@article {pmid40120776, year = {2025}, author = {Din, AU and Sweet, MG and McAmis, AM and Ratliff, JG and Velayutham, ABP and Neilson, AP}, title = {Establishing reliable blood biomarkers for trimethylamine N-oxide status in rodents: effects of oral choline challenge, dietary choline and fasting conditions.}, journal = {The Journal of nutritional biochemistry}, volume = {}, number = {}, pages = {109905}, doi = {10.1016/j.jnutbio.2025.109905}, pmid = {40120776}, issn = {1873-4847}, abstract = {Circulating concentrations of the gut microbial-mammalian metabolite trimethylamine N-oxide (TMAO) is linked to atherosclerosis risk. TMAO biosynthesis begins when dietary choline is converted to trimethylamine (TMA) by gut microbial TMA lyase. TMA is transported to the liver, where flavin-containing monooxygenases convert it to TMAO. While dietary modifications regulate TMAO production, the impact of different intake methods, including oral gavage, dietary supplementation, and conditions such as fasting versus non-fasting, has not been fully explored. Twelve female Sprague-Dawley rats were divided into three diet groups (n = 4 per group): no-choline (0% choline), low-choline (0.08% choline), and high-choline (1% choline). Choline and TMAO fasting and non-fasting blood concentrations, and their kinetics following an acute choline challenge, were assessed before and after a 2-week dietary intervention with the distinct choline dietary levels. Fasting choline was under tight control, with little effect of dietary choline. Non-fasting choline was more variable, with high dietary choline reflected in higher blood choline. Greater levels of dietary choline were reflected in significantly greater levels of TMAO, particularly for non-fasting levels. Kinetic profiling demonstrated additional information regarding the appearance and clearance of these compounds from blood. These results suggest that acute oral choline gavage is likely most suitable for studies targeting acute (direct) inhibitors, whereas a choline-rich diet with assessment of fasting and non-fasting blood levels is more suitable for studying alterations to TMAO production capacity. Future research should examine the impact on atherosclerosis biomarkers and microbiome diversity to deepen the understanding of TMAO regulation and its cardiovascular implications.}, }
@article {pmid40120738, year = {2025}, author = {Liu, ZK and Zhang, L and Ma, X and Chen, W and Chang, Y and Zhao, Y and Hao, X and Shi, S and Shen, JP}, title = {Response of abundant and rare microbial species to 40-year long-term fertilization practices irrespective of bulk and rhizosphere soils.}, journal = {Environmental research}, volume = {275}, number = {}, pages = {121448}, doi = {10.1016/j.envres.2025.121448}, pmid = {40120738}, issn = {1096-0953}, abstract = {Fertilization practices could exert significant influence on the diversity, interactions, and functions of soil microorganisms. However, little is known about how specific microbial groups and their interactions adapt or evolve in response to agricultural practices, especially long-term mineral fertilization. Here we explored the community assembly process shaping the microbial community and co-occurrence networks of abundant and rare groups based on a high-throughput sequencing approach in a field experiment with 40 years of mineral nitrogen (N) and phosphorus (P) fertilization. The results indicated that fertilization (25-51 %) had a strong impact on microbial community structure, while little difference were found between rhizosphere and bulk soils irrespective of abundant and rare microbial groups. Deterministic processes primarily govern the assembly of both abundant and rare bacterial and fungal taxa. Random forest analysis revealed that soil pH and N-related nutrients (i.e. nitrate nitrogen (NO3[-]-N), dissolved organic nitrogen (DON) and ammonium nitrogen (NH4[+]-N)) were the key factors influencing microbial community structure. Structural equation modeling and mantel test further indicated that deterministic factors, particularly soil pH, influence co-occurrence network complexity by modulating the microbiome. Overall, these findings provide insights into factors shaping the microbial community assembly and co-occurrence network dynamics in agroecosystems subjected to long-term fertilization.}, }
@article {pmid40120735, year = {2025}, author = {Chen, P and Yuan, L and Zhou, Z and Xu, G and Chen, W and Cao, Y and Li, C and Fu, Q and Fan, W and Hu, S}, title = {Moso bamboo alleviates Uranium/Cadmium stress through altering the rhizosphere micro-environment and regulating roots carbon and nitrogen metabolism.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121452}, doi = {10.1016/j.envres.2025.121452}, pmid = {40120735}, issn = {1096-0953}, abstract = {Uranium/cadmium (U/Cd) pollution poses a significant global environmental challenge, and phytoremediation offers a sustainable solution for heavy metal contamination. However, the mechanisms by which plants survive U/Cd stress remain unclear. Here, we conducted soil culture experiments of moso bamboo seedlings under U/Cd stress (U, Cd and U + Cd) to examine the effects of it on plant growth, mineral metabolism, and rhizosphere micro-environment. Our findings reveal that U/Cd stress inhibits seedling growth, enhances reactive oxygen species damage, and bolsters the antioxidant system. Additionally, Partial Least Squares Path Modeling (PLS-PM) was employed to uncover potential tolerance mechanisms in moso bamboo under U/Cd stress. U/Cd is mainly distributed in the root cell walls and also exists predominantly in the residual state within the roots. Correspondingly, U and Cd significantly disrupt mineral metabolism in plant. Metabolomic analyses indicate that U/Cd markedly suppress amino acid metabolism pathways, while they stimulate carbon metabolism to mitigate toxicity. Furthermore, U/Cd stress disrupts the rhizosphere microbial community structure, and the competitive interaction of nitrogen functions exists between rhizosphere microorganism and bamboo roots. PLS-PM reveal the U/Cd stress impacts the interaction of the soil-rhizosphere-plant system. Together, these findings offer new insights into the response mechanism of bamboo plants to heavy metal stress, and provide a theoretical foundation for screening heavy metal tolerant plants and managing mining areas.}, }
@article {pmid40120687, year = {2025}, author = {Caffrey, EB and Perelman, D and Ward, CP and Sonnenburg, ED and Gardner, CD and Sonnenburg, JL}, title = {Unpacking food fermentation: Clinically relevant tools for fermented food identification and consumption.}, journal = {Advances in nutrition (Bethesda, Md.)}, volume = {}, number = {}, pages = {100412}, doi = {10.1016/j.advnut.2025.100412}, pmid = {40120687}, issn = {2156-5376}, abstract = {Fermented foods have been consumed for millennia, valued for their extended shelf life, distinctive sensory properties, and potential health benefits. Emerging research suggests that fermented food consumption may contribute to gut microbiome diversity, immune modulation, and metabolic regulation; however, mechanistic insights and clinical validation remain limited. This review synthesizes current scientific evidence on the microbial and metabolite composition of fermented foods, their proposed health effects, and safety considerations for vulnerable populations. Additionally, we highlight the need for standardized definitions, serving sizes, and regulatory frameworks to enhance consumer transparency and research reproducibility. By providing a structured overview of existing data and knowledge gaps, this review establishes a foundation for integrating fermented foods into dietary recommendations and guiding future research directions. STATEMENT OF SIGNIFICANCE: While fermented foods have demonstrated benefits to human health, the gap between scientific research and marketing claims, including lack of regulatory standards in labeling can be disorienting to consumers seeking these potential benefits. This review provides an updated perspective on the role of fermented foods in health, emphasizing clinically relevant tools, research opportunities, and labeling recommendations to guide their identification and use.}, }
@article {pmid40120561, year = {2025}, author = {Ankley, PJ and Challis, J and Xia, P and Gong, Y and Zhou, Y and Hecker, M and Giesy, JP and Brinkmann, M}, title = {Interactions of erythromycin and an antibiotic mixture with the gut microbiome of juvenile rainbow trout.}, journal = {Chemosphere}, volume = {377}, number = {}, pages = {144263}, doi = {10.1016/j.chemosphere.2025.144263}, pmid = {40120561}, issn = {1879-1298}, abstract = {Erythromycin (ERY) is a commonly used antibiotic found in wastewater effluents and the environment globally. Due to the bioactivity by which they kill and prevent bacterial growth, ERY and other antibiotics may have significant unwanted impacts on the gut microbiome of fishes. The overall objective of this project was to assess effects on the gut microbiome in response to exposure to ERY alone or in a mixture with other common antibiotics, which was accomplished in two experiments. The objectives of experiment 1 as a pilot study were to understand uptake and depuration of ERY in juvenile rainbow trout (RBT) over a 7-d exposure to three concentrations of ERY followed by a 7-d depuration period. Furthermore, throughout the study changes in gut microbiome were assessed. In experiment 2, an identical experimental design was used to assess the effects of a mixture of antibiotics containing, in addition to ERY, 100 μg/g each of ampicillin, metronidazole, and ciprofloxacin. In that study, three matrices were analyzed, with gut collected for 16S rRNA metabarcoding, blood plasma for non-targeted metabolomics, and brain tissue for mRNA-seq analysis. ERY was relatively quickly depurated from fish and gut microbiome dysbiosis was observed at 7 d after exposure, with a slight recovery after the 7-d depuration period. A greater number of plasma metabolites was dysregulated at 14 d compared to 7 d revealing distinct temporal dynamics compared to gut microbiome dysbiosis. Furthermore, several transformation products of antibiotics and biomarker metabolites were observed in plasma due to antibiotic exposure. The transcriptome of the brain was only slightly altered due to antibiotic exposure. Results of these studies will help inform aquaculture practitioners and risk assessors when assessing the potential impacts of antibiotics present in fish feed and the environment, with implications for host health.}, }
@article {pmid40120240, year = {2025}, author = {Gao, C and Chen, Y and Zhang, Z and Xu, D and Liu, X and Wang, D and Shi, L and Wang, X and Chen, H and Hao, E}, title = {LAYING RATE WAS CORRELATED WITH MICROBIAL Fecal microbiota transplantation improves the laying performance by changing the gut microbiota composition in late laying period.}, journal = {Poultry science}, volume = {104}, number = {5}, pages = {105064}, doi = {10.1016/j.psj.2025.105064}, pmid = {40120240}, issn = {1525-3171}, abstract = {This research investigated the differences and succession patterns of microbes in different ages, the performance of laying hens, and the effect of Fecal Microbiota Transplantation (FMT) on aged laying hens. First, based on the different laying rates and age, we divided the laying hens into four groups: 75-week-old high-yield (OH, laying rate (LR) > 90%), 75-week-old low-yield (OL, LR < 60%), 75-week-old non-laying hens (OZ, LR = 0%) and 35-week-old high-yield (YH, LR > 90%) with 5 replicates in each group and 6 chickens in each replicate. The microbial metabolic patterns between different ages and laying rates were determined using 16S rDNA technology. Then, to verify the results of microbiome research, we utilized FMT technology to transplant the gut microbiota from OH to OZ (OZFMT-OH), thereby revealing the connection between gut microbes and production performance. The results showed that high-yielding hens (YH and OH groups) had higher levels of Superoxide dismutase (SOD) and Immunoglobulin A (IgA) compared to OL and OZ groups. The Villus height to Crypt depth ratio(V/C) was significantly higher in the YH group than in 75-week-old hens (P < 0.05). Alpha diversity indicated higher microbial diversity in the YH group compared to older hens (P < 0.05), with YH hens harboring more Megamonas, OH hens more Bacteroides, and OL and OZ groups showing higher levels of harmful bacteria. The villus height, V/C, mucosal layer thickness, cup cell number acetic acid level, and LR in the OZFMT-OH group were significantly higher than those in the OZ group (P < 0.05), while the IL-2 level, crypt depth and cecal intestinal wall thickness were significantly lower than those in OZ group (P < 0.05). FMT also changed the morphological structure of grade follicles and small yellow follicles, improved the microbe composition of cecum and increased Bacteroides abundance. In the late laying period, if the intestinal flora cannot maintain the dynamic balance and carry out timely replacement, the production performance may be decreased, and the increase of Bacteroides abundance in the intestinal tract can improve the intestinal health and production performance of laying hens in the late laying period.}, }
@article {pmid40120233, year = {2025}, author = {Hong, Z and Lin, L and Yu, H and Wei, Q and Zhang, Y and He, W and Liao, X and Jing, J and Dong, G and Zhang, Z}, title = {Branched perfluorohexanesulfonic acid (PFHxS) and perfluoroheptanoic acid (PFHpA): 'Safer' per- and polyfluoroalkyl substances (PFASs) alternatives for their effects on gut microbiota and metabolic function in children.}, journal = {Environment international}, volume = {198}, number = {}, pages = {109380}, doi = {10.1016/j.envint.2025.109380}, pmid = {40120233}, issn = {1873-6750}, abstract = {This study examined the effects of branched perfluorohexanesulfonic acid (PFHxS) and perfluoroheptanoic acid (PFHpA), two alternatives to per- and polyfluoroalkyl substances (PFASs), on gut microbiota and metabolic function in Chinese children aged 6-9 years. A total of 336 children were enrolled, providing plasma and fecal samples. Gut microbiota composition was assessed through 16S rRNA gene sequencing, and fecal metabolites and short-chain fatty acids (SCFAs) were analyzed using targeted metabolomics profiling and high-performance liquid chromatography (HPLC), respectively. PFASs in plasma samples were detected using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The results revealed that exposure to PFHpA significantly reduced microbial diversity and richness in the gut microbiota. Specific bacterial genera were found to be positively or negatively associated with branched PFHxS and PFHpA exposures (β = -0.008---0.009, P_fdr = <0.001---0.048), with Parabacteroides positively correlated with branched PFHxS and Lachnospiraceae FCS020 group negatively correlated with PFHpA. Metabolomic analysis showed that branched PFHxS and PFHpA exposures were associated with distinct changes in fecal metabolite profiles (β = -0.182---0.177, P_fdr = 0.015---0.172), particularly reducing fatty acids and amino acids. Additionally, higher exposure to PFHpA was linked to a reduction in SCFA profiles, such as valeric acid (β = -0.691 - -0.341, P = 0.011---0.030). This study offers new insights into the potential adverse effects of PFASs alternatives, specifically branched PFHxS and PFHpA, on the gut microbiome and metabolic health in children.}, }
@article {pmid40119556, year = {2025}, author = {Blonde, C and Caddeo, A and Nasser, W and Reverchon, S and Peyraud, R and Haichar, FEZ}, title = {New insights in metabolism modelling to decipher plant-microbe interactions.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70063}, pmid = {40119556}, issn = {1469-8137}, support = {//CNRS through the MITI interdisciplinary programs through its exploratory research program/ ; }, abstract = {Plant disease outbreaks, exacerbated by climate change, threaten food security and environmental sustainability world-wide. Plants interact with a wide range of microorganisms. The quest for resilient agriculture requires a deep insight into the molecular and ecological interplays between plants and their associated microbial communities. Omics methods, by profiling entire molecular sets, have shed light on these complex interactions. Nonetheless, deciphering the relationships among thousands of molecular components remains a formidable challenge, and studies that integrate these components into cohesive biological networks involving plants and associated microbes are still limited. Systems biology has the potential to predict the effects of biotic and abiotic perturbations on these networks. It is therefore a promising framework for addressing the full complexity of plant-microbiome interactions.}, }
@article {pmid40119548, year = {2025}, author = {Longo, AV and Solano-Iguaran, JJ and Valenzuela-Sánchez, A and Alvarado-Rybak, M and Azat, C and Bacigalupe, LD}, title = {Blurred Lines Between Determinism and Stochasticity in an Amphibian Phylosymbiosis Under Pathogen Infection.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17741}, doi = {10.1111/mec.17741}, pmid = {40119548}, issn = {1365-294X}, support = {1200417, 3210290, 1211587, and 11240453//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; IOS-2011278//Division of Integrative Organismal Systems/ ; }, abstract = {Selection, dispersal and drift jointly contribute to generating variation in microbial composition within and between hosts, habitats and ecosystems. However, we have limited examples of how these processes interact as hosts and their microbes turn over across latitudinal gradients of biodiversity and climate. To bridge this gap, we assembled an extensive dataset of 580 skin bacteriomes from 22 amphibian species distributed across a 10° latitudinal range in Chile. Amphibians are susceptible to the fungal pathogen Batrachochytrium dendrobatidis (Bd), which infects their skin, potentially leading to changes in the normal skin microbiome (i.e., dysbiosis). Using comparative methods, accounting for pathogen infection and implementing resampling schemes, we found evidence of phylosymbiosis, characterised by more similar bacterial communities in closely related amphibian species. We also compared how neutral processes affected the assembly of skin bacteria by focusing on two widespread species from our dataset: the Chilean four-eyed frog (Pleurodema thaul) and Darwin's frog (Rhinoderma darwinii). Neutral models revealed that dispersal and chance largely facilitated the occurrence of ~90% of skin bacteria in both species. Deterministic processes (e.g., phylosymbiosis, active recruitment of microbes, microbe-microbe interactions) explained the remaining fraction of the bacteriomes. Amphibian species accounted for 21%-32% of the variance found in non-neutral bacterial taxa, whereas the interaction with Bd carried a weaker but still significant effect. Our findings provide evidence from ectotherms that most of their skin bacteria are subject to dispersal and chance, yet contemporary and historical contingencies leave strong signatures in their microbiomes even at large geographical scales.}, }
@article {pmid40119394, year = {2025}, author = {Guo, R and Chang, Y and Wang, D and Sun, H and Gu, T and Zong, Y and Zhou, S and Huang, Z and Chen, L and Tian, Y and Xu, W and Lu, L and Zeng, T}, title = {Interaction between cecal microbiota and liver genes of laying ducks with different residual feed intake.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {30}, pmid = {40119394}, issn = {2524-4671}, support = {CARS-42//China Agriculture Research System of MOF and MARA/ ; 2021C02068//Zhejiang Province Agricultural New Breeding Major Science and Technology Special Project/ ; LZ23C170001//Zhejiang Provincial Natural Science Foundation of China/ ; 32472892//National Natural Science Foundation of China/ ; 2022YFD1300100//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: The gut microbiota exerts a critical influence on energy metabolism homeostasis and productive performance in avian species. Given the diminishing availability of arable land and intensifying competition for finite resources between livestock production and human populations, the agricultural sector faces dual imperatives to enhance productive efficiency while mitigating ecological footprints. Within this paradigm, optimizing nutrient assimilation efficiency in commercial waterfowl operations emerges as a strategic priority. This investigation employs an integrated multi-omics approach framework (metagenomic, metabolomic, and transcriptomic analyses) to elucidate the mechanistic relationships between cecal microbial consortia and feed conversion ratios in Shan Partridge ducks.<br><br>RESULTS: Based on the analysis of metagenome data, a total of 34 phyla, 1033 genera and 3262 species of bacteria were identified by metagenomic sequencing analysis. At the phylum level, 31 phylums had higher mean abundance in the low residual feed intake (LRFI) group than in the high residual feed intake (HRFI) group. Among them, the expression of microbiome Elusimicrobiota was significantly higher in the LRFI group than in the HRFI group (P&#x2009;<&#x2009;0.05). And we also found a significant differences in secondary metabolites biosynthesis, transport, and catabolism pathways between the two groups in microbial function (P&#x2009;<&#x2009;0.05). Based on metabolomic analysis, 17 different metabolites were found. Among them, Lipids and lipid molecules accounted for the highest proportion. Whereas the liver is very closely related to lipid metabolism, we are close to understanding whether an individual's energy utilization efficiency is related to gene expression in the liver. We selected six ducks from each group of six ducks each for liver transcriptome analysis. A total of 322 differential genes were identified in the transcriptome analysis results, and 319 genes were significantly down-regulated. Among them, we found that prostaglandin endoperoxide synthase 2 (PTGS2) might be a key hub gene regulating RFI by co-occurrence network analysis. Interestingly, the differential gene PTGS2 was enriched in the arachidonic acid pathway at the same time as the differential metabolite 15-deoxy-delta12,14-prostaglandin J2 (15d-PGJ2). In addition, the results of the association analysis of differential metabolites with microorganisms also revealed a significant negative correlation between 15d-PGJ2 and Elusimicrobiota.<br><br>CONCLUSION: Based on comprehensive analysis of the research results, we speculate that the Elusimicrobiota may affect the feed utilization efficiency in ducks by regulating the expression of the PTGS2 gene.}, }
@article {pmid40119296, year = {2025}, author = {Zhao, W and Ma, L and Xue, L and Jiang, Q and Feng, Y and Wang, S and Tian, J and Tian, X and Gu, Y and Zhang, J}, title = {The rumen microbiome and its metabolome together with the host metabolome regulate the growth performance of crossbred cattle.}, journal = {BMC genomics}, volume = {26}, number = {1}, pages = {278}, pmid = {40119296}, issn = {1471-2164}, support = {2021BEF01002//the Major Project of Science and Technology of Ningxia Autonomous Region/ ; 2023AAC03050//the Natural Science Foundation of Ningxia/ ; }, mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; *Metabolome ; Gastrointestinal Microbiome ; Microbiota ; Hybridization, Genetic ; Metabolomics ; }, abstract = {BACKGROUND: Although it has been demonstrated that gastrointestinal microorganisms greatly influence livestock performance, the effect of gastrointestinal microorganisms on the growth performance of crossbred cattle remains unclear. Due to their superior production characteristics, understanding the impact of gastrointestinal microorganisms on the growth performance of crossbred beef cattle is of significant importance for improving farming efficiency.<br><br>RESULT: In this study, healthy Simmental with similar birth date and weight were selected as dams, Simmental (Combination I), Belgian Blue (Combination II) and Red Angus (Combination III) were used as parents for crossbreeding. The progeny of the three combination crosses were measured for growth performance under identical conditions from birth rearing to 18 months of age (n&#x2009;=&#x2009;30). Rumen fluid and plasma were collected for macro-genomic and non-targeted metabolomic analysis (n&#x2009;=&#x2009;8). The results showed that Combination II was superior to Combination I and Combination III in body weight (BW) and body height (BH) (P&#x2009;<&#x2009;0.05). Mycoplasma, Succinivibrio, Anaerostipes, Methanosphaera, Aspergillus, and Acidomyces were significantly increased in the rumen of Combination II (P&#x2009;<&#x2009;0.05), whereas differentially expressed metabolites (DEMs) 9,10,13-Trihome (11), 9,12,13-Trihome and 9(10)-Epome, and 9(S)-Hpode were reduced in abundance. In addition, plasma DEM PC (14:0/P-18:1(11Z)), PC (16:0/0:0), and PC (17:0/0:0) were down-regulated in combination II. Correlation analysis revealed that Anaerostipes, Methanosphaera, and Succinivibrio were associated with PC (14:0/P-18:1(11Z)), 9(10)-Epome, 9,10,13-Trihome (11), 9(S)-Hpode, 9,10,13-Trihome, PC (17:0/0:0), and PC (16:0/0:0). Growth traits were significantly positively correlated with the three dominant genera, Anaerostipes, Methanosphaera, and Succinivibrio, while significantly negatively correlated with key rumen metabolites and plasma metabolites (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: Our study reveals the role of rumen microorganisms and its metabolites with host metabolism in the regulation of growth performance of crossbred cattle, which will contribute to the development of modern cattle breeding.}, }
@article {pmid40119173, year = {2025}, author = {Attema, B and Kuipers, F}, title = {Microbiome-derived secondary bile acids promote repair of colonic mucosa after injury.}, journal = {EMBO molecular medicine}, volume = {}, number = {}, pages = {}, pmid = {40119173}, issn = {1757-4684}, }
@article {pmid40119155, year = {2025}, author = {Heidrich, V and Valles-Colomer, M and Segata, N}, title = {Human microbiome acquisition and transmission.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {40119155}, issn = {1740-1534}, abstract = {As humans, we host personal microbiomes intricately connected to our biology and health. Far from being isolated entities, our microbiomes are dynamically shaped by microbial exchange with the surroundings, in lifelong microbiome acquisition and transmission processes. In this Review, we explore recent studies on how our microbiomes are transmitted, beginning at birth and during interactions with other humans and the environment. We also describe the key methodological aspects of transmission inference, based on the uniqueness of the building blocks of the microbiome - single microbial strains. A better understanding of human microbiome transmission will have implications for studies of microbial host regulation, of microbiome-associated diseases, and for effective microbiome-targeting strategies. Besides exchanging strains with other humans, there is also preliminary evidence we acquire microorganisms from animals and food, and thus a complete understanding of microbiome acquisition and transmission can only be attained by adopting a One Health perspective.}, }
@article {pmid40118938, year = {2025}, author = {Bhunyakarnjanarat, T and Udompornpitak, K and Wannigama, DL and Ruchusatsawat, A and Aphiboon, P and Sripong, T and Thim-Uam, A and Leelahavanichkul, A}, title = {Intratracheal Candida administration induced lung dysbiosis, activated neutrophils, and worsened lung hemorrhage in pristane-induced lupus mice.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {9768}, pmid = {40118938}, issn = {2045-2322}, support = {grant No 272/2567//University of Phayao and Thailand Science Research and Innovation Fund, Fundamental Fund 2024/ ; B16F640175 and B48G660112//The Program Management Unit for Human Resources and Institutional Development, Research and Innovation/ ; RA-MF-22/65, RA-MF-13/66, and RA-MF-eAsia//Rachadapisek Sompote Matching Fund/ ; HEAF67300087//Thailand Science research and Innovation Fund Chulalongkorn University/ ; N41A640076//The National Research Council of Thailand (NRCT)/ ; }, mesh = {Animals ; *Dysbiosis/microbiology ; Mice ; *Lung/microbiology/pathology ; *Terpenes ; *Lupus Erythematosus, Systemic/complications/immunology ; *Mice, Inbred C57BL ; *Candida albicans ; *Neutrophils/immunology/metabolism ; *Hemorrhage ; Female ; Cytokines/metabolism ; Disease Models, Animal ; }, abstract = {Because the innate immunity might and fungi in the lungs might enhance the severity of lupus-induced diffuse alveolar hemorrhage (DAH), intraperitoneal pristane injection was performed in C57BL6 mice with intratracheal administration by Candida albicans or phosphate buffer solution (PBS). Despite the similar pristane-induced lupus (proteinuria, serum creatinine, and serum anti-dsDNA) at 5 weeks of the model, Candida administration worsened several characteristics, including mortality, body weight, serum cytokines (TNF-α and IL-6), and lung hemorrhage score, and cytokines in the lung tissue (TNF-α, IL-6, and IL-10), but not gut permeability (FITC-dextran assay), serum IL-10, immune cells in the spleens (flow cytometry analysis), and activities of peritoneal macrophages (polymerase-chain reaction). Although Candida administration reduced proteobacterial abundance and altered alpha and beta diversity compared with PBS control, lung microbiota was not different between Candida administration in pristane- and non-pristane-administered mice. Because of the prominent Gram-negative bacteria in lung microbiota and the role of neutrophils in DAH, lipopolysaccharide (LPS) with and without heat-killed Candida preparation was tested. Indeed, Candida preparation with LPS induced more severe pro-inflammatory neutrophils than LPS stimulation alone as indicated by the expression of several genes (TNF-α, IL-6, IL-1β, IL-10, Dectin-1, and NF-κB). In conclusion, the intratracheal Candida worsened pristane-induced lung hemorrhage partly through the enhanced neutrophil responses against bacteria and fungi. More studies on Candida colonization in sputum from patients with lupus-induced DAH are interesting.}, }
@article {pmid40118512, year = {2025}, author = {Gomes, IB}, title = {The Overlooked Interaction of Emerging Contaminants and Microbial Communities: A Threat to Ecosystems and Public Health.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxaf064}, pmid = {40118512}, issn = {1365-2672}, abstract = {Emerging contaminants (ECs) and microbial communities should not be viewed in isolation, but through the One Health perspective. Both ECs and microorganisms lie at the core of this interconnected framework, as they directly influence the health of humans, animals, and the environment. The interactions between ECs and microbial communities can have profound implications for public health, affecting all three domains. However, these ECs-microorganism interactions remain underexplored, potentially leaving significant public health and ecological risks unrecognized. Therefore, this article seeks to alert the scientific community to the overlooked interactions between ECs and microbial communities, emphasizing the pivotal role these interactions may play in the management of "One Health." The most extensively studied interaction between ECs and microbial communities is biodegradation. However, other more complex and concerning interactions demand attention, such as the impact of ECs on microbial ecology (disruptions in ecosystem balance affecting nutrient and energy cycles) and the rise and spread of antimicrobial resistance (a growing global health crisis). Although these ECs-microbial interactions had not been extensively studied, there are scientific evidence that ECs impact on microbial communities may be concerning for public health and ecosystem balance. So, this perspective summarizes the impact of ECs through a One Health lens and underscores the urgent need to understand their influence on microbial communities, while highlighting the key challenges researchers must overcome. Tackling these challenges is vital to mitigate potential long-term consequences for both ecosystems and public health.}, }
@article {pmid40118296, year = {2025}, author = {Wang, W and Zhang, K and Zhang, K and Wu, R and Tang, Y and Li, Y}, title = {Gut microbiota promotes cholesterol gallstone formation through the gut-metabolism-gene axis.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {107446}, doi = {10.1016/j.micpath.2025.107446}, pmid = {40118296}, issn = {1096-1208}, abstract = {BACKGROUND: Gallstone disease, arising from the interplay between host metabolism and gut microbiota, represents a significant health concern. Dysbiosis of the gut microbiome and disruptions in circadian rhythm contribute to the pathogenesis of gallstones. This study conducted a comprehensive analysis of gut microbiota and metabolites derived from stool and serum samples of 28 patients with cholesterol gallstones (CGS) and 19 healthy controls, employing methodologies such as 16S rRNA sequencing, metaproteomics, metabolomics, and host genetic analysis. Additionally, a retrospective cohort study was utilized to assess the efficacy of probiotics or ursodeoxycholic acid (UDCA) in preventing CGS formation post- bariatric surgery.<br><br>RESULTS: In CGS patients, gut microbiota diversity shifted, with harmful bacteria rising and beneficial ones declining. The altered microbiota primarily affected amino acid, lipid, nucleotide, and carbohydrate metabolism. Metabolic abnormalities were noted in amino acids, glucose, lipids, and bile acids with decreased levels of ursodeoxycholic, glycosodeoxycholic, and glycolithocholic acids, and increased glycohyodeoxycholic and allocholic acids. Glutamine and alanine levels dropped, while phenylalanine and tyrosine rosed. Animal studies confirmed gene changes in gallbladder tissues related to bile acid, energy, glucose, and lipid metabolism. Importantly, UDCA and probiotics effectively reduced CGS risk post-bariatric surgery, especially when combined.<br><br>CONCLUSIONS: Multi-omics can clarify CGS pathology, by focusing on the gut-metabolism-gene axis,paving the way for future studies on CGS prevention and treatment through gut microbiota or metabolic interventions.}, }
@article {pmid40118285, year = {2025}, author = {Marchianò, S and Biagioli, M and Giorgio, CD and Massa, C and Bellini, R and Bordoni, M and Urbani, G and Lachi, G and Sepe, V and Morretta, E and Distrutti, E and Zampella, A and Monti, MC and Fiorucci, S}, title = {Allo-lithocholic acid, a microbiome derived secondary bile acid, attenuates liver fibrosis.}, journal = {Biochemical pharmacology}, volume = {}, number = {}, pages = {116883}, doi = {10.1016/j.bcp.2025.116883}, pmid = {40118285}, issn = {1873-2968}, abstract = {Secondary bile acids, lithocholic acid and deoxycholic acid (LCA and DCA), are dehydroxylated derivatives of primary bile acids. However, in addition to LCA and DCA the intestinal microbiota produced a variety of poorly characterized metabolites. Allo-LCA, a LCA metabolite, acts as a dual GPBAR1 agonist and RORγt inverse agonist and modulates intestinal immunity, although is not yet known whether allo-LCA exerts regulatory functions outside the intestine. In the present study we have therefore investigated whether administration of allo-LCA, 10 mg/kg/day, to mice administered a high fat/high fructose diet (HFD-F) and carbon tetrachloride (Ccl4), a model for metabolic dysfunction-associated steatohepatitis (MASH), protects from development of liver damage. In vitro allo-LCA functions as GPBAR1 agonist and RORγt inverse agonist and prevents macrophages M1 polarization and Th17 polarization of CD4 cells. In vivo studies, while exposure to a HFD-F/Ccl4 promoted insulin resistance and development of a pro-atherogenic lipid profile and liver steatosis and fibrosis, allo-LCA reversed this pattern by improving insulin sensitivity and liver lipid accumulation. The liver transcriptomic profile demonstrated that allo-LCA reversed the dysregulation of multiple pathways associated with immunological, inflammatory and metabolic signaling. Allo-LCA also restored bile acid homeostasis, reversing HFD/Ccl4-induced shifts in bile acid pool composition and restored adipose tissue histopathology and function by reducing the expression of leptin and resistin, two pro-inflammatory adipokines, and restored a healthier composition of the intestinal microbiota. In conclusion, present results expand on the characterization of entero-hepatic signaling and suggest that allo-LCA, a microbial metabolite, might have therapeutic potential in liver diseases.}, }
@article {pmid40118220, year = {2025}, author = {Rozera, T and Pasolli, E and Segata, N and Ianiro, G}, title = {Machine learning and artificial intelligence in the multi-omics approach to gut microbiota.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2025.02.035}, pmid = {40118220}, issn = {1528-0012}, abstract = {The gut microbiome is involved in human health and disease, and its comprehensive understanding is necessary to exploit it as a diagnostic or therapeutic tool. Multi-omics approaches, including metagenomics, metatranscriptomics, metabolomics, and metaproteomics, enable depicting the complexity of the gut microbial ecosystem. However, these tools generate a large data stream, which integration is needed to produce clinically useful readouts but, in turn, might be difficult to carry out with conventional statistical methods. Artificial intelligence and machine learning have been increasingly applied to multi-omics datasets in several conditions associated with microbiome disruption, from chronic disorders to cancer. Such tools show potential for clinical implementation, including the discovery of microbial biomarkers for disease classification or prediction, the prediction of response to specific treatments, the fine-tuning of microbiome-modulating therapies. Here we discuss the state of the art, potential, and limits, of artificial intelligence and machine learning in the multi-omics approach to gut microbiome.}, }
@article {pmid40118032, year = {2025}, author = {Ge, AH and Wang, E}, title = {Exploring the plant microbiome: A pathway to climate-smart crops.}, journal = {Cell}, volume = {188}, number = {6}, pages = {1469-1485}, doi = {10.1016/j.cell.2025.01.035}, pmid = {40118032}, issn = {1097-4172}, mesh = {*Microbiota ; *Crops, Agricultural/microbiology ; *Rhizosphere ; Plant Roots/microbiology/metabolism ; Agriculture ; Soil Microbiology ; Climate ; }, abstract = {The advent of semi-dwarf crop varieties and fertilizers during the Green Revolution boosted yields and food security. However, unintended consequences such as environmental pollution and greenhouse gas emissions underscore the need for strategies to mitigate these impacts. Manipulating rhizosphere microbiomes, an aspect overlooked during crop domestication, offers a pathway for sustainable agriculture. We propose that modulating plant microbiomes can help establish "climate-smart crops" that improve yield and reduce negative impacts on the environment. Our proposed framework integrates plant genotype, root exudates, and microbes to optimize nutrient cycling, improve stress resilience, and expedite carbon sequestration. Integrating unselected ecological traits into crop breeding can promote agricultural sustainability, illuminating the nexus between plant genetics and ecosystem functioning.}, }
@article {pmid40118017, year = {2025}, author = {Kehkashan,  and Hussain, A and Murtaza, M and Lee, GJ and Mun, BG and Yun, BW}, title = {Low and high-density polyethylene and expanded polystyrene biodegradation by the greater wax moth Galleria mellonella L reveals a key role of the gut microbiome.}, journal = {Ecotoxicology and environmental safety}, volume = {294}, number = {}, pages = {118074}, doi = {10.1016/j.ecoenv.2025.118074}, pmid = {40118017}, issn = {1090-2414}, abstract = {Polyethylene (PE) is a ubiquitous pollutant that takes long time to degrade naturally. PE breaks down into persistent micro- or nano-plastics that are even more dangerous for the environment and human health. Here we investigated the ability of the wax worm Galleria mellonella (Lepidoptera, Pyralidae) to degrade two different types of PE and expanded polystyrene (EPS). Results showed a reduction of up to 69 %, 73 %, and 50 % in the weight of LDPE, HDPE, and EPS, respectively. Antibiotic treatments indicated that PE consumption is highly dependent upon an intact population of at least eight different bacteria from the Enterococcus, Pseudomonas, and Bacillus genera identified by 16S rRNA sequencing. Antibiotic treatment reduced the gut bacterial population, negatively affecting larval growth. The PE-only diet severely affected the growth and development of G. mellonella larvae, pupae, and male/female adults. SEM analysis of gut bacteria co-incubated LDPE discs revealed biofilm formation and PE biodegradation by all the bacteria in the culture, supporting the great potential of these bacteria for plastic biodegradation. FTIR analysis of frass after feeding on PE only revealed significantly strong PE biodegradation signals as results showed 33 peaks of strong (S) and medium (M) intensity corresponding to wave numbers with PE biodegradation signatures ranging between 1239.50 cm[-1] to 3077.69 cm[-1] coding for vinyl hydrocarbons, vinyl ether, vinylene, vinylene trisubst., ketones, ethers, aldehydes, acrylate, diazo ketones and epoxides which is a convincing evidence of PE metabolism. Further research is required to determine the practical implications of wax worm larvae for plastic degradation in the environment.}, }
@article {pmid40117915, year = {2025}, author = {Ghemrawi, M and Ramírez Torres, A and Netherland, M and Wang, Y and Hasan, NA and El-Fahmawi, B and Duncan, G and McCord, B}, title = {Forensic insights from shotgun metagenomics: Tracing microbial exchange during sexual intercourse.}, journal = {Forensic science international. Genetics}, volume = {78}, number = {}, pages = {103266}, doi = {10.1016/j.fsigen.2025.103266}, pmid = {40117915}, issn = {1878-0326}, abstract = {The microbiome is becoming an emerging field of interest within forensic science with high potential for individualization; however, little is known about bacterial species specific to the genital area or their ability to transfer between individuals during sexual contact. In this proof-of-concept study, we investigated microbial transfer dynamics in seven monogamous, heterosexual couples by collecting pre- and post-sexual intercourse samples from their genital areas, including penile, vaginal, and labial locations. Utilizing Shotgun Metagenomic Sequencing, we sequenced the microbial profiles of these samples. Our findings reveal significant transfer from the vaginal microbiome onto the penile microbiome, predominantly originating from the labial genitalia. Moreover, strain analysis unveiled distinct differentiation between the same species of bacteria across individuals, underscoring the potential for microbial forensics to distinguish individuals. This study contributes to our understanding of microbial transfer during sexual contact and highlights the forensic implications of the genital microbiome.}, }
@article {pmid40117686, year = {2025}, author = {Zhang, C and Cabreiro, F and Barron, LP and Stürzenbaum, SR}, title = {Carbamazepine-exposed earthworms are characterized by tissue-specific accumulation patterns and transcriptional profiles.}, journal = {Environment international}, volume = {198}, number = {}, pages = {109357}, doi = {10.1016/j.envint.2025.109357}, pmid = {40117686}, issn = {1873-6750}, abstract = {Pharmaceutically active compounds enter soils via wastewater reuse and biosolid application. A ubiquitous drug present in wastewater is carbamazepine, a frequently prescribed anti-convulsant. Its mode of action is not species-specific and affects the nervous system of non-target organisms, including most likely the soil dwelling earthworms, which in turn has the potential to negatively impact soil quality. In this project, soils were amended with carbamazepine to explore uptake dynamics and resultant changes in molecular and life cycle endpoints of earthworms (Dendrobaena veneta). Earthworms were maintained, under laboratory conditions, for 28 days in soil spiked with either a solvent control, 0.6 mg/kg carbamazepine (encountered in the terrestrial system) or 10 mg/kg carbamazepine (significantly above an environmental hotspot). Carbamazepine concentrations were quantified in soils and worms by liquid chromatography tandem mass spectrometry (LC-MS/MS) which revealed tissue, dose and time-dependent differences in accumulation. Carbamazepine also modulated the make-up of the microbiome in the soil as well as the earthworm's gut. De novo RNA sequencing identified novel transcripts and complex tissue-specific transcriptomic changes, where, for example, the expression of the tubulin polymerisation promoting protein (tppp) was inhibited (9-fold) in the gut but induced (11-fold) in the cerebral ganglion of exposed earthworms. However, the notable absence of a strong cytochrome P450 response across all conditions suggests that the terrestrial earthworm also relies on detoxification pathways that differ to those observed in well-studied aquatic models. The novel finding that carbamazepine exposure triggers tissue-specific impacts in non-target soil organisms highlights the value and need for a more comprehensive understanding of how contaminants of emerging concern behave within an ecotoxicological context. This, in turn, will lead to informed and reliable risk assessments defining the consequences of wastewater and biosolid amendment practices on soil ecology and ecosystem function.}, }
@article {pmid40117607, year = {2025}, author = {Paz, M and Lio, P}, title = {Dermatological Manifestations and Sebum Composition in Parkinson's Disease.}, journal = {Dermatology practical &amp; conceptual}, volume = {15}, number = {1}, pages = {}, pmid = {40117607}, issn = {2160-9381}, abstract = {INTRODUCTION: Parkinson disease (PD) is a multifaceted neurodegenerative disorder known for its hallmark motor symptoms. However, nonmotor manifestations, specifically dermatological changes, precede motor symptoms and may thus serve as vital early indicators of PD.<br><br>OBJECTIVES: This article explores the skin-related changes associated with PD, focusing on alterations in sebum composition, microbial dysbiosis, and the potential for leveraging dermatological assessments as early, noninvasive diagnostic markers for PD.<br><br>METHODS: A comprehensive literature review was conducted to investigate dermatological manifestations of PD, focusing on sebum changes in affected individuals. Research explored the clinical relevance of altered lipid profiles, volatile organic compound (VOC) contributions, and microbiome dysbiosis in those with PD.<br><br>RESULTS: Individuals with PD exhibit excess sebum production characterized by altered lipid profiles, including elevated short-chain fatty acids (SCFAs) and disruptions in sphingolipid metabolism. The lipid-rich environment also promotes overgrowth of Malessezia yeast, contributing to varied dermatological symptoms in those with PD. VOCs identified in sebum have been linked to unique odors and serve as biomarkers for diagnostic potential. These findings support the potential for early PD diagnosis through dermatologic assessment and sebum analysis.<br><br>CONCLUSION: Dermatological manifestations in PD offer promising noninvasive biomarkers for early diagnosis. Future research should aim to further elucidate the mechanisms underlying sebum dysregulation in PD and validate the clinical relevance of these biomarkers in larger populations.}, }
@article {pmid40117491, year = {2025}, author = {Smith, SRM and Morgan, NV and Brill, A}, title = {Venous Thrombosis Unchained: Pandora's Box of Non-Inflammatory Mechanisms.}, journal = {Blood advances}, volume = {}, number = {}, pages = {}, doi = {10.1182/bloodadvances.2024014114}, pmid = {40117491}, issn = {2473-9537}, abstract = {Venous thromboembolism (VTE), which includes deep vein thrombosis (DVT) and pulmonary embolism (PE), represents a complex pathological process extending far beyond inflammatory mechanisms. This review comprehensively examines the multifaceted non-inflammatory mechanisms underlying thrombosis development, integrating insights from molecular, physiological, and systemic levels. Blood flow dynamics and endothelial function are known to be critical regulators of thrombus development. Platelets and microparticles play important roles beyond conventional inflammatory responses, actively contributing to thrombus formation through intricate molecular interactions. Metabolic syndrome and insulin resistance are associated with thrombotic risk, demonstrating the complex interplay between metabolic disorders and DVT. Certain genetic mutations also predispose individuals to venous thrombosis. Emerging research has discovered the essential role of previously underappreciated factors such as products of gut microbiota or endothelial glycocalyx modifications. Molecular regulators such as microRNAs and hormonal disbalance further illustrate the complex mechanisms of venous thrombosis. Interestingly, circadian rhythms exhibit certain influence on thrombotic potential, introducing chronobiology as emerging variable affecting the risk of thrombosis. Based on these insights, future therapeutic strategies may include various interventions targeting or at least considering metabolic, molecular, and systemic non-inflammatory factors. Potential approaches include personalized risk stratification, microbiome modulation, endothelial protection approaches, and chronotherapy-based therapeutic modalities, that would ensure promising more efficient and safe thrombosis management.}, }
@article {pmid40117176, year = {2025}, author = {Zielińska, K and Udekwu, KI and Rudnicki, W and Frolova, A and Łabaj, PP}, title = {Healthy microbiome-moving towards functional interpretation.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, doi = {10.1093/gigascience/giaf015}, pmid = {40117176}, issn = {2047-217X}, support = {2020/38/E/NZ2/00598//NCN/ ; PLG/2023/016234//Jagiellonian University in Krakow/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; *Metagenomics/methods ; Metagenome ; Phylogeny ; Dysbiosis/microbiology ; Principal Component Analysis ; COVID-19/virology ; }, abstract = {BACKGROUND: Microbiome-based disease prediction has significant potential as an early, noninvasive marker of multiple health conditions linked to dysbiosis of the human gut microbiota, thanks in part to decreasing sequencing and analysis costs. Microbiome health indices and other computational tools currently proposed in the field often are based on a microbiome's species richness and are completely reliant on taxonomic classification. A resurgent interest in a metabolism-centric, ecological approach has led to an increased understanding of microbiome metabolic and phenotypic complexity, revealing substantial restrictions of taxonomy-reliant approaches.<br><br>FINDINGS: In this study, we introduce a new metagenomic health index developed as an answer to recent developments in microbiome definitions, in an effort to distinguish between healthy and unhealthy microbiomes, here in focus, inflammatory bowel disease (IBD). The novelty of our approach is a shift from a traditional Linnean phylogenetic classification toward a more holistic consideration of the metabolic functional potential underlining ecological interactions between species. Based on well-explored data cohorts, we compare our method and its performance with the most comprehensive indices to date, the taxonomy-based Gut Microbiome Health Index (GMHI), and the high-dimensional principal component analysis (hiPCA) methods, as well as to the standard taxon- and function-based Shannon entropy scoring. After demonstrating better performance on the initially targeted IBD cohorts, in comparison with other methods, we retrain our index on an additional 27 datasets obtained from different clinical conditions and validate our index's ability to distinguish between healthy and disease states using a variety of complementary benchmarking approaches. Finally, we demonstrate its superiority over the GMHI and the hiPCA on a longitudinal COVID-19 cohort and highlight the distinct robustness of our method to sequencing depth.<br><br>CONCLUSIONS: Overall, we emphasize the potential of this metagenomic approach and advocate a shift toward functional approaches to better understand and assess microbiome health as well as provide directions for future index enhancements. Our method, q2-predict-dysbiosis (Q2PD), is freely available (https://github.com/Kizielins/q2-predict-dysbiosis).}, }
@article {pmid40116950, year = {2025}, author = {Chan, YL and Liao, JC and Li, TL and Wu, CJ and Chiu, YH}, title = {Bifidobacterium lactis ameliorates AOM/DSS-induced inflammation, dysbiosis, and colonic precancerous lesions.}, journal = {Applied microbiology and biotechnology}, volume = {109}, number = {1}, pages = {69}, pmid = {40116950}, issn = {1432-0614}, support = {MOST 109-2320-B-031-001//Ministry of Science and Technology/ ; }, mesh = {Animals ; *Dysbiosis/microbiology ; *Probiotics/administration &amp; dosage/pharmacology ; *Mice, Inbred C57BL ; Female ; Mice ; *Precancerous Conditions/prevention &amp; control/microbiology/chemically induced/pathology ; *Dextran Sulfate/toxicity ; *Gastrointestinal Microbiome ; *Bifidobacterium animalis ; *Azoxymethane/toxicity ; *Inflammation/prevention &amp; control ; *Disease Models, Animal ; Colonic Neoplasms/prevention &amp; control/pathology ; Cytokines/metabolism ; NF-kappa B/metabolism ; }, abstract = {Bowel cancer is the third most common malignancy of tumors and one of the major causes of cancer-related death. Bowel precancerous conditions can develop without any symptoms, which either makes it difficult for early diagnosis or poses a poor prognosis/gloomy relapse. This study aimed to investigate the effects of Bifidobacterium animalis subsp. lactis TCI604 (B. lactis) on inflammatory responses, gut microbiome, and protectiveness against azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced colonic precancerous lesions. The AOM/DSS-induced colonic precancerous lesion murine model was studied with 24 female C57BL/6 J mice assigned to the control group, AOM/DSS-induced colonic precancerous lesion group (AOM/DSS), AOM/DSS treated with B. lactis probiotic group (B. lactis P), and AOM/DSS treated with B. lactis cell-free supernatant group (B. lactis S). The results showed that both B. lactis P and B. lactis S could attenuate AOM/DSS-induced body weight loss and intestine damage, reduce aberrant crypt foci (ACF) and the formation of colonic polyps, and significantly inhibit pro-inflammatory cytokines and the NF-κB signaling pathway, in which the B. lactis S group outperformed others. Further analysis using 16S rDNA sequencing suggested that both B. lactis P and B. lactis S optimize gut microbiota. Several bacteria, including Muribaculaceae, Prevotellaceae_UCG-001, Anaerostipes, Ruminococcaceae, Mucispirillum, Clostridia_UCG-014, and Clostridia_vadinBB60 that were known in close relation to colonic precancerous lesions, were sequenced at taxonomic level. Our results indicated that both B. lactis P and B. lactis S improved AOM/DSS-induced colonic precancerous lesions by regulating inflammation as well as optimizing gut microbiota, thereby establishing reciprocally cooperative net benefits between probiotics/postbiotics and mice with colonic precancerous lesions. KEY POINTS: • Prophylactic administration of probiotic and postbiotic of B. lactis is capable of alleviating the AOM/DSS-induced body weight loss and colon shortening, as well as diminishing the development of colonic precancerous lesions, such as the formation of ACF and colonic polyps, in an AOM/DSS mouse model • Either probiotic or postbiotic of B. lactis has a positive role in mediating immune imbalance and colonic inflammation via suppression of inflammatory immune cells, pro-inflammatory cytokines, and the NF-κB signaling pathway • AOM/DSS-induced dysbiosis can be reversed with the probiotic and postbiotic of B. lactis supplementation.}, }
@article {pmid40116510, year = {2025}, author = {Lebovics, N and Heering, G and Frishman, WH and Lebovics, E}, title = {Lean MASLD and Cardiovascular Disease: A Review.}, journal = {Cardiology in review}, volume = {}, number = {}, pages = {}, doi = {10.1097/CRD.0000000000000893}, pmid = {40116510}, issn = {1538-4683}, abstract = {Metabolic-associated steatotic liver disease (MASLD), formerly known as nonalcoholic fatty liver disease, is prevalent worldwide and is highly associated with cardiovascular disease (CVD). Lean MASLD is defined by hepatic steatosis and cardiometabolic risk factors in individuals with a body mass index below 25 in Western populations or below 23 in Asian populations. Paradoxically, some studies indicate that lean MASLD is associated with an elevated risk of cardiovascular (CV) disease and CV mortality compared with nonlean MASLD. Lean MASLD patients exhibit distinctive metabolic, genetic, and microbiome profiles contributing to increased visceral adiposity, sarcopenia, hepatic fibrosis, systemic inflammation, and endothelial dysfunction. This review examines the epidemiology, pathophysiology, and CV outcomes associated with lean MASLD, addressing discrepancies in the literature. Furthermore, it highlights current clinical guidelines, emphasizes lifestyle modifications, and discusses emerging pharmacotherapies as potential treatment options.}, }
@article {pmid40116497, year = {2025}, author = {Moreland, RB and Choi, BI and Fontes Noronha, M and Baker, J and Kaindl, J and Wolfe, AJ}, title = {Complete genome sequence of Trueperella bernardiae strain UMB8254, isolated from the bladder of a female with metabolic syndrome and nephrolithiasis.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0126524}, doi = {10.1128/mra.01265-24}, pmid = {40116497}, issn = {2576-098X}, abstract = {Trueperella bernardiae is infrequently isolated, usually in polymicrobial communities, from human hosts with a wide variety of symptoms and diseases. Here, we report a complete genome sequence of Trueperella bernardiae (UMB8254), isolated from the bladder of a human female with metabolic syndrome and nephrolithiasis.}, }
@article {pmid40116459, year = {2025}, author = {Blakeley-Ruiz, JA and Bartlett, A and McMillan, AS and Awan, A and Walsh, MV and Meyerhoffer, AK and Vintila, S and Maier, JL and Richie, TG and Theriot, CM and Kleiner, M}, title = {Dietary protein source alters gut microbiota composition and function.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf048}, pmid = {40116459}, issn = {1751-7370}, support = {7002782//USDA National Institute of Food and Agriculture, Hatch/ ; P30 DK034987/NH/NIH HHS/United States ; }, abstract = {The source of protein in a person's diet affects their total life expectancy. However, the mechanisms by which dietary protein sources differentially impact human health and life expectancy are poorly understood. Dietary choices impact the composition and function of the intestinal microbiota that ultimately modulate host health. This raises the possibility that health outcomes based on dietary protein sources might be driven by interactions between dietary protein and the gut microbiota. In this study, we determined the effects of seven different sources of dietary protein on the gut microbiota of mice using an integrated metagenomics-metaproteomics approach. The protein abundances measured by metaproteomics can provide microbial species abundances, and evidence for the molecular phenotype of microbiota members because measured proteins indicate the metabolic and physiological processes used by a microbial community. We showed that dietary protein source significantly altered the species composition and overall function of the gut microbiota. Different dietary protein sources led to changes in the abundance of microbial proteins involved in the degradation of amino acids and the degradation of glycosylations conjugated to dietary protein. In particular, brown rice and egg white protein increased the abundance of amino acid degrading enzymes. Egg white protein increased the abundance of bacteria and proteins usually associated with the degradation of the intestinal mucus barrier. These results show that dietary protein sources can change the gut microbiota's metabolism, which could have major implications in the context of gut microbiota mediated diseases.}, }
@article {pmid40116078, year = {2025}, author = {Whitlock, JW and Orwin, PM and Stahlschmidt, ZR}, title = {Multigenerational exposure to glyphosate has only modest effects on life history traits, stress tolerance, and microbiome in a field cricket.}, journal = {The Journal of experimental biology}, volume = {}, number = {}, pages = {}, doi = {10.1242/jeb.250210}, pmid = {40116078}, issn = {1477-9145}, support = {//University of the Pacific/ ; }, abstract = {Glyphosate (GLY) is the most used herbicide worldwide, and it can be toxic to off-target species, such as insects. While GLY-based herbicides (GBHs) can influence insect microbiomes, little is known about its cascading effects on fitness-related traits, such as life history or stress tolerance, especially in the context of long-term, multigenerational exposure. Thus, we exposed the variable field cricket, Gryllus lineaticeps, to GBH within- and across-generations to examine the potential role of GBH in developmental plasticity and evolution. Specifically, we measured its effects on life-history traits (e.g., developmental duration, adult body size and mass, and a life-history tradeoff between investment into reproduction and flight), stress (heat and desiccation) tolerance, and the gut microbiome. One generation of exposure to GBH reduced desiccation tolerance, which was also lower in flight-capable individuals. However, after 11 generations of exposure to GBH, this cost of GBH disappeared, and GBH exposure instead increased adult body size and mass in flight-incapable individuals. Flight capacity had a stronger effect on the gut bacterial community than GBH exposure where flight-capable individuals contained more than twice as many Family Oscillospiraceae and fewer than half as many Family Erysipelotrichaceae. The effects of both flight capacity and GBH on the microbiome were only evident in Generation 1. Together, our results indicate that GBH exposure may have quite modest long-term effects on stress tolerance and the gut microbiome. However, GBH may facilitate the evolution of flightlessness given its potential benefits to flight-incapable individuals, which exhibit greater reproductive potential and tolerance to climate stressors compared to flight-capable individuals.}, }
@article {pmid40115756, year = {2025}, author = {Balaji, S and Jeyaraman, N and Jeyaraman, M and Ramasubramanian, S and Muthu, S and Santos, GS and da Fonseca, LF and Lana, JF}, title = {Impact of curcumin on gut microbiome.}, journal = {World journal of experimental medicine}, volume = {15}, number = {1}, pages = {100275}, pmid = {40115756}, issn = {2220-315X}, abstract = {The intricate interplay between natural compounds like curcumin and the gut microbiome has gained significant attention in recent years due to their potential therapeutic implications in various health conditions. Curcumin, a polyphenolic compound derived from turmeric, exhibits diverse pharmacological properties, including anti-inflammatory, antioxidant, and anticancer effects. Understanding how curcumin modulates gut microbiota composition and function is crucial for elucidating its therapeutic mechanisms. This review examines the current literature on the interactions between curcumin and the gut microbiome. A systematic search of relevant databases was conducted to identify studies investigating the effects of curcumin on gut microbial diversity and abundance. Key findings from studies exploring curcumin's efficacy in neurological disorders, gastrointestinal diseases, and metabolic dysfunction are synthesized and discussed. Studies have demonstrated that curcumin supplementation can modulate gut microbiota composition and function, leading to beneficial effects on gut health and homeostasis. Mechanisms underlying curcumin's therapeutic effects include immune modulation, neuroprotection, and inflammation regulation. However, challenges such as poor bioavailability and safety concerns remain significant hurdles to overcome. The interactions between curcumin and the gut microbiome hold promise for therapeutic interventions in a diverse range of health conditions. Further research is needed to optimize curcumin formulations, improve bioavailability, and address safety concerns.}, }
@article {pmid40115744, year = {2025}, author = {Kimmel, M and Tong, B and Devall, AE and Björvang, RD and Schuppe-Koistinen, I and Engstrand, L and Fransson, E and Skalkidou, A and Hugerth, LW}, title = {Investigating the Microbiome in Relation to Mental Distress Across Two Points During Pregnancy: Data From U.S. and Swedish Cohorts.}, journal = {Biological psychiatry global open science}, volume = {5}, number = {3}, pages = {100453}, pmid = {40115744}, issn = {2667-1743}, abstract = {BACKGROUND: In this study, we aimed to characterize the gut microbiome and its potential functioning in 2 populations at 2 time points during pregnancy in relation to mental distress.<br><br>METHODS: During the second and third trimester, individuals from the United States and Sweden completed the Edinburgh Postnatal Depression Scale and provided fecal samples for whole-genome metagenomics. A total of 832 and 161 samples were sequenced and analyzed from the Swedish cohort and the U.S. cohort, respectively. Multiple characterizations of the microbial community were analyzed in relation to distress measured using the Edinburgh Postnatal Depression Scale. Principal coordinate analysis and distance-based redundancy analysis assessed variation in functional gut-brain modules. For the U.S. cohort, the Trier Social Stress Test was administered 8 weeks postpartum while collecting salivary cortisol.<br><br>RESULTS: Principal coordinate analysis identified 4 sample clusters based on the gut-brain modules distinguished by functions such as short-chain fatty acid synthesis and cortisol degradation. While with distance-based redundancy analysis, mental distress subtypes did not significantly contribute to variation in gut-brain modules (p&#xa0;= .085 for Sweden, p&#xa0;= .23 for the U.S.), a U.S. sample cluster distinguished by lower cortisol degradation from another cluster with higher gut microbial cortisol degradation abundance had significantly higher odds of being associated with depression (p&#xa0;= .024). The U.S. sample cluster with lower gut microbial cortisol degradation abundance also had significantly higher cortisol levels after a postpartum social stressor.<br><br>CONCLUSIONS: Further studies are warranted to investigate the potential for the gut microbiome to serve as biomarkers of gut-brain axis health during pregnancy across disparate populations.}, }
@article {pmid40115610, year = {2025}, author = {Waterman, A and Doumas, SA and Fischer, M and Mattar, M and Charbel, S and Jennings, J and Doman, DB}, title = {Uncovering the Hidden Link Between the Aberrant Intestinal Microbiome and Fibromyalgia.}, journal = {Gastroenterology &amp; hepatology}, volume = {21}, number = {2}, pages = {111-121}, pmid = {40115610}, issn = {1554-7914}, abstract = {Fibromyalgia is a multifaceted syndrome primarily characterized by chronic widespread pain and fatigue. Despite its significant prevalence and incidence, the mechanisms mediating the disease pathogenesis have remained poorly understood; however, increasing evidence suggests a potentially central role of intestinal dysbiosis. Researchers have been examining possible diagnostic biomarkers, such as Helicobacter pylori infection, urine metabolite profiles, and cytokine levels, which reflect these microbiome changes. Additionally, evaluation of therapeutic interventions targeting the gut microbiome, including probiotics, fecal microbiota transplantation, and antibiotics for specific infections, has highlighted their potential in alleviating fibromyalgia symptoms. This article delves into the emerging role of the gut microbiome in fibromyalgia pathogenesis, illustrating how alterations in gut bacterial composition and diversity are implicated in the pathophysiology of the disease through the gut-brain axis, and sets a direction for future research to enhance diagnostic accuracy and therapeutic efficacy of this complex condition.}, }
@article {pmid40115534, year = {2025}, author = {Kushkevych, I and Dvořáková, M and Dordevic, D and Futoma-Kołoch, B and Gajdács, M and Al-Madboly, LA and Abd El-Salam, M}, title = {Advances in gut microbiota functions in inflammatory bowel disease: Dysbiosis, management, cytotoxicity assessment, and therapeutic perspectives.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {851-868}, pmid = {40115534}, issn = {2001-0370}, abstract = {Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, have become increasingly prevalent across all human generations. Despite advances in diagnosis, effective long-term therapeutic options remain limited, with many patients experiencing recurrent symptoms after treatment. The multifactorial origins of ulcerative colitis are widely recognized, but the intestinal microbiome, particularly bacteria from the Desulfovibrionaceae family, is thought to play a central role in the pathogenesis of the disease. These bacteria contribute significantly to gut microbial functions, yet their cytotoxic and viability characteristics under disease conditions remain poorly understood. Our review provides insights on recent advancements in methodologies for assessing the cytotoxicity and viability of anaerobic intestinal bacteria, with a specific focus on their relevance to gut health and disease. We introduce overview from current literature on modern techniques including flow cytometry, high-throughput screening, and molecular-based assays, highlighting their applications in understanding the role of Desulfovibrionaceae and other gut microbes in IBD pathogenesis. By bridging methodological advancements with functional implications, this review aims to enhance our understanding of gut microbiota-host interactions, which are crucial for maintaining health and preventing disease through immune modulation, where microbiota help regulate immune responses and prevent excessive inflammation; nutrient metabolism, including the breakdown of dietary fibers into short-chain fatty acids that support gut health; and colonization resistance, where beneficial microbes outcompete harmful pathogens to maintain microbial balance.}, }
@article {pmid40115500, year = {2025}, author = {Liu, Q and Hao, N and Mi, L and Peng, S and Marie-Colette, AK and Zhao, X and Wang, J}, title = {From microbial communities to aroma profiles: A comparative study of spontaneous fermentation in merlot and cabernet sauvignon wines.}, journal = {Food chemistry: X}, volume = {26}, number = {}, pages = {102317}, pmid = {40115500}, issn = {2590-1575}, abstract = {This study aimed to compare the microbial community composition and aroma characteristics during the fermentation of different grape cultivars, Merlot and Cabernet Sauvignon. Principal Component Analysis (PCA), Partial Least Squares Discriminant Analysis (PLS-DA), and Odor Activity Value (OAV) screening identified 15 distinct active compounds. The sensory evaluation indicated that Merlot wine exhibited a more intense fruity aroma and received higher overall scores than Cabernet Sauvignon wine. High-throughput sequencing (HTS) results revealed that the microbial diversity in Merlot was higher than in Cabernet Sauvignon wine. Lachancea, Acremonium, Fructobacillus, and Lactiplantibacillus were unique to the Merlot wine, whereas Penicillium, Wickerhamomyces, Gluconobacter, and Klebsiella were exclusive to Cabernet Sauvignon wine. Saccharomyces and Tatumella were identified as the dominant microorganisms during the fermentation of both Merlot and Cabernet Sauvignon wines. Correlation analysis demonstrated a significant positive association among the dominant microbial communities, which played a crucial role in determining the formation of volatile compounds.}, }
@article {pmid40115072, year = {2025}, author = {Li, J and Hu, X and Tao, X and Li, Y and Jiang, W and Zhao, M and Ma, Z and Chen, B and Sheng, S and Tong, J and Zhang, H and Shen, B and Gao, X}, title = {Deconstruct the link between gut microbiota and neurological diseases: application of Mendelian randomization analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1433131}, pmid = {40115072}, issn = {2235-2988}, mesh = {Humans ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics ; *Nervous System Diseases/genetics/microbiology ; Brain-Gut Axis ; Genome-Wide Association Study ; }, abstract = {BACKGROUND: Recent research on the gut-brain axis has deepened our understanding of the correlation between gut bacteria and the neurological system. The inflammatory response triggered by gut microbiota may be associated with neurodegenerative diseases. Additionally, the impact of gut microbiota on emotional state, known as the "Gut-mood" relationship, could play a role in depression and anxiety disorders.<br><br>RESULTS: This review summarizes recent data on the role of gut-brain axis in the pathophysiology of neuropsychiatric and neurological disorders including epilepsy, schizophrenia, Alzheimer's disease, brain cancer, Parkinson's disease, bipolar disorder and stroke. Also, we conducted a Mendelian randomization study on seven neurological disorders (Epilepsy, schizophrenia, Alzheimer's disease, brain cancer, Parkinson's disease, bipolar disorder and stroke). MR-Egger and MR-PRESSO tests confirmed the robustness of analysis against horizontal pleiotropy.<br><br>CONCLUSIONS: By comparing the protective and risk factors for neurological disorders found in our research and other researches, we can furtherly determine valuable indicators for disease evolution tracking and potential treatment targets. Future research should explore extensive microbiome genome-wide association study datasets using metagenomics sequencing techniques to deepen our understanding of connections and causality between neurological disorders.}, }
@article {pmid40114846, year = {2025}, author = {Changaris, DG}, title = {Rapid Reversal of Forearm Supinator Rigidity With Topical Isomerized Potassium Linoleate: A Novel Perspective on Microbiome-Induced Tetany.}, journal = {Cureus}, volume = {17}, number = {3}, pages = {e80896}, pmid = {40114846}, issn = {2168-8184}, abstract = {Microbes can alter host behavior, immunity, and neurological function at a distance without extension into the brain and spinal cord. Clostridia provides a predicate for such an infection in the periphery by causing "lock jaw" and generalized tetany. This case series presents five patients who showed rigidity or tetany of the forearm. All were diagnosed with vertigo of central origin by video nystagmography (VNG) and posturography. Each had an apparent slow-rolling tetany, most visible in the forearm. Each had a consistent focus of pain within the supinator, diminution of extended wrist rotation, and tender, taut bands. None had clinical evidence of injury to the ulnar, radial, or median nerves, ulnar epicondyles, or wrist. The author applied a commercial preparation of a cleanser containing isomerized potassium linoleate (KCLA) to the skin overlying the forearm's biceps, supinator, and pronator as an "alternative" medical approach to refractory rigidity and tenderness. The tenderness resolved within two to four minutes. After 3-10 minutes, follow-on extended wrist rotation improved toward the norm (p < 0.01). The improved range of motion lasted beyond discharge from the clinic visit. The rapid response in this series suggests the commensal skin biome may contribute to clinical tetany in the forearm supinator.}, }
@article {pmid40114632, year = {2025}, author = {Zhao, X and Büdeyri Gökgöz, N and Xie, Z and Jakobsen, LMA and Nielsen, DS and Bertram, HC}, title = {Effects of calcium supplementation on the composition and activity of in vitro simulated gut microbiome during inulin fermentation.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4fo06365a}, pmid = {40114632}, issn = {2042-650X}, abstract = {The gut microbiome influences the availability of micronutrients in the gastrointestinal tract. However, our insights into how colonic fermentation of prebiotic fibers and lactose is modulated by the presence of micronutrients and local pH environment are limited. Here, we investigated the influence of different calcium salts (calcium phosphate (CaPi), calcium citrate (CaCi), and calcium carbonate (CaCa)) on gut microbiome composition and metabolism using inulin and lactose as carbohydrate sources under low, medium, and high in vitro colonic pH gradients. Our results showed that in vitro colonic pH gradient had a significant effect on gut microbiome diversity (observed ASVs and Shannon diversity index, p < 0.05). After 24 hours of fermentation, the calcium sources had a significant effect on beta diversity at all colonic pH gradients (adjusted p < 0.05). Although changes in GM composition were more pronounced after 24 hours, after 6 hours of fermentation, the CaPi group exhibited a higher abundance of Leuconostoc than other groups. After 24 hours of fermentation, the CaPi group exhibited a higher Blautia abundance at high colonic pH gradient and lower Bacteroides abundance at all colonic pH gradient levels. The CaCi and CaCa groups exhibited a pH-dependent decrease in the abundance of Bacteroides. In addition, Bifidobacterium abundance remained over 1% regardless of colonic pH gradient, calcium source, or fermentation time. In addition, short-chain fatty acid (SCFA) production was dependent on the calcium source. For instance, compared to the control group, the CaCi group exhibited higher acetate production at low and high colonic pH gradients, while the CaPi and CaCa groups showed enhanced lactate production at medium and low pH gradients. These findings can increase our understanding of the impacts of calcium-rich diets on the human gut microbiome and its metabolic activity.}, }
@article {pmid40114628, year = {2025}, author = {Altun, M and Küçük, U and Yıldırım, N}, title = {Modulation of Gut Microbiota Using VSL#3 and Its Impact on Aortic Parameters in a Rat Model.}, journal = {Anatolian journal of cardiology}, volume = {}, number = {}, pages = {}, doi = {10.14744/AnatolJCardiol.2025.5048}, pmid = {40114628}, issn = {2149-2271}, abstract = {BACKGROUND: The increase in aortic stiffness is a significant parameter of cardiovascular diseases (CVDs), posing a substantial global health challenge and economic burden. The gut microbiota and its homeostasis, directly and indirectly, influence CVD. This study investigated the extent to which alterations in the gut microbiota can affect aortic parameters in a rat model through the administration of VSL#3.<br><br>METHODS: Twelve male Wistar rats were divided into VSL#3-treated and control groups. Cardiac function, aortic systolic, and diastolic values were assessed via echocardiography on day 0 and day 42, and fecal specimens were simultaneously collected from each rat. The formation and composition of the gut microbial flora were profiled using 16S rDNA gene sequencing.<br><br>RESULTS: Differences in bacterial density, as indicated by Chao analysis, exhibited statistical significance (P = .037) between the 2 groups. Additionally, in the VSL#3-treated group, significant improvements were observed in aortic systolic and diastolic diameters, as well as in aortic strain parameters, compared to the control group.<br><br>CONCLUSION: This research highlights the potential of gut microbiome modulation, specifically through VSL#3 administration, as a promising strategy to improve aortic parameters, suggesting a novel avenue for cardiovascular health interventions.}, }
@article {pmid40114538, year = {2025}, author = {Salvatore, S and Dinleyici, EC and Szajewska, H and Canani, RB and Gutierrez-Castrellón, P and Hojsak, I and Indrio, F and Mihatsch, W and Orel, R and van Goudoever, JB and Vandenplas, Y and , }, title = {Technical review by the ESPGHAN Special Interest Group on Gut Microbiota and Modifications on the health outcomes of infant formula supplemented with synbiotic.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1002/jpn3.70031}, pmid = {40114538}, issn = {1536-4801}, support = {//None/ ; }, abstract = {This technical review-one of five developed by the European Society for Pediatric Gastroenterology, Hepatology, and Nutrition (ESPGHAN) Special Interest Group on Gut Microbiota and Modifications (SIG-GMM)-supports the preparation of a position paper on the use of biotic- and synbiotic-supplemented infant formulas. This paper also presents the statements made by the SIG-GMM after performing a technical review to evaluate the clinical effects of synbiotic-supplemented infant formulas in healthy full-term infants (0-12 months), as emerged from studies published before 2024. The review focused on the following clinical outcomes (if available): anthropometric measurements, safety, tolerability, stool frequency and consistency, infantile colic or crying, gastrointestinal symptoms, infections and antibiotic use, and allergic disorders. Following the review, all members of the SIG anonymously voted on each statement, scoring them between 0 and 9. A statement was accepted when ≥75% of the members scored >6. The technical review identified 16 randomized controlled trials that evaluated the clinical effects of synbiotic-supplemented infant formula in healthy full-term infants. The studies varied in terms of synbiotic composition, study design, intervention duration, and outcomes. Formulas supplemented with synbiotics studied so far were well tolerated and showed no significant difference compared to the non-supplemented formulas in growth parameters, gastrointestinal symptoms, stool characteristics, or safety. This technical review serves as the background for formulating recommendations on the use of synbiotic-supplemented infant formula in healthy infants studied so far.}, }
@article {pmid40114327, year = {2025}, author = {Żychowska, M and Bakuła, Z and Decewicz, P and Hryncewicz-Gwóźdź, A and Dyląg, M and Jankowska-Konsur, A and Gawor, J and Gromadka, R and Żaczek, A and Jagielski, T}, title = {The Skin Mycobiome of Patients With Atopic Dermatitis and Healthy Volunteers: A Case-Control Study.}, journal = {Experimental dermatology}, volume = {34}, number = {3}, pages = {e70085}, doi = {10.1111/exd.70085}, pmid = {40114327}, issn = {1600-0625}, support = {0258/IP1/2016/74//Ministerstwo Edukacji i Nauki/ ; }, mesh = {Humans ; *Dermatitis, Atopic/microbiology ; *Mycobiome ; Case-Control Studies ; Adult ; Female ; Male ; *Skin/microbiology ; Middle Aged ; Young Adult ; Healthy Volunteers ; Malassezia/isolation &amp; purification ; Adolescent ; }, abstract = {Atopic dermatitis (AD) is a common inflammatory skin disease, for which dysbiosis of the skin mycobiome is considered a triggering factor. The aim of this study was to explore the skin mycobiome of AD patients and healthy volunteers (HV). The study included 50 AD patients and as many HV. Culture-based species identification involved a battery of conventional phenotypic tests and PCR sequencing of the internal transcribed spacer (ITS) 1 and 2 regions within the rDNA cluster. Culture-independent, metataxonomic sequencing was performed with ITS1 as the target region. The overall culture-positive rate was higher in AD patients than in HV (74% vs 28%). Among the former, Rhodotorula spp. dominated, followed by Candida spp., Malassezia spp. and Naganishia albida. The congruence between PCR sequencing and phenotyping was 68.6%. Upon metataxonomy of AD samples, 33 (66%) demonstrated close clustering with HV samples ('control-like' AD), while 17 (34%) displayed a remarkably different mycobiome composition ('AD-specific'), with Cladosporium, Malassezia, Candida, Diplodia, Saccharomyces, Penicillium and Aspergillus genera showing increased abundance. Patients with 'AD-specific' mycobiomes were more commonly exposed to air-conditioning compared to 'control-like' AD patients (p = 0.030). A subset of patients with AD has a different cutaneous mycobiome make-up dominated by environmental moulds, and Malassezia and Candida yeasts. Anthropogenic factors may affect the cutaneous mycobiome composition in AD and should be taken into account in microbiome studies.}, }
@article {pmid40114168, year = {2025}, author = {Wu, Y and Qu, Z and Wu, Z and Zhuang, J and Wang, Y and Wang, Z and Chu, J and Qi, Q and Han, S}, title = {Multiple primary malignancies and gut microbiome.}, journal = {BMC cancer}, volume = {25}, number = {1}, pages = {516}, pmid = {40114168}, issn = {1471-2407}, support = {2022E50008, 2024ZY01056//Zhejiang Provincial Clinical Research Center for CANCER/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; Middle Aged ; *Metagenomics/methods ; *Neoplasms, Multiple Primary/microbiology/virology ; Colorectal Neoplasms/microbiology/virology ; Adult ; Aged ; Bacteria/classification/genetics/isolation &amp; purification ; Enterovirus/isolation &amp; purification/genetics ; Case-Control Studies ; Feces/microbiology/virology ; }, abstract = {BACKGROUND: Multiple primary malignancies (MPM) are two or more independent primary malignancies. Recently, the relationship between microbiome and various tumors has been gradually focused on.<br><br>OBJECTIVE: To describe the relationship between MPM patients (MPMs) and gut microbiome.<br><br>METHODS: A total of 27 MPMs, 30 colorectal cancer patients (CRCs), and 30 healthy individuals were included to obtain metagenomic sequencing data. The knowledge graphs of gut bacteria and enteroviruses were plotted based on metagenomics. Wilcoxon rank-sum test was used to screen the characteristic gut microbiome.<br><br>RESULTS: The knowledge graph of gut microbiome in MPM patients was plotted. A total of 26 different gut bacteria, including Dialister, Fecalibacterium and Mediterraneibacter, were found between MPMs and healthy individuals. Twenty gut bacteria, including Parvimonas, Dialister and Mediterraneibacter, were more abundant in MPM complicated by CRC compared with CRCs. Twenty-one different enterovirus, including Triavirus, Punavirus and Lilyvirus, were screened between MPMs and healthy individuals. Triavirus, Punavirus and Lilyvirus were less abundant in MPM than healthy individuals. The abundance of Triavirus, Punavirus and Lilyvirus in CRC patients were also lower than MPM complicated by CRC patients.<br><br>CONCLUSION: The knowledge graph of gut microbiome in MPM patients was plotted. It may provide basic data support for future research of MPM.}, }
@article {pmid40114065, year = {2025}, author = {Pyakurel, S and Caddey, BJ and Dias, AP and De Buck, J and Morck, DW and Orsel, K}, title = {Profiling bacterial communities in feedlot cattle affected with bovine foot rot and bovine digital dermatitis lesions using 16S rRNA gene sequencing and quantitative real-time PCR.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {158}, pmid = {40114065}, issn = {1471-2180}, mesh = {Animals ; Cattle ; *RNA, Ribosomal, 16S/genetics ; *Real-Time Polymerase Chain Reaction/methods ; *Digital Dermatitis/microbiology ; *Cattle Diseases/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *DNA, Bacterial/genetics ; Microbiota ; Foot Diseases/microbiology/veterinary ; Skin/microbiology/pathology ; Treponema/genetics/classification/isolation &amp; purification ; Fusobacterium necrophorum/genetics/isolation &amp; purification ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: The primary infectious foot diseases in cattle, bovine foot rot (BFR) and bovine digital dermatitis (BDD), commonly associated with Fusobacterium necrophorum and Treponema spp., respectively, are considered polybacterial in etiology with several additional bacteria involved such as Porphyromonas levii, Bacteroides pyogenes, and Fusobacterium mortiferum. BDD is further classified into several M-stages (M2: active and ulcerative; M4: chronic proliferative). Using quantitative real-time PCR and 16S rRNA gene (V3-V4 region) sequencing, we quantified several specific bacteria and analyzed bacterial communities present in biopsies of visually diagnosed cases of BFR (n = 32), M2 (n = 17), and M4 (n = 12) stages of BDD in feedlot cattle in contrast to inconclusive (n = 14) clinical cases and healthy (n = 25) cattle.<br><br>RESULTS: Bacterial composition of healthy skin differed significantly from that of skin lesions, and between BFR and both lesion stages of BDD, which also differed from each other. All animal groups had generally the same bacterial species, albeit in distinct ratios. Differential abundance analysis relative to the healthy group identified a higher abundance of Fusobacterium spp. in BFR and Treponema spp. in both BDD-M2 and BDD-M4. P. levii had the highest absolute abundance in all animal groups. A significantly higher abundance of F. necrophorum was observed in BFR compared to BDD-M2, and F. mortiferum in both stages of BDD compared to the inconclusive group. Both BDD M-stages had a significantly higher abundance of Treponema phagedenis and Treponema pedis. Treponema medium was significantly more abundant in BDD-M4 compared to BDD-M2.<br><br>CONCLUSION: These results further the evidence of the involvement of Treponema spp., in BDD in feedlot cattle. However, it suggests further exploration of the role of Fusobacterium spp. in BFR and BDD. Importantly, a discriminating polybacterial involvement in these infections was evident demonstrated by changes in the population of multiple bacteria when compared to healthy animals.}, }
@article {pmid40113967, year = {2025}, author = {Mannaa, M and Park, AR and Kim, JC and Seo, YS}, title = {Microbial allies recruited by Bacillus subtilis JCK-1398 to defend pine trees against pinewood nematode.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {9670}, pmid = {40113967}, issn = {2045-2322}, mesh = {Animals ; *Pinus/parasitology/microbiology ; *Plant Diseases/parasitology/microbiology/prevention &amp; control ; *Bacillus subtilis/physiology ; Rhizosphere ; Microbiota ; Nematoda/microbiology/physiology ; Soil Microbiology ; Disease Resistance ; Pantoea/physiology/genetics ; }, abstract = {Pine wilt disease (PWD) is a devastating disease caused by the pinewood nematode (Bursaphelenchus xylophilus). Its substantial ecological disruption harms global forestry and poses serious economic challenges. Although previous research has demonstrated that Bacillus subtilis JCK-1398 has the potential to induce systemic resistance in pine trees, the ecological mechanisms underlying its biocontrol efficacy remain underexplored. This study investigated how JCK-1398 treatment influences rhizosphere- and nematode-associated microbial communities to mitigate PWD. Metabarcoding analyses revealed that JCK-1398 treatment increased the abundance of beneficial microbial taxa (e.g., Nocardioides and Mesorhizobium) in the rhizosphere microbiome. Concurrently, nematode-associated microbial communities became dominated by Pantoea, a genus with known nematicidal properties. Isolation and characterization of Pantoea dispersa BC11 confirmed that it significantly limits nematode viability. These findings highlight the multifaceted defense that JCK-1398 offers, not only inducing systemic resistance, but also orchestrating beneficial microbiome dynamics. This study emphasizes the potential of manipulating a microbial holobiont for eco-friendly and sustainable disease management. The ability of JCK-1398 to recruit and enhance microbial allies offers a novel framework for developing biocontrol agents, with implications for managing PWD and other plant-pathogen systems.}, }
@article {pmid40113862, year = {2025}, author = {Groen-van Schooten, TS and Cabeza-Segura, M and Ferreira, RM and Martínez-Ciarpaglini, C and Barros, R and Santos-Antunes, J and Costa, A and Fernández-Figueroa, EA and Lino-Silva, L and Hernandez-Guerrero, AI and Ruiz-García, E and Caballero, C and Boggino, H and Gauna, C and Cantero, D and Freile, B and Esteso, F and O Connor, J and Riquelme, A and Owen, G and Riquelme, E and Roa, JC and Latorre, G and Garrido, M and Ruiz-Pace, F and Diez García, M and Alsina, M and Lordick, F and Farrés, J and Carbonell-Asins, JA and Villagrasa, R and Pereira, R and Pouw, RE and Jimenez-Martí, E and Miralles, A and Dientsmann, R and Figueiredo, C and Carneiro, F and Cervantes, A and Derks, S and Fleitas, T}, title = {Immune profiling of gastric adenocarcinomas in EU and LATAM countries identifies global differences in immune subgroups and microbiome influence.}, journal = {British journal of cancer}, volume = {}, number = {}, pages = {}, pmid = {40113862}, issn = {1532-1827}, abstract = {BACKGROUND: Gastric cancer (GC) patients from European (EU) and especially Latin American (LATAM) countries are underrepresented in previous large-scale multi-omic studies that have identified clinically relevant subgroups. The LEGACY study aimed to profile the molecular and immunological features of GCs from EU and LATAM countries.<br><br>METHODS: Tumor biopsies from 95 EU and 56 LATAM GCs were profiled with immunohistochemistry (CD3, CD8, FOXP3, PD-L1, MSI and HER2), Nanostring mRNA expression analyses, and microbiome sequencing.<br><br>RESULTS: Immune profiling identified four distinct immune clusters: a T cell dominant cluster with enriched activation pathways, a macrophage dominant cluster and an immune excluded microenvironment which were equally distributed among the countries. A fourth cluster of mostly Mexican patients consisted of excessive T cell numbers accompanied by enhanced cytokine signaling in absence of enhanced antigen presentation and cytotoxicity signatures and a strong association with H. pylori infection.<br><br>DISCUSSION: Both EU and LATAM countries have GCs with a T cell inflamed microenvironment that might benefit from checkpoint inhibition. We identified a highly inflamed GC subgroup that lacked antigen presentation and cytotoxicity associated with H. pylori CagA-positive strains, suggesting their contribution to tumor immune tolerance. Future studies are needed to unravel whether these cancers benefit from immunotherapy as well.}, }
@article {pmid40113782, year = {2025}, author = {Park, G and Johnson, K and Miller, K and Kadyan, S and Singar, S and Patoine, C and Hao, F and Lee, Y and Patterson, AD and Arjmandi, B and Kris-Etherton, PM and Berryman, CE and Nagpal, R}, title = {Almond snacking modulates gut microbiome and metabolome in association with improved cardiometabolic and inflammatory markers.}, journal = {NPJ science of food}, volume = {9}, number = {1}, pages = {35}, pmid = {40113782}, issn = {2396-8370}, support = {ECP-Nagpal-NR-001//Almond Board of California/ ; 24A05//Florida Department of Health/ ; }, abstract = {Western-style dietary patterns have been linked with obesity and associated metabolic disorders and gut dysbiosis, whereas prudent dietary and snacking choices mitigate these predispositions. Using a multi-omics approach, we investigated how almond snacking counters gut imbalances linked to adiposity and an average American Diet (AAD). Fifteen adults with overweight or obesity underwent a randomized, crossover-controlled feeding trial comparing a 4-week AAD with a similar isocaloric diet supplemented with 42.5 g/day of almonds (ALD). Almond snacking increases functional gut microbes, including Faecalibacterium prausnitzii, while suppressing opportunistic pathogens, thereby favorably modulating gut microecological niches through symbiotic and microbe-metabolite interactions. Moreover, ALD elevates health-beneficial monosaccharides and fosters bacterial consumption of amino acids, owing to enhanced microbial homeostasis. Additionally, ALD enhances metabolic homeostasis through a ketosis-like effect, reduces inflammation, and improves satiety-regulating hormones. The findings suggest that prudent dietary choices, such as almond snacking, promote gut microbial homeostasis while modulating immune metabolic state.}, }
@article {pmid40113766, year = {2025}, author = {Nodit, L and Kelley, JR and Panella, TJ and Bruckbauer, A and Nodit, PG and Shope, GA and Peyton, K and Klingeman, DM and Zaretzki, R and Carrell, A and Podar, M}, title = {Oral microbiome and mycobiome dynamics in cancer therapy-induced oral mucositis.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {463}, pmid = {40113766}, issn = {2052-4463}, mesh = {Humans ; *Stomatitis/microbiology/etiology ; *Microbiota ; *Mycobiome ; Longitudinal Studies ; Mouth/microbiology ; Carcinoma, Squamous Cell/therapy/microbiology ; Chemoradiotherapy/adverse effects ; Oropharyngeal Neoplasms/therapy/microbiology ; }, abstract = {Cancer therapy-induced oral mucositis is a frequent major oncological problem, secondary to cytotoxicity of chemo-radiation treatment. Oral mucositis commonly occurs 7-10 days after initiation of therapy; it is a dose-limiting side effect causing significant pain, eating difficulty, need for parenteral nutrition and a rise of infections. The pathobiology derives from complex interactions between the epithelial component, inflammation, and the oral microbiome. Our longitudinal study analysed the dynamics of the oral microbiome (bacteria and fungi) in nineteen patients undergoing chemo-radiation therapy for oral and oropharyngeal squamous cell carcinoma as compared to healthy volunteers. The microbiome was characterized in multiple oral sample types using rRNA and ITS sequence amplicons and followed the treatment regimens. Microbial taxonomic diversity and relative abundance may be correlated with disease state, type of treatment and responses. Identification of microbial-host interactions could lead to further therapeutic interventions of mucositis to re-establish normal flora and promote patients' health. Data presented here could enhance, complement and diversify other studies that link microbiomes to oral disease, prophylactics, treatments, and outcome.}, }
@article {pmid40113321, year = {2025}, author = {Yan, ZH and Cheng, X and Hu, TH and Zhong, QH}, title = {[Accumulation and Clearance of Polystyrene Microplastics in Brine Shrimp and the Responses of Microbiome and Metabolism].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {46}, number = {3}, pages = {1841-1849}, doi = {10.13227/j.hjkx.202403163}, pmid = {40113321}, issn = {0250-3301}, mesh = {Animals ; *Artemia ; *Microplastics/toxicity/metabolism ; *Polystyrenes/toxicity/metabolism ; *Water Pollutants, Chemical/metabolism ; *Microbiota ; Particle Size ; }, abstract = {To investigate the accumulation kinetics of microplastics （MPs） with different characteristics in zooplankton and the related biological effects, the accumulation and clearance of polystyrene microplastics （PS-MPs） with different concentrations and particle sizes in brine shrimp （Artemiasaline） were analyzed under different nutritional conditions. The responses of microbial communities and metabolic functions in brine shrimp were revealed using the combination methods of microbiome and metabolome. The results showed that the accumulation and clearance rate of PS-MPs in brine shrimp increased with the increase in exposure concentrations, showing a concentration-dependent manner. On the contrary, the accumulation and clearance of PS-MPs in brine shrimp were negatively correlated with their particle sizes. The nutritional condition did not alter the accumulation kinetics of PS-MPs in brine shrimp, indicating that short-term feeding may have had no effect on the uptake and clearance of PS-MPs in brine shrimp. Compared to that in the control, exposure to PS-MPs significantly enhanced the diversity of the microbial community in brine shrimp. The proportions of Proteobacteria and Acinetobacter were increased by 0.4 folds and 12.3 folds, respectively, whereas the proportions of Firmicutes and Bacillus were decreased by 43% and 86%, respectively. This finding indicates that PS-MPs may have caused an imbalance of the bacterial community in brine shrimp by inhibiting the beneficial bacteria and stimulating the harmful bacteria, thus disrupting the metabolic function in brine shrimp. In addition, exposure to PS-MPs resulted in a production of 2 311 different metabolites in brine shrimp and mainly disrupted the pyrimidine metabolism and the biosynthesis of dermal sulfate/chondroitin sulfate in brine shrimp, leading to toxicity in the shrimp. The accumulation and biological effects of MPs with different characteristics in zooplankton may further affect the stability of aquatic systems, leading to unpredictable ecological risks.}, }
@article {pmid40113228, year = {2025}, author = {Cavon, J and Basso, M and Kadosh, KC and Gibbons, SM}, title = {The human gut microbiome and sleep across adulthood: associations and therapeutic potential.}, journal = {Letters in applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/lambio/ovaf043}, pmid = {40113228}, issn = {1472-765X}, abstract = {Sleep is an essential homeostatic process that undergoes dynamic changes throughout the lifespan, with distinct life stages predisposed to specific sleep pathologies. Similarly, the gut microbiome also varies with age, with different signatures associated with health and disease in the latest decades of life. Emerging research has shown significant cross-talk between the gut microbiota and the brain through several pathways, suggesting the microbiota may influence sleep, though the specific mechanisms remain to be elucidated. Here, we critically examine the existing literature on the potential impacts of the gut microbiome on sleep and how this relationship varies across adulthood. We suggest that age-related shifts in gut microbiome composition and immune function may, in part, drive age-related changes in sleep. We conclude with an outlook on the therapeutic potential of microbiome-targeted interventions aimed at improving sleep across adulthood, particularly for individuals experiencing high stress or with sleep complaints.}, }
@article {pmid40113076, year = {2025}, author = {Xu, HS and Chen, Y and Lin, YJ and Eldefrawy, F and Kramer, NE and Siracusa, JS and Kong, F and Guo, TL}, title = {Nanocellulose dysregulated glucose homeostasis in female mice on a Western diet: The role of gut microbiome.}, journal = {Life sciences}, volume = {}, number = {}, pages = {123567}, doi = {10.1016/j.lfs.2025.123567}, pmid = {40113076}, issn = {1879-0631}, abstract = {There is currently increased interest in nanocellulose as a food emulsifier and dietary supplement. It was hypothesized that nanocellulose could modulate behaviors and glucose homeostasis in female mice using mechanisms of altered gut microbiome and immune modulation. An initial experiment was conducted with the objective of examining whether three common types of nanocellulose affected the gut microbiome of female C57BL/6 mice on a Western diet. Cellulose nanofibrils (CNF), TEMPO-CNF and cellulose nanocrystals were administered at the physiologically relevant dose of 30 mg/kg/day for 30 days by gavage, with cellulose and water groups as the positive and negative controls, respectively. Findings suggested that CNF had the strongest effect on the gut microbiome. CNF was therefore selected for a chronic 6-month study on the gut microbiome, immune system and behaviors in female NOD mice, a model for type 1 diabetes. Gut microbiome analysis suggested that there might be some beneficial changes following subchronic exposure (e.g., at the two-month timepoint), however, this effect was no longer seen after chronic consumption (e.g., at the six-month timepoint). CNF treatment also altered the immune homeostasis, including decreases in the splenic Mac-3[+] population and serum level of proinflammatory chemokine LIX. Additionally, CNF consumption decreased diabetic incidences but had no effect on the depressive-like behavior and grip strength. However, further analysis, e.g., the insulin tolerance test, indicated that CNF-treated NOD mice might exhibit signs of insulin resistance. Taken together, nanocellulose dysregulated glucose homeostasis in female mice on a Western diet involving mechanisms related to alteration of the gut microbiome.}, }
@article {pmid40112923, year = {2025}, author = {Majenka, P and Hoffmann, M and Strobel, S and Rötzer, I and Enk, A and Hassel, JC}, title = {Influence of high-fiber diet on ipilimumab-induced gastrointestinal toxicity in metastatic melanoma.}, journal = {Clinical nutrition ESPEN}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.clnesp.2025.03.026}, pmid = {40112923}, issn = {2405-4577}, abstract = {BACKGROUND: The anti-cytotoxic T-lymphocyte-associated protein (CTLA)-4 antibody ipilimumab (ipi) and the anti-programmed death (PD)-1 antibody nivolumab (nivo) are routinely used to treat metastatic melanoma. One of the most frequent severe immune-related adverse events (irAEs) induced by ipi is diarrhea as a symptom of ir-colitis. Here, the composition of the gut microbiome was shown to correlate with the risk of developing colitis. Stimulated by a patient case and the knowledge that nutrition influences the gut microbiome, we performed a retrospective analysis to evaluate dietary habits and the frequency of colitis in patients with ipi +/- nivo therapy.<br><br>METHODS: Patients with metastasized stage III or IV melanoma who were treated with ipi +/- nivo and who were willing to take part in a nutritional survey and interview at least three months after the first ipi dose were included into the study. Dietary habits were investigated using the food frequency questionnaire (FFQ) and personal interviews. The calculated daily intake of calories, carbohydrates, fats, proteins, sugars, and dietary fiber was correlated with the development of ir-colitis.<br><br>RESULTS: 20 patients were included into this study, and all but one received ipi-nivo combination therapy. The median age was 59.5 years, and 60% were male. 4 of 20 patients (20%) developed ir-colitis grade 3 after two cycles in the median and were managed with at least high-dose corticosteroids. The FFQ and interview were conducted in a median of six months after treatment initiation. In general, the interviewed patients followed a typical western-pattern diet based on carbohydrates as the main, followed by fat as the second most important energy substrate. Comparing patients with and without colitis our investigation revealed that the achieved amount of recommended dietary fiber intake per total energy intake (TEI) was negatively associated with diarrhea and colitis (p = 0.061). No significant differences concerning daily intake of calories, carbohydrates, fats, proteins, and sugar were found. In addition, no significant differences were found among patients in terms of their age, gender, tobacco use, supplement intake, therapy regime, or body mass index (BMI).<br><br>CONCLUSIONS: This pilot study gives first hints that nutritional habits might influence treatment tolerability to ipi +/- nivo therapy. A high-fiber diet might protect against ir-colitis and diarrhea in ipi-treated patients. This observation should be validated by a prospective randomized interventional trial. However, if it is possible to prevent ir-colitis by a high-fiber diet that would be of great impact on routine patient treatment.}, }
@article {pmid40112626, year = {2025}, author = {Sun, N and Xin, J and Zhao, Z and Chen, Y and Gan, B and Duan, L and Luo, J and Wang, D and Zeng, Y and Pan, K and Jing, B and Zeng, D and Ma, H and Wang, H and Ni, X}, title = {Improved effect of antibiotic treatments on the hippocampal spatial memory dysfunction of mice induced by high fluoride exposure: Insight from assembly processes and co-occurrence networks of gut microbial community.}, journal = {Ecotoxicology and environmental safety}, volume = {294}, number = {}, pages = {118048}, doi = {10.1016/j.ecoenv.2025.118048}, pmid = {40112626}, issn = {1090-2414}, abstract = {High fluoride exposure was widely demonstrated to be related with brain memory impairment. Since the absorption of F[-] enters the body mainly through the gastrointestinal tract, studying the effects of excessive intake of fluoride on brain memory function in various gut microbiome states might have profound implications for the prevention of fluorosis because growing evidence revealed the significance of the "microbiota-gut-brain" axis (MGBA). In the present study, we aimed to illustrate the potential mechanism of gut microbiota on high fluoride exposure-induced hippocampal lesions and spatial memory dysfunction in mice by the various intestinal microecological environments, which were constructed by antibiotic treatment. Mice fed with normal (CG1 and Exp1 groups) or sodium-fluoride (CG2 and Exp2 groups; 24 mg/kg sodium fluoride per mouse) by gavage administration with or without antibiotic treatments, a combination of metronidazole (1 g/L) and ciprofloxacin (0.2 g/L) in drinking water. Mice gavaged with excessive sodium fluoride alone exhibited reduced weight gain, hippocampal tissue damages, spatial memory levels dysfunction, impaired intestinal permeability, decreased inflammatory cytokines expression and antioxidant capability in the hippocampal and ileal tissues. In contrast, antibiotic intervention significantly reversed these high fluoride exposure-induced hippocampal and ileal changes.16S rRNA high throughput sequencing found that ileal microbiota were dominated by abundant taxa, which is conducive to constructing microbial interaction networks and module communities, and identifying keystone species targeted by high fluoride exposure compared with colonic microbiome. In addition, the microbial community composition and assembly mechanism of ileal microbiome under the effects of antibiotics were suitable for revealing the characteristics of high fluoride environment. In the later analysis, Lactobacillus, Staphylococcus, Muribaculaceae and Robinsoniella were considered as the keystone species targeted by high fluoride-exposed mice based on the analysis of network node properties and niche overlap of ileal microbes. Spearman rank correlation demonstrated that these keystone species had significant effects on hippocampal memory levels and intestinal health, as well as microbial communities functions. Compared to previous researches, this study further revealed intestinal microbial coummunity mediated the underlying mechanism through antibiotic treatment against high fluoride-induce hippocampal spatial memory impairment.}, }
@article {pmid40112608, year = {2025}, author = {Chen, J and Wang, Z and Shen, X and Chen, R and Peng, Y and Cai, Y and Zeng, S and Liu, D and Yang, J and Zhuang, W and Wang, S and Xu, J and Ying, H}, title = {Solid-state fermentation through synthetic microbiome: An effective strategy for converting Chinese distillers' grains into functional protein feed.}, journal = {International journal of food microbiology}, volume = {435}, number = {}, pages = {111154}, doi = {10.1016/j.ijfoodmicro.2025.111154}, pmid = {40112608}, issn = {1879-3460}, abstract = {Chinese distillers' grains (CDGs), a byproduct of liquor production, have low protein, high fiber, and elevated alcohol/lactic acid levels, limiting their use as animal feed. This study utilised a synthetic microbiome composed of Candida utilis (protein enhancement), Trichoderma viride (fiber reduction), Bacillus subtilis (detoxification), and Lactobacillus casei (functional enhancement) for solid-state fermentation. The results showed that crude protein content increased to 23.61 %, and true protein content to 20.45 %. Crude fiber, ethanol, lactic acid, and acetic acid contents decreased by 22.31 %, 77.25 %, 85.08 %, and 73.89 %, respectively. Amino acid content increased by 23.80 %, and flavour compounds rose by 140.76 %. Mycotoxins like aflatoxin B1 (AFB1) and ochratoxin A (OTA) were undetectable, while vomitoxin (DON) remained below EU limits. In vitro digestibility of dry matter increased by 98.36 %. Pilot-scale trials showed a 1.42-fold increase in crude protein and a 1.34-fold increase in true protein, contributing to more efficient CDG utilisation and reduced agricultural costs.}, }
@article {pmid40111997, year = {2025}, author = {Nikitashina, L and Chen, X and Radosa, L and Li, K and Straßburger, M and Seelbinder, B and Böhnke, W and Vielreicher, S and Nietzsche, S and Heinekamp, T and Jacobsen, ID and Panagiotou, G and Brakhage, AA}, title = {The murine lung microbiome is disbalanced by the human-pathogenic fungus Aspergillus fumigatus resulting in enrichment of anaerobic bacteria.}, journal = {Cell reports}, volume = {44}, number = {3}, pages = {115442}, doi = {10.1016/j.celrep.2025.115442}, pmid = {40111997}, issn = {2211-1247}, abstract = {Here, we report significant changes in the composition of the lung microbiome and metabolome of mice under immune suppression, infection of immunosuppressed mice with virulent and avirulent strains of the clinically important human-pathogenic fungus Aspergillus fumigatus, and treatment with the clinically used antifungal drug voriconazole. Our data also indicate the important role of the gut microbiome for lung homeostasis mediated by the plasma metabolome. In the lung microbiome, DNA sequencing indicates that infection by A. fumigatus leads to a significant increase of anaerobic bacteria, most prominently of Ligilactobacillus murinus; the latter has been confirmed by qPCR analyses. We also isolated live bacteria, including L. murinus, from the murine lower respiratory tract. Co-cultivation of L. murinus and A. fumigatus leads to a reduction in oxygen concentration accompanied by an increase of L. murinus cells, suggesting that A. fumigatus establishes a microaerophilic niche, thereby promoting growth of anaerobic bacteria.}, }
@article {pmid40111698, year = {2025}, author = {Vernon, JJ}, title = {Modulation of the Human Microbiome: Probiotics, Prebiotics, and Microbial Transplants.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {277-294}, pmid = {40111698}, issn = {0065-2598}, mesh = {Humans ; *Prebiotics/administration &amp; dosage ; *Probiotics/therapeutic use ; *Microbiota/physiology ; Mouth/microbiology ; Gastrointestinal Microbiome/physiology ; Fecal Microbiota Transplantation/methods ; }, abstract = {The balance between health and disease is intrinsically linked to the interactions between microbial communities and the host. This complex environment of antagonism and synergy involves both prokaryotic and eukaryotic cells, whose collaborative metabolic pathways and immunomodulatory elements influence system homeostasis. As with the gut and other niches, the oral microbiome has the capacity to affect distal host sites. The ability to manipulate this environment holds the potential to impact local and systemic disease.With the increasing threat of antimicrobial resistance, novel approaches to reduce the burden of disease are essential. The use of probiotics and prebiotics is one such strategy. Probiotics introduce non-pathogenic bacteria into the environment to compete with pathogens for nutrients and attachment sites, or to produce metabolites that counteract disease aetiologies. Prebiotic compounds enhance the growth of health-associated organisms, offering additional benefits, whilst a conjunctive approach with probiotics potentially holds even greater promise. Though widely studied in the gastrointestinal context, their potential for treating oral diseases, such as dental caries and periodontitis, is less understood. Additionally, the use of microbial transplantations has demonstrated efficacy in other areas, reducing systemic inflammation and recolonising with commensal bacteria. Here we evaluate their use in the oral context and their modulatory impact on overall health.In this chapter, we discuss how pro- and prebiotic strategies seek to modulate both the oral and gut environments to promote oral health and prevent disease. We assess novel approaches for utilising health-associated microorganisms to combat oral disorders, either administered locally in the mouth or imparting influence through immune modulation via the oral-gut axis. By examining available clinical trial data, we aim to further understand the intricacies involved in this discipline. Furthermore, we consider the challenges facing the research community, including optimal candidate organism/compound selection and colonisation retention, as well as considerations for future research.}, }
@article {pmid40111697, year = {2025}, author = {Bartsch, S and Scholz, KJ and Al-Ahmad, A and Cieplik, F}, title = {Effects of Antimicrobial Agents Used for Dental Treatments: Impacts on the Human Oral Ecosystem and the Resistome.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {261-275}, pmid = {40111697}, issn = {0065-2598}, mesh = {Humans ; *Mouth/microbiology/drug effects ; *Drug Resistance, Bacterial/genetics/drug effects ; *Microbiota/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Anti-Infective Agents/pharmacology ; Bacteria/drug effects/genetics ; }, abstract = {Antimicrobial resistance (AMR) is a major public health concern, especially with regard to bacterial resistance to antibiotics. Dentists are responsible for approximately 10% of all antibiotic prescriptions. In addition, there seems to be a lack of awareness of potential resistance toward antiseptics and biocides such as chlorhexidine digluconate (CHX) or cetylpyridinium chloride (CPC), which are commonly used in dental practice but also included in over-the-counter products. In comparison to the gut microbiome, only a small number of studies have investigated the impact of antibiotics on the oral microbiome. Amoxicillin is a commonly prescribed antibiotic in dentistry, often used in combination with metronidazole. Several studies have addressed its impact on the oral microbiome. Similarly, the effects of ciprofloxacin, clindamycin, cephazolin, and benzylpenicillin have also been examined in various studies. However, due to variations in study designs, it is difficult to compare the effects of antibiotics on the oral microbiota, and conclusions can only be drawn at the phyla level. In contrast, studies on CPC and CHX have also focused on the genus level. The oral resistome mainly contains genes involved in resistance to macrolides, MLSB (macrolide, lincosamide, and streptogramin B), lincosamide and streptogramin A, fluoroquinolone, tetracycline, or penicillin. The oral cavity therefore serves as a reservoir for antibiotic resistance genes (ARGs), which are of crucial importance both for inflammations in the oral cavity and for the treatment of the entire human organism. Therefore, dentists must weigh up the benefits and risks of using antibiotics very carefully.}, }
@article {pmid40111696, year = {2025}, author = {Zeng, Y and Lin, D and Chen, A and Ning, Y and Li, X}, title = {Periodontal Treatment to Improve General Health and Manage Systemic Diseases.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {245-260}, pmid = {40111696}, issn = {0065-2598}, mesh = {Humans ; *Periodontitis/microbiology/therapy/immunology ; Dysbiosis/therapy/microbiology ; Microbiota ; Cardiovascular Diseases/therapy/microbiology/immunology ; }, abstract = {Periodontitis is increasingly recognized for its role in overall health and its associations with systemic conditions. Shared etiological factors, including microbiological, immunological, genetic, and environmental influences, have prompted interest in the potential impact of periodontal therapy on broader health outcomes. The oral microbiome plays a key role in the pathogenesis of periodontitis, with microbial imbalances (dysbiosis) contributing to inflammation and systemic disease progression. Additionally, immune responses to periodontal infection, such as chronic inflammation and dysregulated immune activity, are central to linking periodontitis with conditions like diabetes, cardiovascular disease, and autoimmune disorders. This chapter explores the connections between periodontal treatment and systemic diseases, such as diabetes, rheumatoid arthritis, cardiovascular disease, chronic kidney disease, Alzheimer's disease, digestive disorders, and respiratory disease. It also reviews the current research on the mechanisms, including microbial and immune factors, that underlie these associations. By emphasizing the role of periodontal health, the oral microbiome, and immune regulation in disease prevention and management, this chapter underscores the importance of integrated healthcare approaches to improve patient outcomes.}, }
@article {pmid40111695, year = {2025}, author = {Rus, MJ and Sauco Carballo, C and Faria, FD and Simon-Soro, A}, title = {Hormonal Environment Shapes the Oral Microbiome.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {225-242}, pmid = {40111695}, issn = {0065-2598}, mesh = {Humans ; *Microbiota/physiology ; *Mouth/microbiology ; *Saliva/microbiology/metabolism ; Hormones/metabolism ; Host Microbial Interactions/physiology ; Biofilms/growth &amp; development ; Female ; }, abstract = {Hormones are present in oral fluids and undergo dynamic changes throughout life. Hormonal changes can influence the interactions between the microbial community and the host. The oral microbiome is sensitive to changes in the oral environment, and hormonal fluctuations can create conditions that favour the growth of certain types of bacteria over others. Since the gingival niche harbours the resident microbial community in the biofilm form, while saliva has a transient microbiota in the planktonic form, both could modulate the host-microbial interaction under hormonal oscillations.The microbiome and hormones have a dynamic bidirectional interaction. Specific oral microorganisms can metabolize steroid hormones, disrupting their host regulation. Hormones can serve as host-microbial crosstalk related to health and disease. Hormonal imbalances are associated with systemic diseases such as polycystic ovary syndrome, endometriosis, cortisol-related conditions and oral cancer. Elucidating the complex relationship between steroid hormones and the oral microbiome offers valuable insights into the mechanisms of the disease and potential therapeutic avenues for maintaining oral and systemic health.}, }
@article {pmid40111694, year = {2025}, author = {Vieira Lima, CP and Pauletto, P and Lataro, RM and De Luca Canto, G and Dame-Teixeira, N and Stefani, CM}, title = {The Oral Microbiome in Diabetes, Arterial Hypertension, and Obesity: A Scoping Review.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {201-223}, pmid = {40111694}, issn = {0065-2598}, mesh = {Humans ; *Obesity/microbiology ; *Hypertension/microbiology ; *Diabetes Mellitus, Type 2/microbiology ; *Microbiota/genetics ; *Mouth/microbiology ; Saliva/microbiology ; }, abstract = {BACKGROUND: Changes in the oral microbiome are expected in the presence of chronic conditions such as type 2 diabetes mellitus (T2D), arterial hypertension (AH), and obesity (OB).<br><br>OBJECTIVE: We aimed to map the literature regarding oral microbiome changes in people with T2D, AH, or OB compared to those without these conditions.<br><br>METHODS: This scoping review was guided by the JBI Manual for Evidence Synthesis and reported according to the PRISMA extension for scoping reviews (PRISMA-ScR). A search strategy was developed and adapted to five databases (Embase, LILACS, PubMed, Scopus, and Web of Science) and gray literature (Google Scholar and ProQuest Dissertation and Thesis). Two reviewers individually screened studies for inclusion. Data from the studies, including the molecular method to evaluate the microbiome and the type of sample, were extracted and analyzed. The focus was significant changes in phylum and genera.<br><br>RESULTS: A total of 1413 records were retrieved from databases, 86 from gray literature, and 7 from reference lists. After the screening process, 50 records were included, 28 on T2D, 8 on AH, and 12 on OB. Two studies addressed metabolic syndromes. Most studies identified the oral microbiome in saliva using 16S rRNA amplicon sequencing.<br><br>CONCLUSION: At the phylum level, Fusobacteria was enriched in &#x2265;3 studies in people with T2D. Firmicutes enrichment was associated with T2D and OB. Genera enriched in T2D comprised Catonella, Leptotrichia, Prevotella, and Rothia. Aggregatibacter and Prevotella were enriched in OB. No phylum or genera were consistently enriched in AH.OSF protocol registration: DOI 10.17605/OSF.IO/XK72V (available at https://osf.io/z5fp4).}, }
@article {pmid40111693, year = {2025}, author = {Yu, X and Mankia, K and Do, T and Meade, J}, title = {Oral Microbiome Dysbiosis and Citrullination in Rheumatoid Arthritis.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {185-199}, pmid = {40111693}, issn = {0065-2598}, mesh = {*Arthritis, Rheumatoid/immunology/microbiology/metabolism ; Humans ; *Dysbiosis/microbiology/immunology ; *Citrullination ; *Microbiota/immunology ; *Mouth/microbiology/immunology ; Porphyromonas gingivalis/pathogenicity/immunology/metabolism ; Animals ; Autoimmunity ; Periodontal Diseases/microbiology/immunology/metabolism ; }, abstract = {Rheumatoid arthritis and periodontal diseases, both characterized by chronic inflammation, share many common risk factors, sparking interest in understanding their established association. Emerging research has shed light on the link between these two diseases potentially occurring through the intricate interactions within the oral microbiome. The enrichment of pathogenic strains and species in this microbial community disrupts the delicate balance of both ecological and immunological homeostasis with the host. Particular attention has been paid to the role of key pathogens, such as Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans, known for their immunomodulatory abilities. The generation of an autoimmune response against proteins modified by citrullination is known to be a key step in the pathogenesis of RA. Importantly, the bidirectional citrullination mediated by both host innate immune cells and oral bacteria generates citrullinated peptide neoepitopes, which may serve as potential triggers for the loss of tolerance and subsequent autoimmunity in susceptible individuals. This review highlights the importance of understanding the mechanisms through which oral microbiome dysbiosis and citrullination contribute to the onset and progression of RA. Insights into these mechanisms not only advance pathobiological understanding but also offer potential therapeutic targets. Furthermore, we discuss the potential impact of nonsurgical periodontal treatment in modifying disease progression or mitigating RA, underscoring the critical role of periodontal health in managing systemic inflammatory conditions.}, }
@article {pmid40111692, year = {2025}, author = {Gao, C and Kang, J}, title = {Oral Diseases Are Associated with Cognitive Decline and Dementia.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {171-183}, pmid = {40111692}, issn = {0065-2598}, mesh = {Humans ; *Dementia/epidemiology/etiology ; *Cognitive Dysfunction/epidemiology ; Risk Factors ; Mouth Diseases/epidemiology ; Oral Health ; }, abstract = {Common oral diseases, including periodontitis and dental caries, and their endpoint as tooth loss are controllable yet highly prevalent among adults worldwide. Cognitive decline also poses significant global public health challenges during the aging process, especially the pathological form of cognitive decline such as dementia. Dementia is irreversible and is one of the leading causes of death, disability, and dependency in the aging population. Emerging research suggests a bidirectional association between oral diseases and cognitive decline or dementia. This potential link has implications for designing better oral care plans for patients with dementia and recognizing oral diseases as modifiable risk factors for dementia prevention.This chapter provides an overview of the association between oral diseases and cognitive decline, followed by a discussion of current evidence on such associations in two directions: (1) the impact of cognitive decline or dementia on oral health and (2) the role of oral diseases as modifiable risk factors for dementia. We critically evaluate several hypotheses regarding the underlying mechanisms of this association, including (1) life-course hypothesis, (2) shared inflammation and bacterial infection mechanisms, (3) malnourishment mechanism, (4) pain pathway, and (5) sensory feedback pathway.However, the association between oral diseases and cognitive decline or dementia remains controversial due to limited high-quality evidence, particularly from biomedical research. Much of the existing evidence is from observational studies prone to confounding bias, with inconclusive questions about causation and the direction of causality.This chapter concludes by emphasizing the need for future studies with robust methodological designs, including randomized controlled trials, biomedical studies, and innovative research techniques such as Mendelian randomization. Such studies are crucial for disease prevention and enhancing patient care and quality of life. By providing a comprehensive overview, this chapter contributes to an advanced understanding of this field, addresses current study gaps, and suggests future research directions.}, }
@article {pmid40111691, year = {2025}, author = {Deng, J and Sun, C and Xu, G and Wang, B and Tzortzopoulou, E and Deng, D and Giovannetti, E}, title = {The Oral Microbiome and Cancer.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {151-170}, pmid = {40111691}, issn = {0065-2598}, mesh = {Humans ; *Mouth/microbiology ; *Microbiota ; Neoplasms/microbiology/immunology ; Mouth Neoplasms/microbiology/immunology/pathology ; Animals ; Periodontal Diseases/microbiology ; Bacteria/classification/pathogenicity ; }, abstract = {There is growing evidence suggesting a strong association between members of the oral microbiota and various types of cancer, including oral cancer, colorectal cancer, esophageal squamous cell carcinoma, and pancreatic cancer. Periodontal diseases closely associated with pathogenic bacteria in the oral cavity have been shown to be correlated with the occurrence and development of cancers. Among the periodontal disease-associated bacteria in the oral cavity, two prominent oral pathogens, Porphyromonas gingivalis and Fusobacterium nucleatum, have been found to promote tumor cell proliferation, invasion, and migration, as well as to inhibit immune cell function, thereby facilitating tumor progression. The presence of other oral pathogenic bacteria, such as Treponema denticola, Tannerella forsythia, Parvimonas micra, and Aggregatibacter actinomycetemcomitans, has also been found to be associated with cancer worsening. Oral commensal bacteria play a crucial role in maintaining the normal oral homeostasis. However, the relationship between oral commensal bacteria and the occurrence and development of cancers remains controversial. Some studies suggest an increase in oral commensal bacteria during tumor development, while others suggest an association of certain commensal bacteria with lower tumor risk. The microbiota can significantly alter responses and toxicity to various forms of cancer treatment through interactions with the human body, thereby influencing disease progression. In this chapter, we provide a concise overview of current understanding of the role of the oral microbiota in cancer.}, }
@article {pmid40115491, year = {2024}, author = {Parizi, MK and Matsukawa, A and Alimohammadi, A and Klemm, J and Tsuboi, I and Fazekas, T and Laukhtina, E and Chiujdea, S and Karakiewicz, PI and Shariat, SF}, title = {Genitourinary microbiomes and prostate cancer: a systematic review and meta-analysis of tumorigeneses and cancer characteristics.}, journal = {Central European journal of urology}, volume = {77}, number = {3}, pages = {447-455}, pmid = {40115491}, issn = {2080-4806}, abstract = {INTRODUCTION: We assessed the association of genitourinary microbiomes with prostate cancer (PCa) tumorigeneses and cancer characteristics.<br><br>MATERIAL AND METHODS: A systematic search and meta-analysis was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement. The primary endpoints were the association between relative abundance of genitourinary microbiomes and PCa compared to non-cancerous men/prostate specimen, high grade disease, and disease progression. The odds ratio (OR) was used as the summary statistic, and results were reported with 95% confidence intervals (CI).<br><br>RESULTS: Seventeen studies, comprising 2,195 patients were eligible for review and meta-analysis. The specific microbiomes in urine, prostate tissue, and prostate (or seminal) secretions were significantly more abundant in patients with PCa compared to men in the control groups in individual studies. Certain bacterial phyla, genuses, and species were significantly associated with PCa aggressiveness and disease progression in individual studies. The relative abundance meta-analysis of five urine microbiomes revealed no statistically significant differences between PCa patients and control groups (pooled OR, 1.35; 95% CI: 0.70-2.59).<br><br>CONCLUSIONS: Our systematic review indicates that specific genitourinary microbiomes are more abundant in PCa and have a potential to predict/prognosticate disease aggressiveness and clinical outcomes. Nevertheless, these findings should be interpreted with caution owing to the significant heterogeneity among studies in terms of microbiome analysis method, assessed sample's characteristics, and individual biological behavior of microbiomes for analysis. Further studies are needed to validate these observations and shed more light on the role of the microbiome across the development and natural history of PCa.}, }
@article {pmid40114931, year = {2024}, author = {Dockman, RL and Ottesen, EA}, title = {Purified fibers in chemically defined synthetic diets destabilize the gut microbiome of an omnivorous insect model.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {}, pmid = {40114931}, issn = {2813-4338}, abstract = {The macronutrient composition of a host's diet shapes its gut microbial community, with dietary fiber in particular escaping host digestion to serve as a potent carbon source for gut microbiota. Despite widespread recognition of fiber's importance to microbiome health, nutritional research often fails to differentiate hyper-processed fibers from cell-matrix-derived intrinsic fibers, limiting our understanding of how individual polysaccharides influence the gut community. We use the American cockroach (Periplaneta americana) as a model system to dissect the response of complex gut microbial communities to dietary modifications that are difficult to test in traditional host models. Here, we designed synthetic diets from lab-grade, purified ingredients to identify how the cockroach microbiome responds to six different carbohydrates (chitin, methylcellulose, microcrystalline cellulose, pectin, starch, and xylan) in otherwise balanced diets. We show via 16S rRNA gene profiling that these synthetic diets reduce bacterial diversity and alter the phylogenetic composition of cockroach gut microbiota in a fiber-dependent manner, regardless of the vitamin and protein content of the diet. Comparisons with cockroaches fed whole-food diets reveal that synthetic diets induce blooms in common cockroach-associated taxa and subsequently fragment previously stable microbial correlation networks. Our research leverages an unconventional microbiome model system and customizable lab-grade artificial diets to shed light on how purified polysaccharides, as opposed to nutritionally complex intrinsic fibers, exert substantial influence over a normally stable gut community.}, }
@article {pmid40111690, year = {2025}, author = {He, J and Cheng, L}, title = {The Oral Microbiome: A Key Determinant of Oral Health.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {133-149}, pmid = {40111690}, issn = {0065-2598}, mesh = {Humans ; *Microbiota/physiology ; *Oral Health ; *Mouth/microbiology ; Dental Caries/microbiology ; Mouth Diseases/microbiology ; Periodontal Diseases/microbiology ; Bacteria/classification/genetics ; }, abstract = {As the second largest reservoir of human microbes, the oral cavity is colonized by millions of tiny creatures collectively named as oral microbiome. Species detected in human mouth are diverse, including bacteria, fungi, viruses, and protozoa. Active bidirectional interaction exists between the oral microbiome and the host. Stresses from hosts shape the composition, distribution pattern, and the community behaviors of the oral microbiome, while any changes occurring on the oral microbiome may disrupt its symbiosis relationship with the host and ultimately lead to oral and systemic diseases that jeopardize the host's health. In this chapter, the latest understanding about the role of oral microbiome in common oral diseases, including dental caries, periodontal disease, oral candidiasis, and hyposalivation, is discussed.}, }
@article {pmid40111689, year = {2025}, author = {Mattos, MCO and Vivacqua, A and Carneiro, VMA and Grisi, DC and Guimarães, MDCM}, title = {Interaction of the Systemic Inflammatory State, Inflammatory Mediators, and the Oral Microbiome.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {121-132}, pmid = {40111689}, issn = {0065-2598}, mesh = {Humans ; *Microbiota/immunology ; *Mouth/microbiology/immunology ; *Inflammation Mediators/metabolism ; *Inflammation/microbiology/immunology ; *Periodontitis/microbiology/immunology ; Dysbiosis/microbiology/immunology ; Animals ; }, abstract = {Humans are biological units that host numerous microbial symbionts and their genomes, which together form a superorganism or holobiont. Changes in the balance of the oral ecosystem can have consequences for both general and oral health, such as cavities, gingivitis, and periodontitis. Periodontitis is initiated by a synergistic and dysbiotic microbial community that causes local inflammation and destruction of the tooth's supporting tissues, potentially leading to systemic inflammation. This inflammation caused by periodontal disease has been associated with various systemic alterations, and the immune system is largely responsible for the body's exacerbated response, which can induce and exacerbate chronic conditions. Studies indicate that subgingival microorganisms found in periodontitis reach the bloodstream and are distributed throughout the body and, therefore, can be found in distant tissues and organs. Among all diseases associated with periodontal disease, diabetes mellitus presents the strongest and most elucidated link, and its bidirectional relationship has already been demonstrated. Chronic hyperglycemia favors the worsening of periodontal parameters, while the aggravation of periodontal parameters can promote an increase in glycemic indexes. Other systemic diseases have been related to periodontitis, such as Alzheimer's, chronic kidney disease, atherosclerosis, and respiratory diseases. The importance of periodontal control may suggest a reduction in the chances of developing chronic inflammatory diseases because these two alterations often share inflammatory pathways and, for this reason, may influence each other.}, }
@article {pmid40111688, year = {2025}, author = {Heller, D and Nery, GB and Bachi, ALL and Al-Hashimi, I}, title = {Positive Role of Saliva in the Oral Microbiome.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {103-118}, pmid = {40111688}, issn = {0065-2598}, mesh = {*Saliva/microbiology/metabolism/immunology ; Humans ; *Microbiota/physiology/immunology ; *Mouth/microbiology/immunology ; Dysbiosis/microbiology/immunology ; Salivary Proteins and Peptides/immunology/metabolism ; Immunoglobulin A, Secretory/immunology/metabolism ; Oral Health ; Antimicrobial Peptides/metabolism/immunology ; Animals ; }, abstract = {Saliva plays a pivotal role in shaping the oral microbiome and maintaining oral homeostasis and health. This chapter explores the importance of saliva in promoting eubiosis of the oral microbiome and its implications for oral and systemic health. Saliva is a dynamic fluid rich in antimicrobial components and buffering agents that contribute to the microbial balance and homeostasis within the oral cavity. It provides a cleansing mechanism that facilitates the removal of bacteria and debris and limits the growth and colonization of microorganisms. The salivary antimicrobial proteins and peptides, in combination with antibodies, predominantly secretory immunoglobulin A (sIgA), are crucial for combating microbial pathogens and preventing oral infections. Saliva also possesses a buffering mechanism that regulates the pH levels within the oral cavity, which creates an environment that is inimical for the growth of acid-producing pathogens and promotes remineralization of the teeth. Furthermore, salivary proteins and glycoproteins form an inter-face (tissue coat) over the oral mucosa and teeth to protect the oral tissue from external environmental insults, maintain tissue integrity, and promote wound healing. Understanding the positive role of saliva in the oral microbiome provides an insight into potential novel strategies for promoting oral health and combating microbial dysbiosis. Recognizing the multifaceted roles of saliva as a guardian (gatekeeper) of oral microbial balance, we can unlock the therapeutic potential of saliva in enhancing the well-being of the body and averting oral and systemic diseases.}, }
@article {pmid40111687, year = {2025}, author = {Washio, J and Takahashi, N}, title = {Nitrite Production from Nitrate in the Oral Microbiome and Its Contribution to Oral and Systemic Health.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {89-101}, pmid = {40111687}, issn = {0065-2598}, mesh = {Humans ; *Nitrates/metabolism ; *Nitrites/metabolism ; *Mouth/microbiology/metabolism ; *Microbiota/physiology ; Saliva/metabolism/microbiology ; Oral Health ; Animals ; }, abstract = {The metabolism of nitrate to nitrite by the oral microbiome has recently attracted considerable attention. Nitrate is abundant in the green and yellow vegetables comprising our daily diet. Nitrate is reduced to nitrite by the oral microbiome in the oral cavity, absorbed through the gastrointestinal tract after ingestion, and transferred to the bloodstream, where it is gradually reoxidized to nitrate, some of which is secreted back into the oral cavity as saliva (enterosalivary circulation). Consequently, the oral environment is constantly supplied with nitrate from food and saliva. Nitrite has antibacterial and vasodilatory effects, which may contribute to the suppression of oral or intestinal bacteria and decrease blood pressure through systemic vasodilation in the enterosalivary circulation. Thus, the nitrate metabolism of oral bacteria may play an important role in maintaining and improving both oral and systemic health. On the other hand, there has been concerns that nitrate may contribute to the production of carcinogenic substances such as nitrosamines. However, there is currently a mainstream view that this idea should be reconsidered. Given the growing number of reports showing the relationship between the oral microbiome and systemic health from the perspective of nitrate metabolism; accordingly, this review summarizes the latest findings on the mechanisms of nitrite production by the oral microbiome and its relationship with oral and systemic health.}, }
@article {pmid40111686, year = {2025}, author = {Colombo, APV and Lourenço, TGB and de Oliveira, AM and da Costa, ALA}, title = {Link Between Oral and Gut Microbiomes: The Oral-Gut Axis.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {71-87}, pmid = {40111686}, issn = {0065-2598}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Mouth/microbiology ; *Dysbiosis/microbiology ; Animals ; Gastrointestinal Tract/microbiology ; }, abstract = {In the last decades, groundbreaking research on the human microbiome has changed our reductionist conception of the etiology and pathogenesis of several chronic diseases. As a result, we have come to appreciate the significance of a balanced microbiome in maintaining human health. In this context, the upper and lower gastrointestinal tracts (GITs) comprise the most abundant and diverse microbiotas of the human body. In addition to its diversity, functional redundancy, and temporal stability, a healthy GIT microbiome is characterized by its body site specificity. In fact, current evidence has indicated that the translocation of oral species to the gut environment through the oral-gut axis is increased in an array of illnesses, including chronic inflammatory and metabolic diseases, neurological disorders, and cancer. Oral pathogens have also been shown to promote gut dysbiosis and systemic inflammation in animal models. Yet, some level of overlapping between oral and gut microbiomes may occur without disruption of these microbial communities and loss of site specificity. The uniqueness of each host-microbiome entity may hinder our ability to define a "universal" normal GIT microbiome. Despite that, this chapter summarizes the predominant health-related taxa along the human GIT, as well as their role in the physiology and immunity of the digestive system. Some mechanisms that may lead to disturbances and relevant shifts in the oral and gut microbiomes of major inflammatory chronic diseases are also pointed out. Lastly, oral-fecal microbial signatures are presented as potential biomarkers for several oral and systemic disorders. The recognition of such symbiotic/dysbiotic microbial profiles may provide insights into the development of more accurate early diagnosis and therapeutic ecological approaches to restore the balance of the GIT microbiome.}, }
@article {pmid40111685, year = {2025}, author = {Santonocito, S and Polizzi, A and Isola, G}, title = {The Impact of Diet and Nutrition on the Oral Microbiome.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {53-69}, pmid = {40111685}, issn = {0065-2598}, mesh = {Humans ; *Mouth/microbiology ; *Microbiota/physiology ; *Diet/history ; *Oral Health/history ; Nutritional Status ; }, abstract = {At present, it is well known that oral health is essential for the well-being of the body as a whole, thanks to the increasing awareness of how various oral diseases, including periodontal disease, oral carcinomas, and other conditions, have a close connection with various systemic disorders. In recent decades, studies on the oral microbiome have increasingly emphasized how the balance between the host and the microbial species that coexist there is essential for oral health at all stages of life. However, there are many factors capable of interfering with that balance, and diet is precisely one of them. The real influence of diet on the oral microbiota, and consequently on oral health, has been much debated. In this context, the observation of two key periods in human history, the Neolithic and the Industrial Revolution, has proved to be diriment. The foods and processing techniques that emerged in these two historical periods, in association with changes in customs and habits, significantly altered the central constituents of the human diet, including macronutrient proportions, glycemic load, fatty acid composition, sodium and potassium levels, micronutrient levels, dietary pH, and fiber content taken in by human beings. The introduction of these foods into the daily human routine has been linked to a decline in oral health and an increase of several other diseases, including cardiovascular diseases, inflammatory bowel disease, rheumatic diseases, many cancers, and obesity. The aim of this chapter is to update the current knowledge and further discuss the role of diet and nutrition on oral health.}, }
@article {pmid40111684, year = {2025}, author = {de Barros Santos, HS and Pagnussatti, MEL and Arthur, RA}, title = {Symbiosis Between the Oral Microbiome and the Human Host: Microbial Homeostasis and Stability of the Host.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {31-51}, pmid = {40111684}, issn = {0065-2598}, mesh = {Humans ; *Symbiosis ; *Mouth/microbiology ; *Microbiota/physiology ; *Homeostasis ; *Host Microbial Interactions ; Bacteria/metabolism/genetics/classification ; Metagenomics/methods ; Oral Health ; }, abstract = {The oral cavity presents a highly diverse microbial composition. All the three domains of life, Bacteria, Eukarya, and Archaea, as well as viruses constitute the oral microbiome. Bacteria are among the most abundant microorganisms in the oral cavity, followed by viruses, fungi, and Archaea. These microorganisms tend to live in harmony with each other and with the host by preventing the colonization of oral sites by exogenous microorganisms. Interactions between the host and its microbiota are crucial for keeping ecological stability in the oral cavity and a condition compatible with oral health. This chapter focuses on describing the oral microbiota in healthy individuals based on both targeted and nontargeted genome sequencing methods and the functional activity played by those microorganisms based on metagenomic, metatranscriptomic, metaproteomic, and metabolomic analyses. Additionally, this chapter explores mutualistic and antagonistic microbe-microbe relationships. These interactions are mediated by complex mechanisms like cross-feeding networks, production of bacteriocins and secondary metabolites, synthesis of pH-buffering compounds, and the use of universal signaling molecules. At last, the role played by host-microbe interactions on colonization resistance and immune tolerance will help provide a better understanding about the harmonious and peaceful coexistence among host and microbial cells under oral health-related conditions.}, }
@article {pmid40111683, year = {2025}, author = {Azevedo, MJ and Kaan, AM and Costa, CFFA and Sampaio-Maia, B and Zaura, E}, title = {Acquisition of the Oral Microbiome.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {13-29}, pmid = {40111683}, issn = {0065-2598}, mesh = {Humans ; *Mouth/microbiology ; *Microbiota/physiology ; Bacteria/genetics/classification/growth &amp; development/isolation &amp; purification ; Animals ; }, abstract = {The oral cavity hosts a diverse range of microorganisms that are essential for maintaining oral and general health. These communities include bacteria, fungi, archaea, viruses, and protozoa, and they inhabit distinct niches within the oral cavity. While most research has been dedicated to the study of bacteria, knowledge regarding the acquisition and maintenance of other members of the oral microbiota is still scarce. This chapter aims to explore the process of oral microbiota acquisition from the prenatal to the postnatal stages, emphasizing the intricate interplay between host and environmental factors that shape these microbial communities. However, it is important to acknowledge that significant gaps in knowledge persist, particularly regarding the understanding of these processes beyond bacteria.}, }
@article {pmid40111682, year = {2025}, author = {Dame-Teixeira, N and Do, T and Deng, D}, title = {The Oral Microbiome and Us.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {3-9}, pmid = {40111682}, issn = {0065-2598}, mesh = {Humans ; *Mouth/microbiology ; *Microbiota/physiology ; *Dysbiosis/microbiology ; Periodontitis/microbiology ; Animals ; Oral Health ; }, abstract = {Oral and systemic human health depend on the symbiotic relationship between the human host and its microbiome. As the second most diverse site of the human microbiome, the oral cavity is instrumental in symbiotic relationships, transforming nutrients and acting as the human body's initial barrier against pathogens. However, under certain conditions, the typically beneficial oral microbiome can become harmful. Systemic inflammatory diseases can send signals through the oral-gut axis, such as cytokines and host defensins, altering gene expression and, consequently, the composition of the oral microbiome. These changes can be responsible for causing oral diseases, such as periodontitis and candidiasis. Evidence of metabolic syndrome, including obesity, hypertension, hyperglycemia, and dyslipidemia, exacerbates oral microbiome dysbiosis. On the other hand, the oral microbiota can also influence systemic health. Inflammatory processes in the gingival structures caused by a dysbiotic oral microbiome are linked to worsen glycemic levels in diabetics, premature birth, and rheumatoid arthritis, among others. The idea for this book emerged from the need to explore the multifaceted nature of this relationship in its various dimensions. We discuss multispecies characteristics from an ecological perspective, focusing on how the host affects the microbiome and vice versa. Understanding how the oral microbiome influences human health will guide tailored strategies for disease prevention and treatment, which is discussed in the last section of the book. Looking ahead, predictive health and disease models will enable personalized therapies centered on restoring the healthy human microbiome.}, }
@article {pmid40111647, year = {2025}, author = {Choi, Y and Jeong, J and Kim, M and Cha, S and Han, K}, title = {Backtracking identification techniques for predicting unclear bacterial taxonomy at species level: molecular diagnosis-based bacterial classification.}, journal = {Genes &amp; genomics}, volume = {}, number = {}, pages = {}, pmid = {40111647}, issn = {2092-9293}, support = {RS-2024-00355393//National Institute for International Education/ ; }, abstract = {Bacterial 16S rRNA genes are widely used to classify bacterial communities within interesting environments (e.g., plants, water, human body) because they contain nine hyper-variable regions (V1-V9) reflecting a large number of sequence variation sites between species. Short-read sequencing platform (targeting partial region of 16S rRNA gene; approximately 150-500 bp) commonly used in the 16S-based microbiome study is favored by many researchers because it is economical and can generate highthroughput sequencing data faster than long-read sequencing platforms. However, this sequencing platform has technical limitations in that it cannot clarify bacterial classification at the species level compared to long-read sequencing technology, which can cover the unclassification issue due to sequence similarity between species by targeting the 16S full-length region. In recent microbiome research-related industries, species-level high-resolution microbial classification is considered a key challenge to secure microbial resources among institutions in the field. However, the long-read sequencing platforms currently offered are still under price adjustment (demanding higher cost than short-read sequencing platforms) and have the disadvantage of low base-calling accuracy compared to short-read sequencing platforms. Therefore, this brief communication introduces the'Molecular diagnosis-based bacterial classification' technology to predict candidate species by backtracking for unclassified bacterial taxonomy at the species level in the NGS-based 16S microbiome study.}, }
@article {pmid40111427, year = {2025}, author = {Rukavina Mikusic, NL and Prince, PD and Choi, MR and Chuffa, LGA and Simão, VA and Castro, C and Manucha, W and Quesada, I}, title = {Microbiota, mitochondria, and epigenetics in health and disease: converging pathways to solve the puzzle.}, journal = {Pflugers Archiv : European journal of physiology}, volume = {}, number = {}, pages = {}, pmid = {40111427}, issn = {1432-2013}, support = {PICT2018-3965//ANPCyT FONCyT/ ; PICT 2000 Serie A 4000//ANPCyT FONCyT/ ; J029-T1 SIIP 2022-2024//ANPCyT FONCyT/ ; }, abstract = {Dysbiosis, which refers to an imbalance in the composition of the gut microbiome, has been associated with a range of metabolic disorders, including type 2 diabetes, obesity, and metabolic syndrome. Although the exact mechanisms connecting gut dysbiosis to these conditions are not fully understood, various lines of evidence strongly suggest a substantial role for the interaction between the gut microbiome, mitochondria, and epigenetics. Current studies suggest that the gut microbiome has the potential to affect mitochondrial function and biogenesis through the production of metabolites. A well-balanced microbiota plays a pivotal role in supporting normal mitochondrial and cellular functions by providing metabolites that are essential for mitochondrial bioenergetics and signaling pathways. Conversely, in the context of illnesses, an unbalanced microbiota can impact mitochondrial function, leading to increased aerobic glycolysis, reduced oxidative phosphorylation and fatty acid oxidation, alterations in mitochondrial membrane permeability, and heightened resistance to cellular apoptosis. Mitochondrial activity can also influence the composition and function of the gut microbiota. Because of the intricate interplay between nuclear and mitochondrial communication, the nuclear epigenome can regulate mitochondrial function, and conversely, mitochondria can produce metabolic signals that initiate epigenetic changes within the nucleus. Given the epigenetic modifications triggered by metabolic signals from mitochondria in response to stress or damage, targeting an imbalanced microbiota through interventions could offer a promising strategy to alleviate the epigenetic alterations arising from disrupted mitochondrial signaling.}, }
@article {pmid40111342, year = {2025}, author = {Castonguay-Paradis, S and Demers-Potvin, &#xc9; and Rochefort, G and Lacroix, S and Perron, J and Martin, C and Flamand, N and Raymond, F and Di Marzo, V and Veilleux, A}, title = {Seasonal variations in circulating endocannabinoidome mediators and gut microbiota composition in humans.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2476563}, doi = {10.1080/19490976.2025.2476563}, pmid = {40111342}, issn = {1949-0984}, mesh = {Humans ; *Seasons ; *Endocannabinoids/blood ; *Gastrointestinal Microbiome ; Female ; Male ; *Feces/microbiology ; Middle Aged ; Adult ; Longitudinal Studies ; Bacteria/classification/isolation &amp; purification/genetics ; Quebec ; Aged ; Diet ; Feeding Behavior ; }, abstract = {BACKGROUND: The human gut microbiome-endocannabinoidome axis is crucial for several homeostatic processes, including inflammation and energy metabolism, and is influenced by many endogenous and exogenous factors, such as dietary habits. Changes in the gut microbiome in response to seasonal variations were previously reported and tentatively attributed to shifts in dietary patterns. However, there is a need for longitudinal studies in industrialized populations to comprehensively explore seasonal variations independently of lifestyle confounding factors.<br><br>OBJECTIVE: To investigate the longitudinal effects of seasonal variations on the composition of the gut microbiome and the circulating levels of endocannabinoidome mediators in humans, while elucidating the contributing factors underlying these changes.<br><br>METHODS: Plasma and fecal samples were collected at the end of both the winter and summer in a longitudinal cohort of 48 individuals living in Qu&#xe9;bec City (Canada). Dietary habits, medical history, fecal microbiota taxonomic composition and plasma levels of circulating N&#x2011;acyl&#x2011;ethanolamines (NAEs) and 2&#x2011;monoacyl-glycerols (2&#x2011;MAGs) were obtained at each time point.<br><br>RESULTS: Lower circulating levels of most NAEs were observed at the end of summer. These changes were accompanied by a reduction in the relative abundance of the Bifidobacteriaceae and Lachnospiraceae families, along with an increase in the abundance of the Bacteroidaceae and Ruminococcaceae families. These seasonal variations were not associated with concurrent changes in adiposity parameters, dietary intakes, physical activity habits, or vitamin D status. Importantly, the magnitude of the shift in gut microbiota composition from winter to summer was found to be associated with the seasonal variations in circulating endocannabinoidome (eCBome) mediators.<br><br>CONCLUSION: This study identified specific seasonal changes in gut microbiota composition and circulating levels of several NAEs, which were not associated with vitamin D status and lifestyle habits. It underscores the importance of the gut microbiota-endocannabinoidome axis in the pathophysiology of seasonal changes, and of considering seasons in clinical trials on these systems.}, }
@article {pmid40111075, year = {2025}, author = {Zhang, X and Gaballa, MMS and Hasan, AA and Liu, Y and Hocher, JG and Chen, X and Liu, L and Li, J and Wigger, D and Reichetzeder, C and Elitok, S and Kleuser, B and Krämer, BK and Hocher, B}, title = {Effects of High-Salt Intake on Glucose Metabolism, Liver Function, and the Microbiome in Rats: Influence of ACE Inhibitors and Angiotensin II Receptor Blockers.}, journal = {American journal of physiology. Cell physiology}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpcell.01036.2024}, pmid = {40111075}, issn = {1522-1563}, support = {2022RC40//Hunan High-Level Talent Aggregation Project/ ; //Boehringer Ingelheim (Boehringer Ingelheim International GmbH)/ ; YNXM-202304//Researsch Grant of CITIC-Xiangya/ ; 202008430176//China Scholarship Council (CSC)/ ; //Deutschland-Stipendium der Charite Universitatsmedizin Berlin/ ; }, abstract = {Abstract Background: High-salt diets (HSD) are known to impact blood pressure and cardiovascular health, but their effects on glucose metabolism, liver function, and gut microbiota remain poorly understood. This study investigates how long-term HSD affects these physiological processes and evaluates the potential therapeutic effects of ACE inhibitors (ACEIs) and angiotensin II receptor blockers (ARBs). Methods: Male Sprague-Dawley rats were fed a normal salt diet (0.3% NaCl), a moderate salt diet (2% NaCl), or a high-salt diet (8% NaCl) for 12 weeks. Two subgroups in the HSD condition received telmisartan or enalapril. We assessed blood pressure, glucose homeostasis, liver inflammation, pancreatic function, and gut microbiota composition. Results: HSD rats exhibited significantly higher blood pressure (130 ± 2 mmHg in ND vs. 144 ± 4 mmHg in HSD; p < 0.01), reduced fasting insulin (1.33 ± 0.14 ng/mL in ND vs. 0.60 ± 0.05 ng/mL in HSD; p < 0.01), and gut microbiota dysbiosis, with a 71% reduction in Ruminococcus species (p = 0.018). Liver inflammation, indicated by an increase in CD68+ macrophages, was also observed in the HSD group. Telmisartan treatment significantly reduced liver inflammation but did not fully restore metabolic homeostasis. Conclusion: HSD disrupts multiple physiological systems, including glucose metabolism and liver function, partly through gut microbiota alterations. ACEIs and ARBs provided partial protection, highlighting the need for multi-targeted interventions to mitigate high-salt diet effects.}, }
@article {pmid40111053, year = {2025}, author = {Jian, N and Yu, L and Ma, L and Zheng, B and Huang, W}, title = {BCG therapy in bladder cancer and its tumor microenvironment interactions.}, journal = {Clinical microbiology reviews}, volume = {}, number = {}, pages = {e0021224}, doi = {10.1128/cmr.00212-24}, pmid = {40111053}, issn = {1098-6618}, abstract = {SUMMARYBacillus Calmette-Guérin (BCG) has been the standard treatment for non-muscle-invasive bladder cancer for over 30 years. Despite its proven efficacy, challenges persist, including unclear mechanisms of action, resistance in 30%-50% of patients, and significant side effects. This review presents an updated and balanced discussion of the antitumor mechanisms of BCG, focusing on its direct effects on bladder cancer and its interactions with various cell types within the bladder tumor microenvironment. Notably, recent research on the interactions between BCG and the bladder microbiome is also incorporated. We further summarize and analyze the latest preclinical and clinical studies regarding both intrinsic and adaptive resistance to BCG in bladder cancer. Based on the current understanding of BCG's therapeutic principles and resistance mechanisms, we systematically explore strategies to improve BCG-based tumor immunotherapy. These include the development of recombinant BCG, combination therapy with different drugs, optimization of therapeutic regimens and management, and the exploration of new approaches by targeting changes in the bladder microbiota and its metabolites. These measures aim to effectively address the BCG resistance in bladder cancer, reduce its toxicity, and ultimately enhance the clinical anti-tumor efficacy. Bacterial therapy, represented by genetically engineered oncolytic bacteria, has gradually emerged in the field of cancer treatment in recent years. As the only bacterial drug successfully approved for oncology use, BCG has provided decades of clinical experience. By consolidating lessons from BCG's successes and limitations, we hope to provide valuable insights for the development and application of bacterial therapies in cancer treatment.}, }
@article {pmid40110742, year = {2025}, author = {Dutta, S and Chatterjee, N and Gallina, NLF and Kar, S and Koley, H and Nanda, PK and Biswas, O and Das, AK and Biswas, S and Bhunia, AK and Dhar, P}, title = {Diet, microbiome, and probiotics establish a crucial link in vaccine efficacy.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-26}, doi = {10.1080/1040841X.2025.2480230}, pmid = {40110742}, issn = {1549-7828}, abstract = {Vaccination plays a critical role in public health by reducing the incidence and prevalence of infectious diseases. The efficacy of a vaccine has numerous determinants, which include age, sex, genetics, environment, geographic location, nutritional status, maternal antibodies, and prior exposure to pathogens. However, little is known about the role of gut microbiome in vaccine efficacy and how it can be targeted through dietary interventions to improve immunological responses. Unveiling this link is imperative, particularly in the post-pandemic world, considering impaired COVID-19 vaccine response observed in dysbiotic individuals. Therefore, this article aims to comprehensively review how diet and probiotics can modulate gut microbiome composition, which is linked to vaccine efficacy. Dietary fiber and polyphenolic compounds derived from plant-based foods improve gut microbial diversity and vaccine efficacy by promoting the growth of short-chain fatty acids-producing microbes. On the other hand, animal-based foods have mixed effects - whey protein and fish oil promote gut eubiosis and vaccine efficacy. In contrast, lard and red meat have adverse effects. Studies further indicate that probiotic supplements exert varied effects, mostly strain and dosage-specific. Interlinking diet, microbiome, probiotics, and vaccines will reveal opportunities for newer research on diet-induced microbiome-manipulated precision vaccination strategies against infectious diseases.}, }
@article {pmid40110651, year = {2025}, author = {Saini, S and Sabaeifard, P and Coughlin, L and Poulides, N and Gan, S and Zhan, X and Dang, M and Koh, AY and Zia, A}, title = {Identifying Microbiota and Immune Host Factors Associated With Bleeding Risk in Children With Immune Thrombocytopenia.}, journal = {American journal of hematology}, volume = {}, number = {}, pages = {}, doi = {10.1002/ajh.27669}, pmid = {40110651}, issn = {1096-8652}, support = {1R01HL153963/NH/NIH HHS/United States ; K24AI123163/NH/NIH HHS/United States ; 20IPA35320263//American Heart Association/ ; R38HL150214/HL/NHLBI NIH HHS/United States ; }, }
@article {pmid40110597, year = {2025}, author = {Mason, B and Sahoo, DK and Iennarella-Servantez, CA and Kathrani, A and Morgan, SM and Bourgois-Mochel, A and Bray, AM and Gabriel, V and Zdyrski, C and Groeltz, JM and Cassmann, E and Ackermann, MR and Suchodolski, JS and Mochel, JP and Allenspach, K and Jergens, AE}, title = {Effects of a Western Diet on Colonic Dysbiosis, Bile Acid Dysmetabolism and Intestinal Inflammation in Clinically Healthy Dogs.}, journal = {Journal of veterinary internal medicine}, volume = {39}, number = {2}, pages = {e70035}, doi = {10.1111/jvim.70035}, pmid = {40110597}, issn = {1939-1676}, support = {//Iowa State University Veterinary Clinical Sciences Incentive Grant Program 2021/ ; //VCA Sponsored Resident Funding/ ; }, mesh = {Animals ; Dogs ; *Dysbiosis/veterinary ; *Dog Diseases/microbiology/diet therapy ; *Bile Acids and Salts/metabolism ; *Feces/microbiology/chemistry ; Male ; Female ; *Diet, Western/adverse effects ; Inflammation/veterinary ; Colon/pathology/microbiology ; Gastrointestinal Microbiome/drug effects ; Animal Feed/analysis ; }, abstract = {BACKGROUND: Consumption of a high-fat, high-carbohydrate Western-style diet (WD) associated with obesity and inflammation in humans has not been investigated in dogs.<br><br>AIMS: To determine the effects of WD on inflammatory indices, microbiome, and fecal bile acids (BAs) in dogs.<br><br>ANIMALS: Ten adult clinically healthy dogs.<br><br>METHODS: A dietary trial compared the effects of two home-prepared diets: a high-fiber, low-fat control diet (CD) to a diet containing the macronutrient composition of WD (low-fiber, high fat). Dietary treatments were given sequentially for three feeding periods, each lasting 1 month. Outcome measures included molecular/microbiologic testing of colonic biopsies, histopathology, inflammatory biomarkers, and quantification of fecal BA following each feeding period.<br><br>RESULTS: Cell markers of apoptosis (TUNEL-positive cells: CD1, 0.36%&#x2009;&#xb1;&#x2009;0.2%; WD, 0.79%&#x2009;&#xb1;&#x2009;0.5%; CD2, 0.42%&#x2009;&#xb1;&#x2009;0.3%; 95% CI) and&#xa0;inflammation (NF-&#x138;B area: CD1, 8.09%&#x2009;&#xb1;&#x2009;3.3%; WD, 11.58%&#x2009;&#xb1;&#x2009;3.4%; CD2 7.25%&#x2009;&#xb1;&#x2009;3.8%; 95% CI), as well as serum high-sensitivity C-reactive protein (CD1, 2.0&#x2009;&#xb1;&#x2009;0.4&#x2009;ng/mL; WD, 2.76&#x2009;&#xb1;&#x2009;0.23&#x2009;ng/mL; CD2, 2.29&#x2009;&#xb1;&#x2009;0.25&#x2009;ng/mL; 95% CI), were increased (p&#x2009;<&#x2009;0.05) in dogs fed WD versus CD. Other perturbations seen with WD ingestion included altered (p&#x2009;<&#x2009;0.05) colonic mucosal bacteria (bacterial counts: CD1, 301.5&#x2009;&#xb1;&#x2009;188.5; WD, 769.8&#x2009;&#xb1;&#x2009;431.9; CD2, 542.1&#x2009;&#xb1;&#x2009;273.9; 95% CI) and increased (p&#x2009;<&#x2009;0.05) fecal cholic acid (median and interquartile range/IQR: CD1, 9505 [2384-33&#x2009;788] peak heights; WD, 34&#x2009;131 [10&#x2009;113-175&#x2009;909] peak heights) and serum myeloperoxidase (CD1, 46.98&#x2009;&#xb1;&#x2009;16.6&#x2009;ng/mL; WD, 82.93&#x2009;&#xb1;&#x2009;33.6&#x2009;ng/mL; CD2, 63.52&#x2009;&#xb1;&#x2009;29.5&#x2009;ng/mL; 95% CI).<br><br>WD fed to clinically healthy dogs promotes colonic dysbiosis, altered fecal BA, and low-grade inflammation independent of obesity.}, }
@article {pmid40110560, year = {2025}, author = {Adachi, A and Zhang, F and Kanaya, S and Ono, N}, title = {Quantifying uncertainty in microbiome-based prediction using Gaussian processes with microbial community dissimilarities.}, journal = {Bioinformatics advances}, volume = {5}, number = {1}, pages = {vbaf045}, pmid = {40110560}, issn = {2635-0041}, abstract = {SUMMARY: The human microbiome is closely associated with the health and disease of the human host. Machine learning models have recently utilized the human microbiome to predict health conditions and disease status. Quantifying predictive uncertainty is essential for the reliable application of these microbiome-based prediction models in clinical settings. However, uncertainty quantification in such prediction models remains unexplored. In this study, we have developed a probabilistic prediction model using a Gaussian process (GP) with a kernel function that incorporates microbial community dissimilarities. We evaluated the performance of probabilistic prediction across three regression tasks: chronological age, body mass index, and disease severity, using publicly available human gut microbiome datasets. The results demonstrated that our model outperformed existing methods in terms of probabilistic prediction accuracy. Furthermore, we found that the confidence levels closely matched the empirical coverage and that data points predicted with lower uncertainty corresponded to lower prediction errors. These findings suggest that GP regression models incorporating community dissimilarities effectively capture the characteristics of phylogenetic, high-dimensional, and sparse microbial abundance data. Our study provides a more reliable framework for microbiome-based prediction, potentially advancing the application of microbiome data in health monitoring and disease diagnosis in clinical settings.<br><br>The code is available at https://github.com/asahiadachi/gp4microbiome.}, }
@article {pmid40110548, year = {2024}, author = {Phiri, TN and Weatherill, JW and Monford-Sanchez, E and Serrano-Contreras, JI and Melvin, C and Kunaka, M and Chisenga, I and Ngalande, P and Mweetwa, MN and Besa, E and Haider, T and Mandal, N and Thompson, AJ and Edwards, CA and Bourke, CD and Robertson, RC and Posma, JM and Banda, R and Mwiinga, M and Kazhila, L and Katsidzira, L and Bwakura-Dangarembizi, M and Amadi, B and Garcia-Perez, I and Maitland, K and Marchesi, JR and Morrison, DJ and Frost, G and Kelly, P}, title = {Novel gastrointestinal tools (GI Tools) for evaluating gut functional capacity in adults with environmental enteropathy in Zambia and Zimbabwe: A cross-sectional study protocol.}, journal = {F1000Research}, volume = {13}, number = {}, pages = {956}, pmid = {40110548}, issn = {2046-1402}, mesh = {Humans ; Cross-Sectional Studies ; Zambia ; Adult ; Middle Aged ; Adolescent ; *Intestinal Diseases ; Zimbabwe ; Young Adult ; Aged ; Female ; Male ; Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: Environmental enteropathy (EE) is a highly prevalent subclinical inflammatory intestinal disorder associated with growth failure, impaired neurocognitive development, poor response to oral vaccines, and micronutrient deficiencies. However, EE research and clinical trials are hampered by the lack of non-invasive tools for measuring intestinal function in detail. This study aims to develop new tools for the measurement of multiple domains of gut functional capacity.<br><br>METHODS: The GI TOOLS project is a cross-sectional study that will recruit adults aged 18-65 years with EE in Lusaka, Zambia. Each participant will undergo assessment of gut functional capacity using novel near-point-of-care tools and provide multiple samples for detailed laboratory analyses. Participants will also undergo endoscopy for collection of duodenal biopsies. Novel techniques include stable isotopes approaches to measuring digestion, absorption, and bidirectional transmucosal amino acid flux, a non-invasive fluorescence tool for real-time evaluation of gut permeability, and assessment of reverse permeation of intravenous antibiotics to be carried out separately in Zimbabwe. Stool and duodenal microbiome sequencing using MinION sequencing, metabolome analysis applied to plasma and intestinal fluids, blood immune cell phenotyping, in vitro epithelial barrier models, and duodenal immunohistochemistry will also be used to explore EE in depth. These will all be integrated with gold standard histology and mucosal morphometry, alongside lactulose permeation data, and stool and plasma biomarker analysis. The protocol has been approved by ethics committees and regulators in Zambia, Zimbabwe, and the UK. Participants will give informed consent before they can participate.<br><br>ANTICIPATED OUTCOMES: Based on this extensive phenotyping, tests will be developed which can be simplified and refined for use in adults and children with EE, and for clinical trials. Findings from this project will be disseminated through in-person meetings with caregivers and regulatory bodies, presentations at conferences and in peer-reviewed journals.}, }
@article {pmid40110359, year = {2025}, author = {Ahmed, W and Ye, W and Pan, J and Liu, S and Ji, W and Zhou, S and Wang, F and Li, Z and Mohany, M and Wang, X}, title = {Evaluation the role of Luteibacter pinisoli DP2-30 in mitigating pine wilt disease caused by Bursaphelenchus xylophilus through modulation of host microbiome.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1515506}, pmid = {40110359}, issn = {1664-462X}, abstract = {BACKGROUND AND AIM: Pine wilt disease (PWD), caused by the pine wood nematode (PWN) Bursaphelenchus xylophilus, poses a significant threat to pine forests worldwide. This study aimed to isolate bacterial strains from the rhizosphere of healthy Pinus massoniana and elucidate their biocontrol potential in mitigating PWD through direct nematicidal activity and manipulation of host microbiome.<br><br>RESULTS: We successfully isolated the rhizobacterium strain DP2-30 from rhizosphere of healthy pine plants, which was identified as Luteibacter pinisoli on the basis of morphological, biochemical, and molecular analyses. The fermentation filtrates of strain DP2-30 displayed direct nematicidal activity of >95% (corrected mortality rate) on PWN after 48 hours of treatment. The fermentation broth and filtrates of strain DP2-30 significantly inhibited PWN egg hatching by 49.38% and 43.05%, respectively. Additionally, root drenching of strain DP2-30 fermentation broth significantly reduced PWD severity in pine seedlings (2 years old), with a control effect of 62.50%. Microbiome analyses revealed significant variations in the diversity, structure, and relative abundance of bacterial and fungal communities of pine plants combined treated with DP2-30 and PWN (T2), solely treated with PWN (T1), and control (treated with water). Bacterial phyla, Proteobacteria, Actinobacteriota, Chloroflexi, Acidobacteriota, and Armatimonadota and fungal phyla Ascomycota, Basidiomycota and Mortierellomycota were dominant in the all root and stem samples. The application of L. pinisoli DP2-30 significantly increased the relative abundance of the family Rhodanobacteraceae in the roots and stems of pine seedlings. Additionally, intra-kingdom co-occurrence network analysis revealed reduced complexity in the bacterial networks but increased complexity in the fungal networks of treated plants, suggesting enhanced functional redundancy and ecosystem stability.<br><br>CONCLUSIONS: Overall, this study highlights the potential of L. pinisoli DP2-30 as an effective biocontrol agent against PWD by directly killing PWN and manipulating the host microbiota.}, }
@article {pmid40110355, year = {2025}, author = {Lane, BR and Kuhs, MA and Zaret, MM and Song, Z and Borer, ET and Seabloom, EW and Schlatter, DC and Kinkel, LL}, title = {Foliar fungi-imposed costs to plant productivity moderate shifts in composition of the rhizosphere microbiome.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1558191}, pmid = {40110355}, issn = {1664-462X}, abstract = {Plants in grasslands navigate a complex landscape of interactions including competition for resources and defense against pathogens. Foliar fungi can suppress plant growth directly through pathogenic interactions, or indirectly via host growth-defense tradeoffs. The exclusion of foliar fungi allows the reallocation of resources from defense to growth and reproduction. In addition, plants also invest photosynthates in rhizodeposition, or root exudates, which play a significant role in shaping the rhizosphere microbial community. However, it remains unclear what impact the exclusion of foliar fungi has on the allocation of resources to rhizodeposition and the composition of the rhizosphere microbial community. Using a 6-year foliar fungicide study in plots planted with 16 species of native prairie plants, we asked whether foliar fungi influence the rhizosphere microbial composition of a common prairie grass (Andropogon gerardii) and a common legume (Lespedeza capatita). We found that foliar fungicide increased aboveground biomass and season-long plant production, but did not alter root biomass, seed production, or rhizosphere microbial diversity. The magnitude of change in aboveground season-long plant production was significantly associated with the magnitude of change in the rhizosphere microbial community in paired foliar fungicide-treated vs. control plots. These results suggest important coupling between foliar fungal infection and plant investment in rhizodeposition to modify the local soil microbial community.}, }
@article {pmid40110195, year = {2025}, author = {Carneiro, KO and Araújo, TMT and Da Silva Mourão, RM and Casseb, SMM and Demachki, S and Moreira, FC and Dos Santos, &#xc2;KCR and Ishak, G and Da Costa, DSA and Magalhães, L and Vidal, AF and Burbano, RMR and de Assumpção, PP}, title = {Transcriptional and microbial profile of gastric cancer patients infected with Epstein-Barr virus.}, journal = {Frontiers in oncology}, volume = {15}, number = {}, pages = {1530430}, pmid = {40110195}, issn = {2234-943X}, abstract = {INTRODUCTION: Gastric cancer (GC), which has low survival rates and high mortality, is a major concern, particularly in Asia and South America, with over one million annual cases. Epstein-Barr virus (EBV) is recognized as a carcinogen that may trigger gastric carcinogenesis by infecting the stomach epithelium via reactivated B cells, with growing evidence linking it to GC. This study investigates the transcriptional and microbial profiles of EBV-infected versus EBV-non-infected GC patients.<br><br>METHODS: Using Illumina NextSeq, cDNA libraries were sequenced, and reads were aligned to the human genome and analyzed with DESeq2. Kegg and differential analyses revealed key genes and pathways. Gene sensitivity and specificity were assessed using ROC curves (p < 0.05, AUC > 0.8). Non-aligned reads were used for microbiome analysis with Kraken2 for bacterial identification. Microbial analysis included LDA score, Alpha and Beta diversity metrics, with significance set at p &#x2264; 0.05. Spearman's correlation between differentially expressed genes (DEGs) and bacteria were also examined.<br><br>RESULTS: The data revealed a gene expression pattern in EBV-positive gastric cancer, highlighting immune response, inflammation, and cell proliferation genes (e.g., GBP4, ICAM1, IL32, TNFSF10). ROC analysis identified genes with high specificity and sensitivity for discriminating EBV+ gastric cancer, including GBP5, CMKLR1, GM2A and CXCL11 that play pivotal roles in immune response, inflammation, and cancer. Functional enrichment pointed to cytokine-cytokine receptor interactions, antigen processing, and Th17 immune response, emphasizing the role of the tumor microenvironment, shaped by inflammation and immunomodulation, in EBV-associated GC. Microbial analysis revealed changes in the gastric microbiota in EBV+ samples, with a significant reduction in bacterial taxa. The genera Choristoneura and Bartonella were more abundant in EBV+ GC, while more abundant bacteria in EBV- GC included Citrobacter, Acidithiobacillus and Biochmannia. Spearman's correlation showed a strong link between DE bacterial genera and DEGs involved in processes like cell differentiation, cytokine production, digestion, and cell death.<br><br>CONCLUSION: These findings suggest a complex interaction between the host (EBV+ GC) and the microbiota, possibly influencing cancer progression, and offering potential therapeutic targets such as microbiota modulation or gene regulation. Comparing with EBV- samples further highlights the specific impact of EBV and the microbiota on gastric cancer pathogenesis.}, }
@article {pmid40110165, year = {2025}, author = {Liu, C and Zhang, J and Li, Q and Zhang, Y and Zhang, S and Yu, Z and Li, J and Li, J}, title = {Horizontal transmission of symbiotic bacteria and host selective sweep in the giant clam Tridacna crocea.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf037}, pmid = {40110165}, issn = {2730-6151}, abstract = {Giant clams, with their significant ecological importance, depend on associated bacteria for their health and development, yet the transmission modes and succession of community dynamics of these bacteria remain poorly understood. This study employed 16S rRNA gene sequencing and microscopy to investigate the transmission and community dynamics of symbiotic bacteria in the giant clam Tridacna crocea during early developmental stages (fertilized eggs, blastocyst, D-larvae, and pediveliger larvae). Fluorescence in situ hybridization and transmission electron microscopy did not detect internal symbiotic bacteria in fertilized eggs and adult gonad gametes, but scanning electron microscopy revealed microbial structures on egg surface microvilli, suggesting their role as microbial carriers. 16S rRNA sequencing confirmed microbial presence in fertilized eggs, indicating bacterial acquisition via external vertical transmission (adherence to microvilli) or horizontal transmission. Given the lack of internalized bacteria in reproductive organs, we prefer to classify the symbiotic bacteria acquisition as horizontal transmission. Microbial community analysis showed that T. crocea acquired a significant portion of its microbiome from seawater throughout its development. Before reaching the pediveliger stage, the bacterial community composition closely resembled that of the surrounding seawater, primarily featuring the family Rhodobacteraceae. As T. crocea matured, the host's selective pressure increased (e.g. deterministic assembly), which simplified the microbial community and reduced diversity. During the pediveliger stage, the genus Endozoicomonas became dominant, forming a large proportion of the bacterial community within the gonads. This highlights the ecological significance of host-microbe interactions in maintaining biodiversity and driving ecosystem stability through dynamic community assembly processes.}, }
@article {pmid40109991, year = {2025}, author = {Xu, CC and Zhao, WX and Sheng, Y and Yun, YJ and Ma, T and Fan, N and Song, JQ and Wang, J and Zhang, Q}, title = {Serum homocysteine showed potential association with cognition and abnormal gut microbiome in major depressive disorder.}, journal = {World journal of psychiatry}, volume = {15}, number = {3}, pages = {102567}, pmid = {40109991}, issn = {2220-3206}, abstract = {BACKGROUND: Cognitive impairment is one of the common clinical manifestations of depression, causing negative distress to patients. Elevated homocysteine (Hcy) concentrations and gut microbiome dysfunction may be observed in patients with depression.<br><br>AIM: To investigate the relationship between Hcy, microbiome, and cognition in depressive patients.<br><br>METHODS: We recruited 67 patients with major depressive disorder (MDD) (MDD group) and 94 healthy controls (HCs) individuals (HCs group). Serum Hcy levels were determined using the enzyme circulation method. 16s rRNA sequencing was used to classify and identify the fecal bacteria. 17 Hamilton depression rating scale and MATRICS consensus cognitive battery were used to evaluate mood states and cognition in patients with MDD. Correlation analysis was performed to explore the correlation between fecal flora, Hcy, and depressive cognitive function.<br><br>RESULTS: Elevated serum levels of Hcy were seen in patients with MDD compared to healthy individuals. Patients with MDD indicated significant decreases in cognitive scores (P < 0.001) in six modules: Speed of processing, working memory, visual learning, reasoning and problem-solving, social cognition, and total scores. Hcy levels showed a negative correlation with processing speed, social cognition, and total MDD scores (P < 0.05). Hcy was also significantly negatively correlated with Alistipes, Ruminococcae, Tenericides, and Porphyromonas (P < 0.05).<br><br>CONCLUSION: Our results highlight that Hcy was correlated with cognition and gut microbiome in MDD. This interaction may be related to the physiological and pathological mechanisms underlying cognitive deficits in depression.}, }
@article {pmid40109976, year = {2025}, author = {Ku, JY and Lee, MJ and Jung, Y and Choi, HJ and Park, J}, title = {Changes in the gut microbiome due to diarrhea in neonatal Korean indigenous calves.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1511430}, pmid = {40109976}, issn = {1664-302X}, abstract = {Studies on gut microbiome changes in neonatal Korean indigenous calves with diarrhea are rare. In this study, 14 normal calves and 11 calves with diarrhea were selected from Korean indigenous calves up to 30 days of age and classified into three groups at 10-day intervals (1-10, 11-20, and 21-30 days). Feces from 25 calves were collected, and the diversity, similarity, structure, and correlation of the gut microbiome were analyzed. Firmicutes, Bacteroidetes, and Proteobacteria were predominant in the taxonomic composition of the gut microbiome of the calves regardless of the presence of diarrhea. However, Proteobacteria increased and Bacteroidetes and Actinobacteria decreased in calves with diarrhea. In addition, calves with diarrhea showed a significant decrease in the diversity of the gut microbiome, especially for anaerobic microorganisms Faecalibacterium prausnitzii, Gemmiger formicilis, and Collinsella aerofaciens. The microbial communities in calves with diarrhea and normal calves were distinct. By analyzing the microorganisms that showed correlation with diarrhea and age using linear discriminant analysis effect size, at the genus level, Prevotella and Lachnospiraceae_uc were significantly related in the normal (11-20 days) group whereas Enterobacterales, Gammaproteobacteria, Enterobacteriaceae, Escherichia, and Proteobacteria were significantly associated with diarrhea in the 11-20 days group. Futhermore, the normal (21-30 days) group showed significant correlation with Blautia, Provotellaceae, Muribaculaceae, Christensenellaceae, and Catenella, whereas the diarrhea (21-30 days) group showed significant correlation with Dorea. The microorganisms associated with diarrhea in calves were mainly known as harmful microorganisms, we confirmed that there is a relationship between the increase in harmful bacteria and diarrhea. These results show that diarrhea significantly affects the gut microbiome of Korean indigenous calves. The changes in the gut microbiome of Korean indigenous calves observed in this study could be helpful in predicting and managing diarrhea calves, and furthermore, in establishing preventive measures for calf diarrhea through management of gut microbiome.}, }
@article {pmid40109720, year = {2025}, author = {Merelim, AS and Zacca, R and Moreira-Gonçalves, D and Costa, PP and Baptista, LC}, title = {Distinct exercise modalities on GUT microbiome in sarcopenic older adults: study protocol of a pilot randomized controlled trial.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1504786}, pmid = {40109720}, issn = {2296-858X}, abstract = {BACKGROUND: Sarcopenia is a progressive and age-related skeletal muscle disease related to adverse health outcomes and to an increased economic burden. Recent evidence pinpoints the human gut microbiota (GM) as a contributing factor in the development of sarcopenia via the gut-muscle axis. To date, no study specifically analyzed the optimal type of exercise modality in older adults with sarcopenia considering the impact of GM composition in skeletal muscle mass and function. Therefore, the DEMGUTS study intents to explore the impact of three different exercise regimens on GM composition and gut-derived metabolites in older adults with sarcopenia.<br><br>METHODS: This pilot single center three-arm parallel open-label randomized control trial (RCT) will randomly assign eligible participants to: (i) moderate aerobic exercise (AER); (ii) resistance exercise (RES); or (iii) concurrent exercise training (RES&#x202f;+&#x202f;AER). Participants will engage in a supervised center-based exercise intervention (12-weeks, 3 d/week, 60&#x202f;min/d), and will be assessed at (i) baseline, (ii) end of intervention (14&#x202f;weeks), and (iii) at close-out (26-weeks). The primary outcome will be the change in the relative abundance of Faecalibacterium prausnitzii and other short-chain fatty acid producing bacteria after the intervention (14-weeks). A set of complementary outcomes will also be assessed to broadly characterize the impact of each exercise intervention on body composition, skeletal muscle function, functional performance and general GM composition.<br><br>CONCLUSION: Unraveling the impact of these exercise regimens on GM is crucial to help clarify the optimal exercise modality to manage sarcopenia disease, contributing to clinical guidance and enhancing exercise prescription in older adults with sarcopenia.<br><br>CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/, identifier NCT06545123.}, }
@article {pmid40109716, year = {2025}, author = {Tian, X and Wang, L and Zhong, L and Zhang, K and Ge, X and Luo, Z and Zhai, X and Liu, S}, title = {The research progress and future directions in the pathophysiological mechanisms of type 2 diabetes mellitus from the perspective of precision medicine.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1555077}, pmid = {40109716}, issn = {2296-858X}, abstract = {Type 2 diabetes mellitus (T2DM) is a complex metabolic disorder characterized by pathophysiological mechanisms such as insulin resistance and β-cell dysfunction. Recent advancements in T2DM research have unveiled intricate multi-level regulatory networks and contributing factors underlying this disease. The emergence of precision medicine has introduced new perspectives and methodologies for understanding T2DM pathophysiology. A recent study found that personalized treatment based on genetic, metabolic, and microbiome data can improve the management of T2DM by more than 30%. This perspective aims to summarize the progress in T2DM pathophysiological research from the past 5 years and to outline potential directions for future studies within the framework of precision medicine. T2DM develops through the interplay of factors such as gut microbiota, genetic and epigenetic modifications, metabolic processes, mitophagy, NK cell activity, and environmental influences. Future research should focus on understanding insulin resistance, β-cell dysfunction, interactions between gut microbiota and their metabolites, and the regulatory roles of miRNA and genes. By leveraging artificial intelligence and integrating data from genomics, epigenomics, metabolomics, and microbiomics, researchers can gain deeper insights into the pathophysiological mechanisms and heterogeneity of T2DM. Additionally, exploring the combined effects and interactions of these factors may pave the way for more effective prevention strategies and personalized treatments for T2DM.}, }
@article {pmid40109342, year = {2025}, author = {Zhan, P and Chen, W and Chen, J and Zhao, J and Ding, M and Fu, S and Wang, J}, title = {Commentary: Exploring the gut microbiome and immunological landscape in kidney cancer: a Mendelian randomization analysis.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1506205}, pmid = {40109342}, issn = {1664-3224}, }
@article {pmid40109036, year = {2025}, author = {Xu, Q and Xue, L and Wu, Z and Kang, S and Li, J and Wu, Y and Wu, Y and Zhao, J and Wu, R and Lv, H and Wang, J and Han, D}, title = {Dietary Qiwenghuangbo powder-enriched Limosilactobacillus reuteri protects the intestinal epithelium and alleviates inflammation via a strain-specific mechanism.}, journal = {Animal models and experimental medicine}, volume = {}, number = {}, pages = {}, doi = {10.1002/ame2.70016}, pmid = {40109036}, issn = {2576-2095}, support = {6232024//Beijing Municipal Natural Science Foundation/ ; 2021YFD1300201//National Key Research and Development Program of China/ ; 2022YFA1304201//National Key Research and Development Program of China/ ; B16044//111 Project/ ; 32125036//National Natural Science Foundation of China/ ; 32172750//National Natural Science Foundation of China/ ; 32302765//National Natural Science Foundation of China/ ; 32330100//National Natural Science Foundation of China/ ; CARS-35//China Agricultural Research System/ ; //2115 Talent Development Program of China Agricultural University/ ; }, abstract = {BACKGROUND: Qiwenghuangbo powder (QP), composed of Astragalus, Phellodendron chinensis, and Radix pulsatilla, is a traditional Chinese herbal formula, but its effects on weaned piglets remained unclear.<br><br>METHODS: Weaned piglets fed with 0.5&#x2009;kg/t QP (QP1), 1&#x2009;kg/t QP (QP2), low-zinc oxide (ZnO; negative control), and high-ZnO (positive control) diets in two phases, respectively, and the growth performance, intestinal morphology, cytokines, and microbial communities were profiled. The mouse models of colitis induced by Citrobacter rodentium and dextran sulfate sodium (DSS) were employed to elucidate the potential role of QP-fed enriched key species.<br><br>RESULTS: Dietary 1.0&#x2009;kg/t QP alleviated diarrhea and inflammation and improved intestinal development and growth performance of weaned piglets. Moreover, this dietary intervention notably altered microbiota composition, characterized by the enrichment of Limosilactobacillus reuteri. Furthermore, out of three isolated L. reuteri, two strains could alleviate pathogen infection and intestinal inflammation, respectively. Specifically, the anti-inflammatory effect of one strain was achieved by promoting the colonization resistance of C. rodentium as significantly reduced pathogen loads. The other strain mitigated DSS-induced colitis by enhancing the goblet cell function and inhibiting the secretion of pro-inflammatory cytokines, particularly interleukin-1&#x3b2; (IL-1&#xdf;) and tumor necrosis factor-&#x3b1; (TNF-&#x3b1;).<br><br>CONCLUSIONS: Dietary QP improved the growth performance and intestinal health of weaned piglets by promoting the colonization of L. reuteri. The isolated commensal L. reuteri control colitis in a strain-specific mechanism, highlighting the potential of QP and L. reuteri in providing evidence for gut health promotion.}, }
@article {pmid40108947, year = {2025}, author = {Zhang, C and Qu, L and Huang, Y and Tang, L and Ma, J and Xie, K and Wu, H}, title = {Association of Oral Microbiome Diversity With Depression Status: NHANES 2009-2012.}, journal = {Journal of public health dentistry}, volume = {}, number = {}, pages = {}, doi = {10.1111/jphd.12671}, pmid = {40108947}, issn = {1752-7325}, abstract = {OBJECTIVES: To investigate the relationship between oral microbial diversity and depression symptoms in the U.S.<br><br>METHODS: We utilized the US National Health and Nutrition Examination Survey (NHANES; 2009-2012) to assess the association between oral microbial diversity and depression symptoms. A cut-off PHQ-9 score of 15 was used to define severe depression symptoms. We conducted the multivariate linear regression to explore the association of the amplicon sequence variants (ASVs) with PHQ-9 scores. A restricted cubic spline (RCS) model was introduced to curve the dose-response relationship. A logistic regression model was used to calculate the odds ratio (OR) and 95% confidence interval (CI) of the association between ASVs and the risk of severe depression symptoms. Based on Bray-Curtis dissimilarity of beta diversity, analysis of similarity (ANOSIM) is used to assess the dissimilarity between different depression groups.<br><br>RESULTS: A total of 1497 participants were included, with 111 (7.41%) meeting the criteria for severe depression. After adjusting for confounders, we found that ASVs were negatively correlated with PHQ-9 scores (&#x3b2;&#x2009;=&#x2009;-0.008, p&#x2009;=&#x2009;0.014). The RCS plot showed a linear relationship (pnon-linear&#x2009;=&#x2009;0.232). Logistic regression showed that ASVs were associated with a decreased risk of severe depression symptoms (OR&#x2009;=&#x2009;0.992, p&#x2009;=&#x2009;0.003). Analysis of &#x3b2; diversity identified a statistically significant difference (R&#x2009;=&#x2009;0.087, p&#x2009;=&#x2009;0.003). Additionally, we developed a nomogram to estimate an individual's risk of severe depression symptoms.<br><br>CONCLUSIONS: Alpha diversity of the oral microbiota was associated with a reduced risk of severe depression symptoms, which could contribute to the early identification and intervention of severe depression.}, }
@article {pmid40108935, year = {2025}, author = {O'Grady, K and Grabrucker, AM}, title = {Metal Dyshomeostasis as a Driver of Gut Pathology in Autism Spectrum Disorders.}, journal = {Journal of neurochemistry}, volume = {169}, number = {3}, pages = {e70041}, doi = {10.1111/jnc.70041}, pmid = {40108935}, issn = {1471-4159}, support = {//University of Limerick/ ; }, mesh = {Humans ; *Autism Spectrum Disorder/metabolism/pathology ; *Homeostasis/physiology ; *Gastrointestinal Microbiome/physiology ; *Brain-Gut Axis/physiology ; Animals ; Metals, Heavy/metabolism/toxicity ; Gastrointestinal Tract/metabolism/pathology ; }, abstract = {Despite being classified as neurodevelopmental disorders, in recent years, there has been a growing interest in the association between autism spectrum disorders (ASDs) and gut pathology. This comprehensive and systematic review explores a potential mechanism underlying gut pathology in ASDs, including alterations in gut microbiota, intestinal permeability, immune dysregulation, and gastrointestinal (GI) symptoms. Specifically, it delves into the role of toxic and essential metals and their interplay, affecting the development and function of the GI tract. The review also discusses the potential implications of this gut pathology in the development and management of ASDs. Studies have shown that heavy metal exposure, whether through environmental sources or dietary intake, can disrupt the delicate balance of trace elements in the gut. This disruption can adversely affect zinc homeostasis, potentially exacerbating gut pathology in individuals with ASDs. The impaired zinc absorption resulting from heavy metal exposure may contribute to the immune dysregulation, oxidative stress, and inflammation observed in the gut of individuals with ASDs. By shedding light on the multifaceted nature of gut pathology, including the impact of metal dyshomeostasis as a non-genetic factor in ASD, this review underscores the significance of the gut-brain axis in the etiology and management of ASDs.}, }
@article {pmid40108902, year = {2025}, author = {Khalili, L and Park, G and Nagpal, R and Bhide, P and Salazar, G}, title = {The Impact of Akkermansia muciniphila on Mouse Models of Depression, Anxiety, and Stress: A Systematic Review and Meta-Analysis.}, journal = {Current neuropharmacology}, volume = {}, number = {}, pages = {}, doi = {10.2174/011570159X360149250225041829}, pmid = {40108902}, issn = {1875-6190}, abstract = {BACKGROUND: Akkermansia muciniphila (A. muciniphila), a bacterial species within the human gut microbiome, has shown beneficial effects on host health. Emerging research suggests that A. muciniphila also influences neurobehavioral domains through the microbiota-gut-brain axis. This meta-analysis evaluates A. muciniphila's impact on depression, anxiety, and stress in mouse models.<br><br>METHODS: We conducted a systematic search of PubMed, Science Direct, Embase, and Web of Science databases up to March 2024, identifying 15 eligible studies.<br><br>RESULTS: Supplementation with A. muciniphila, its outer membrane protein (Amuc_1100), and extracellular vesicles (EVs) alleviated anxiety, depressive-like behaviors, and enhanced memory in mice. Compared to controls, intervention groups exhibited reduced anxiety-like behaviors, including increased travel distance in the open-field test (OFT) and more time spent in the lightbox during the light-dark box (LDB) test and open arms in the elevated plus maze (EPM). Depression-like symptoms were reduced, with lower immobility time in the tail suspension and forced swim tests. Memory function also improved, and learning time was reduced in the Y-maze and Barnes circular maze tests. Serotonin levels increased significantly in the serum and hippocampus, while corticosterone levels decreased, though not significantly. The intervention reduced hippocampal and serum inflammatory markers (TNF&#x3b1;, IL1&#x3b2;, IL6) and altered gut microbiome composition, increasing Akkermansia, Roseburia, Caldicoprobacter, and Lachnospiraceae.<br><br>CONCLUSION: This meta-analysis provides evidence supporting the health-promoting effects of A. muciniphila, one of the next-generation probiotics, in alleviating neuropsychiatric disorders. Given the high prevalence and clinical significance of depression, anxiety, and stress, further investigation into the therapeutic utility of A. muciniphila is warranted.}, }
@article {pmid40108895, year = {2025}, author = {Dagdeviren, M and Bozcal, E}, title = {Inflecting Factors on Alzheimer's Disease Progression: The Interaction of Gut Microbiome, Oxidative Stress, and Nutritional Interventions.}, journal = {Current topics in medicinal chemistry}, volume = {}, number = {}, pages = {}, doi = {10.2174/0115680266342624241127071044}, pmid = {40108895}, issn = {1873-4294}, abstract = {Alzheimer's Disease (AD) is a complex neurological condition caused by various factors. Diet, oxidative stress, and the gut microbiota all play critical roles in the development of AD. Recent studies suggested a bidirectional relationship between the gut and the brain, emphasizing the pivotal role of the gut microbiome in influencing cognitive functions. For instance, dysbiosis, a disruption in the balance of gut microbial communities, has been linked to neuroinflammation and the accumulation of amyloid-beta plaques, hallmark features of AD. Oxidative stress, arising from an imbalance between free radicals and antioxidants, contributes significantly to AD pathology. The molecular mechanisms through which oxidative stress impacts neuronal health and exacerbates the cognitive decline in AD patients are also relevant. Moreover, nutritional interventions emerge as promising strategies to modulate these inflecting factors. Dietary components, such as antioxidants, omega-3 fatty acids, and polyphenols, exhibit neuroprotective effects, potentially mitigating AD progression. In contrast, the Western diet has a high potential to abet AD onset. Mediterranean diet and/or intermittent fasting are more valuable diets that may help delay the AD onset or progression. Limitations like individual differences affect the efficacy of nutritional interventions. As a supporting therapy, personalized diets should be applied according to the patients' special needs/microbiomes in the future. To gather current knowledge on the interconnected roles of the gut microbiome, oxidative stress, and nutritional interventions in AD is crucial. Understanding these interactions may pave the way for novel therapeutic approaches, as well as disputing the potential diets that can help improve AD patients' quality of life.}, }
@article {pmid40108741, year = {2025}, author = {Gamboa, DA and Flynn, PJ and Horna-Lowell, ES and Pinter-Wollman, N}, title = {Social organization and physical environment shape the microbiome of harvester ants.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {29}, pmid = {40108741}, issn = {2524-4671}, support = {000886211//National Science Foundation Graduate Research Fellowship Program/ ; GM115509//Foundation for the National Institutes of Health/ ; }, abstract = {All animals harbor microbiomes, which are obtained from the surrounding environment and are impacted by host behavior and life stage. To determine how two non-mutually exclusive drivers - physical environment and social organization - affect an organism's microbiome, we examined the bacterial communities within and around nests of harvester ants (Veromessor andrei). We collected soil and nest content samples from five different ant nests. We used 16S rRNA gene sequencing and calculated alpha and beta diversity to compare bacterial diversity and community composition across samples. To test the hypotheses that physical environment and/or social organization impact ant colonies' community of microbes we compared our samples across (i) sample types (ants, brood, seeds and reproductives (winged alates), and soil), (ii) soil inside and outside the nest, and (iii) soil from different chamber types. Interestingly, we found that both the environment and social organization impact the bacterial communities of the microbiome of V. andrei colonies. Soil from the five nests differed from one another in a way that mapped onto their geographical distance. Furthermore, soil from inside the nests resembled the surrounding soil, supporting the physical environment hypothesis. However, the bacterial communities associated with the contents within the nest chambers, i.e., ants, brood, seeds, and reproductives, differed from one another and from the surrounding soil, supporting the social organization hypotheses. This study highlights the importance of considering environmental and social factors in understanding microbiome dynamics.}, }
@article {pmid40108657, year = {2025}, author = {Ruiz-Moreno, AJ and Del Castillo-Izquierdo, &#xc1; and Tamargo-Rubio, I and Fu, J}, title = {MicrobeRX: a tool for enzymatic-reaction-based metabolite prediction in the gut microbiome.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {78}, pmid = {40108657}, issn = {2049-2618}, support = {101001678/ERC_/European Research Council/International ; VI.C.202.022//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; Bacteria/metabolism/classification/genetics ; Pharmaceutical Preparations/metabolism ; Enzymes/metabolism ; Software ; Biotransformation ; Metabolomics/methods ; }, abstract = {BACKGROUND: The gut microbiome functions as a metabolic organ, producing numerous enzymes that influence host health; however, their substrates and metabolites remain largely unknown.<br><br>RESULTS: We present MicrobeRX, an enzyme-based metabolite prediction tool that employs 5487 human reactions and 4030 unique microbial reactions from 6286 genome-scale models, as well as 3650 drug metabolic reactions from the DrugBank database (v.5.1.12). MicrobeRX includes additional analysis modules for metabolite visualization and enzymatic and taxonomic analyses. When we applied MicrobeRX to 1083 orally administered drugs that have been approved in at least one jurisdiction at some point in time (DrugBank), it predicted metabolites with physicochemical properties and structures similar to metabolites found in biosamples (from MiMeDB). It also outperformed another existing metabolite prediction tool (BioTransformer 3.0) in terms of predictive potential, molecular diversity, reduction of redundant predictions, and enzyme annotation.<br><br>CONCLUSIONS: Our analysis revealed both unique and overlapping metabolic capabilities in human and microbial metabolism and chemo- and taxa-specific microbial biotransformations. MicrobeRX bridges the genomic and chemical spaces of the gut microbiome, making it a valuable tool for unlocking the chemical potential of the gut microbiome in human health, the food and pharmaceutical industries, and environmental safety. Video Abstract.}, }
@article {pmid40108637, year = {2025}, author = {Gangiah, TK and Alisoltani, A and Potgieter, M and Bell, L and Ross, E and Iranzadeh, A and McDonald, Z and Allali, I and Dabee, S and Barnabas, S and Blackburn, JM and Tabb, DL and Bekker, LG and Jaspan, HB and Passmore, JS and Mulder, N and Masson, L}, title = {Exploring the female genital tract mycobiome in young South African women using metaproteomics.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {76}, pmid = {40108637}, issn = {2049-2618}, support = {SP.2011.41304.038//European and Developing Countries Clinical Trials Partnership Strategic Primer/ ; }, mesh = {Female ; Humans ; South Africa ; *Mycobiome ; *Proteomics ; Adult ; Young Adult ; *Vagina/microbiology ; Fungi/classification/isolation &amp; purification/genetics ; Vaginosis, Bacterial/microbiology ; Adolescent ; Genitalia, Female/microbiology ; Microbiota ; Candida/classification/isolation &amp; purification/genetics ; Chromatography, Liquid ; Tandem Mass Spectrometry ; Sexually Transmitted Diseases/microbiology ; }, abstract = {BACKGROUND: Female genital tract (FGT) diseases such as bacterial vaginosis (BV) and sexually transmitted infections are prevalent in South Africa, with young women being at an increased risk. Since imbalances in the FGT microbiome are associated with FGT diseases, it is vital to investigate the factors that influence FGT health. The mycobiome plays an important role in regulating mucosal health, especially when the bacterial component is disturbed. However, we have a limited understanding of the FGT mycobiome since many studies have focused on bacterial communities and have neglected low-abundance taxonomic groups, such as fungi. To reduce this knowledge deficit, we present the first large-scale metaproteomic study to define the taxonomic composition and potential functional processes of the FGT mycobiome in South African reproductive-age women.<br><br>RESULTS: We examined FGT fungal communities present in 123 women by collecting lateral vaginal wall swabs for liquid chromatography-tandem mass spectrometry. From this, 39 different fungal genera were identified, with Candida dominating the mycobiome (53.2% relative abundance). We observed changes in relative abundance at the protein, genus, and functional (gene ontology biological processes) level between BV states. In women with BV, Malassezia and Conidiobolus proteins were more abundant, while Candida proteins were less abundant compared to BV-negative women. Correspondingly, Nugent scores were negatively associated with total fungal protein abundance. The clinical variables, Nugent score, pro-inflammatory cytokines, chemokines, vaginal pH, Chlamydia trachomatis, and the presence of clue cells were associated with fungal community composition.<br><br>CONCLUSIONS: The results of this study revealed the diversity of FGT fungal communities, setting the groundwork for understanding the FGT mycobiome. Video Abstract.}, }
@article {pmid40108579, year = {2025}, author = {Feng, Q and Huang, W and Zhao, X and Sheng, T and Peng, B and Meng, S and Liu, W and Ge, L and Wang, L and Pathak, JL and Jiang, Q and Lin, R and Zeng, S}, title = {Investigation of dental health and salivary microbiota characteristics of children with visual impairment in Guangzhou, China.}, journal = {BMC oral health}, volume = {25}, number = {1}, pages = {408}, pmid = {40108579}, issn = {1472-6831}, support = {No.20241A010079//the General Guidelines of Guangzhou Health Science, Technology Project/ ; No.20241A010079//the General Guidelines of Guangzhou Health Science, Technology Project/ ; 201904010085//the Science and Technology Planning Project of Guangzhou/ ; 201904010085//the Science and Technology Planning Project of Guangzhou/ ; 2023E02J0004//the Guangzhou Liwan District science popularization "One District One Brand" project/ ; }, mesh = {Humans ; Child ; China ; *Saliva/microbiology ; Female ; Male ; *Microbiota ; Adolescent ; *Oral Health ; *Vision Disorders/microbiology ; Dental Caries/microbiology ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: The prevalence of visual impairment (VS) among children in China is increasing. The oral microbiome is crucial for maintaining homeostasis and health. This study aimed to investigate the oral health and hygiene habits of children with VS in Guangzhou and explore the differences in salivary microbiota (SM) between children with VS and healthy vision (HS).<br><br>METHOD: This study included oral health examinations and surveys of oral hygiene habits among 101 children with VS. Saliva samples from 20 children with VS and 20 with HS were analysed for oral microbiota. The 16s rRNA V3-V4 regions were sequenced using the Illumina MiSeq platform and operational taxonomic units were clustered using QIIME for statistical analysis.<br><br>RESULTS: Inadequate oral hygiene was observed among 101 children with VS, aged 6-16, who displayed a high caries rate of 92.1%. There was no significant difference in the overall composition of the salivary microbiota between the two groups. HS group had a higher abundance of Bacillota, Patescibacteria, and Spirochaetota at the phylum level; Bacilli, Negativicutes, and Saccharimonadia at the class level; and Streptococcus at the genus level. In contrast, VS group showed a greater abundance of Actinomycetota, Bacteroidota, Pseudomonadota, and Fusobacteriota (at the phylum level) and Actinomycetia, Bacteroidia, Gammaproteobacteria, Fusobacteriia, and Clostridia (at the class level), along with Rothia, Neisseria, Veillonella, Prevotella_7, Actinomyces, Leptotrichia, and Lactobacillales (at the genus level). Actinomycetota was significantly and positively correlated with gingivitis and dental caries, and Streptococcus salivarius was more abundant in children with VS.<br><br>CONCLUSION: This study underscores the importance of improving oral healthcare for schoolchildren with VS in Guangzhou, China and provides valuable insights into the characteristics of the salivary microbiota of this population, identifying potential targets for interventions aimed at enhancing oral health.}, }
@article {pmid40108399, year = {2025}, author = {Xu, J and Dong, L and Xie, X and Geng, BD and Lu, J and Dong, Y and Hu, Y and Liu, C and Mao, Y and Ge, G and Ren, Z}, title = {Human umbilical cord-derived mesenchymal stem cells improve thymus and spleen functions in D-galactose-induced aged mice.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {9470}, pmid = {40108399}, issn = {2045-2322}, support = {82160126//National Natural Science Foundation of China/ ; gzwkj2023-230//Science and Technology Fund Project of Guizhou Province Health Commission/ ; HY2402//Cooperation projects of Guizhou Medical University-Guizhong Biotechnology Co., Ltd/ ; Qiankehe Foundation-ZK 2024 General 182//Natural Science Foundation Project of Guizhou Provincial Science and Technology Department/ ; XBHJ[2024]018 &amp; [2020]018//Guizhou Medical University Doctoral Start-up Fund/ ; }, mesh = {Animals ; *Galactose ; *Thymus Gland/metabolism ; *Mesenchymal Stem Cells/metabolism/cytology ; *Spleen/metabolism ; Mice ; *Umbilical Cord/cytology ; Humans ; *Mesenchymal Stem Cell Transplantation/methods ; Gastrointestinal Microbiome ; Aging ; Cellular Senescence ; Male ; NF-E2-Related Factor 2/metabolism ; }, abstract = {As aging progresses, the structures and functions of immune organs such as the thymus and spleen deteriorate, leading to impaired immune function and immune senescence. This study investigated the potential of umbilical cord mesenchymal stem cells (UC-MSCs) to mitigate D-galactose-induced immune senescence by enhancing the structural and functional integrity of aging immune organs and regulating the gut microbiota. The findings show that UC-MSCs treatment significantly delayed thymus and spleen atrophy and reduced the number of senescence-associated β-galactosidase (SA-β-gal) positive cells. At the molecular level, UC-MSCs treatment downregulated the expression of aging-related genes, including p16, p53, p21, and RB. It also boosted antioxidant enzyme activity, increasing the levels of catalase (CAT), superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px), while decreasing serum malondialdehyde (MDA) levels by activating the Nrf2/HO-1 pathway. Additionally, UC-MSCs treatment restored the balance of the gut microbiota. These results demonstrate that UC-MSCs significantly improve the structural and functional integrity of immune organs and enhance the composition of the gut microbiome, offering a potential strategy for delaying immune senescence.}, }
@article {pmid40108347, year = {2025}, author = {Bashandy, SR and Mohamed, OA and Abdalla, OA and Elfarash, A and Abd-Alla, MH}, title = {Harnessing plant growth-promoting bacteria to combat watermelon mosaic virus in squash.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {9440}, pmid = {40108347}, issn = {2045-2322}, mesh = {*Plant Diseases/microbiology/virology ; *Potyvirus/physiology ; *Cucurbita/virology/microbiology/growth &amp; development ; *Bacteria/metabolism/genetics ; Rhizosphere ; Soil Microbiology ; Indoleacetic Acids/metabolism ; RNA, Ribosomal, 16S/genetics ; Carbon-Carbon Lyases/metabolism ; Plant Growth Regulators/metabolism ; Plant Development ; }, abstract = {Plant diseases significantly threaten global food security, with viral infections, particularly Watermelon Mosaic Virus (WMV), causing substantial losses in economically important crops such as squash. This study aims to investigate the efficacy of beneficial bacteria isolated from various plants in promoting growth and mitigating the effects of WMV in squash. Understanding the interactions between plants and beneficial microbes could provide sustainable solutions for managing viral infections in agriculture. Sixty-two bacterial isolates were obtained from the rhizosphere of basil, mint, thyme, and squash plants. Among these, six strains exhibited notable plant growth-promoting activities, including the synthesis of indole acetic acid, solubilization of phosphate and zinc, ammonia production, and activity of 1-aminocyclopropane-1-carboxylate deaminase (ACCD). Morphological observations and 16S rRNA gene sequencing identified these isolates as Pseudomonas indica, Bacillus paramycoides, Bacillus thuringiensis, Bacillus mycoides, Paenibacillus glucanolyticus, and Niallia circulans. In pot experiments, squash plants inoculated with these bacterial strains demonstrated significant reductions in disease severity after being infected with WMV. Specifically, foliar applications of the bacteria resulted in the following reductions in disease severity: B. mycoides (87%), B. thuringiensis (73%), Paenibacillus glucanolyticus (73%), Niallia circulans (70%), B. paramycoides (65%), and Pseudomonas indica (65%). Additionally, plants treated with B. mycoides showed increased plant height and shoot dry weight, indicating enhanced growth performance relative to infected controls. Statistical analysis revealed that these growth promotions and disease severity reduction were significant (p < 0.05). GC-MS analysis of the six bacterial strains revealed a diverse array of 73 chemical metabolites, including common compounds such as 9-Octadecenoic acid (Z), benzene derivatives, and cyclopentanones. These findings suggest shared metabolic pathways among the strains and indicate potential roles in ecological interactions, plant defense mechanisms, and antiviral properties. These metabolites likely contribute to the observed reductions in viral severity and enhance plant resilience. The study indicates that inoculating squash plants with specific beneficial bacteria, especially B. mycoides, through foliar or soil application can significantly decrease the severity of WMV and promote plant growth. This approach offers an environmentally friendly alternative to chemical antiviral treatments and may reduce reliance on pesticides. This research highlights the potential of using plant growth-promoting bacteria (PGPB)as a sustainable approach to control viral infections in crops. Further field trials are necessary to PGPB validate the scalability of these findings and assess their effectiveness under diverse agricultural conditions. Incorporating these beneficial microbes into agricultural practices could enhance the resilience of cropping systems, ultimately fostering sustainable agriculture and enhancing food security.}, }
@article {pmid40108202, year = {2025}, author = {Redgwell, TA and Thorsen, J and Petit, MA and Deng, L and Vestergaard, G and Russel, J and Chawes, B and Bønnelykke, K and Bisgaard, H and Nielsen, DS and Sørensen, S and Stokholm, J and Shah, SA}, title = {Prophages in the infant gut are pervasively induced and may modulate the functionality of their hosts.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {46}, pmid = {40108202}, issn = {2055-5008}, mesh = {*Gastrointestinal Microbiome ; *Prophages/genetics/physiology ; Humans ; Infant ; *Metagenome ; Virome ; Female ; Feces/microbiology/virology ; Bacteria/genetics/classification/virology ; Bacteroides/genetics/virology ; }, abstract = {Gut microbiome (GM) composition and function is pivotal for human health and disease, of which the virome's importance is increasingly recognised. However, prophages and their induction patterns in the infant gut remain understudied. Here, we identified 10645 putative prophages in 662 metagenomes from 1-year-old children in the COPSAC2010 mother-child cohort and investigated their potential functions. No core provirome was found as the most prevalent vOTU was identified in only ~70% of the samples. The most dominant cluster of vOTUs in the cohort was related to Bacteroides phage Hanky p00', and it carried both diversity generating retroelements and genes involved in capsular polysaccharide synthesis. Paired analysis of viromes and metagenomes from the same samples revealed that most prophages within the infant gut were induced and that induction was unaffected by a range of environmental perturbers. In summary, prophages are major components of the infant gut that may have far reaching influences on the microbiome and its host.}, }
@article {pmid40108178, year = {2025}, author = {Hong, MG and Song, EJ and Yoon, HJ and Chung, WH and Seo, HY and Kim, D and Lee, D and Seo, JG and Lee, H and Kim, SI and Kim, GJ and Kim, KN and Lee, SN and Kim, KS and Nam, YD}, title = {Clade-specific extracellular vesicles from Akkermansia muciniphila mediate competitive colonization via direct inhibition and immune stimulation.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2708}, pmid = {40108178}, issn = {2041-1723}, mesh = {*Akkermansia ; *Extracellular Vesicles/metabolism/immunology ; *Gastrointestinal Microbiome ; Animals ; Immunoglobulin A/immunology ; Mice ; Humans ; Probiotics ; Mice, Inbred C57BL ; }, abstract = {Akkermansia muciniphila, a promising candidate for next-generation probiotics, exhibits significant genomic diversity, classified into several distinct clades (AmI to AmIV). Notably, a single Akkermansia clade tends to predominate within individual hosts, with co-occurrence of different clades being rare. The mechanisms driving such clade-specific exclusion remain unclear. Here, we show that extracellular vesicles (EVs) derived from AmII clade inhibit the growth of clade I (AmI), conferring a competitive advantage to AmII. Moreover, we observe clade-specific immunoglobulin A (IgA) responses, where AmII clade-specific IgAs, induced by EVs from AmII, facilitate niche occupancy and competitive exclusion of AmI. These findings provide insights into the competitive dynamics of A. muciniphila clades and suggest that future personalized microbiome interventions could be optimized by considering the clade composition of A. muciniphila in individual hosts.}, }
@article {pmid40108151, year = {2025}, author = {Krueger, ME and Boles, JS and Simon, ZD and Alvarez, SD and McFarland, NR and Okun, MS and Zimmermann, EM and Forsmark, CE and Tansey, MG}, title = {Comparative analysis of Parkinson's and inflammatory bowel disease gut microbiomes reveals shared butyrate-producing bacteria depletion.}, journal = {NPJ Parkinson's disease}, volume = {11}, number = {1}, pages = {50}, pmid = {40108151}, issn = {2373-8057}, support = {PF-RCE-1945//Parkinson's Foundation (Parkinson's Foundation, Inc.)/ ; PF-RCE-1945//Parkinson's Foundation (Parkinson's Foundation, Inc.)/ ; PF-RCE-1945//Parkinson's Foundation (Parkinson's Foundation, Inc.)/ ; }, abstract = {Epidemiological studies reveal that inflammatory bowel disease (IBD) is associated with an increased risk of Parkinson's disease (PD). Gut dysbiosis has been documented in both PD and IBD, however it is currently unknown whether gut dysbiosis underlies the epidemiological association between both diseases. To identify shared and distinct features of the PD and IBD microbiome, we recruited 54 PD, 26 IBD, and 16 healthy control individuals and performed the first joint analysis of gut metagenomes. Larger, publicly available PD and IBD metagenomic datasets were also analyzed to validate and extend our findings. Depletions in short-chain fatty acid (SCFA)-producing bacteria, including Roseburia intestinalis, Faecalibacterium prausnitzii, Anaerostipes hadrus, and Eubacterium rectale, as well depletion in SCFA-synthesis pathways were detected across PD and IBD datasets, suggesting that depletion of these microbes in IBD may influence the risk for PD development.}, }
@article {pmid40107863, year = {2025}, author = {Emerson, KJ and Shaikh, SS and Bradley-Slagle, DP and Woodley, SK}, title = {The Aquatic Microbial Environment Shapes the Tadpole Microbiome and Antipredator Behavior.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icaf009}, pmid = {40107863}, issn = {1557-7023}, abstract = {Host-associated microbial communities impact the brain and behavior through the microbiota-gut-brain (MGB) axis. Most studies of the gut microbiota use mammals in biomedical contexts; much less is known regarding wildlife species. We used larval amphibians to study the impact of the aquatic microbial environment on the gut and skin microbiota, brain, and antipredator behavior. We raised Northern Leopard Frog (Lithobates pipiens) tadpoles in pond water that was autoclaved or not autoclaved (natural); other studies show that these treatments produce variation in the tadpole gut microbiota. Tadpoles were also raised in the presence of stressors: predation-derived chemical cues and corticosterone. Compared to tadpoles raised in natural pond water, tadpoles raised in autoclaved pond water had altered gut and skin microbial communities, body size, brain size, brain shape and behavioral responses to alarm pheromones. There was no effect of microbial environment or stressors on differential gene expression of the whole brain. The gut microbiota, but not the skin microbiota, was a significant predictor of behavioral endpoints. We found surprisingly few impacts of stressors on the tadpoles, although stressor treatments interacted with pond water treatments to influence the composition of the gut microbiota. Our findings demonstrate that tadpole behavior is modulated by the aquatic microbial community experienced during development in ways that are likely to affect survival.}, }
@article {pmid40107677, year = {2025}, author = {Pasquier, JC and Plourde, M and Ramanathan, S and Chaillet, N and Boivin, G and Laforest-Lapointe, I and Allard-Chamard, H and Baron, G and Beaulieu, JF and Fülöp, T and Généreux, M and Mâsse, B and Robitaille, J and Valiquette, L and Bilodeau, S and H Buch, D and Piche, A}, title = {P robiotics i nfluencing r esponse of a ntibodies over t ime in s eniors after CO VID-19 v accine (PIRATES-COV): a randomised controlled trial protocol.}, journal = {BMJ open}, volume = {15}, number = {3}, pages = {e088231}, doi = {10.1136/bmjopen-2024-088231}, pmid = {40107677}, issn = {2044-6055}, mesh = {Humans ; Aged ; *COVID-19/prevention &amp; control ; Aged, 80 and over ; *Probiotics/therapeutic use ; Double-Blind Method ; *SARS-CoV-2/immunology ; Male ; Female ; *COVID-19 Vaccines/immunology ; Quebec ; Antibodies, Viral/blood ; Lacticaseibacillus casei/immunology ; Lacticaseibacillus rhamnosus ; Randomized Controlled Trials as Topic ; }, abstract = {INTRODUCTION: The elderly are particularly vulnerable to morbidity and mortality from COVID-19, the disease caused by the SARS-CoV-2. Approximately 20% of the elderly showed no antibodies 3-5 months post-second dose of the COVID-19 vaccine. As probiotics have been shown to increase influenza-specific antibody levels post-influenza vaccination, we aim to reduce the percentage of participants without antibodies against the SARS-CoV-2 spike protein receptor-binding domain (anti-S1-RBD) at 6 months post-vaccination.<br><br>METHODS AND ANALYSIS: Our study design is a double-blind randomised controlled trial, using intention-to-treat analysis. Eligible participants are a purposive sample of 688 adults aged 65-89 years, in Quebec, Canada, not diagnosed with COVID-19 in the 3 months prior to recruitment and who wish to receive a government-recommended mRNA booster (Pfizer-BioNTech, Moderna) vaccine. The intervention consists of one capsule/day of a probiotic dietary supplement of Lacticaseibacillus rhamnosus and Lacticaseibacillus casei 6&#xd7;10[9]&#x2009;CFU/capsule or a placebo, for 15 days pre-booster and post-booster vaccine. All participants provide dried blood spot samples at three timepoints (inclusion, 3 and 6&#x2009;months post-vaccination) and a stool sample for microbiome analysis. A subgroup of 100 participants living near Sherbrooke, Quebec, is expected to volunteer for two onsite blood-test visits (at inclusion and 6 months post-vaccination). The primary outcome is the percentage of participants without anti-S1-RBD antibodies at 6 months post-vaccination. Secondary outcomes include longitudinal analysis of anti-S1-RBD and anti-N antibodies at three timepoints. In the subgroup, serum levels of neutralising antibodies will be determined at inclusion and 6 months post-vaccination. Probiotic and vaccine side effects are monitored. At the end of the study, we expect to identify the adjuvant effect of probiotic on vaccine-induced immune response.<br><br>ETHICS AND DISSEMINATION: The study was approved by Research Ethics Board of the Centre Int&#xe9;gr&#xe9; Universitaire de Sant&#xe9; et des Services Sociaux de l'Estrie- Centre Hospitalier Universitaire de Sherbrooke (CIUSSS de l'Estrie-CHUS) and the CHU de Qu&#xe9;bec-Universit&#xe9; Laval # MP-31-2022-4598 as well as Health Canada. All participants will provide informed consent. Results will be disseminated to the scientific community and to all networks related in this research.<br><br>TRIAL REGISTRATION NUMBER: NCT05195151.}, }
@article {pmid40107222, year = {2025}, author = {Yatera, K and Nishida, C and Mukae, H}, title = {Up-to-date nucleic acid assays for diagnosing respiratory infection.}, journal = {Respiratory investigation}, volume = {63}, number = {3}, pages = {383-393}, doi = {10.1016/j.resinv.2025.03.004}, pmid = {40107222}, issn = {2212-5353}, abstract = {Nucleic acid assays have been widely used as rapid tests for diagnosing respiratory infections during and after the coronavirus disease 2019 (COVID-19) pandemic. An ideal point-of-care diagnostic must be affordable, sensitive, specific, user-friendly, rapid/robust, equipment-free and deliverable (ASSURED), and in addition to improvements to conventional methods based on polymerase chain reaction (PCR), point-of-care testing aiming for "REASSURED" are emerging through integration with microfluidic technology. Compared to conventional immunoassays, nucleic acid assays, especially rapid nucleic acid assays as point-of-care testing, contribute to improvements in various clinical outcomes, such as diagnostic yield, turnaround time, length of hospital stay, disease treatment, and infection control management. Rapid and diverse development of new nucleic acid-based molecular diagnostic technologies, such as those based on the CRISPR/Cas system or biosensor nucleic acid assays, is expected to become increasingly diverse in the future as point-of-care testing. In addition, laboratory-based DNA sequencing technology has been used to perform microbiome analyses over a wide area and is expected to shed light on the pathological mechanisms of various respiratory infectious diseases. One example of the benefits of nucleic acid amplification analysis methods is their ability to reveal the true nature of the bacterial flora in pneumonia lesions. This has been demonstrated based on the results of 16S ribosomal RNA gene sequencing analyses using bronchoalveolar lavage fluid directly obtained from pneumonia lesions in patients with pneumonia.}, }
@article {pmid40106906, year = {2025}, author = {Pan, H and Bi, J and Hu, H and Huang, Y and Li, A and Zhang, H and Wan, Y and Zhan, K and Wang, K and Zhao, Z and Bai, X}, title = {Chinese herbal medicine improves antioxidant capacity of chicken liver at high stocking density involved gut-liver microbiota axis based on multi-omics technologies.}, journal = {Poultry science}, volume = {104}, number = {5}, pages = {105015}, doi = {10.1016/j.psj.2025.105015}, pmid = {40106906}, issn = {1525-3171}, abstract = {Traditional Chinese Medicine (TCM), such as artemisinin, berberine and proanthocyanidin, has been considered an effective additive for broiler production. High density farming (HDF), which is the primary modern mode of chicken production, is associated with animal health problems. This work aimed to evaluate the effects of dietary TCMs (dihydroartemisinin, hydrochloride, and oligomeric proanthocyanidins) on improving the antioxidant capacity of chickens under HDF and their underlying mechanisms. A total of 360 Wuding chickens (134-day-old) were divided into five experimental groups: one normal stocking density (8 birds/m[2], control group) and four high stocking density (16 birds/m[2]), with six replicates for each group. For four HDF groups, one group was fed the basal diet, and the other three groups were fed the basal diet supplemented with 80 mg/kg dihydroartemisinin, 600 mg/kg berberine hydrochloride, and 250 mg/kg grape oligomeric proanthocyanidins, respectively. HDF increased malondialadehyde level, but decreased superoxide dismutase, glutathione and glutathione peroxidase levels in the liver of broiler; however, dietary TCMs apparently alleviated this attenuation. Dietary TCMs significantly decreased the expression of genes involved in cholesterol synthesis in the liver and the levels of tripepides in the intestine of the HDF chickens. Meanwhile, dietary TCMs significantly altered the composition of the liver microbiome in the HDF chickens, expressing by reduced Pseudomonas but enriched Bradyrhizobium. The gut microbiota of the HDF chickens was also altered following dietary TCM administration, with a decreased abundance of Microbacter margulisiae and an increased abundance of acetate synthesis genes. Association analysis of the multi-omics results revealed negative correlations between liver cholesterol synthesis and antioxidant factors that could be regulated by gut microbiota-produced short-chain fatty acids. Furthermore, alleviating of oxidative stress by dietary TCMs also showed significant correlations with the liver microbiome, which could be mediated by tripeptides produced by the gut microbiota. These results indicated that dietary TCM is beneficial in improving antioxidant defenses in HDF chickens and interpreted the mechanisms of action of TCM from the perspective of modern science.}, }
@article {pmid40106821, year = {2025}, author = {Yang, CC and Washio, J and Lin, YC and Hsu, ML and Wang, DH and Tsai, FT and Lin, YM and Tu, HF and Chang, HC and Takahashi, N}, title = {Microbiome Signatures and Dysbiotic Patterns in Oral Cancer and Precancerous Lesions.}, journal = {Oral diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/odi.15317}, pmid = {40106821}, issn = {1601-0825}, support = {112-2314-B-A49-027//the National Science and Technology Council, Taiwan/ ; 111-2314-B-A49-028-MY2//the National Science and Technology Council, Taiwan/ ; 111-2314-B-A49-026-MY3//the National Science and Technology Council, Taiwan/ ; 112-2314-B-A49-058//the National Science and Technology Council, Taiwan/ ; 111-2314-B-A49-087-MY3//the National Science and Technology Council, Taiwan/ ; 21H03151//the Japan Society for the Promotion of Science/ ; 20K10241//the Japan Society for the Promotion of Science/ ; 23K18349//the Japan Society for the Promotion of Science/ ; 23K21499//the Japan Society for the Promotion of Science/ ; //the National Yang Ming Chiao Tung University and Ministry of Education (MOE), Taiwan/ ; }, abstract = {BACKGROUND: The oral microbiome has been shown to be associated with the development of oral squamous cell carcinoma (OSCC). Research has primarily focused on elucidating the oncogenic mechanisms of specific pathogens by comparing the microbiomes of OSCC and normal tissues. However, the characteristics of the microbiome in the precancerous state remain less understood, as does the influence of metabolic and environmental factors on OSCC-associated microbiomes.<br><br>METHODS: In this study, we analyzed mucosa-associated microbiomes in normal, precancerous, and OSCC lesions from a cohort of 51 patients using 16S rRNA amplicon sequencing. We investigated compositional changes in the microbiome, including the specific abundances and co-occurrences of OSCC-associated bacteria.<br><br>RESULTS: Our findings indicate that the microbiome associated with precancerous lesions is indistinguishable from that of the normal mucosa, whereas the OSCC microbiome significantly differs from both normal and precancerous conditions. Specifically, the OSCC microbiome harbors less Streptococcus, coupled with an increase in amino-acid-degrading anaerobes such as Fusobacterium and Prevotella. The metabolic properties of individual microbes reported suggest that the overrepresentation of OSCC-specific bacteria is a result of metabolic adaptation to tumor microenvironments, although this possibility needs to be experimentally confirmed.<br><br>CONCLUSIONS: Our results demonstrate oral microbiome patterns across OSCC progression, offering insights into microbial ecological perspectives.}, }
@article {pmid40106235, year = {2025}, author = {Frenn, M and Salzman, N and Lam, V and Holtz, M and Moosreiner, A and Garnier-Villarreal, M and Singh, M}, title = {Childhood Obesity Body Mass Index and Gut Microbiome: A Cluster Randomized Controlled Pilot Feasibility Study.}, journal = {Childhood obesity (Print)}, volume = {}, number = {}, pages = {}, doi = {10.1089/chi.2024.0344}, pmid = {40106235}, issn = {2153-2176}, abstract = {Background: Prebiotic fiber has been examined as a way to foster gut bacteria less associated with obesity. Tests of prebiotic fiber in reducing obesity have occurred mainly in animals, adults, and Caucasians when the highest obesity rates are in African American and Latinx youth. Response to prebiotic fiber is determined by the pre-existing intestinal microbiota. The type of microbiota varies based on diet and physical activity (PA), so it is important to examine acceptability and response to prebiotic fiber in those most at risk for obesity. Methods: This cluster randomized controlled feasibility trial included an online program designed to improve diet and PA along with administration of prebiotic fiber for 12 weeks in 123 4th and 5th grade students where 98% were eligible for free or reduced fee lunch. Of these 56% were male; 71% Latinx; 15% African American; and 14% Other. Results: A decrease in body fat (BF) was associated with higher pre-test BF. Lower BMI was associated with a decrease in fecal Tenericutes and an increase in Actinobacteria. Conclusion: Prebiotic fiber was evaluated in additional studies. Determining those most responsive to prebiotic fiber can also permit individual recommendations for greater inclusion in usual diet choices.}, }
@article {pmid40105993, year = {2025}, author = {Ge, Y and Yang, H and Fu, Y and Zhou, J and Cheng, Z and Fan, X and Yu, Y}, title = {A Mendelian randomization study to reveal gut-disc axis: causal associations between gut microbiota with intervertebral disc diseases.}, journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society}, volume = {}, number = {}, pages = {}, pmid = {40105993}, issn = {1432-0932}, support = {No.cstc2021jcyj-msxmX0853//Natural Science Foundation of Chongqing, China/ ; No.2024ZYZD006//Chongqing Traditional Chinese Medicine scientific research project (Joint project of Chongqing Health Commission and Science and Technology Bureau)/ ; Grant No.KJQN202215120//The Science and Technology Research Program of Chongqing Municipal Education Commission/ ; }, abstract = {PURPOSE: Emerging evidence suggests a link between gut microbiota and intervertebral disc diseases (IDDs); however, the causal relationships remain unclear. This study aimed to evaluate the causal effects of gut microbiota on the risk of cervical disc disorders (CDD), other intervertebral disc disorders (OIDD), pyogenic intervertebral disc infections, and discitis, shedding light on the potential "gut-disc axis".<br><br>METHODS: Genetic variation data for 202 gut microbiota taxa were obtained from the Dutch Microbiome Project, and disease outcome data were sourced from the FinnGen consortium. A Mendelian Randomization (MR) approach was employed to assess causal relationships, using genetic variants as instrumental variables. Sensitivity analyses, including tests for pleiotropy, heterogeneity, and reverse causation, ensured robust findings.<br><br>RESULTS: The study identified 20 gut microbial taxa with significant associations to IDDs. Notably, taxa within the Erysipelotrichaceae family showed consistent protective effects against OIDD after Bonferroni correction (P&#x2009;<&#x2009;0.05). Associations between several species and specific diseases, such as Alistipes senegalensis with CDD and Ruminococcus lactaris with discitis, were also observed. Sensitivity analyses confirmed no evidence of confounding or reverse causation.<br><br>CONCLUSION: This study provides evidence of causal relationships between specific gut microbiota and IDDs, supporting the existence of a "gut-disc axis." The findings suggest that microbial dysbiosis may influence spinal health through systemic inflammation and immune regulation. These insights open new possibilities for microbiota-targeted interventions, such as probiotics or dietary modifications, to prevent or manage IDDs. However, further research is required to validate these therapeutic strategies.}, }
@article {pmid40105301, year = {2025}, author = {Qiu, W and Kang, J and Ye, Z and Yang, S and Tu, X and Xie, P and Ge, J and Ping, W and Yuan, J}, title = {Arbuscular mycorrhizal fungi build a bridge for soybeans to recruit Pseudomonas putida.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.70064}, pmid = {40105301}, issn = {1469-8137}, support = {42322708//National Natural Science Foundation of China/ ; 42277297//National Natural Science Foundation of China/ ; HST2022TR004//the Scientific Research Project of Ecological Environment Protection of Heilongjiang Provincial Department of Ecological Environment, China/ ; 2023-KYYWF-1448//the Basic Scientific Research Operating Expenses of Colleges and Universities in Heilongjiang Province, China/ ; PL2024D015//Heilongjiang Provincial Natural Science Foundation of China/ ; }, abstract = {The assembly of the rhizosphere microbiome determines its functionality for plant fitness. Although the interactions between arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) play important roles in plant growth and disease resistance, research on the division of labor among the members of the symbionts formed among plants, AMF, and PGPR, as well as the flow of carbon sources, is still insufficient. To address the above questions, we used soybean (Glycine max), Funneliformis mosseae, and Pseudomonas putida KT2440 as research subjects to establish rhizobiont interactions and to elucidate the signal exchange and division of labor among these components. Funneliformis mosseae can attract P. putida KT2440 by secreting cysteine as a signaling molecule and can promote the colonization of P. putida KT2440 in the soybean rhizosphere. Colonized P. putida KT2440 can stimulate the l-tryptophan secretion of the host plant and can lead to the upregulation of genes involved in converting methyl-indole-3-acetic acid (Me-IAA) into IAA in response to l-tryptophan stimulation. Collectively, we decipher the tripartite mechanism of rhizosphere microbial community assembly via cross-kingdom interactions.}, }
@article {pmid40104597, year = {2025}, author = {Zhang, Z and Wang, J and Dang, S and Liu, X and Zhang, Y and Zhang, H}, title = {The worldview of Akkermansia muciniphila, a bibliometric analysis.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1500893}, pmid = {40104597}, issn = {1664-302X}, abstract = {Akkermansia muciniphila (A. muciniphila), a critical bacterium within the gut microbiota, plays a key role in human health and immunomodulation. Since its identification in 2004, A. muciniphila has emerged as a significant agent in treating metabolic diseases, gastroenterological diseases, and tumor immunotherapy. Its rapid ascent in scientific translation underscores its importance in gut microbiome research. However, there has been a lack of visualization and analysis of the rapidly occurring commercialization in this field, which has critically hindered insights into the current knowledge structure and understanding of the cutting-edge of the discipline. This study employs the Web of Science Core Collection (WOSCC) and Innography platforms to provide the first comprehensive analysis of A. muciniphila's academic progresses and commercialization over the past two decades, highlighting its growing prominence in global health research. Our analysis delineates that, following the academic trajectory, the evolution of A. muciniphila patents from foundational research through to application development and maturity, with particular emphasis on its expansive potential in emerging fields, including gastroenterological disorders, non-alcoholic fatty liver disease, cancer immunotherapy, stress management, and neurodegenerative disease treatment. Concluding, A. muciniphila presents as a next-generation probiotic with vast implications for human health. Our findings provide essential insights for future research and product development, contributing to the advancement of this burgeoning field.}, }
@article {pmid40104591, year = {2025}, author = {Yang, S and Liu, H and Liu, Y}, title = {Advances in intestinal epithelium and gut microbiota interaction.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1499202}, pmid = {40104591}, issn = {1664-302X}, abstract = {The intestinal epithelium represents a critical interface between the host and external environment, serving as the second largest surface area in the human body after the lungs. This dynamic barrier is sustained by specialized epithelial cell types and their complex interactions with the gut microbiota. This review comprehensively examines the recent advances in understanding the bidirectional communication between intestinal epithelial cells and the microbiome. We briefly highlight the role of various intestinal epithelial cell types, such as Paneth cells, goblet cells, and enteroendocrine cells, in maintaining intestinal homeostasis and barrier function. Gut microbiota-derived metabolites, particularly short-chain fatty acids and bile acids, influence epithelial cell function and intestinal barrier integrity. Additionally, we highlight emerging evidence of the sophisticated cooperation between different epithelial cell types, with special emphasis on the interaction between tuft cells and Paneth cells in maintaining microbial balance. Understanding these complex interactions has important implications for developing targeted therapeutic strategies for various gastrointestinal disorders, including inflammatory bowel disease, metabolic disorders, and colorectal cancer.}, }
@article {pmid40104590, year = {2025}, author = {Pakostova, E and Falagan, C and Mazuelos Rojas, A}, title = {Editorial: Exploring processes and applications of metal-microbe interactions.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1575076}, doi = {10.3389/fmicb.2025.1575076}, pmid = {40104590}, issn = {1664-302X}, }
@article {pmid40104586, year = {2025}, author = {Safarchi, A and Al-Qadami, G and Tran, CD and Conlon, M}, title = {Understanding dysbiosis and resilience in the human gut microbiome: biomarkers, interventions, and challenges.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1559521}, pmid = {40104586}, issn = {1664-302X}, abstract = {The healthy gut microbiome is important in maintaining health and preventing various chronic and metabolic diseases through interactions with the host via different gut-organ axes, such as the gut-brain, gut-liver, gut-immune, and gut-lung axes. The human gut microbiome is relatively stable, yet can be influenced by numerous factors, such as diet, infections, chronic diseases, and medications which may disrupt its composition and function. Therefore, microbial resilience is suggested as one of the key characteristics of a healthy gut microbiome in humans. However, our understanding of its definition and indicators remains unclear due to insufficient experimental data. Here, we review the impact of key drivers including intrinsic and extrinsic factors such as diet and antibiotics on the human gut microbiome. Additionally, we discuss the concept of a resilient gut microbiome and highlight potential biomarkers including diversity indices and some bacterial taxa as recovery-associated bacteria, resistance genes, antimicrobial peptides, and functional flexibility. These biomarkers can facilitate the identification and prediction of healthy and resilient microbiomes, particularly in precision medicine, through diagnostic tools or machine learning approaches especially after antimicrobial medications that may cause stable dysbiosis. Furthermore, we review current nutrition intervention strategies to maximize microbial resilience, the challenges in investigating microbiome resilience, and future directions in this field of research.}, }
@article {pmid40104324, year = {2025}, author = {Gu, C and Sha, G and Zeng, B and Cao, H and Cao, Y and Tang, D}, title = {Therapeutic potential of fecal microbiota transplantation in colorectal cancer based on gut microbiota regulation: from pathogenesis to efficacy.}, journal = {Therapeutic advances in gastroenterology}, volume = {18}, number = {}, pages = {17562848251327167}, pmid = {40104324}, issn = {1756-283X}, abstract = {Colorectal cancer (CRC) remains a leading cause of cancer-related deaths worldwide, with its progression intricately linked to gut microbiota dysbiosis. Disruptions in microbial homeostasis contribute to tumor initiation, immune suppression, and inflammation, establishing the microbiota as a key therapeutic target. Fecal microbiota transplantation (FMT) has emerged as a transformative approach to restore microbial balance, enhance immune responses, and reshape the tumor microenvironment. This review explores the mechanisms underlying FMT's therapeutic potential, evaluates its advantages over other microbiota-based interventions, and addresses challenges such as donor selection, safety concerns, and treatment standardization. Looking forward, the integration of FMT into personalized CRC therapies requires robust clinical trials and the identification of predictive biomarkers to optimize its efficacy and safety.}, }
@article {pmid40104285, year = {2025}, author = {Yu, N and Yang, Y and Wang, G and Wang, Y and Feng, M and Yang, P and Liu, S and Wang, RR and Zhang, L}, title = {Investigating the Gut Microbiota Profile in Prehypertensive Individuals Exhibiting Phlegm-Dampness Constitution.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1507076}, pmid = {40104285}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Prehypertension/microbiology ; *RNA, Ribosomal, 16S/genetics ; Male ; Female ; Middle Aged ; *Feces/microbiology ; *Dysbiosis/microbiology ; Adult ; Bacteria/classification/genetics/isolation &amp; purification ; Medicine, Chinese Traditional ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Prehypertension is the preclinical stage of hypertension, which is more likely to develop into hypertension than normal blood pressure. Although the body may experience pathological changes at this stage, there are often no symptoms. Chinese medicine constitution theory is widely used to assess an individual's health and disease status, which provides a new method for disease prevention. The phlegm-dampness constitution (PDC) is the main constitution in prehypertension. Dysbiosis of the intestinal flora is considered to be related to the development of hypertension. However, the characteristics of the intestinal flora in prehypertensive populations with PDCs are still unknown.<br><br>METHODS: 16S rRNA gene sequencing of fecal samples was performed in this study, which included 30 prehypertensive subjects with PDCs, 30 nonphlegm-dampness constitution (NPDC) prehypertensive individuals with balanced constitution, and 30 ideal blood pressure subjects with balanced constitution (BC). On the basis of the composition of the intestinal flora, a random forest classifier was constructed to screen the specific bacteria of the prehypertensive PDC population, and the diagnostic efficiency was determined by the area under the curve (AUC).<br><br>RESULTS: At the phylum level, the abundance of Bacteroidetes decreased in the PDC group compared with the NPDC group. Bacteroides was the most important genus at the genus level. Compared with those in the NPDC or BC group, the relative abundances of o_RF39, f_Porphyromonadaceae, f_Christensenellaceae, g_parabacteroides, and g_nitrobacteria in the PDC group were significantly greater. The random forest analysis results revealed that Alistipes, Butyricimonas, Odoribacter, Parabacteroides, and Corynebacterium are bacterial genera that significantly differ between the PDC and NPDC groups and greatly contribute to group differentiation. Receiver operating characteristic (ROC) analysis revealed that the AUC range of differential bacteria and its combined diagnostic model ranged from 0.653 (95% CI: 0.511-0.794) to 0.706 (95% CI: 0.573-0.838), suggesting that it is a potential risk marker for phlegm-dampness constitution with prehypertension.<br><br>CONCLUSIONS: Our study indicates that PDC individuals with prehypertension can be distinguished from NPDC individuals according to their gut microbiome characteristics. Prevention and treatment measures based on these biomarkers may be beneficial in opening new ideas and directions for identifying more aggressive and effective interventions for prehypertensive populations.}, }
@article {pmid40104089, year = {2024}, author = {Mousa, W and Alramadan, N and Ghemrawi, R and Abu Izneid, T}, title = {Revealing culturable fungal microbiome communities from the Arabian Peninsula desert representing a unique source of biochemicals for drug discovery and biotechnology.}, journal = {F1000Research}, volume = {13}, number = {}, pages = {1527}, pmid = {40104089}, issn = {2046-1402}, mesh = {*Desert Climate ; *Fungi/drug effects ; *Drug Discovery ; Biotechnology/methods ; Mycobiome ; Antioxidants/pharmacology ; Soil Microbiology ; Microbiota ; }, abstract = {BACKGROUND: Microbes living at extremes evolve unique survival strategies to adapt to challenging environmental conditions. Among these strategies is their distinctive metabolic potential and ability to produce specialized metabolites enabling them to compete for limited resources and defend against predators. These metabolites have significant potential in pharmaceutical and industrial applications, particularly in the development of drugs and biochemicals.<br><br>OBJECTIVES: This study aimed to investigate the culturable fungal communities associated with four desert plants and their surrounding soils in the Arabian Peninsula desert to identify their bioactive properties.<br><br>METHODS: A total of 12 distinct fungal species were isolated from the plants and soils. Each plant hosted a unique set of fungi, demonstrating the diversity of desert-adapted fungal communities. Biological activities of the fungal extracts were evaluated through various assays, including antimicrobial, antifungal, anticancer, and antioxidant properties.<br><br>RESULTS: Panicum turgidum harbors the most diverse fungal community, dominated by genera such as Mucor, Aspergillus, Colletotrichum, Alternaria, and Chaetomium. Aspergillus species comprise 33% of the total isolates, followed by Fusarium at 16%. All extracts exhibit diverse activities, with Aspergillus species demonstrating the highest antioxidant activities and total phenolic and flavonoid content. Fungi from P. turgidum, particularly Mucor sp., Aspergillus sp., and Curvularia sp., display potent activity against Staphylococcus aureus, while Mucor sp., Chaetomium sp., and Curvularia sp. exhibit moderate inhibition against Pseudomonas aeruginosa.<br><br>CONCLUSION: This study highlights the importance of exploring extremophilic microorganisms, such as those found in desert ecosystems, as they offer a wealth of compounds that could address current challenges in drug discovery and biotechnology.}, }
@article {pmid40104059, year = {2025}, author = {Sharma, P and Jain, T and Sorgen, A and Iyer, S and Tarique, M and Roy, P and Kurtom, S and Sethi, V and Bava, EP and Gutierrez-Garcia, AK and Vaish, U and Suresh, DS and Sahay, P and Edwards, D and Afghani, J and Putluri, S and Reddy, KRK and Amara, CS and Kamal, AHM and Fodor, A and Dudeja, V}, title = {Smoking-induced gut microbial dysbiosis mediates cancer progression through modulation of anti-tumor immune response.}, journal = {iScience}, volume = {28}, number = {3}, pages = {112002}, pmid = {40104059}, issn = {2589-0042}, abstract = {Cigarette smoke exposure (CSE) increases the risk for a plethora of cancers. Recent evidence indicates that the gut microbiome can influence cancer progression by immune system modulation. Since CSE alters the gut microbiome, we hypothesized that the gut microbiome serves as a causative link between smoking and cancer growth. Through a combination of syngeneic animal models and fecal microbiota transplantation studies, we established an essential role for smoke-induced dysbiosis in cancer growth. 16s rRNA sequencing and liquid chromatography-mass spectrometry indicated a unique CSE-associated microbial and metabolomic signature. Immunophenotyping of tumor specimens and experiments in Rag1-KO and CD8-KO demonstrated that smoke-induced tumor growth requires functional adaptive immunity. Finally, utilizing gut microbial ablation strategies with broad- and narrow-spectrum antibiotics, we demonstrated the reversal of phenotypic effects of CSE. Our study provides evidence for gut microbiome as an actionable target to mitigate CSE-induced tumor promotion.}, }
@article {pmid40103748, year = {2025}, author = {Lee, M and Vindenes, HK and Fouladi, F and Shigdel, R and Ward, JM and Peddada, SD and London, SJ and Bertelsen, RJ}, title = {Oral microbiota related to allergy in Norwegian adults.}, journal = {The journal of allergy and clinical immunology. Global}, volume = {4}, number = {2}, pages = {100435}, pmid = {40103748}, issn = {2772-8293}, abstract = {BACKGROUND: Oral microbiome composition has been linked to onset and progression of several localized and systemic diseases. Associations with allergy in adults have been less explored.<br><br>OBJECTIVE: We sought to identify oral microbiota associated with allergy outcomes in adults using high-throughput sequencing data.<br><br>METHODS: We characterized bacterial communities of gingival samples from 453 Norwegian adults (average age, 28 years) using 16S rRNA gene amplicon sequencing. We examined more than 2200 bacterial taxa in relation to self-reported current asthma, eczema, or rhinitis, and seroatopy (IgE&#xa0;> 0.70 kU/L). We used linear regression to determine whether overall bacterial diversity differed by each allergic outcome and analysis of composition of microbiomes with bias correction (ANCOM-BC2) to identify differentially abundant taxa.<br><br>RESULTS: Less diverse oral bacterial communities were observed (P&#xa0;< .05) in individuals with atopy or rhinitis compared with those without. Bacterial diversity did not differ by asthma and eczema status. While no bacterial taxa were differentially abundant by asthma, many were differentially abundant (P&#xa0;<&#xa0;.05 after multiple-testing correction) in relation to atopy, eczema, and rhinitis. These taxa include several from the genera Leptotrichia and Fusobacterium. Some, including Streptococcus, were previously implicated in respiratory health, whereas others were novel. We also found taxa related to nasal medication use in individuals with rhinitis. Notably, microbial network interconnections differed by allergy status.<br><br>CONCLUSIONS: Bacterial community compositions of oral gingival samples may play a role in allergic outcomes in adults. These findings could contribute to the development of novel treatment strategies.}, }
@article {pmid40103612, year = {2025}, author = {Starke, S and Harris, DMM and Paulay, A and Aden, K and Waschina, S}, title = {Comparative analysis of amino acid auxotrophies and peptidase profiles in non-dysbiotic and dysbiotic small intestinal microbiomes.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {821-831}, pmid = {40103612}, issn = {2001-0370}, abstract = {Small Intestinal Bacterial Overgrowth (SIBO) is linked to various diseases and has been associated with altered serum amino acid levels. However, the direct role of the gut microbiome in these changes remains unconfirmed. This study employs genome-scale metabolic modeling to predict amino acid auxotrophy and peptidase gene profiles in the small intestinal microbiomes of SIBO and non-SIBO subjects. Auxotrophy and peptidase gene profiles were further examined in the large intestinal microbiome under non-dysbiotic conditions to assess their similarity to the microbial SIBO profile. Our analysis revealed that the abundance of auxotrophic bacteria is higher in the microbiota of the small intestine than in the large intestine in non-dysbiotic controls. In patients with SIBO, the abundance of auxotrophies in the small intestine decreased compared to non-SIBO subjects. Peptidase gene profiles in non-dysbiotic individuals were distinct between small and large intestinal microbiomes, with fewer extracellular peptidase genes in small intestine microbiomes. In SIBO, extracellular peptidase genes increased compared to non-SIBO subjects. Further, there were more significant associations between the abundance of auxotrophies and peptidase genes in microbiomes of the small intestine compared to the large intestine. In conclusion, the auxotrophy and peptidase gene profiles of the small and large intestinal microbiomes were distinct. In SIBO, the small intestinal microbiome shifts towards a metabolic state resembling that of the large intestine, particularly in its increased abundance of extracellular peptidase genes. This highlights the potential of genome-scale metabolic modeling in identifying metabolic disruptions associated with SIBO, which could inform the development of targeted interventions.}, }
@article {pmid40103525, year = {2025}, author = {Park, S and Jung, S and Lee, G and Lee, E and Black, R and Hong, J and Jeong, S}, title = {Self-Nourishing and Armored Probiotics via Egg-Inspired Encapsulation.}, journal = {Advanced healthcare materials}, volume = {}, number = {}, pages = {e2405219}, doi = {10.1002/adhm.202405219}, pmid = {40103525}, issn = {2192-2659}, support = {HN21C1410000021//Korea Drug Development Fund/ ; HI22C193900//Korea Health Industry Development Institute/Republic of Korea ; RS-2023-00212494//National Research Foundation of Korea/ ; R35 GM147513/GM/NIGMS NIH HHS/United States ; }, abstract = {The gut microbiota plays an essential role in regulating overall physiology, including metabolism and neurological and immune functions. Therefore, their dysregulation is closely associated with metabolic disorders, such as obesity and diabetes, as well as other pathological conditions, including inflammatory bowel diseases, cancer, and neurological disorders. Probiotics are commonly used to maintain a healthy gut microbiome, but their oral delivery is inefficient mainly due to their poor stability in the harsh gastrointestinal (GI) environment. This work presents an innovative encapsulation strategy, inspired by the natural structure of an egg, for the effective oral delivery of probiotics, termed PIE (Probiotics-In-Egg). The PIE technology is based upon encapsulating probiotics with phosvitin and ovalbumin derived from egg yolk and egg white, respectively. PIE exhibits significantly enhanced survival and proliferation in a simulated GI tract, as well as the ability to neutralize harmful reactive oxygen species (ROS) and sustain in nutrient-depleted conditions. Moreover, when administered orally in mouse models, PIE demonstrates excellent bioavailability and enhanced colonization in the GI tract. This egg-inspired encapsulation technology has great potential as a practical and effective platform for oral delivery of probiotics, which can significantly help maintain a healthy gut microbiome.}, }
@article {pmid40103411, year = {2025}, author = {Li, JH and Xu, J and Hu, JX and Xu, HM and Guo, X and Zhang, Y and Xu, JK and Huang, C and Nie, YQ and Zhou, YL}, title = {PPARγ/β/δ Agonists Can Ameliorate Dextran Sodium Sulfate-Induced Colitis and Modulate Gut Microbiota.}, journal = {Journal of gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jgh.16929}, pmid = {40103411}, issn = {1440-1746}, support = {82270577//National Natural Science Foundation of China/ ; 82370552//National Natural Science Foundation of China/ ; 2023A1515030214//Natural Science Foundation of Guangdong Province/ ; KY17010003//Guangzhou Key Laboratory of Digestive Diseases/ ; }, abstract = {BACKGROUND AND AIM: Peroxisome proliferator-activated receptors (PPARs), as nuclear receptors, modulate both lipid metabolism and inflammatory/immune processes. This study examines the impact of modulating the activities of the PPAR subtypes PPARβ/ð and PPARγ on the gut microbiota in inflammatory bowel disease (IBD).<br><br>METHODS: Mice with dextran sulfate sodium (DSS)-induced acute colitis were treated with the PPAR&#x3b3; agonist pioglitazone, PPAR&#x3b2;/&#x3b4; agonist GW0742, or their respective antagonists (GW9662, GSK3787). Weight loss, diarrhea severity, hematochezia, and disease activity index were assessed daily. Upon study completion, colon length, histopathology, and mRNA levels of the intestinal barrier and inflammatory markers were measured. Occludin and E-cadherin levels were assessed via immunofluorescence analysis, and cecal samples underwent 16S rRNA sequencing for gut microbiota analysis.<br><br>RESULTS: Our findings revealed that the agonists pioglitazone and GW0742 effectively suppressed DSS-induced colitis, improved clinical symptoms, reversed colon shortening, and mitigated histological damage. Conversely, their antagonists, GW9662 and GSK3787, failed to alleviate inflammation and sometimes exacerbated disease indicators. Both agonists modulated DSS-induced dysbiosis by reducing the abundance of proinflammatory cytokine-associated microbiota, including Bacteroides, Enterococcus, and Escherichia-Shigella, while enhancing both &#x3b1;-diversity and &#x3b2;-diversity of the gut microbiome, to restore equilibrium.<br><br>CONCLUSION: Our findings reveal that activation of PPAR&#x3b3; and PPAR&#x3b2;/&#x3b4; can balance the gut microbiota in mice and ameliorate experimental colitis in mice. Thus, PPAR&#x3b3; and PPAR&#x3b2;/&#x3b4; have protective effects against IBD and could serve as novel therapeutic targets for its treatment.}, }
@article {pmid40103015, year = {2025}, author = {Wu, Y and Alomeir, N and Li, T and Falsetta, ML and Yang, R and Liu, Y and Sun, E and Wu, TT and Wood, R and Kenney, MH and Almulhim, A and Watson, G and Torres Ballester, KA and Fiscella, K and Xiao, J}, title = {Effect of L. plantarum on Caries Prevention and the Oral-Gut Microbiome In Vivo.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {220345251325807}, doi = {10.1177/00220345251325807}, pmid = {40103015}, issn = {1544-0591}, abstract = {While Lactiplantibacillus plantarum has shown promise against cariogenic pathogens, its in vivo effects on caries prevention remain unexplored. This study used a rat model to investigate the effect of L. plantarum early-life oral inoculation on oral and gut microbiomes, host immune responses, and serum metabolites. Forty 14-day Sprague-Dawley rat pups were randomly allocated into 5 groups: (1) blank control, (2) L. plantarum colonization alone, (3) Streptococcus mutans and Candida albicans co-colonization, (4) L. plantarum precolonization before S. mutans and C. albicans exposure, and (5) 2-wk treatment of L. plantarum after S. mutans and C. albicans exposure. Dynamic colonization of L. plantarum, S. mutans, and C. albicans in saliva and plaque was assessed using a culture-dependent method. Saliva, plaque, and fecal microbiomes were assessed using 16S ribosomal RNA gene sequencing. Caries scoring was performed using Keyes' scoring system and microcomputed tomography. Serum metabolite and immune markers were assessed through liquid chromatography tandem mass spectrometry untargeted metabolomics and multiplex immune profiling. We found that 3-d L. plantarum inoculation established stable L. plantarum colonization in the oral cavity of young rats. Inoculation timing of L. plantarum was critical for caries prevention. L. plantarum precolonization significantly reduced caries lesions compared with the S. mutans and C. albicans group, whereas 2 wk of postexposure treatment did not demonstrate a protective effect. L. plantarum precolonization led to distinct microbial shifts in saliva, plaque, and gut microbiomes, with an increased abundance of beneficial bacteria, such as Streptococcus azizii, Bifidobacterium animalis, Faecalibaculum rodentium, and Allobaculum stercoricanis, and a decrease in S. mutans. L. plantarum preinoculation also influenced metabolic profiles, with 1 metabolite upregulated and 24 downregulated, although immune marker differences were minimal. In conclusion, L. plantarum oral colonization before host exposure to oral cariogenic pathogens effectively reduced caries and modulated the profile of oral and gut microbiomes and serum metabolic profile.}, }
@article {pmid40102971, year = {2025}, author = {Luo, Z and Ou, H and Tan, Z and Jiao, J}, title = {Rumen-protected methionine and lysine supplementation to the low protein diet improves animal growth through modulating colonic microbiome in lambs.}, journal = {Journal of animal science and biotechnology}, volume = {16}, number = {1}, pages = {46}, pmid = {40102971}, issn = {1674-9782}, abstract = {BACKGROUND: Dietary protein level and amino acid (AA) balance are crucial determinants of animal health and productivity. Supplementing rumen-protected AAs in low-protein diets was considered as an efficient strategy to improve the growth performance of ruminants. The colon serves as a crucial conduit for nutrient metabolism during rumen-protected methionine (RPMet) and rumen-protected lysine (RPLys) supplementation, however, it has been challenging to clarify which specific microbiota and their metabolites play a pivotal role in this process. Here, we applied metagenomic and metabolomic approaches to compare the characteristic microbiome and metabolic strategies in the colon of lambs fed a control diet (CON), a low-protein diet (LP) or a LP diet supplemented with RPMet and RPLys (LR).<br><br>RESULTS: The LP treatment decreased the average daily weight gain (ADG) in lambs, while the LR treatment tended to elicit a remission in ADG. The butyrate molar concentration was greater (P&#x2009;<&#x2009;0.05), while acetate molar concentration (P&#x2009;<&#x2009;0.05) was lower for lambs fed the LP and LR diets compared to those fed the CON diet. Moreover, the LP treatment remarkably decreased total AA concentration (P&#x2009;<&#x2009;0.05), while LR treatment showed an improvement in the concentrations of methionine, lysine, leucine, glutamate, and tryptophan. Metagenomic insights proved that the microbial metabolic potentials referring to biosynthesis of volatile fatty acids (VFAs) and AAs in the colon were remarkably altered by three dietary treatments. Metagenomic binning identified distinct microbial markers for the CON group (Alistipes spp., Phocaeicola spp., and Ruminococcus spp.), LP group (Fibrobacter spp., Prevotella spp., Ruminococcus spp., and Escherichia coli), and LR group (Akkermansia muciniphila and RUG099 spp.).<br><br>CONCLUSIONS: Our findings suggest that RPMet and RPLys supplementation to the low-protein diet could enhance the microbial biosynthesis of butyrate and amino acids, enriche the&#xa0;beneficial bacteria in the colon, and&#xa0;thereby improve the growth performance of lambs.}, }
@article {pmid40102827, year = {2025}, author = {Mehdipour, A and Masoumi, M and Fateh, R and Aghaali, M and Mohammadidana, F and Saleh, A and Rasouli, A and Kabiri, F}, title = {Comparative study of the profile of supragingival dental plaque and tooth decay in patients with lupus erythematosus and rheumatoid arthritis.}, journal = {BMC oral health}, volume = {25}, number = {1}, pages = {399}, pmid = {40102827}, issn = {1472-6831}, mesh = {Humans ; *Dental Plaque/microbiology ; *Lupus Erythematosus, Systemic/complications/microbiology ; *Dental Caries/microbiology ; *Arthritis, Rheumatoid/complications/microbiology ; Female ; Cross-Sectional Studies ; Male ; Adult ; Middle Aged ; DMF Index ; Candida albicans/isolation &amp; purification ; Streptococcus mutans/isolation &amp; purification ; Lactobacillus/isolation &amp; purification ; }, abstract = {BACKGROUND AND OBJECTIVES: Systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) are complex autoimmune diseases that present with a range of systemic and oral manifestations including dental decay and alterations in the oral microbiome profile. The purpose of this study was to compare the fungal and bacterial profile of supragingival dental plaque and dental caries in patients with SLE and RA.<br><br>METHODS: The present descriptive-cross-sectional-analytical study was conducted on 91 participants (31 RA, 30 lupus, and 30 control groups). Decayed, Missing, and Filled teeth (DMFT) and The International Caries Detection Assessment System (ICDAS) indices were used to investigate tooth decay. The DAS-28 index was used to assess the severity of RA, and the SLEDAI-2&#xa0;K index was used to evaluate the severity of lupus. The number of supragingival dental plaque Streptococcus mutans, Lactobacillus spp. and Candida albicans colonies were evaluated using Mitis Salivarius Agar (MSA), deMan-Rogosa-Sharpe agar (MRS) and Sabouraud Dextrose Agar with Chloramphenicol (SC) culture medium, respectively. Data were analyzed using one-way ANOVA, Kruskal -Wallis, k2, Fisher's tests, and Spearman's correlation coefficient.<br><br>RESULTS: A statistically significant relationship was observed between the education level (P&#x2009;=&#x2009;0.030), mean of DMFT, ICDAS, MSA and SC indices (P&#x2009;<&#x2009;0.001) with the type of disease. The control and RA group showed significantly higher MRS index than the lupus group (P&#x2009;<&#x2009;0.001). There was significant and positive correlation between the severity of the disease in lupus patients and SC (Candida albicans) (P&#x2009;<&#x2009;0.001, R&#x2009;=&#x2009;0.698) and MRS (P&#x2009;=&#x2009;0/020, R&#x2009;=&#x2009;0.408) indices.<br><br>CONCLUSION: Dental decay and the fungal and bacterial flora of supragingival dental plaque patients are higher than in the healthy group. It is recommended that these patients pay more attention to their oral hygiene and undergo periodic oral examinations.}, }
@article {pmid40102775, year = {2025}, author = {Shi, H and Guo, P and Wang, Z and Zhou, J and He, M and Shi, L and Huang, X and Guo, P and Guo, Z and Zhang, Y and Hou, F}, title = {Cellulase enhancing rumen microbiome of Tan sheep indicates plastic responses to seasonal variations of diet in the typical steppe.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {154}, pmid = {40102775}, issn = {1471-2180}, support = {2021YFD1300504//National Key Research and Development Plan/ ; U21A20242//National Natural Science Foundation of China/ ; 32161143028//NSFC Projects of International Cooperation and Exchanges/ ; IRT17R50//Program for Innovative Research Team in University/ ; 2022002//Scientific and technological support project for grassland ecological restoration in Gansu Province/ ; }, mesh = {Animals ; *Rumen/microbiology ; *Seasons ; Sheep ; *Cellulase/metabolism ; *Animal Feed/analysis ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fermentation ; Diet/veterinary ; Dietary Supplements ; }, abstract = {BACKGROUND: Climate and geographical changes significantly influence food availability and nutrient composition over time and space, Which in turn affects the selection of microbial communities essential for maintaining gastrointestinal homeostasis and facilitating dietary adaptation. Therefore, it is essential to understand the specific responses of the gut microbiota to dietary and seasonal variations in order to improve animal conservation strategies based on solid scientific knowledge.<br><br>RESULTS: In summer, due to the higher nutritional quality of forage, Tan sheep exhibited enhanced forage degradation and fermentation. This was reflected by increased populations of key rumen bacteria, including Bacteroidetes, Prevotella_1, Prevotellaceae_UCG-003, Ruminococcus_1, Saccharofermentans, and Ruminococcaceae_UCG-014. Supplementation with cellulase further facilitated these processes, optimizing the utilization of available nutrients. In contrast, during winter, when the nutritional quality of forage decline, we observed lower indicators of forage degradation and fermentation in Tan sheep. Additionally, there was a significant increase in the Firmicutes/Bacteroidetes ratio, microbial diversity, microbial interactions, and metabolic activity.<br><br>CONCLUSIONS: The rumen microbiota adapts to enhance the breakdown of forage biomass and maintain energy balance during periods of inadequate nutritional value. Supplementing the diet with cellulase during these times can help mitigate the reduced digestibility associated with low-quality forage. This study highlights the dynamic adaptation of the rumen microbiota to seasonal variations in forage quality and emphasizes the potential benefits of cellulase supplementation in supporting rumen function and improving animal performance under varying environmental conditions.}, }
@article {pmid40102723, year = {2025}, author = {Guo, X and Shao, Y}, title = {Role of the oral-gut microbiota axis in pancreatic cancer: a new perspective on tumor pathophysiology, diagnosis, and treatment.}, journal = {Molecular medicine (Cambridge, Mass.)}, volume = {31}, number = {1}, pages = {103}, pmid = {40102723}, issn = {1528-3658}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Pancreatic Neoplasms/therapy/diagnosis/microbiology/etiology ; Animals ; Mouth/microbiology ; Carcinoma, Pancreatic Ductal/therapy/microbiology/diagnosis ; }, abstract = {Pancreatic cancer, one of the most lethal malignancies, remains challenging due to late diagnosis, aggressive progression, and therapeutic resistance. Recent advances have revealed the presence of intratumoral microbiota, predominantly originating from the oral and gut microbiomes, which play pivotal roles in pancreatic cancer pathogenesis. The dynamic interplay between oral and gut microbial communities, termed the "oral-gut microbiota axis," contributes multifacetedly to pancreatic ductal adenocarcinoma (PDAC). Microbial translocation via anatomical or circulatory routes establishes tumor-resident microbiota, driving oncogenesis through metabolic reprogramming, immune regulation, inhibition of apoptosis, chronic inflammation, and dysregulation of the cell cycle. Additionally, intratumoral microbiota promote chemoresistance and immune evasion, further complicating treatment outcomes. Emerging evidence highlights microbial signatures in saliva and fecal samples as promising non-invasive diagnostic biomarkers, while microbial diversity correlates with prognosis. Therapeutic strategies targeting this axis-such as antibiotics, probiotics, and engineered bacteria-demonstrate potential to enhance treatment efficacy. By integrating mechanisms of microbial influence on tumor biology, drug resistance, and therapeutic applications, the oral-gut microbiota axis emerges as a critical regulator of PDAC, offering novel perspectives for early detection, prognostic assessment, and microbiome-based therapeutic interventions.}, }
@article {pmid40102641, year = {2025}, author = {Kalvapalle, PB and Staubus, A and Dysart, MJ and Gambill, L and Reyes Gamas, K and Lu, LC and Silberg, JJ and Stadler, LB and Chappell, J}, title = {Information storage across a microbial community using universal RNA barcoding.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {40102641}, issn = {1546-1696}, support = {2021-33522-35356//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; W911NF-24-2-0073//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; 1805901//National Science Foundation (NSF)/ ; 1828869//National Science Foundation (NSF)/ ; 2227526//National Science Foundation (NSF)/ ; 2237052//National Science Foundation (NSF)/ ; 2237512//National Science Foundation (NSF)/ ; FWP 78814//U.S. Department of Energy (DOE)/ ; A23-0202-004//Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation/ ; }, abstract = {Gene transfer can be studied using genetically encoded reporters or metagenomic sequencing but these methods are limited by sensitivity when used to monitor the mobile DNA host range in microbial communities. To record information about gene transfer across a wastewater microbiome, a synthetic catalytic RNA was used to barcode a highly conserved segment of ribosomal RNA (rRNA). By writing information into rRNA using a ribozyme and reading out native and modified rRNA using amplicon sequencing, we find that microbial community members from 20 taxonomic orders participate in plasmid conjugation with an Escherichia coli donor strain and observe differences in 16S rRNA barcode signal across amplicon sequence variants. Multiplexed rRNA barcoding using plasmids with pBBR1 or ColE1 origins of replication reveals differences in host range. This autonomous RNA-addressable modification provides information about gene transfer without requiring translation and will enable microbiome engineering across diverse ecological settings and studies of environmental controls on gene transfer and cellular uptake of extracellular materials.}, }
@article {pmid40102546, year = {2025}, author = {Lechleiter, N and Wedemeyer, J and Schütz, A and Sehl-Ewert, J and Schaufler, K and Homeier-Bachmann, T}, title = {Metagenomic analysis of the faecal microbiota and AMR in roe deer in Western Pomerania.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {9288}, pmid = {40102546}, issn = {2045-2322}, mesh = {Animals ; *Deer/microbiology ; *Feces/microbiology ; *Metagenomics/methods ; Escherichia coli/genetics/isolation &amp; purification ; Microbiota/genetics ; Drug Resistance, Bacterial/genetics ; Germany ; Metagenome ; Gastrointestinal Microbiome/genetics ; Bacteria/genetics/classification ; Anti-Bacterial Agents/pharmacology ; }, abstract = {As an integral part of the global wellbeing, the health of wild animals should be regarded just as important as that of humans and livestock. The investigation of wildlife health, however, is limited by the availability of samples. In an attempt to implement a method with little invasiveness and broad areas of application, shotgun metagenomics were utilised to investigate the faecal microbiome and its antimicrobial resistance genes (AMRG) in roe deer. These genes can facilitate antimicrobial resistances (AMR) in bacteria and are therefore of increasing importance in global health. Accordingly, the abundance in potential vectors like wildlife needs to be assessed. The samples were additionally investigated for ESBL-E. coli, an antibiotic resistant pathogen of global concern, via cultivation. Twenty-seven hunt-harvested animals in Western Pomerania were sampled. This study is the first to our knowledge to describe the faecal microbiome of the European roe deer (Capreolus capreolus), providing insights into the bacterial and archaeal composition. Among the animals, the microbiome was mostly similar and showed a comparable composition to what has been reported in related species, with a ratio of 1.76 between Bacillota and Bacteroidota. The normalised abundance of AMR genes was found to be 0.035 on average, which is similar to other investigations on wild ruminants. Selective cultivation found no ESBL-E. coli in the animals. The prevalence of AMRG in roe deer of Western Pomerania was found to be in line with previous results. The use of shotgun metagenomics allowed for the simultaneous investigation of composition and AMR genes in the faecal microbiome of roe deer, which suggests it as a promising method for the health monitoring of wildlife. This study is the first to describe the prokaryotic assemblage in the faeces of roe deer and its differences to the microbiomes published on other cervids were discussed.}, }
@article {pmid40102379, year = {2025}, author = {Deng, L and Taelman, S and Olm, MR and Toe, LC and Balini, E and Ouédraogo, LO and Bastos-Moreira, Y and Argaw, A and Tesfamariam, K and Sonnenburg, ED and Hanley-Cook, GT and Ouédraogo, M and Ganaba, R and Van Criekinge, W and Huybregts, L and Stock, M and Kolsteren, P and Sonnenburg, JL and Lachat, C and Dailey-Chwalibóg, T}, title = {Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2683}, pmid = {40102379}, issn = {2041-1723}, support = {OPP1175213//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Female ; *Dietary Supplements ; Infant ; Pregnancy ; Adult ; Burkina Faso ; *Carbohydrate Metabolism ; Infant, Newborn ; Feces/microbiology ; Dietary Proteins/metabolism ; Male ; Lactation ; }, abstract = {Balanced energy-protein (BEP) supplementation during pregnancy and lactation can improve birth outcomes and infant growth, with the gut microbiome as a potential mediator. The MISAME-III randomized controlled trial (ClinicalTrial.gov: NCT03533712) assessed the effect of BEP supplementation, provided during pregnancy and the first six months of lactation, on small-for-gestational age prevalence and length-for-age Z-scores at six months in rural Burkina Faso. Nested within MISAME-III, this sub-study examines the impact of BEP supplementation on maternal and infant gut microbiomes and their mediating role in birth outcomes and infant growth. A total of 152 mother-infant dyads (n = 71 intervention, n = 81 control) were included for metagenomic sequencing, with stool samples collected at the second and third trimesters, and at 1-2 and 5-6 months postpartum. BEP supplementation significantly altered maternal gut microbiome diversity, composition, and function, particularly those with immune-modulatory properties. Pathways linked to lipopolysaccharide biosynthesis were depleted and the species Bacteroides fragilis was enriched in BEP-supplemented mothers. Maternal BEP supplementation also accelerated infant microbiome changes and enhanced carbohydrate metabolism. Causal mediation analyses identified specific taxa mediating the effect of BEP on birth outcomes and infant growth. These findings suggest that maternal supplementation modulates gut microbiome composition and influences early-life development in resource-limited settings.}, }
@article {pmid40102109, year = {2025}, author = {Parkhill, M and Salmaso, N and D'Angiulli, A and Lee, V and Aguilar-Valles, A}, title = {Emerging autism and Fragile X syndrome treatments.}, journal = {Trends in pharmacological sciences}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tips.2025.02.004}, pmid = {40102109}, issn = {1873-3735}, abstract = {The limitations of current symptom-focused treatments drive the urgent need for effective therapies for autism and Fragile X syndrome (FXS). Currently, no approved pharmacological interventions target the core symptoms of these disorders. Advances in understanding the underlying biology of autism and FXS make this an important time to explore novel options. Indeed, several treatments have recently been tested in clinical trials, with promising results in treating core symptoms of autism and FXS. We focus on emerging interventions, such as gut microbiome therapies, anti-inflammatory approaches, bumetanide, phosphodiesterase 4D inhibitors, and endocannabinoid modulators. We also discuss factors, such as disorder heterogeneity, which may have contributed to poor efficacy in previously failed late-phase trials and impact recent trials, emphasizing the need for personalized treatment approaches.}, }
@article {pmid40102030, year = {2025}, author = {Batalha, MA and LeCroy, MN and Lin, J and Peters, BA and Qi, Q and Wang, Z and Wang, T and Gallo, LC and Talavera, GA and McClain, AC and Thyagarajan, B and Daviglus, ML and Hou, L and Llabre, M and Cai, J and Kaplan, RC and Isasi, CR}, title = {Life-course socioeconomic position and the gut microbiome in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2479772}, doi = {10.1080/19490976.2025.2479772}, pmid = {40102030}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Hispanic or Latino/statistics &amp; numerical data ; Female ; Male ; Adult ; *Feces/microbiology ; Middle Aged ; United States/epidemiology ; Bacteria/classification/genetics/isolation &amp; purification ; Cohort Studies ; Young Adult ; Socioeconomic Factors ; Adolescent ; Child ; Social Class ; White ; }, abstract = {Socioeconomic position (SEP) in childhood and beyond may influence the gut microbiome, with implications for disease risk. Studies evaluating the relationship between life-course SEP and the gut microbiome are sparse, particularly among Hispanic/Latino individuals, who have a high prevalence of low SEP. We use the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), a population-based cohort study conducted in four field centers in the United States (U.S.), to evaluate the association between life-course SEP and gut microbiome composition. Life-course SEP indicators included parental education (proxy of childhood SEP), current SEP (n = 2174), and childhood (n = 988) and current economic hardship (n = 994). Shotgun sequencing was performed on stool samples. Analysis of Compositions of Microbiomes was used to identify associations of life-course SEP indicators with gut microbiome species and functions. Parental education and current SEP were associated with the overall gut microbiome composition; however, parental education and current education explained more the gut microbiome variance than the current SEP. A lower parental education and current SEP were associated with a lower abundance of species from genus Bacteroides. In stratified analysis by nativity, we found similar findings mainly among foreign-born participants. Early-life SEP may have long-term effects on gut microbiome composition underscoring another biological mechanism linking early childhood factors to adult disease.}, }
@article {pmid40101943, year = {2025}, author = {Lai, TV and Ryder, MH and Rathjen, JR and Riley, IT and Denton, MD}, title = {Seed-applied micronutrient toxicity to rhizobia and impaired legume nodulation.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxaf067}, pmid = {40101943}, issn = {1365-2672}, abstract = {AIMS: Micronutrients are sometimes mixed with rhizobial inoculants in liquid solutions to promote the growth and development of legume crops. The compatibility of rhizobia with micronutrients is poorly documented. The objective of this study was to assess the effect of some frequently used micronutrients on rhizobial inoculant survival, nodulation, nutrition of chickpea and field pea.<br><br>METHODS AND RESULTS: Four Australian commercial rhizobia (CC1192, SARDI969, WSM1455 and WU425) were assessed in vitro for their compatibility with plant micronutrients as used in a liquid mixture (4% MnSO4, 2% ZnSO4, 0.2% CuSO4 and 0.04% Na2MoO4). The impact of this mixture on nodulation and plant nutrition was tested on chickpea and field pea under glasshouse conditions. The micronutrient mixture was toxic to all tested rhizobia. While MnSO4 and Na2MoO4 were not inhibitory to rhizobia, individual CuSO4 (>20&#xa0;&#xb5;mol L-1 or 0.0005%) and ZnSO4 (>250&#xa0;&#xb5;mol L-1 or 0.007%) were lethal to rhizobia. Rhizobial survival was relatively low in a combination of 20&#xa0;&#xb5;mol L-1 CuSO4 and 250&#xa0;&#xb5;mol L-1 ZnSO4 due to their interactive effect. When rhizobial peat inoculants were suspended in the micronutrient mix, only 35% of rhizobia were recovered at sowing time (1&#xa0;h after preparation), resulting in poor nodulation of both legumes. Separation of rhizobia (inoculants on seeds) from the micronutrient mixture (applied in-furrow) reduced the risk of inadequate nodulation, while meeting plant nutritional requirements and symbiosis.}, }
@article {pmid40101773, year = {2025}, author = {Ashey, J and Putnam, HM and McManus, MC}, title = {Guided by the northern star coral: a research synthesis and roadmap for Astrangia poculata.}, journal = {Biology letters}, volume = {21}, number = {3}, pages = {20240469}, doi = {10.1098/rsbl.2024.0469}, pmid = {40101773}, issn = {1744-957X}, support = {//National Science Foundation/ ; }, mesh = {Animals ; *Symbiosis ; *Anthozoa/physiology ; Climate Change ; Ecosystem ; Microbiota ; Genomics ; Transcriptome ; }, abstract = {The northern star coral, Astrangia poculata, is a temperate, facultatively symbiotic, scleractinian coral spanning the coastal western Atlantic. This calcifying species is mixotrophic with a broad geographical range, and therefore has high utility in addressing questions related to community ecology, symbiosis, population genetics, biomineralization and resilience to environmental perturbations. Here, we review the current A. poculata peer-reviewed literature, which is primarily found in six focal areas: geographic range, habitat and ecology, symbiosis, life history, microbiome and genomics and transcriptomics. A cross-cutting theme of these studies emerges as the value of an experimental system that is facultatively symbiotic. Yet, the historic overgeneralization of symbiotic versus 'aposymbiotic' A. poculata has constrained the interpretation of the basic biology and generalizability of conclusions. Emergent from our review, and timely with respect to climate change, is the value that A. poculata brings as an experimental system with the potential to test questions on range adaptability and environmental resilience. We identify future avenues of research for A. poculata studies that include integration of population genetics with organismal-molecular-cellular biology across the geographical range, while leveraging the power of the facultative symbiosis context.}, }
@article {pmid40101714, year = {2025}, author = {Lynn, HM and Gordon, JI}, title = {Sequential co-assembly reduces computational resources and errors in metagenome-assembled genomes.}, journal = {Cell reports methods}, volume = {}, number = {}, pages = {101005}, doi = {10.1016/j.crmeth.2025.101005}, pmid = {40101714}, issn = {2667-2375}, abstract = {Generating metagenome-assembled genomes from DNA shotgun sequencing datasets can demand considerable computational resources. Here, we describe a sequential co-assembly method that reduces the assembly of duplicate reads through successive application of single-node computing tools for read assembly and mapping. Using a simulated mouse microbiome DNA shotgun sequencing dataset, we demonstrated that this approach shortens assembly time, uses less memory than traditional co-assembly, and produces significantly fewer assembly errors. Applying sequential co-assembly to shotgun sequencing reads from (1) a longitudinal study of gut microbiomes from undernourished Bangladeshi children and (2) a 2.3-terabyte dataset generated from gnotobiotic mice colonized with pooled microbiomes from these children that was too large to be handled by a traditional co-assembly approach also demonstrated significant reductions in assembly time and memory requirements. These results suggest that this approach should be useful in resource-constrained settings, including in low- and middle-income countries.}, }
@article {pmid40101713, year = {2025}, author = {Antonini Cencicchio, M and Montini, F and Palmieri, V and Massimino, L and Lo Conte, M and Finardi, A and Mandelli, A and Asnicar, F and Pavlovic, R and Drago, D and Ungaro, F and Andolfo, A and Segata, N and Martinelli, V and Furlan, R and Falcone, M}, title = {Microbiota-produced immune regulatory bile acid metabolites control central nervous system autoimmunity.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {102028}, doi = {10.1016/j.xcrm.2025.102028}, pmid = {40101713}, issn = {2666-3791}, abstract = {The commensal gut microbiota has a role in the pathogenesis of extra-intestinal autoimmune diseases such as multiple sclerosis (MS) with unknown mechanisms. Deoxycholic acid (DCA) and lithocholic acid (LCA) are secondary bile acid metabolites (BAMs) produced from primary bile acids by gut microbiota that play key immune regulatory functions by promoting FOXP3[+] regulatory T (Treg) cell differentiation at the expense of Th17 cells. Here, we show that bacteria releasing enzymes responsible for secondary BAMs production are under-represented in the gut of MS patients, resulting in significantly reduced intestinal concentration of DCA and immune dysregulation with increased percentage of Th17 cells. We validated our human findings in a preclinical model of MS by showing that DCA/LCA administration prevents experimental autoimmune encephalomyelitis (EAE) by dampening Th17 cell differentiation and the effector phenotype of myelin-reactive T cells. Our data highlight the key role of immune regulatory BAMs for the prevention of central nervous system (CNS) autoimmunity.}, }
@article {pmid40100630, year = {2025}, author = {Feng, W and Wan, X and Zhang, Y and Quensen, J and Williams, TA and Thompson, M and Streeter, M and Zhang, Y and Jiao, S and Wei, G and Zhu, Y and Gu, J and Tiedje, JM and Qian, X}, title = {Diversification, niche adaptation, and evolution of a candidate phylum thriving in the deep Critical Zone.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {12}, pages = {e2424463122}, doi = {10.1073/pnas.2424463122}, pmid = {40100630}, issn = {1091-6490}, mesh = {*Bacteria/genetics/metabolism/classification ; *Phylogeny ; *Soil Microbiology ; Microbiota/genetics ; Adaptation, Physiological/genetics ; Genome, Bacterial ; Evolution, Molecular ; Biological Evolution ; }, abstract = {The deep subsurface soil microbiome encompasses a vast amount of understudied phylogenetic diversity and metabolic novelty, and the metabolic capabilities and ecological roles of these communities remain largely unknown. We observed a widespread and relatively abundant bacterial phylum (CSP1-3) in deep soils and evaluated its phylogeny, ecology, metabolism, and evolutionary history. Genome analysis indicated that members of CSP1-3 were actively replicating in situ and were widely involved in the carbon, nitrogen, and sulfur cycles. We identified potential adaptive traits of CSP1-3 members for the oligotrophic deep soil environments, including a mixotrophic lifestyle, flexible energy metabolisms, and conservation pathways. The ancestor of CSP1-3 likely originated in an aquatic environment, subsequently colonizing topsoil and, later, deep soil environments, with major CSP1-3 clades adapted to each of these distinct niches. The transition into the terrestrial environment was associated with genome expansion, including the horizontal acquisition of a range of genes for carbohydrate and energy metabolism and, in one lineage, high-affinity terminal oxidases to support a microaerophilic lifestyle. Our results highlight the ecology and genome evolution of microbes in the deep Critical Zone.}, }
@article {pmid40100361, year = {2025}, author = {Suresh, R and Jayachandiran, S and Balu, P and Ramasamy, D}, title = {Comparative genomics reveals genetic diversity and differential metabolic potentials of the species of Arachnia and suggests reclassification of Arachnia propionica E10012 (=NBRC_14587) as novel species.}, journal = {Archives of microbiology}, volume = {207}, number = {4}, pages = {93}, pmid = {40100361}, issn = {1432-072X}, mesh = {*Phylogeny ; *Genetic Variation ; *Genomics ; Genome, Bacterial ; Microbiota/genetics ; }, abstract = {The genus Arachnia, including Arachnia propionica and Arachnia rubra, are part of the normal oral and respiratory microbiota but can act as opportunistic pathogens in humans. This study investigates the functional, phylogenomic and taxonomic characteristics of 10 completely sequenced Arachnia strains, to elucidate their evolutionary relationships and divergence patterns, focusing on genomic variability and functional diversity. Phylogenetic analyses revealed distinct patterns, with Arachnia propionica strains showing significant divergence compared to the conserved Arachnia rubra strains. Notably, E10012 (=NBRC 14587) emerged as a distinct lineage with unique adaptations, while NCTC11666 exhibited a unique phylogenetic position, suggesting subspecies-level classification. Functional analyses highlighted variability among Arachnia propionica strains, with E10012 (=NBRC 14587) showing genes linked to choline metabolism and metal resistance, and NCTC11666 enriched in carbohydrate-active enzymes like GH179. In contrast, Arachnia rubra demonstrated genomic conservation, indicative of evolutionary specialization. This study reveals that strains E10012 (=NBRC 14587) and NCTC11666 displayed unique genomic features and distinct phylogenetic positioning, suggesting their reclassification as potential novel species and subspecies respectively. This underscores the balance between genomic conservation and diversification in Arachnia, reflecting their ecological adaptability and functional roles in the oral microbiome.}, }
@article {pmid40099907, year = {2025}, author = {Reetz, L and Schulze, L and Kronenberger, T and Selim, KA and Schaefle, T and Dema, T and Zipperer, A and Mößner, J and Poso, A and Grond, S and Peschel, A and Krismer, B}, title = {The human microbiome-derived antimicrobial lugdunin self-regulates its biosynthesis by a feed-forward mechanism.}, journal = {mBio}, volume = {}, number = {}, pages = {e0357124}, doi = {10.1128/mbio.03571-24}, pmid = {40099907}, issn = {2150-7511}, abstract = {Many human microbiome members inhibit bacterial competitors by production of antimicrobial compounds whose expression needs to be tightly controlled to balance the costs and benefits of compound biosynthesis. The nasal commensal Staphylococcus lugdunensis outcompetes Staphylococcus aureus using the antimicrobial lugdunin. The lugdunin biosynthetic gene cluster (BGC) encodes two potential regulators whose roles have remained unknown. Deletion of the regulator genes lugR or lugJ led to increased lugdunin production and/or immunity. While LugR was found to repress the transcription of the biosynthetic lugRABCTDZ operon, LugJ repressed the lugIEFGH export and immunity genes. Both regulators bound to different inverted repeats in the controlled promoter regions. Notably, both repressors were released from cognate promoters to allow transcription upon addition of exogenous lugdunin. Even minor structural changes disabled lugdunin derivatives to induce expression of its BGC, which is consistent with inferior binding to the predicted LugR and LugJ binding pockets. Thus, lugdunin controls its own biosynthesis through a feed-forward mechanism probably to avoid futile production.IMPORTANCEBiosynthetic gene clusters (BGCs) are usually tightly controlled to avoid production of costly goods at inappropriate time points or unfavorable conditions. However, in most cases, the regulatory signals of these clusters have remained unknown. Frequently, quorum sensing or two-component regulatory systems are involved in BGC expression control. This study elucidates the sophisticated regulation of lugdunin biosynthesis and secretion via two independent regulators, LugR and LugJ. Although belonging to different families of repressors, both directly interact with the antimicrobial lugdunin and thereby enhance biosynthesis and secretion in a feed forward-like mechanism.}, }
@article {pmid40099185, year = {2025}, author = {Li, Y and Lyu, L and Ding, H}, title = {The potential roles of gut microbiome in porto-sinusoidal vascular disease: an under-researched crossroad.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1556667}, pmid = {40099185}, issn = {1664-302X}, abstract = {Accumulating evidence indicates that patients with liver diseases exhibit distinct microbiological profiles, which can be attributed to the bidirectional relationship of the gut-liver axis. Porto-sinusoidal vascular disease (PSVD) has recently been introduced to describe a group of vascular diseases of the liver, involving the portal venules and sinusoids. Although the pathophysiology of PSVD is not yet fully understood, several predisposing conditions, including immunodeficiency, inflammatory bowel disease, abdominal bacterial infections are associated with the increasing in intestinal permeability and microbial translocation, supporting the role of altered gut microbiota and gut-derived endotoxins in PSVD etiopathogenesis. Recent studies have proposed that the gut microbiome may play a crucial role in the pathophysiology of intrahepatic vascular lesions, potentially influencing the onset and progression of PSVD in this context. This review aims to summarize the current understanding of the gut microbiome's potential role in the pathogenesis of hepatic microvascular abnormalities and thrombosis, and to briefly describe their interactions with PSVD. The insights into gut microbiota and their potential influence on the onset and progression of PSVD may pave the way for new diagnostic, prognostic, and therapeutic strategies.}, }
@article {pmid40099159, year = {2025}, author = {Tourlousse, DM and Sekiguchi, Y}, title = {Synthetic DNA spike-in standards for cross-domain absolute quantification of microbiomes by rRNA gene amplicon sequencing.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf028}, pmid = {40099159}, issn = {2730-6151}, abstract = {Microbiome studies using high-throughput sequencing are increasingly incorporating absolute quantitative approaches to overcome the inherent limitations of relative abundances. In this study, we have designed and experimentally validated a set of 12 unique synthetic rRNA operons, which we refer to as rDNA-mimics, to serve as spike-in standards for quantitative profiling of fungal/eukaryotic and bacterial microbiomes. The rDNA-mimics consist of conserved sequence regions from natural rRNA genes to act as binding sites for common universal PCR primers, and bioinformatically designed variable regions that allow their robust identification in any microbiome sample. All constructs cover multiple rRNA operon regions commonly targeted in fungal/eukaryotic microbiome studies (SSU-V9, ITS1, ITS2, and LSU-D1D2) and two of them also include an artificial segment of the bacterial 16S rRNA gene (SSU-V4) for cross-domain application. We validated the quantitative performance of the rDNA-mimics using defined mock communities and representative environmental samples. In particular, we show that rDNA-mimics added to extracted DNA or directly to the samples prior to DNA extraction precisely reflects the total amount of fungal and/or bacterial rRNA genes in the samples. We demonstrate that this allows accurate estimation of differences in microbial loads between samples, thereby confirming that the rDNA-mimics are suitable for absolute quantitative analyses of differential microbial abundances.}, }
@article {pmid40099142, year = {2025}, author = {Lee, Y and Yoon, Y and Choi, KH}, title = {Correlation of periodontitis with hepatic and intestinal inflammation and glycemic control, and effects of bioconverted Artemisia herba-alba by Lactiplantibacillus plantarum SMFM2016-RK.}, journal = {Journal of oral microbiology}, volume = {17}, number = {1}, pages = {2473246}, pmid = {40099142}, issn = {2000-2297}, abstract = {Periodontitis has been linked to systemic inflammation, however research on its role in causing systemic diseases remains limited. Recent studies explore probiotics for microbiome modulation and enhancing natural compound bioavailability. This study investigated periodontitis-related systemic disease mechanisms, and evaluated the mitigation effects of bioconversion product using Lactiplantibacillus plantarum SMFM2016-RK and Artemisia herba-alba extracts. Four types of bioconverted milk [BM1 (L. plantarum SMFM2016-RK), BM2 (BM1 + A. herba-alba ethanol extract), BM3 (BM1 + A. herba-alba hot-water extract), and BM4 (BM1+ both A. herba-alba extracts)] were studied in a periodontitis-induced rat model. Rats were divided into six groups: normal control, skim milk with ligature, and four BM groups with ligature. Periodontitis induction elevated trabecular resorption (0.325 ± 0.057 mm[3]) and histopathological symptoms. Serum ALT (55.6 ± 6.6 U/L), glucose (261.7 ± 64.3 mg/dL), insulin (1.90 ± 0.87 ng/mL), inflammation in the liver and colon, and gluconeogenesis-related enzyme expression increased. Periodontitis-induced rats showed gut dysbiosis, with decreased Lactobacillaceae level and increased Oscillospiraceae level. BM3 administration significantly reduced the serum glucose (190.9 ± 27.8 mg/dL), ALT (40.5 ± 5.0 U/L), inflammation, and gluconeogenesis-related enzymes, while increasing tight junction proteins expression and phylum Actinobacteria levels in the gut microbiome. The findings highlight the systemic impact of periodontitis on inflammation, glycemic control, and gut microbiome balance. BM3 effectively alleviated these effects suggesting therapeutic potential.}, }
@article {pmid40098979, year = {2025}, author = {Palmer, E and Hammer, A and Sharpton, T and Jiang, Y}, title = {A group penalization framework for detecting time-lagged microbiota-host associations.}, journal = {Frontiers in genetics}, volume = {16}, number = {}, pages = {1504443}, pmid = {40098979}, issn = {1664-8021}, abstract = {There is rising interest in using longitudinal microbiome data to understand how the past status of the microbiome impacts the current state of the host, referred to as "time-lagged" effects, as these effects may take time to occur. While existing works used previous states of the microbiome in their analysis, they did not use methods that identify both the time-lagged associations and their corresponding time lags. In this article, we present a framework to identify time-lagged associations between abundances of longitudinally sampled microbiota and a stationary response (final health outcome, disease status, etc.). We start with a definition of the time-lagged effect by imposing a particular structure on the association pattern of longitudinal microbial measurements. Using group penalization methods, we identify these time-lagged associations including their strengths, signs, and timespans. Through simulation studies, we demonstrate accurate identification of time lags and estimation of signal strengths by our approach. We further apply our approach to find specific gut microbial taxa and their time-lagged effects on increased parasite worm burden in zebrafish.}, }
@article {pmid40098966, year = {2025}, author = {Johnson, MJ and Lazarus, SK and Bennett, AE and Tovar-Salazar, A and Robertson, CE and Kofonow, JM and Li, S and McCollister, B and Nunes, MC and Madhi, SA and Frank, DN and Weinberg, A}, title = {Gut microbiota and other factors associated with increased T cell regulation in HIV-exposed uninfected infants.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1533003}, pmid = {40098966}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Female ; *HIV Infections/immunology/microbiology ; *T-Lymphocytes, Regulatory/immunology ; Infant ; Male ; Infant, Newborn ; Pregnancy ; T-Lymphocyte Subsets/immunology/metabolism ; Adult ; }, abstract = {INTRODUCTION: Infants exposed to HIV and uninfected (HEUs) are at higher risk of infectious morbidity than HIV-unexposed uninfected infants (HUUs). Multiple immune defects of unknown origin were observed in HEUs. We hypothesized that HEUs have more regulatory and inhibitory checkpoint-expressing T cells (Treg, Tici) than HUUs, which may dampen their immune defenses against pathogens.<br><br>METHOD: We used flow cytometry to measure 25 Treg/Tici subsets in HEUs and HUUs at birth, 6, 28, and 62 weeks of life. We used maternal and infant gut microbiome data reported in a previous study to establish correlations with the Treg/Tici.<br><br>RESULTS: At birth, 3 Treg subsets, including the prototypic CD4+FOXP3+ and CD4+FOXP3+CD25+, had higher frequencies in 123 HEUs than in 117 HUUs, and 3 subsets had higher frequencies in HUUs. At 28 and 62 weeks of age, 5 Treg/Tici subsets had higher proportions in HEUs than HUUs. The frequencies of the Treg/Tici subsets that diverged between HEUs and HUUs at birth correlated with differential relative abundances of bacterial taxa in the maternal gut microbiome. The Treg/Tici subsets with significantly different frequencies at subsequent visits correlated with the concurrent composition of the infant gut microbiome. In vitro, treatment of HUU peripheral blood mononuclear cells (PBMC) with bacterial taxa most abundant in HEUs expanded Treg/Tici subsets with higher frequencies in HEUs than HUUs, recapitulating the in vivo correlations. Conversely, in vitro treatment of HEU PBMC did not increase Treg/Tici frequencies. Other factors that correlated with increased Treg/Tici frequencies were low maternal CD4+ T cells in HEUs at birth and male sex in the HUUs at 28 weeks of life.<br><br>DISCUSSION: This study shows that maternal and infant gut dysbiosis are central to the increase in Treg/Tici in HEUs and may be targeted by mitigating interventions.}, }
@article {pmid40098961, year = {2025}, author = {Ikewaki, N and Ichiyama, K and Senthilkumar, R and Preethy, S and Abraham, SJK}, title = {Modulation of neutrophil-to-lymphocyte ratio and gut microbiome balance in astronauts: potential benefits of novel beta-glucans during space missions.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1538147}, pmid = {40098961}, issn = {1664-3224}, }
@article {pmid40098807, year = {2025}, author = {Herrnreiter, CJ and Murray, MG and Luck, M and Ganesa, C and Kuprys, PV and Li, X and Choudhry, MA}, title = {Bacterial dysbiosis and decrease in SCFA correlate with intestinal inflammation following alcohol intoxication and burn injury.}, journal = {eGastroenterology}, volume = {3}, number = {1}, pages = {e100145}, pmid = {40098807}, issn = {2976-7296}, abstract = {BACKGROUND: Patients intoxicated at the time of burn experience increased rates of sepsis and death compared with that observed in similarly sized burns alone. We sought to characterise changes in the intestinal microbiome and short-chain fatty acids (SCFAs) following alcohol intoxication and burn injury and to determine whether these changes are associated with intestinal inflammation.<br><br>METHODS: 10-12-week-old C57BL/6 male and female mice were subjected to ethanol intoxication and a 12.5% total body surface area scald burn injury. The following day, mice were euthanised and faecal contents from the caecum and small intestine (SI) were harvested for 16S sequencing for microbial analysis and caecum contents underwent high-performance liquid chromatography mass spectroscopy to assess SCFAs.<br><br>RESULTS: The intestinal microbiome of ethanol burn (EB) mice exhibited decreased alpha diversity and distinct beta diversity compared with sham vehicle (SV). EB faeces were marked by increased Proteobacteria and many pathobionts. EB caecum faeces exhibited a significant decrease in butyrate and a downward trend in acetate and total SCFAs. SCFA changes correlated with microbial changes particularly in the SI. Treatment of murine duodenal cell clone-K (MODE-K) cells with faecal slurries led to upregulation of interleukin-6 (IL-6) from EB faeces compared with SV faeces which correlated with levels of Enterobacteriaceae. However, supplementation of butyrate reduced faecal slurry-induced MODE-K cells IL-6 release.<br><br>CONCLUSION: Together, these findings suggest that alcohol and burn injury induce bacterial dysbiosis and a decrease in SCFAs, which together can promote intestinal inflammation and barrier disruption, predisposing to postinjury pathology.}, }
@article {pmid40098681, year = {2025}, author = {Orouskhani, M and Rauniyar, S and Morella, N and Lachance, D and Minot, SS and Dey, N}, title = {Deep learning imaging analysis to identify bacterial metabolic states associated with carcinogen production.}, journal = {Discover imaging}, volume = {2}, number = {1}, pages = {2}, pmid = {40098681}, issn = {3004-9776}, abstract = {BACKGROUND: Colorectal cancer (CRC) is a globally prevalent cancer. Emerging research implicates the gut microbiome in CRC pathogenesis. Bacteria such as Clostridium scindens can produce the carcinogenic bile acid deoxycholic acid (DCA). It is unknown whether imaging methods can differentiate DCA-producing and DCA-non-producing C. scindens cells.<br><br>METHODS: Light microscopy images of anaerobically cultured C. scindens in four conditions were acquired at 100&#xd7; magnification using the Tissue FAX system: C. scindens in media alone (DCA-non-producing state), C. scindens in media with cholic acid (DCA-producing state), or C. scindens in co-culture with one of two Bacteroides species (intermediate DCA production states). We evaluated three approaches: whole-image classification, per-cell classification, and image segmentation-based classification. For whole-image classification, we used a custom Convolutional Neural Network (CNN), pre-trained DenseNet, pre-trained ResNet, and ResNet enhanced by integrating the Digital Images of Bacterial Species (DIBaS) dataset. For cell detection and classification, we applied thresholding (OTSU or adaptive thresholding) followed by a ResNet model. Finally, image segmentation-based classification was performed using nnU-Net.<br><br>RESULTS: For whole-image analysis, DIBaS-enhanced ResNet models achieved the best performance in distinguishing C. scindens states in monoculture (accuracy 0.89&#x2009;&#xb1;&#x2009;0.006) and in co-cultures (accuracy 0.86&#x2009;&#xb1;&#x2009;0.004). Per-cell analysis was optimal at a C constant value of 3, with the ResNet model achieving 62-74% accuracy for C. scindens states&#xa0;in monoculture. Segmentation-based analysis using nnU-Net resulted in Dice coefficients of 87% for C. scindens and 74-76% for the Bacteroides species.<br><br>CONCLUSIONS: This study demonstrates feasibility of image-based deep learning models in identifying health-relevant gut bacterial metabolic states.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s44352-025-00006-1.}, }
@article {pmid40098675, year = {2025}, author = {Jing, X and Gong, Y and Diao, Z and Ma, Y and Meng, Y and Chen, J and Ren, Y and Liang, Y and Li, Y and Sun, W and Zhang, J and Ji, Y and Cong, Z and Li, S and Ma, B and Cui, Z and Ma, L and Xu, J}, title = {Phylogeny-metabolism dual-directed single-cell genomics for dissecting and mining ecosystem function by FISH-scRACS-seq.}, journal = {Innovation (Cambridge (Mass.))}, volume = {6}, number = {3}, pages = {100759}, pmid = {40098675}, issn = {2666-6758}, abstract = {Microbiome-wide association studies (MWASs) have uncovered microbial markers linked to ecosystem traits, but the mechanisms underlying their functions can remain elusive. This is largely due to challenges in validating their in situ metabolic activities and tracing such activities to individual genomes. Here, we introduced a phylogeny-metabolism dual-directed single-cell genomics approach called fluorescence-in situ-hybridization-guided single-cell Raman-activated sorting and sequencing (FISH-scRACS-seq). It directly localizes individual cells from target taxon via an FISH probe for marker organism, profiles their in situ metabolic functions via single-cell Raman spectra, sorts cells of target taxonomy and target metabolism, and produces indexed, high-coverage, and precisely-one-cell genomes. From cyclohexane-contaminated seawater, cells representing the MWAS-derived marker taxon of γ-Proteobacteria and that are actively degrading cyclohexane in situ were directly identified via FISH and Raman, respectively, then sorted and sequenced for one-cell full genomes. In such a Pseudoalteromonas fuliginea cell, we discovered a three-component cytochrome P450 system that can convert cyclohexane to cyclohexanol in vitro, representing a previously unknown group of cyclohexane-degrading enzymes and organisms. Therefore, by unveiling enzymes, pathways, genomes, and their in situ cellular functions specifically for those organisms with ecological relevance at one-cell resolution, FISH-scRACS-seq is a rational and generally applicable approach to dissecting and mining microbiota functions.}, }
@article {pmid40098416, year = {2025}, author = {Tanfouri, N and Guerfali, MM and Asimakis, E and Mokhtar, NB and Apostolopoulou, G and Hamden, H and Charaabi, K and Fadhl, S and Stathopoulou, P and Cherif, A and Tsiamis, G}, title = {Characterization of the microbial communities in Tunisian wild populations of the Mediterranean fruit fly (Ceratitis capitata) and their implications for the future implementation of the sterile insect technique.}, journal = {Insect science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1744-7917.70016}, pmid = {40098416}, issn = {1744-7917}, support = {22662//International Atomic Energy Agency/ ; }, abstract = {Insects and their associated microbiota have developed a sustained and mutually beneficial relationship, characterized by the influence of the symbiotic microorganisms on the host's physiological processes and fitness parameters. The Mediterranean fruit fly, Ceratitis capitata (Diptera: Tephritidae), is one of the world's most ubiquitous, invasive, and harmful agricultural pests. In Tunisia, the medfly is widely distributed across all bioclimatic zones. However, in the absence of surveillance, infestations can escalate drastically, causing damage levels as high as 100%. Our study aimed to characterize the microbiome profile of Tunisian medfly populations from Zaghouan, Tozeur, Siliana, and Bizerte to understand the microbial dynamics implicated in the invasiveness and adaptability potential if SIT is applied. We conducted amplicon sequencing using MiSeq Illumina and a culture-dependent approach. Our findings revealed notable differences in symbiotic communities across regions. For instance, Serratia was prevalent in Tozeur populations, while Klebsiella showed high abundance in Bizerte. The composition of the bacterial communities within the medfly populations was influenced by several factors including the environmental conditions, geographical location, developmental stage, and the sex of the insects. Investigating the intricate relationship between insects and their microbiota is pivotal for understanding their biology and developing effective pest management strategies. Additionally, the isolation of bacteria from adult and larval medflies collected in the Bizerte region revealed the presence of bacterial species that could be utilized as attractants or supplements in larval artificial diets in the case of application of the SIT aiming at producing competitive sterile males.}, }
@article {pmid40098333, year = {2025}, author = {Kumar, V and Bahuguna, A and Kumar, S and Kim, M}, title = {Xylooligosaccharides mediated gut microbiome modulation: prebiotics to postbiotics.}, journal = {Critical reviews in biotechnology}, volume = {}, number = {}, pages = {1-19}, doi = {10.1080/07388551.2025.2460852}, pmid = {40098333}, issn = {1549-7801}, abstract = {An increasing trend toward harnessing nutraceuticals as food supplements rather than pharmaceuticals as curative and preventive agents against various ailments has been observed. Owing to their health benefits, prebiotics have received notable attention from the pharmaceutical and food industries. Among the different prebiotic oligosaccharides, xylooligosaccharides (XOS) exhibited a remarkable capacity to stimulate the growth of the gut microbiota and benefit individuals with metabolic abnormalities. Additionally, XOS can be produced from various renewable agricultural wastes, which supports their economic feasibility for use as prebiotics at the industrial level. This review explains gut microbiome modulation based on in vivo, in vitro, and clinical findings. Gut microbiome modulation leads to the production of postbiotics that stimulate various beneficial health effects. The current review entails the mechanisms of different health-promoting activities mediated by XOS, including immunomodulation and anticancer effects. Additionally, the concept of converting prebiotics to synbiotics using XOS has been established for nutraceutical applications. Synbiotics based on XOS and probiotics may be good alternatives to nutraceuticals for improving human health.}, }
@article {pmid40098322, year = {2025}, author = {Huang, L and Zhao, X and Wang, J and Guan, J and Huang, B and Feng, J and Li, X and Zhang, Y and Zhang, J}, title = {Gut microbiota and risk of heart failure in European population-A comprehensive Mendelian randomization study.}, journal = {ESC heart failure}, volume = {}, number = {}, pages = {}, doi = {10.1002/ehf2.15267}, pmid = {40098322}, issn = {2055-5822}, support = {7222143//Natural Science Foundation of Beijing Municipality/ ; 2022-GSP-GG-9//National High-Level Hospital Clinical Research Funding/ ; 2023-GSP-GG-26//National High-Level Hospital Clinical Research Funding/ ; 2020-I2M-1-002//CAMS Innovation Fund for Medical Science/ ; }, abstract = {AIMS: Gut dysbiosis is proven to be involved in the pathogenesis and progression of heart failure (HF). Hindering the detrimental effects of gut-heart axis is an emerging trend. Our goal is to investigate the causal relationship between gut microbiota and HF, with the aim of facilitating future exploration of microbiome-targeted approaches to prevent and delay the progression of HF.<br><br>METHODS AND RESULTS: Two-sample Mendelian randomization (MR) analysis was applied to investigate the causal association of the gut microbiome with HF among individuals of European ancestry. Genetic variants associated with the 196 bacterial taxa from MiBioGen consortium were used as exposure data, summary statistics for HF derived from Heart Failure Molecular Epidemiology for Therapeutic Targets (HERMES) consortium were used as outcome data. Five MR methods were applied, including inverse variance weighted, maximum likelihood, MR-Egger, weighted median, and weighted mode. Reverse causality of instrumental variables (IVs) was tested by MR Steiger test of directionality. Strength of IVs was evaluated by F-statistics. Cochrane's Q test, MR-Egger regression analysis, and MR Pleiotropy RESidual Sum and Outlier (MR-PRESSO) tests were used to detect heterogeneity and pleiotropy. Leave-one-out method was used for testing the stability of results. Seven microbiomes were found to be associated with HF. Five of them were associated with higher risks of developing HF, these included Order_Selenomonadales (odds ratio [OR]&#xa0;=&#xa0;1.11, P&#xa0;=&#xa0;0.024), Family_Peptococcaceae (OR&#xa0;=&#xa0;1.07, P&#xa0;=&#xa0;0.045), Genus_Eubacterium eligens group (OR&#xa0;=&#xa0;1.14, P&#xa0;=&#xa0;0.022), Genus_Eubacterium oxidoreducens group (OR&#xa0;=&#xa0;1.12, P&#xa0;=&#xa0;0.011) and Genus_Flavonifractor (OR&#xa0;=&#xa0;1.14, P&#xa0;=&#xa0;0.012). Genus_Anaerostipes and Order_Bacillales were associated with lower risks of HF (OR&#xa0;=&#xa0;0.90, P&#xa0;=&#xa0;0.014; OR&#xa0;=&#xa0;0.95, P&#xa0;=&#xa0;0.042, respectively). Evidence of pleiotropy or heterogeneity was not observed.<br><br>CONCLUSIONS: We identified seven intestinal microbiomes that were causally associated with HF at the level of gene prediction. This study will help with the discovery of potential preventive and therapeutic targets for HF.}, }
@article {pmid40098172, year = {2025}, author = {Raziq, MF and Khan, N and Manzoor, H and Tariq, HMA and Rafiq, M and Rasool, S and Kayani, MUR and Huang, L}, title = {Prioritizing gut microbial SNPs linked to immunotherapy outcomes in NSCLC patients by integrative bioinformatics analysis.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {343}, pmid = {40098172}, issn = {1479-5876}, mesh = {Humans ; *Polymorphism, Single Nucleotide/genetics ; *Carcinoma, Non-Small-Cell Lung/genetics/microbiology/drug therapy ; *Computational Biology/methods ; *Gastrointestinal Microbiome/genetics ; *Lung Neoplasms/genetics/drug therapy/microbiology ; *Immunotherapy ; Treatment Outcome ; Male ; Female ; Metagenome/genetics ; }, abstract = {BACKGROUND: The human gut microbiome has emerged as a potential modulator of treatment efficacy for different cancers, including non-small cell lung cancer (NSCLC) patients undergoing immune checkpoint inhibitor (ICI) therapy. In this study, we investigated the association of gut microbial variations with response against ICIs by analyzing the gut metagenomes of NSCLC patients.<br><br>METHODS: Strain identification from the publicly available metagenomes of 87 NSCLC patients, treated with nivolumab and collected at three different timepoints (T0, T1, and T2), was performed using StrainPhlAn3. Variant calling and annotations were performed using Snippy and associations between microbial genes and genomic variations with treatment responses were evaluated using MaAsLin2. Supervised machine learning models were developed to prioritize single nucleotide polymorphisms (SNPs) predictive of treatment response. Structural bioinformatics approaches were employed using MUpro, I-Mutant 2.0, CASTp and PyMOL to access the functional impact of prioritized SNPs on protein stability and active site interactions.<br><br>RESULTS: Our findings revealed the presence of strains for several microbial species (e.g., Lachnospira eligens) exclusively in Responders (R) or Non-responders (NR) (e.g., Parabacteroides distasonis). Variant calling and annotations for the identified strains from R and NR patients highlighted variations in genes (e.g., ftsA, lpdA, and nadB) that were significantly associated with the NR status of patients. Among the developed models, Logistic Regression performed best (accuracy&#x2009;>&#x2009;90% and AUC ROC&#x2009;>&#x2009;95%) in prioritizing SNPs in genes that could distinguish R and NR at T0. These SNPs included Ala168Val (lpdA) in Phocaeicola dorei and Tyr233His (lpdA), Leu330Ser (lpdA), and His233Arg (obgE) in Parabacteroides distasonis. Lastly, structural analyses of these prioritized variants in objE and lpdA revealed their involvement in the substrate binding site and an overall reduction in protein stability. This suggests that these variations might likely disrupt substrate interactions and compromise protein stability, thereby impairing normal protein functionality.<br><br>CONCLUSION: The integration of metagenomics, machine learning, and structural bioinformatics provides a robust framework for understanding the association between gut microbial variations and treatment response, paving the way for personalized therapies for NSCLC in the future. These findings emphasize the potential clinical implications of microbiome-based biomarkers in guiding patient-specific treatment strategies and improving immunotherapy outcomes.}, }
@article {pmid40098090, year = {2025}, author = {Xiao, P and Li, Y and Li, X and Ge, T and Li, D and Xu, Q and Ruan, Y and Xiao, F and Xiao, Y and Zhang, T}, title = {Long-term safety of fecal microbiota transplantation in Chinese children from 2013 to 2023: a single-center retrospective study.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {152}, pmid = {40098090}, issn = {1471-2180}, mesh = {Humans ; Retrospective Studies ; Male ; Female ; *Fecal Microbiota Transplantation/methods/adverse effects ; Child ; Child, Preschool ; China ; Adolescent ; Infant ; *Gastrointestinal Microbiome ; Treatment Outcome ; Feces/microbiology ; East Asian People ; }, abstract = {BACKGROUND: The gut microbiome plays a vital role in influencing various health conditions. Fecal Microbiota Transplantation (FMT) has emerged as a rapid, safe, and effective method for modifying the microbiome. However, there is a lack of long-term safety data regarding FMT in children. This study presents the largest single-center analysis of the long-term safety outcomes of FMT in pediatric patients in China, featuring a substantial sample size and an extended follow-up period to thoroughly examine its safety in children.<br><br>METHODS: A retrospective study was conducted on 813 patients who underwent FMT treatments at our hospital from December 2013 to December 2023. All FMT procedures adhered to standardized protocols. The safety of these treatments was retrospectively assessed, focusing on adverse events (AEs) and serious adverse events (SAEs). AEs associated with FMT were categorized as short-term (within 48 h post-FMT) and long-term (within 3 months). Various potential influencing factors for AEs, including sex, age, route of administration, disease type, and consanguineous donor, were examined as independent variables. Significant independent factors and their associated risk ratios with 95% confidence intervals (CI) were determined through multivariate logistic regression analysis. A p-value of less than 0.05 was considered statistically significant.<br><br>RESULTS: A total of 813 patients underwent FMT, with a median age of 93 months (range 4-215) and 68.0% being males. The average follow-up time was 32.3 months (range 1-122). All short-term AEs resolved within 48&#xa0;h, with an overall occurrence rate of 5.8% (47/813). The most common short-term AEs included vomiting (2.0%), abdominal pain (1.6%), diarrhea (0.9%), fever (0.7%), dysphoria (0.4%), and nausea (0.4%). Multivariable analysis revealed that patients with inflammatory bowel disease (IBD) (OR: 3.98, 95% CI: 1.78-8.92, P&#x2009;=&#x2009;0.001) and those who received FMT via capsules (OR: 0.09, 95% CI: 0.03-0.27, P&#x2009;=&#x2009;0.000) were independent risk factors for FMT-related AEs. All 813 patients were followed up for at least 1 month, with 78.8% followed for more than 12 months. No long-term AEs occurred during the longest follow-up period of 122 months.<br><br>CONCLUSIONS: FMT is a promising treatment option that appears to be safe and well tolerated. This study stands out for its substantial sample size, making it's the largest reported series in pediatrics, as well as for having the longest follow-up period for FMT in this population.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid40098052, year = {2025}, author = {Oami, T and Shimazui, T and Yumoto, T and Otani, S and Hayashi, Y and Coopersmith, CM}, title = {Gut integrity in intensive care: alterations in host permeability and the microbiome as potential therapeutic targets.}, journal = {Journal of intensive care}, volume = {13}, number = {1}, pages = {16}, pmid = {40098052}, issn = {2052-0492}, support = {GM148217//Foundation for the National Institutes of Health/ ; }, abstract = {BACKGROUND: The gut has long been hypothesized to be the "motor" of critical illness, propagating inflammation and playing a key role in multiple organ dysfunction. However, the exact mechanisms through which impaired gut integrity potentially contribute to worsened clinical outcome remain to be elucidated. Critical elements of gut dysregulation including intestinal hyperpermeability and a perturbed microbiome are now recognized as potential therapeutic targets in critical care.<br><br>MAIN BODY: The gut is a finely tuned ecosystem comprising ~&#xa0;40 trillion microorganisms, a single cell layer intestinal epithelia that separates the host from the microbiome and its products, and the mucosal immune system that actively communicates in a bidirectional manner. Under basal conditions, these elements cooperate to maintain a finely balanced homeostasis benefitting both the host and its internal microbial community. Tight junctions between adjacent epithelial cells selectively transport essential molecules while preventing translocation of pathogens. However, critical illness disrupts gut barrier function leading to increased gut permeability, epithelial apoptosis, and immune activation. This disruption is further exacerbated by a shift in the microbiome toward a "pathobiome" dominated by pathogenic microbes with increased expression of virulence factors, which intensifies systemic inflammation and accelerates organ dysfunction. Research has highlighted several potential therapeutic targets to restore gut integrity in the host, including the regulation of epithelial cell function, modulation of tight junction proteins, and inhibition of epithelial apoptosis. Additionally, microbiome-targeted therapies, such as prebiotics, probiotics, fecal microbiota transplantation, and selective decontamination of the digestive tract have also been extensively investigated to promote restoration of gut homeostasis in critically ill patients. Future research is needed to validate the potential efficacy of these interventions in clinical settings and to determine if the gut can be targeted in an individualized fashion.<br><br>CONCLUSION: Increased gut permeability and a disrupted microbiome are common in critical illness, potentially driving dysregulated systemic inflammation and organ dysfunction. Therapeutic strategies to modulate gut permeability and restore the composition of microbiome hold promise as novel treatments for critically ill patients.}, }
@article {pmid40097931, year = {2025}, author = {Boutin, S and Käding, N and Belheouane, M and Merker, M and Rupp, J and Nurjadi, D}, title = {Towards unraveling antimicrobial resistance dynamics: a longitudinal exploration of rectal swab metagenomes.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {150}, pmid = {40097931}, issn = {1471-2180}, mesh = {Humans ; *Rectum/microbiology ; *Metagenome ; *Metagenomics/methods ; Bacteria/genetics/drug effects/isolation &amp; purification/classification ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Whole Genome Sequencing ; Longitudinal Studies ; Male ; Microbial Sensitivity Tests ; Female ; Middle Aged ; Microbiota/genetics/drug effects ; Aged ; Genome, Bacterial/genetics ; Adult ; }, abstract = {The increasing prevalence of antimicrobial resistance (AMR) poses significant challenges in clinical settings. In particular, early screening and detection of colonization by multidrug-resistant organisms (MDROs) in patients at admission is crucial. In this context, the clinical use of metagenomics (mNGS) holds promise for fast and untargeted diagnostic methods. Here, we aimed to evaluate the long-term stability of the rectal microbiome and the diagnostic accuracy of mNGS in comparison to culture and whole-genome sequencing (WGS) of MDROs. We analyzed rectal swabs from 26 patients with two consecutive admissions over a four-year period. The detected antimicrobial resistance genes and assembled metagenomes were compared to those obtained via classical culture-based antimicrobial susceptibility testing and WGS of isolated MDROs. Our results showed that the rectal microbiome is variable during the two timepoints, highlighting the variability in the niche. Nevertheless, we also observed strong co-occurrence of taxa, suggesting that the rectal swab microbiome is also a regulated environment with cooperative biotic interactions. In total, we isolated and sequenced 6 MDROs from 6 patients at individual timepoints. Almost all AMR genes from the genomes of the isolates (median: 100%, range: 84.6-100%) could be detected by mNGS of the rectal swabs at the time of isolation of the MDRO but not at the time of culture negativity. In addition, we detected AMR genes and potentially pathogenic species in patients with negative cultures. In conclusion, our study showed that, in principle, mNGS of rectal swabs can detect clinically relevant AMR profiles. However, the cooccurrence of AMR genes and potentially-pathogenic species does not always correlate with culture-based diagnostic results but rather indicates a potential risk of horizontal AMR gene transfer. However, it is unclear whether the observed discrepancies are due to transient or locally confined colonization of MDROs, limits of detection, or variability of the sampling method and specimens.}, }
@article {pmid40097884, year = {2025}, author = {Zhang, H and Xia, M and Li, H and Zeng, X and Jia, H and Zhang, W and Zhou, J}, title = {Implication of Immunobiological Function of Melanocytes in Dermatology.}, journal = {Clinical reviews in allergy &amp; immunology}, volume = {68}, number = {1}, pages = {30}, pmid = {40097884}, issn = {1559-0267}, support = {202403AC100011//Key research and development program of Yunnan Province/ ; No.82473537//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Melanocytes/immunology/metabolism ; Animals ; Dermatology ; Skin/immunology ; Ultraviolet Rays/adverse effects ; Immunity, Innate ; Skin Diseases/immunology/etiology ; Vitiligo/immunology ; Skin Pigmentation ; Immunomodulation ; }, abstract = {Melanocytes are essential for regulating pigmentation and providing photoprotection in human skin. Originating from neural crest cells, these cells migrate to the basal layer of the epidermis and hair follicles during embryogenesis. Melanosomes, the specialized, membrane-bound organelles are essential for melanin synthesis. Beyond their role in pigmentation, melanocytes exhibit complex immune functions, expressing a variety of immune-related markers and receptors, such as pattern recognition receptors (PRRs), major histocompatibility complex class II (MHC-II) molecules, CD40, intercellular adhesion molecule 1 (ICAM-1), and programmed death-ligand 1 (PD-L1). These receptors allow melanocytes to detect environmental signals and engage in the innate immune response. Furthermore, melanocytes release various immunomodulatory substances, including proinflammatory cytokines, chemokines, and damage-associated molecular patterns (DAMPs), contributing to immune regulation. The immune functions of melanocytes are significantly influenced by external factors such as ultraviolet radiation (UVR), the microbiome, and oxidative stress. In different skin diseases, these immune functions may vary. For example, vitiligo, a common hypopigmentary disorder, is primarily driven by an autoimmune response targeting melanocytes, giving rise to depigmentation and the appearance of white patches. In contrast, melanoma, a form of skin cancer that arises from melanocytes, is closely linked to UV exposure. This review highlights the diverse immunobiological functions of melanocytes and their implications in dermatology.}, }
@article {pmid40097762, year = {2025}, author = {Nabakhteh, S and Lotfi, A and Afsartaha, A and Khodadadi, ES and Abdolghaderi, S and Mohammadpour, M and Shokri, Y and Kiani, P and Ehtiati, S and Khakshournia, S and Khatami, SH}, title = {Nutritional Interventions in Amyotrophic Lateral Sclerosis: From Ketogenic Diet and Neuroprotective Nutrients to the Microbiota-Gut-Brain Axis Regulation.}, journal = {Molecular neurobiology}, volume = {}, number = {}, pages = {}, pmid = {40097762}, issn = {1559-1182}, abstract = {Amyotrophic lateral sclerosis (ALS) is a complex neurodegenerative disease with significant challenges in diagnosis and treatment. Recent research has highlighted the complex nature of ALS, encompassing behavioral impairments in addition to its neurological manifestations. While several medications have been approved to slow disease progression, ongoing research is focused on identifying new therapeutic targets. The current review focuses on emerging therapeutic strategies and personalized approaches aimed at improving patient outcomes. Recent advancements highlight the importance of targeting additional pathways such as mitochondrial dysfunction and neuroinflammation to develop more effective treatments. Personalized medicine, including genetic testing and biomarkers, is proving valuable in stratifying patients and tailoring treatment options. Complementary therapies, such as nutritional interventions like the ketogenic diet and microbiome modulation, also show promise. This review emphasizes the need for a multidisciplinary approach that integrates early diagnosis, targeted treatments, and supportive care to address the multisystemic nature of ALS and improve the quality of life for patients.}, }
@article {pmid40097696, year = {2025}, author = {Ambaye, TG and Hassani, A and Vaccari, M and Franzetti, A and Prasad, S and Aminabhavi, TM and Rtimi, S}, title = {Nano-bioremediation for the removal of inorganic and organic pollutants from the soil.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {40097696}, issn = {1614-7499}, abstract = {Soil pollution is a significant problem due to harmful toxic substances, particularly organic compounds and heavy metals, resulting from various anthropogenic activities. To address this issue, a synergistic approach involving the use of nanotechnology and bioremediation has been proposed. Nano-bioremediation is a very efficient, cost-effective, and environmentally benign approach for reducing both organic and inorganic pollutants. Nanoparticles (NPs) enhance catalytic, adsorptive, and reactive properties, whereas microorganisms and extracts serve as eco-friendly catalysts. The combination of nanomaterials (NMs) and bioremediation techniques has the potential to significantly transform toxic substances either in situ or ex-situ to clean polluted environments. This article reviews recent developments in nano-bioremediation to eliminate organic and inorganic pollutants from contaminated soils. The use of NPs has the potential to enhance soil bioremediation for the removal of harmful substances through immobilization or stimulation of microbial activities and enzymes involved in the remediation process. It also discusses the mechanism of the interaction of NMs with other microorganisms and their roles in the remediation of polluted environments. Finally, the review discusses future perspectives and challenges regarding the importance of interactions between the soil microbiome, NPs, and contaminants to develop microbe-based nano-remediation strategies for organically and inorganically polluted environments.}, }
@article {pmid40097303, year = {2025}, author = {Watanabe, K and Kamei, Y and Igarashi, M and Shibuya, S and Shimizu, T and Kimura, I and Maruyama, M}, title = {Impact of a water-soluble soy extract on inflammation and gut microbiota in physiologically aged mice.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/bbb/zbaf032}, pmid = {40097303}, issn = {1347-6947}, abstract = {Soy isoflavones are involved deeply in our diet as beneficial to the health. It is known to have anti-inflammatory and antioxidant effects and also to be effective in alleviating various lifestyle diseases, as well as the maintenance of endocrine function especially with age-related diseases such as osteoporosis. Here we investigated the impact of age-dependent changes with the intestinal microbiota in physiologically aged C57BL/6 N by free drinking water with soluble soybean-derived isoflavone glycosides (SIFs) for 4 weeks. Consequently, Akkermansia muciniphila (A. muciniphila) species represented age-dependent increase with SIF treatment, subsequently, generally age-dependent decreased goblet cells are retained in the large intestine. These results invoke that SIF plays a beneficial role on intestinal barrier function to maintain the large intestine homeostasis. Interestingly, we also revealed that SIF had an alleviating effect on age-dependent bone loss. Taken together, SIF has fruitful effect on the intestinal environment and maintenance of homeostasis in physiological aging.}, }
@article {pmid40097230, year = {2025}, author = {Nair, SS and Kutty Narayanan, A and Nair, K and Mallick, S and Zackariah, NM and Biswas, L and Praseedom, R and G Nair, BK and Surendran, S}, title = {Microbiota-directed intervention in living donor liver transplant recipients: protocol for a randomised double-blind placebo-controlled trial.}, journal = {BMJ open}, volume = {15}, number = {3}, pages = {e092984}, doi = {10.1136/bmjopen-2024-092984}, pmid = {40097230}, issn = {2044-6055}, mesh = {Humans ; *Liver Transplantation ; *Living Donors ; Double-Blind Method ; *Synbiotics/administration &amp; dosage ; *Gastrointestinal Microbiome ; Randomized Controlled Trials as Topic ; Acute-On-Chronic Liver Failure/therapy ; Probiotics/therapeutic use ; Adult ; Postoperative Complications/microbiology ; Male ; Female ; }, abstract = {INTRODUCTION: Acute-on-chronic liver failure (ACLF) patients have the highest propensity for post-liver transplantation (LT) infections and mortality. Liver-associated diseases have been one of the primary targets for synbiotic therapy to augment immunity and mitigate infections. However, despite multiple studies showing benefits of synbiotics in liver diseases, data on their use following LT are sparse.<br><br>METHODS AND ANALYSIS: This randomised placebo-controlled study aims to assess the impact of synbiotics in ACLF patients undergoing living donor liver transplantation (LDLT). Following randomisation by computer-generated block number sequence, 3&#x2009;days prior to LDLT, the intervention arm will receive standard medical treatment and synbiotics (VSL#3 a probiotic, and Yogut, prebiotic and probiotic combination) for 6&#x2009;weeks, while the control arm will receive standard medical treatment with a placebo. The patients will be followed up for 6&#x2009;months to study the clinical and biochemical outcomes. The primary objective is to compare the difference in the occurrence of infectious complications between the patients who receive synbiotics versus placebo during the 6-month period following LDLT. The secondary objectives include assessing the qualitative and quantitative change in microbiota with synbiotics and LDLT, adverse reactions due to synbiotics, and post-LT morbidity and mortality. The minimum sample size comes to 71 in each group. The first 50 patients in the study protocol will undergo gut microbiome analysis using 16s metagenomic and nanopore sequencing to analyse the microbial composition before starting synbiotics/placebo and at 6 weeks after LDLT.<br><br>ETHICS AND DISSEMINATION: The study is approved by the Research Ethics Committee of Amrita Institute of Medical Sciences, Kochi, India (IEC-AIMS-2022-GISUR-203) and registered in the Clinical Trial Registry of India (CTRI) CTRI/2022/10/046327. The results of the trial will be disseminated by presentation at national/international conferences and publication in peer-reviewed journals.<br><br>TRIAL REGISTRATION NUMBER: CTRI/2022/10/046327 - Clinical Trial Registry of India.}, }
@article {pmid40097060, year = {2025}, author = {Bénet, T and Dardinier, A and Tytgat, HLP and Austin, S}, title = {Quantitative determination of human milk oligosaccharides in faecal matter.}, journal = {Analytical biochemistry}, volume = {}, number = {}, pages = {115845}, doi = {10.1016/j.ab.2025.115845}, pmid = {40097060}, issn = {1096-0309}, abstract = {Human milk oligosaccharides (HMOs) are a major component of human milk and colostrum, yet they are non-digestible and thus not utilized directly by the infant. Nevertheless, they are important for infant health and development and have been implicated in immune development, pathogen deflection, cognitive development and the development of healthy microbiome. To understand how HMOs may be utilized it is important to be able to measure them both in milk and faeces. Many methods for the determination of HMOs in milk have been published. However, there are fewer reports of methods describing the quantitative determination of oligosaccharides in faeces. Here we report a validated method for the determination of 30 oligosaccharides in faeces. Oligosaccharides are labelled with 2-aminobenzamide and determined by liquid chromatography with fluorescence detection. The method precision determined as relative standard deviation under intermediate reproducibility conditions is below 12 % for all of the oligosaccharides. Recoveries were in the range 86.6 - 115% for the 8 oligosaccharides for which quantitative standards were available, and are estimated to be in the range 81-117% when using 2'-fucosyllactose as a universal calibrant assuming equimolar response factors of the 2-aminobenzamide labelled oligosaccharides.}, }
@article {pmid40096759, year = {2025}, author = {Wei, D and Zhang, X and Guo, Y and Saleem, K and Jia, J and Li, M and Yu, H and Hu, Y and Yao, X and Wang, Y and Chang, X and Song, C}, title = {CuO nanoparticles facilitate soybean suppression of Fusarium root rot by regulating antioxidant enzymes, isoflavone genes, and rhizosphere microbiome.}, journal = {Plant physiology and biochemistry : PPB}, volume = {222}, number = {}, pages = {109788}, doi = {10.1016/j.plaphy.2025.109788}, pmid = {40096759}, issn = {1873-2690}, abstract = {BACKGROUND: Fusarium root rot is a widespread soil-borne disease severely impacting soybean yield and quality. Compared to traditional fertilizers' biological and environmental toxicity, CuO nanoparticles (NPs) hold promise for disease control in a low dose and high efficiency manner.<br><br>METHODS: We conducted both greenhouse and field experiments, employing enzymatic assays, elemental analysis, qRT-PCR, and microbial sequencing (16S rRNA, ITS) to explore the potential of CuO NPs for sustainable controlling Fusarium-induced soybean disease.<br><br>RESULTS: Greenhouse experiments showed that foliar spraying of CuO NPs (10, 100, and 500&#xa0;mg&#xa0;L[-1]) promoted soybean growth more effectively than EDTA-CuNa2 at the same dose, though 500 CuO NPs caused mild phytotoxicity. CuO NPs effectively controlled root rot, while EDTA-CuNa2 worsened the disease severity by 0.85-34.04 %. CuO NPs exhibited more substantial antimicrobial effects, inhibiting F. oxysporum mycelial growth and spore germination by 5.04-17.55 % and 10.24-14.41 %, respectively. 100&#xa0;mg&#xa0;L[-1] CuO NPs was the optimal concentration for balancing soybean growth and disease resistance. Additionally, CuO NPs boosted antioxidant enzyme activity (CAT, POD, and SOD) in leaves and roots, aiding in ROS clearance during pathogen invasion. Compared to the pathogen control, 100&#xa0;mg&#xa0;L[-1] CuO NPs upregulated the relative expression of seven isoflavone-related genes (Gm4CL, GmCHS8, GmCHR, GmCHI1a, GmIFS1, GmUGT1, and GmMYB176) by 1.18-4.51 fold, thereby enhancing soybean disease resistance in place of progesterone-receptor (PR) genes. Field trials revealed that CuO NPs' high leaf-to-root translocation modulated soybean rhizosphere microecology. Compared to the pathogen control, 100&#xa0;mg&#xa0;L[-1] CuO NPs increased nitrogen-fixing bacteria (Rhizobium, Azospirillum, Azotobacter) and restored disease-resistant bacteria (Pseudomonas, Burkholderia) and fungi (Trichoderma, Penicillium) to healthy levels. Furthermore, 100&#xa0;mg&#xa0;L[-1] CuO NPs increased beneficial bacteria (Pedosphaeraceae, Xanthobacteraceae, SCI84, etc.) and fungi (Trichoderma, Curvularia, Hypocreales, etc.), which negatively correlated with F. oxysporum, while recruiting functional microbes to enhance soybean yield.<br><br>CONCLUSION: 100&#xa0;mg&#xa0;L[-1] CuO NPs effectively promoting soybean growth and providing strong resistance against root rot disease by improving antioxidant enzyme activity, regulating the relative expression of isoflavone-related genes, increasing beneficial bacteria and fungi and restoring disease-resistant. Our findings suggest that CuO NPs offer an environmentally sustainable strategy for managing soybean disease, with great potential for green production.}, }
@article {pmid40096354, year = {2025}, author = {Dongre, DS and Saha, UB and Saroj, SD}, title = {Exploring the role of gut microbiota in antibiotic resistance and prevention.}, journal = {Annals of medicine}, volume = {57}, number = {1}, pages = {2478317}, doi = {10.1080/07853890.2025.2478317}, pmid = {40096354}, issn = {1365-2060}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Dysbiosis/microbiology ; Drug Resistance, Multiple, Bacterial/genetics ; Fecal Microbiota Transplantation ; Drug Resistance, Microbial/genetics ; Bacteria/drug effects/genetics ; Probiotics/administration &amp; dosage/therapeutic use ; }, abstract = {BACKGROUND/INTRODUCTION: Antimicrobial resistance (AMR) and the evolution of multiple drug-resistant (MDR) bacteria is of grave public health concern. To combat the pandemic of AMR, it is necessary to focus on novel alternatives for drug development. Within the host, the interaction of the pathogen with the microbiome plays a pivotal role in determining the outcome of pathogenesis. Therefore, microbiome-pathogen interaction is one of the potential targets to be explored for novel antimicrobials.<br><br>MAIN BODY: This review focuses on how the gut microbiome has evolved as a significant component of the resistome as a source of antibiotic resistance genes (ARGs). Antibiotics alter the composition of the native microbiota of the host by favouring resistant bacteria that can manifest as opportunistic infections. Furthermore, gut dysbiosis has also been linked to low-dosage antibiotic ingestion or subtherapeutic antibiotic treatment (STAT) from food and the environment.<br><br>DISCUSSION: Colonization by MDR bacteria is potentially acquired and maintained in the gut microbiota. Therefore, it is pivotal to understand microbial diversity and its role in adapting pathogens to AMR. Implementing several strategies to prevent or treat dysbiosis is necessary, including faecal microbiota transplantation, probiotics and prebiotics, phage therapy, drug delivery models, and antimicrobial stewardship regulation.}, }
@article {pmid40096210, year = {2025}, author = {Lazaros, K and Adam, S and Krokidis, MG and Exarchos, T and Vlamos, P and Vrahatis, AG}, title = {Non-Invasive Biomarkers in the Era of Big Data and Machine Learning.}, journal = {Sensors (Basel, Switzerland)}, volume = {25}, number = {5}, pages = {}, pmid = {40096210}, issn = {1424-8220}, support = {TAEDR-0535850.//This work was supported by the European Union-Next Generation EU, Greece 2.0 National Re-covery and Resilience Plan Flagship program TAEDR-0535850./ ; }, mesh = {Humans ; *Biomarkers/metabolism/analysis ; *Machine Learning ; *Big Data ; Precision Medicine/methods ; Artificial Intelligence ; Breath Tests/methods ; Wearable Electronic Devices ; }, abstract = {Invasive diagnostic techniques, while offering critical insights into disease pathophysiology, are often limited by high costs, procedural risks, and patient discomfort. Non-invasive biomarkers represent a transformative alternative, providing diagnostic precision through accessible biological samples or physiological data, including blood, saliva, breath, and wearable health metrics. They encompass molecular and imaging approaches, revealing genetic, epigenetic, and metabolic alterations associated with disease states. Furthermore, advances in breathomics and gut microbiome profiling further expand their diagnostic scope. Even with their strengths in terms of safety, cost-effectiveness, and accessibility, non-invasive biomarkers face challenges in achieving monitoring sensitivity and specificity comparable to traditional clinical approaches. Computational advancements, particularly in artificial intelligence and machine learning, are addressing these limitations by uncovering complex patterns in multi-modal datasets, enhancing diagnostic accuracy and facilitating personalized medicine. The present review integrates recent innovations, examines their clinical applications, highlights their limitations and provides a concise overview of the evolving role of non-invasive biomarkers in precision diagnostics, positioning them as a compelling choice for large-scale healthcare applications.}, }
@article {pmid40095592, year = {2025}, author = {Kiełbratowski, M and Kuśka-Kiełbratowska, A and Mertas, A and Bobela, E and Wiench, R and Kępa, M and Trzcionka, A and Korkosz, R and Tanasiewicz, M}, title = {Evaluation of the Effectiveness of a Mouthwash Containing Spilanthol and Cannabidiol on Improving Oral Health in Patients with Gingivitis-Clinical Trial.}, journal = {Journal of clinical medicine}, volume = {14}, number = {5}, pages = {}, pmid = {40095592}, issn = {2077-0383}, abstract = {Background/Objectives: Plaque-associated gingivitis is widely regarded as a local inflammatory condition initiated by the accumulation of a non-specific dental biofilm in the interaction with the host immune system. The initial symptom noticed by the patient is bleeding gums. The use of mouthwash can serve to supplement mechanotherapy. However, there is an increasing interest in mouthwashes comprising natural ingredients, including cannabidiol (CBD) and spilanthol. The objective of this study was to evaluate the effect of an oral rinse containing spilanthol and CBD oil compared to a rinse containing tea tree oil on the oral microbiota and the values of selected oral status indicators in patients with gingivitis. Methods: The study included 40 patients treated with a rinse containing tea tree oil (TTO)/TTO + spilanthol + CBD for a period of 42 days. Patients rinsed their mouth twice daily for 30 s. The patients' oral microbiome was assessed before and after treatment, and bleeding on probing (BOP) and approximal plaque index (API) were assessed. The study was double-blind. Results: API and BOP were reduced in all groups, both the test and control. The most significant decrease in baseline BOP-1 scores was observed in test groups A and D (p = 0.005062 and p = 0.005062, respectively). A significant difference in API improvement was observed between the initial and final visits in the test (A, D) and control (B, C) groups (p = 0.012516, p = 0.005062, p = 0.004028, p = 0.003172, respectively). Conclusions: Firstly, the use of a mouthwash containing cannabidiol (CBD) and spilanthol was demonstrated to be efficacious in the maintenance of oral microbiota homeostasis. Secondly, the combination of TTO with spilanthol and CBD in the rinse was shown to result in a more significant reduction in selected oral health parameters (BOP and API) and anti-inflammatory effects when compared to a rinse with TTO alone. It should be noted that this is a pilot study and will continue.}, }
@article {pmid40095191, year = {2025}, author = {Ramos, C and Magistro, D and Walton, GE and Whitham, A and Camp, N and Poveda, C and Gibson, GR and Hough, J and Kinnear, W and Hunter, K}, title = {Assessing the gut microbiota composition in older adults: connections to physical activity and healthy ageing.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {40095191}, issn = {2509-2723}, abstract = {The composition and functionality of the gut microbiota (GM) changes throughout the life course. As we move into older age, it starts to shift towards a less healthy one, which may lead to an imbalance in the GM community. Strategies that can reverse age-related dysbiosis are an important part of healthy aging. Little is known about the GM composition of older adults with different physical activity (PA) levels and whether it might contribute to healthy ageing. The aim of this study was to compare the GM composition of older adults with different PA levels and assess if it is associated with healthy ageing. 101 participants aged between 65-85 years undertook anthropometric measures, a 6-min walking test, wore an accelerometer for 7 days and provided a faecal sample. Faecal GM composition was analysed using 16S rRNA sequencing. We found that those who fulfilled the WHO/UK PA recommendations had higher relative abundance of several health-related bacteria such as Lactobacillus, F. prausnitzii and Roseburia intestinalis and lower abundance of disease-associated bacteria such as D.piger or Enterobacterales when compared to those who did not reach PA recommendations. These findings suggest that PA might improve the GM composition and has the potential to, at least partially, revert age-associated dysbiosis and promote healthy ageing.}, }
@article {pmid40095168, year = {2025}, author = {Hu, S and Dong, J and Che, Y and Guo, J}, title = {Causal association of the skin microbiome with human infertility: insights from a bidirectional two-sample Mendelian randomization.}, journal = {Archives of dermatological research}, volume = {317}, number = {1}, pages = {565}, pmid = {40095168}, issn = {1432-069X}, support = {82074443//National Natural Science Foundation of China/ ; 22CP1423//Program of Science and Technology Department of Sichuan Province/ ; 2021MS307//Sichuan Provincial Administration of Traditional Chinese Medicine/ ; }, mesh = {Humans ; Female ; *Microbiota/genetics ; *Skin/microbiology/pathology ; *Mendelian Randomization Analysis ; Infertility, Female/microbiology ; Male ; Genome-Wide Association Study ; Pregnancy ; }, abstract = {Infertility is a disorder characterized by the inability to achieve a clinical pregnancy after 12 months of regular and unprotected sexual activity. Affecting 8-12% of the global population, with the continuous progress of microbial research in recent years, a variety of microorganisms may be associated with the onset of infertility. We therefore used a two-sample MR Analysis to investigate the association between skin microbes and infertility. we used preprocessed exposure data to correlate infertility measures (infertility in women, associated with anovulation; Female infertility, cervical infertility, vaginal infertility, other infertility or unknown causes; Female infertility, fallopian tube origin; ED; Based on this, the positive results were subjected to horizontal pleiotropy analysis and heterogeneity analysis. Finally, Steiger test was performed to confirm the absence of reverse causality. The data used in this study were obtained from the published GWAS data sets. skin microbiota from the study conducted by Moitinho-Silva et al., and the exposure from the Finn. In this study, we found a positive causal association between Lactobacillales, Clostridiales, Pseudomonadales, and Moraxellaceae and female infertility and anovulation by MR Analysis of two samples. Enhydrobacter, Betaproteobacteria have a negative causal association with female infertility and anovulation. Lactobacillales and Alphaproteobacteria had positive causal association with female infertility, cervical infertility, vaginal infertility, other infertility or unknown causes. There was a negative causal association between Haemophilus and female infertility, cervical infertility, vaginal infertility, other infertility or unknown causes. Alphaproteobacteria are positively correlated with female infertility and fallopian tube origin. Bacteroidetes is negatively correlated with female infertility and fallopian tube origin. Rhodobacteraceae, Clostridiales and Flavobacteriaceae had a negative causal association with male infertility. Corynebacterium had a positive causal association with ED, and Micrococcus had a negative causal association with ED. Our study reveals a causal association between skin microbiota and infertility, and provides a theoretical basis for the inclusion of skin microbiota in the prevention and treatment of infertility. To the best of our knowledge, our study is the first MR Analysis to explore the potential causal association between skin microbiota and infertility. On this basis, we make a reasonable hypothesis that skin microbes cause infertility, and propose possible mechanisms. Our research contributes to the prevention and treatment of clinical infertility.}, }
@article {pmid40095096, year = {2025}, author = {Salem, A}, title = {Revealing the viral culprits: the hidden role of the oral virome in head and neck cancers.}, journal = {Archives of microbiology}, volume = {207}, number = {4}, pages = {73}, pmid = {40095096}, issn = {1432-072X}, mesh = {Humans ; *Virome ; *Mouth/virology/microbiology ; *Head and Neck Neoplasms/virology ; Microbiota ; Oropharyngeal Neoplasms/virology ; }, abstract = {The oral viral microbiome (or virome), encompassing a diverse community of viruses within the oral cavity, has emerged as a significant yet underexplored factor in head and neck cancers (HNCs). This review synthesizes recent evidence linking the oral virome to head and neck carcinogenesis, particularly oropharyngeal and nasopharyngeal carcinomas-the most common virus-associated subtypes of HNCs. Beyond pathogenesis, the diagnostic and therapeutic implications of the oral virome are explored, including non-invasive salivary detection of viral biomarkers for early cancer diagnosis, the development of targeted antiviral therapies, and preventive vaccination strategies-exemplified by the success of HPV vaccines in reducing the incidence of oropharyngeal cancers. Despite these advancements, challenges persist, including technical limitations, the need for longitudinal studies, and the integration of multi-omics approaches. A comprehensive understanding of the oral virome could revolutionize cancer diagnostics, therapeutics, and prevention. Moving forward, collaborative interdisciplinary efforts will be essential to fully leverage virome research for improving HNC outcomes.}, }
@article {pmid40094958, year = {2025}, author = {Alizhan, D and Ukybassova, T and Bapayeva, G and Aimagambetova, G and Kongrtay, K and Kamzayeva, N and Terzic, M}, title = {Cervicovaginal Microbiome: Physiology, Age-Related Changes, and Protective Role Against Human Papillomavirus Infection.}, journal = {Journal of clinical medicine}, volume = {14}, number = {5}, pages = {}, pmid = {40094958}, issn = {2077-0383}, support = {BR24992853//the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, abstract = {Background/Objectives: Persistent high-risk human papillomavirus (HPV) infections are the leading cause of cervical cancer. Developing evidence suggests that the cervicovaginal microbiome plays a significant role in modulating HPV persistence and progression to cervical neoplasia. This review synthesizes the current knowledge on the interplay between the cervicovaginal microbiome and local immunity in HPV infections, emphasizing microbial diversity, immune responses, and potential therapeutic implications. Methods: A thorough review of the literature was performed using Embase, PubMed, Scopus, and Google Scholar, encompassing studies published between 2000 and 2024. Studies examining the composition of the microbiome, immune responses, and HPV-related outcomes were evaluated and synthesized into a comprehensive review. Results: A Lactobacillus-dominant microbiome, particularly with L. crispatus, creates a protective environment through lactic acid production, maintenance of low pH, and anti-inflammatory immune modulation, facilitating HPV clearance. Dysbiosis, often characterized by a dominance of L. iners and overgrowth of anaerobic bacteria, fosters chronic inflammation, cytokine imbalance, and a microenvironment conducive to HPV persistence and progression. Hormonal changes and menopause exacerbate these microbial shifts, increasing the risk of cervical lesions. Studies suggest that cytokine profiles and antimicrobial peptides significantly influence local immune responses, further modulating infection outcomes. Conclusions: The cervicovaginal microbiome is a critical determinant in HPV infection outcomes, with therapeutic potential for modulating the microbiome to enhance immune responses and prevent cervical cancer. Personalized microbiome-targeted therapies may offer a novel avenue for managing HPV and reducing cervical cancer incidence.}, }
@article {pmid40094861, year = {2025}, author = {Stanford, J and Stefoska-Needham, A and Jiang, X and McWhinney, B and Cheikh Hassan, HI and El-Omar, E and Charlton, K and Lambert, K}, title = {High-Diversity Plant-Based Diet and Gut Microbiome, Plasma Metabolome, and Symptoms in Adults with CKD.}, journal = {Clinical journal of the American Society of Nephrology : CJASN}, volume = {}, number = {}, pages = {}, doi = {10.2215/CJN.0000000682}, pmid = {40094861}, issn = {1555-905X}, abstract = {BACKGROUND: Research suggests that eating a plant-dominant dietary pattern is beneficial to people with chronic kidney disease (CKD). The aim was to investigate how increasing the diversity of plant food intake would impact metabolomic, microbiome and clinical parameters in people with CKD.<br><br>METHODS: This study was a cross-over, randomized controlled trial involving 25 Australian adults diagnosed with stage 3-4 CKD. Participants were randomly allocated to follow two diets for 6 weeks each, separated by a minimum 4-week washout period: a high-diversity plant-based diet (HDPD, &#x2265;30 unique plant foods weekly) and a low-diversity plant-based diet (LDPD, &#x2264;15 unique plant foods weekly), alongside a usual kidney diet prescription. Data collection was completed at four timepoints (beginning and end of each intervention period). Primary outcome included a change in uremic toxins (indoxyl sulfate and p-Cresyl sulfate) concentrations. Secondary and exploratory outcomes included diet quality and nutritional status, fecal microbiome composition and diversity, plasma metabolome, symptom burden, quality of life scores, blood pressure, biochemical and anthropometric measures.<br><br>RESULTS: Plasma and urinary uremic toxin levels did not consistently decrease across the cohort; however, significant reductions were observed in responders to the HDPD, particularly those with poorer kidney function and higher baseline uremic toxin levels. Neither diet caused electrolyte imbalances. The HDPD significantly improved diet quality, reduced potential renal acid load by an average of 47% from baseline, with an estimated marginal mean reduction of 9.96 (95% CI: -16.28 to -3.64), and compared to the LDPD, decreased total symptom burden, including constipation (95% CI: -4.11 to -0.54 and -0.91 to -0.22, respectively). It also shifted the gut microbiome toward increased production of beneficial metabolites like butyrate/isobutyrate. In contrast, the LDPD reduced microbial diversity and decreased the abundance of 27 species and 33 functional genes.<br><br>CONCLUSIONS: This study demonstrated the safety and clinically relevant therapeutic benefits of aiming to incorporate 30 or more unique plant foods weekly in the diet of individuals with moderate CKD. It was observed that individuals with more advanced kidney disease and higher levels of uremic toxins may derive the greatest benefit from adopting a HDPD.<br><br>TRIAL REGISTRATION: ACTRN12619000442101.}, }
@article {pmid40094490, year = {2025}, author = {File, TM and Ramirez, JA}, title = {Pulmonary Infections in Adults: Community-Acquired Pneumonia.}, journal = {FP essentials}, volume = {550}, number = {}, pages = {6-15}, pmid = {40094490}, issn = {2159-3000}, mesh = {Humans ; *Community-Acquired Infections/diagnosis/epidemiology ; *Anti-Bacterial Agents/therapeutic use ; Pneumonia/diagnosis ; Adult ; Streptococcus pneumoniae/isolation &amp; purification ; Procalcitonin/blood ; Antimicrobial Stewardship ; Pneumonia, Bacterial/diagnosis/drug therapy/epidemiology ; Smoking Cessation ; }, abstract = {Community-acquired pneumonia (CAP) is a common and potentially serious illness, particularly in older patients and those with significant comorbidities. Recent evidence indicates diverse communities of microbes reside within the alveoli as part of the lung microbiome and may play a role in the development of pneumonia. A CAP diagnosis is based on the demonstration of a new infiltrate on imaging in a patient with symptoms and signs of pneumonia. Although vaccination has decreased its incidence, Streptococcus pneumoniae (pneumococcus) remains the most common bacterial cause of CAP. Macrolide resistance to S pneumoniae has increased in the United States. With their increasing availability, newer molecular testing methods (eg, respiratory pathogen polymerase chain reaction panel) play a significant role in the evaluation of respiratory viruses. Antimicrobial therapy for hospitalized patients should be based on the results of diagnostic studies to allow pathogen-directed therapy and optimal antimicrobial stewardship. The recommended duration for antimicrobial therapy is 3 to 5 days if there is good clinical improvement by day 2 or 3. Procalcitonin levels can be useful as an adjunct to clinical judgment for determining the appropriate duration of therapy. Smoking cessation and vaccination should be prioritized because they significantly reduce the incidence and severity of CAP.}, }
@article {pmid40094398, year = {2025}, author = {Lee, R and Ong, J and Waisberg, E and Mader, T and Berdahl, J and Suh, A and Panzo, N and Memon, H and Sampige, R and Katsev, B and Kadipasaoglu, CM and Mason, CE and Beheshti, A and Zwart, SR and Smith, SM and Lee, AG}, title = {Potential Risks of Ocular Molecular and Cellular Changes in Spaceflight.}, journal = {Seminars in ophthalmology}, volume = {}, number = {}, pages = {1-11}, doi = {10.1080/08820538.2025.2471443}, pmid = {40094398}, issn = {1744-5205}, abstract = {PURPOSE: Many fundamental cellular and molecular changes are known to occur in biological systems during spaceflight, including oxidative stress, DNA damage, mitochondrial damage, epigenetic factors, telomere lengthening, and microbial shifts. We can apply the consequences of these molecular changes in ocular cells, such as the retinal ganglion cells and corneal epithelium, to identify ophthalmologic risks during spaceflight. This review aims to discuss the potential molecular changes in greater detail and apply the principles to ocular cells and ophthalmic disease risk in astronauts.<br><br>METHODS: A targeted, relevant search of the literature on the topic and related topics of ocular surface and spaceflight was conducted with scholarly databases PubMed, Web of Science, and Embase from inception to July2024 with search terms "oxidative stress"; "DNA damage"; "Mitochondrial Dysfunction"; "Epigenetics"; "Telomeres"; "Microbiome"; "ocular cells"; "spaceflight"; "microgravity"; "radiation."<br><br>RESULTS: A total of 115 articles were included following screening and eligibility assessment. Key findings include molecular changes and their contributions to ophthalmic diseases like cataracts, spaceflight-associated neuro-ocular syndrome, and dry eye syndrome.<br><br>CONCLUSION: This review provides a comprehensive overview of risks to vision associated with long-duration spaceflight missions beyond low Earth orbit (LEO). Further investigation into targeted countermeasures is imperative to mitigate vision-threatening sequelae in astronauts undertaking deep-space exploration.}, }
@article {pmid40094367, year = {2025}, author = {Cabello, FC and Millanao, A and Godfrey, HP}, title = {Piscirickettsia salmonis pathogenicity: using the damage-response framework to look beyond smoke and mirrors.}, journal = {mBio}, volume = {}, number = {}, pages = {e0382124}, doi = {10.1128/mbio.03821-24}, pmid = {40094367}, issn = {2150-7511}, abstract = {Piscirickettsia salmonis is a globally distributed aquatic bacterium and a component of the normal salmon microbiome. It has significant biological and economic impact on Chilean salmon aquaculture due to the highly fatal disease, piscirickettsiosis. Unsuccessful attempts to prevent and treat this disease have resulted in heavy use of antimicrobials with adverse effects on the aquatic environment and piscine and human health. Evidence suggests P. salmonis could be a bacterium with relative pathogenic potential on farmed salmonids and other fishes that triggers piscirickettsiosis under particular conditions in the salmon and its environment. Application of a damage-response framework analysis could define the steps from asymptomatic P. salmonis infection to symptomatic disease, help tailor improved approaches to disease prevention and management, and, in turn, help avoid heavy use of antimicrobials which have global effects on animal health, human health, and environmental biodiversity (the One Health concept).}, }
@article {pmid40094201, year = {2025}, author = {Masaadeh, AH and Eletrebi, M and Parajuli, B and De Jager, N and Bosch, DE}, title = {Human colitis-associated colorectal carcinoma progression is accompanied by dysbiosis with enriched pathobionts.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2479774}, doi = {10.1080/19490976.2025.2479774}, pmid = {40094201}, issn = {1949-0984}, mesh = {Humans ; *Dysbiosis/microbiology ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; *Disease Progression ; *Colorectal Neoplasms/microbiology/pathology ; *Bacteria/classification/isolation &amp; purification/genetics ; Inflammatory Bowel Diseases/microbiology/pathology/complications ; Colitis-Associated Neoplasms/microbiology/pathology ; Adult ; RNA, Ribosomal, 16S/genetics ; Colitis/microbiology/pathology ; Metagenomics ; Intestinal Mucosa/microbiology/pathology ; }, abstract = {Dysbiosis and pathobionts contribute to inflammation and the risk of colitis-associated carcinoma (CAC) in animal models, but their roles in humans with this uncommon disease are unknown. We identified microbiome differences in human CAC compared with longstanding inflammatory bowel disease (IBD) and sporadic colorectal carcinoma (CRC). Twenty-four CAC resections were matched with CRC and IBD controls. Methods included histopathology, 16S rDNA metagenomics, and pathobiont-specific qPCR. Beta diversity differed by diagnosis (PERMANOVA p = 0.007). The distinguishing taxa included Akkermansia enriched in CRC, and Bacteroides spp. enriched in IBD. The non-neoplastic mucosae presented distinct beta diversity (p = 0.005), but the CAC/CRC tumor microbiomes were similar (p = 0.7). Within metastases and margins, Enterobacteriaceae were enriched in CAC, and Bacteroidales in CRC. Pathobiont-specific qPCR confirmed a greater frequency of pks+ E. coli and enterotoxigenic Bacteroides fragilis in CAC than IBD. High alpha diversity was associated with active inflammation, advanced cancer stage, and shorter overall survival (log-rank p = 0.008). Mucosal microbiomes distinguish CAC from longstanding IBD, implicating pathobionts as markers for disease progression. Integrating our findings with prior animal model research, pathobionts promote carcinogenesis in IBD patients through genotoxicity and host cell signaling.}, }
@article {pmid40093983, year = {2025}, author = {Cheng, H and Guo, H and Wen, C and Sun, G and Tang, F and Li, Y}, title = {The dual role of gut microbiota in pancreatic cancer: new insights into onset and treatment.}, journal = {Therapeutic advances in medical oncology}, volume = {17}, number = {}, pages = {17588359251324882}, pmid = {40093983}, issn = {1758-8340}, abstract = {Pancreatic cancer ranks among the most lethal digestive malignancies, exhibiting a steadily increasing incidence and mortality worldwide. Despite significant advances in cancer research, the 5-year survival rate remains below 10%, predominantly due to delayed diagnosis and limited therapeutic options. Concurrently, the gut microbiota-an integral component of host physiology-has emerged as a crucial player in the pathogenesis of pancreatic cancer. Mounting evidence indicates that alterations in gut microbial composition and function may influence tumor initiation, progression, and response to therapy. This review provides an in-depth examination of the intricate interplay between the gut microbiome and pancreatic cancer, highlighting potential diagnostic biomarkers and exploring microbiome-targeted therapeutic strategies to improve patient outcomes.}, }
@article {pmid40093880, year = {2025}, author = {Palathinkara, M and Aljadah, M and Thorgerson, A and Dawson, AZ and Widlansky, ME}, title = {Association of probiotic supplementation and cardiovascular risk profiles of patients with coronary artery disease-a cross-sectional analysis of the NHANES database between 1999-2019.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1495633}, pmid = {40093880}, issn = {2296-861X}, abstract = {BACKGROUND: Atherosclerotic cardiovascular disease (ASCVD) is a chronic inflammatory disease that leads to adverse events such as myocardial infarctions and stroke. Gut microbiome modulation is a promising target to reduce chronic inflammation and improve outcomes for patients with coronary artery disease (CAD). Risk profile patterns of CAD patients who target gut health with probiotics could provide insight into how gut modulation improves CAD clinical biomarkers. This study aims to evaluate the association between probiotic use and clinical markers of known atherosclerotic risk factors, in patients with CAD.<br><br>METHODS: We conducted a cross-sectional large-database study using National Health and Nutrition Examination Survey (NHANES) data from years 1999-2020. The cohort included adults with at least a diagnosis of coronary heart disease, angina, and heart attack or two of the following: diabetes, high blood pressure, and high cholesterol. Analyses of clinical biomarkers compared probiotic to non-probiotic groups, between probiotic type groups, and between probiotic supplement strains.<br><br>RESULTS: Our cohort included 14,992 survey responders. After weighting, this sample represented 46,217,980 US adults. There were 4,062,022 adults exposed to probiotics, 763,288 to probiotic supplements and 3,179,008 to probiotic foods. Probiotic exposure was associated with lower A1c (p&#x202f;<&#x202f;0.001), lower triglycerides (p&#x202f;<&#x202f;0.001), lower ASCVD risk score (p&#x202f;=&#x202f;0.01) and higher HDL-C (p&#x202f;<&#x202f;0.001). Probiotic supplement exposure was associated with lower LDL-C (p&#x202f;=&#x202f;0.003) and total cholesterol (p&#x202f;=&#x202f;0.047).<br><br>CONCLUSION: Our study reinforces the beneficial association between probiotic ingestion and cardiovascular health in patients with existing atherosclerotic disease. Further studies to better determine potential mechanistic connections between the gut microbiota on cardiovascular risk factors is warranted.}, }
@article {pmid40093799, year = {2025}, author = {Chen, LK and Chang, SJ and Chen, CL and Yan, JH and Cherng, JH and Fan, GY and Meng, E and Hsu, YC}, title = {Dextrose Prolotherapy's Impact on the Urinary Microbiome in Interstitial Cystitis/Bladder Pain Syndrome.}, journal = {International journal of medical sciences}, volume = {22}, number = {7}, pages = {1516-1527}, pmid = {40093799}, issn = {1449-1907}, mesh = {Humans ; *Cystitis, Interstitial/drug therapy/microbiology/urine ; *Microbiota/drug effects ; *Glucose ; Female ; Middle Aged ; *RNA, Ribosomal, 16S/genetics ; Adult ; *Prolotherapy ; Male ; Administration, Intravesical ; Urinary Bladder/microbiology/drug effects ; Aged ; Bacteria/isolation &amp; purification/genetics/drug effects/classification ; Treatment Outcome ; }, abstract = {Background: Interstitial cystitis/bladder pain syndrome (IC/BPS) is a debilitating chronic condition affecting millions globally. Dextrose prolotherapy, a minimally invasive and safe treatment, has emerged as a potential way to promote tissue healing in these patients. This study investigates how dextrose prolotherapy impacts the urinary microbiome, aiming to uncover the underlying mechanisms involved in its effectiveness. Methods: Midstream urine samples from healthy controls and IC/BPS patients were collected before and after administering intravesical 10% dextrose injections. Microbiome profiling was conducted using 16S rRNA gene sequencing to analyze bacterial composition. Results: Significant differences in urinary microbiome diversity were observed between healthy controls and IC/BPS patients. Proteobacteria, Firmicutes, and Bacteroidota were more abundant in IC/BPS patients. Importantly, dextrose prolotherapy led to a decrease in harmful bacteria (Subgroup_22, Chryseolinea, and Ureaplasma) while enriching beneficial species such as Luteolibacter, Lactococcus, and L. lactis, correlating with improved clinical symptoms. Conclusions: Dextrose prolotherapy (DP) not only reduces the presence of harmful bacteria but also fosters the growth of beneficial microbes in IC/BPS patients. These findings suggest that the modulation of the urinary microbiome may be a key factor in its therapeutic success.}, }
@article {pmid40093639, year = {2025}, author = {Yeo, S and Lee, C and Park, H and Eo, K and Yeom, SC and Kim, H and Huh, CS}, title = {Overcrowding Stress in Livestock Production Alters Gut Microbiota Composition and Neuronal Nitric Oxide Synthase (nNOS) Expression in nNOS-HiBiT Knock-in Mouse Model.}, journal = {Food science of animal resources}, volume = {45}, number = {2}, pages = {598-613}, pmid = {40093639}, issn = {2636-0780}, abstract = {Overcrowding stress in livestock farming is a significant concern for animal health and livestock products such as meats, milk, and eggs. It affects gut health by altering microbiota and regulating neuronal nitric oxide synthase (nNOS). This study aimed to investigate the effects of overcrowding stress on the gut microbiota composition and nNOS expression. We generated an nNOS-HiBiT knock-in mouse model using the HiBiT system, a highly sensitive tool for accurately quantifying gene expression. Overcrowding stress was induced by housing twenty mice per cage (MPC20) and compared with a control group of two mice per cage (MPC2). Overcrowding stress increases nNOS levels in the hypothalamus and ileum and serum corticosterone levels. Gut microbial composition differed between the control and overcrowding stress-induced groups in the ileum, cecum, and colon. Specifically, Bifidobacterium and Akkermansia decreased in all three regions of MPC20, whereas Helicobacter in the ileum and colon and Parasuterella in the cecum increased in MPC20. Notably, Bifidobacterium consistently decreased when nNOS and corticosterone expression were used as covariates under overcrowding stress. These regional variations reflect the differential impact of overcrowding stress on the intestinal tract, indicating complex interactions through nNOS expression within the brain-gut-microbiome axis. Importantly, the addition of probiotic feed, particularly those containing Bifidobacterium, may counteract these decreases, leading to enhanced gut health and improved quality of livestock food products. This study enhances our understanding of the correlation between overcrowding stress and the gut microbiota, providing valuable data for improving the management environment in livestock farming.}, }
@article {pmid40093613, year = {2025}, author = {Huang, X and Yuan, T and Huang, Y and Qazi, IH and Liu, J}, title = {Analysis of causal pathogens of mulberry bacterial blight in samples collected from eight provinces of China using culturomics and metagenomic sequencing methods.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1517050}, pmid = {40093613}, issn = {1664-462X}, abstract = {Mulberry bacterial blight (MBB) is a complex and one of the devastating diseases of mulberry that causes serious reduction in the yield and quality of mulberry. In recent years, the transformation of sericulture industry, mulberry production system, and increasing seedling trade have resulted in the spread of MBB to different parts of China, posing a major economic threat to the farmers and industry. This study investigated the occurrence of MBB in eight provinces of China during years 2023 and 2024. The MBB disease samples were collected and the composition of the MBB pathogenic microbiome was analyzed by combining culturomics and metagenomic sequencing methods. A total of 498 bacterial strains were isolated and identified through culturomics, and then 109 suspected pathogen strains were preliminarily screened based on metagenomic sequencing data. Finally, 10 pathogens including, Pseudomonas syringae, P. fulva, P. fluorescens, Pantoea ananatis, Pectobacterium parvum, P. carotovorum, Flavobacterium fluviale, Citrobacter portucalensis, Klebsiella grimontii, Stenotrophomonas maltophilia, were identified through Koch's postulates. Based on the distribution pattern of pathogens and the changes in the microbiome community of mulberry following infection with P. syringae, we infer that P. syringae, and P. fulva are important pathogens of MBB. In addition, based on the analysis of meteorological data, different bacteria showed adaptability to different environments, leading to differences in the pathogens of MBB under different climate conditions and latitudes. The data presented herein provides a foundation for understanding the occurrence, spatial distribution and pathogenic mechanism of MBB and its major pathogens.}, }
@article {pmid40093612, year = {2025}, author = {Bonanomi, G and Idbella, A and Amoroso, G and Iacomino, G and Gherardelli, M and De Sio, A and Saccocci, F and Abd-ElGawad, AM and Moreno, M and Idbella, M}, title = {Agronomic impacts of chemically and microbiologically characterized compost tea in Mediterranean volcanic soils.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1524884}, pmid = {40093612}, issn = {1664-462X}, abstract = {Compost tea is widely recognized for its beneficial effects on crop growth and soil health. However, its efficacy varies depending on the composition of the feedstock and brewing conditions. This study investigates the chemical composition and agronomic impact of compost tea prepared from a commercial mixture of plant residues and animal manure. Standard chemical analyses, combined with solid-state [13]C CPMAS NMR spectroscopy, were employed to characterize the organic chemistry of the feedstock. High-throughput sequencing of bacterial and eukaryotic rRNA gene markers was used to profile the microbiota. Compost tea was applied to three crops, Allium cepa, Beta vulgaris, and Lactuca sativa, grown in protected Mediterranean environments on volcanic soils. The [13]C CPMAS NMR analysis revealed that the feedstock is predominantly composed of plant-derived tissues, including grass straw, nitrogen-fixing hay, and animal manure, with a significant presence of O-alkyl-C and di-O-alkyl-C regions typical of sugars and polysaccharides. Additionally, the chemical profile indicated the presence of an aliphatic fraction (alkyl-C), characteristic of lipids such as waxes and cutins. The compost tea microbiome was dominated by Pseudomonadota, with Pseudomonas, Massilia, and Sphingomonas being the most prevalent genera. Compost tea application resulted in significant yield increases, ranging from +21% for lettuce to +58% for onion and +110% for chard. Furthermore, compost tea application reduced slug damage and enhanced the shelf life of lettuce. These findings highlight the bio-stimulant potential of this standardized compost tea mixture across different vegetable crops.}, }
@article {pmid40093541, year = {2025}, author = {Toledo-Perona, R and Gómez-Martín, &#xc1; and Contreras, A and Toquet, M and Quereda, JJ and Esnal, A and González-Torres, P and Gomis, J}, title = {Metabarcoding analysis of the microbiota in flocks naturally infected by Coxiella burnetii: First description of the global microbiota in domestic small ruminants.}, journal = {One health (Amsterdam, Netherlands)}, volume = {20}, number = {}, pages = {100996}, pmid = {40093541}, issn = {2352-7714}, abstract = {This study investigates Q fever in sheep and goats, key reservoirs for human infection, by metabarcoding and comparing it with q-PCR and serology. Samples from 26 small ruminants (aborted and normal-delivery) and six males across three Q fever-affected herds were analyzed. In sheep herds, seropositivity was 50 and 80 % respectively, with Coxiella (C.) burnetii shedding detected vaginally in the second herd. In goats, 100 % seropositivity and 90 % C. burnetii detection were observed, with nasal and vaginal samples showing the highest detection rates. Metabarcoding revealed significant differences in alpha diversity, with greater richness in blood and evenness in milk from normal-delivery sheep and higher evenness in faeces from aborted sheep. Beta diversity showed distinct vaginal microbiota in normal-delivery females compared to aborted ones. Firmicutes was the most abundant phylum observed. Dominant genera included: Moraxella (nasal), Mycoplasma (blood), Streptococcus (milk), Ureaplasma (vaginal and preputial), Rikenellaceae RC9 gut group (faeces). Significant differences in bacterial composition, including infertility-linked vaginal pathogens, were found across female groups in all herds in the anatomical locations studied, revealing new species and tropisms. Moreover, taxonomic analysis identified C. burnetii in vaginal, milk and environmental samples. This first report of C. burnetii in the caprine nasal cavity suggests an underestimated tropism that may improve Q fever diagnosis. These findings underscore the need for herd-wide Q fever control measures, including males and normal-delivery females. Our findings contribute to new insights into the pathogen's impact on small ruminant microbiota and a novel approach to studying infectious diseases in this sector.}, }
@article {pmid40093272, year = {2025}, author = {Nie, LJ and Cheng, Z and He, YX and Yan, QH and Sun, YH and Yang, XY and Tian, J and Zhu, PF and Yu, JY and Zhou, HP and Zhou, XQ}, title = {Role of duodenal mucosal resurfacing in controlling diabetes in rats.}, journal = {World journal of diabetes}, volume = {16}, number = {3}, pages = {102277}, pmid = {40093272}, issn = {1948-9358}, abstract = {BACKGROUND: The duodenum plays a significant role in metabolic regulation, and thickened mucous membranes are associated with insulin resistance. Duodenal mucosal resurfacing (DMR), a new-style endoscopic procedure using hydrothermal energy to ablate this thickened layer, shows promise for enhancing glucose and lipid metabolism in type 2 diabetes (T2D) patients. However, the mechanisms driving these improvements remain largely unexplored.<br><br>AIM: To investigate the mechanisms by which DMR improves metabolic disorders using a rat model.<br><br>METHODS: Rats with T2D underwent a revised DMR procedure via a gastric incision using a specialized catheter to abrade the duodenal mucosa. The duodenum was evaluated using histology, immunofluorescence, and western blotting. Serum assays measured glucose, lipid profiles, lipopolysaccharide, and intestinal hormones, while the gut microbiota and metabolomics profiles were analyzed through 16S rRNA gene sequencing and ultra performance liquid chromatography-mass spectrum/mass spectrum, severally.<br><br>RESULTS: DMR significantly improved glucose and lipid metabolic disorders in T2D rats. It increased the serum levels of cholecystokinin, gastric inhibitory peptide, and glucagon-like peptide 1, and reduced the length and depth of duodenal villi and crypts. DMR also enhanced the intestinal barrier integrity and reduced lipopolysaccharide translocation. Additionally, DMR modified the gut microbiome and metabolome, particularly affecting the Blautia genus. Correlation analysis revealed significant links between the gut microbiota, metabolites, and T2D phenotypes.<br><br>CONCLUSION: This study illustrates that DMR addresses metabolic dysfunctions in T2D through multifaceted mechanisms, highlighting the potential role of the Blautia genus on T2D pathogenesis and DMR's therapeutic impact.}, }
@article {pmid40093270, year = {2025}, author = {Yang, YJ and Zhou, XC and Tian, HR and Liang, FX}, title = {Electroacupuncture relieves type 2 diabetes by regulating gut microbiome.}, journal = {World journal of diabetes}, volume = {16}, number = {3}, pages = {103032}, pmid = {40093270}, issn = {1948-9358}, abstract = {Cumulative studies have shown that the composition of the gut microbiome is strongly associated with the development of type 2 diabetes mellitus (T2DM). Electroacupuncture (EA) therapy has been reported to alleviate various diseases, including T2DM, by targeting specific acupuncture points and regulating metabolic homeostasis. A recent review published in the World Journal of Diabetes detailed the role of the gut microbiome in T2DM, discussing the role of therapeutic strategies developed to alleviate T2DM and its complications based on gut microbiome in ameliorating T2DM, as well as the effects of multiple diabetes medications on gut microbiome. However, the review did not elucidate the therapeutic role of EA therapy, a common non-pharmacological intervention for T2DM. This letter complemented the effect of EA therapy on glucose metabolism by adjusting the gut microbiome composition, which reveals the underlying mechanism of glucose lowering by EA therapy and provides a scientific basis for the application of EA therapy in clinical treatment.}, }
@article {pmid40093214, year = {2025}, author = {McDonald, T and Aqeel, A and Neubert, B and Bauer, A and Jiang, S and Osborne, O and Jiang, D and Bucardo, F and Gutiérrez, L and Zambrana, L and Jenkins, K and Gilner, J and Rodriguez, J and Lai, A and Smith, JP and Song, R and Ahsan, K and Ahmed, S and Soomro, SI and Umrani, F and Barratt, M and Gordon, J and Ali, A and Iqbal, N and Hurst, J and Martin, V and Shreffler, W and Yuan, Q and Brown, J and Surana, NK and Vilchez, S and Becker-Dreps, S and David, L}, title = {Dietary plant diversity predicts early life microbiome maturation.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.28.25323117}, pmid = {40093214}, abstract = {Between birth and adulthood, the human gut is colonized by a complex microbial community. Despite established links between the infant gut microbiome and health, knowledge is limited for how complementary feeding influences colonization. Using FoodSeq, an objective DNA-based dietary assessment technique, we analyzed 1,036 fecal samples from 729 children aged 0-3 years across countries in North America, Central America, Africa, and Asia. We detected a wide diversity of 199 unique plant food sequences, of which only eight staple foods were consistently present across all countries. Despite this variation in global diet, we identified universal trajectories in early life dietary exposure: weaning stage, which tracked with dietary diversity, emerged as the dominant dietary signature across populations. Still, dietary diversity did not correlate with gut microbial diversity. Instead, dietary diversity and weaning stage specifically predicted the abundance of adult-like bacterial taxa, including known fiber-degrading taxa, which colonized after age 1. Our findings support a two-stage model of microbiome maturation: an early phase dominated by milk-adapted taxa independent of complementary feeding, followed by a maturation phase where diet shapes adult-like microbiota colonization. This model suggests that tracking and promoting plant dietary diversity may support the timely emergence of an adult-like microbiome.}, }
@article {pmid40093191, year = {2025}, author = {Chtioui, N and Duval, C and St-Pierre, DH}, title = {The impact of an active lifestyle on markers of intestinal inflammation in Parkinson's disease: Preliminary findings.}, journal = {Clinical parkinsonism &amp; related disorders}, volume = {12}, number = {}, pages = {100301}, pmid = {40093191}, issn = {2590-1125}, abstract = {UNLABELLED: Alterations in the gut microbiota leading to intestinal inflammation and decreased levels of Short Chain Fatty Acids (SCFA) has been observed in Parkinson's disease (PD).<br><br>OBJECTIVE: The aim of this study was to compare these factors between physically active and less active people with PD.<br><br>METHODS: Stool, plasma samples and clinical data were collected from 35 people with PD (20 men and 15 women, mean age 66&#xa0;years). Their level of physical activity was retrospectively assessed using the International Physical Activity Questionnaire (IPAQ). Participants were divided into two groups based on their physical activity level: Active and Inactive. Both SCFA and calprotectin, a marker of intestinal inflammation, were respectively measured by GC-MS and ELISA, according to standardized, validated protocols.<br><br>RESULTS: Age, disease stage (Hoen &amp; Yahr) and Montreal Cognitive Assessments (MoCA) were similar between groups. Acetate, propionate, and butyrate levels were significantly higher in the Active group than in the Inactive group. In addition, fecal calprotectin was significantly lower in the Active group than in the Inactive group. The constipation values were significantly lower in the Active group.<br><br>CONCLUSION: Our results suggest that an active lifestyle with regular physical activity is beneficial in patients with PD, through increased production of SCFA by the gut microbiome, and reduced intestinal inflammation and constipation.}, }
@article {pmid40093185, year = {2025}, author = {France, MT and Chaudry, I and Rutt, L and Quain, M and Shirtliff, B and McComb, E and Maros, A and Alizadeh, M and Hussain, FA and Elovitz, MA and Relman, DA and Rahman, A and Brotman, RM and Price, J and Kassaro, M and Holm, JB and Ma, B and Ravel, J}, title = {VIRGO2: Unveiling the Functional and Ecological Complexity of the Vaginal Microbiome with an Enhanced Non-Redundant Gene Catalog.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.03.04.641479}, pmid = {40093185}, issn = {2692-8205}, abstract = {Despite the importance of the cervicovaginal microbiome, the mechanisms that govern its composition and drive its impact on host physiology remain poorly understood. This study expands our understanding of the function and ecology of the vaginal microbiome using VIRGO2, an enhanced non-redundant gene catalog comprising over 1.7 million well-annotated genes from body-site specific microbes and viruses. Analyses using VIRGO2 revealed novel insights, including the identification of previously uncharacterized vaginal bacteria, features of the vaginal mycobiome and phageome, and differential expression of bacterial carbohydrate catabolic genes. Constructed from over 2,500 metagenomes and 4,000 bacterial genomes, VIRGO2 broadens geographic representation and microbial diversity compared to its predecessor. This updated catalog enables more precise profiling of taxonomic and functional composition from metagenomic and metatranscriptomic datasets. VIRGO2 is a critical resource for integrative analyses of vaginal microbial communities and their interactions with host tissues, thereby enhancing our mechanistic understanding of vaginal health and disease.}, }
@article {pmid40093002, year = {2025}, author = {Wang, QW and Zheng, H and Yang, Y and Chang, X and Du, Z and Hang, ZN and Li, ZS and Liao, Z}, title = {Distinct microbial signatures and their predictive value in recurrent acute pancreatitis: insights from 5-region 16S rRNA gene sequencing.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1558983}, pmid = {40093002}, issn = {1664-3224}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Pancreatitis/microbiology/diagnosis ; Animals ; Humans ; *Recurrence ; Male ; Mice ; Female ; Middle Aged ; Prospective Studies ; Microbiota/genetics ; Adult ; Bacteria/genetics/classification/isolation &amp; purification ; Disease Models, Animal ; Predictive Value of Tests ; }, abstract = {BACKGROUND: Recurrent acute pancreatitis (RAP) poses significant clinical challenges, with 32.3% developing to chronic pancreatitis within 5 years. The underlying microbial factors contributing to RAP remain poorly understood. This study aims to identify blood microbial signatures associated with RAP and explore the potential microbial predictors for RAP.<br><br>METHODS: In this prospective cohort, 90 acute pancreatitis patients are classified into non-recurrent acute pancreatitis (NRAP, n=68) and RAP (n=22) groups based on the number of pancreatitis episodes. Microbial composition of blood samples is analyzed using 5-region (5R) 16S rRNA gene sequencing. Key microbial taxa and functional predictions are made. A random forest model is used to assess the predictive value of microbial features for RAP. The impact of Staphylococcus hominis (S. hominis) on RAP is further evaluated in an experimental mouse model.<br><br>RESULTS: Linear discriminant analysis effect size (LEfSe) analysis highlights significant microbial differences, with Paracoccus aminovorans, Corynebacterium glucuronolyticum and S. hominis being prominent in RAP. Functional predictions indicate enrichment of metabolic pathways in the RAP group. Random forest analysis identifies key microbial taxa with an AUC value of 0.759 for predicting RAP. Experimental validation shows that S. hominis exacerbates pancreatic inflammation in mice.<br><br>CONCLUSIONS: This study identifies distinct clinical and microbial features associated with RAP, emphasizing the role of specific bacterial taxa in pancreatitis recurrence. The findings suggest that microbial profiling could enhance the diagnosis and management of RAP, paving the way for personalized therapeutic approaches.}, }
@article {pmid40092793, year = {2025}, author = {Abakumov, S and Ruppeka-Rupeika, E and Chen, X and Bouwens, A and Leen, V and Dedecker, P and Hofkens, J}, title = {DeepMAP: Deep CNN Classifiers Applied to Optical Mapping for Fast and Precise Species-Level Metagenomic Analysis.}, journal = {ACS omega}, volume = {10}, number = {9}, pages = {9224-9232}, pmid = {40092793}, issn = {2470-1343}, abstract = {DNA optical mapping is a powerful technique commonly used for structural variant calling and genome assembly verification. Despite being inherently high-throughput, the method has not yet been applied to highly complex settings such as species identification in microbiome analysis due to the lack of alignment algorithms that can both assign large numbers of reads in minutes and handle large database size. In this work, we present a novel genomic classification pipeline based on deep convolutional neural networks for optical mapping data (DeepMAP), which can perform fast and accurate assignment of individual optical maps to their respective genomes. We furthermore achieve a superior performance of DeepMAP in the presence of evolutionary divergent sequences, making it robust to the presence of unknown strains within metagenomic samples. We evaluate DeepMAP on genomic DNA extracted from bacterial mixtures, reaching species-level resolution with true positive rates of around 75% and a false positive rate of less than 1%, with measured classification speeds significantly outpacing those of previously developed approaches for high-density optical mapping data alignment.}, }
@article {pmid40092662, year = {2025}, author = {Mahdavi, M and Kim, TY and Prévost, K and Balthazar, P and Gagné-Ouellet, V and Hus, IF and Duchesne, &#xc9; and Harvey, S and Gagnon, C and Laforest-Lapointe, I and Dumont, NA and Massé, E}, title = {Influence of CTG repeats from the human DM1 locus on murine gut microbiota.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {733-743}, pmid = {40092662}, issn = {2001-0370}, abstract = {Myotonic Dystrophy type 1 (DM1) is caused by a CTG repeat expansion in the 3' untranslated region of the DMPK gene. This expansion leads to the production of toxic RNA transcripts, which accumulate in the nucleus and interfere with normal RNA processing. DM1 affects a broad range of tissues and systems such as the skeletal muscle, the central nervous system, cardiac, visual, reproductive, and gastrointestinal (GI) system. GI dysfunction is a significant but poorly understood aspect of DM1. Particularly, it is unknown if there are alterations in the intestinal microbiome in DM1. Here, we used a transgenic humanized mouse model (DMSXL) to explore how the gut microbiome may be linked to GI issues in DM1. For this purpose, 68 stool samples from Homozygous, Heterozygous, and Wild-Type (WT) mice were collected. These samples were sequenced by MiSeq and analyzed with DADA2 to generate taxonomic profiles. Our analysis indicated that the overexpression of CTG repeats significantly influences the bacterial structure of the gut microbiome in Homozygous mice samples, especially in terms of the relative abundance of the Patescibacteria and Defferibacterota Phyla. These results provide valuable information about the gut microbiota structure thus improving the understanding of the role of these changes in the pathogenicity as well as GI problems of DM1 patients.}, }
@article {pmid40092654, year = {2025}, author = {JanssenDuijghuijsen, L and Fransen, K and Deng, R and Perenboom, C and de Wit, N and Hooiveld, G and van Trijp, M}, title = {How to Study the Effects of Dietary Lipids on the Small Intestinal Microbiome? Methodological Design and Evaluation of the Human HealThy fAt, haPpy mIcRobiome (TAPIR) Proof-of-Concept Study.}, journal = {Current developments in nutrition}, volume = {9}, number = {3}, pages = {104564}, pmid = {40092654}, issn = {2475-2991}, abstract = {BACKGROUND: Emerging evidence highlights the importance of the small intestinal microbiota in digestion and metabolism, underscoring the challenging need for human studies beyond fecal analyses.<br><br>OBJECTIVE: The TAPIR (acronym of "healthy fat, happy microbiome") proof-of-concept study was primarily designed to confirm the interaction between the small intestinal microbiota and dietary lipids in healthy adults with a challenge test. We also aimed to assess the impact of a plant-based mild-ketogenic preconditioning diet on microbiome composition and function. Here, we comprehensively describe our extensive study protocol and evaluate the study execution.<br><br>METHODS: Participants consumed an 8-day preconditioning diet, followed by a high-fat shake challenge test on day 9. During this test, fasting and postprandial small intestinal aspirates were collected every 20 min via a naso-intestinal catheter, and blood samples were collected hourly. Participants ingested small intestine aspiration capsules before (day 0), on day 6 of the preconditioning diet, and during the challenge test. Dietary compliance, capsule retrieval, sample collection, stool pattern, and gastrointestinal complaints were monitored to evaluate study execution.<br><br>RESULTS: Twenty adults with a mean age of 48 y (19-88 y) and a mean body mass index (BMI) of 24.3 kg/m[2] (19.5-30 kg/m[2]) consumed a preconditioning diet with a 96% compliance. There were no significant changes in gastrointestinal complaints and stool patterns during the study. Mean aspiration capsule retrieval rate was 94.7%, with mean sample weights per timepoint between 84.2 and 95.4 mg and median transit times between 32.8 and 49.3 h. The average success rate of aspirate collection by catheter was 49%, varying significantly between time points.<br><br>CONCLUSION: The dietary intervention was successful and well-tolerated. We sampled in the small intestine with capsules and catheters, each with its own (dis)advantages. The comprehensive description and evaluation of our study execution offer practical insights supporting future study designs in food-microbe interactions in the small intestine.The trial is registered at clinicaltrials.gov as NCT06064266.}, }
@article {pmid40092632, year = {2025}, author = {Pich, EM and Tarnanas, I and Brigidi, P and Collo, G}, title = {Gut Microbiome-Liver-Brain axis in Alcohol Use Disorder. The role of gut dysbiosis and stress in alcohol-related cognitive impairment progression: possible therapeutic approaches.}, journal = {Neurobiology of stress}, volume = {35}, number = {}, pages = {100713}, pmid = {40092632}, issn = {2352-2895}, abstract = {The Gut Microbiome-Liver-Brain Axis is a relatively novel construct with promising potential to enhance our understanding of Alcohol Use Disorder (AUD), and its therapeutic approaches. Significant alterations in the gut microbiome occur in AUD even before any other systemic signs or symptoms manifest. Prolonged and inappropriate alcohol consumption, by affecting the gut microbiota and gut mucosa permeability, is thought to contribute to the development of behavioral and cognitive impairments, leading to Alcohol-Related Liver Disorders and potentially progressing into alcoholic cirrhosis, which is often associated with severe cognitive impairment related to neurodegeneration, such as hepatic encephalopathy and alcoholic dementia. The critical role of the gut microbiota is further supported by the efficacy of FDA-approved treatments for hepatic encephalopathy in alcoholic cirrhosis (i.e., lactulose and rifaximin). To stimulate new research, we hypothesize that interactions between a maladaptive stress response and a constitutional predisposition to neurodegeneration underlie the progression of AUD to conditions of Alcohol-Related Clinical Concerns with severe cognitive impairment, which represent a significant and costly burden to society. Early identification of AUD individuals at risk for developing these conditions could help to prioritize integrated therapeutic interventions targeting different substrates of the Gut Microbiome-Liver-Brain axis. Specifically, addiction medications, microbiome modulators, stress-reducing interventions, and, possibly soon, novel agents that reduce hepatic steatosis/fibrosis will be discussed in the context of digitally supported integrated therapeutic approaches. The explicit goal of this AUD treatment performed on the early stage of the disorder would be to reduce the transition from AUD to those conditions of Alcohol-Related Common Clinical Concerns associated with severe cognitive impairment, a strategy recommended for most neurological neurodegenerative disorders.}, }
@article {pmid40092580, year = {2025}, author = {Li, G and Wang, Z and Wu, C and Wang, D and Han, I and Lee, J and Kaeli, DR and Dy, JG and Weinberger, KQ and Gu, AZ}, title = {Towards high-accuracy bacterial taxonomy identification using phenotypic single-cell Raman spectroscopy data.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf015}, pmid = {40092580}, issn = {2730-6151}, abstract = {Single-cell Raman Spectroscopy (SCRS) emerges as a promising tool for single-cell phenotyping in environmental ecological studies, offering non-intrusive, high-resolution, and high-throughput capabilities. In this study, we obtained a large and the first comprehensive SCRS dataset that captured phenotypic variations with cell growth status for 36 microbial strains, and we compared and optimized analysis techniques and classifiers for SCRS-based taxonomy identification. First, we benchmarked five dimensionality reduction (DR) methods, 10 classifiers, and the impact of cell growth variances using a SCRS dataset with both taxonomy and cellular growth stage labels. Unsupervised DR methods and non-neural network classifiers are recommended for at a balance between accuracy and time efficiency, achieved up to 96.1% taxonomy classification accuracy. Second, accuracy variances caused by cellular growth variance (<2.9% difference) was found less than the influence from model selection (up to 41.4% difference). Remarkably, simultaneous high accuracy in growth stage classification (93.3%) and taxonomy classification (94%) were achievable using an innovative two-step classifier model. Third, this study is the first to successfully apply models trained on pure culture SCRS data to achieve taxonomic identification of microbes in environmental samples at an accuracy of 79%, and with validation via Raman-FISH (fluorescence in situ hybridization). This study paves the groundwork for standardizing SCRS-based biotechnologies in single-cell phenotyping and taxonomic classification beyond laboratory pure culture to real environmental microorganisms and promises advances in SCRS applications for elucidating organismal functions, ecological adaptability, and environmental interactions.}, }
@article {pmid40092554, year = {2025}, author = {Staun-Ram, E and Volkowich, A and Miller, A}, title = {Immunotherapy-mediated modulation of the gut microbiota in multiple sclerosis and associations with diet and clinical response-the effect of dimethyl fumarate therapy.}, journal = {Therapeutic advances in neurological disorders}, volume = {18}, number = {}, pages = {17562864241306565}, pmid = {40092554}, issn = {1756-2856}, abstract = {BACKGROUND: Accumulating evidence supports a role of the microbiota in health and disease, including in multiple sclerosis (MS). How MS drugs affect the microbiota and whether this is part of their mode of action is yet unknown.<br><br>OBJECTIVES: To assess how dimethyl fumarate (DMF) affects the gut microbiota and whether the microbiota is associated with clinical response or adverse events (AEs) to DMF or diet.<br><br>DESIGN: An observational cohort study, in which the microbiota from 45 patients with relapsing-remitting MS pre-DMF initiation and following 6&#x2009;months of DMF therapy, and from 47 matched healthy controls, were compared, and associations with clinical and dietary data assessed.<br><br>DATA SOURCES AND METHODS: Microbial DNA was sequenced and analyzed using MicrobiomeAnalyst. The clinical response was assessed after 1-year DMF therapy based upon evidence of disease activity (relapse, &#x394;EDSS increase >1, or MRI activity compared to pre-treatment). Dietary data were obtained by food questionnaires.<br><br>RESULTS: Alterations in relative abundance of several microbes were identified post 6-month DMF therapy compared to pre-treatment, including an increase in Firmicutes, Lachnospiraceae, and Ruminococcaceae, while reduction in Bacteroidetes and Proteobacteria. Patients who showed disease activity within 1&#x2009;year from DMF initiation had pre-treatment higher abundance of Proteobacteria, Flavonifractor, and Acidaminococcaceae, while lower abundance of Firmicutes, Ruminococcaceae, Butyricicoccus, and Massiliprevotella massiliensis, compared to patients without disease activity. Patients who discontinued DMF therapy due to AEs had pre-treatment higher abundance of Proteobacteria, Bacteroidetes, Eggerthella, and Lachnoclostridium and lower abundance of Ruminococcaceae, Megamonas, and Holdemanella, among others. Differentially abundant microbes correlated with intake of several nutrients.<br><br>CONCLUSION: DMF immunotherapy is associated with modifications of the microbiota. The microbiota may affect the severity of AEs and the clinical response to DMF, and is potentially modulated by diet. Microbiota-based, personalized treatment approach, integrating pharmacotherapy with dietary components, carries potential to improved clinical outcome.}, }
@article {pmid40092263, year = {2025}, author = {Bhadani, JS and Agashe, VM and Shyam, A and Mukhopadhaya, J}, title = {The Gut Feeling: The Role of Gut Microbiome in Orthopedics.}, journal = {Journal of orthopaedic case reports}, volume = {15}, number = {3}, pages = {308-311}, pmid = {40092263}, issn = {2250-0685}, }
@article {pmid40092039, year = {2025}, author = {Zhang, N and Chen, X and Ren, T and Luo, J and Liang, J and Wang, ET and Shi, F}, title = {Differentiation of soil metabolic function and microbial communities between plantations and natural reforestation.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1544641}, pmid = {40092039}, issn = {1664-302X}, abstract = {Reforestation plays a vital role in restoring the soil degradation areas. However, the mechanisms by which different restoration approaches affect the soil properties and microbial communities remain unclear. Aiming to understand the interactions between plant species, soil properties, and microbial communities in different restoration approaches, we investigated the soil microbial community using nontargeted metabolomics to explore how the reforestation approach affects soil physicochemical properties, soil metabolites, and soil microbial communities. The results showed that the reforestation approach, soil layer, and their interactive effects significantly affected soil organic carbon, total nitrogen, dissolved organic carbon, available phosphorus concentrations, and root traits. The diversity and composition of bacterial and fungal communities in natural reforestation (NR) were different from those in artificial mono-plantations, and their network interactions were more significant in NR than in artificial plantations. A clear separation of metabolites between the artificial plantations and NR was observed in the soil metabolite analysis. Two pathways, linoleic acid metabolism, and valine, leucine, and isoleucine biosynthesis, were significantly regulated between the artificial mono-plantations and NR. Different soil traits were significantly correlated with dominant microbial taxa in the four reforestation approaches. 13-L-hydroperoxylinoleic acid, 13-S-hydroxyoctadecadienoic acid, homovanillin, and 9,10-epoxyoctadecenoic acid showed the highest correlation with the microbial taxa in the network. Partial least squares path modeling (PLS-PM) shows that root-mediated soil physicochemical properties were the primary factors affecting the bacterial community among the reforestation approaches. The soil fungal community is directly regulated by plant roots in the subsoil and indirectly regulated by the root-mediated physicochemical properties in the topsoil. We conclude that different reforestation approaches affect the soil microbial community through root and soil physicochemical properties rather than soil metabolites.}, }
@article {pmid40092031, year = {2025}, author = {Berbé, L and Machouart, M and Luc, A and Albuisson, E and Strazielle, C and Bisson, C}, title = {High prevalence of periodontal disease and periodontopathogen colonization in adults with autism spectrum disorder: a pilot study.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1552656}, pmid = {40092031}, issn = {1664-302X}, abstract = {INTRODUCTION: Alteration of the oral microbiome could potentially play a role in the etiology of certain patients with Autism Spectrum Disorder (ASD), similar to the established link between gut microbiota dysbiosis and ASD. Most studies have assessed oral microbiota in children only and few have explored the oral flora composition in adults with ASD.<br><br>METHODS: In our study, periodontal and dental status was evaluated in 30 adults with ASD using appropriate indices. Oral microbiota samples were collected in crevicular fluid and supra-gingival plaque at inflamed sites in each patient and analyzed using PCR for bacteria and qPCR for protozoa. Demographic data, co-morbidities, medication and oral hygiene habits were also collected.<br><br>RESULTS: A total of 86.7% of the patients recruited suffering from severe ASD had periodontal disease and 67% had a high level of supra-gingival plaque. Two major periodontopathogens belonging to the red complex, Treponema denticola and Tannerella forsythia, were both detected in the supra-gingival plaque of 86.2% of patients and in the gingival crevicular fluid of 80 and 86.7% of patients, respectively. Certain microorganisms were statistically more frequently detected in patients with digestive disorders and taking certain medications.<br><br>DISCUSSION: The oral microbiota composition of the adults with ASD showed significant differences compared to neurotypical individuals, particularly in the prevalence of the specific microorganisms P. gingivalis, T. tenax and E. gingivalis ST1. The detection frequency of periodontitis and periodontopathogens may have been underestimated due to the lack of cooperation of the adults with ASD during clinical examination and microbiota sampling. Further studies on larger cohorts are needed to consolidate these results to gain a better understanding of variations in oral microbiota.}, }
@article {pmid40091996, year = {2025}, author = {Chandra Nayak, S and Latha, PB and Kandanattu, B and Pympallil, U and Kumar, A and Kumar Banga, H}, title = {The Oral Microbiome and Systemic Health: Bridging the Gap Between Dentistry and Medicine.}, journal = {Cureus}, volume = {17}, number = {2}, pages = {e78918}, pmid = {40091996}, issn = {2168-8184}, abstract = {The oral microbiome, consisting of a mixture of bacteria, fungi, and viruses, is an important contributor to oral and systemic health. Microbial balance disruptions are associated with oral pathologies like dental caries and periodontitis as well as systemic diseases such as cardiovascular diseases, adverse pregnancy outcomes, and respiratory diseases. This review explores the mechanistic pathways linking oral dysbiosis to systemic inflammation, endothelial dysfunction, and immune modulation. The roles of key microbial species in health and disease are analyzed, with an emphasis on how hematogenous dissemination leads to systemic pathologies through inflammatory signaling. Also, advances in high throughput sequencing are discussed, as well as microbial diversity and its implications for diagnostics and therapeutics. The review highlights the potential of oral microbiota-targeted interventions to mitigate systemic diseases through dentistry and medicine integration, by throwing light on interdisciplinary strategies. Future work should focus on the evaluation of the mechanisms by which the oral microbiome plays a role in systemic diseases through the integration of multi-omics approaches such as metagenomics, transcriptomics, and metabolomics. Furthermore, clinical trials need to be designed in a way to evaluate the efficacy of microbiome-targeted therapies in the prevention of cardiovascular diseases, adverse pregnancy outcomes, and autoimmune disorders.}, }
@article {pmid40091902, year = {2025}, author = {Patel, P and Patel, B and Vyas, SD and Patel, MS and Hirani, T and Haque, M and Kumar, S}, title = {A Narrative Review of Periodontal Vaccines: Hope or Hype?.}, journal = {Cureus}, volume = {17}, number = {3}, pages = {e80636}, pmid = {40091902}, issn = {2168-8184}, abstract = {Globally, periodontal diseases, mainly driven by polymicrobial biofilms, are a widespread concern of social medicine due to their considerable incidence and tie-up to systemic disorders like diabetes, cardiovascular diseases, and complications during pregnancy. Traditional treatments focus on mechanical debridement and antimicrobial therapies, but these approaches have limitations, including recurrence and antibiotic resistance. Periodontal vaccines offer a promising alternative by targeting the immunological mechanisms underlying periodontal disease. This review explores the current state of periodontal vaccine development, highlighting key antigens, vaccine delivery systems, and preclinical and clinical advancements. Special emphasis is placed on antigen selection, host variability, immune tolerance, and future directions to overcome these barriers. This article highlights the advancements and challenges in periodontal vaccine research, offering insights into the capability of immunoprophylaxis as a groundbreaking way to manage periodontal diseases.}, }
@article {pmid40091861, year = {2025}, author = {Carrier, TJ and Elder, H and Macrander, J and Dimond, JL and Bingham, BL and Reitzel, AM}, title = {Symbiont-Mediated Metabolic Shift in the Sea Anemone Anthopleura elegantissima.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17722}, doi = {10.1111/mec.17722}, pmid = {40091861}, issn = {1365-294X}, support = {//National Science Foundation Graduate Research Fellowship Program/ ; //University of North Carolina at Charlotte/ ; //Western Washington University/ ; }, abstract = {Coral reefs and their photosynthetic algae form one of the most ecologically and economically impactful symbioses in the animal kingdom. The stability of this nutritional mutualism and this ecosystem is, however, at risk due to increasing sea surface temperatures that cause corals to expel their symbionts. Symbioses with these microeukaryotes have independently evolved multiple times, and non-coral cnidarians (e.g., sea anemones) serve as a valuable and insightful comparative system due to their ease of husbandry in the laboratory and their ability to shuffle different strains of their photosymbionts to acclimate to thermal conditions. This breadth of symbiont shuffling is exemplified by the sea anemone Anthopleura elegantissima, which naturally occurs in symbiosis with the dinoflagellate Breviolum muscatinei (formerly Symbiodinium) or the chlorophyte Elliptochloris marina as well as being aposymbiotic. Here, we assembled a draft genome and used multi-omics to characterise multiple physiological levels of each phenotype. We find that A. elegantissima has symbiont-specific transcriptional and metabolomic signatures, but a similar bacterial community dominated by a single Sphingomonas species that is commonly found in the cnidarian microbiome. Symbiosis with either eukaryotic symbiont resulted in differential gene expression and metabolic abundance for diverse processes spanning metabolism and immunity to reproduction and development, with some of these processes being unique to either symbiont. The ability to culture A. elegantissima with its phylogenetically divergent photosymbionts and perform experimental manipulations makes A. elegantissima another tractable sea anemone system to decode the symbiotic conversations of coral reef ecosystems and aid in wider conservation efforts.}, }
@article {pmid40091684, year = {2025}, author = {Nagano, F and Yoshimura, Y and Wakabayashi, H and Matsumoto, A and Shimazu, S and Shiraishi, A and Bise, T and Kido, Y and Hamada, T and Kuzuhara, A and Yoneda, K and Maeda, K}, title = {Gut microbiome diversity and nutrition intake in post-stroke patients.}, journal = {Geriatrics &amp; gerontology international}, volume = {}, number = {}, pages = {}, doi = {10.1111/ggi.70017}, pmid = {40091684}, issn = {1447-0594}, support = {22-4//Research Funding of Longevity Sciences/ ; 23K21639//Japan Society for the Promotion of Science/ ; }, abstract = {AIM: This study aimed to investigate the association between energy intake and gut microbiome diversity in patients following stroke.<br><br>METHODS: A cross-sectional study was conducted with 156 patients following stroke aged &#x2265;65&#x2009;years admitted to a rehabilitation hospital (mean age, 78&#x2009;&#xb1;&#x2009;7&#x2009;years; 69 women). Energy intake was calculated from average food consumption during the first week after admission. Gut microbiome diversity was assessed using three indices derived from 16S rRNA sequencing of stool samples: the Shannon index, operational taxonomic unit (OTU) richness and Faith's phylogenetic diversity (PD). Sex-stratified multiple linear regression analysis evaluated the association between energy intake and gut microbiome diversity, adjusting for confounders such as age, body weight, inflammation markers, nutritional status, and medication.<br><br>RESULTS: The study included 156 patients following stroke (mean age, 78&#x2009;&#xb1;&#x2009;7&#x2009;years; 69 women). The median energy intake was 1600 (interquartile range [IQR], 1400-1800] kcal/day for all participants. The median for gut microbiome diversity indices were Shannon index, 6.3 (IQR, 5.9-6.5); OTU richness, 217.3 (IQR, 181.9-258.1); and Faith's PD, 22.4 (IQR, 19.3-27.2). In women, energy intake was significantly positively associated with the Shannon index (&#x3b2;&#x2009;=&#x2009;0.233, P&#x2009;=&#x2009;0.026), OTU richness (&#x3b2;&#x2009;=&#x2009;0.228, P&#x2009;=&#x2009;0.036), and Faith's PD (&#x3b2;&#x2009;=&#x2009;0.212, P&#x2009;=&#x2009;0.038). In men, energy intake was significantly positively associated with the Shannon index (&#x3b2;&#x2009;=&#x2009;0.230, P&#x2009;=&#x2009;0.027), OTU richness (&#x3b2;&#x2009;=&#x2009;0.211, P&#x2009;=&#x2009;0.040), and Faith's PD (&#x3b2;&#x2009;=&#x2009;0.198, P&#x2009;=&#x2009;0.043).<br><br>CONCLUSIONS: Adequate energy intake may play an important role in preserving gut microbiome diversity in patients. Further longitudinal studies are needed to confirm these associations, clarify causality, and explore underlying mechanisms. Geriatr Gerontol Int 2025; &#x2022;&#x2022;: &#x2022;&#x2022;-&#x2022;&#x2022;.}, }
@article {pmid40091636, year = {2025}, author = {Lee, EH and Kwon, H and Park, SY and Park, JY and Hong, JH and Paeng, JW and Kim, YK and Han, PL}, title = {Sphingomonas Paucimobilis-derived Extracellular Vesicles Reverse Aβ-induced Dysregulation of Neurotrophic Factors, Mitochondrial Function, and Inflammatory Factors through MeCP2-mediated Mechanism.}, journal = {Experimental neurobiology}, volume = {34}, number = {1}, pages = {20-33}, doi = {10.5607/en25001}, pmid = {40091636}, issn = {1226-2560}, abstract = {Recent studies have shown an increased abundance of Sphingomonas paucimobilis, an aerobic, Gram-negative bacterium with a distinctive cell envelope rich in glycosphingolipids, within the gut microbiome of individuals with Alzheimer Disease (AD). However, the fact that S. paucimobilis is a well-known pathogen associated with nosocomial infections presents a significant challenge in investigating whether its presence in the gut microbiome is detrimental or beneficial, particularly in the context of AD. This study examines the impact of S. paucimobilis-derived extracellular vesicles (Spa-EV) on Aβ-induced pathology in cellular and animal models of AD. Microarray analysis reveals that Spa-EV treatment modulates Aβ42-induced alterations in gene expression in both HT22 neuronal cells and BV2 microglia cells. Among the genes significantly affected by Spa-EV, notable examples include Bdnf, Nt3/4, and Trkb, which are key players of neurotrophic signaling; Pgc1α, an upstream regulator of mitochondrial biogenesis; Mecp2 and Sirt1, epigenetic factors that regulate numerous gene expressions; and Il1β, Tnfα, and Nfκb-p65, which are associated with neuroinflammation. Remarkably, Spa-EV effectively reverses Aβ42-induced alteration in the expression of these genes through the upregulation of Mecp2. Furthermore, administration of Spa-EV in Tg-APP/PS1 mice restores the reduced expression of neurotrophic factors, Pgc1α, MeCP2, and Sirt1, while suppressing the increased expression of proinflammatory genes in the brain. Our results indicate that Spa-EV has the potential to reverse Aβ-induced dysregulation of gene expression in neuronal and microglial cells. These alterations encompass those essential for neurotrophic signaling and neuronal plasticity, mitochondrial function, and the regulation of inflammatory processes.}, }
@article {pmid40091547, year = {2025}, author = {Solek, P and Nurfitri, E and Sahril, I and Prasetya, T and Rizqiamuti, AF and Burhan, B and Rachmawati, I and Gamayani, U and Rusmil, K and Chandra, LA and Afriandi, I and Gunawan, K}, title = {The Role of Artificial Intelligence for Early Diagnostic Tools of Autism Spectrum Disorder: A Systematic Review.}, journal = {Turkish archives of pediatrics}, volume = {60}, number = {2}, pages = {126-140}, doi = {10.5152/TurkArchPediatr.2025.24183}, pmid = {40091547}, issn = {2757-6256}, abstract = {Objective: Autism Spectrum Disorder (ASD) is a complex neurodevelopmental condition characterized by challenges in social communication and repetitive behaviors. This systematic review examines the application of artificial intelligence (AI) in diagnosing ASD, focusing on pediatric populations aged 0-18 years. Materials and methods: A systematic review was conducted following Preferred Reporting Items for Systematic Reviews and Meta-Analyses 2020 guidelines. Inclusion criteria encompassed studies applying AI techniques for ASD diagnosis, primarily evaluated using metriclike accuracy. Non-English articles and studies not focusing on diagnostic applications were excluded. The literature search covered PubMed, ScienceDirect, CENTRAL, ProQuest, Web of Science, and Google Scholar up to November 9, 2024. Bias assessment was performed using the Joanna Briggs Institute checklist for critical appraisal. Results: The review included 25 studies. These studies explored AI-driven approaches that demonstrated high accuracy in classifying ASD using various data modalities, including visual (facial, home videos, eye-tracking), motor function, behavioral, microbiome, genetic, and neuroimaging data. Key findings highlight the efficacy of AI in analyzing complex datasets, identifying subtle ASD markers, and potentially enabling earlier intervention. The studies showed improved diagnostic accuracy, reduced assessment time, and enhanced predictive capabilities. Conclusion: The integration of AI technologies in ASD diagnosis presents a promising frontier for enhancing diagnostic accuracy, efficiency, and early detection. While these tools can increase accessibility to ASD screening in underserved areas, challenges related to data quality, privacy, ethics, and clinical integration remain. Future research should focus on applying diverse AI techniques to large populations for comparative analysis to develop more robust diagnostic models.}, }
@article {pmid40091534, year = {2025}, author = {Lu, YM and Lu, JQ and Zhao, Q and Chen, J and Xiong, JB}, title = {Pathogenic mechanisms of Enterocytozoon hepatopenaei through the parasite-gut microbiome-shrimp (Litopenaeus vannamei) physiology axis.}, journal = {Zoological research}, volume = {46}, number = {2}, pages = {401-413}, doi = {10.24272/j.issn.2095-8137.2024.411}, pmid = {40091534}, issn = {2095-8137}, mesh = {Animals ; *Penaeidae/microbiology ; *Gastrointestinal Microbiome/physiology ; *Enterocytozoon/physiology/genetics ; Host-Parasite Interactions ; }, abstract = {The progressive impact of Enterocytozoon hepatopenaei (EHP) infection on gut microbial function in Litopenaeus vannamei remains poorly understood beyond static comparisons between healthy and infected individuals. To close this knowledge gap, metagenomic sequencing was used to characterize the gut microbiomes of normal, long, medium, and short-sized adult shrimp categorized by increasing severity of infection. EHP infection suppressed digestive activity while inducing immune responses compared with healthy shrimp. Increasing infection severity was associated with a gradual decline in gut α-diversity and an expansion of potential pathogens and virulence factors (VFs). In addition, dysbiosis in gut microbiota composition and function, as well as reduced network stability among differential species, intensified with infection severity. Accordingly, we identified 24 EHP-discriminatory species that contributed an overall 83.3% accuracy in diagnosing infection severity without false negatives. Functional pathway analysis revealed significant suppression of metabolic, degradative, and biosynthetic processes in EHP-infected shrimp compared with healthy controls. Among them, map00630 glyoxylate and dicarboxylate metabolism and map00280 valine, leucine and isoleucine degradation were consistently depleted in infected individuals, thereby impairing their digestive function and anti-inflammatory responses. Additionally, EHP infection diversified VFs directly affecting shrimp gut microbiome. These findings support a conceptual model linking EHP pathogenesis to the parasite-gut microbiome-shrimp physiology axis.}, }
@article {pmid40091533, year = {2025}, author = {Sha, HN and Lu, YM and Zhan, PP and Chen, J and Qiu, QF and Xiong, JB}, title = {Beneficial effects of probiotics on Litopenaeus vannamei growth and immune function via the recruitment of gut Rhodobacteraceae symbionts.}, journal = {Zoological research}, volume = {46}, number = {2}, pages = {388-400}, doi = {10.24272/j.issn.2095-8137.2024.364}, pmid = {40091533}, issn = {2095-8137}, mesh = {Animals ; *Probiotics/pharmacology/administration &amp; dosage ; *Penaeidae/immunology/microbiology/growth &amp; development ; *Gastrointestinal Microbiome/drug effects ; *Symbiosis ; *Rhodobacteraceae ; }, abstract = {Probiotic supplementation enhances the abundance of gut-associated Rhodobacteraceae species, critical symbionts contributing to the health and physiological fitness of Litopenaeus vannamei. Understanding the role of Rhodobacteraceae in shaping the shrimp gut microbiota is essential for optimizing probiotic application. This study investigated whether probiotics benefit shrimp health and fitness via the recruitment of Rhodobacteraceae commensals in the gut. Probiotic supplementation significantly enhanced feed conversion efficiency, digestive enzyme activity, and immune responses, thereby promoting shrimp growth. Additionally, probiotics induced pronounced shifts in gut microbial composition, enriched gut Rhodobacteraceae abundance, and reduced community variability, leading to a more stable gut microbiome. Network analysis revealed that the removal of Rhodobacteraceae nodes disrupted gut microbial connectivity more rapidly than the removal of non-Rhodobacteraceae nodes, indicating a disproportionate role of Rhodobacteraceae in maintaining network stability. Probiotic supplementation facilitated the migration of Rhodobacteraceae taxa from the aquatic environment to the shrimp gut while reinforcing deterministic selection in gut microbiota assembly. Transcriptomic analysis revealed that up-regulation of amino acid metabolism and NF-κB signaling pathways was positively correlated with Rhodobacteraceae abundance. These findings demonstrate that probiotic supplementation enriches key Rhodobacteraceae taxa, stabilizes gut microbial networks, and enhances host digestive and immune functions, ultimately improving shrimp growth performance. This study provides novel perspectives on the ecological and molecular mechanisms underlying the beneficial effects of probiotics on shrimp fitness.}, }
@article {pmid40091493, year = {2025}, author = {Wang, J and Li, D and Wu, R and Feng, D}, title = {Cutting-Edge Advancements in the Antibiotics-Gut Microbiota-Urinary Tumour Axis.}, journal = {Cell proliferation}, volume = {}, number = {}, pages = {e70023}, doi = {10.1111/cpr.70023}, pmid = {40091493}, issn = {1365-2184}, abstract = {Gut microbiota regulates urological tumors. Antibiotics induce dysbiosis, altering tumor progression/therapy: reducing carcinogen metabolism but impairing immunity. Specific bacteria enhance immune responses and combat endocrine resistance. Future research should unravel microbiota-cancer links and develop microbiome-targeted therapies to optimize outcomes while preserving diversity.}, }
@article {pmid40091479, year = {2025}, author = {Dong, L and Zhang, H and Kang, Y and Wang, F and Bai, T and Yang, Y}, title = {NLRP3 and Gut-Liver Axis: New Possibility for the Treatment of Alcohol-Associated Liver Disease.}, journal = {Journal of gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jgh.16935}, pmid = {40091479}, issn = {1440-1746}, support = {2024-MSLH-010//Natural Science Foundation of Liaoning Province/ ; 81700523//National Natural Science Foundation of China/ ; 81900532//National Natural Science Foundation of China/ ; DLUXK-2024-QN-012//Interdisciplinary project of Dalian University/ ; }, abstract = {Alcohol-associated liver disease (ALD) is one of the most prevalent chronic diseases worldwide, with persistently high morbidity and mortality rates. Previous studies have identified NLRP3 inflammasome as a class of receptors of intracellular intrinsic immunity. These receptors can be activated by both intrinsic and extracellular danger signals, leading to the release of downstream pro-inflammatory factors, including interleukin IL-1β and IL-18. These vesicles are critical for maintaining host defense. Concurrently, researchers have identified a close relationship between the microbiome, gut-liver axis, and NLRP3 inflammasome with ALD. Consequently, the present study focus on the structure and activation of the NLRP3 inflammasome, the gut-liver axis, and intestinal microecological regulation, as well as the relationship between bile acid metabolism and the gut-liver axis. The objective of this study is to provide a foundation of knowledge and references for the development of targeted therapeutic interventions of ALD that are informed by the dynamic interplay between the NLRP3 inflammasome and the gut-liver axis.}, }
@article {pmid40091465, year = {2025}, author = {Velmurugan, S and Ganesan, K and Rajasundaram, A and Thangam, C and Cyril, R and Subbaraj, GK}, title = {Nanoparticles and the Vaginal Microbiota: Diagnostic and Therapeutic Innovations in Human Papilloma Virus-associated Cervical Cancer - A Systematic Review.}, journal = {The Nigerian postgraduate medical journal}, volume = {32}, number = {1}, pages = {1-13}, doi = {10.4103/npmj.npmj_265_24}, pmid = {40091465}, issn = {1117-1936}, mesh = {Humans ; *Uterine Cervical Neoplasms/diagnosis/virology/therapy/microbiology ; Female ; *Papillomavirus Infections/diagnosis/complications ; *Nanoparticles ; *Microbiota ; *Vagina/microbiology/virology ; Dysbiosis ; Drug Delivery Systems ; Human Papillomavirus Viruses ; }, abstract = {Cervical cancer (CC) remains a significant global health challenge, with the interplay between microbiome and cancer progression becoming increasingly evident. A comprehensive literature search was conducted across multiple databases, including Embase, NCBI, Google Scholar, Elsevier, Science Direct and PubMed, utilising the specific keywords such as 'cervical cancer', 'cervical microbiome', 'vaginal microbiome', 'Human papillomavirus', 'nanoparticles', 'drug delivery' and 'dysbiosis'. Studies published over the past 15 years were reviewed. A total of 400 articles were identified and 65 research articles were finally included. This systematic approach identified relevant studies, enabling an in-depth analysis of microbial species, such as Parabacteroides, Escherichia, Shigella, Gardnerella and Fusobacterium which are recognised as the potential biomarkers for CC diagnosis and progression. Dysbiosis is characterised by a reduction in helpful bacteria and a proliferation of harmful ones. It is linked to chronic inflammation and human papillomavirus infection, both of which facilitate the CC progression. Advanced nanotechnology presents innovative therapeutic options for CC treatment, enhancing drug delivery systems and targeting tumour cells more effectively. Moreover, incorporating nanocarriers into treatment regimens aims to improve the bioavailability and efficacy of existing therapies, potentially transforming the clinical approaches to CC management. This review highlights the dual role of the microbiome as both a diagnostic and prognostic biomarker and elucidates the potential of nanotechnology in optimising treatment strategies, advocating for further research on microbial interactions in cancer pathology.}, }
@article {pmid40091425, year = {2025}, author = {Lai, Y and Shen, H and Wang, S and Ouyang, Y and Zhang, X and Hu, B and Zhang, X and Li, G and Xu, L and Zhao, J}, title = {Hydrogel-Transformable Probiotic Powder for Targeted Eradication of Helicobacter pylori with Enhanced Gastric Mucosal Repair and Microbiota Preservation.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2500478}, doi = {10.1002/advs.202500478}, pmid = {40091425}, issn = {2198-3844}, abstract = {Lactobacillus reuteri (L. reuteri) therapies represent a potentially effective approach to eradicating Helicobacter pylori (H. pylori). However, the difficulty in bacterial viability preservation and harsh gastric environment compromises the survival and on-target delivery of L. reuteri. This study presents a novel bacterium-mediated bacterial elimination strategy using an edible L. reuteri@HTP probiotic powder for targeted bacterial elimination. The probiotic powder is obtained by grinding a lyophilized hydrogel composed of L. reuteri, hyaluronic acid (HA), tannic acid (TA), and polyvinyl alcohol (PVA). Upon contact with water, the powder quickly transforms into a hydrogel, enhancing L. reuteri's survival in the harsh gastric environment and ensuring selective release at H. pylori-infected inflammatory sites. L. reuteri targets and reduces H. pylori colonization while secreting reuterin to eliminate the bacteria. Additionally, TA's antioxidant properties help alleviate inflammation, and HA supports gastric mucosal repair. L. reuteri@HTP powder preserves the integrity of the gut microbiota, facilitating the restoration of a healthy microbiome. In particular, the probiotic powder remains stable at room temperature for at least six months, providing a promising alternative to traditional antibiotics for H. pylori treatment. This strategy combines targeted eradication, mucosal healing, and microbiome restoration, offering a new approach to treating gastric infections.}, }
@article {pmid40091309, year = {2025}, author = {Li, H and Zhang, L and Zong, F and Tian, B and Chen, X and Wang, H}, title = {Microbiome-Metabolomics Analysis of the Impacts of Balantidium Coli Infection in Rhesus Monkeys (Macaca mulatta).}, journal = {Journal of medical primatology}, volume = {54}, number = {2}, pages = {e70013}, doi = {10.1111/jmp.70013}, pmid = {40091309}, issn = {1600-0684}, support = {31960121//National Natural Science Foundation of China/ ; 202001BC070001//Natural Science Foundation of Yunnan Province/ ; 202102AA100053//Natural Science Foundation of Yunnan Province/ ; }, mesh = {Animals ; *Macaca mulatta ; *Balantidiasis/veterinary/metabolism ; *Balantidium/metabolism ; *Gastrointestinal Microbiome ; *Monkey Diseases/microbiology/parasitology/metabolism ; *Feces/microbiology/parasitology/chemistry ; Metabolomics ; Male ; Female ; Metabolome ; Gas Chromatography-Mass Spectrometry/veterinary ; }, abstract = {Balantidium coli (B. coli) is a prevalent intestinal parasite in monkeys, significantly impacting their health. Previous studies have demonstrated that B. coli infection in pigs leads to severe dysregulation of the gut microbiota. However, there has been no report on the alterations in fecal microbiota and metabolites in rhesus monkeys infected with B. coli. In order to investigate the differences in gut microbiota and metabolites between healthy rhesus monkeys and those infected with B. coli, we conducted gene sequencing and gas chromatography-mass spectrometry (GC-MS) analysis of fecal samples from 6 healthy rhesus monkeys and 5 rhesus monkeys infected with B. coli. The results revealed significant differences in the composition of gut microbiota between rhesus monkeys infected with B. coli and healthy ones (p < 0.01). The abundance of Campylobacterota was significantly increased (p < 0.01), while the abundance of Bacteroidota was significantly decreased (p < 0.05). Prevotella 9 was the dominant genus in both groups, showing a significant increase in the infected group (p < 0.05). At the species level, Brachyspira hampsonii was significantly increased in the infected group (p < 0.01), whereas Prevotella copri, which was the dominant species in both groups, showed a significant decrease in the infected group (p < 0.05). Metabolomics studies indicated a significant decrease in levels of metabolites such as dihydrolipoamide, 9(Z),11(E)-Conjugated Linoleic Acid, and 8,9-DiHETrE within fecal samples from rhesus monkeys infected with B. coli (p < 0.05). Correlation analysis of the microbiome and metabolome suggested a close relationship between differential microbiota and metabolites. In conclusion, this study suggests that the colonization of B. coli is associated with dysbiosis of the monkey gut microbiota. This study provides a new insight that using intestinal microbes instead of antibiotics to treat balantidiosis can also serve as a reference for further research on the relationship between gut microbiota and metabolomics in host infections by other protozoa.}, }
@article {pmid40091084, year = {2025}, author = {Streb, LM and Cholewińska, P and Gschwendtner, S and Geist, J and Rath, S and Schloter, M}, title = {Age matters: exploring differential effects of antimicrobial treatment on gut microbiota of adult and juvenile brown trout (Salmo trutta).}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {28}, pmid = {40091084}, issn = {2524-4671}, support = {03F090fA//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 03F090fA//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 03F090fA//Bundesministerium f&#xfc;r Bildung und Forschung/ ; 03F090fA//Bundesministerium f&#xfc;r Bildung und Forschung/ ; }, abstract = {BACKGROUND: Antibiotics and antiparasitics are essential tools in controlling infectious disease outbreaks in commercial aquaculture. While the negative effects of antimicrobials on the gut microbiome of various farmed fish species are well documented, the influence of underlying host factors, such as age, on microbiome responses remains poorly understood. This is especially evident for peracetic acid, whose impact on the gut microbiome has not yet been studied. Understanding how microbiome dynamics vary by host age is critical to improving antibiotic stewardship in aquaculture. In this study, juvenile and sexually mature brown trout (Salmo trutta) were used as a model to investigate the age-dependent effects of florfenicol and peracetic acid on the gut microbiome using a 16S rRNA metabarcoding approach.<br><br>RESULTS: Fish age significantly shaped taxonomic composition and microbial co-occurrence network structure of the gut microbiome, regardless of treatment. Juvenile trout exhibited greater microbiome volatility and a stronger response to both florfenicol and peracetic acid compared to adult fish, with disruptions persisting up to 11&#xa0;days post-treatment. Temporal dynamics were also evident, with microbial shifts characterized by a decline in beneficial commensals like Cetobacterium and Lactococcus. Although overall abundance recovered by 18&#xa0;days post-treatment, network positions of key microbial community members remained altered, particularly in juvenile fish. Opportunistic pathogens, including Aeromonas and Streptococcus, were enriched and assumed more central roles within the microbial networks in treated fish.<br><br>CONCLUSION: The initial composition of the gut microbiome in brown trout is strongly influenced by fish age, which in turn affects the microbiome's response to antibiotic disruption. Juveniles displayed higher susceptibility to microbiome perturbation, and although recovery was observed at the community level, network properties remained altered. This study also provides the first evidence that external peracetic acid application can disrupt gut microbial communities. Since compositional shifts are often linked to functional alterations, even short-term disruptions may have important consequences for host health in developing fish. These findings emphasize the importance of considering gut microbial community structure in relation to fish age in aquaculture management practices.}, }
@article {pmid40091072, year = {2025}, author = {Liu, Y and Liu, J and Ren, R and Xin, Z and Luo, Y and Chen, Y and Huang, C and Liu, Y and Yang, T and Wang, X}, title = {Short-term and long-term high-fat diet promote metabolic disorder through reprogramming mRNA m[6]A in white adipose tissue by gut microbiota.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {75}, pmid = {40091072}, issn = {2049-2618}, support = {32330098//National Natural Science Foundation of China/ ; 2022R52023//Science and technology innovation leading talent project of Zhejiang Province/ ; 2023YFD1301303//National Key Research and Development Program of China/ ; }, mesh = {*Gastrointestinal Microbiome ; *Diet, High-Fat/adverse effects ; Animals ; *Adipose Tissue, White/metabolism ; Mice ; Male ; *Metabolic Diseases/metabolism/microbiology/genetics ; *RNA, Messenger/genetics/metabolism ; *Mice, Inbred C57BL ; Endogenous Retroviruses/genetics ; Fecal Microbiota Transplantation ; Long Interspersed Nucleotide Elements/genetics ; Epigenesis, Genetic ; Adenosine/analogs &amp; derivatives ; }, abstract = {BACKGROUND: Although short-term high-fat diet (S-HFD) and long-term high-fat diet (L-HFD) induce metabolic disorder, the underlying epigenetic mechanism is still unclear.<br><br>RESULTS: Here, we found that both 4&#xa0;days of S-HFD and 10&#xa0;weeks of L-HFD increased mRNA m[6]A level in epididymal white adipose tissue (eWAT) and impaired metabolic health. Interestingly, S-HFD activated transposable elements (TEs), especially endogenous retroviruses (ERVs) in eWAT, while L-HFD activated long interspersed elements (LINEs). Subsequently, we demonstrated that both S-HFD and L-HFD increased m[6]A level of Ehmt2 and decreased EHMT2 protein expression and H3K9me2 level, accounting for activation of ERVs and LINEs. Overexpression of EHMT2 in eWAT or inhibition of ERVs and LINEs by antiviral therapy improved metabolic health under HFD feeding. Notably, we found that both short-term and long-term HFD feeding increased Fimicutes/Bacteroidota ratio and decreased the gut microbiome health index. Fecal microbiota transplantation (FMT) experiments demonstrated that gut microbiota from S-HFD and L-HFD was responsible for increased m[6]A level in eWAT, resulting in glucose intolerance and insulin insensitivity. Furthermore, we identified that both S-HFD and L-HFD increased the abundance of the gut microbial metabolite homogentisic acid (HGA), and HGA level was positively correlated with unclassified_f__Lachnospiraceae which was both increased in S-HFD and L-HFD feeding mice. Administration of HGA increased the m[6]A level of Ehmt2 and decreased the EHMT2 protein expression and H3K9me2 level in eWAT, leading to metabolic disorder in mice.<br><br>CONCLUSIONS: Together, this study reveals a novel mechanism that S-HFD and L-HFD induce metabolism disorder through gut microbiota-HGA-m[6]A-Ehmt2-ERV/LINE signaling. These findings may provide a novel insight for prevention and treatment of metabolism disorder upon short-term or long-term dietary fat intake. Video Abstract.}, }
@article {pmid40091070, year = {2025}, author = {Lin, YC and Wu, CC and Li, YE and Chen, CL and Lin, CR and Ni, YH}, title = {Full-length 16S rRNA Sequencing Reveals Gut Microbiome Signatures Predictive of MASLD in children with obesity.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {146}, pmid = {40091070}, issn = {1471-2180}, support = {MOST 111-2314-B-418-010//National Science and Technology Council/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; Child ; Female ; Male ; Case-Control Studies ; *Pediatric Obesity/microbiology ; Bacteria/genetics/classification/isolation &amp; purification ; Adolescent ; Feces/microbiology ; High-Throughput Nucleotide Sequencing ; Non-alcoholic Fatty Liver Disease/microbiology ; Obesity/microbiology/complications ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: The gut microbiota plays a crucial role in metabolic dysfunction-associated steatotic liver disease (MASLD). Next-generation sequencing technologies are essential for exploring the gut microbiome. While recent advancements in full-length 16S (FL16S) rRNA sequencing offer better taxonomic resolution, whether they establish stronger associations with the risk of MASLD remains to be determined.<br><br>METHOD: This study utilized long-read FL16S and short-read V3-V4 16S rRNA sequencing to profile gut microbiome compositions in age-, sex-, and BMI-matched case-control pairs of obese children with and without MASLD. A random forest predictive model was employed, using gut-microbiota features selected based on the top 35 most abundant taxa or a linear discriminant analysis score greater than 3. The model's performance was evaluated by comparing the area under the receiver operating characteristic curve (AUC) through a tenfold cross-validation method.<br><br>RESULTS: Subjects with MASLD exhibited significantly elevated serum alanine aminotransferase, triglycerides, and homeostasis model assessment of insulin resistance levels compared to controls. At the genus level, the gut microbiome compositions detected by both FL16S and V3-V4 sequencing were similar, predominantly comprising Phocaeicola and Bacteroides, followed by Prevotella, Bifidobacterium, Parabacteroides, and Blautia. The AUC for the model based on FL16S sequencing data (86.98%) was significantly higher than that based on V3-V4 sequencing data (70.27%), as determined by DeLong's test (p&#x2009;=&#x2009;0.008).<br><br>CONCLUSION: FL16S rRNA sequencing data demonstrates stronger associations with the risk of MASLD in obese children, highlighting its potential for real-world clinical applications.}, }
@article {pmid40090966, year = {2025}, author = {Ngambia Freitas, FS and De Vooght, L and Njiokou, F and Abeele, JVD and Bossard, G and Tchicaya, B and Corrales, RM and Ravel, S and Geiger, A and Berthier-Teyssedre, D}, title = {Evaluation of two candidate molecules-TCTP and cecropin-on the establishment of Trypanosoma brucei gambiense into the gut of Glossina palpalis gambiensis.}, journal = {Insect science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1744-7917.70012}, pmid = {40090966}, issn = {1744-7917}, support = {//Institut&#xa0;de Recherche pour le D&#xe9;veloppement/ ; //Labex ParaFrap/ ; //Research Infrastructures for the control of vector-borne diseases/ ; 731060//European Union's Horizon 2020/ ; }, abstract = {Trypanosomiasis, transmitted by tsetse flies (Glossina spp.), poses a significant health threat in 36 sub-Saharan African countries. Current control methods targeting tsetse flies, while effective, allow reinfestation. This study investigates paratransgenesis, a novel strategy to engineer symbiotic bacteria in tsetse flies, Sodalis glossinidius, to deliver anti-trypanosome compounds. Disrupting the trypanosome life cycle within the fly and reducing parasite transmission could offer a sustainable solution for trypanosomiasis control. In this context, we tested the effect of cecropin, reported to be lethal for Trypanosoma cruzi (Chagas disease) and TbgTCTP (Translationally Controlled Tumor Protein from Trypanosoma brucei gambiense), previously reported to modulate the growth of bacteria isolated from the fly microbiome, to delay the first peak of parasitemia and the death of trypanosome-infected mice. We have successfully cloned and transfected the genes encoding the two proteins into Sodalis strains. These Sodalis recombinant strains (recSodalisTbgTCTP and recSodaliscecropin) have been then microinjected into the L3 larval stage of Glossina palpalis gambiensis flies. The stability of the cloned genes was checked up to the 20th day after microinjection of recSodalis. The rate of fly emergence from untreated pupae was 95%; it was reduced by nearly 50% due to the mechanical injury caused by microinjection. It decreased to nearly 7% when larvae were injected with recSodalisTbgTCTP, which suggests TCTP could have a lethal impact to larvae development. When challenged with T. brucei gambiense, a slightly lower, but statistically non-significant, infection rate was recorded in flies harboring recSodaliscecropin compared to control flies. The effect of recSodalisTbgTCTP could not be measured due to the very low rate of fly emergence after corresponding treatment of the larvae. The results do not allow to conclude on the effect of cecropin or TCTP, delivered by para-transgenesis into the fly's gut, on the fly infection by the trypanosome. Nevertheless, the results are encouraging insofar as the technical approach works on the couple G. p. gambiensis/T. brucei gambiense. The next step will be to optimize the system and test other targets chosen among the ESPs (Excreted-Secreted Proteins) of the trypanosome secretum, or the differentially expressed genes associated with the sensitivity/resistance of the fly to trypanosome infection.}, }
@article {pmid40090884, year = {2025}, author = {Steinert, RE and Rehman, A and Sadabad, MS and Milanese, A and Wittwer-Schegg, J and Burton, JP and Spooren, A}, title = {Microbial micronutrient sharing, gut redox balance and keystone taxa as a basis for a new perspective to solutions targeting health from the gut.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2477816}, doi = {10.1080/19490976.2025.2477816}, pmid = {40090884}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Oxidation-Reduction ; *Micronutrients/metabolism ; *Prebiotics ; *Bacteria/metabolism/classification/genetics ; *Probiotics ; Animals ; Gastrointestinal Tract/microbiology/metabolism ; }, abstract = {In health, the gut microbiome functions as a stable ecosystem maintaining overall balance and ensuring its own survival against environmental stressors through complex microbial interaction. This balance and protection from stressors is maintained through interactions both within the bacterial ecosystem as well as with its host. As a consequence, the gut microbiome plays a critical role in various physiological processes including maintaining the structure and function of the gut barrier, educating the gut immune system, and modulating the gut motor, digestive/absorptive, as well as neuroendocrine system all of which are crucial for human health and disease pathogenesis. Pre- and probiotics, widely available and clinically established, offer various health benefits primarily by beneficially modulating the gut microbiome. However, their clinical outcomes can vary significantly due to differences in host physiology, diets, individual microbiome compositions, and other environmental factors. This perspective paper highlights emerging scientific insights into the importance of microbial micronutrient sharing, gut redox balance, keystone species, and the gut barrier in maintaining a diverse and functional microbial ecosystem, and their relevance to human health. We propose a novel approach that targets microbial ecosystems and keystone taxa performance by supplying microbial micronutrients in the form of colon-delivered vitamins, and precision prebiotics [e.g. human milk oligosaccharides (HMOs) or synthetic glycans] as components of precisely tailored ingredient combinations to optimize human health. Such a strategy may effectively support and stabilize microbial ecosystems, providing a more robust and consistent approach across various individuals and environmental conditions, thus, overcoming the limitations of current single biotic solutions.}, }
@article {pmid40090524, year = {2025}, author = {Kh, H and S, D and T, L and A, L and Sk, M and Cl, P and S, R and P, R and Gb, R and I, S and C, S and S, S and Sl, T and A, G}, title = {Relationship between Sputum Bacterial Load and Lung Function in Children with Cystic Fibrosis Receiving Tobramycin.}, journal = {Respiratory medicine}, volume = {}, number = {}, pages = {108042}, doi = {10.1016/j.rmed.2025.108042}, pmid = {40090524}, issn = {1532-3064}, abstract = {BACKGROUND: Chronic pulmonary infection with pathogens such as Pseudomonas aeruginosa is associated with lung function decline and increased mortality in people with cystic fibrosis (CF). The relationship between sputum bacterial load and the severity of pulmonary exacerbations remains unclear. This study aimed to explore the relationship between sputum bacterial load and clinical response to antibiotic treatment of pulmonary exacerbations in children with CF.<br><br>METHODS: Multicentre prospective longitudinal study of children with CF receiving IV tobramycin for a pulmonary exacerbation and who had prior isolation of Gram-negative bacteria and able to expectorate sputum. Lung function (FEV1) and sputum bacterial load were assessed. Bacterial load was performed using quantitative PCR on either intact (live) bacterial cells or all bacterial DNA (live+dead) and targeted either P. aeruginosa only or all bacteria.<br><br>RESULTS: Twelve children (14 admissions) were enrolled and each provided &#x2265;2 sputum samples; 11 children (13 admissions) also had &#x2265;2 FEV1 measurements. In 10 admissions where FEV1 improved, five showed a reduction in all live bacteria, with a median reduction by 8.65&#xd7;10[6] copies/g (73% reduction). Live P. aeruginosa was detected in 8/10 children and in seven, a median reduction of 2.99&#xd7;10[7] copies/g (90% reduction) was observed. Improved FEV1 correlated with greater reductions in live+dead P. aeruginosa (&#x3c1; = -0.63, p = 0.04).<br><br>CONCLUSION: A greater reduction in total sputum P. aeruginosa bacterial load (live+dead) was associated with improved lung function (FEV1) in children with CF receiving tobramycin.}, }
@article {pmid40090501, year = {2025}, author = {Mehta, D and Krishnani, KK and Verma, AK and Kumar, N and Abisha, R and Roy, U}, title = {Hydrogel and fish mucus mediated semi-biofloc formation, nitrogenous stress mitigation and growth performance of fish in integrated bioremediation system of aquaculture.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {107487}, doi = {10.1016/j.micpath.2025.107487}, pmid = {40090501}, issn = {1096-1208}, abstract = {Intensive aquaculture system tends to produce excessive ammonia and other nitrogenous metabolites and microbial load, which lead to abiotic and biotic stresses in fish. Eco-friendly alternatives such as probiotics are needed to prevent economically relevant infectious diseases for a successful disease-free harvest in aquaculture. In the present study, 90-days experiments were conducted at two stocking densities 80 and 160 per m[3] fish (7.15±0.05 g) coupled with xanthan gum (ED1) and sweet potato powder (ED2) for mitigation of priority stresses in Labeo rohita. Highest average body weight (17.71±0.15 g), average daily gain (0.12±0.01 g), specific growth rate (1.02 ± 0.01 g day[-1]), percentage weight gain (150.73±1.01) and feed efficiency ratio (1.00±0.01) were found in 80 fish per m[3] coupled with ED2. Bacterial counts (2.6×10[6] CFU ml[-1]) and removal efficiency of total ammonia-N (97.6%) and nitrite-N (99.99%) were significantly(P<0.05) higher in 160 fish per m[3] coupled with ED2. Maturation of biofloc bacterial biomass and bio-stimulatory effects were found to be the major mechanism. Fish mucus was found to be bactericidal mostly against fish pathogenic bacteria Aeromonas hydrophila and Edwardsiella tarda due to antagonistic effect of probiotic microbiome of green slime. Bacteria as safe candidate probionts in fish health management have been isolated and identified as Bacillus spp based on 16S rDNA and FAME approaches. Low level of catalase and SOD was observed in gill, muscle and liver in treatments, indicating stress alleviation to the culture organisms. For the first time, coupling of fish green slime with hydrogel has newly been coined an integrated hydrogel-mucus-based bioremediation system. The investigation of fish mucus has a very important biological and environmental roles in potential applications in species diversification and climate-resilient aquaculture and culture-based fisheries.}, }
@article {pmid40090309, year = {2025}, author = {Nnorom, MA and Avery, L and Hough, R and Saroj, D and Guo, B}, title = {Anaerobic digestion at hyper-mesophilic temperatures: Microbiome and antibiotic resistome in full-scale agricultural biogas plants.}, journal = {Journal of hazardous materials}, volume = {491}, number = {}, pages = {137922}, doi = {10.1016/j.jhazmat.2025.137922}, pmid = {40090309}, issn = {1873-3336}, abstract = {Temperatures between 40°C and 50°C are increasingly implemented in full-scale agricultural anaerobic digestion (AD), yet the microbial diversity and antibiotic resistome dynamics within this temperature range remain poorly understood. Here, we defined this range as "hyper-mesophilic" and surveyed five full-scale sites. Significant differences were found in the bacterial community structure, potentially stemming from feedstock combination (high vs low/non-manure) and operating temperature. Sites operating at 44°C exhibited superior attenuation efficiency (81-92 %) for antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) than sites operating at 41°C (41-83 %). High-risk clinically important ARGs such as sul1, lnuA, tet(O), and tet(L) persisted in sites blending livestock manure. Potential hosts of ARGs were identified and included opportunistic human pathogens like Enterococcus faecalis, Staphylococcus aureus, and Clostridioides difficile. The tnpA transposon accounted for > 50 % of the total MGEs and frequently co-localised with ARGs, while the class 1 integrase, intI1, was only detected in manure-blended AD. Based on prevalence in plasmids, ARGs showed higher mobility potential in sites blending chicken manure. The results obtained here provided initial insights into hyper-mesophilic AD and reinforced the importance of conducting surveillance for crop AD, with or without manure, as part of wider efforts to mitigate antimicrobial resistance in agroecosystems.}, }
@article {pmid40090240, year = {2025}, author = {Tao, Y and Yi, X and Zhou, X and Qu, J and Diogene, T and Wang, A and Zhang, Y}, title = {Link between gut damage and neurotoxicity with gender differences in zebrafish: Dibutyl phthalate-driven microbiota dysbiosis as a possible major cause.}, journal = {The Science of the total environment}, volume = {972}, number = {}, pages = {179102}, doi = {10.1016/j.scitotenv.2025.179102}, pmid = {40090240}, issn = {1879-1026}, abstract = {Among plasticizers, dibutyl phthalate (DBP) is widely used in in industry, posing significant health risks to aquatic organisms. In this study, adult male and female zebrafish were exposed to 0 and 30 μg/L DBP for 15 days. Behavioral monitoring, immunofluorescence, protein immunoblotting, and high-throughput sequencing were used to investigate the critical role of the gut microbiome in DBP-induced dysfunction of the zebrafish gut-brain axis. The results showed pronounced, sex-specific toxic effects of acute DBP exposure in adult zebrafish, with males experiencing more severe neurological damage, while females exhibited greater intestinal damage. DBP exposure caused marked anxiety behaviors in males and significant weight loss in females. Males showed reduced neuronal expression, while females exhibited increased intestinal permeability and lower levels of the tight junction protein (ZO-1). The Firmicutes/Bacteroidota (F/B) ratio decreased, indicating severe gut microbiota dysbiosis. Changes in the gut and fecal microbiota composition, along with PICRUSt2 functional predictions, suggest that female zebrafish experienced more severe metabolic disturbances than males. Analysis of key gene expression in the brain-derived neurotrophic factor (bdnf) pathway revealed that changes in the abundance of tryptophan-metabolizing bacteria in the gut may explain the sex-specific effects of DBP on neurotransmitter serotonin levels in the brain, which influence the gut-brain axis in zebrafish. This study contributes to the understanding of toxic effects of DBP on aquatic organisms and provides strong evidence for assessing its environmental risks.}, }
@article {pmid40089976, year = {2025}, author = {Amato, KR and Lake, BR and Ozminkowski, S and Jiang, H and Moy, M and Sardaro, MLS and Fultz, A and Hopper, LM}, title = {Exploring the Utility of the Gut Microbiome as a Longitudinal Health Monitoring Tool in Sanctuary Chimpanzees (Pan troglodytes).}, journal = {American journal of primatology}, volume = {87}, number = {3}, pages = {e70004}, pmid = {40089976}, issn = {1098-2345}, support = {//This project was made possible by funding from the Arcus Foundation. K.R.A. is supported as a fellow in CIFAR's "Humans and the Microbiome" program./ ; }, mesh = {Animals ; *Pan troglodytes/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; *Animal Welfare ; Longitudinal Studies ; Feces/microbiology ; Animals, Zoo/microbiology ; }, abstract = {The primary goal of captive primate management is to ensure optimal health and welfare of the animals in our care. Given that the gut microbiome interacts closely with host metabolism, immunity, and even cognition, it represents a potentially powerful tool for identifying subtle changes in health status across a range of body systems simultaneously. However, thus far, it has not been widely tested or implemented as a monitoring tool. In this study, we used longitudinal microbiome sampling of newly arrived chimpanzees at Chimp Haven to explore the feasibility of using the gut microbiome as a health and welfare biomarker in a sanctuary environment. We also tested the hypothesis that a transition to a new living environment, and integration into new social groupings, would result in temporal changes in chimpanzee gut microbiome composition. The collection of longitudinal microbiome data at Chimp Haven was feasible, and it revealed temporal shifts that were unique to each individual and, in some cases, correlated to other known impacts on health and behavior. We found limited evidence for microbial change over time after arrival at Chimp Haven that was consistent across individuals. In contrast, social group and enclosure, and to a lesser extent, age and sex, were associated with differences in gut microbiome composition. Microbiome composition was also associated with overall health status categories. However, many of the effects we detected were most apparent when using longitudinal data, as opposed to single time point samples. Additionally, we found important effects of technical factors, specifically outdoor temperature and time to collection, on our data. Overall, we demonstrate that the gut microbiome has the potential to be effectively deployed as a tool for health and environmental monitoring in a population of sanctuary chimpanzees, but the design must be carefully considered. We encourage other institutions to apply these approaches and integrate health and physiology data to build on the utility of gut microbiome analysis for ensuring the welfare of captive primates in a range of contexts.}, }
@article {pmid40089763, year = {2025}, author = {Chandrasekaran, P and Krausz, M and Han, Y and Mitsuiki, N and Gabrysch, A and Nöltner, C and Proietti, M and Heller, T and Grou, C and Calderon, V and Subramanian, P and Jones, DR and Siu, Y and Deming, C and Conlan, S and Holland, SM and Segre, JA and Uzel, G and Grimbacher, B and Falcone, EL}, title = {Correction: The intestinal microbiome and metabolome discern disease severity in cytotoxic T-lymphocyte-associated protein 4 deficiency.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {74}, pmid = {40089763}, issn = {2049-2618}, }
@article {pmid40089527, year = {2025}, author = {Eriksen, E and Graff, P and Eiler, A and Straumfors, A and Komlavi Afanou, A}, title = {DNA metabarcoding and its potential in microbial risk assessment in waste sorting plants.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8941}, pmid = {40089527}, issn = {2045-2322}, mesh = {*DNA Barcoding, Taxonomic/methods ; Risk Assessment ; Humans ; *Microbiota/genetics ; *Air Microbiology ; Fungi/genetics/isolation &amp; purification/classification ; Bacteria/genetics/classification/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Waste Disposal Facilities ; Environmental Monitoring/methods ; }, abstract = {Exposure to hazardous microorganisms during waste handling is a potential health concern. Molecular biological techniques provide means of profiling the microbial community at high taxonomic resolution, allow the identification of critical human pathogens on the species level and thereby aid the risk assessment of work tasks. The present study used high-throughput sequencing to characterise the microbiome in personal full-shift air samples collected at contemporary waste sorting plants (WSPs) and identified large variations in community composition within (alpha diversity) and between (beta diversity) WSPs. Seasonality did not contribute to differences in the community composition. Cladosporium sp. was dominant among fungi, whereas Aerococcus sp. was dominant among bacteria. The personal air-samples contained potential human pathogens, such as Aspergillus sp., Fusarium sp. and Enterobacteriaceae, that encompass strains with the potential to develop drug-resistance. This study provided characterization of the microbial community composition of personal bioaerosol samples and provided evidence for the occurrence of potential human pathogens in contemporary waste sorting plants. Furthermore, this study highlighted the potential of microbial metabarcoding to detect critical human pathogens that may be encountered in working environments.}, }
@article {pmid40089085, year = {2025}, author = {Saadh, MJ and Allela, OQB and Kareem, RA and Sanghvi, G and Ballal, S and Naidu, KS and Bareja, L and Chahar, M and Gupta, S and Sameer, HN and Yaseen, A and Athab, ZH and Adil, M}, title = {Exploring preventive and treatment strategies for oral cancer: Modulation of signaling pathways and microbiota by probiotics.}, journal = {Gene}, volume = {}, number = {}, pages = {149380}, doi = {10.1016/j.gene.2025.149380}, pmid = {40089085}, issn = {1879-0038}, abstract = {The evidence suggests that the microbiome plays a crucial role in cancer development. The oral cavity has many microorganisms that can influence oral cancer progression. Understanding the mechanisms and signaling pathways of the oral, gum, and teeth microbiome in tumor progression can lead to new treatment strategies. Probiotics, which are friendly microorganisms, have shown potential as anti-cancer agents. These positive characteristics of probiotic strains make them suitable for cancer prevention or treatment. The oral-gut microbiome axis supports health and homeostasis, and imbalances in the oral microbiome can disrupt immune signaling pathways, epithelial barriers, cell cycles, apoptosis, genomic stability, angiogenesis, and metabolic processes. Changes in the oral microbiome in oral cancer may suggest using probiotics-based treatments for their direct or indirect positive roles in cancer development, progression, and metastasis, specifically oral squamous cell carcinoma (OSCC). Here, reported relationships between probiotics, oral microbiota, and oral cancer are summarized.}, }
@article {pmid40089059, year = {2025}, author = {Fan, J and Wu, Y and Wang, X and Ullah, H and Ling, Z and Liu, P and Wang, Y and Feng, P and Ji, J and Li, X}, title = {The probiotic enhances donor microbiota stability and improves the efficacy of fecal microbiota transplantation for treating colitis.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2025.03.017}, pmid = {40089059}, issn = {2090-1224}, abstract = {INTRODUCTION: The stability and metabolic functionality of donor microbiota are critical determinants of fecal microbiota transplantation (FMT) efficacy in inflammatory bowel disease (IBD). While probiotics show potential to enhance microbiota resilience, their role in optimizing donor microbiota for FMT remains underexplored.<br><br>OBJECTIVES: This study investigated whether pretreatment of donor microbiota with L. plantarum GR-4 could improve FMT outcomes in a DSS-induced colitis model by modulating microbial stability, metabolic activity, and host-microbiome interactions.<br><br>METHODS: Donor mice received L. plantarum GR-4 for 3&#x202f;weeks to generate modified FMT (MFMT). DSS-colitis mice were treated with MFMT, conventional FMT, or 5-aminosalicylic acid (5-ASA). Multi-omics analyses and functional assays (stress resistance, engraftment efficiency) were used to evaluate therapeutic mechanisms.<br><br>RESULTS: GR-4 pretreatment conferred three key advantages to donor microbiota: Ecological stabilization: 1. GR-4-driven acidification (pH 3.97 vs. 4.59 for LGG, p&#x202f;<&#x202f;0.0001) enriched butyrogenic Butyricicoccus (73&#x202f;% butyrate increase, p&#x202f;<&#x202f;0.05) and improved stress resistance to bile acids/gastric conditions (1.25&#x202f;&#xd7;&#x202f;survival vs. FMT). 2. Metabolic reprogramming: GR-4 metabolized 25.3&#x202f;% of tryptophan (vs. 10.3&#x202f;% for LGG) to generate immunomodulatory indoles (ILA, IAA), activating aryl hydrocarbon receptor (AHR) signaling and upregulating anti-inflammatory IL-10/IL-22. 3. Bile acid remodeling: MFMT restored sulfolithocholic acid and &#x3b2;-MCA levels, outperforming FMT in resolving DSS-induced dysregulation. MFMT achieved an 83&#x202f;% remission rate (vs. 50&#x202f;% for FMT), enhanced gut barrier integrity, and reversed colitis-associated metabolic dysregulation (e.g., elevated spermidine, 7-sulfocholic acid). Probiotic preconditioning improved donor engraftment by 1.25&#x202f;&#xd7;&#x202f;and enriched success-associated taxa (Sporobacter, Butyricimonas), while suppressing pathogens (Clostridium papyrosolvens).<br><br>CONCLUSIONS: L. plantarum GR-4 optimizes donor microbiota via pH-driven niche engineering, immunometabolic reprogramming, and bile acid modulation, addressing key limitations of conventional FMT. The multi-targeted efficacy of MFMT, evidenced by superior remission rates and metabolic restoration, establishes this approach as a translatable strategy for IBD therapy. This study establishes probiotic-enhanced FMT as a paradigm for precision microbiome interventions.}, }
@article {pmid40088440, year = {2025}, author = {Černá, K and Šíma, R and Němcová, J}, title = {Molecular detection of infectious agents in the pathology laboratory.}, journal = {Ceskoslovenska patologie}, volume = {60}, number = {4}, pages = {169-175}, pmid = {40088440}, issn = {1210-7875}, mesh = {Humans ; *Molecular Diagnostic Techniques/methods ; }, abstract = {Using molecular methods, infectious organisms of viral, bacterial and fungal origin, as well as protozoa and helminths, can be detected. Molecular methods detect specific segments in the nucleic acid sequences of infectious agents and therefore do not require the maintenance of viability of the microorganisms of interest. Therefore, these methods can also be used for direct detection of infectious agents from fixed tissue, the most commonly available material in pathology. This short review article is based on more than 20 years of molecular microbiology within pathology and our aim is to present the possibilities of molecular detection of infectious organisms for pathological diagnosis.}, }
@article {pmid40087795, year = {2025}, author = {Scalzo, PL and Marshall, AG and Soriano, S and Curry, K and Dulay, M and Hodics, T and Quigley, EMM and Treangen, TJ and Piskorz, MM and Villapol, S}, title = {Gut Microbiome dysbiosis and immune activation correlate with somatic and neuropsychiatric symptoms in COVID-19 patients.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {327}, pmid = {40087795}, issn = {1479-5876}, support = {T15LM007093//Gulf Coast Consortia/ ; R21NS106640/NS/NINDS NIH HHS/United States ; R56AG080920/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; *COVID-19/immunology/microbiology ; *Dysbiosis/microbiology/immunology ; Female ; Male ; *Gastrointestinal Microbiome ; Middle Aged ; SARS-CoV-2/isolation &amp; purification ; Adult ; Aged ; Depression/immunology/microbiology/complications ; Cytokines/blood ; Anxiety/complications/microbiology ; Inflammation/immunology ; Severity of Illness Index ; Mental Disorders/microbiology/immunology ; }, abstract = {BACKGROUND: Infection with SARS-CoV-2, the virus responsible for COVID-19, can lead to a range of physical symptoms and mental health challenges, including stress, anxiety, and depression. These effects are particularly pronounced in hospitalized patients, likely due to the virus's direct and indirect impact on the nervous system. Gut dysbiosis, an imbalance in the gut microbiome, has been implicated in immune dysfunction and chronic inflammation in COVID-19 patients. However, the interactions between gut microbiome composition and the physical and mental symptoms of COVID-19 remain incompletely understood.<br><br>METHODS: We investigated the association between physical and mental symptoms, cytokine profiles, and gut microbiota composition in 124 hospitalized COVID-19 patients. We collected data on demographics, COVID-19 severity, and mental health indicators (stress, anxiety, and depression). Gut microbiome profiling was performed using full-length 16&#xa0;S rRNA gene sequencing to evaluate microbial diversity and composition.<br><br>RESULTS: COVID-19 severity was categorized as low (27.4%), moderate (29.8%), or critical (42.8%). Common symptoms included fever (66.1%) and cough (55.6%), while somatic symptoms (27.3%), anxiety (27.3%), depressive symptoms (39%), and stress (80.5%) were frequently self-reported. Elevated interleukin-6 levels in severe cases highlighted systemic inflammation, reduced gut bacterial diversity, particularly among women and obese patients, correlated with higher disease severity. Notably, the genus Mitsuokella was associated with increased physical symptoms and mental distress, while Granulicatella was linked to critical illness.<br><br>CONCLUSIONS: Our findings reveal significant associations between mental health status, systemic inflammation, and gut dysbiosis in hospitalized COVID-19 patients. These results indicate the potential for microbiome-targeted therapies to mitigate psychological and physical complications and improve recovery outcomes in this population.}, }
@article {pmid40087791, year = {2025}, author = {Centeno-Delphia, RE and Glidden, N and Long, E and Ellis, A and Hoffman, S and Mosier, K and Ulloa, N and Cheng, JJ and Davidson, JL and Mohan, S and Kamel, M and Szasz, JI and Schoonmaker, J and Koziol, J and Boerman, JP and Ault, A and Verma, MS and Johnson, TA}, title = {Nasal pathobiont abundance is a moderate feedlot-dependent indicator of bovine respiratory disease in beef cattle.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {27}, pmid = {40087791}, issn = {2524-4671}, support = {2020-68014-31302//National Institute of Food and Agriculture/ ; 2018-006//Purdue University's Colleges of Agriculture and Engineering Collaborative Projects Program/ ; }, abstract = {BACKGROUND: Bovine respiratory disease (BRD) poses a persistent challenge in the beef cattle industry, impacting both animal health and economic aspects. Several risk factors make an animal susceptible to BRD, including bacteria such as Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis. Despite efforts to characterize and quantify these bacteria in the nasal cavity for disease diagnosis, more research is needed to understand if there is a pathobiont abundance threshold for clinical signs of respiratory disease, and if the results are similar across feedlots. This study aims to compare the nasal microbiome community diversity and composition, along with the abundance of four bacterial pathogens and associated serotypes, in apparently healthy and BRD-affected beef cattle. Nasal swabs were collected from four beef feedlots across the US, covering the years 2019 to 2022. The study included post-weaned beef cattle with diverse housing conditions.<br><br>RESULTS: Quantification of BRD-associated pathogens effectively distinguished BRD-affected from apparently healthy beef cattle, surpassing the efficacy of 16S rRNA gene sequencing of the nasal microbiome community. Specifically, H. somni, M. bovis, and M. haemolytica had higher abundance in the BRD-affected group. Utilizing the abundance of these pathobionts and analyzing their combined abundance with machine learning models resulted in an accuracy of approximately 63% for sample classification into disease status. Moreover, there were no significant differences in nasal microbiome diversity (alpha and beta) between BRD-affected and apparently healthy cattle; instead, differences were detected between feedlots.<br><br>CONCLUSIONS: Notably, this study sheds light on the beef cattle nasal microbiome community composition, revealing specific differences between BRD-affected and apparently healthy cattle. Pathobiont abundance was increased in some, but not all farms. Nonetheless, more research is needed to determine if these differences are consistent across other studies. Additionally, future research should consider bacterial-viral interactions in the beef nasal metagenome.}, }
@article {pmid40087775, year = {2025}, author = {Duret, M and Wallner, A and Besaury, L and Aziz, A}, title = {Diversity and functional features of the root-associated bacteriome are dependent on grapevine susceptibility to Plasmopara viticola.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {30}, pmid = {40087775}, issn = {2524-6372}, support = {1564//French National Research Agency through the PRIMA-MiDiVine project/ ; 1564//French National Research Agency through the PRIMA-MiDiVine project/ ; 1564//French National Research Agency through the PRIMA-MiDiVine project/ ; }, abstract = {BACKGROUND: Plant health depends on beneficial interactions between the roots and their microbiomes. Despite recent progress on the role of the grapevine microbiome, the taxonomic identity and functional traits of microbial taxa specific to healthy or Plasmopara viticola-diseased plants, as well as to the susceptible or resistant cultivar are unknown. Using metabarcoding and shotgun metagenomics sequencing, we investigated the effect of downy mildew on the root-associated microbiome (rhizospheric soil, rhizoplane and endosphere) of 41B-grafted susceptible cultivar (Chardonnay) and resistant interspecific hybrid (Voltis) at flowering and veraison stages. The impact of conventional treatment on the rhizomicrobiome assembly of Chardonnay was also evaluated.<br><br>RESULTS: Analyses revealed a core bacteriome shared between both susceptible and resistant cultivars. This also highlighted common functional traits between the rhizosphere and rhizoplane bacteriomes in both cultivars. A dysbiosis state was also evidenced by a loss of beneficial communities in the rhizosphere of the P. viticola-infected cultivar. Microbial genome assemblies showed functional differences between healthy and diseased plants, with a loss of Pseudomonas and Phyllobacterium taxa at veraison. This state was mainly characterized by a loss of genes involved in polyamine transport and metabolism in the susceptible cultivar. It was also marked by an increase in population evenness and total bacterial diversity, and the presence of pathogenic species in susceptible plants.<br><br>CONCLUSIONS: This study reveals distinct and overlapping bacterial communities and functional genes in the rhizospheric soil, rhizoplane and root endosphere of both susceptible and resistant grapevine cultivars to downy mildew. Microbial diversity and abundant taxa of grapevine roots are influenced by downy mildew and cultivar susceptibility. Common bacterial functions are shared among rhizocompartments of susceptible and resistant cultivars, revealing a dysbiosis state and functional signatures related to plant immunity, especially in the infected-susceptible plants.}, }
@article {pmid40060671, year = {2025}, author = {Trunfio, M and Scutari, R and Fox, V and Vuaran, E and Dastgheyb, RM and Fini, V and Granaglia, A and Balbo, F and Tortarolo, D and Bonora, S and Perno, CF and Di Perri, G and Alteri, C and Calcagno, A}, title = {The cerebrospinal fluid virome in people with HIV: links to neuroinflammation and cognition.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {40060671}, issn = {2692-8205}, support = {R25 MH081482/MH/NIMH NIH HHS/United States ; }, abstract = {Despite effective HIV suppression, neuroinflammation and neurocognitive issues are prevalent in people with HIV (PWH) yet poorly understood. HIV infection alters the human virome, and virome perturbations have been linked to neurocognitive issues in people without HIV. Once thought to be sterile, the cerebrospinal fluid (CSF) hosts a recently discovered virome, presenting an unexplored avenue for understanding brain and mental health in PWH. This cross-sectional study analyzed 85 CSF samples (74 from PWH on suppressive antiretroviral therapy, and 11 from controls without HIV, CWH) through shotgun metagenomics for DNA/RNA viruses. Taxonomic composition (reads and contigs), α and β diversity, and relative abundance (RA) of prokaryotic (PV), human eukaryotic (hEV), and non-human eukaryotic viruses (nhEV) were evaluated in relation to HIV infection, markers of neuroinflammation and neurodegeneration, cognitive functions, and depressive symptoms. Sensitivity analyses and post-hoc cluster analysis on the RA of viral groups and blood-brain barrier permeability were also performed. Of 46 read-positive CSF samples, 93.5% contained PV sequences, 47.8% hEV, and 45.6% nhEV. Alpha diversity was lower in PWH versus CWH, although p>0.05. At β diversity analysis, HIV status explained 3.3% of the variation in viral composition (p=0.016). Contigs retained 13 samples positive for 8 hEV, 2 nhEV, and 6 PV. Higher RA of PV was correlated with higher CSF S100β (p=0.002) and β-Amyloid 1-42 fragment (βA-42, p=0.026), while higher RA of nhEV with poorer cognitive performance (p=0.022). Conversely, higher RA of hEV correlated with better cognition (p=0.003) and lower βA-42 (p=0.012). Sensitivity analyses in virome-positive samples only confirmed these findings. Three CSF clusters were identified and showed differences in astrocytosis, βA-42, tau protein, and cognitive functions. Participants with hEV-enriched CSF showed better cognitive performance compared to those with virus-devoid and nhEV-enriched CSF (models'p<0.05). This study provides the first comprehensive description of the CSF virome in PWH, revealing associations with neuroinflammation and cognition. These findings highlight the potential involvement of the CSF virome in brain health and inform about its composition, origin, and potential clinical implications in people with and without HIV.}, }
@article {pmid40087729, year = {2025}, author = {Bauer, IL}, title = {Putting the mouth back in the body - the neglected area of dental and oral travel health.}, journal = {Tropical diseases, travel medicine and vaccines}, volume = {11}, number = {1}, pages = {7}, pmid = {40087729}, issn = {2055-0936}, abstract = {The lack of dental travel health care has been deplored for some time. Travel medicine's remit is to prepare people for travel. People travel with their mouth firmly in their body, yet the mouth's wellbeing does not rate a mention. This article represents the first exploration of a range of topics relevant to an until now neglected, yet potentially highly important, area of health care. A range of dental mishaps can occur while away from home, from simple toothache to accidents, serious emergencies, or restoration failures. Other problems originate in unwise behaviour, including holiday-inspired body modifications.Unless there is pain, teeth are typically not thought about much. However, examining the practical side of dental hygiene during travels, several overlooked and perhaps surprising topics emerge that - through the travel lens - take on a different and important role: the oral microbiome, toothbrush hygiene, the toilet plume, and traveller diarrhoea. Based on this discussion, recommendations are made for clinical practice, education, and further research.The historical chasm between dentistry and medicine, despite long-standing calls for change, does not seem to go away and impairs holistic high quality travel health care. Travel medicine can bypass this unproductive division. It has the unique opportunity to be the first medical specialty cooperating closely with dentists to bridge this gap by providing quality travel health care to travellers with all their body parts attached.}, }
@article {pmid40087655, year = {2025}, author = {Sheng, Z and Xu, J and Wang, M and Xu, X and Zhu, J and Zeng, S and Xu, C and Zhang, Z}, title = {The role of urinary microbiota in primary and recurrent bladder cancer: insights from a propensity score matching study.}, journal = {BMC cancer}, volume = {25}, number = {1}, pages = {468}, pmid = {40087655}, issn = {1471-2407}, support = {82172871//National Natural Science Foundation of China/ ; 82272950//National Natural Science Foundation of China/ ; 2022YQ010//Shanghai Municipal Health Commission/ ; 2024MS013//Basic Research Project of Naval Medical University/ ; }, mesh = {Humans ; *Urinary Bladder Neoplasms/microbiology/urine/pathology ; Female ; Male ; *Microbiota ; *Neoplasm Recurrence, Local/microbiology/urine ; Aged ; Middle Aged ; *Propensity Score ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; }, abstract = {BACKGROUND: Bladder cancer (BCa) is a common urinary malignancy with high recurrence rates in non-muscle invasive bladder cancer (NMIBC), posing significant clinical challenges. Emerging evidence links urinary microbiota to cancer progression; however, their role in BCa recurrence remains unclear. This study aimed to explore urinary microbiota differences between primary and recurrent BCa to identify potential microbiological markers and mechanisms associated with recurrence.<br><br>METHODS: Urine samples were collected from 170 BCa patients, including 125 with primary Bca(BCa_P) and 45 with recurrent BCa (BCa_R). All samples underwent 16&#xa0;S rRNA gene sequencing, and clinical data were collected, including age, sex, body mass index (BMI), smoking history, pathological grade, and other biological characteristics. Propensity score matching (1:1 ratio, caliper&#x2009;=&#x2009;0.02) minimized baseline differences, resulting in 39 matched pairs. Microbial diversity was analyzed using &#x3b1; and &#x3b2; diversity indices. Differential taxa were identified with Linear Discriminant Analysis Effect Size (LEfSe), and functional pathways were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt).<br><br>RESULTS: Alpha diversity was significantly higher in BCa_P than BCa_R, particularly in Chao1 indices. &#x3b2; diversity revealed distinct microbial structures (ADONIS, P&#x2009;=&#x2009;0.004, R&#xb2; = 0.025). At the phylum level, both BCa_P and BCa_R were dominated by Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria, with Firmicutes significantly higher and Bacteroidetes lower in BCa_R. At the genus level, BCa_P was enriched in Sphingomonas, Corynebacterium, Capnocytophaga, Massilia, and Aquabacterium, while BCa_R showed higher levels of Aeromonas, Cupriavidus, and Bradyrhizobium. Functional predictions revealed glucose metabolism and oxidative stress pathways enriched in BCa_R, while pollutant degradation and TCA cycle pathways were prominent in BCa_P.<br><br>CONCLUSION: These findings reveal significant differences in urinary microbiota compositions and functional profiles between primary and recurrent BCa patients, with recurrent cases exhibiting reduced microbial diversity and enrichment of potentially pathogenic communities, highlighting their potential roles in tumor progression and recurrence.<br><br>TRIAL REGISTRATION: Registered with the Chinese Clinical Trial Registry (ChiCTR2300070969) on April 27, 2023.}, }
@article {pmid40087603, year = {2025}, author = {Zou, Y and Ma, H and Yang, X and Wei, XY and Chen, C and Jiang, J and Jiang, T}, title = {Interaction between the liver transcriptome and gut microbiota in mice during Toxoplasma gondii infection as identified by integrated transcriptomic and microbiome analysis.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {137}, pmid = {40087603}, issn = {1471-2180}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Liver/microbiology/metabolism ; Mice ; *Mice, Inbred BALB C ; *Transcriptome ; *Toxoplasma/genetics ; Gene Expression Profiling ; MicroRNAs/genetics/metabolism ; Female ; Toxoplasmosis, Animal/immunology/microbiology ; Toxoplasmosis/immunology/microbiology/genetics ; Feces/microbiology/parasitology ; RNA, Messenger/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; RNA, Long Noncoding/genetics/metabolism ; }, abstract = {BACKGROUND: Toxoplasma gondii is a single-cell parasite capable of infecting both humans and a variety of animal species. Although T. gondii infection is known to adversely affect the liver and gut microbiota, the precise interplay between the gut microbiome and the liver transcriptome in infected mice remains largely unknown. In this study, we artificially induced acute and chronic stages of T. gondii infection in BALB/c mice via the oral of low doses (n = 10) of PRU (Type II) bradyzoites. Then, we performed fecal 16S rRNA gene amplicon sequencing and RNA transcriptome sequencing to investigate the composition of the gut microbiota and the expression profiles of long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs) in the livers of mice infected with T. gondii at different stages of infection.<br><br>RESULTS: Analysis revealed dynamic alterations in the gut microbiota of mice following infection with T. gondii over the course of the infection cycle. Notably, we observed a significant increase in the abundance of Enterobacteriaceae during the acute stage of infection, while the abundance of Lactobacteriaceae was elevated during the chronic stage. Liver transcriptome analysis identified numerous differentially expressed (DE) non-coding RNAs and mRNAs potentially potentially involved in mediating liver immune responses and inflammation induced by T. gondii. During the acute stage of infection, several pro-inflammatory genes, including Lpin1, Usp2, Pim3, and Il6ra were significantly up-regulated in the liver. Among these, Lpin1 may be closely associated with the development of Enterobacteriaceae overgrowth. Conversely, some anti-inflammatory genes, such as Dmbt1, and Ddit4, were exclusively up-regulated during the chronic stage of infection. Gene ontology (GO) enrichment analysis further revealed the stage-specific features of liver functionality. Specifically, during the acute stage of infection, pathways associated with inflammation were significantly enriched. Interestingly, during the chronic stage of infection, pathways related to microbiota regulation, such as 'defense response to Gram-negative bacterium', 'antimicrobial humoral immune response mediated by antimicrobial peptide', and 'antimicrobial humoral response' were enriched. Additionally, competing endogenous RNAs (CeRNAs) networks revealed that numerous DElncRNAs and DEcircRNAs competitively regulated DEmiRNA mmu-miR-690, which targets the Nr1d1 gene. These findings provide insights into the complex interplay between the liver and gut microbiota during different stages of T. gondii infection.<br><br>CONCLUSIONS: In summary, our results highlight the intricate interaction between the liver and gut microbiota in mice during T. gondii infection, with dynamic alterations observed in both the gut microbiota composition and the expression profiles of key genes in the liver over the course of the infection cycle.}, }
@article {pmid40087562, year = {2025}, author = {Cai, X and Xu, M and Lu, Y and Shen, W and Kang, J and Wang, W and Chen, Y}, title = {Bacterial translocation and gut microbiome imbalance in an experimental infection model of legionellosis in guinea pigs.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {139}, pmid = {40087562}, issn = {1471-2180}, support = {82270107//National Natural Science Foundation of China/ ; 81170009//National Natural Science Foundation of China/ ; 2017YFC1309702//National Key Research and Development Program of China/ ; }, mesh = {Animals ; Guinea Pigs ; *Gastrointestinal Microbiome ; *Disease Models, Animal ; *Bacterial Translocation ; *RNA, Ribosomal, 16S/genetics ; *In Situ Hybridization, Fluorescence ; DNA, Bacterial/genetics ; Legionellosis/microbiology ; Lung/microbiology/pathology ; Intestine, Small/microbiology ; Legionella pneumophila/isolation &amp; purification/genetics ; Liver/microbiology/pathology ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Recent studies have shown that in critically ill patients such as those with sepsis and shock, the lung and gut microbiomes undergo profound changes. Legionella pneumophila (Lp) can cause fatal infection, however, such changes have not been investigated in legionellosis. Here, we evaluated the microbiome of the lungs, blood, liver, and small intestine content in Lp-infected guinea pigs.<br><br>METHODS: We used a culture-independent method by analysing the conserved 16S rDNA sequences of bacteria from the organs of guinea pigs infected with legionellosis. Bacterial DNA was also identified through bacterial probe-fluorescence in situ hybridisation (BP-FISH). Bacterial entry from the intestinal lumen into the submucosa was examined via ultrastructural visualisation.<br><br>RESULTS: Anoxybacillus kestanbolensis, Geobacillus vulcani, and other bacteria were identified in the small intestine content of healthy guinea pigs but not in other tissues. However, in Lp-infected guinea pigs, DNA from these bacteria was detected in the small intestine, lungs, blood, and liver tissues at 24&#xa0;h and 48&#xa0;h post-infection, indicating the possible translocation of gut bacteria to the remote tissues. This was validated through BP-FISH and ultrastructural visualisation. At 72&#xa0;h post-infection, Pseudomonadota were the dominant gut bacteria, highlighting an imbalance in the gut microbiome.<br><br>CONCLUSION: Infection with the Legionella pneumophila serotype 1 disrupted the intestinal microbiota in a subset of guinea pigs during a 72-hour period post-infection, with possible translocation of gut-associated anaerobic bacteria to the lungs and liver based on the presence of genomic DNA detected in tissue from infected guinea pigs.}, }
@article {pmid40087549, year = {2025}, author = {Wang, X and Shang, Y and Xing, Y and Chen, Y and Wu, X and Zhang, H}, title = {Captive environments reshape the compositions of carbohydrate active enzymes and virulence factors in wolf gut microbiome.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {142}, pmid = {40087549}, issn = {1471-2180}, support = {2022KJ177//the Youth Innovation Team in Colleges and Universities of Shandong Province/ ; 32001228//the National Natural Science Foundation of China/ ; 32270444//the National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Virulence Factors/genetics ; *Wolves/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/enzymology ; Dogs ; *Foxes/microbiology ; Animals, Zoo/microbiology ; Animals, Wild/microbiology ; Carbohydrate Metabolism ; Metagenomics ; }, abstract = {Species in the family Canidae occupy different spatial ecological niches, and some (e.g., wolf) can be kept in zoos. The gut microbiome may differ among various wild and captive canids. Therefore, we compared the gut microbiomes of wild canids (wolf, red fox, and corsac fox) in the Hulun Lake area, captive wolves, and domestic dogs in different regions using metagenomic data. A random forest analysis revealed significant enrichment for bacterial species producing short-chain fatty acids and the thermogenesis pathway (ko04714) in the gut microbiome of wild wolf, potentially providing sufficient energy for adaptation to a wide range of spatial ecological niches. The significantly enriched bacterial species and functional pathways in the gut microbiome of corsac foxes were related to physiological stability and adaptation to arid environments. Alpha diversity of carbohydrate-active enzymes in the gut microbiome was higher in the red fox than in the corsac fox and wild wolf, which may be related to the abundance of plant seeds (containing carbohydrates) in their diets (red foxes inhabit seed-rich willow bosk habitats). However, the influence of host genetic factors cannot be excluded, and further experimental studies are needed to verify the study results. In addition, captive environments drove similarity in carbohydrate-active enzymes (CAZymes) and virulence factors (VFs) in the gut microbiomes of captive wolf and domestic dog, and increased the diversity of CAZymes and VFs in the gut microbiome of captive wolf. Increased VFs diversity may increase the pathogenic potential of the gut microbiome in captive wolves. Therefore, it is necessary to continue monitoring the health status of captive wolves and develop appropriate management strategies.}, }
@article {pmid40087408, year = {2025}, author = {Jiang, Z and He, L and Li, D and Zhuo, L and Chen, L and Shi, RQ and Luo, J and Feng, Y and Liang, Y and Li, D and Congmei, X and Fu, Y and Chen, YM and Zheng, JS and Tao, L}, title = {Human gut microbial aromatic amino acid and related metabolites prevent obesity through intestinal immune control.}, journal = {Nature metabolism}, volume = {}, number = {}, pages = {}, pmid = {40087408}, issn = {2522-5812}, support = {2023YFC2308403//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 2024SSYS0032//Science and Technology Department of Zhejiang Province/ ; 2024SSYS0032//Science and Technology Department of Zhejiang Province/ ; 32430002//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82471502//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82073546//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82073529//National Natural Science Foundation of China (National Science Foundation of China)/ ; LRG25C010001//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; LZ23H260001//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; }, abstract = {Obesity affects millions of people in the world. The gut microbiome influences body fat accumulation, but the mechanisms remain to be investigated. Here, we show an association between microbial aromatic amino acid metabolites in serum and body fat accumulation in a large Chinese longitudinal cohort. We next identify that 4-hydroxyphenylacetic acid (4HPAA) and its analogues effectively protect male mice from high-fat-diet-induced obesity. These metabolites act on intestinal mucosa to regulate the immune response and control lipid uptake, which protects against obesity. We further demonstrate that T cells and B cells are not vital for 4HPAA-mediated obesity prevention, and innate lymphoid cells have antagonistic roles. Together, these findings reveal specific microbial metabolites as pivotal molecules to prohibit obesity through immune control, establishing mechanisms of host modulation by gut microbial metabolites.}, }
@article {pmid40087237, year = {2025}, author = {Ferreira, DD and Ferreira, LG and Amorim, KA and Delfino, DCT and Ferreira, ACBH and Souza, LPCE}, title = {Assessing the Links Between Artificial Intelligence and Precision Nutrition.}, journal = {Current nutrition reports}, volume = {14}, number = {1}, pages = {47}, pmid = {40087237}, issn = {2161-3311}, mesh = {Humans ; *Artificial Intelligence ; *Precision Medicine ; *Gastrointestinal Microbiome ; Obesity ; Nutritional Status ; }, abstract = {PURPOSE OF REVIEW: To conduct an overview of the potentialities of artificial intelligence in precision nutrition.<br><br>RECENT FINDINGS: A keyword co-occurrence analysis of 654 studies on artificial intelligence (AI) and precision nutrition (PN) highlighted the potential of AI techniques like Random Forest and Gradient Boosting in improving personalized dietary recommendations. These methods address gastrointestinal symptoms, weight management, and cardiometabolic markers, especially when incorporating data on gut microbiota. Despite its promise, challenges like data privacy, bias, and ethical concerns remain. AI must complement healthcare professionals, necessitating clear guidelines, robust governance, and ongoing research to ensure safe and effective applications. The integration of AI into PN enables highly personalized dietary recommendations by accounting for metabolic variability, genetics, and microbiome data. AI-driven strategies show potential in managing conditions like obesity and diabetes through accurate predictions of individual dietary responses. However, ethical, regulatory, and practical challenges must be addressed to ensure safe, equitable, and effective application of AI in nutrition.}, }
@article {pmid40087204, year = {2025}, author = {Lin, D and Howard, A and Raihane, AS and Di Napoli, M and Cáceres, E and Ortiz, M and Davis, J and Abdelrahman, AN and Divani, AA}, title = {Traumatic Brain Injury and Gut Microbiome: The Role of the Gut-Brain Axis in Neurodegenerative Processes.}, journal = {Current neurology and neuroscience reports}, volume = {25}, number = {1}, pages = {23}, pmid = {40087204}, issn = {1534-6293}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Neurodegenerative Diseases/microbiology/physiopathology ; *Brain Injuries, Traumatic/microbiology/physiopathology/complications ; *Brain-Gut Axis/physiology ; Animals ; Dysbiosis ; Brain/physiopathology ; }, abstract = {PURPOSE OF REVIEW: A deeper understanding of the communication network between the gut microbiome and the central nervous system, termed the gut-brain axis (GBA), has revealed new potential targets for intervention to prevent the development of neurodegenerative disease associated with tramatic brain injury (TBI). This review aims to comprehensively examine the role of GBA post-traumatic brain injury (TBI).<br><br>RECENT FINDINGS: The GBA functions through neural, metabolic, immune, and endocrine systems, creating bidirectional signaling pathways that modulate brain and gastrointestinal (GI) tract physiology. TBI perturbs these signaling pathways, producing pathophysiological feedback loops in the GBA leading to dysbiosis (i.e., a perturbed gut microbiome, impaired brain-blood barrier, impaired intestinal epithelial barrier (i.e., "leaky gut"), and a maladaptive, systemic inflammatory response. Damage to the CNS associated with TBI leads to GI dysmotility, which promotes small intestinal bacterial overgrowth (SIBO). SIBO has been associated with the early stages of neurodegenerative conditions such as Parkinson's and Alzheimer's disease. Many of the bacteria associated with this overgrowth promote inflammation and, in rodent models, have been shown to compromise the structural integrity of the intestinal mucosal barrier, causing malabsorption of essential nutrients and further exacerbating dysbiosis. TBI-induced pathophysiology is strongly associated with an increased risk of neurodegenerative diseases, including Parkinson's and Alzheimer's diseases, which represents a significant public health burden and challenge for patients and their families. A healthy gut microbiome has been shown to promote improved recovery from TBI and prevent the development of neurodegenerative disease, as well as other chronic complications. The role of the gut microbiome in brain health post-TBI demonstrates the potential for microbiome-targeted interventions to mitigate TBI-associated comorbidities. Promising new evidence on prebiotics, probiotics, diet, and fecal microbiota transplantation may lead to new therapeutic options for improving the quality of life for patients with TBI. Still, many of these preliminary findings must be explored further in clinical settings. This review covers the current understanding of the GBA in the setting of TBI and how the gut microbiome may provide a novel therapeutic target for treatment in this patient population.}, }
@article {pmid40087147, year = {2025}, author = {Ziogou, A and Giannakodimos, A and Giannakodimos, I and Schizas, D and Charalampakis, N}, title = {Effect of Helicobacter Pylori infection on immunotherapy for gastrointestinal cancer: a narrative review.}, journal = {Immunotherapy}, volume = {}, number = {}, pages = {1-14}, doi = {10.1080/1750743X.2025.2479410}, pmid = {40087147}, issn = {1750-7448}, abstract = {Immunotherapy for gastrointestinal cancers has elicited considerable amount of attention as a viable therapeutic option for several cancer types. Gut microbiome as a whole plays a critical role in shaping immune responses and influencing cancer progression. Recent evidence suggests that Helicobacter pylori (H. pylori), may influence immunotherapy efficacy by modulating the tumor microenvironment. Infection with H. pylori is common as it affects approximately 50% of the global population and remains the leading risk factor for gastric cancer. Interestingly, recent clinical and preclinical data has associated H. pylori with colorectal cancer carcinogenesis. Gut microbiome appears to be a modulator of the relationship between the immune system, gastrointestinal cancer development and existing therapies. Infection with H. pylori may affect immunotherapy results in both gastroesophageal and colorectal cancer; favorable results were noticed in H. pylori positive patients with gastric cancer, while in colorectal cancer patients the pathogen seemed to impede immunotherapy's action. This article aims to review current data on the role of H. pylori in triggering gastric inflammation and cancer, as well as its potential involvement in colorectal cancer development. Additionally, it seeks to highlight the impact of H. pylori infection on the response to immunotherapy in gastrointestinal cancers.}, }
@article {pmid40087126, year = {2025}, author = {Kamal, F and Kim, J and Lafayette, R}, title = {Current Biomarkers of IgA Nephropathy.}, journal = {Seminars in nephrology}, volume = {}, number = {}, pages = {151572}, doi = {10.1016/j.semnephrol.2025.151572}, pmid = {40087126}, issn = {1558-4488}, abstract = {IgA nephropathy (IgAN) is the most prevalent primary glomerular disease and has been recognized to carry a poor prognosis. It is therefore critical to identify the patients that will progress to ESKD and start treatments early. The current gold standard for diagnosis remains kidney biopsy. Histopathologic findings along with proteinuria, glomerular filtration rate, and hypertension remain the best-validated biomarkers for prognosis but do not provide enough granularity to guide treatment decisions. The current understanding of the pathophysiology of IgAN with the four-hit hypothesis has helped identify potential additional biomarkers that could become available in the foreseeable future. In this review we detail the existing data for the most promising biomarkers including galactose-deficient IgA1 and its corresponding autoantibody, markers of complement activation, as well as more nascent assays such as MicroRNAs, genomic, and microbiome biomarkers.}, }
@article {pmid40086991, year = {2025}, author = {Peng, Q and Zhou, H and Zheng, H and Xie, G}, title = {Investigating the role of primary fungi in Huangjiu fermentation: Insights from flavor orientation and synthetic microbiomes.}, journal = {Food microbiology}, volume = {129}, number = {}, pages = {104765}, doi = {10.1016/j.fm.2025.104765}, pmid = {40086991}, issn = {1095-9998}, mesh = {*Fermentation ; *Volatile Organic Compounds/metabolism/analysis ; *Alcoholic Beverages/microbiology/analysis ; *Fungi/genetics/metabolism/classification/isolation &amp; purification ; *Microbiota ; *Taste ; *Flavoring Agents/metabolism ; Humans ; Food Microbiology ; }, abstract = {Huangjiu, a traditional alcoholic beverage, presents a complex fermentation ecosystem primarily influenced by specific fungal species. This study utilized a culture-dependent approach and amplicon sequencing to explore fungal community succession during Huangjiu fermentation. Key fungi identified include Saccharomyces cerevisiae, Aspergillus species (flavus, oryzae, niger), Saccharomycopsis fibuligera, Thermomyces lanuginosus, Rhizopus arrhizus, Issatchenkia orientalis, Wickerhamomyces anomalus, and Diutina rugosa. Employing a synthetic microbiome, we developed a dual-strain fermentation system to evaluate the impact of these fungi on Huangjiu's organoleptic properties. Introduction of these fungi significantly altered the flavor profile, enhancing 23 volatile organic compounds (VOCs), with S. fibuligera notably increasing nine distinct VOCs. While molds contributed to bitterness by increasing bitter amino acids, S. fibuligera effectively mitigated these components, enhancing the beverage's alcohol body, smoothness, and balance. These findings provide crucial insights for optimizing Huangjiu fermentation to improve its quality and appeal.}, }
@article {pmid40086705, year = {2025}, author = {Ma, G and Chai, Y and Tye, KD and Xie, H and Meng, L and Tang, X and Luo, H and Xiao, X}, title = {Predictive analysis of the impact of probiotic administration during pregnancy on the functional pathways of the gut microbiome in healthy infants based on 16S rRNA gene sequencing.}, journal = {Gene}, volume = {952}, number = {}, pages = {149414}, doi = {10.1016/j.gene.2025.149414}, pmid = {40086705}, issn = {1879-0038}, abstract = {Maternal probiotic supplementation altered the microbial composition in infants' gut, yet its effect on the functional pathways of the microbiota remains unclear. This study aimed to explore the potential impact of maternal probiotic intake on the predicted functional pathways of the gut microbiome in healthy infants. A total of 24 pregnant women were randomly allocated to either the control group or the probiotic group. The women in the probiotic group began receiving probiotics at the 32nd week of pregnancy and continued until delivery. Meconium and fecal samples were collected from infants at birth, as well as on the 3rd day, 14th day, and 6th month after birth. The functional characteristics of the microbial community were inferred using 16S rRNA gene analysis, processed with PICRUSt software, and cross-referenced with the KEGG database. The probiotic group had lower levels of Actinobacteria and Bacteroidetes, while Bifidobacterium growth was notably increased in the infant gut microbiota. At day 0 postpartum, the control group exhibited higher levels of Prevotellaceae compared to the probiotic group (P < 0.05). However, no significant differences were found by day 3. At day 14, the control group exhibited higher levels of Bacteroidaceae and Bacteroides, while Bacteroides_thetaiotaomicron was more abundant in the probiotic group (P < 0.05). By 6 months, the control group showed a higher abundance of Firmicutes (P < 0.05). On day 0 postpartum, maternal probiotic consumption increased the Environmental information processing pathway at KEGG Level 1, and increased Energy metabolism, Metabolism of cofactors and vitamins, and Cell growth and death pathways at KEGG Level 2. It also increased Histidine metabolism, One carbon pool by folate, and Folate biosynthesis at KEGG Level 3. No changes were observed in the infant gut microbiota's functional metabolic pathways at 3 days postpartum. At 14 days postpartum, probiotics reduced Lipid metabolism pathways at KEGG Level 2 and the Citrate cycle at KEGG Level 3. At 6 months postpartum, probiotics decreased Carbohydrate metabolism pathways at KEGG Level 2. Our findings suggest that probiotic supplementation during pregnancy affects the functional metabolism of the gut microbiota in healthy infants. This, in turn, may influence the development of the infant's immune system, metabolism, and overall health by modifying the gut microbial environment.}, }
@article {pmid40086700, year = {2025}, author = {Xu, T and Yasuda, S and Oba, K and Kuroiwa, M and Riya, S and Zhou, Y and Duan, J and Hori, T and Ookawa, T and Zhan, X and Terada, A}, title = {Single cell protein production potential of enriched microbial populations from rice paddy soils and roots: Insights into protein yield enhancement by Methylophilaceae.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132397}, doi = {10.1016/j.biortech.2025.132397}, pmid = {40086700}, issn = {1873-2976}, abstract = {This study aimed to determine key factors for enriching methylotrophic populations for single-cell protein (SCP) production and to determine the predominant active methylotrophs. Microbial populations from rice paddy soils and roots, hotspots for CH4 oxidation, underwent serial incubation by feeding CH4 and O2. The protein content was primarily influenced by the incubation stage, with a lesser effect from the rice plant roots as an inoculum source, reaching a maximum of 20 % in biomass dominated by Methylomonadaceae and Methylophilaceae. While Methylomonadaceae as CH4 oxidizers exhibited lower abundance but high transcription activity, Methylophilaceae as methanol oxidizers were more abundant and strongly correlated with protein content (Pearson's coefficient >0.8, p < 0.05). Enhancing Methylophilaceae in the mixed cultures may improve SCP yields via interactions with Methylomondaceae, likely mediated by methanol. The cooperative relation plausibly offers a promising strategy for sustainable CH4-based SCP production.}, }
@article {pmid40086405, year = {2025}, author = {Sulivan, J and Thomas, L and Gérald, T}, title = {A bioelectronic tongue to estimate the toxicological intensity of pollutants in wastewater treatment plant.}, journal = {Water research}, volume = {279}, number = {}, pages = {123470}, doi = {10.1016/j.watres.2025.123470}, pmid = {40086405}, issn = {1879-2448}, abstract = {With 360 km[3] of wastewater produced each year in Europe, the management and control of units responsible for their treatment appear as major challenges in preserving the environment. Nevertheless, these processes remain vulnerable to the presence of toxic compounds likely to compromise their performance. Although many toxicity tests exist to evaluate the impact of pollutants on the environment, these are generally not easily transferable to the monitoring of wastewater treatment processes (constraints of implementation, representativeness of the information provided). This innovative project leverages the concept of a "bioelectronic tongue" integrated into a biosensor to evaluate the toxic impact of pollutants on wastewater treatment plant (WWTP) microbiomes. This work presents a holistic approach, covering the entire process from the selection of representative microorganisms to in situ application. The strategy hinges on the synergistic implementation of 8 bioreporters, coupled with a data processing algorithm to generate relevant toxicity assessments. In parallel, a significant focus was placed on developing a biosensor optimized for in situ deployment of this innovative measurement strategy. The developed approach (TOXLAB) has been compared to reference methods currently used to assess the toxicological intensity of effluents. As expected, significant differences were highlighted between the standardized methods, particularly the method based on marine bioluminescent bacteria (lack of representativeness - 9 out of the 11 tested conditions could not be quantified with this method). However, the results provided by the TOXLAB approach show a certain adequacy with the toxicity data obtained on the urban WWTP microbiome. On the other hand, the results obtained on the industrial site (34 samples) are much more contrasted. Indeed, no correlation (r[2] = 0.033) could be established between the data from the TOXLAB approach and the effects induced on the autochthonous microbial community of the site. To explain these results, the work focused on the composition of these specific ecosystems, thus showing important differences between the microbiomes of WWTPs and the industrial site. Thus, in light of these results, the conclusion of the study shows the need to use a specific set of bioreporters, dedicated to each industrial site, in order to ensure a relative representativeness of the information provided.}, }
@article {pmid40086306, year = {2025}, author = {Russo, A and D'Alessandro, A and Di Paola, M and Cerasuolo, B and Renzi, S and Meriggi, N and Conti, L and Costa, J and Pogni, R and Martellini, T and Cincinelli, A and Ugolini, A and Cavalieri, D}, title = {On the role of bacterial gut microbiota from supralittoral amphipod Talitrus saltator (Montagu, 1808) in bioplastic degradation.}, journal = {The Science of the total environment}, volume = {972}, number = {}, pages = {179109}, doi = {10.1016/j.scitotenv.2025.179109}, pmid = {40086306}, issn = {1879-1026}, abstract = {Despite the promise of a reduced environmental impact, bioplastics are subjected to dispersion and accumulation similarly to traditional plastics, especially in marine and coastal environments. The environmental impact of bioplastics is attracting increasing attention due to the growing market demand. The ability of the supralittoral amphipod Talitrus saltator to ingest and survive on pristine starch-based bioplastic has already been assessed. However, the involvement of the gut microbiota of this key coastal species in making bioplastics a dietary supplement, remains unknown. In this study, we investigated the modification of T. saltator gut microbiota following bioplastic ingestion and the effect of this change on the modification of their chemical composition. Groups of adult amphipods were fed with: 1 - two different kinds of starch-based bioplastic; 2 - a 50 %/50 % chitosan-starch mixture; and 3 - paper and dry-fish-food. Freshly collected, unfed individuals were used as control group. Faecal pellets from the amphipods were collected and characterized using ATR-FTIR spectroscopy. DNA was extracted from gut samples for metagenomic analysis. Spectroscopic investigation suggested a partial digestion of polysaccharide components in the experimental polymeric materials. The analysis of the gut microbiota revealed that bioplastic feeding induced modification of sandhopper's gut microbial communities, shifting the abundance of specific microbial genera already present in the gut, towards bacterial genera associated with plastic/bioplastic degradation, especially in groups fed with starch-based bioplastics. Overall, our results highlight the involvement of T. saltator's gut microbiota in bioplastic modification, providing new insights into the potential role of microbial consortia associated to sandhoppers in bioplastic management.}, }
@article {pmid40086090, year = {2025}, author = {Goudriaan, M and Ndhlovu, RT and Brouwer, M and Vreugdenhil, S and van der Meer, MTJ and Niemann, H}, title = {Degradation and habitat-dependent colonization of plastics in Caribbean coastal waters and sediments by bacterial communities.}, journal = {Marine pollution bulletin}, volume = {214}, number = {}, pages = {117787}, doi = {10.1016/j.marpolbul.2025.117787}, pmid = {40086090}, issn = {1879-3363}, abstract = {This study investigates microbial colonization of plastics in Caribbean coastal waters. We deployed five polymer types, on set with a mild UV-pretreatment and one set without UV-pretreatment, for 4.5 months in the water column and sediment at two locations, and analyzed the epiplastic biofilms with 16S rRNA gene sequencing. While a significant influence of location and habitat was apparent, we could not detect notable effects related to polymer type or UV-pretreatment on microbial community composition. Nevertheless, potential plastic and hydrocarbon degraders constituted up to 43 % of sequences from epiplastic biofilms, suggesting an affinity for plastic. Indeed, utilizing [13]C-labeled PE and PP, we determined incorporation of plastic-derived carbon into microbial biomass. We measured isotopically labeled fatty acids in incubations with [13]C labeled plastics in both water column and sediments, whether virgin or pre-weathered with UV light. The apparent biodegradation of plastic in benthic habitats challenges the perception of marine sediments as a final sink for polyolefins.}, }
@article {pmid40086049, year = {2025}, author = {Pan, L and Wang, X and Yang, B and Liu, Y and Tang, D}, title = {Importance of intestinal microflora: Dried toad skin-radix clematidis plasma component analysis and anti-CRC core target study.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {260}, number = {}, pages = {116802}, doi = {10.1016/j.jpba.2025.116802}, pmid = {40086049}, issn = {1873-264X}, abstract = {The focus of this study is to explore the impact of gut microbiota in different states on the blood components of couplet medications (dried toad skin and radix clematidis) and to identify drug metabolites associated with the gut microbiota. By constructing a pseudo-sterile rat model and combining non-targeted metabolomics with plasma pharmacology, we found that the plasma metabolites of couplet medications underwent significant changes in different gut microbiome environments. The GABA and PGE1 levels in the model group and the model+TCM (traditional chinese medicine) group were both significantly lower than those in the normal+TCM group. When the gut microbiota is imbalanced, drug interventions cannot significantly increase the levels of GABA and PGE1. It further confirmed the correlation between the levels of GABA and PGE1 and the gut microbiota. Based on the results of non-targeted metabolomics, we applied network pharmacology and molecular docking to explore the core targets for colorectal cancer treatment based on gut microbiota. In the end, we identified TNF and PPARG as the two core targets. These research findings provide a possibility for clarifying the molecular mechanisms of couplet medications in the treatment of colorectal cancer. It also laid the foundation for further clarifying the molecular mechanisms of Chanling Paste in the treatment of colorectal cancer.}, }
@article {pmid40085697, year = {2025}, author = {Kang, Z and Chen, L and Li, P and Zheng, Z and Shen, J and Xiao, Z and Miao, Y and Yang, Y and Chen, Q}, title = {A polyvalent vaccine for selectively killing tumor-associated bacteria to prevent cancer metastasis.}, journal = {Science advances}, volume = {11}, number = {11}, pages = {eadt0341}, pmid = {40085697}, issn = {2375-2548}, mesh = {Animals ; Mice ; *Neoplasm Metastasis/prevention &amp; control ; Female ; *Bacterial Vaccines/immunology/administration &amp; dosage ; *Cancer Vaccines/immunology/administration &amp; dosage ; Humans ; Cell Line, Tumor ; Bacteria/immunology/drug effects ; Disease Models, Animal ; Breast Neoplasms/immunology/pathology ; Antigens, Bacterial/immunology ; Enterococcus faecalis/immunology ; }, abstract = {Specific bacteria, including Fusobacterium nucleatum, Streptococcus sanguis, Enterococcus faecalis, and Staphylococcus xylosus, have been identified as contributors to breast cancer metastasis. Due to limitations such as lack of selectivity, traditional antibiotic therapies face obstacles in eliminating intratumoral bacteria. Herein, this work proposes the use of therapeutic vaccines to selectively target and eliminate harmful bacteria within tumors. A multivalent vaccine encapsulating both insoluble and soluble bacterial antigens was developed, addressing the shortcomings of traditional antibacterial vaccines by balancing broad antigen coverage with effective immune activation. This vaccine induces robust downstream immune responses to eliminate F. nucleatum, S. sanguis, E. faecalis, and S. xylosus, demonstrating notable therapeutic and preventive efficacy in bacteria-induced cancer metastasis models. Unexpectedly, vaccinated infected mice showed even slower tumor metastasis than uninfected mice. Overall, this study validates the potential of nanovaccines in modulating the intratumoral microbiome for tumor therapy and highlights tumor-associated bacterial infections as potential promising antitumor targets.}, }
@article {pmid40085302, year = {2025}, author = {Pardiñas López, S and García-Caro, ME and Vallejo, JA and Aja-Macaya, P and Conde-Pérez, K and Nión-Cabeza, P and Khouly, I and Bou, G and Cendal, AIR and Díaz-Prado, S and Poza, M}, title = {Anti-inflammatory and antimicrobial efficacy of coconut oil for periodontal pathogens: a triple-blind randomized clinical trial.}, journal = {Clinical oral investigations}, volume = {29}, number = {4}, pages = {182}, pmid = {40085302}, issn = {1436-3771}, mesh = {Humans ; *Coconut Oil/therapeutic use ; Male ; Female ; *Saliva/microbiology ; *Chlorhexidine/therapeutic use ; Middle Aged ; *Anti-Inflammatory Agents/therapeutic use/pharmacology ; Adult ; Periodontitis/microbiology/therapy/drug therapy ; Gingival Crevicular Fluid/chemistry ; Biomarkers/analysis ; Interleukin-6/analysis ; Tumor Necrosis Factor-alpha/analysis ; Treatment Outcome ; DNA, Bacterial/analysis ; Anti-Infective Agents, Local/therapeutic use ; }, abstract = {OBJECTIVES: To evaluate the effect of coconut oil on the oral bacteriome and inflammatory response in patients with periodontitis by integrating next-generation sequencing analyses of pathogenic bacterial shifts and quantification of inflammatory markers, thereby assessing its potential as a natural adjunct to standard nonsurgical periodontal therapy.<br><br>MATERIALS AND METHODS: A triple-blind clinical trial was conducted with 30 participants diagnosed with periodontitis, randomized into 3 groups: (1) coconut oil, (2) chlorhexidine and (3) placebo. Saliva and gingival crevicular fluid (GCF) samples were collected before treatment, one month after treatment, and one month post-non-surgical periodontal therapy. Bacterial DNA was extracted, and the V3-V4 region of the 16&#xa0;S rRNA gene was PCR-amplified and sequenced using Illumina MiSeq technologies. Inflammatory biomarkers, including Interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-&#x3b1;), were quantified from GCF samples.<br><br>RESULTS: Coconut oil treatment significantly reduced pathogenic bacterial families such as Spirochaetaceae and Tannerellaceae while promoting beneficial bacteria such as Streptococcaceae. At the genus and species levels, coconut oil reduced pathogens such as Tannerella forsythia and Treponema denticola along with increase in beneficial bacteria such as Streptococcus. The subgingival microbial dysbiosis index improved significantly in both coconut oil and chlorhexidine groups. Furthermore, the coconut oil demonstrated a reduction in IL-6 and TNF-&#x3b1; levels, indicating decreased local inflammation.<br><br>CONCLUSIONS: Coconut oil treatment significantly modulated the oral microbiome and reduced inflammatory markers in patients with periodontitis, suggesting its potential as a natural and effective adjunct in periodontal therapy.<br><br>CLINICAL RELEVANCE: This study highlights coconut oil's potential as a natural adjunct in periodontal therapy, effectively reducing pathogenic bacteria and inflammatory markers (IL-6, TNF-&#x3b1;). It offers a safe alternative to chlorhexidine, promoting microbiome balance and improved periodontal health.}, }
@article {pmid40085266, year = {2025}, author = {Li, J and Alperstein, L and Tatsumi, M and de Nys, R and Nappi, J and Egan, S}, title = {Bacterial Supplements Significantly Improve the Growth Rate of Cultured Asparagopsis armata.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {27}, number = {2}, pages = {65}, pmid = {40085266}, issn = {1436-2236}, support = {RG220026//UNSW Science Faculty/ ; RG0027//Sea Forest Ltd./ ; }, mesh = {*Pseudoalteromonas/genetics/growth &amp; development ; *Aquaculture ; *RNA, Ribosomal, 16S/genetics ; Seaweed/microbiology ; Rhodobacteraceae/genetics/growth &amp; development ; Rhodophyta ; Microbiota ; }, abstract = {Seaweed aquaculture is an expanding industry with innovative applications beyond the traditional uses as human foods and phycocolloids. Asparagopsis armata, a red seaweed, is cultivated as a feed supplement to reduce methane emission from ruminants. The manipulation of microbiota with seaweed beneficial microorganisms (SBMs) has shown promise in enhancing disease resistance and growth in seaweeds and has potential to aid the cultivation of A. armata. In this study, we developed a growth assay for the rapid selection of bacteria that promote the growth of A. armata tetrasporophytes. We tested bacterial strains from the genera Phaeobacter and Pseudoalteromonas for their impact on the growth of A. armata, as these bacteria have been recognized for their beneficial traits in other seaweeds. All strains significantly enhanced the specific growth rate (SGR) of A. armata tetrasporophytes compared to controls without bacterial treatment. Bacterial 16S rRNA gene amplicon sequencing confirmed the presence of the inoculated growth-promoting SBMs (SBM-Gs) in A. armata cultures with no significant impacts on the resident microbial community. Co-occurrence network analysis of the resulting communities demonstrated that the inoculated Phaeobacter spp. formed distinct modules, exclusively interacting with resident Phaeobacter species, while the Pseudoalteromonas sp. was absent from the network. These results demonstrate that microbial inoculation is an effective strategy for incorporating SBM-Gs into the A. armata microbiota to promote growth. The tested SBM-Gs may exert their influence by interacting with specific resident species or by directly affecting host physiology, resulting in minimal undesired effects on the microbiome.}, }
@article {pmid40085258, year = {2025}, author = {Dinleyici, M and Harmanci, K and Arslantas, D and Vandenplas, Y and Dinleyici, EC}, title = {A web-based questionnaire to evaluate risk factors to develop cow milk allergy.}, journal = {European journal of pediatrics}, volume = {184}, number = {4}, pages = {250}, pmid = {40085258}, issn = {1432-1076}, mesh = {Humans ; Female ; Risk Factors ; Cross-Sectional Studies ; *Milk Hypersensitivity/epidemiology ; Male ; Surveys and Questionnaires ; Pregnancy ; Infant ; Child, Preschool ; Gastrointestinal Microbiome ; Internet ; Case-Control Studies ; Finland/epidemiology ; Animals ; Adult ; Pets ; Child ; Infant, Newborn ; }, abstract = {UNLABELLED: Many environmental, genetic, and epigenetic variables are considered to influence the evolution of cow's milk allergy (CMA). The gastro-intestinal microbiota may play a direct role in or inhibit tolerance development. In this study, we planned to evaluate the presence of previously identified risk factors for microbiota composition. This study used a cross-sectional electronic survey in Turkiye, utilizing a national convenience sample of 270 children with CMA, as reported by their caregivers, and 2154 healthy controls. We developed a web-based questionnaire to gather information on pregnancy and maternal-related factors, delivery mode, feeding patterns, antibiotic use, and the presence of pets in the home. The risk factors affecting CMA were maternal age (OR 0.897; 0.862-0.934, p < 0.01), presence of maternal allergic disorders (OR 3.070; 1.891-4.983, p < 0.001) and in both parents (OR 3.831; 1.202-12.210, p < 0.001), maternal weight at conception (OR 1.016; 1.003-1.030, p < 0.05), maternal weight gain during pregnancy (OR 1.033; 1.012-1.056, p < 0.01), (absence of a) pet at home (OR 1.394; 1.003-1.938, p < 0.05), intrapartum antibiotic use (OR 1.469; 1.092-1.975, p < 0.05), antibiotic use during the first 6 months of life (OR 1.933; 1.306-2.863, p < 0.001), and number of householders (OR 0.794; 0.650-0.969, p < 0.05).<br><br>CONCLUSION: In addition to allergic disorders in parents, maternal weight and weight gain during pregnancy, intrapartum and first 6 months of life antibiotic use, and the presence of pets at home were found to be microbiota-related risk factors in children with CMA. Potential strategies related to microbiota composition may contribute positively to the disease's development and progression.<br><br>WHAT IS KNOWN: &#x2022;&#xa0;The gut microbiome contributes to the development of cow milk allergy, and disrupted microbiota&#xa0;maturation during the first year of life appears to be common in pediatric food allergies. &#x2022;&#xa0;Factors that influence an infant's microbiota within the first 1000 days and the relationship between these&#xa0;factors and microbiota may enhance allergy diagnosis, prevention, and treatment.<br><br>WHAT IS NEW: &#x2022;&#xa0;Besides parental allergy disorders, maternal weight and weight gain during pregnancy, antibiotic use&#xa0;during intrapartum and first six months of life, and the presence of pets at home were identified as microbiota-related&#xa0;risk factors in children with CMA.}, }
@article {pmid40085117, year = {2025}, author = {Sands, N and Malka, S and Vecere, G and Lee, M and Stockman, J and Krumbeck, JA}, title = {Determining the Fecal Microbiome of Healthy Cockatiels (Nymphicus hollandicus) Fed Seeds Versus Formulated Pelleted Diets by Next-Generation DNA Sequencing.}, journal = {Journal of avian medicine and surgery}, volume = {39}, number = {1}, pages = {2-11}, doi = {10.1647/AVIANMS-D-24-00010}, pmid = {40085117}, issn = {1082-6742}, mesh = {Animals ; *Cockatoos/microbiology ; *Feces/microbiology ; *Animal Feed/analysis ; *Diet/veterinary ; Seeds/microbiology ; Bacteria/classification/isolation &amp; purification/genetics ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/veterinary ; Microbiota ; }, abstract = {Fecal samples were collected from 34 clinically healthy cockatiels (Nymphicus hollandicus), with 15 consuming a commercially available seed diet and 19 on a formulated pelleted diet. Next-generation DNA sequencing was used to analyze the samples, revealing a diverse microbial landscape. A total of 179 bacterial species from 94 genera and 244 fungal species from 156 genera were identified across both diet groups. Although no significant differences in microbial diversity were observed between the 2 groups, distinct microbial compositions were noted. Notably, Corynebacterium kroppenstedtii and Enterococcus durans/faecium were enriched in the pellet-fed group, whereas Lactobacillus oris and a species in the Brevinemataceae family were more abundant in the seed-fed group. In the mycobiome, Aspergillus penicillioides, Meyerozyma sp, and Fusarium sp were enriched in the pelleted diet group, whereas Bulleribasidium oberjochense was more prevalent in the seed diet group. These findings highlight the nuanced effects of diet on the fecal microbiome of cockatiels, providing valuable insights for avian health management and potential probiotic interventions.}, }
@article {pmid40084919, year = {2025}, author = {Baalbaki, N and Slob, EMA and Kazer, SW and I Abdel-Aziz, M and Bogaard, HJ and Golebski, K and Maitland-van der Zee, AH}, title = {The Omics Landscape of Long COVID-A Comprehensive Systematic Review to Advance Biomarker, Target and Drug Discovery.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.16526}, pmid = {40084919}, issn = {1398-9995}, support = {//Health~Holland/ ; }, abstract = {An estimated 10% of coronavirus disease (COVID-19) survivors suffer from persisting symptoms referred to as long COVID (LC), a condition for which approved treatment options are still lacking. This systematic review (PROSPERO: CRD42024499281) aimed to explore the pathophysiological mechanisms underlying LC and potential treatable traits across symptom-based phenotypes. We included studies with primary data, written in English, focusing on omics analyses of human samples from LC patients with persistent symptoms of at least 3 months. Our search in PubMed and Embase, conducted on January 8, 2024, identified 642 studies, of which 29 met the inclusion criteria after full-text assessment. The risk of bias was evaluated using the Joanna Briggs Institute appraisal tool. The synthesis of omics data, including genomics, transcriptomics, proteomics, metabolomics, and metagenomics, revealed common findings associated with fatigue, cardiovascular, pulmonary, neurological, and gastrointestinal phenotypes. Key findings included mitochondrial dysfunction, dysregulated microRNAs associated with pulmonary dysfunction, tissue impairment, blood-brain barrier disruption, coagulopathy, vascular dysfunction, microbiome disturbances, microbial-derived metabolite production and persistent inflammation. Limitations include cross-study heterogeneity and variability in sampling methods. Our review emphasizes the complexity of LC and the need for further longitudinal omics-integrated studies to advance the development of biomarkers and targeted treatments.}, }
@article {pmid40084911, year = {2025}, author = {Mojica, MF and Hausman, BS and Pearlmutter, BS and Zink, EG and Wilson, BM and Villamil, V and Saiz, C and Mahler, G and Vila, AA and Sangwan, N and Donskey, CJ and Bonomo, RA}, title = {Impact of tebipenem pivoxil on the intestinal microbiota and on establishment of colonization with carbapenem-resistant Klebsiella pneumoniae in mice.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0234624}, doi = {10.1128/spectrum.02346-24}, pmid = {40084911}, issn = {2165-0497}, abstract = {Tebipenem pivoxil has potent in vitro activity against Enterobacterales pathogens, but requires combination with β-lactamase inhibitor to achieve activity against carbapenemase producers, including metallo-β-lactamases (MBLs). Herein, we evaluate the potential of tebipenem pivoxil, alone and in combination with the prodrug of the experimental MBL inhibitor CS319 (CS319-piv-SAc), to disrupt the indigenous mice microbiota of the colon and promote colonization by pathogens. The effect of antibiotic treatment (daily for 3 days with subcutaneous saline [control], subcutaneous clindamycin, oral tebipenem pivoxil alone and in combination with CS319-piv-Sac, or oral CS319-piv-Sac) on the intestinal microbiota was assessed by culture for enterococci and facultative Gram-negative bacilli and by 16S rRNA amplicon sequencing. Mice were also challenged with 10,000 colony-forming units (CFU) of multidrug-resistant (MDR) strain Klebsiella pneumoniae blaNDM-1, 6 h after the second dose. The concentrations of the MDR K. pneumoniae in stool were measured on days 1, 3, and 6 after challenge. In comparison to saline controls, clindamycin (P = 0.001) and tebipenem pivoxil plus CS319-piv-SAc (P = 0.02) treatment resulted in significant changes in the alpha diversity patterns, whereas tebipenem pivoxil and CS319-piv-SAc individual treatments did not (P > 0.05). Moreover, clindamycin treatment resulted in substantial overgrowth of MDR K. pneumoniae (mean concentration after 6 days of infection, 6.1 vs 2.9 log10 CFU/g stool), whereas the other treatments did not (≤3.6 log10 CFU/g). Although tebipenem pivoxil alone or in combination with an MBL inhibitor, CS319, caused alteration of the mice intestinal microbiota, neither treatment promoted overgrowth of carbapenem-resistant K. pneumoniae.IMPORTANCEIn this work, we used a mouse model to determine the impact of tebipenem pivoxil alone and in combination with a prodrug of an experimental metallo-β-lactamase inhibitor, CS319, on the intestinal microbiota and on the establishment of colonization with carbapenem-resistant Klebsiella pneumoniae. We found that while treatment with tebipenem pivoxil plus the prodrug of CS319 caused alteration of the intestinal microbiota, it did not promote the overgrowth of carbapenem-resistant K. pneumoniae. Although additional studies are needed to examine the impact of tebipenem pivoxil treatment on other multidrug-resistant Gram-negative bacilli, Clostridioides difficile, and Candida spp., our study is a step forward in the understanding of the potential effect of this oral carbapenem on the indigenous microbiota of the colon and on the promotion of colonization by pathogens.}, }
@article {pmid40084893, year = {2025}, author = {Yuan, S and Wu, Y and Balcazar, JL and Wang, D and Zhu, D and Ye, M and Sun, M and Hu, F}, title = {Expanding the potential soil carbon sink: unraveling carbon sequestration accessory genes in vermicompost phages.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0029625}, doi = {10.1128/aem.00296-25}, pmid = {40084893}, issn = {1098-5336}, abstract = {The compost microbiome is important in regulating soil carbon sequestration. However, there is limited information concerning phage communities and phage-encoded auxiliary metabolic genes (AMGs) in compost-applied soils. We combined metagenomics and meta-viromes to explore the potential role of bacterial and phage communities in carbon sequestration in the compost microbiome. The experiment comprised swine manure compost (SW) and vermicompost (VE) applied to the soil along with a control treatment (CK). The bacterial community richness decreased after swine manure application and increased after vermicomposting compared to the control treatment. The phage community in the vermicompost-applied soil was dominated (63.1%) by temperate phages. In comparison, the communities of the swine manure compost-applied soil (92.7%) and control treatments (75.4%) were dominated by virulent phages. Phage-encoded carbon sequestration AMGs were detected in all three treatments, with significant enrichment in the vermicompost-applied soil. The average carbon sequestration potential (the coverage ratio of phage AMGs:total genes) of phage AMGs (aceF, GT11, and GT6) in the vermicompost-applied soil (65.18%) was greater than in the swine manure-applied (0) and control soils (50.21%). The results highlight the role of phage-encoded AMGs in improving soil carbon sequestration in vermicompost-applied soil. The findings provide new avenues for increasing soil carbon sequestration.IMPORTANCEThe phage-bacteria interactions have a significant impact on the global carbon cycle. Soil microbial carbon sequestration is a process in combination withcarbon sequestration genes and growth activity. This is the first study aimed at understanding the carbon sequestration potential of phage communities in vermicompost. The results of this study provide variations in carbon sequestration genes in vermicompost microbial communities, and some novel phage auxiliary metabolic genes were revealed to assist bacterial communities to increase soil carbon sequestration potential. Our results highlight the importance of phages in soil carbon sequestration from the perspective of phage-bacterial community interactions.}, }
@article {pmid40084887, year = {2025}, author = {Sun, Y-Y and Liu, N-N}, title = {Mycobiome: an underexplored kingdom in cancer.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {}, number = {}, pages = {e0026124}, doi = {10.1128/mmbr.00261-24}, pmid = {40084887}, issn = {1098-5557}, abstract = {SUMMARYThe human microbiome, including bacteria, fungi, archaea, and viruses, is intimately linked to both health and disease. The relationship between bacteria and disease has received much attention and intensive investigation, while that of the fungal microbiome, also known as mycobiome, has lagged far behind bacteria. There is growing evidence showing mycobiome dysbiosis in cancer patients, and certain cancer-specific fungi may contribute to cancer progression by interacting with both host and bacteria. It was also demonstrated that the role of fungi-derived products in cancer should also not be underestimated. Therefore, investigating how fungal pathogenesis contributes to the onset and spread of cancer would yield crucial information for cancer diagnosis, prevention, and anti-cancer therapy.}, }
@article {pmid40084873, year = {2025}, author = {Soh, M and Er, S and Low, A and Jaafar, Z and de Boucher, R and Seedorf, H}, title = {Spatial and temporal changes in gut microbiota composition of farmed Asian seabass (Lates calcarifer) in different aquaculture settings.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0198924}, doi = {10.1128/spectrum.01989-24}, pmid = {40084873}, issn = {2165-0497}, abstract = {UNLABELLED: The microbiota composition of healthy farmed fishes remains poorly characterized for many species. This study explores the influence of the external environment and innate factors that may shape the gut microbiota of farmed Asian seabass, Lates calcarifer. The α-diversity based on Shannon, Simpson, and Chao1 indices was lower for fishes reared in sea cages and tanks than for fishes that experienced a transfer from sea cages to tanks. Longitudinal analyses of gut segments revealed no significant differences in alpha diversity between segments within the same containment type, except for the Chao1 index between the stomach and pyloric cecum of sea-caged fishes. β-diversity analysis using weighted UniFrac distance and Bray-Curtis dissimilarity demonstrated that fish reared in the same containment type shared similar microbial communities. PERMANOVA tests confirmed that containment type, farm, and batch significantly influenced these distances. Containment type accounted for 10.4% of the observed diversity, farm for 29.8%, and batch for 10.7%. Genera comprising potential pathogens such as Aeromonas, Flavobacterium, and Vibrio were differentially abundant along the guts of fish from different containment types and particularly increased in tanks. Microbiota changes were observed with host age and gut segment, with differentially abundant microbial genera identified along the gut and as the seabass grew. Comparing the hindgut microbiota of Asian seabass to other species of farmed fishes revealed host-specific clustering as indicated by PERMANOVA. Overall, these findings underscore the significance of containment conditions on the gut microbiota of Asian seabass, with broad implications for aquaculture practices.<br><br>IMPORTANCE: Understanding the microbiota composition of healthy farmed fishes is crucial for optimizing aquaculture practices. This study highlights the significant influence of containment conditions on the gut microbiota of farmed Asian seabass (Lates calcarifer). By demonstrating that gut microbiota diversity and community composition are shaped by containment type, farm location, and batch, the research provides valuable insights into how external environmental factors and innate host factors interact to influence fish health. The findings, particularly the differential abundance of potential pathogens in various containment types, underscore the need for tailored management strategies in aquaculture. This research not only advances our knowledge of fish microbiota but also has broad implications for improving the sustainability and productivity of aquaculture practices.}, }
@article {pmid40084403, year = {2025}, author = {Vanhentenrijk, S and Grodin, JL and Augusto, SN and Tang, WHW}, title = {Hereditary Transthyretin Cardiac Amyloidosis With the p.V142I Variant: Mechanistic Insights and Diagnostic Challenges.}, journal = {Circulation. Heart failure}, volume = {}, number = {}, pages = {e012469}, doi = {10.1161/CIRCHEARTFAILURE.124.012469}, pmid = {40084403}, issn = {1941-3297}, abstract = {The most common form of hereditary transthyretin cardiac amyloidosis (hATTR-CA) in the United States and the United Kingdom is the p.V142I variant. About 3% to 4% of patients with African ancestry carry this genetic predisposition to develop signs and symptoms of hATTR-CA. Nevertheless, clinical manifestations of hATTR-CA appear only late in the fifth and sixth decades of life, despite its clear genetic background. Imbalances in native protein-stabilizing and elementary breakdown cellular mechanisms are postulated as potential causes for affecting transthyretin structural integrity and myocardial fibril deposition. Noncoding variants, epigenetic and environmental factors, as well as gut microbiome derangements may serve as disease-modifying factors that feature detrimental amyloidogenic organ involvement and impact disease severity. Organ amyloid deposition varies widely among different carriers of a genetic transthyretin variant. The genotype-phenotype interdependence causes unpredictable phenotypic penetrance that results in a variety of signs and symptoms and patient outcomes. Cardiovascular biomarkers and multimodality imaging may identify initial amyloidogenic organ involvement. These early clinical clues through the course of hATTR-CA offer a window of opportunity for early treatment onset to cease disease progression and alter prognosis. Identifying at-risk patients requires information on the genetic background of probands and their relatives. Initiatives to reveal asymptomatic gene carriers early in the disease should be encouraged, as it necessitates stringent patient follow-up and immediate treatment onset to reduce the burden of heart failure hospitalization and mortality in hATTR-CA.}, }
@article {pmid40084003, year = {2025}, author = {Oliwa-Libumska, K and Jaworska-Czerwinska, A and Mallek-Grabowska, M and Wlodarski, R and Zuratynski, P and Kozlowski, B}, title = {Fecal microbiota transplantation in a patient hospitalized in the intensive care unit - Case report.}, journal = {Heliyon}, volume = {11}, number = {4}, pages = {e42793}, pmid = {40084003}, issn = {2405-8440}, abstract = {Clostridioides difficile infections are difficult and serious problem occurring in patients staying in intensive care units. In recent years, the number and severity of these infections, as well as the mortality rate, have been increasing, posing a serious epidemiological problem. This is caused, among other factors, by stressors, artificial nutrition, and sepsis, which lead to disturbances in the patients' microbiome. Basic method of treatment is antibiotic therapy, however some patients experience recurrences of the infection. Fecal Microbiota Transplantation (FMT) is one of the alternative methods used in treating recurring infections of Clostridioides difficile etiology (Clostridioides Difficile Infection, CDI). The presented case refers to a patient with severe pseudomembranous enterocolitis who underwent FMT twice. This report highlights the role of FMT in the treatment of severe Clostridioides difficile infections in critically ill patients.}, }
@article {pmid40083911, year = {2025}, author = {Intze, E and Schaubeck, M and Pourjam, M and Neuhaus, K and Lagkouvardos, I and Hitch, TCA and Clavel, T}, title = {The infant microbiota hopscotches between community states toward maturation-longitudinal stool parameters and microbiota development in a cohort of European toddlers.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf016}, pmid = {40083911}, issn = {2730-6151}, abstract = {The development of the gut microbiome is critical during early life and is associated with infant health. To test whether this development is deterministic and how it is influenced by factors such as diet and mode of birth, we studied microbiota profiles and fecal parameters of 540 European infants, fed a synbiotic or control infant formula during their first year of life, up to 36 months of age. The diversity of the microbiota gradually increased until 36 months, at which point it resembled adult community states, indicating that microbiota maturation had occurred. However, distinct gut microbiota community states were observed that differed at each stage of maturation. The distribution of infants within the communities even at 36 months was significantly influenced by early life events, with a higher prevalence of infants born by cesarean section having the immature M36-C1 community state at 36 months. The microbial community state at one time point was not predictive of the next; instead, we observed hopscotching of the infant microbiota between different community states. This work provides new longitudinal data on the infant gut microbiome in relation to diet, suggesting that ecosystem development is not deterministic, but that early life events influence the community state of an individual's gut microbiota beyond infancy.}, }
@article {pmid40083787, year = {2025}, author = {Štempelová, L and Micenková, L and Andrla, P and Strompfová, V}, title = {The skin microbiome on healthy and inflammatory altered canine skin determined by next generation sequencing.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1528747}, pmid = {40083787}, issn = {1664-302X}, abstract = {INTRODUCTION: Human and animal skin is colonized by a complex microbial population. An imbalance of these microorganisms is often associated with dermatological diseases.<br><br>METHODS: The aim of this work was to describe the skin bacterial microbiota composition of healthy dogs and dogs with inflammatory skin lesions. Genomic DNA was sequenced using primers that target the V4 region of the bacterial 16S rRNA gene. Superficial skin swabs were collected from eight body areas of six healthy dogs (n =&#x202f;48) and directly from inflammatory altered canine skin (n =&#x202f;16).<br><br>RESULTS: The skin of healthy dogs was predominantly colonized by phylum Bacillota (34.4&#x202f;&#xb1;&#x202f;27.2%), followed by Actinomycetota (32.2&#x202f;&#xb1;&#x202f;20.3%), Pseudomonadota (16.4&#x202f;&#xb1;&#x202f;12.2%), and Bacteroidota (8.7&#x202f;&#xb1;&#x202f;11.6%). At the level of genera, Streptococcus spp. (19.4&#x202f;&#xb1;&#x202f;26.1%) was the most abundant genus across all samples collected from healthy skin, followed by Curtobacterium (5.4&#x202f;&#xb1;&#x202f;12.1%), Bacteroides (5.2&#x202f;&#xb1;&#x202f;11.1%) and Corynebacterium_1 (4.3&#x202f;&#xb1;&#x202f;13.2%). More specifically, Streptococcus spp. was the most abundant on the chin (49.0&#x202f;&#xb1;&#x202f;35.5%), nose (37.9&#x202f;&#xb1;&#x202f;32.1%), perianal region (21.1&#x202f;&#xb1;&#x202f;28.2%), abdomen (11.0&#x202f;&#xb1;&#x202f;12.8%), dorsal back (12.4&#x202f;&#xb1;&#x202f;10.3%) and interdigital area (5.5&#x202f;&#xb1;&#x202f;2.2%). Curtobacterium spp. was predominant on inner pinna (17.8&#x202f;&#xb1;&#x202f;24.8%) and axilla (6.7&#x202f;&#xb1;&#x202f;10.8%). Alpha diversity analysis (Shannon index) showed maximum on interdigital area but minimum on a chin (p-value: 0.0416). Beta diversity analysis showed clustering across samples from the individual skin sites but also across samples collected from individual dogs. Staphylococcus spp. was the most abundant genus in 12/16 samples collected from inflammatory skin. In addition, a lower bacterial diversity was observed in samples from skin lesions compared to samples from healthy canine skin.<br><br>DISCUSSION: The results confirm the fact that the microbiome of healthy skin is very diverse. Compared to other studies, streptococci predominated on healthy canine skin. Shannon index showed only minor differences in diversity between different parts of canine skin. Results of beta-diversity showed the fact that the main force driving the skin microbiota composition is the individual, followed by the skin site. On the area of skin lesions, dysbiosis was observed with a significant predominance of staphylococci.}, }
@article {pmid40083779, year = {2025}, author = {Liu, Y and Yan, D and Chen, R and Zhang, Y and Wang, C and Qian, G}, title = {Recent insights and advances in gut microbiota's influence on host antiviral immunity.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1536778}, pmid = {40083779}, issn = {1664-302X}, abstract = {A diverse array of microbial organisms colonizes the human body, collectively known as symbiotic microbial communities. Among the various pathogen infections that hosts encounter, viral infections represent one of the most significant public health challenges worldwide. The gut microbiota is considered an important biological barrier against viral infections and may serve as a promising target for adjuvant antiviral therapy. However, the potential impact of symbiotic microbiota on viral infection remains relatively understudied. In this review, we discuss the specific regulatory mechanisms of gut microbiota in antiviral immunity, highlighting recent advances in how gut microbiota regulate the host immune response, produce immune-related molecules, and enhance the host's defense against viruses. Finally, we also discuss the antiviral potential of oral probiotics.}, }
@article {pmid40083725, year = {2025}, author = {Irwin, MT and Rahalinarivo, V and Ramorasata, B and Raharison, JL and Ranaivoarisoa, JF and Gherardi, CNM and Rothman, JM}, title = {More Choosy for Minor Foods: Diet, Seasonality and Food Selection in Sympatric Frugivorous and Folivorous Lemurs.}, journal = {Ecology and evolution}, volume = {15}, number = {3}, pages = {e71069}, pmid = {40083725}, issn = {2045-7758}, abstract = {Despite traditional dietary categories common in primatology (folivore, frugivore, insectivore), most primates use one or more food types beyond their primary one. Among lemurs, folivores tend to have a complicated, long gastrointestinal tract with an enlarged cecum, shearing teeth, and microbiome adaptations to foliage, while frugivores have simple teeth and guts and fast gut passage. Yet frugivores often eat some leaves, and folivores eat some fruit, and little is known about the selection rules they follow within each food type. We quantified diet and food chemistry for two sympatric rainforest lemurs: a cathemeral frugivore (brown lemur, Eulemur fulvus) and a diurnal folivore (diademed sifaka, Propithecus diadema) over 18 and 13 months. Brown lemurs ate 78.3% fruit and 13.0% leaves; sifakas ate 52.8% leaves and 37.9% fruit/seed; both ate fruit/seed most in the resource-abundant season, increasing leaf/flower consumption in the lean season. Both had diverse diets (128 and 81 plant species) but selected almost entirely different species; however, within fruit and leaf categories, their foods overlapped substantially in nutritional content. They were more selective in their secondary foods: sifakas selected higher-energy fruits and brown lemurs selected leaves higher in protein and minerals. This indicates a balancing function: frugivores selecting leaves strategically to compensate for low-protein, low-mineral fruit and folivores selecting fruit/seed to compensate for low-energy leaves. That said, it is puzzling why sifakas ignored some leaf species eaten by brown lemurs that were high in protein and minerals-this suggests these nutrients are not prioritized or limiting for sifakas. Other factors likely contribute to the mutual exclusivity in food selection, particularly plant secondary metabolites not measured here or the (poorly-understood) metabolic costs of eating nutrients in excess. More research is needed to fully understand food choices, how these promote niche differentiation, and their consequences for animals, communities, and ecosystems.}, }
@article {pmid40083550, year = {2025}, author = {Ng, HY and Liao, Y and Cheung, CL and Zhang, R and Chan, KH and Seto, WK and Leung, WK and Hung, IFN and Lam, TTY and Cheung, KS}, title = {Gut microbiota is associated with persistence of longer-term BNT162b2 vaccine immunogenicity.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1534787}, pmid = {40083550}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Male ; Female ; Middle Aged ; Adult ; *BNT162 Vaccine/immunology ; *SARS-CoV-2/immunology ; *COVID-19/immunology ; Antibodies, Neutralizing/blood/immunology ; Immunogenicity, Vaccine ; Prospective Studies ; Antibodies, Viral/blood/immunology ; Hong Kong ; Feces/microbiology ; }, abstract = {INTRODUCTION: BNT162b2 immunogenicity wanes with time and we investigated association between gut microbiota and longer-term immunogenicity.<br><br>METHODS: This cohort study prospectively recruited adult BNT162b2 two-dose recipients from three vaccination centers in Hong Kong. Blood samples were collected at baseline and day 180 after first dose, and tested for neutralizing antibodies (NAb) against receptor-binding domain (RBD) of wild type SARS-CoV-2 virus using chemiluminescence immunoassay. Shotgun DNA metagenomic sequencing was performed to characterize baseline stool microbiome. Baseline metabolites were measured by gas and liquid chromatography-tandem mass spectrometry (GC-MS/MS and LC-MS/MS). Primary outcome was persistent high NAb response (defined as top 25% of NAb level) at day 180. Putative bacterial species and metabolic pathways were identified using linear discriminant analysis [LDA] effect size analysis. Multivariable logistic regression adjusting for clinical factors was used to derive adjusted odds ratio (aOR) of outcome with bacterial species and metabolites.<br><br>RESULTS: Of 242 subjects (median age: 50.2 years [IQR:42.5-55.6]; male:85 [35.1%]), 61 (25.2%) were high-responders while 33 (13.6%) were extreme-high responders (defined as NAb&#x2265;200AU/mL). None had COVID-19 at end of study. Ruminococcus bicirculans (log10LDA score=3.65), Parasutterella excrementihominis (score=2.82) and Streptococcus salivarius (score=2.31) were enriched in high-responders, while Bacteroides thetaiotaomicron was enriched in low-responders (score=-3.70). On multivariable analysis, bacterial species (R. bicirculans-aOR: 1.87, 95% CI: 1.02-3.51; P. excrementihominis-aOR: 2.2, 95% CI: 1.18-4.18; S. salivarius-aOR: 2.09, 95% CI: 1.13-3.94) but not clinical factors associated with high response. R. bicirculans positively correlated with most metabolic pathways enriched in high-responders, including superpathway of L-cysteine biosynthesis (score=2.25) and L-isoleucine biosynthesis I pathway (score=2.16) known to benefit immune system. Baseline serum butyrate (aOR:10.00, 95% CI:1.81-107.2) and isoleucine (aOR:1.17, 95% CI:1.04-1.35) significantly associated with extreme-high vaccine response.<br><br>CONCLUSION: Certain gut bacterial species, metabolic pathways and metabolites associate with longer-term COVID-19 vaccine immunogenicity.}, }
@article {pmid40083091, year = {2025}, author = {Chen, Z and Ma, L and Chen, S and Huang, Y and Qin, Z and Lin, L and Shi, F}, title = {Effects of enrofloxacin and povidone-iodine on immunity, the intestinal microbiome and transcriptome of juvenile grass carp (Ctenopharyngodon idella).}, journal = {Journal of fish biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jfb.70018}, pmid = {40083091}, issn = {1095-8649}, support = {4210061024//National Natural Science Foundation of China/ ; }, abstract = {Gut microbiota stability is crucial for maintaining fish health. In aquaculture, antibiotics and disinfectants are frequently used to manipulate the host gut microbiota, but the combined effects on asymptomatic fish remain unclear. We investigated the effects of single and combined treatments with antibiotics and disinfectants on grass carp (Ctenopharyngodon idella) gut health, immune response, microbiome dynamics and transcriptome profile. In a 2-week trial, grass carp were exposed to enrofloxacin (10 mg/kg) in the basal diet or povidone-iodine (0.05 mg/L) in fresh water. A 14-day treatment led to significant oxidative stress, as indicated by reduced catalase and total superoxide dismutase activities. Digestive enzyme activities, including amylase and lipase, were also significantly suppressed. Gut microbiota diversity decreased, with notable shifts in dominant bacterial phyla, including reduced abundances of Firmicutes and Bacteroidetes and increased Proteobacteria and Fusobacteria. Transcriptomic analysis revealed downregulation of immune-related pathways, including those linked to IgA production, and suppression of key immune-related genes, such as major histocompatibility complex 2 (MHC2) and tumour necrosis factor alpha (TNF-α). Histopathological analysis showed damaged intestinal villi, increased goblet cell numbers and significant apoptosis in intestinal epithelial cells, as confirmed by terminal deoxynucleotidyl transferase (TdT) dUTP Nick-End Labeling (TUNEL) staining and upregulation of caspase-3, caspase-8 and caspase-9. These findings demonstrate that enrofloxacin and povidone-iodine disrupt gut microbiota balance, impair mucosal immunity and induce apoptosis in grass carp.}, }
@article {pmid40082895, year = {2025}, author = {Chen, C and Deng, C and Li, Y and He, S and Liu, Y and Pan, S and Xu, W and Fang, L and Zhu, Y and Wang, Y and Jiang, X}, title = {Machine learning-derived diagnostic model of epithelial ovarian cancer based on gut microbiome signatures.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {319}, pmid = {40082895}, issn = {1479-5876}, support = {2023JJ60350//Natural Science Foundation of Hunan Province/ ; JCYJ20210324131414040//Science, Technology and Innovation Commission of Shenzhen Municipality/ ; 2019JJ80064//Hunan Natural Science Foundation/ ; }, mesh = {Humans ; Female ; *Machine Learning ; *Carcinoma, Ovarian Epithelial/microbiology/diagnosis/pathology ; *Gastrointestinal Microbiome ; *Ovarian Neoplasms/microbiology/diagnosis/pathology ; Middle Aged ; Cell Line, Tumor ; Models, Biological ; Metabolomics ; Case-Control Studies ; ROC Curve ; RNA, Ribosomal, 16S/genetics ; Adult ; Feces/microbiology ; }, abstract = {BACKGROUND: Prior studies have elucidated that alterations in gut microbiota are associated with a spectrum of tumors and metabolic disorders. However, the diagnostic value of gut microbiota in epithelial ovarian cancer remains insufficiently investigated.<br><br>METHODS: A total of 34 patients with a diagnosis of epithelial ovarian cancer (EOC), 15 patients with benign ovarian tumors (TB), and 30 healthy volunteers (NOR) were enrolled in this study. Fecal samples were collected, followed by sequencing of the V3-V4 region of the 16S rRNA gene. The clinical data and pathological characteristics were comprehensively recorded for further analysis, PICRUSt2 was utilized to conduct an analysis of microbial functional predictions, WGCNA networks were constructed by integrating microbiome and clinical data. LEfSe analysis was employed to identify microbial diagnostic markers, LASSO and SVM analyses were used to screen microbial diagnostic markers in conjunction with the Cally index, to establish a Microbial-Cally diagnostic model. Bootstrap resampling was utilized for the internal validation of the model, whereas the Hosmer-Lemeshow test and decision curve analysis (DCA) were employed to evaluate the diagnostic performance of the model. Plasma samples were subjected to untargeted metabolomics profiling, followed by differential analysis to identify key metabolites that are significantly altered in epithelial ovarian cancer. At the same time, Spearman correlation analysis was used to study the association between key microbiota and differential metabolites. The supernatants from Escherichia coli and Bifidobacterium cultures were co-cultured with SKOV3 cells. Cell proliferation, migration, and invasion were evaluated using Cell Counting Kit-8 (CCK-8) assay, Transwell migration and invasion assays. Apoptosis was assessed by flow cytometry analysis of fluorescence signals from Annexin V and propidium iodide (PI) staining.<br><br>RESULTS: Compared to Nor and TB populations, individuals diagnosed with EOC demonstrated a significantly diminished gut microbiota diversity when contrasted with both normal controls and those presenting benign conditions. Specifically, the relative abundance of Bilophila, Bifidobacterium, and other probiotics was significantly reduced in patients diagnosed with epithelial ovarian cancer (EOC), while Escherichia and Shigella demonstrated a marked enrichment within this cohort. Differential microorganisms were identified through the application of machine learning techniques to delineate the characteristic microbial profiles associated with the EOC patients. A significant correlation was identified between the Cally index and microorganisms. In conclusion, we utilized microbial biomarkers alongside the Cally to establish a diagnostic model for epithelial ovarian cancer, receiver operating characteristic (ROC) curve Area Under Curve (AUC) of 0.976 (95%CI 0.943-1.00), The AUC obtained from the Bootstrap internal validation was 0.974. The Hosmer-Lemeshow test revealed a robust concordance between the observed probabilities and the predicted probabilities generated by the model. The decision curve analysis revealed that the model provided a significant net clinical benefit. A total of 233 differential metabolites were identified between the EOC group and the NT (NOR and TB) groups. Among these, eight specific metabolites (HMDB0243492, C09265, HMDB0242046, HMDB0240606, C04171, HMDB0060557, HMDB0252797, and C21412) were exclusively derived from the microbiome. Notably, metabolite HMDB0240606 exhibited a significant positive correlation with Escherichia coli and Shigella, while it showed a significant negative correlation with Ruminococcus. In vitro studies demonstrated that Bifidobacterium possessed anti-tumor activity, whereas Escherichia coli exhibited pro-tumor activity.<br><br>CONCLUSION: This study provides the inaugural comprehensive analysis of gut microbiota composition and its differential profiles among patients with epithelial ovarian cancer, those with benign ovarian tumors, and healthy controls in Hunan province, China.}, }
@article {pmid40082677, year = {2025}, author = {Lee, S and Sfanos, K and Singla, N}, title = {The role of the urinary microbiome in genitourinary cancers.}, journal = {Nature reviews. Urology}, volume = {}, number = {}, pages = {}, pmid = {40082677}, issn = {1759-4820}, abstract = {Genitourinary cancers account for 20% of cancer instances globally and pose a substantial burden. The microbiome, defined as the ecosystem of organisms that reside within and on the human body, seems to be closely related to multiple cancers. Research on the gut microbiome has yielded substantial insights into the interactions of this entity with the immune system and cancer therapeutic efficacy, whereas the urinary microbiome has been relatively less well-studied. Advances in next-generation sequencing technologies led to new discoveries in the urinary microbiome, which might aid in early detection, risk stratification and personalized treatment strategies in genitourinary cancers. Mechanistic investigations have also suggested a role for the urinary microbiome in modulating the tumour microenvironment and host immune response. For example, distinct urinary microbial signatures have been linked to bladder cancer occurrence and recurrence risk, with specific taxa associated with cytokine production and inflammation. Urinary microbiome signatures have also been explored as potential biomarkers for non-invasive cancer detection. However, challenges remain in standardizing methodologies, validating findings across studies, and establishing causative mechanisms. As investigations into the urinary microbiome continue to evolve, so does the potential for developing microbiome-modulating therapies and enhancing diagnostic capabilities to improve outcomes in patients with genitourinary cancers.}, }
@article {pmid40082490, year = {2025}, author = {Naspolini, NF and Natividade, AP and Asmus, CIF and Moreira, JC and Dominguez-Bello, MG and Meyer, A}, title = {Early-life gut microbiome is associated with behavioral disorders in the Rio birth cohort.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8674}, pmid = {40082490}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; *Meconium/microbiology ; Infant ; RNA, Ribosomal, 16S/genetics ; Birth Cohort ; Infant, Newborn ; Brazil ; Bacteria/genetics/classification/isolation &amp; purification ; Pregnancy ; }, abstract = {Emerging evidence has been linking changes in the early-life gut microbiome and neurodevelopmental outcomes. The founder bacteria that first colonize the infant's gut determine the microbial succession that signals host tissues and impact development including the brain. Here we investigated the association between the meconium microbiome and neurobehavior. To this end, we surveyed the 16S rRNA gene on meconium samples and assessed behavioral outcomes at six-months of age by the Denver Developmental Screening Test II (DDST-II). Among the four behavioral domains investigated, the personal-social domain was associated with significant differences in meconium bacterial beta diversity (unweighted UniFrac; R[2] 0.078, p = 0.021) and reduced alpha diversity (β = -2.290, 95% CI = -4.212; CI = -0.368), after adjustment for gestational antibiotics, preterm delivery, and delivery mode. Besides, this altered neurobehavior (failing to meet the milestone) was associated with overrepresented Ruminococcaceae, Christensenellaceae, and Eubacterium, Treponema, Senegalimassilia, Ruminiclostridium, Roseburia, Romboutsia, Prevotella, and Veillonella seminalis. Predicted functional genes showed reduced abundance in association with altered neurobehavior (all q < 0.15). Fine and gross motor skills presented no associations with the microbiome. This pilot study shows associations between the first gut microbiome and behavioral outcomes that deserve further studies in different neonate populations.}, }
@article {pmid40082445, year = {2025}, author = {Manns, MP and Bergquist, A and Karlsen, TH and Levy, C and Muir, AJ and Ponsioen, C and Trauner, M and Wong, G and Younossi, ZM}, title = {Primary sclerosing cholangitis.}, journal = {Nature reviews. Disease primers}, volume = {11}, number = {1}, pages = {17}, pmid = {40082445}, issn = {2056-676X}, mesh = {Humans ; *Cholangitis, Sclerosing/physiopathology/therapy/epidemiology/diagnosis/complications ; Liver Transplantation/methods ; Ursodeoxycholic Acid/therapeutic use ; }, abstract = {Primary sclerosing cholangitis (PSC) is a chronic biliary inflammation associated with periductular fibrosis of the intrahepatic and extrahepatic bile ducts leading to strictures, bacterial cholangitis, decompensated liver disease and need for liver transplantation. This rare focal liver disease affects all races and ages, with a predominance of young males. There is an up to 88% association with inflammatory bowel disease. Although the aetiology is unknown and the pathophysiology is poorly understood, PSC is regarded as an autoimmune liver disease based on a strong immunogenetic background. Further, the associated risk for various malignancies, particularly cholangiocellular carcinoma, is also poorly understood. No medical therapy has been approved so far nor has been shown to improve transplant-free survival. However, ursodeoxycholic acid is widely used since it improves the biochemical parameters of cholestasis and is safe at low doses. MRI of the biliary tract is the primary imaging technology for diagnosis. Endoscopic interventions of the bile ducts should be limited to clinically relevant strictures for balloon dilatation, biopsy and brush cytology. End-stage liver disease with decompensation is an indication for liver transplantation with recurrent PSC in up to 38% of patients. Several novel therapeutic strategies are in various stages of development, including apical sodium-dependent bile acid transporter and ileal bile acid transporter inhibitors, integrin inhibitors, peroxisome proliferator-activated receptor agonists, CCL24 blockers, recombinant FGF19, CCR2/CCR5 inhibitors, farnesoid X receptor bile acid receptor agonists, and nor-ursodeoxycholic acid. Manipulation of the gut microbiome includes faecal microbiota transplantation. This article summarizes present knowledge and defines unmet medical needs to improve quality of life and survival.}, }
@article {pmid40082312, year = {2025}, author = {Yagel, Y and Motro, Y and Green, S and Klapper-Goldstein, H and Pardo, E and Moran-Gilad, J and Weintraub, AY}, title = {Investigation of the female genital tract microbiome and its association with hydrosalpinx in women undergoing salpingectomy.}, journal = {Archives of gynecology and obstetrics}, volume = {}, number = {}, pages = {}, pmid = {40082312}, issn = {1432-0711}, abstract = {OBJECTIVE: To describe the microbiome of the vagina and fallopian tubes (FT) and its relation with hydrosalpinx.<br><br>METHODS: Case-control study was conducted in women who underwent salpingectomy for hydrosalpinx (case) or other indications (controls). Samples were obtained during surgery and subjected to 16S rRNA amplicon sequencing, and analyses of alpha diversity and beta diversity measures were compared between sites and groups. Differential abundance of bacteria associated with vaginal dysbiosis was compared between cases and controls.<br><br>RESULTS: Nine women with hydrosalpinx and 23 women without hydrosalpinx were included in the study. The mean age of studied women was 41 (range: 29-54) and most (89%) were premenopausal. After in silico decontamination, only 30% of control FT samples and 10% of case FT samples had evidence of bacterial presence. The vaginal microbiome of control patients showed greater abundance of lactobacilli, whereas the vaginal microbiome of case patients contained relatively more bacterial vaginosis-associated bacteria, such as Prevotella and Atopobium. A significant difference was found in alpha and beta diversity between vaginal and FT microbiomes in control patients as FT samples were more diverse. We found that women with hydrosalpinx had a more "dysbiotic" vaginal microbiome and in women without hydrosalpinx, microbial composition within the vagina and FT differed, possibly representing two distinct ecological environments.<br><br>CONCLUSION: Women undergoing salpingectomy for various reasons harbored bacteria within their FT, while women with hydrosalpinx generally did not. This suggests that even though infection may be an underlying cause of hydrosalpinx, bacteria may not be present by the time patients require surgery.}, }
@article {pmid40082232, year = {2025}, author = {Shu-Ting, MO and Zhe, T and Xin, L and Chao, H and Yu-Hua, C}, title = {Research Progress in Effects of Vermiform Appendix on the Occurrence and Development of Diseases Related to Gut-Brain Axis.}, journal = {Zhongguo yi xue ke xue yuan xue bao. Acta Academiae Medicinae Sinicae}, volume = {47}, number = {1}, pages = {95-101}, doi = {10.3881/j.issn.1000-503X.16046}, pmid = {40082232}, issn = {1000-503X}, mesh = {Humans ; *Appendix/microbiology ; *Brain-Gut Axis/physiology ; *Appendectomy ; *Appendicitis/microbiology ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Brain ; }, abstract = {The gut-brain axis is a bidirectional communication pathway connecting the central nervous system and gastrointestinal tract,playing a key role in the occurrence and development of diseases related to this axis.The vermiform appendix,as a part of the gut that is connected to the cecum,has a unique anatomical location,a rich microbiome,and abundant immune cells.Appendicitis and appendectomy have been found to be associated with the development of diseases related to the gut-brain axis.This review first introduces the anatomy and functions of the vermiform appendix and then expounds the associations of appendicitis and appendectomy with diseases related to the gut-brain axis.Furthermore,this review summarizes and prospects the mechanisms of the vermiform appendix in affecting the occurrence and development of diseases related to the gut-brain axis.}, }
@article {pmid40082000, year = {2025}, author = {Massaro, CA and Meade, S and Lemarié, FL and Kaur, G and Bressler, B and Rosenfeld, G and Leung, Y and Williams, AJ and Lunken, G}, title = {Gut microbiome predictors of advanced therapy response in Crohn's disease: protocol for the OPTIMIST prospective, longitudinal, observational pilot study in Canada.}, journal = {BMJ open}, volume = {15}, number = {3}, pages = {e094280}, doi = {10.1136/bmjopen-2024-094280}, pmid = {40082000}, issn = {2044-6055}, mesh = {Humans ; *Crohn Disease/microbiology/therapy ; *Gastrointestinal Microbiome ; Pilot Projects ; Prospective Studies ; Longitudinal Studies ; Observational Studies as Topic ; Feces/microbiology ; British Columbia/epidemiology ; Canada ; }, abstract = {INTRODUCTION: Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis, is characterised by chronic and relapsing inflammation of the gastrointestinal tract, leading to significant morbidity and reduced quality of life. The global rise in IBD incidence is driven by a complex interplay of genetic, environmental, dietary and microbiome-related factors. Despite advancements in treatment, such as biologics, response rates remain variable, highlighting the need for personalised approaches. Recent research suggests that specific microbiome signatures may serve as biomarkers for predicting therapeutic efficacy, offering a potential tool for optimising treatment strategies in CD. The aim of the Optimising IBD Patient Treatment with Integrated Microbiome Investigation for Specialised Therapeutics (OPTIMIST) study is to evaluate microbiome profiles across various sample types in a Canadian CD cohort starting or already on advanced therapy, with the goal of developing predictive models for personalised therapeutics.<br><br>METHODS AND ANALYSIS: This study is a two-phase, longitudinal, prospective observational pilot study conducted in British Columbia, Canada, involving both CD patients and non-IBD controls. Phase 1 focuses on baseline microbiome differences across participant cohorts through cross-sectional analysis. Phase 2 follows participants over 12 months to assess microbiome changes and their association with treatment response. Stool samples, intestinal biopsies from the left colon, right colon and ileum, as well as mucosal wash samples from the proximal part of the distal colon, will undergo metagenomics, metaproteomics and metabolomics analyses to explore compositional and functional differences. Data will be analysed using alpha and beta diversity metrics, differential abundance analyses and multivariate analyses to identify microbiome-based predictors of therapeutic response.<br><br>ETHICS AND DISSEMINATION: Ethical approval was received by the Research Ethics Board (REB) of University of British Columbia-Providence Healthcare (UBC-PHC) with a REB number H23-02927. All amendments to the protocol are reported and adapted based on the requirements of the REB. The results of this study will be submitted to peer-reviewed journals and will be communicated in editorials/articles by the IBD Centre of BC and BC Children's Hospital Research Institute.<br><br>TRIAL REGISTRATION NUMBER: NCT06453720.<br><br>PROTOCOL VERSION: 2024-06-21, version 3.0.}, }
@article {pmid40081897, year = {2025}, author = {Dehghanizai, AB and Stewart, CJ and Thomas, RH}, title = {The microbiome: what a neurologist needs to know.}, journal = {Practical neurology}, volume = {}, number = {}, pages = {}, doi = {10.1136/pn-2024-004400}, pmid = {40081897}, issn = {1474-7766}, abstract = {The gastrointestinal tract is inhabited by trillions of micro-organisms that form the gut microbiome, which serves various functions that can influence neurological pathways. It can release metabolites that could affect the nervous system. The bidirectional communication between the intestine and the central nervous system is known as the gut-brain axis. This communication can be impacted by the microbiota in various direct and indirect ways. There has been a suggested connection between the microbiome and many neurological disorders, including epilepsy, Alzheimer's disease, Parkinson's disease and multiple sclerosis. This has been explored in human and animal studies. While no microbial biomarkers have been identified yet, alterations in several taxa have been suggested to be associated with disease states. The potential of the microbiome to modulate neurological function has sparked multiple clinical trials using gut-altering treatments, some with positive preliminary results.}, }
@article {pmid40081885, year = {2025}, author = {Min, H and Choi, KS and Yun, S and Jang, S}, title = {Live Biotherapeutic Products for Metabolic Diseases: Development Strategies, Challenges, and Future Directions.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2410054}, doi = {10.4014/jmb.2410.10054}, pmid = {40081885}, issn = {1738-8872}, mesh = {Humans ; *Metabolic Diseases/therapy/microbiology ; *Probiotics/therapeutic use ; *Gastrointestinal Microbiome ; Animals ; Diabetes Mellitus, Type 2/therapy ; Non-alcoholic Fatty Liver Disease/therapy/microbiology ; Biological Products/therapeutic use ; Obesity/therapy ; }, abstract = {Metabolic diseases, such as obesity, type 2 diabetes, and non-alcoholic fatty liver disease, have emerged as major global health challenges. Recent research has revealed that the gut microbiome is closely associated with the development of these conditions. The Food and Drug Administration has recognized certain probiotic strains with therapeutic potential, classifying them as live biotherapeutic products (LBPs). LBPs, which are derived from naturally occurring microorganisms, may present an effective strategy for treating metabolic diseases by restoring gut microbiota balance and regulating metabolic functions. This review explores the development of LBPs specifically for metabolic disease treatments, covering every phase from strain identification, non-clinical and clinical trials, manufacturing and formulation to regulatory approval. Furthermore, it addresses the challenges involved in the commercialization of these therapies. By offering critical insights into the research and development of LBPs for metabolic disease treatment, this review aims to contribute to the progress of these promising therapies.}, }
@article {pmid40081757, year = {2025}, author = {Armengaud, J}, title = {The dawn of the revolution that will allow us to precisely describe how microbiomes function.}, journal = {Journal of proteomics}, volume = {}, number = {}, pages = {105430}, doi = {10.1016/j.jprot.2025.105430}, pmid = {40081757}, issn = {1876-7737}, abstract = {The community of microorganisms inhabiting a specific environment, such as the human gut - including bacteria, fungi, archaea, viruses, protozoa, and others - is known as the microbiota. A holobiont, in turn, refers to an integrated ecological unit where microbial communities function and interact with their host, thus is a more integrative concept. To understand the processes involved, the diversity of microorganisms present must be identified and their molecular components quantified, especially proteins. Indeed, proteins - through their roles as catalytic units, structural components, and signaling molecules - are the main drivers of biological processes. Metagenomics has significantly expanded what we know about the genetic material present in microbiota, revealing their functional potential; metabolomics delivers an overall snapshot of the metabolites produced by the community. But metaproteomics offers a complementary approach to explore microbiome and holobiont functionality by focusing on the active proteins and functional pathways from each taxon. Significant recent advances in high-resolution tandem mass spectrometry have greatly expanded the catalog of peptide sequences accessible in each sample, creating the conditions for unprecedented taxonomical profiling, while also providing more accurate biomass quantification, more detailed protein characterization, and a greater capacity to monitor abundance and distinguish host biomarkers. By integrating artificial intelligence into the metaproteomics pipeline, extended datasets can now be efficiently mined to gain a more comprehensive functional view of complex biological systems, paving the way for next-generation metaproteomics. In this perspective, I discuss the transformative potential of this methodology. We are on the cusp of a remarkable omic revolution that promises to uncover the intricate workings of microbiomes by producing a vast array of new knowledge with multiple applications. SIGNIFICANCE: Metaproteomics provides a powerful lens to investigate microbiome and holobiont functionality by identifying and quantifying active proteins and functional pathways within each taxon. Recent breakthroughs in high-resolution tandem mass spectrometry have dramatically expanded the repertoire of peptide sequences detectable per sample. This progress enables unprecedented taxonomic resolution for microbial identification, more precise biomass quantification, comprehensive protein characterization, abundance monitoring, and the unique identification of host biomarkers. In this commentary, I delve into the distinctive features that make metaproteomics a transformative tool. I discuss the recent advancements in tandem mass spectrometry and argue that the primary challenge in analyzing complex samples is shifting from data acquisition to data interpretation. With the integration of artificial intelligence, I believe next-generation metaproteomics is poised to become the next Big Thing in microbiome research, unlocking profound insights into microbial functionality and ecosystem dynamics.}, }
@article {pmid40081698, year = {2025}, author = {Zong, G and Deng, R and Pan, Y and Liu, M and Zhu, H and Tao, R and Shan, Y and Wei, Z and Lu, Y}, title = {Ginseng polysaccharides ameliorate colorectal tumorigenesis through Lachnospiraceae-mediated immune modulation.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {142015}, doi = {10.1016/j.ijbiomac.2025.142015}, pmid = {40081698}, issn = {1879-0003}, abstract = {Probiotics and their metabolites play a critical role in immunotherapy for colorectal cancer (CRC) and intestinal damage. Identifying specific probiotics from natural products and elucidating the underlying mechanisms represent promising strategies for CRC research. This study investigated the structural characterization and therapeutic potential of ginseng polysaccharides (GPS) in inhibiting tumor growth. The results showed that the molecular weight of GPS was 2425.512 kDa, which was mainly composed of Man, GluA, Gal, Glc, Xyl, and Ara contained in its structure. GPS (100, 200, and 400 mg/kg) significantly ameliorates colorectal tumorigenesis in AOM/DSS-induced and MC38-induced CRC models. 16S rRNA shows that GPS supplementation significantly increased the abundance of Lachnospiraceae compared to the model group. Mechanistically, GPS supplementation promoted the proliferation of beneficial Lachnospiraceae bacterium (L.B.), leading to increased short-chain fatty acids (SCFAs) production. The effective anti-CRC effects of key probiotics were further substantiated by their ability to inhibit myeloid-derived suppressor cells (MDSCs) and enhance the infiltration and activation of CD8[+] T cells. These findings highlight the pivotal role of GPS-induced alterations in the potential probiotics L.B. production in CRC suppression, emphasizing the potential of GPS in immune regulation for microbiome-targeted cancer therapies.}, }
@article {pmid40081368, year = {2025}, author = {Dai, R and Zhang, J and Liu, F and Xu, H and Qian, JM and Cheskis, S and Liu, W and Wang, B and Zhu, H and Pronk, LJU and Medema, MH and de Jonge, R and Pieterse, CMJ and Levy, A and Schlaeppi, K and Bai, Y}, title = {Crop root bacterial and viral genomes reveal unexplored species and microbiome patterns.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2025.02.013}, pmid = {40081368}, issn = {1097-4172}, abstract = {Reference genomes of root microbes are essential for metagenomic analyses and mechanistic studies of crop root microbiomes. By combining high-throughput bacterial cultivation with metagenomic sequencing, we constructed comprehensive bacterial and viral genome collections from the roots of wheat, rice, maize, and Medicago. The crop root bacterial genome collection (CRBC) significantly expands the quantity and phylogenetic diversity of publicly available crop root bacterial genomes, with 6,699 bacterial genomes (68.9% from isolates) and 1,817 undefined species, expanding crop root bacterial diversity by 290.6%. The crop root viral genome collection (CRVC) contains 9,736 non-redundant viral genomes, with 1,572 previously unreported genus-level clusters in crop root microbiomes. From these, we identified conserved bacterial functions enriched in root microbiomes across soils and host species and uncovered previously unexplored bacteria-virus connections in crop root ecosystems. Together, the CRBC and CRVC serve as valuable resources for investigating microbial mechanisms and applications, supporting sustainable agriculture.}, }
@article {pmid40081332, year = {2025}, author = {Pinel, G and Marette, A}, title = {Rewild your gut: Fighting modern diseases with ancient microbes.}, journal = {Cell host &amp; microbe}, volume = {33}, number = {3}, pages = {327-329}, doi = {10.1016/j.chom.2025.02.012}, pmid = {40081332}, issn = {1934-6069}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Limosilactobacillus reuteri/physiology ; Diet ; Animals ; Gastrointestinal Tract/microbiology ; }, abstract = {Industrialization alters the gut microbiome, increasing chronic disease risk. In a recent study published in Cell, Li et al. show that a diet mimicking non-industrialized patterns ("Restore" diet) enhances Limosilactobacillus reuteri persistence and improves microbiome-derived metabolites, leading to cardiometabolic benefits and highlighting the potential of interventions aimed at restoring the gut microbiota.}, }
@article {pmid40081329, year = {2025}, author = {Zeng, S and Wang, H and Mu, D and Wang, S}, title = {The African gut microbiome: A window into the hidden human microbial diversity.}, journal = {Cell host &amp; microbe}, volume = {33}, number = {3}, pages = {320-322}, doi = {10.1016/j.chom.2025.02.015}, pmid = {40081329}, issn = {1934-6069}, mesh = {Humans ; *Gastrointestinal Microbiome ; *HIV Infections/microbiology/virology ; Africa ; Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; }, abstract = {Studies on industrialized populations have uncovered gut microbiome diversity and its disease associations. However, non-industrialized populations remain underrepresented. In a recent paper, Maghini et al. present findings from the AWI-Gen 2 Microbiome Project, substantially expanding our knowledge of the African gut bacterial and viral diversity and its linkage with HIV infection.}, }
@article {pmid40081220, year = {2025}, author = {Dong, S and Li, X and Huang, Q and Li, Y and Li, J and Zhu, X and Xue, C and Chen, R and Zeng, Y and Wu, J and Zhong, Y and Hu, S}, title = {Resistance to immunotherapy in non-small cell lung cancer: Unraveling causes, developing effective strategies, and exploring potential breakthroughs.}, journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy}, volume = {81}, number = {}, pages = {101215}, doi = {10.1016/j.drup.2025.101215}, pmid = {40081220}, issn = {1532-2084}, abstract = {Over the last two decades, advancements in deciphering the intricate interactions between oncology and immunity have fueled a meteoric rise in immunotherapy for non-small cell lung cancer, typified by an explosive growth of immune checkpoint inhibitors. However, resistance to immunotherapy remains inevitable. Herein we unravel the labyrinthine mechanisms of resistance to immunotherapy, characterized by their involvement of nearly all types of cells within the body, beyond the extrinsic cancer cells, and importantly, such cells are not only (inhibitory or excitatory, or both) signal recipients but also producers, acting in a context-dependent manner. At the molecular level, these mechanisms underlie genetic and epigenetic aberrations, which are regulated by or regulate various protein kinases, growth factors, and cytokines with inherently dynamic and spatially heterogeneous properties. Additionally, macroscopic factors such as nutrition, comorbidities, and the microbiome within and around organs or tumor cells are involved. Therefore, developing therapeutic strategies combined with distinct action informed by preclinical, clinical, and real-world evidence, such as radiotherapy, chemotherapy, targeted therapy, antibody-drug conjugates, oncolytic viruses, and cell-based therapies, may stand as a judicious reality, although the ideality is to overcome resistance point-by-point through a novel drug. Notably, we highlight a realignment of treatment aims, moving the primary focus from eliminating cancer cells -- such as through chemotherapy and radiotherapy -- to promoting immune modulation and underscore the value of regulating various components within the host macro- or micro-environment, as their effects, even if seemingly minimal, can cumulatively contribute to visible clinical benefit when applied in combination with ICIs. Lastly, this review also emphasizes the current hurdles scattered throughout preclinical and clinical studies, and explores evolving directions in the landscape of immunotherapy for NSCLC.}, }
@article {pmid40080967, year = {2025}, author = {Fang, X and Li, P and Luo, C and Wu, C and Shi, X and Lan, J and Zhao, F and Wang, F and Zhang, K and Yang, C and Ren, Z and Zheng, S}, title = {Epiphytic bacterial consortia drive growth regulation in potato under methyl jasmonate elicitation: A leaf surface multi-omics perspective.}, journal = {Plant physiology and biochemistry : PPB}, volume = {222}, number = {}, pages = {109737}, doi = {10.1016/j.plaphy.2025.109737}, pmid = {40080967}, issn = {1873-2690}, abstract = {Methyl jasmonate (MeJA), a lipid-derived signaling molecule widely reported as a plant growth regulator, was revealed in this study to coordinate oxidative stress adaptation and delay senescence in potato through metabolite-microbe interactions, ultimately improving yield. MeJA triggered leaf oxidative stress while integrating rapid enzymatic scavenging, sustained osmoprotectant accumulation, and membrane stabilization, effectively delaying senescence initiation. Metabolic reprogramming under MeJA suppressed endogenous jasmonic acid synthesis while promoting saturated fatty acid biosynthesis, altering leaf surface lipid composition. These lipid changes, combined with MeJA-induced alkaloids, drove functional restructuring of phyllosphere epiphytic bacteria through fatty acid-mediated niche specialization, enhancing bacterial metabolism and enriching stress-resistant Proteobacteria. Notably, the enrichment of saturated fatty acids correlated with microbial taxa exhibiting specialized lipid metabolism. Field trials demonstrated that 200 μmol/L MeJA optimized redox homeostasis and photosynthetic longevity in early-maturing cultivar 'Favorita', translating delayed senescence into significant yield increases. This study proposes a "metabolite-guided microbial niche construction" model, where host lipid metabolism and secondary metabolites jointly shape stress-adapted microbial communities, providing new strategies for precision agrochemical design targeting phyllosphere microbiome engineering.}, }
@article {pmid40080496, year = {2025}, author = {Alizadeh, M and Oladokun, S and Fletcher, C and Boodhoo, N and Fazel, F and Shojadoost, B and Raj, S and Zheng, J and Abdelaziz, K and Sharif, S}, title = {Evaluating the protective effects of the Toll-like receptor (TLR) 21 ligand, CpG ODN, against necrotic enteritis in broiler chickens.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0319404}, doi = {10.1371/journal.pone.0319404}, pmid = {40080496}, issn = {1932-6203}, mesh = {Animals ; *Chickens/immunology/microbiology ; *Oligodeoxyribonucleotides/pharmacology/administration &amp; dosage ; *Enteritis/veterinary/microbiology/prevention &amp; control/immunology/drug therapy ; *Poultry Diseases/microbiology/immunology/prevention &amp; control ; *Clostridium perfringens ; *Clostridium Infections/veterinary/immunology/prevention &amp; control ; Necrosis ; Toll-Like Receptors/metabolism/genetics ; Ligands ; Cytokines/metabolism ; }, abstract = {Necrotic enteritis (NE), caused by Clostridium perfringens (C. perfringens), presents a challenge to the global broiler industry. Evidence suggests that Toll-like receptor (TLR) ligands can enhance the immune responses in chickens and protect them against infectious diseases. This study investigated the protective effects of TLR21 ligand class B CpG oligonucleotides (ODN) against NE in broiler chickens. On day 21 of age, chickens were injected with 50 or 100 μg CpG intramuscularly, and one group was injected with 50 μg CpG followed by a booster dose on day 22. Subsequently, birds were orally challenged with C. perfringens twice daily for three days, starting on day 22. On day 22, intestinal samples were collected for gene expression analysis. On day 25, all birds were euthanized, intestinal lesions were scored, and tissue samples were collected from the intestine for gene expression analysis, lymphocyte subset determination, and histomorphological analysis. Cecal contents were also collected for microbiome analysis. The results demonstrated that CpG pre-treatment, either at a single dose of 100 μg or two doses of 50 μg per bird, reduced lesion scores compared to the positive control. C. perfringens infection increased crypt depth in both the jejunum and ileum in the positive control group compared to both the CpG-treated group. At 22 days of age, CpG administration at doses of 100 μg per bird enhanced expression of TLR21, interleukin (IL)-2, CXCL8, IL-10, and interferon (IFN)-γ mRNA transcripts in both the jejunum and ileum. Additionally, at 25 days of age, the group pretreated with two doses of 50 μg of CpG per bird showed increased expression of all cytokines in both the jejunum and ileum compared to the control groups. The percentage of intestinal lymphocytes was not affected by CpG pre-treatment. However, CpG pretreatment at doses of 100 μg resulted in a higher abundance of the members of families Lactobacillaceae and Bacteroidaceae, which are crucial for maintaining gut health. In conclusion, our findings suggest that pretreatment of chickens with intramuscular administration of CpG may be effective in maintaining gut health during C. perfringens infection.}, }
@article {pmid40080332, year = {2025}, author = {Murphy, SC and Russell, SP and Harty, JA and O'Loughlin, P}, title = {Microbiologic features of prosthetic joint infections at a tertiary referral orthopaedic unit.}, journal = {Irish journal of medical science}, volume = {}, number = {}, pages = {}, pmid = {40080332}, issn = {1863-4362}, abstract = {BACKGROUND: Prosthetic joint infections (PJI) are a potential devasting consequence of arthroplasty surgery. Knowledge of the causative organism and antimicrobial sensitivity increases eradication success rates for PJI.<br><br>AIMS: This study aimed to: 1) Observe the PJI microbiome at a tertiary referral arthroplasty unit; 2) Make comparison to similar published observations; and; 3) Establish empiric local antibiotic PJI guidelines.<br><br>METHODS: All patients with positive tissue cultures for PJIs over a 4&#xa0;year period were included. An electronic microbiology laboratory database search was performed to identify isolated microorganisms, sensitivities and resistances. Time from index procedure to PJI onset was recorded. The identified PJI microbiome was compared to current literature.<br><br>RESULTS: 86 patients involving 88 joints were included. 56% (n&#x2009;=&#x2009;49) related to hip, 42% (n&#x2009;=&#x2009;37) to knee and 2% (2) to shoulder arthroplasty procedures. Coagulase Negative Staphylococci (CoNS) were isolated in 32% of cases, Staphylococcus aureus (SA) in 23%, Enterococcus species and Streptococcus species in 9.0%. 19% of case occurred within 3&#xa0;months of index surgery, 17% from 3-12&#xa0;months and 64% after 12&#xa0;months. The microbiome identified varied comparable studies.<br><br>CONCLUSION: This study describes a local PJI microbiome with contrasting results from comparable studies. Empiric antibiotic guidelines have been established to target treatment and a local PJI register has since been established to improve patient outcomes and antimicrobial stewardship in an era of antibiotic resistance.}, }
@article {pmid40080268, year = {2025}, author = {Fan, X and Ge, AH and Qi, S and Guan, Y and Wang, R and Yu, N and Wang, E}, title = {Root exudates and microbial metabolites: signals and nutrients in plant-microbe interactions.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {40080268}, issn = {1869-1889}, abstract = {Plant roots meticulously select and attract particular microbial taxa from the surrounding bulk soil, thereby establishing a specialized and functionally diverse microbial community within the rhizosphere. Rhizosphere metabolites, including root exudates and microbial metabolites, function as both signals and nutrients that govern the assembly of the rhizosphere microbiome, playing crucial roles in mediating communications between plants and microbes. The environment and their feedback loops further influence these intricate interactions. However, whether and how specific metabolites shape plant-microbe interactions and facilitate diverse functions remains obscure. This review summarizes the current progress in plant-microbe communications mediated by chemical compounds and their functions in plant fitness and ecosystem functioning. Additionally, we raise some prospects on future directions for manipulating metabolite-mediated plant-microbe interactions to enhance crop productivity and health. Unveiling the biological roles of specific metabolites produced by plants and microbes will bridge the gap between fundamental research and practical applications.}, }
@article {pmid40080232, year = {2025}, author = {Wang, Y and Sun, Y and Liao, H}, title = {Causal associations between 26 musculoskeletal disorders and gut microbiota: a Mendelian randomization analysis with Bayesian validation.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {3}, pages = {106}, pmid = {40080232}, issn = {1573-0972}, support = {No. B2023192//Guangdong Medical Research Foundation/ ; No.2022B33//Medical and Medicine Research Project of Meizhou City, Guangdong Province of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bayes Theorem ; *Mendelian Randomization Analysis ; *Musculoskeletal Diseases/microbiology/genetics/etiology ; *Genome-Wide Association Study ; Finland ; }, abstract = {Emerging evidence suggests that gut microbiota imbalances may influence the onset of musculoskeletal disorders (MSDs), yet conclusive evidence establishing causation remains limited. This study investigates the causal relationship between gut microbiota and a range of MSDs, aiming to identify potential therapeutic targets. Using data on 211 gut microbiome taxa from a genome-wide association study (GWAS) and summary statistics for 26 MSDs from the Finnish Biobank, we employed Mendelian randomization (MR) with inverse-variance weighting (IVW) as the primary analytical approach, complemented by Bayesian model validation to ensure robust results. Our MR analyses revealed significant causal associations between gut microbiota and nine MSDs within four categories, including osteoporosis (IVW-Beta = 0.011, P = 0.025), rheumatoid arthritis (IVW-Beta = - 0.016, P < 0.001), rotator cuff syndrome (IVW-Beta = - 0.007, P = 0.022), and calcific tendonitis of the shoulder (IVW-Beta = - 0.021, P = 0.034). Bayesian validation underscored the plausibility of these relationships, supporting the potential causal role of gut microbiota in the development of these disorders. Our findings present a library of causal associations that underscore the gut microbiome's role in MSD pathogenesis, providing genetic evidence that highlights specific gut microbiota taxa as prospective therapeutic targets. This research offers novel insights into the pathogenic mechanisms underlying MSDs and points toward new directions for future investigation into microbiome-based therapies.}, }
@article {pmid40080167, year = {2025}, author = {Kouakou, AK and Collart, P and Perron, T and Kolo, Y and Gay, F and Brauman, A and Brunel, C}, title = {Soil Microbial Recovery to the Rubber Tree Replanting Process in Ivory Coast.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {13}, pmid = {40080167}, issn = {1432-184X}, support = {(PFI : 7250A1, Centre de co&#xfb;t : 210F2CVNB)//Institut Fran&#xe7;ais du Caoutchouc/ ; (PFI : 7250A1, Centre de co&#xfb;t : 210F2CVNB)//Institut Fran&#xe7;ais du Caoutchouc/ ; (PFI : 7250A1, Centre de co&#xfb;t : 210F2CVNB)//Institut Fran&#xe7;ais du Caoutchouc/ ; (PFI : 7250A1, Centre de co&#xfb;t : 210F2CVNB)//Institut Fran&#xe7;ais du Caoutchouc/ ; ARTS, 2019//IRD PhD Grant Program/ ; }, mesh = {*Soil Microbiology ; *Hevea/microbiology/growth &amp; development ; Cote d'Ivoire ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Soil/chemistry ; Agriculture/methods ; RNA, Ribosomal, 18S/genetics ; }, abstract = {The resistance and resilience of soil microbial communities to an environmental disturbance are poorly documented, due to the lack on onfield diachronic experiments, limiting our ability to design adapted agroecological practices. This is especially true in rubber plantations, one of the most planted tree in tropical areas. We aimed to understand (1) how soil disturbances occurring during the rubber replanting phase affect the soil microbiome, (2) how agricultural practices combining legumes cover crops and tree logging residues shape community resilience and (3) how microbial responses vary across different edaphic contexts. In two plantations with distinct soil properties in Ivory Coast, soil microbial communities were surveyed every 6 months for 24 months after soil perturbation. Community structure, functioning and networks were described based on a 16S/18S rRNA gene investigation. Prokaryotes were generally more resistant to soil perturbation than microeukaryote communities. Prokaryotic resilience dynamics were faster than those of microeukaryotes, the latter being deeply modulated by cover treatments. These specific dynamics were exacerbated in the sandy site. Co-occurrence network modelling provided useful insights into microbial resilience trajectories. We argue that this tool should be more widely used to describe microbial community dynamics. Practices involving a combination of logging residues and legume cover crops have shown beneficial effects on the community resilience in the sandy site and appears as promising agroecological practices. However, the major influence of soil texture warns of the need to consider pedological context when designing pertinent agroecological practices.}, }
@article {pmid40080091, year = {2025}, author = {Wagner, CA and Frey-Wagner, I and Ortiz, A and Unwin, R and Liabeuf, S and Suzumoto, Y and Iervolino, A and Stasi, A and Di Marzo, V and Gesualdo, L and Massy, ZA and , }, title = {The role of the intestinal microbiome in cognitive decline in patients with kidney disease.}, journal = {Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association}, volume = {40}, number = {Supplement_2}, pages = {ii4-ii17}, doi = {10.1093/ndt/gfae253}, pmid = {40080091}, issn = {1460-2385}, support = {CA19127//COST/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Renal Insufficiency, Chronic/microbiology/complications ; Dysbiosis/complications ; Cognition Disorders/etiology/microbiology ; Cognitive Dysfunction/etiology/microbiology ; }, abstract = {Cognitive decline is frequently seen in patients with chronic kidney disease (CKD). The causes of cognitive decline in these patients are likely to be multifactorial, including vascular disease, uraemic toxins, blood-brain barrier leakage, and metabolic and endocrine changes. Gut dysbiosis is common in patients with CKD and contributes to the increase in uraemic toxins. However, the gut microbiome modulates local and systemic levels of several metabolites such as short-chain fatty acids or derivatives of tryptophan metabolism, neurotransmitters, endocannabinoid-like mediators, bile acids, hormones such as glucagon-like peptide 1 (GLP1) or cholecystokinin (CCK). These factors can affect gut function, immunity, autonomic nervous system activity and various aspects of brain function. Key areas include blood-brain barrier integrity, nerve myelination and survival/proliferation, appetite, metabolism and thermoregulation, mood, anxiety and depression, stress and local inflammation. Alterations in the composition of the gut microbiota and the production of biologically active metabolites in patients with CKD are well documented and are favoured by low-fiber diets, elevated urea levels, sedentary lifestyles, slow stool transit times and polypharmacy. In turn, dysbiosis can modulate brain function and cognitive processes, as discussed in this review. Thus, the gut microbiome may contribute to alterations in cognition in patients with CKD and may be a target for therapeutic interventions using diet, prebiotics and probiotics.}, }
@article {pmid40080061, year = {2025}, author = {Childers, L and Park, J and Wang, S and Liu, R and Barry, R and Watts, SA and Rawls, JF and Bagnat, M}, title = {Protein absorption in the zebrafish gut is regulated by interactions between lysosome rich enterocytes and the microbiome.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {40080061}, issn = {2050-084X}, support = {DK132120/NH/NIH HHS/United States ; DK121007/NH/NIH HHS/United States ; }, mesh = {Animals ; *Zebrafish/metabolism ; *Enterocytes/metabolism ; *Gastrointestinal Microbiome/physiology ; *Lysosomes/metabolism ; Dietary Proteins/metabolism ; Intestinal Absorption ; }, abstract = {Dietary protein absorption in neonatal mammals and fishes relies on the function of a specialized and conserved population of highly absorptive lysosome-rich enterocytes (LREs). The gut microbiome has been shown to enhance absorption of nutrients, such as lipids, by intestinal epithelial cells. However, whether protein absorption is also affected by the gut microbiome is poorly understood. Here, we investigate connections between protein absorption and microbes in the zebrafish gut. Using live microscopy-based quantitative assays, we find that microbes slow the pace of protein uptake and degradation in LREs. While microbes do not affect the number of absorbing LRE cells, microbes lower the expression of endocytic and protein digestion machinery in LREs. Using transgene-assisted cell isolation and single cell RNA-sequencing, we characterize all intestinal cells that take up dietary protein. We find that microbes affect expression of bacteria-sensing and metabolic pathways in LREs, and that some secretory cell types also take up protein and share components of protein uptake and digestion machinery with LREs. Using custom-formulated diets, we investigated the influence of diet and LRE activity on the gut microbiome. Impaired protein uptake activity in LREs, along with a protein-deficient diet, alters the microbial community and leads to an increased abundance of bacterial genera that have the capacity to reduce protein uptake in LREs. Together, these results reveal that diet-dependent reciprocal interactions between LREs and the gut microbiome regulate protein absorption.}, }
@article {pmid40079755, year = {2025}, author = {Menozzi, E and Schapira, AHV and Borghammer, P}, title = {The Gut-Brain Axis in Parkinson disease: Emerging Concepts and Therapeutic Implications.}, journal = {Movement disorders clinical practice}, volume = {}, number = {}, pages = {}, doi = {10.1002/mdc3.70029}, pmid = {40079755}, issn = {2330-1619}, support = {ASAP-000420//Aligning Science Across Parkinson's/ ; MR/T046007/1//EU Joint Programme - Neurodegenerative Disease Research/ ; }, abstract = {BACKGROUND: The gut-brain axis, i.e. the bidirectional communication system between the gut and the brain, has become of central importance in Parkinson disease (PD) research over the past 20 years.<br><br>AIMS: We aimed to describe the milestones of the gut-brain axis research in PD and the development of theories proposing the involvement of the gastrointestinal tract in PD pathogenesis.<br><br>METHODS: We searched PubMed using the terms 'gut-brain axis' AND 'Parkinson disease', and selected relevant articles to provide the foundation for reconstructing an historical overview of the gut-brain axis research in PD.<br><br>RESULTS: Mounting evidence from preclinical, clinical and post-mortem studies suggests that a subgroup of PD patients present with a range of prodromal symptoms (e.g., autonomic dysfunction, rapid eye movement sleep behaviour disorder) which reflect initial accumulation and later spread of pathological &#x3b1;-synuclein rostrally from the gastrointestinal tract ("body-first" PD). Through neural connections along the gut-brain axis, pathological &#x3b1;-synuclein may spread to the brain, producing clinically manifest disease. Recently, two mechanisms involving the gut-brain axis have attracted increasing attention for their role in PD pathogenesis and progression, namely the perturbation of the composition of the microorganisms living in the gut (the gut microbiome), and the dysfunction of enteroendocrine cells.<br><br>CONCLUSION: Treatments targeting the gut-brain axis, especially the gut microbiome and the enteroendocrine cells pathway, could potentially slow disease progression or even prevent disease onset. Among these, pre/probiotics, faecal microbiota transplantation, and glucagon-like peptide-1 receptor agonists, have entered advanced stages of clinical trials in humans and shown potential symptomatic and disease-modifying effects.}, }
@article {pmid40079595, year = {2025}, author = {Kumar, M and Sayavedra, L and Baker, DJ and Shouche, YS and Narbad, A}, title = {Genome sequence of Eubacterium callanderi AM6, isolated from a Parkinson's disease patient.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0003925}, doi = {10.1128/mra.00039-25}, pmid = {40079595}, issn = {2576-098X}, abstract = {Here, we report the genome sequence of Eubacterium callanderi AM6, isolated from a fecal sample obtained from a Parkinson's disease patient. The bacterial genome was sequenced using Illumina technology on a NextSeq 500 platform. The assembled genome of Eubacterium callanderi comprises 4,318,463 base pairs with a G + C content of 47.5%.}, }
@article {pmid40079503, year = {2025}, author = {Leonard, JM and Cecconi, M and Kaplan, LJ}, title = {ICU imperatives in open abdomen management after trauma or emergency surgery.}, journal = {Current opinion in critical care}, volume = {}, number = {}, pages = {}, doi = {10.1097/MCC.0000000000001264}, pmid = {40079503}, issn = {1531-7072}, abstract = {PURPOSE OF REVIEW: This review is both timely and relevant as the open abdomen approach to manage injury, emergency general surgery (EGS) conditions, as well as secondary intra-abdominal hypertension (IAH) and the abdominal compartment syndrome (ACS) remain prevalent throughout ICUs.<br><br>RECENT FINDINGS: IAH is not limited to those with injury or EGS conditions, as it is increasingly recognized following cardiac surgery as well as cardiac transplantation. IAH monitoring techniques benefit from technological advances including noninvasive devices. Time to primary fascial closure (PFC) is a key determinant of patient-centered outcomes, with worse outcomes in those with delayed or failed closure attempts. Visceral edema avoidance or mitigation techniques remain controversial. Nutrition support and its impact on the gastrointestinal microbiome appear to influence infection risk and anastomotic integrity. Team-based approaches to successful as well as failed open abdomen management help optimize outcomes.<br><br>SUMMARY: These findings bear broad implications for intensive care medicine clinicians who care for open abdomen patients, as they address resuscitation, intra-abdominal pressure monitoring, and nutrition support all of which influence the likelihood of achieving PFC - a key goal regardless of whether the abdomen was initially left open after injury, EGS, or intestinal ischemia management.}, }
@article {pmid40079420, year = {2025}, author = {Jurburg, SD}, title = {Short Read Lengths Recover Ecological Patterns in 16S rRNA Gene Amplicon Data.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14102}, doi = {10.1111/1755-0998.14102}, pmid = {40079420}, issn = {1755-0998}, abstract = {16S rRNA gene metabarcoding, the study of amplicon sequences of the 16S rRNA gene from mixed environmental samples, is an increasingly popular and accessible method for assessing bacterial communities across a wide range of environments. As metabarcoding sequence data archives continue to grow, data reuse will likely become an important source of novel insights into the ecology of microbes. While recent work has demonstrated the benefits of longer read lengths for the study of microbial communities from 16S rRNA gene segments, no studies have explored the use of shorter (< 200 bp) read lengths in the context of data reuse. Nevertheless, this information is essential to improve the reuse and comparability of metabarcoding data across existing datasets. This study reanalyzed nine 16S rRNA datasets targeting aquatic, animal-associated and soil microbiomes, and evaluated how processing the sequence data across a range of read lengths affected the resulting taxonomic assignments, biodiversity metrics and differential (i.e., before-after treatment) analyses. Short read lengths successfully recovered ecological patterns and allowed for the use of more sequences. Limited increases in resolution were observed beyond 150 bp reads across environments. Furthermore, abundance-weighted diversity metrics (e.g., Inverse Simpson index, Morisita-Horn dissimilarities or weighted Unifrac distances) were more robust to variation in read lengths. Read lengths alone contributed to consistent increases in the total number of ASVs detected, highlighting the need to consider metabarcoding-derived diversity estimates within the context of the bioinformatics parameters selected. This study provides evidence-based guidelines for the processing of short reads.}, }
@article {pmid40079375, year = {2025}, author = {Zhang, Y and Chen, Q and Yang, X and Hao, L and Lu, L and Kleindienst, S and Lin, J and Li, S}, title = {Unravelling the Activity and Presence of N2O Reducers on Urban Greening Tree Leaves.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.15463}, pmid = {40079375}, issn = {1365-3040}, support = {//This work was financially supported by the National Natural Science Foundation of China (Grant No. 42007294 and 42021005) and the State Key Laboratory of Microbial Technology Open Projects Fund (M2024-02). L.H. acknowledges the Guizhou Provincial Department of Science and Technology (E2DF028)./ ; }, abstract = {Nitrous oxide (N2O) is a potent greenhouse gas and can be biotically emitted from soils, water, and the less recognised plant leaves. Leaves can produce N2O and may host N2O-reducing microbes that use it as a respiratory substrate, potentially mitigating climate warming. This study examines the ecophysiology of N2O reducers in the plant phyllosphere. Anoxic microcosm experiments, quantification of N2O reduction kinetics, and analysis of nosZ gene governing N2O reduction were conducted to assess the activity and presence of N2O reducers in leaf epiphytes from various canopy positions of Photinia fraseri, an urban greenery plant. Results revealed canopy position-dependent N2O reduction activity in the leaf microbiota. We identified previously unrecognised atypical Clade II nosZ gene in the phyllosphere microbiome, with its absolute abundance positively correlated with N2O reduction activity, highlighting its significance in this process. Sequencing of bacterial and archaeal 16S rRNA genes revealed keystone taxa as primary drivers of N2O reduction activity. These findings underscore the functional potential for N2O reduction and the presence of the Clade II nosZ group within epiphytic microbes. This work provides insights into the ecophysiology of epiphytic N2O reducers and underpins the development of leaf-based microbial solutions for N2O mitigation under future warming.}, }
@article {pmid40079338, year = {2025}, author = {Su, L and Wang, X and Lin, Y and Zhang, Y and Yao, D and Pan, T and Huang, X}, title = {Exploring the Causal Relationship Between Gut Microbiota and Pulmonary Artery Hypertension: Insights From Mendelian Randomization.}, journal = {Journal of the American Heart Association}, volume = {}, number = {}, pages = {e038150}, doi = {10.1161/JAHA.124.038150}, pmid = {40079338}, issn = {2047-9980}, abstract = {BACKGROUND: Research into the "gut-lung" axis links gut microbiota to pulmonary artery hypertension (PAH). However, the mechanisms by which gut microbiota influence PAH remain unclear. We aimed to investigate the causal relationship between the gut microbiota and PAH using Mendelian randomization analysis, identify key microbiota and metabolites, and explore the regulatory role of associated genes in PAH pathogenesis.<br><br>METHODS AND RESULTS: We examined the association between gut microbiota taxa and PAH using inverse variance weighted 2-sample Mendelian randomization analysis, Mendelian randomization-Egger, weighted median, and weighted mode methods. Additionally, we identified PAH-regulating genes in the intestinal microbiome using bioinformatics tools and validated their expression levels in the lung tissue of hypoxia-induced PAH mice models by quantitative reverse transcription polymerase chain reaction. Eleven gut microbiota taxa were associated with PAH. The order Clostridiales and genera Eubacterium fissicatena group, Lachnospiraceae UCG004, and Ruminococcaceae UCG002 were positively associated with PAH, whereas the order Bifidobacteriales; family Bifidobacteriaceae; and genera Eubacterium eligens group, Sutterella, Methanobrevibacter, Sellimonas, and Tyzzerella3 were negatively associated with PAH, with some exhibiting bidirectional causality. These microbiota modulate 24 metabolites, including palmitoylcholine, oleoylcholine, and 3,7-dimethylurate, to influence PAH. Hypoxia-induced PAH mice had significantly downregulated 1,4,5-trisphosphate receptor type 2, degrading enzyme, nuclear receptor-interacting protein 1, and growth factor-binding protein 1 in lung tissues, indicating their potential role in PAH regulation.<br><br>CONCLUSIONS: These findings suggest that gut microbiota composition and associated metabolites contribute to PAH development by regulating lung tissue gene expression. Our findings have implications for advancing gut microbiota-based PAH diagnostic technologies and targeted therapies.}, }
@article {pmid40079058, year = {2025}, author = {Manhães, LM and Santana, L and Alves, MR and Leal, PM and de Velasco, PC and Santana, I and de Brito, JS and Mafra, D and Borges, NA}, title = {Trimethylamine N-Oxide Plasma Levels Following Red Meat and Cod Fish Intake: A Pilot Crossover Trial in Hemodialysis Patients.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e70031}, doi = {10.1002/mnfr.70031}, pmid = {40079058}, issn = {1613-4133}, support = {E-26/202.524/2019//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; E-26/211.440/2019//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; }, abstract = {SCOPE: The uremic toxin trimethylamine N-oxide (TMAO) accumulates in patients with chronic kidney disease (CKD) and is associated with its progression, cardiovascular disease, and other complications. The gut microbiota produces TMAO from substrates mainly found in red meat, eggs, and dairy. However, some saltwater fish also contain high levels of TMAO. Although fish consumption is generally linked to beneficial effects, its effects on CKD patients require further research.<br><br>METHODS AND RESULTS: This study compares the effect of red meat and cod fish intake on TMAO plasma levels in CKD patients undergoing hemodialysis (HD). Participants received a single animal protein source (red meat vs. cod fish) for lunch and dinner for four consecutive days (each intervention), with a 2-week washout period in between. TMAO plasma levels were analyzed using LC-MS/MS. All 14 patients concluded the red meat intervention, while one refused to participate in the fish intervention. No significant difference in TMAO plasma levels was found post-red meat (p = 0.21) or fish intervention (p = 0.91), as well as between groups (p = 0.43).<br><br>CONCLUSION: In this study, 4 days of red meat and cod fish intake did not significantly impact TMAO levels in HD patients, while other factors may be associated with their circulating levels.}, }
@article {pmid40078943, year = {2024}, author = {Wang, Y and Qu, M and Bi, Y and Liu, WJ and Ma, S and Wan, B and Hu, Y and Zhu, B and Zhang, G and Gao, GF}, title = {The multi-kingdom microbiome catalog of the chicken gastrointestinal tract.}, journal = {Biosafety and health}, volume = {6}, number = {2}, pages = {101-115}, pmid = {40078943}, issn = {2590-0536}, abstract = {Chicken is an important food animal worldwide and plays an important role in human life by providing meat and eggs. Despite recent significant advances in gut microbiome studies, a comprehensive study of chicken gut bacterial, archaeal, and viral genomes remains unavailable. In this study, we constructed a chicken multi-kingdom microbiome catalog (CMKMC), including 18,201 bacterial, 225 archaeal, and 33,411 viral genomes, and annotated over 6,076,006 protein-coding genes by integrating 135 chicken gut metagenomes and publicly available metagenome-assembled genomes (MAGs) from ten countries. We found that 812 and 240 MAGs in our dataset were putative novel species and genera, respectively, far beyond what was previously reported. The newly unclassified MAGs were predominant in Phyla Firmicutes_A (n = 263), followed by Firmicutes (n = 126), Bacteroidota (n = 121), and Proteobacteria (n = 87). Most of the classified species-level viral operational taxonomic units belong to Caudovirales. Approximately, 63.24 % of chicken gut viromes are predicted to infect two or more hosts, including complete circular viruses. Moreover, we found that diverse auxiliary metabolic genes and antibiotic resistance genes were carried by viruses. Together, our CMKMC provides the largest integrated MAGs and viral genomes from the chicken gut to date, functional insights into the chicken gastrointestinal tract microbiota, and paves the way for microbial interventions for better chicken health and productivity.}, }
@article {pmid40078791, year = {2025}, author = {Gonzales, G and Malka, R and Bizios, R and Dion, GR and Guda, T}, title = {Burn inhalation injury and intubation with dexamethasone-eluting endotracheal tubes modulate local microbiome and alter airway inflammation.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {13}, number = {}, pages = {1524013}, pmid = {40078791}, issn = {2296-4185}, abstract = {BACKGROUND: Inhalation injuries, caused by exposure to extreme heat and chemical irritants, lead to complications with speaking, swallowing, and breathing. This study investigates the effects of thermal injury and endotracheal tube (ETT) placement on the airway microbiome and inflammatory response. A secondary aim is to assess the impact of localized dexamethasone delivery via a drug-eluting ETT to reduce laryngeal scarring.<br><br>METHODS: Inhalation injury was developed in swine by administering heated air (150&#xb0;C-160&#xb0;C) under endoscopic visualization. Following injury, segments of regular or dexamethasone-loaded endotracheal tubes (ETTs) were placed in the injured airways for 3 or 7&#xa0;days. Computed tomography (CT) scans were used to assess airway narrowing post-injury. Biofilm formation on the ETTs was investigated using micro-CT and microscopy. The airway microbiome was analyzed via 16S rRNA sequencing. Inflammatory markers were quantified using an immunoassay and macrophage populations in laryngeal tissue were assessed with CD86 and CD206 staining. Tracheal tissues were also histologically examined for epithelial thickness, collagen area, and mucin production.<br><br>RESULTS: CT scans confirmed airway narrowing post-injury, particularly around ETT sites. Biofilm formation was more extensive on dexamethasone-coated ETTs at later timepoints. Beta diversity analysis revealed significant shifts in microbial composition related to ETT type (R[2] = 0.04, p < 0.05) and duration of placement (R[2] = 0.22, p < 0.05). Differential abundance analysis demonstrated significant positive log fold changes in genera such as Bergeriella, Peptostreptococcus, and Bacteriodes with thermal injury over time. Inflammatory markers IFN-&#x3b3;, IL-4, and IL-1&#x3b2; were elevated in dexamethasone-ETT groups at 3&#xa0;days, then decreased by 7&#xa0;days. Macrophage markers CD86 and CD206 were significantly greater in dexamethasone groups compared to regular ETT groups at 7&#xa0;days (p = 0.002 and p = 0.0213, respectively). Epithelial thickness was significantly greater with regular ETT placement compared to dexamethasone ETT placement in the burn-injured airway at 3&#xa0;days (p = 0.027).<br><br>CONCLUSION: Thermal inhalation injury and ETT placement significantly impact airway inflammation, structural integrity, and microbiome composition. Dexamethasone-eluting ETTs, intended to reduce inflammation, increased biofilm formation and elevated cytokine levels, suggesting complex interactions between the drug coating and the host immune response. The airway microbiome shifted significantly with specific taxa thriving in the inflamed environment.}, }
@article {pmid40078785, year = {2025}, author = {Shin, HK and Bang, YJ}, title = {Aromatic Amino Acid Metabolites: Molecular Messengers Bridging Immune-Microbiota Communication.}, journal = {Immune network}, volume = {25}, number = {1}, pages = {e10}, pmid = {40078785}, issn = {1598-2629}, abstract = {Aromatic amino acid (AAA) metabolites, derived from tryptophan, phenylalanine, and tyrosine through coordinated host and microbial metabolism, have emerged as critical modulators of immune function. We examine the complex journey of AAAs from dietary intake through intestinal absorption and metabolic transformation, highlighting the crucial role of host-microbe metabolic networks in generating diverse immunomodulatory compounds. This review provides a unique integrative perspective by mapping the molecular mechanisms through which these metabolites orchestrate immune responses. Through detailed analysis of metabolite-receptor and metabolite-transporter interactions, we reveal how specific molecular recognition drives cell type-specific immune responses. Our comprehensive examination of signaling networks-from membrane receptor engagement to nuclear receptor activation to post-translational modifications- demonstrates how the same metabolite can elicit distinct functional outcomes in different immune cell populations. The context-dependent nature of these molecular interactions presents both challenges and opportunities for therapeutic development, particularly in inflammatory conditions where metabolite signaling pathways are dysregulated. Understanding the complexity of these regulatory networks and remaining knowledge gaps is fundamental for advancing metabolite-based therapeutic strategies in immune-mediated disorders.}, }
@article {pmid40078553, year = {2025}, author = {Wang, B and Shang, N and Feng, X and Hu, Z and Li, P and Chen, Y and Hu, B and Ding, M and Xu, J}, title = {Understanding the microbiome-crop rotation nexus in karst agricultural systems: insights from Southwestern China.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1503636}, pmid = {40078553}, issn = {1664-302X}, abstract = {Understanding how soil properties and microbial communities respond to crop rotation is essential for the sustainability of agroecosystems. However, there has been limited research on how crop rotation alters below-ground microbial communities in soils with serious bacterial wilt within the karst agricultural system. This study investigated the effects of continuous planting of corn, tobacco, and tobacco-corn rotation on soil microbial communities in the karst regions of Southwestern China. High-throughput sequencing was used to evaluate the responses of the soil microbial community structure to crop monoculture and rotation patterns. As expected, the tobacco-corn rotation mitigated the negative effects of continuous cropping and reduced soil acidification. The tobacco-corn rotation also significantly altered the composition of microbial communities and promoted plant growth by fostering a higher abundance of beneficial microorganisms. The predominant bacteria genera Sphingomonas and Gaiella and the predominant fungal genera Mortierella and Saitozyma were identified as discriminant biomarkers that are critical to soil ecosystem health. pH, available potassium (AK), and available phosphorus (AP) were the primary soil factors related to the soil microbiome assembly. This study aimed to demonstrate the association between crop rotation and microbiomes, suggesting that altering cultivation patterns could enhance karst agricultural systems.}, }
@article {pmid40078549, year = {2025}, author = {Gurung, B and Courreges, MC and Pollak, J and Malgor, R and Jiang, L and Wang, B and Wang, S}, title = {Non-invasive treatment of Clostridioides difficile infection with a human-origin probiotic cocktail through gut microbiome-gut metabolome modulations.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1555220}, pmid = {40078549}, issn = {1664-302X}, abstract = {Clostridioides difficile (C. difficile) is a leading cause of hospital-associated diarrhea, primarily due to gut dysbiosis following antibiotic use. Probiotics have been found to provide several benefits to hosts via modulation of the gut microbiota and their metabolites. However, till now, no conventional probiotics have been clearly proven to be an effective prophylactic option for CDI prevention. Therefore, more studies on developing specific probiotic candidates targeting CDI and improving diversity of probiotics administrated are needed. In this study, a human-origin highly diverse and highly targeted probiotic cocktail (Pro11) containing 11 various probiotic species was developed against C. difficile. Pro11 protected mice against CDI with lower clinical scores and higher survival rates, and inhibited C. difficile in vivo with less C. difficile burden and toxins production determined in colon. Histological analysis demonstrated that Pro11 strengthened gut barrier, reducing gut permeability (less secreted sCD14 in serum) and gut inflammation. In addition, gut microbiome analysis demonstrated that Pro11 increased gut microbiome diversity and beneficial species. Along with gut microbiome modulation, gut metabolites including butyrate, were significantly increased in the probiotics-fed group. Results from this study highlighted probiotics as a promising CDI therapy as gut microbiota modulators, which will lay the foundation for translating probiotics in mitigating CDI and other intestinal pathogens for clinical use.}, }
@article {pmid40084234, year = {2019}, author = {Werlang, C and Cárcarmo-Oyarce, G and Ribbeck, K}, title = {Engineering mucus to study and influence the microbiome.}, journal = {Nature reviews. Materials}, volume = {4}, number = {2}, pages = {134-145}, pmid = {40084234}, issn = {2058-8437}, abstract = {Mucus is a 3D hydrogel that houses the majority of the human microbiome. The mucous environment plays an important role in the differentiation and behaviour of microbial phenotypes and enables the creation of spatial distributions. Dysregulation of mucus is further associated with various diseases. Therefore, mucus is the key ingredient to study the behaviour of commensal and pathogenic microbiota in vitro. Indeed, microorganisms cultured in mucus exhibit phenotypes substantially different from those exhibited in standard laboratory media. In this Review, we discuss the impact of mucus on the microbiome and examine the structure and glycosylation of mucins - the main building blocks of mucus. We investigate the impact of glycans on mucin function and highlight different approaches for the engineering of synthetic mucins, including synthesis of the backbone, the design of mucin-mimetic hydrogels and the engineering of glycans. Finally, mucin mimetics for 3D in vitro cell culture and for modulating microbial community structure and function are discussed.}, }
@article {pmid40078547, year = {2025}, author = {Peng, T and Yang, T and Sha, J and Zhao, J and Shi, J}, title = {Dynamics of endophytic fungi composition in paris polyphylla var. chinensis (franch.) hara seeds during storage and growth, and responses of seedlings to phytohormones.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1540651}, doi = {10.3389/fmicb.2025.1540651}, pmid = {40078547}, issn = {1664-302X}, abstract = {INTRODUCTION: Endophytic fungi exhibit diverse interactions with plants, from pathogenic to mutualistic symbiosis, and the community composition is regulated by phytohormones. Yet, the composition and dynamics of endophytic fungi in Paris polyphylla var. chinensis (Franch.) Hara (PPC) during fresh seed (FD), sand-stored seed (SSD), and seedling (SS) stages remain unclear. Similarly, the overall impact of phytohormones on the management of endophytic fungal communities is yet to be elucidated.<br><br>METHODS: We carried out a pot experiment to examine the effects of various stages of PPC seeds and the external addition of three phytohormones, namely, melatonin (MT), strigolactone (SL), and 24-epibrassinolide (BR) on the endophytic fungi of PPC seedlings. This was done through internal transcribed spacer (ITS) amplicon sequencing.<br><br>RESULTS: The study of the endophytic fungal microbiome in FD, SSD, and SS stages of PPC revealed an increased richness and diversity of fungi during the SS stage, with significant changes in community composition observed. We found that Sordariomycetes played a crucial role in this process, potentially contributing to the establishment and growth of PPC seedlings. Additionally, this study investigated the influence of phytohormones on the phenotypic and physiological characteristics of PPC and its endophytic fungal community. Our results demonstrated that MT and SL significantly increased PPC biomass by 69.32 and 15.23%, respectively, while 2 mg/L of BR hindered the growth of PPC roots. MT, SL, and BR not only induced significant changes in the composition and diversity of the endophytic fungal community in PPC but also affected biomass potentially through specific regulation of potential biomarkers. Furthermore, phytohormones were shown to indirectly modify the endophytic fungal community by altering antioxidant system in plants.<br><br>CONCLUSION: This study provides novel insights into the dynamic changes of microbial communities in the FD, SSD, and SS stages. Furthermore, the differences among various phytohormones ultimately enhance our predictive understanding of how to directly or indirectly manipulate the plant microbiome to improve plant health.}, }
@article {pmid40078411, year = {2025}, author = {Huang, Y and Yang, C and Fu, B and Guo, H and Chen, Y and Xu, D}, title = {Impact of Ligilactobacillus salivarius Li01 on benzo[a]pyrene-induced colitis, based on host-microbiome interactions in Mongolian gerbils.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1494525}, doi = {10.3389/fnut.2025.1494525}, pmid = {40078411}, issn = {2296-861X}, abstract = {BACKGROUND: Probiotics supplementations have been regarded as an effective strategy for colitis treatment. However, the effect of Ligilactobacillus salivarius Li01 on benzo[a]pyrene (BaP)-induced colitis in Mongolian gerbils remains unclear. In this study, we leverage a BaP-induced model of colitis that exhibits significant remission following Ligilactobacillus salivarius Li01 intervention, to conduct an animal experiment that integrates histopathological assessment, inflammatory cytokines, 16S rRNA sequencing, targeted metabolomic profiling to investigate the relationship between Ligilactobacillus salivarius Li01, gut microbiota, and colitis.<br><br>RESULTS: We demonstrated that the improvements in colon histopathological assessment and inflammatory cytokines by Ligilactobacillus salivarius Li01 supplementation are accompanied by alterations in gut microbiota structure marked by increased abundance of strains with probiotic potential belonging to Bifidobacterium and Eubacterium_coprostanoligenes. Targeted metabolomic profiling analysis showed that Ligilactobacillus salivarius Li01 supplementation increases the concentration of acetic, propionic, butyric, and valeric acid. Correlation analysis showed that the alteration in the indicators associated with colitis is closely correlated to the changed microbial taxa and short-chain fatty acids (SCFAs).<br><br>CONCLUSION: These data highlighted that Ligilactobacillus salivarius Li01 supplementation ameliorated the BaP-induced colitis, probably via modulating the structure of gut microbiota and promoting the production of SCFAs. Our findings provide preliminary evidence for a possible therapeutic strategy for the treatment of colitis based on host-microbiome interactions.}, }
@article {pmid40078367, year = {2025}, author = {Ullah, H and Arbab, S and Chang, C and Bibi, S and Muhammad, N and Rehman, SU and Suleman,  and Ullah, I and Hassan, IU and Tian, Y and Li, K}, title = {Gut microbiota therapy in gastrointestinal diseases.}, journal = {Frontiers in cell and developmental biology}, volume = {13}, number = {}, pages = {1514636}, doi = {10.3389/fcell.2025.1514636}, pmid = {40078367}, issn = {2296-634X}, abstract = {The human gut microbiota, consisting of trillions of microorganisms, plays a crucial role in gastrointestinal (GI) health and disease. Dysbiosis, an imbalance in microbial composition, has been linked to a range of GI disorders, including inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), celiac disease, and colorectal cancer. These conditions are influenced by the interactions between the gut microbiota, the host immune system, and the gut-brain axis. Recent research has highlighted the potential for microbiome-based therapeutic strategies, such as probiotics, prebiotics, fecal microbiota transplantation (FMT), and dietary modifications, to restore microbial balance and alleviate disease symptoms. This review examines the role of gut microbiota in the pathogenesis of common gastrointestinal diseases and explores emerging therapeutic approaches aimed at modulating the microbiome. We discuss the scientific foundations of these interventions, their clinical effectiveness, and the challenges in their implementation. The review underscores the therapeutic potential of microbiome-targeted treatments as a novel approach to managing GI disorders, offering personalized and alternative options to conventional therapies. As research in this field continues to evolve, microbiome-based interventions hold promise for improving the treatment and prevention of gastrointestinal diseases.}, }
@article {pmid40078316, year = {2025}, author = {Zhao, C and Escalante, C and Jacobson, AL and Balkcom, KS and Conner, KN and Martin, KM}, title = {Metatranscriptomic and metagenomic analyses of cotton aphids (Aphis gossypii) collected from cotton fields in Alabama, USA.}, journal = {Frontiers in insect science}, volume = {5}, number = {}, pages = {1461588}, doi = {10.3389/finsc.2025.1461588}, pmid = {40078316}, issn = {2673-8600}, }
@article {pmid40078208, year = {2025}, author = {Wu, L and Xue, L and Ding, X and Jiang, H and Zhang, R and Zheng, A and Zu, Y and Tan, S and Wang, X and Liu, Z}, title = {Integrated microbiome and metabolomics analysis reveals the alleviating effect of Pediococcus acidilactici on colitis.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1520678}, doi = {10.3389/fvets.2025.1520678}, pmid = {40078208}, issn = {2297-1769}, abstract = {Colitis is a complicated disease caused by multiple factors, seriously threatening the host health and the development of animal husbandry. Probiotics have been demonstrate to participate in the active regulation of multiple gastrointestinal disease, gut microbiota and metabolism, but research on the efficacy of Pediococcus acidilactici isolated from dogs in alleviating colitis remains scarce. Here, we aimed to investigate the ameliorative effects of Pediococcus acidilactici isolated from dogs on colitis induced by LPS and its underlying molecular mechanisms. For this purpose, we collected colon contents from 15 mice for amplicon sequencing and metabolic analysis. Results showed that Pediococcus acidilactici could relieve the colon damage and cytokine disorder caused by colitis. Microbiome analysis showed that colitis could cause a significant decrease in the gut microbial diversity and abundance, but Pediococcus acidilactici administration could restore the microbial index to the control level. Metabolomics analysis showed that 8 metabolic pathways and 5 (spermine, L-Arginine, 15-Deoxy-Delta12,14-PGJ2, prostaglandin J2, and 15(S)-HETE) metabolites may be involved in the alleviation of colitis by Pediococcus acidilactici. In summary, these findings demonstrated that the positive regulation effect of Pediococcus acidilactici on gut microbiota and metabolism may be one of its underlying mechanisms to alleviate colitis. Additionally, this study also conveyed a vital message that Pediococcus acidilactici isolated from dogs may serve as a promising candidate to ameliorate Pediococcus acidilactici.}, }
@article {pmid40077904, year = {2025}, author = {Brunet, M and Le Duff, N and Barbeyron, T and Thomas, F}, title = {Year-Round Quantification, Structure and Dynamics of Epibacterial Communities From Diverse Macroalgae Reveal a Persistent Core Microbiota and Strong Host Specificities.}, journal = {Environmental microbiology reports}, volume = {17}, number = {2}, pages = {e70077}, doi = {10.1111/1758-2229.70077}, pmid = {40077904}, issn = {1758-2229}, support = {ANR-10-BTBR-04//Agence Nationale de la Recherche/ ; ANR-18-CE02-0001-01//Agence Nationale de la Recherche/ ; }, mesh = {*Seaweed/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Seasons ; Phylogeny ; Host Specificity ; Ulva/microbiology ; Phaeophyceae/microbiology ; DNA, Bacterial/genetics ; Ecosystem ; Biodiversity ; Rhodophyta/microbiology ; }, abstract = {Macroalgae-bacteria interactions play pivotal ecological roles in coastal ecosystems. Previous characterisation of surface microbiota from various macroalgae evidenced fluctuations based on host tissues, physicochemical and environmental parameters. However, the dynamics and degree of similarity of epibacterial communities colonising phylogenetically distant algae from the same habitat are still elusive. We conducted a year-long monthly epimicrobiota sampling on five algal species inhabiting an English Channel rocky shore: Laminaria digitata, Ascophyllum nodosum, Fucus serratus (brown algae), Palmaria palmata (red alga) and Ulva sp. (green alga). To go beyond relative compositional data and estimate absolute variations in taxa abundance, we combined qPCR measurements of 16S rRNA gene copies with amplicon metabarcoding. A core microbiome composed of 10 genera was consistently found year-round on all algae. Notably, the abundant genus Granulosicoccus stood out for being the only one present in all samples and displayed an important microdiversity. Algal host emerged as the primary driver of epibacterial community composition, before seasonality, and bacterial taxa specifically associated with one or several algae were identified. Moreover, the impact of seasons on the epimicrobiota varied depending on algal tissues. Overall, this study provides an extensive characterisation of the microbiota of intertidal macroalgae and enhances our understanding of algal-bacteria holobionts.}, }
@article {pmid40077821, year = {2025}, author = {Arokiaraj, SR and Prathiviraj, R and Chaiyasut, C and Sivamaruthi, BS}, title = {Bacteriocins from Lactic Acid Bacteria Could Modulate the Wnt Pathway: A Possible Therapeutic Candidate for the Management of Colorectal Cancer- An In silico Study.}, journal = {Anti-cancer agents in medicinal chemistry}, volume = {}, number = {}, pages = {}, doi = {10.2174/0118715206367950250228100833}, pmid = {40077821}, issn = {1875-5992}, abstract = {INTRODUCTION: Colorectal cancer (CRC) is a type of cancer that develops due to abnormal cell growth in the colon and rectum. Existing conventional CRC treatment strategies have side effects. Hence, exploring new and advanced techniques for bacterial CRC therapy is crucial. Bacteriocins are peptides produced by bacteria, including lactic acid bacteria (LAB), that have bactericidal effects. In the present study, we have focused on searching for effective and safe bacteriocins from LAB as alternatives to clinical therapeutics for treating CRC, leaving healthy cells unaffected.<br><br>METHODS: We selected nine bacteriocin-like peptides that are effective in the human gut microbiome. These peptides were derived from LAB species using online database resources. We then conducted an in silico phylogenetic analysis of other LAB species present in the gut microbiome using the KEGG Genome database. We established the phylogenetic relationship of these LAB species with others observed in the database to determine their closeness and similarity. Further, the bacteriocin-like peptides were modeled and refined to interact with the plausible target. The systematic network analysis was performed to find the highly interconnected targets involved in the Wnt target genes of CRC.<br><br>RESULTS: The network analysis observed that the genes CTNNB1 and LRP5 were found as hub genes to upregulate CRC. In silico protein-peptide docking between the target bacteriocins like peptides and the therapeutic targets of CRC was performed, significantly our findings revealed that the peptide PE4 and PE9 (Lactacin F and Lactacin B) exhibited better binding affinity with CTNNB1. In contrast, the peptides PE7 and PE9 (Doderlin and Lactacin B) revealed better binding affinity with LRP5. Furthermore, we conducted molecular dynamics (MD) simulations to confirm the stability and bonding interactions of the bacteriocins derived from the LAB species.<br><br>CONCLUSION: Our findings indicate that bacteriocins (Lactacin B, Lactacin F and Doderlin) may have significant potential as therapeutics for CRC.}, }
@article {pmid40077792, year = {2025}, author = {Costa, CJ and Prescott, S and Fourie, NH and Abey, SK and Sherwin, LB and Rahim-Williams, B and Joseph, PV and Posada-Quintero, H and Hoffman, RK and Henderson, WA}, title = {Host Transcriptome and Microbial Variation in Relation to Visceral Hyperalgesia.}, journal = {Nutrients}, volume = {17}, number = {5}, pages = {}, doi = {10.3390/nu17050921}, pmid = {40077792}, issn = {2072-6643}, support = {1ZIANR000018-01-09; K22MD006143-01/GF/NIH HHS/United States ; }, mesh = {Humans ; *Hyperalgesia/microbiology ; *Transcriptome ; Male ; Female ; Adult ; Visceral Pain/microbiology ; Microbiota ; RNA, Messenger/metabolism ; Middle Aged ; Mouth/microbiology ; Gastrointestinal Microbiome ; Bacteria/genetics/classification ; Young Adult ; }, abstract = {BACKGROUND: Chronic visceral hypersensitivity is associated with an overstressed pain response to noxious stimuli (hyperalgesia). Microbiota are active modulators of host biology and are implicated in the etiology of visceral hypersensitivity.<br><br>OBJECTIVES: we studied the association between the circulating mRNA transcriptome, the intensity of induced visceral pain (IVP), and variation in the oral microbiome among participants with and without baseline visceral hypersensitivity.<br><br>METHODS: Transcriptomic profiles and microbial abundance were correlated with IVP intensity. Host mRNA and microbes associated with IVP were explored, linking variation in the microbiome to host RNA biology.<br><br>RESULTS: 259 OTUs were found to be associated with IVP through correlation to differential expression of 471 genes in molecular pathways related to inflammation and neural mechanisms, including Rho and PI3K/AKT pathways. The bacterial families Lachnospiraceae, Prevotellaceae, and Veillonellaceae showed the highest degree of association. Oral microbial profiles with reduced diversity were characteristic of participants with visceral hypersensitivity.<br><br>CONCLUSIONS: Our results suggest that the oral microbiome may be involved in systemic immune and inflammatory effects and play a role in nervous system and stem cell pathways. The interactions between visceral hypersensitivity, differentially expressed molecular pathways, and microbiota described here provide a framework for further work exploring the relationship between host and microbiome.}, }
@article {pmid40077784, year = {2025}, author = {Bomar, MC and Ewell, TR and Brown, RL and Brown, DM and Kwarteng, BS and Abbotts, KSS and Butterklee, HM and Williams, NNB and Wrigley, SD and Walsh, MA and Hamilton, KL and Thomson, DP and Weir, TL and Bell, C}, title = {Short-Term Magnesium Supplementation Has Modest Detrimental Effects on Cycle Ergometer Exercise Performance and Skeletal Muscle Mitochondria and Negligible Effects on the Gut Microbiota: A Randomized Crossover Clinical Trial.}, journal = {Nutrients}, volume = {17}, number = {5}, pages = {}, doi = {10.3390/nu17050915}, pmid = {40077784}, issn = {2072-6643}, support = {0//New Capstone, Inc./ ; }, mesh = {Humans ; Male ; *Cross-Over Studies ; *Gastrointestinal Microbiome/drug effects ; Female ; *Dietary Supplements ; Double-Blind Method ; Adult ; *Oxygen Consumption/drug effects ; Muscle, Skeletal/drug effects/metabolism ; Young Adult ; Magnesium/blood ; Exercise/physiology ; Mitochondria, Muscle/metabolism/drug effects ; Exercise Test ; Athletic Performance/physiology ; Magnesium Chloride/pharmacology ; }, abstract = {Background/Objectives: Although the importance of magnesium for overall health and physiological function is well established, its influence on exercise performance is less clear. The primary study objective was to determine the influence of short-term magnesium supplementation on cycle ergometer exercise performance. The hypothesis was that magnesium would elicit an ergogenic effect. Methods: A randomized, double-blind, placebo-controlled, two-period crossover design was used to study men and women who were regular exercisers. Fifteen participants ingested either a placebo or magnesium chloride (MgCl2 300 mg) twice per day, for 9 days, separated by a 3-week washout. During days 8 and 9, participants completed a battery of cycle ergometer exercise tests, and whole blood, vastus lateralis, and stools were sampled. The primary outcomes were the maximal oxygen uptake (VO2max), a simulated 10 km time trial, and the sprint exercise performance. Additional outcomes included skeletal muscle mitochondrial respiration, and, on account of the known laxative effects of magnesium, the gut microbiota diversity. Results: Compared with a placebo, MgCl2 supplementation increased the circulating ionized Mg concentration (p < 0.03), decreased the VO2max (44.4 ± 7.7 vs. 41.3 ± 8.0 mL/kg/min; p = 0.005), and decreased the mean power output during a 30 s sprint (439 ± 88 vs. 415 ± 88 W; p = 0.03). The 10 km time trial was unaffected (1282 ± 126 vs. 1281 ± 97 s; p = 0.89). In skeletal muscle, MgCl2 decreased mitochondrial respiration in the presence of fatty acids at complex II (p = 0.04). There were no significant impacts on the gut microbiota richness (CHAO1; p = 0.68), Shannon's Diversity (p = 0.23), or the beta-diversity (Bray-Curtis distances; p = 0.74). Conclusions: In summary, magnesium supplementation had modest ergolytic effects on cycle ergometer exercise performance and mitochondrial respiration. We recommend that regular exercisers, free from hypomagnesemia, should not supplement their diet with magnesium.}, }
@article {pmid40077761, year = {2025}, author = {Eleftheriades, A and Koulouraki, S and Belegrinos, A and Eleftheriades, M and Pervanidou, P}, title = {Maternal Obesity and Neurodevelopment of the Offspring.}, journal = {Nutrients}, volume = {17}, number = {5}, pages = {}, doi = {10.3390/nu17050891}, pmid = {40077761}, issn = {2072-6643}, mesh = {Humans ; Female ; Pregnancy ; *Pregnancy in Obesity ; *Neurodevelopmental Disorders/etiology/epidemiology ; *Prenatal Exposure Delayed Effects ; Animals ; Epigenesis, Genetic ; Maternal Nutritional Physiological Phenomena ; }, abstract = {BACKGROUND: An increasing amount of evidence, derived from both human epidemiological studies and animal research, suggests that exposure to maternal obesity in utero is linked to adverse neurodevelopmental outcomes in the offspring. These can include attention deficit hyperactivity disorder, autism spectrum disorders, intellectual disability, and cerebral palsy.<br><br>METHODS: A thorough search in Medline/PubMed and Google Scholar databases was performed by two independent reviewers in order to investigate the link between the exposure to maternal obesity and neurodevelopmental outcomes in the offspring. A list of keywords, including maternal obesity, maternal overweight, maternal diet, neurodevelopment, and neuropsychiatric disorders, was used in the search algorithm.<br><br>RESULTS: The existing evidence regarding the potential mechanisms through which maternal obesity may impact offspring neurodevelopment and programming, such as inflammation, hormone dysregulation, alterations to the microbiome, and epigenetics, as well as evidence from animal studies, was summarized in this narrative review.<br><br>CONCLUSIONS: Maternal obesity seems to be overall associated with various neuropsychiatric and neurodevelopmental disorders. However, more robust data from future studies are needed to establish this association, which will take into account the role of potential confounders such as genetic factors and gene-environment interactions.}, }
@article {pmid40077728, year = {2025}, author = {Rondinella, D and Raoul, PC and Valeriani, E and Venturini, I and Cintoni, M and Severino, A and Galli, FS and Mora, V and Mele, MC and Cammarota, G and Gasbarrini, A and Rinninella, E and Ianiro, G}, title = {The Detrimental Impact of Ultra-Processed Foods on the Human Gut Microbiome and Gut Barrier.}, journal = {Nutrients}, volume = {17}, number = {5}, pages = {}, doi = {10.3390/nu17050859}, pmid = {40077728}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis ; Fast Foods/adverse effects ; Probiotics ; Dietary Fiber ; Brain-Gut Axis/physiology ; Food Handling ; Diet/adverse effects ; Permeability ; Food, Processed ; }, abstract = {Ultra-processed foods (UPFs) have become a widely consumed food category in modern diets. However, their impact on gut health is raising increasing concerns. This review investigates how UPFs impact the gut microbiome and gut barrier, emphasizing gut dysbiosis and increased gut permeability. UPFs, characterized by a high content of synthetic additives and emulsifiers, and low fiber content, are associated with a decrease in microbial diversity, lower levels of beneficial bacteria like Akkermansia muciniphila and Faecalibacterium prausnitzii, and an increase in pro-inflammatory microorganisms. These alterations in the microbial community contribute to persistent inflammation, which is associated with various chronic disorders including metabolic syndrome, irritable bowel syndrome, type 2 diabetes, and colorectal cancer. In addition, UPFs may alter the gut-brain axis, potentially affecting cognitive function and mental health. Dietary modifications incorporating fiber, fermented foods, and probiotics can help mitigate the effects of UPFs. Furthermore, the public needs stricter regulations for banning UPFs, along with well-defined food labels. Further studies are necessary to elucidate the mechanisms connecting UPFs to gut dysbiosis and systemic illnesses, thereby informing evidence-based dietary guidelines.}, }
@article {pmid40077697, year = {2025}, author = {Borer, KT}, title = {Relevance of Milk Composition to Human Longitudinal Growth from Infancy Through Puberty: Facts and Controversies.}, journal = {Nutrients}, volume = {17}, number = {5}, pages = {}, doi = {10.3390/nu17050827}, pmid = {40077697}, issn = {2072-6643}, mesh = {Humans ; Infant ; *Milk, Human/chemistry ; *Infant Nutritional Physiological Phenomena/physiology ; Animals ; *Child Development/physiology ; *Puberty/physiology ; Infant, Newborn ; Female ; Infant Formula ; Child ; Child, Preschool ; Milk/chemistry ; Gastrointestinal Microbiome/physiology ; Energy Intake ; Male ; }, abstract = {Milk is the principal nutrient of newborn humans and a diagnostic feature of the order Mammalia. Its release is elicited as a reflex by infant sucking under the control of the hormone oxytocin. While it is recognized that breast milk optimally promotes infant longitudinal growth and development, this review explores facts and controversies regarding the extent to which the milks of several dairy animals and infant formula milk (IF) approximate special properties and bioactivities of breast milk. It also provides evidence that early exposure to undernutrition during the very rapid fetal and early infancy growth predominantly and permanently stunts longitudinal growth trajectory in both animals and humans and is often followed in later life by obesity and metabolic dysfunction, and sometimes also by precocious timing of sexual maturation. There is a knowledge gap as to whether there may be additional critical periods of nutritional vulnerability in human development, which is characterized by a relatively prolonged period of slow childhood growth bracketed by the rapid fetal-neonatal and pubertal growth spurts. It is also unclear whether any quantitative differences in caloric intake and supply during neonatal period may influence developmental fatness programming. A further knowledge gap exists regarding the role of infant microbiome composition and development in the possible epigenetic programming of longitudinal growth or fatness in later life. Extending the research of early developmental programming to the entire period of human growth from conception to the end of puberty, examining infant caloric intake and supply as possible factors modulating the epigenetic programming in favor of obesity, and examining the role of infant gut microbiome in developing infant's capacity to process nutrients may provide a better understanding of the interaction between critical nutritional influences in the control of human longitudinal growth and later-life obesity.}, }
@article {pmid40077695, year = {2025}, author = {Shremo Msdi, A and Haghparast, A and Garey, KW and Wang, EM}, title = {Microbiome-Based Therapeutics for Salt-Sensitive Hypertension: A Scoping Review.}, journal = {Nutrients}, volume = {17}, number = {5}, pages = {}, doi = {10.3390/nu17050825}, pmid = {40077695}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome ; Animals ; *Hypertension/therapy/microbiology ; *Probiotics/therapeutic use ; *Sodium Chloride, Dietary ; Prebiotics/administration &amp; dosage ; Diet, Sodium-Restricted ; Blood Pressure/drug effects ; Rats ; Mice ; Fatty Acids, Volatile/metabolism ; }, abstract = {The purpose of this scoping review was to provide a comprehensive understanding of the current knowledge concerning the gut microbiome and SCFAs as emerging treatments for salt-sensitive hypertension. Relevant animal and human studies were identified via PubMed through August 2024. Twenty-four human (n = 9) and animal (n = 15) trials were included. Most human studies were observational (n = 6), aiming to compare gut microbiota differences between hypertensive and normotensive individuals. Three human studies evaluated microbiome-based interventions either via a sodium-restricted diet (n = 2) or prebiotic supplementation (n = 1). Fifteen animal trials involving either mice or rats were identified, all of which were interventional. These included dietary changes (n = 9), probiotic treatments (n = 1), postbiotic primarily bacterial metabolites (n = 4), and live biotherapeutic products (n = 4). All interventions were effective in decreasing blood pressure. Microbiome-based therapies as biologic modifiers for salt-sensitive hypertension are emerging. Substantial knowledge gaps remain, warranting further research to fully explore this promising therapeutic avenue.}, }
@article {pmid40077676, year = {2025}, author = {Baldeon, ME and Cardenas, P and Arevalo, V and Prado-Vivar, B and Uchimiya, M and Peña, L and Benitez, AD and Suárez-Jaramillo, A and Edison, AS and Herrera, A and Arturo, L and Fornasini, M}, title = {Human Milk Microbiota Across Lactation Stages and Free Glutamate Concentrations in Healthy Ecuadorian Women.}, journal = {Nutrients}, volume = {17}, number = {5}, pages = {}, doi = {10.3390/nu17050805}, pmid = {40077676}, issn = {2072-6643}, support = {NA//International Glutamate Technical Committee to MEB and by Universidad Internacional del Ec-uador/ ; }, mesh = {Humans ; *Milk, Human/chemistry/microbiology ; Female ; Ecuador ; Adult ; *Lactation ; *Glutamic Acid/analysis ; *Microbiota ; Bacteria/classification/genetics ; Young Adult ; RNA, Ribosomal, 16S/genetics ; Male ; Colostrum/microbiology/chemistry ; }, abstract = {Background/Objectives: There is limited information on human milk (HM) microbiome composition and function in Latin America. Also, interactions between HM constituents and its microbiome have received partial attention. Objective: To characterize the HM microbiota composition considering lactation stages (colostrum, transition, and mature HM) and free glutamate concentrations in Ecuadorian mothers. Methods: We recruited 20 mothers that gave birth to normal full-term babies and donated colostrum, transition, and mature milk. Samples were assessed by 16S rRNA gene sequencing by Oxford Nanopore Technologies (ONT). Free glutamate concentrations were measured by proton nuclear magnetic resonance (NMR) spectroscopy. Results: For each lactation stage and in order of frequency, the majority of ASVs were assigned to Staphylococcus, Streptococcus, (Firmicutes); Escherichia, Acinetobacter, (Proteobacteria); Corynebacterium, Lactobacillus, Cutibacterium, (Actinobacteriota); Chryseobacterium, and Flavobacterium (Bacteroidota). Alfa diversity was similar in HM samples and tended to be higher in milk intended for male infants. We observed significant differences in qualitative β-diversity metrics between samples with low and high glutamate concentrations. Functional predictions of HM microbiota demonstrated the presence of polyamine biosynthesis II super pathway in samples with high glutamate concentrations. Conclusions: The core bacterial components of the HM microbiota in Ecuadorian women were similar to those reported from different parts of the world, with variations at the genus level. Free glutamate dynamics in HM need to be studied considering maternal production and bacterial metabolism to better understand HM composition for optimal infant nutrition.}, }
@article {pmid40077643, year = {2025}, author = {Schwartz, LT and Ladouceur, JG and Russell, MM and Xie, SYL and Bu, S and Kerver, JM and Comstock, SS}, title = {The Relationship Between Fiber Intake and Gut Bacterial Diversity and Composition During the Third Trimester of Pregnancy.}, journal = {Nutrients}, volume = {17}, number = {5}, pages = {}, doi = {10.3390/nu17050773}, pmid = {40077643}, issn = {2072-6643}, support = {R01 DK135054/GF/NIH HHS/United States ; UG3OD023285/GF/NIH HHS/United States ; UH3OD023285/GF/NIH HHS/United States ; G-1608-140432//Michigan Health Endowment Fund/ ; R-1605-140007//Michigan Health Endowment Fund/ ; none//Michigan State C-RAIND/ ; none//CHARM small grant/ ; }, mesh = {Humans ; Female ; *Dietary Fiber/administration &amp; dosage ; Pregnancy ; *Gastrointestinal Microbiome ; *Pregnancy Trimester, Third ; Adult ; Feces/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Vegetables ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; Butyrates/metabolism/analysis ; Young Adult ; Diet ; }, abstract = {BACKGROUND/OBJECTIVES: High fiber (34-36 g/day) diets are recommended during pregnancy due to inverse associations with constipation and adverse pregnancy health outcomes, including pre-eclampsia and gestational diabetes. However, the mechanism for this protective effect is poorly defined. Fiber may be protective due to its impact on the composition and function of specific bacteria within the pregnancy gut microbiome. The purpose of this analysis was to investigate whether a sub-sample of cohort study participants in their third trimester met daily dietary fiber and vegetable intake recommendations and, in turn, how this impacted bacterial composition and butyrate-producing genes within the gut microbiome.<br><br>METHODS: Pregnant participants (n = 52) provided stool samples and survey data, which were used to calculate fiber and vegetable intake. Genomic DNA was extracted from the stool samples, followed by PCR to amplify the V4 region of the 16S rRNA gene. Amplicons were sequenced and mapped to the RDP reference. Quantitative real-time PCR was used to measure the abundance of bacterial genes for butyrate production.<br><br>RESULTS: Of the pregnant participants in this sample, 84.7% and 92.3% failed to meet recommendations in the Dietary Guidelines for Americans for dietary fiber and vegetable intake, respectively. All four participants who met the vegetable recommendation were a subset of those who met the fiber recommendation. The participants who met the pregnancy fiber recommendation had gut microbiotas with greater alpha diversity (Shannon and Inverse Simpson) than those who did not. However, there was no association between dietary fiber intake and the abundance of bacterial genes for butyrate production.<br><br>CONCLUSIONS: This research suggests that general fiber intake during pregnancy has a modest association with the gut bacterial community. These preliminary results demonstrate a need to improve fiber intake during pregnancy. Further, studies that measure the relationship between dietary intake of specific types of fiber and associations with specific gut bacterial community members and their functions are needed.}, }
@article {pmid40077613, year = {2025}, author = {Noles, DL and Matzeller, KL and Frank, DN and Krebs, NF and Tang, M}, title = {Complementary Feeding and Infant Gut Microbiota: A Narrative Review.}, journal = {Nutrients}, volume = {17}, number = {5}, pages = {}, doi = {10.3390/nu17050743}, pmid = {40077613}, issn = {2072-6643}, support = {5R01DK126710-04/DK/NIDDK NIH HHS/United States ; T32DK067009-20/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Infant ; *Infant Nutritional Physiological Phenomena ; Diet ; Infant Food ; }, abstract = {Background: The complementary feeding period, spanning from 6 to 24 months of age, marks the transition from an exclusive liquid diet in infants to a dietary pattern requiring the introduction of solid foods to meet nutritional demands. Complementary feeding coincides with other critical development windows, including the maturation of the gut microbiome. However, the effects of specific solid foods on gut microbiota and the subsequent influence on health outcomes require further investigation. Methods: This narrative review analyzes published research from January 2004 to October 2024 and aims to summarize the current evidence of the effects of complementary feeding on the infant gut microbiota. Results: A total of 43 studies were included in this review. Overall, multiple studies reported an increase in alpha-diversity after solid food introduction. Bifidobacteriaceae is the predominant bacterial family during the first 6 months of life, shifting to Lachnospiraceae, Ruminococcaceae, and Clostridium spp. after the introduction of solid foods. The timing of solid food introduction may also influence gut microbiota, though results were inconclusive. The effect of individual dietary components on the gut microbiota was conflicting, with limited evidence to make inferences. Conclusions: Because of variations in study design, dietary intake quantification, and minimal follow-up, a lack of conclusive evidence exists describing the relationship between complementary feeding and gut microbiota outcomes in infants. Future research to describe these relationships should focus on the impact of individual foods on microbial diversity and maturation, as well as the relationship between microbiota and infant health outcomes.}, }
@article {pmid40077577, year = {2025}, author = {Wu, Y and Sun, J and Xie, W and Xue, S and Li, X and Guo, J and Shan, J and Peng, G and Zheng, Y}, title = {Immunomodulation of Glycyrrhiza Polysaccharides In Vivo Based on Microbiome and Metabolomics Approaches.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/foods14050874}, pmid = {40077577}, issn = {2304-8158}, support = {No. 81973482 and No. 82474116; No. 2022A02013-3//the National Natural Science Foundation of China; the Xinjiang Autonomous Region Key R&amp;D Program of China/ ; }, abstract = {Glycyrrhiza uralensis Fisch. is a medicinal herb that can be added to food to provide therapeutic effects and reduce the burden of medications. Herein, the immunomodulatory effects of Glycyrrhiza polysaccharides (GPs) were verified and illustrated by intervening immunocompromised rats treated with different doses of GPs, which were reflected for adjusting the composition and structure of the intestinal microbiota and altering the metabolic profile. The immunomodulatory effects of GPs were exerted by regulating the intestinal microenvironment. In particular, GPs could promote the growth of probiotic bacteria Allobaculum, norank__o_Clostridia_UCG-014, Dubosiella, and g__norank_o___RF39 and curb the growth of harmful bacteria Enterococcus. The results showed that GPs had a prebiotic effect, which contributed to improving the intestinal environment and maintaining intestinal health. In addition, the content of beneficial differential metabolites was up-regulated, especially short-chain fatty acids, with alanine, aspartate, and glutamate metabolism; arginine biosynthesis; glyoxylate and dicarboxylate metabolism being the most enriched pathways. These metabolic pathways imply the metabolic process of GPs, and the metabolic pathways and differential effector metabolites of it are focused. Overall, the purpose of this article lies in providing support for the application of GPs for regulating immune function.}, }
@article {pmid40077533, year = {2025}, author = {Yan, Y and Zhao, N and Liu, J and Zhang, S and Zhang, Y and Qin, X and Zhai, K and Du, C}, title = {Ziziphi Spinosae Semen Flavonoid Ameliorates Hypothalamic Metabolism and Modulates Gut Microbiota in Chronic Restraint Stress-Induced Anxiety-like Behavior in Mice.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/foods14050828}, pmid = {40077533}, issn = {2304-8158}, support = {20210302123470, 20210302123237//Natural Science Foundation of Shanxi Province/ ; }, abstract = {Ziziphi Spinosae Semen (ZSS), a homology of medicine and a type of seed, has been widely used to improve sleep quality. The present study aimed to assess the effects of ZSS flavonoid (ZSSF) extracted and isolated from ZSS on gut microbiota and hypothalamus metabolomic profiles in a chronic restraint stress (CRS)-induced anxiety mouse model. ZSSF was prepared using microporous resin chromatography, and seven compounds were determined by UPLC-MS. ZSSF treatment dramatically reduced anxiety-like behaviors, exerted sedative-hypnotic effects, increased hippocampal 5-HT and 5-HTP, and enhanced intestinal barrier function through inhibiting colon ZO-1, Claudin-1, and Occludin expression and reducing TNF-α, IL-6, and IL-1β levels. Compared with the CRS group, the diversity of gut microbiota in ZSSF-group mice was increased, with an increase in Bacteroidetes and a decrease in Firmicutes, and it was accompanied by an increase in fecal SCFAs. Hypothalamus metabolomics and lipidomics were performed to achieve 25 differential metabolites and 44 lipids, respectively. Serum metabolomics showed a total of 13 metabolites associated with anxiety were remarkably regulated by ZSSF. Weighted correlation network analysis (WGCNA) showed that glycerophospholipids (GPs) as well as phenylalanine, tyrosine, and L-tryptophan in peripheral and central parts were significant metabolites, which contributed to the pharmacological action of ZSSF. The mRNA expression of TPH2 and DDC key enzymes associated with tryptophan metabolism were upregulated, and PLA2G12A, LACT, and PLA2G6 key enzymes associated with GP metabolism were downregulated in ZSSF compared with CRS. Briefly, ZSSF improved tryptophan and GP metabolism and regulated the gut microbiome. This study may lay a theoretical basis for potentially developing ZSSF as a natural functional food ingredient for the improvement of anxiety and sleep disorders.}, }
@article {pmid40077522, year = {2025}, author = {Zhu, F and Xu, J and Wang, T and Yang, R and He, B and Wang, HL and Xu, Y}, title = {Royal Jelly Enhances the Social Status of Submissive Rats by Restoring Balance to the Disturbed Gut-Brain Communication.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/foods14050819}, pmid = {40077522}, issn = {2304-8158}, support = {No. JZ2019YYPY0029//Fundamental Research Funds for the Central Universities of China/ ; }, abstract = {Royal jelly (RJ) has long been considered a crucial dietary component in dictating caste differentiation in honeybees. As a nutritional additive, royal jelly imparts a broad range of benefits to mammals and humans; however, its precise impact on the social hierarchy of these advanced animals is not yet fully understood. This study aims to determine whether the benefits of royal jelly can be transferred to rats to alter their social ranks and uncover the underlying mechanisms. A submissive model was established by inducing dysbiosis in rats, via the persistent exposure of vancomycin. Royal jelly at a dose of 2.5 g/kg was daily administered to the subject rats during postnatal weeks (PNW) 6 and 7. At the end of the intervention, animals were subjected to agonistic, water and tube competition tests, in order to assess their dominance status. As revealed by the results, the RJ treatment significantly improved the social rank of the dysbiotic rats, demonstrating that RJ can elicit positive effect on the social behaviors (caused by dysbiosis) of rats. All behavioral paradigms yielded consistent results, with no notable differences in body weight or anxiety levels. Regarding gut microbiome, vancomycin exposure caused the dysbiosis of the subject rats, which was partially reversed by treatment with royal jelly. Specifically, the intestinal presence of Proteobacteria was profoundly attenuated by the RJ supplementation, resulting in a comparable level with the intact/dominant rats. At the genus level, both Escherichia and Clostridium displayed similar dynamics in relation to Proteobacteria, implying their involvement with the RJ-mediated dominance switching. Transcriptomic analysis in the medial prefrontal context showed that the expression of a broad range of genes was influenced by RJ intake, embodying various pathways related to neuronal transmission such as neuroactive ligan-receptor interaction, the synaptic vesicle cycle, etc. By virtue of correlation analysis, Escherichia, Akkermansia and Clostridium were strongly associated with a set of gene modules around gastrin releasing peptide (Grp) and signaling pathways around Rps6ka3, establishing an intrinsic gut-brain communication. Furthermore, the infection trials of Escherichia significantly degraded the social ranks of the RJ-remedied rats in tube tests, while a series of cerebral genes like Grpr and Grpel1, as well as prefrontal spine density, were concordantly altered, underscoring the critical role of the gut-brain link in deciding the outcomes of the dyadic contests. In summary, this is an intriguing example of how royal jelly can influence the social ranks of mammals, emphasizing the importance of microbe-host interaction in mediating this species-spanning function of royal jelly in shaping social hierarchy.}, }
@article {pmid40077496, year = {2025}, author = {Mou, D and Ding, D and Pu, J and Zhou, P and Cao, E and Zhang, X and Lan, J and Ye, L and Wen, W}, title = {Effects of Dietary Pretreatment with All-trans Lycopene on Lipopolysaccharide-Induced Jejunal Inflammation: A Multi-Pathway Phenomenon.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/foods14050794}, pmid = {40077496}, issn = {2304-8158}, support = {2023NSFSC1140//Sichuan Science and Technology Program/ ; }, abstract = {This study was conducted to investigate the effects and mechanisms of all-trans lycopene on intestinal health by establishing lipopolysaccharide-induced (LPS-induced) jejunal inflammation model. Dietary lycopene supplementation enhanced serum and jejunum antioxidant capacity. Lycopene significantly reduced LPS-induced upregulation of toll-like receptor-4 (TLR-4) and nuclear factor kappa-B (NF-κB), suggesting that lycopene reduced the activation of TLR-4/NF-κB signaling pathway induced by LPS challenge, and further protected mice from LPS induced jejunal inflammation. Furthermore, lycopene increased jejunal zonula occludens-1 (ZO-1) protein expression that was reduced by LPS challenge, and increased abundance of Rikenella, Lachnospiraceae_NK4A136_group and Mucispirillum potentially associated with reducing gut inflammation. Overall, these results showed that pretreatment with lycopene can improve jejunal inflammation and ensure intestinal health in mice by improving antioxidant capacity, intestinal barrier function, microorganisms potentially associated with anti-inflammatory effects and reducing the activation of TLR-4/NF-κB signaling pathway by LPS. We provided a new insight into lycopene prevented LPS-induced jejunal inflammation by corresponding alterations in serum metabolites and gut microbiota, improving antioxidant capacity and regulating the TLR-4/NF-κB signaling pathway in mice.}, }
@article {pmid40076961, year = {2025}, author = {Gu, M and Jiang, H and Ma, F and Li, S and Guo, Y and Zhu, L and Shi, C and Na, R and Wang, Y and Zhang, W}, title = {Multi-Omics Analysis Revealed the Molecular Mechanisms Affecting Average Daily Gain in Cattle.}, journal = {International journal of molecular sciences}, volume = {26}, number = {5}, pages = {}, doi = {10.3390/ijms26052343}, pmid = {40076961}, issn = {1422-0067}, support = {2023YFHH0058//the Technology Plan Project in Inner Mongolia Autonomous Region/ ; 2021GG0025//the Technology Plan Project in Inner Mongolia Autonomous Region/ ; 2024QN03051//the Natural Science Foundation of Inner Mongolia/ ; 2022JBGS0025//the Inner Mongolia Open Competition Projects/ ; TL2024TW002//the Tongliao City Open Competition Projects/ ; QF202202//the College of Animal Science, Inner Mongolia Agricultural University Special project of high-level achievement cultivation/ ; }, mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome ; Transcriptome ; Metabolomics/methods ; Weight Gain/genetics ; Metabolome ; Feces/microbiology/chemistry ; Gene Expression Profiling ; Female ; Multiomics ; }, abstract = {The average daily gain (ADG) is a critical index for evaluating growth rates in cattle and is closely linked to the economic benefits of the cattle industry. Heredity is one of the factors affecting the daily gain of cattle. However, the molecular mechanisms regulating ADG remain incompletely understood. This study aimed to systematically unravel the molecular mechanisms underlying the divergence in ADG between high average daily gain (HADG) and low average daily gain (LADG) Angus cattle through integrated multi-omics analyses (microbiome, metabolome, and transcriptome), hypothesizing that the gut microbiota-host gene-metabolism axis is a key regulatory network driving ADG divergence. Thirty Angus cattle were classified according to their HADG and LADG. Fecal and serum samples were collected for 16S, fecal metabolome, and blood transcriptome analysis. The results showed that compared with the LADG group, the abundance of Firmicutes increased in the HADG group, while the abundance of Bacteroidetes and Proteobacteria decreased. Metabolomics and transcriptomic analysis revealed that KEGG pathways associated with differentially expressed genes (DEGs) and differentially abundant metabolites (DAMs) were enriched in bile acid metabolism. Spearman correlation analysis showed that Oscillospira was positively correlated with ZBTB20 and negatively correlated with RADIL. ZBTB20 was negatively correlated with dgA-11_gut_group. This study analyzed the regulatory mechanism of average daily gain of beef cattle from genetic, metabolic, and microbial levels, providing a theoretical basis for analyzing the mechanism of differential daily gain of beef cattle, and has important significance for improving the production performance of beef cattle. The multi-omics network provides biomarker foundations for machine learning-based ADG prediction models, offering potential applications in precision breeding. While these biomarkers show promise for precision breeding, their causal roles require further validation. The conclusions are derived from a single breed (Angus) and gender (castrated males). Future studies should include females and diverse breeds to assess generalizability.}, }
@article {pmid40076957, year = {2025}, author = {Kumagai, K and Ishikawa, S and Iino, M and Edamatsu, K and Okuyama, N and Yusa, K and Shimizu, Y and Aoki, R and Masuda, C and Ohashi, Y and Horie, A and Hoshi, K and Hamada, Y}, title = {Characterization of Salivary Microbiota in Japanese Patients with Oral Cancer.}, journal = {International journal of molecular sciences}, volume = {26}, number = {5}, pages = {}, doi = {10.3390/ijms26052339}, pmid = {40076957}, issn = {1422-0067}, support = {JP 22K10113//JSPS KAKENHI Grant-in-Aid for Scientific Research (C)/ ; }, mesh = {Humans ; *Saliva/microbiology ; Male ; Female ; *Microbiota/genetics ; Middle Aged ; *RNA, Ribosomal, 16S/genetics ; *Mouth Neoplasms/microbiology ; Aged ; Bacteria/classification/genetics/isolation &amp; purification ; Japan ; Case-Control Studies ; Adult ; Metagenomics/methods ; East Asian People ; }, abstract = {This study aimed to characterize salivary microbiota in patients with oral cancer using 16S rRNA amplicon sequencing. DNA was extracted from saliva samples of 23 patients with oral cancer and 95 age-matched controls. A metagenomic analysis was performed using 16S rRNA amplicon sequencing. Patients with oral cancer exhibited lower α-diversity, as indicated by the Chao-1 index, compared to the control group, and significant differences in β-diversity were observed between the two groups. At the genus level, 25 bacterial species such as Lautropia, Megasphaera, Lactobacillus, Kingella, Gemella, Staphylococcus, and Propionibacterium were identified in patients with oral cancer, with more than half being Gram-positive facultative anaerobes or anaerobes. The reduced bacterial diversity in saliva of patients with oral cancer suggests dysbiosis during oral carcinogenesis may contribute to changes in bacterial distribution within the oral cavity.}, }
@article {pmid40076864, year = {2025}, author = {Hatamnejad, MR and Medzikovic, L and Dehghanitafti, A and Rahman, B and Vadgama, A and Eghbali, M}, title = {Role of Gut Microbial Metabolites in Ischemic and Non-Ischemic Heart Failure.}, journal = {International journal of molecular sciences}, volume = {26}, number = {5}, pages = {}, doi = {10.3390/ijms26052242}, pmid = {40076864}, issn = {1422-0067}, support = {R01HL162124/NH/NIH HHS/United States ; R01HL147586/NH/NIH HHS/United States ; R01HL159865/NH/NIH HHS/United States ; 24CDA1263497//American Heart Association/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Heart Failure/metabolism ; Animals ; Hydrogen Sulfide/metabolism ; Fatty Acids, Volatile/metabolism ; Myocardial Ischemia/metabolism/microbiology ; Methylamines/metabolism ; }, abstract = {The effect of the gut microbiota extends beyond their habitant place from the gastrointestinal tract to distant organs, including the cardiovascular system. Research interest in the relationship between the heart and the gut microbiota has recently been emerging. The gut microbiota secretes metabolites, including Trimethylamine N-oxide (TMAO), short-chain fatty acids (SCFAs), bile acids (BAs), indole propionic acid (IPA), hydrogen sulfide (H2S), and phenylacetylglutamine (PAGln). In this review, we explore the accumulating evidence on the role of these secreted microbiota metabolites in the pathophysiology of ischemic and non-ischemic heart failure (HF) by summarizing current knowledge from clinical studies and experimental models. Elevated TMAO contributes to non-ischemic HF through TGF-ß/Smad signaling-mediated myocardial hypertrophy and fibrosis, impairments of mitochondrial energy production, DNA methylation pattern change, and intracellular calcium transport. Also, high-level TMAO can promote ischemic HF via inflammation, histone methylation-mediated vascular fibrosis, platelet hyperactivity, and thrombosis, as well as cholesterol accumulation and the activation of MAPK signaling. Reduced SCFAs upregulate Egr-1 protein, T-cell myocardial infiltration, and HDAC 5 and 6 activities, leading to non-ischemic HF, while reactive oxygen species production and the hyperactivation of caveolin-ACE axis result in ischemic HF. An altered BAs level worsens contractility, opens mitochondrial permeability transition pores inducing apoptosis, and enhances cholesterol accumulation, eventually exacerbating ischemic and non-ischemic HF. IPA, through the inhibition of nicotinamide N-methyl transferase expression and increased nicotinamide, NAD+/NADH, and SIRT3 levels, can ameliorate non-ischemic HF; meanwhile, H2S by suppressing Nox4 expression and mitochondrial ROS production by stimulating the PI3K/AKT pathway can also protect against non-ischemic HF. Furthermore, PAGln can affect sarcomere shortening ability and myocyte contraction. This emerging field of research opens new avenues for HF therapies by restoring gut microbiota through dietary interventions, prebiotics, probiotics, or fecal microbiota transplantation and as such normalizing circulating levels of TMAO, SCFA, BAs, IPA, H2S, and PAGln.}, }
@article {pmid40076778, year = {2025}, author = {Escuela-Escobar, A and Perez-Garcia, J and Martín-González, E and González Martín, C and Hernández-Pérez, JM and González Pérez, R and Sánchez Machín, I and Poza Guedes, P and Mederos-Luis, E and Pino-Yanes, M and Lorenzo-Díaz, F and González Carracedo, MA and Pérez Pérez, JA}, title = {Impact of Saharan Dust and SERPINA1 Gene Variants on Bacterial/Fungal Balance in Asthma Patients.}, journal = {International journal of molecular sciences}, volume = {26}, number = {5}, pages = {}, doi = {10.3390/ijms26052158}, pmid = {40076778}, issn = {1422-0067}, support = {2022CLISA19//Fundaci&#xf3;n CajaCanarias and Fundaci&#xf3;n "la Caixa"/ ; SAF2017-83417R//MICIU/AEI/ 10.13039/501100011033 and by "ERDF A way of making Europe"/ ; FPI2024010017//co-financed by the Canarian Agency for Research, Innovation and the Information Society of the Counseling of Universities, Science and Innovation and Culture, and by the European Social Fund Plus (FSE+) Integrated Operational Program of the Canary Islands/ ; TESIS2022010045//co-financed by the Canarian Agency for Research, Innovation and the Information Society of the Counseling of Universities, Science and Innovation and Culture, and by the European Social Fund Plus (FSE+) Integrated Operational Program of the Canary Islands/ ; }, mesh = {Humans ; *Asthma/microbiology/genetics ; *alpha 1-Antitrypsin/genetics ; Male ; Female ; *Dust/analysis ; Middle Aged ; Adult ; DNA, Fungal/genetics ; DNA, Bacterial/genetics ; Fungi/genetics ; Africa, Northern ; Polymorphism, Single Nucleotide ; Microbiota/genetics ; }, abstract = {The Canary Islands, a region with high asthma prevalence, are frequently exposed to Saharan Dust Intrusions (SDIs), as are a wide range of countries in Europe. Alpha-1 antitrypsin (SERPINA1 gene) regulates the airway's inflammatory response. This study analyzed the combined effect of SDI exposure and SERPINA1 variants on bacterial/fungal DNA concentrations in saliva and pharyngeal samples from asthmatic patients. Bacterial and fungal DNAs were quantified by qPCR in 211 asthmatic patients (GEMAS study), grouped based on their exposure to daily PM10 concentrations. Associations between SDI exposure, microbial DNA concentrations, and nine variants in SERPINA1 were tested using linear regression models adjusted for confounders. The ratio between bacterial and fungal DNA was similar in saliva and pharyngeal samples. SDI exposure for 1-3 days was enough to observe significant microbial DNA change. Increased bacterial DNA concentration was detected when SDI exposure occurred 4-10 days prior to sampling, while exposure between days 1 and 3 led to a reduction in the fungal DNA concentration. The T-allele of SERPINA1 SNV rs2854254 prevented the increase in the bacterial/fungal DNA ratio in pharyngeal samples after SDI exposure. The bacterial/fungal DNA ratio represents a potential tool to monitor changes in the microbiome of asthmatic patients.}, }
@article {pmid40076773, year = {2025}, author = {Qi, M and Shi, X and Huang, W and Wei, Q and Zhang, Z and Zhang, R and Dong, S and Anwar, S and Bakhat, HF and Wang, B and Ge, Y}, title = {Microbiome and Metabolome Illustrate the Correlations Between Endophytes and Flavor Metabolites in Passiflora ligularis Fruit Juice.}, journal = {International journal of molecular sciences}, volume = {26}, number = {5}, pages = {}, doi = {10.3390/ijms26052151}, pmid = {40076773}, issn = {1422-0067}, support = {XDYC-QNRC-2022-0711//Young Talents of "Xingdian Talent Support Program" of Yunnan Province/ ; 202403AP140018//Project of Yunnan Province to build a Science and Technology Innovation Center for South and Southeast Asia/ ; 202410676028; 202410676030//Innovation and entrepreneurship training program for college students/ ; 2024SJJX036//Yunnan Agricultural University Undergraduate Practical Teaching, Labor Education and Rural Education Teaching Reform Research and Practice Project/ ; 202405//Education and Teaching Reform Research Project, School of Tropical Crops, Yunnan Agricultural University/ ; YNAUJG2024010//Yunnan Agricultural University undergraduate teaching reform project/ ; }, mesh = {*Passiflora/microbiology/metabolism ; *Microbiota ; *Metabolome ; *Fruit and Vegetable Juices/microbiology/analysis ; Endophytes/metabolism ; Volatile Organic Compounds/metabolism/analysis ; Fruit/metabolism/microbiology ; Metabolomics/methods ; Basidiomycota/metabolism ; Flavoring Agents/metabolism ; Bacteria/classification/metabolism/genetics ; }, abstract = {This study investigates the interplay between volatile and non-volatile flavor metabolites and endophytic microbial communities during three developmental stages of Passiflora ligularis fruit juice. Using bioinformatics and metabolomics, we characterize microbial diversity and metabolic variations to understand flavor development. A total of 1490 bacterial and 1158 fungal operational taxonomic units (OTUs) were identified. Young fruits had higher microbial diversity, dominated by Proteobacteria and Firmicutes (bacteria) and Ascomycota and Basidiomycota (fungi). As the fruit matured, Proteobacteria increased while Firmicutes decreased, indicating that microbial succession is tied to development. Metabolomic profiling identified 87 volatile and 1002 non-volatile metabolites, with distinct chemical classes varying across stages. Saturated hydrocarbons and fatty alcohols were the main volatile metabolites, while organic acids and lipids among non-volatile metabolites showed stage-dependent changes, influencing flavor complexity. Correlation analysis showed microbial-flavor interactions: Proteobacteria negatively correlated with metabolites, while Firmicutes positively correlated with metabolites. Ascomycota positively correlated with volatile metabolites, whereas Basidiomycota showed an inverse relationship, highlighting their differential contributions to flavor biosynthesis. This study enhances understanding of microbial and metabolic factors shaping P. ligularis fruit flavor, highlighting the importance of microbial influence on fruit metabolomics. The findings suggest the potential for microbiome engineering to improve flavor quality, aiding postharvest management and industrial processing in the food and beverage industry.}, }
@article {pmid40076732, year = {2025}, author = {Du, D and Li, Q and Wei, Z and Wang, Z and Xu, L}, title = {Exploring the CDCA-Scd1 Axis: Molecular Mechanisms Linking the Colitis Microbiome to Neurological Deficits.}, journal = {International journal of molecular sciences}, volume = {26}, number = {5}, pages = {}, doi = {10.3390/ijms26052111}, pmid = {40076732}, issn = {1422-0067}, support = {CSTB2022NSCQ-BHX0666//Natural Science Foundation of Chongqing/ ; KJQN202400419//Scientific and Technological Research Program of Chongqing Municipal Education Commission/ ; }, mesh = {Animals ; *Colitis/metabolism/microbiology/chemically induced ; Mice ; *Stearoyl-CoA Desaturase/metabolism/genetics ; *Dextran Sulfate ; Gastrointestinal Microbiome ; Male ; Disease Models, Animal ; Brain/metabolism ; Depression/metabolism/microbiology ; Mice, Inbred C57BL ; Anxiety/microbiology/metabolism ; }, abstract = {Inflammatory bowel disease is a risk factor for brain dysfunction; however, the underlying mechanisms remain largely unknown. In this study, we aimed to explore the potential molecular mechanisms through which intestinal inflammation affects brain function and to verify these mechanisms. Mice were treated with multiple cycles of 1% w/v dextran sulfate sodium (DSS) in drinking water to establish a chronic colitis model. Behavioral tests were conducted using the open field test (OFT), tail suspension test (TST), forced swimming test (FST), and Morris water maze test (MWM). Brain metabolomics, transcriptomics, and proteomics analyses were performed, and key target proteins were verified using qPCR and immunofluorescence. Four cycles of DSS administration induced colitis, anxiety, depression, and spatial memory impairment. The integrated multi-omics characterization of colitis revealed decreased brain chenodeoxycholic acid (CDCA) levels as well as reduced stearoyl-CoA desaturase (Scd1) gene and protein expression. Transplantation of the colitis microbiome resulted in anxiety, depression, impaired spatial memory, reduced CDCA content, decreased Scd1 gene and protein expression, and lower concentrations of monounsaturated fatty acids (MUFAs), palmitoleate (C16:1), and oleate (C18:1) in the brain. In addition, CDCA supplementation improved DSS-induced colitis, alleviated depression and spatial memory impairment, and increased Scd1 gene and protein expression as well as MUFA levels in the brain. The gut microbiome induced by colitis contributes to neurological dysfunction, possibly through the CDCA-Scd1 signaling axis. CDCA supplementation alleviates colitis and depressive behavior, likely by increasing Scd1 expression in the brain.}, }
@article {pmid40076682, year = {2025}, author = {Guo, H and Yang, R and Cheng, W and Li, Q and Du, M}, title = {An Update of Salivary Biomarkers for the Diagnosis of Alzheimer's Disease.}, journal = {International journal of molecular sciences}, volume = {26}, number = {5}, pages = {}, doi = {10.3390/ijms26052059}, pmid = {40076682}, issn = {1422-0067}, support = {82301091//National Natural Science Foundation of China/ ; }, mesh = {*Alzheimer Disease/diagnosis/metabolism/cerebrospinal fluid ; Humans ; *Biomarkers/cerebrospinal fluid ; *Saliva/metabolism ; Amyloid beta-Peptides/metabolism/cerebrospinal fluid/analysis ; tau Proteins/metabolism/cerebrospinal fluid ; }, abstract = {Alzheimer's disease (AD) is characterized by progressive cognition and behavior impairments. Diagnosing AD early is important for clinicians to slow down AD progression and preserve brain function. Biomarkers such as tau protein and amyloid-β peptide (Aβ) are used to aid diagnosis as clinical diagnosis often lags. Additionally, biomarkers can be used to monitor AD status and evaluate AD treatment. Clinicians detect these AD biomarkers in the brain using positron emission tomography/computed tomography or in the cerebrospinal fluid using a lumbar puncture. However, these methods are expensive and invasive. In contrast, saliva collection is simple, inexpensive, non-invasive, stress-free, and repeatable. Moreover, damage to the brain parenchyma can impact the oral cavity and some pathogenic molecules could travel back and forth from the brain to the mouth. This has prompted researchers to explore biomarkers in the saliva. Therefore, this study provides an overview of the main finding of salivary biomarkers for AD diagnosis. Based on these available studies, Aβ, tau, cholinesterase enzyme activity, lactoferrin, melatonin, cortisol, proteomics, metabolomics, exosomes, and the microbiome were changed in AD patients' saliva when compared to controls. However, well-designed studies are essential to confirm the reliability and validity of these biomarkers in diagnosing and monitoring AD.}, }
@article {pmid40076626, year = {2025}, author = {Kabisch, S and Hajir, J and Sukhobaevskaia, V and Weickert, MO and Pfeiffer, AFH}, title = {Impact of Dietary Fiber on Inflammation in Humans.}, journal = {International journal of molecular sciences}, volume = {26}, number = {5}, pages = {}, doi = {10.3390/ijms26052000}, pmid = {40076626}, issn = {1422-0067}, mesh = {*Dietary Fiber/metabolism ; Humans ; *Inflammation/metabolism ; Diabetes Mellitus, Type 2/prevention &amp; control/metabolism/diet therapy ; Gastrointestinal Microbiome ; Metabolic Syndrome/diet therapy/metabolism ; }, abstract = {Cohort studies consistently show that a high intake of cereal fiber and whole-grain products is associated with a decreased risk of type 2 diabetes (T2DM), cancer, and cardiovascular diseases. Similar findings are also reported for infectious and chronic inflammatory disorders. All these disorders are at least partially caused by inflammaging, a chronic state of inflammation associated with aging and Metabolic Syndrome. Surprisingly, insoluble (cereal) fiber intake consistently shows stronger protective associations with most long-term health outcomes than soluble fiber. Most humans consume soluble fiber mainly from sweet fruits, which usually come with high levels of sugar, counteracting the potentially beneficial effects of fiber. In both observational and interventional studies, high-fiber diets show a beneficial impact on inflammation, which can be attributed to a variety of nutrients apart from dietary fiber. These confounders need to be considered when evaluating the effects of fiber as part of complex dietary patterns. When assessing specific types of fiber, inulin and resistant starch clearly elicit anti-inflammatory short-term effects, while results for pectins, beta-glucans, or psyllium turn out to be less convincing. For insoluble fiber, promising but sparse data have been published so far. Hypotheses on putative mechanisms of anti-inflammatory fiber effects include a direct impact on immune cells (e.g., for pectin), fermentation to pleiotropic short-chain fatty acids (for fermentable fiber only), modulation of the gut microbiome towards higher levels of diversity, changes in bile acid metabolism, a differential release of gut hormones (such as the glucose-dependent insulinotropic peptide (GIP)), and an improvement of insulin resistance via the mTOR/S6K1 signaling cascade. Moreover, the contribution of phytate-mediated antioxidative and immune-modulatory means of action needs to be considered. In this review, we summarize the present knowledge on the impact of fiber-rich diets and dietary fiber on the human inflammatory system. However, given the huge heterogeneity of study designs, cohorts, interventions, and outcomes, definite conclusions on which fiber to recommend to whom cannot yet be drawn.}, }
@article {pmid40076607, year = {2025}, author = {Neidhöfer, C and Condic, M and Hahn, N and Otten, LA and Ralser, DJ and Wetzig, N and Thiele, R and Hoerauf, A and Parčina, M}, title = {Homogeneity Between Cervical and Vaginal Microbiomes and the Diagnostic Limitations of 16S Sequencing for STI Pathogens at Higher Ct Values.}, journal = {International journal of molecular sciences}, volume = {26}, number = {5}, pages = {}, doi = {10.3390/ijms26051983}, pmid = {40076607}, issn = {1422-0067}, mesh = {Humans ; Female ; *Vagina/microbiology ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; *Cervix Uteri/microbiology ; *Sexually Transmitted Diseases/microbiology/diagnosis ; Adult ; Middle Aged ; Chlamydia trachomatis/genetics/isolation &amp; purification ; Bacteria/genetics/isolation &amp; purification/classification ; Vaginal Smears/methods ; }, abstract = {Understanding the interactions between the cervico-vaginal microbiome, immune responses, and sexually transmitted infections (STIs) is crucial for developing targeted diagnostic and therapeutic strategies. Although microbiome analyses are not yet standard practice, integrating them into routine diagnostics could enhance personalized medicine and therapies. We investigated the extent to which partial 16S short-read amplicon microbiome analyses could inform on the presence of six commonly encountered STI-causing pathogens in a patient cohort referred for colposcopy, and whether relevant taxonomic or diagnostic discrepancies occur when using vaginal rather than cervical swabs. The study cohort included cervical and vaginal samples collected from women referred for colposcopy at the University Hospital Bonn between November 2021 and February 2022, due to an abnormal PAP smear or positive hrHPV results. 16S rRNA gene sequencing libraries were prepared targeting the V1-V2 and V4 regions of the 16S RNA gene and sequenced on the Illumina MiSeq. PCR diagnostics for common STI-causing pathogens were conducted using the Allplex STI Essential Assay Kit (Seegene, Seoul, Republic of Korea). Concerning the bacterial microbiome, no significant differences were found between vaginal and cervical samples in terms of prevalence of taxa present or diversity. A total of 95 patients and 171 samples tested positive for at least one among Ureaplasma parvum, Ureaplasma urealyticum, Mycoplasma hominis, Mycoplasma genitalium, Chlamydophila trachomatis or Neisseria gonorrhoeae. Sequencing the V1-V2 region enabled detection of one-third to half of the PCR-positive samples, with the detection likelihood increasing at lower cycle threshold (Ct) values. In contrast, sequencing the V4 region was less effective overall, yielding fewer species-level identifications and a higher proportion of undetermined taxa. We demonstrate that the vaginal microbiome closely mirrors the cervical microbiome, a relationship that has not been explored previously, but which broadens the possibilities for microbiome analysis and pathogen detection and establishes vaginal swabs as a reliable method for detecting the investigated pathogens, with sensitivities comparable with or superior to endocervical swabs. On the other hand, the sensitivity of partial 16S amplicon sequencing appears insufficient for effective STI diagnostics, as it fails to reliably identify or even detect pathogens at higher Ct values.}, }
@article {pmid40076446, year = {2025}, author = {Li, Y and Zhang, ZJ and Saarela, O and Sharma, D and Xu, W}, title = {Mediation CNN (Med-CNN) Model for High-Dimensional Mediation Data.}, journal = {International journal of molecular sciences}, volume = {26}, number = {5}, pages = {}, doi = {10.3390/ijms26051819}, pmid = {40076446}, issn = {1422-0067}, support = {RGPIN-2024-06081//Natural Sciences and Engineering Research Council/ ; }, mesh = {Humans ; *Algorithms ; *Neural Networks, Computer ; *Microbiota ; Female ; Computer Simulation ; }, abstract = {Complex biological features such as the human microbiome and gene expressions play a crucial role in human health by mediating various biomedical processes that influence disease progression, such as immune responses and metabolic processes. Understanding these mediation roles is essential for gaining insights into disease pathogenesis and improving treatment outcomes. However, analyzing such high-dimensional mediation features presents challenges due to their inherent structural and correlations, such as the hierarchical taxonomic structures in microbial operational taxonomic units (OTUs), gene-pathway relationships, and the high dimensionality of the datasets, which complicates mediation analysis. We propose the Med-CNN model, an iterative approach using Convolutional Neural Networks (CNNs) to incorporate the complex biological network of the mediation features. The output values from network-specific CNN models are condensed into an integrative mediation metric (IMM), which captures essential biological information for estimating mediation effects. Our approach is designed to handle high-dimensional data and accommodate their unique structures and non-linear interactive mediation effects. Through comprehensive simulation studies, we evaluated the performance of our algorithm across different scenarios, including various mediation effects, effect sizes, and sample sizes, and we compared it to conventional methods. Our simulations demonstrated consistently lower biases in mediation effect estimates, with values ranging from 0.17 to 0.56, which were lower than other established methods ranging from 0.24 to 13.27. In a real data application, our method identified a mediation effect of 0.06 between ethnicity and vaginal pH levels.}, }
@article {pmid40076406, year = {2025}, author = {Hu, L and Luo, Y and Yang, J and Cheng, C}, title = {Botanical Flavonoids: Efficacy, Absorption, Metabolism and Advanced Pharmaceutical Technology for Improving Bioavailability.}, journal = {Molecules (Basel, Switzerland)}, volume = {30}, number = {5}, pages = {}, doi = {10.3390/molecules30051184}, pmid = {40076406}, issn = {1420-3049}, support = {No.82260746//National Natural Science Foundation of China/ ; jxsq2023101038//Jiangxi Province Double Thousand Talent-Leader of Natural Science Project/ ; 2022BCJ25027 &amp; 2023BBG70014//Jiangxi Province Urgently Overseas Talent Project/ ; S2024KXJJ0001//Natural Science Foundation of Jiujiang/ ; }, mesh = {*Flavonoids/pharmacokinetics/chemistry/pharmacology ; *Biological Availability ; Humans ; Gastrointestinal Microbiome/drug effects ; Animals ; Technology, Pharmaceutical/methods ; Antioxidants/pharmacokinetics/pharmacology/chemistry ; }, abstract = {Flavonoids represent a class of natural plant secondary metabolites with multiple activities including antioxidant, antitumor, anti-inflammatory, and antimicrobial properties. However, due to their structural characteristics, they often exhibit low bioavailability in vivo. In this review, we focus on the in vivo study of flavonoids, particularly the effects of gut microbiome on flavonoids, including common modifications such as methylation, acetylation, and dehydroxylation, etc. These modifications aim to change the structural characteristics of the original substances to enhance absorption and bioavailability. In order to improve the bioavailability of flavonoids, we discuss two feasible methods, namely dosage form modification and chemical modification, and hope that these approaches will offer new insights into the application of flavonoids for human health. In this article, we also introduce the types, plant sources, and efficacy of flavonoids. In conclusion, this is a comprehensive review on how to improve the bioavailability of flavonoids.}, }
@article {pmid40076400, year = {2025}, author = {Newman, PP and Schmitt, BL and Maurmann, RM and Pence, BD}, title = {Polysaccharides with Arabinose: Key Players in Reducing Chronic Inflammation and Enhancing Immune Health in Aging.}, journal = {Molecules (Basel, Switzerland)}, volume = {30}, number = {5}, pages = {}, doi = {10.3390/molecules30051178}, pmid = {40076400}, issn = {1420-3049}, support = {R15AG078906/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; *Polysaccharides/pharmacology/chemistry ; *Aging/drug effects/immunology ; *Inflammation/metabolism/drug therapy ; *Arabinose/pharmacology ; Animals ; Oxidative Stress/drug effects ; Chronic Disease ; Antioxidants/pharmacology ; }, abstract = {Aging is associated with a decline in physiological performance leading to increased inflammation and impaired immune function. Polysaccharides (PLs) found in plants, fruits, and fungi are emerging as potential targets for therapeutic intervention, but little is known about their effects on chronic inflammation and aging. This review aims to highlight the current advances related to the use of PLs, with the presence of arabinose, to attenuate oxidative stress and chronic and acute inflammation, and their immunomodulatory effects associated with antioxidant status in monocytes, macrophages, and neutrophil infiltration, and leukocyte rolling adhesion in neutrophils. In addition, recent studies have shown the importance of investigating the 'major' monosaccharide, such as arabinose, present in several of these polysaccharides, and with described effects on gut microbiome, glucose, inflammation, allergy, cancer cell proliferation, neuromodulation, and metabolic stress. Perspectives and opportunities for further investigation are provided. By promoting a balanced immune response and reducing inflammation, PLs with arabinose or even arabinose per se may alleviate the immune dysregulation and inflammation seen in the elderly, therefore providing a promising strategy to mitigate a variety of diseases.}, }
@article {pmid40076325, year = {2025}, author = {Zolotareva, D and Zazybin, A and Belyankova, Y and Bayazit, S and Dauletbakov, A and Seilkhanov, T and Kemelbekov, U and Aydemir, M}, title = {Heterocyclic Antidepressants with Antimicrobial and Fungicide Activity.}, journal = {Molecules (Basel, Switzerland)}, volume = {30}, number = {5}, pages = {}, doi = {10.3390/molecules30051102}, pmid = {40076325}, issn = {1420-3049}, support = {AP19578051 and BR28713241//Ministry of Science and Higher Education of the Republic of Kazakhstanr/ ; }, mesh = {*Antidepressive Agents/pharmacology/chemistry ; Humans ; Anti-Infective Agents/pharmacology/chemistry ; Gastrointestinal Microbiome/drug effects ; Heterocyclic Compounds/pharmacology/chemistry ; Bacteria/drug effects/growth &amp; development ; Animals ; Antifungal Agents/pharmacology/chemistry ; }, abstract = {In this review, the presence of antimicrobial and fungicidal activity in heterocyclic antidepressants was investigated. The already proven connection between the intestinal microbiome and mental health prompted the idea of whether these drugs disrupt the normal intestinal microflora. In addition, there is a serious problem of increasing resistance of microorganisms to antibiotics. In this article, we found that almost all of the antidepressants considered (except moclobemide, haloperidol, and doxepin) have antimicrobial activity and can suppress the growth of not only pathogenic microorganisms but also the growth of bacteria that directly affect mental health (such as Lactobacillus, Lactococcus, Streptococcus, Enterococcus, and Bifidobacterium).}, }
@article {pmid40076040, year = {2025}, author = {Li, D and Zhang, K and Xue, X and Bai, Z and Yang, L and Qi, J and Suolang, S}, title = {Treatment-Related Mechanisms of Tibetan Medicine Terminalia chebula (TC) Aqueous Extract Against Mouse Gastroenteritis Caused by Yak-Origin Salmonella Determined Using Intestinal Microbiome Analysis and Metabolomics.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/ani15050755}, pmid = {40076040}, issn = {2076-2615}, support = {This work was supported by the China Agriculture Research System of MOF and MARA (CARS-37), as well as received financial support for the establishment of the veterinary medicine discipline at Tibet Agriculture and Animal Husbandry College.//Sizhu Suolang/ ; }, abstract = {This study aimed to evaluate the therapeutic effect of Terminalia chebula (TC) on Tibetan yak-origin Salmonella-induced diarrhea and dysentery in mice. The levels of pro-inflammatory cytokines (IL-1β, IL-6, IL-8, and TNF-α), anti-inflammatory cytokines (IL-4 and IL-10), and the oxidative stress markers malondialdehyde (MDA), superoxide dismutase (T-SOD), total antioxidant capacity (T-AOC), reduced glutathione (GSH-PX), and catalase (CAT) in the serum of mice were measured using ELISA kits. Using microbial diversity sequencing and non-targeted metabolomics detection techniques, the relevant mechanisms of TC treatment in a mouse Salmonella infection model were evaluated. The results showed the following: TC can effectively reduce the diarrhea rate; alleviate weight loss caused by Salmonella invasion; reduce the pro-inflammatory cytokines IL-1β, IL-6, IL-8, and TNF-α in serum; and increase the concentrations of the anti-inflammatory cytokines IL-4 and IL-10. TC can improve the body's antioxidant levels to heal the damage caused by oxidative stress and lipid peroxidation. The histological section results show that TC can significantly improve gastric and intestinal tissue lesions and has no toxic effects on the liver and kidneys. 16S rRNA and ITS sequencing analysis suggests that Lactobacillus, Enterorhabdus, Alistipes (bacterial community), Lodderomyces, Saccharomyces, and Penicillium (fungal community) may be key functional microbial communities in TC. Non-targeted metabolomics also suggests that the antibacterial treatment of dysentery with chebulic acid may be related to regulation of the Ras signaling pathway, long-term potentiation, the MAPK signaling pathway, metabolic pathways, and gut microbiome composition. Conclusion: TC has clear clinical efficacy in treating bacterial diarrhea, presenting anti-inflammatory and antioxidant effects. Its roles in regulating the gut microbiome and metabolic pathways and products were determined as the main reason for its therapeutic effect in a mouse gastroenteritis model caused by Salmonella infection.}, }
@article {pmid40076036, year = {2025}, author = {Bai, X and Gu, Y and Li, D and Li, M}, title = {Gut Metagenome Reveals the Microbiome Signatures in Tibetan and Black Pigs.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/ani15050753}, pmid = {40076036}, issn = {2076-2615}, support = {National Key R &amp; D Program of China (2020YFA0509500 and 2023YFD1301302)//Mingzhou Li/ ; the Biological Breeding-Major Projects in National Science and Technology (2023ZD0404404)//Mingzhou Li/ ; the Sichuan Science and Technology Program (2021ZDZX0008 and 2021YFYZ0009)//Mingzhou Li/ ; the National Natural Science Foundation of China (32421005, 32225046 and 32494802)//Mingzhou Li/ ; }, abstract = {The harsh conditions of the Qinghai-Tibet Plateau pose significant physiological challenges to local fauna, often resulting in gastrointestinal disorders. However, Tibetan pigs have exhibited remarkable adaptability to the high-altitude stress of the Tibetan Plateau, a phenomenon that remains not fully understood in terms of their gastrointestinal microbiota. This study collected 57 gastrointestinal tract samples from Tibetan pigs (n = 6) and plain black pigs (n = 6) with comparable genetic backgrounds. Samples from the stomach, jejunum, cecum, colon, and rectum, underwent comprehensive metagenomic analysis to elucidate the gut microbiota-related adaptive mechanisms in Tibetan pigs to the extreme high-altitude environment. A predominance of Pseudomonadota was observed within gut microbiome of Tibetan pigs. Significant differences in the microbial composition were also identified across the tested gastrointestinal segments, with 18 genera and 141 species exhibiting differential abundance. Genera such as Bifidobacterium, Megasphaera, Fusobacterium, and Mitsuokella were significantly more abundant in Tibetan pigs than in their lowland counterparts, suggesting specialized adaptations. Network analysis found greater complexity and modularity in the microbiota of Tibetan pigs compared to black pigs, indicating enhanced ecological stability and adaptability. Functional analysis revealed that the Tibetan pig microbiota was particularly enriched with bacterial species involved in metabolic pathways for propionate and butyrate, key short-chain fatty acids that support energy provision under low-oxygen conditions. The enzymatic profiles of Tibetan pigs, characterized by elevated levels of 4-hydroxybutyrate dehydrogenase and glutaconyl-CoA decarboxylase, highlighted a robust fatty acid metabolism and enhanced tricarboxylic acid cycle activity. In contrast, the gut microbiome of plain black pigs showed a reliance on the succinate pathway, with a reduced butyrate metabolism and lower metabolic flexibility. Taken together, these results demonstrate the crucial role of the gastrointestinal microbiota in the adaptation of Tibetan pigs to high-altitude environments by optimizing carbohydrate metabolism and short-chain fatty acid production for efficient energy utilization. This study not only highlights the metabolic benefits conferred by the gut microbiota of Tibetan pigs in extreme environments, but also advances our understanding of the adaptive gastrointestinal mechanisms in plateau-dwelling animals. These insights lay the foundation for exploring metabolic interventions to support health and performance in high-altitude conditions.}, }
@article {pmid40076031, year = {2025}, author = {Bae, DY and Moon, SH and Lee, TG and Ko, YS and Cho, YC and Kang, H and Park, CS and Kang, JS and Oh, Y and Cho, HS}, title = {Consequences of Domestication on Gut Microbiome: A Comparative Analysis Between Wild Boars and Domestic Pigs.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/ani15050747}, pmid = {40076031}, issn = {2076-2615}, support = {No. 321081-4//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET)/ ; }, abstract = {The gut microbiota plays a vital role in the physiological functions and health of animals. Domestic pigs (Sus scrofa domesticus) and wild boars (Sus scrofa scrofa), which share a common ancestor, present a unique model for exploring the evolutionary changes in gut microbiota due to domestication. Comparing the gut microbiota of these two groups provides a unique opportunity to identify microorganisms that may have been lost or altered during domestication. This study employed 16S rRNA sequencing to compare the gut microbiota compositions of domestic pigs and wild boars, analyzing 69 fecal samples from both groups. Our results indicate significant differences in the taxonomic profiles of the gut microbiota between the two groups. Specifically, the genera Bifidobacterium and Lactobacillus, were found in higher abundance in wild boars. In contrast, domestic pigs exhibited a decreased variety of these potentially health-enhancing bacteria, likely due to factors such as simplified diets and antibiotic use. Functional gene analysis revealed that pathways related to carbohydrate metabolism, lipid metabolism, immune response, and environmental adaptability were more enriched in wild boars. These findings demonstrate significant differences in the gut microbiota composition between domestic pigs and wild boars, underscoring the impact of domestication on microbial diversity. Further research is necessary to explore the potential of transferring beneficial microbes from wild to domestic populations.}, }
@article {pmid40075947, year = {2025}, author = {Min, BR and Yutaka, U and Ismael, H and Abdo, H and Chaudhary, S and Hilaire, M and Kanyi, V}, title = {Malted Barley as a Potential Feed Supplementation for the Reduction of Enteric Methane Emissions, Rumen Digestibility, and Microbiome Community Changes in Laboratory Conditions.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/ani15050664}, pmid = {40075947}, issn = {2076-2615}, support = {# ALX-SRS22.//USDA-NIFA/ ; }, abstract = {Three sets of in vitro rumen fermentation experiments were conducted to determine the effects of diets that included malted barley (MB) and basal diets (grain- and forage-based) on the in vitro gas production, greenhouse gas (GHG) emissions, rumen fermentation profiles, and microbiome changes in the rumen when supplemented with feedlot or dairy rations. The first experiment (Exp. 1) was conducted to evaluate the effects of various levels of MB (0% [referred to as a control], 10%, 20%, and 30%, as-fed basis) supplemented with a grain-based diet in a feedlot ration (2.5 g/bottle) after 48 h ruminal incubation on the in vitro gas production, GHG emissions, and rumen fermentation rate. The second two sets of in vitro experiments (Exp. 2a, b) were conducted to determine (1) the effects of linear dose levels of malted barley (MB; 0%, 10%, 20%, 30%, and 40% as-fed) with two different basal diets (grain-based and forage-based) and (2) the effects of different sources of MB (control, Korean, Canadian, and the USA; 30% MB, as-fed) in a dairy ration after 24 h incubation on in vitro gas production, rumen fermentation profiles, GHG emissions (methane [CH4] and nitrous oxide [N2O]), in vitro dry matter disappearance rate (IVDMD), and microbiome changes. Commercially available α-amylase (0.2 g/100 mL) was used as a sub-control in Exp. 2a. Using gas chromatography, all gases were collected using an ANKOM Gas Production system and analyzed for CH4 and N2O. In Exp. 1, total gas production, cumulative gas, and GHG productions (CH4, N2O) linearly decreased (p ≤ 0.05) with increasing MB supplementation. In Exp. 2a, cumulative in vitro gas, total gas production, and rumen fermentation profiles (e.g., total VFA, acetate, butyrate, iso-butyrate, valerate, and iso-valerate) linearly decreased (p < 0.05-0.01) with increasing MB supplementation, with diet-treatment interactions (p < 0.001). In addition, CH4 and N2O production (mL/g DM) linearly and quadratically decreased (p < 0.01) with increasing MB supplementation across the diets. However, IVDMD linearly and/or quadratically increased (p < 0.01) with increasing MB, with diet-treatment interactions (p < 0.001). The average populations of Bacteroidetes, Proteobacteria, and Spirochaetes were significantly decreased (p < 0.01-0.001) for MB treatment groups compared to the control group. Therefore, it may be possible to suppress methane production directly and indirectly by adding MB and α-amylase by modifying ruminal fermentation profiles.}, }
@article {pmid40075934, year = {2025}, author = {Lyu, Y and Pu, J and Deng, B and Wu, C}, title = {Gut Metabolome in Companion Animal Nutrition-Linking Diets to Health.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/ani15050651}, pmid = {40075934}, issn = {2076-2615}, abstract = {Tailoring diet to support a healthy gut microbiome is key for animal well-being. The gut metabolome, including all small molecules in the gut, is central to diet-microbiome-health interactions. While comprehension of the gut metabolome in companion animal nutrition is emerging, a substantial number of studies have been undertaken to elucidate the metabolomic shifts and identify specific marker metabolites influenced by diverse dietary interventions. By employing various metabolomic approaches, researchers have extensively documented the effects of different diet types, nutrient compositions, and dietary supplements on the gut metabolome in dogs and cats. Despite these advancements, there remains several notable limitations, including a lack of integrated microbiome analysis, incomplete understanding of specific marker metabolites, and an over-reliance on extrapolating findings from human studies. Therefore, this review aims to summarize the current understanding of the canine and feline gut metabolome, while exploring future possibilities and challenges for the field.}, }
@article {pmid40075931, year = {2025}, author = {Huang, F and Ma, Z and Du, X and Wang, C and Liu, G and Zhou, M}, title = {Methionine Alters the Fecal Microbiota and Enhances the Antioxidant Capacity of Lactating Donkeys.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/ani15050648}, pmid = {40075931}, issn = {2076-2615}, abstract = {This study looked at how methionine (Met) affects on serum biochemical indicators, antioxidant indicators, and the fecal microbiota of lactating donkeys. A total of 18 healthy donkeys at the mid-lactation stage were used in this study. They were given concentrate meals with varying concentrations of Met after being randomly split into three groups: Met group I (M1) received 5 g/d of Met, Met group II (M2) received 15 g/d of Met, and the control group (C) received 0 g/d of Met. The trial lasted for five weeks in total. Fecal microbes, antioxidant markers, and blood biochemical indicators were examined. The findings showed that while the levels of malondialdehyde (MDA) decreased (p < 0.05), the addition of Met (15 g/d) significantly enhanced the total antioxidant capacity (T-AOC) and catalase (CAT) activity. Milk samples from the different groups trended towards having significant differences in the levels of the serum biochemical indicators albumin (ALB) and lactate dehydrogenase (LDH) (0.05 < p < 0.1). A fecal microbiome analysis revealed that the addition of Met (5 g/d) increased the abundance of Methanocorpusculum and Ruminococcus, and the addition of 15 g/d of Met increased the abundance of Ruminococcus, Peptococcus, and Anaeroplasma while decreasing the abundance of the [Eubacterium]_ruminantium_group. A correlation analysis revealed that Ruminococcus and Methanocorpusculum were positively correlated with the T-AOC and CAT activity (M1 group). Peptococcus was significantly negatively correlated with MDA levels and positively correlated with the T-AOC (M2 group). Anaeroplasma was positively correlated with CAT activity (M2 group). The above results indicated that Met increased donkey antioxidant levels and modulated the abundance of the fecal microbial community. These findings lay the groundwork for boosting the production performance and general health of nursing donkeys.}, }
@article {pmid40075903, year = {2025}, author = {Xiao, S and Feng, K and Li, S and Li, M and Yan, X and Wu, Y and Mi, J and Liao, X and Wang, Y}, title = {Influence of Astragalus extract on Gut Microbiome Regulation and Ammonia Emission Mitigation in Laying Hens.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/ani15050620}, pmid = {40075903}, issn = {2076-2615}, support = {32372931//The National Natural Science Foundation of China/ ; 2022KJ128//The Construction Project of Modern Agricultural Science and Technology Innovation Alliance in Guangdong Province/ ; 2023KJ128//The Construction Project of Modern Agricultural Science and Technology Innovation Alliance in Guangdong Province/ ; YUECAINONG202137//The Guangdong agricultural research projects/ ; DT20220020//The Heyuan Branch, Guangdong Laboratory for Lingnan Modern Agriculture Project/ ; CARS-40//The earmarked fund for Modern Agroindustry Technology Research System/ ; }, abstract = {Astragalus extract plays a dual role in gut microbiome regulation and ammonia (NH3) emission mitigation in laying hens. This study explored its effects through feeding experiments, with a focus on gut microbial metabolic pathways and NH3 reduction mechanisms. To achieve this, both in vitro fermentation experiments and in vivo feeding trials were conducted. In the in vitro study, cecal contents from laying hens were incubated with different concentrations of AE and Yucca extract (YE) to evaluate NH3 production, while in the feeding trial, 58-week-old Lohmann Pink laying hens were allocated into three groups (control, 0.1% YE, and 0.1% AE) and housed in controlled-environment respiration chambers for 21 days. Measurements included NH3 emissions, serum biochemical indices, immune parameters, gut physicochemical properties, and 16S rRNA-based microbiota analysis. Results showed that Astragalus extract reduced NH3 emissions by 29.3%, achieved by lowering urease and uricase activities and promoting the conversion of ammonium nitrogen to nitrate nitrogen. Additionally, it significantly enhanced gut immune function by increasing intestinal immunoglobulin levels. Microbial community analysis revealed an increased relative abundance of Bacteroides, Muribaculaceae, and Faecalibacterium, which are negatively correlated with NH3 emissions. These microbial shifts improved ammonium nitrogen utilization via the upregulation of CTP synthase and GMP synthase activities, contributing to higher NH3 reduction efficiency. This study highlights Astragalus extract as a cost-effective and sustainable strategy to regulate gut microbiota, optimize nitrogen metabolism, and mitigate NH3 emissions in laying hens.}, }
@article {pmid40075661, year = {2025}, author = {Chacon, J and Faizuddin, F and McKee, JC and Sheikh, A and Vasquez, VM and Gadad, SS and Mayer, G and Siby, S and McCabe, M and Dhandayuthapani, S}, title = {Unlocking the Microbial Symphony: The Interplay of Human Microbiota in Cancer Immunotherapy Response.}, journal = {Cancers}, volume = {17}, number = {5}, pages = {}, doi = {10.3390/cancers17050813}, pmid = {40075661}, issn = {2072-6694}, abstract = {INTRODUCTION: The emergence of cancer immunotherapy has revolutionized cancer treatment, offering remarkable outcomes for patients across various malignancies. However, the heterogeneous response to immunotherapy underscores the necessity of understanding additional factors influencing treatment efficacy. Among these factors, the human microbiota has garnered significant attention for its potential role in modulating immune response. Body: This review explores the intricate relationship between the human microbiota and cancer immunotherapy, highlighting recent advances and potential mechanisms underlying microbial influence on treatment outcomes.<br><br>CONCLUSION: Insights into the microbiome's impact on immunotherapy response not only deepen our understanding of cancer pathogenesis but also hold promise for personalized therapeutic strategies aimed at optimizing patient outcomes.}, }
@article {pmid40075558, year = {2025}, author = {Molnar, NB and Weigel, BL and Fales, RJ and Pfister, CA}, title = {Warming Seawater Temperature and Nutrient Depletion Alters Microbial Community Composition on a Foundational Canopy Kelp Species.}, journal = {Environmental microbiology}, volume = {27}, number = {3}, pages = {e70077}, doi = {10.1111/1462-2920.70077}, pmid = {40075558}, issn = {1462-2920}, support = {//Washington State Legislature/ ; G17AC000218//U.S. Geological Survey/ ; //University of Chicago/ ; }, mesh = {*Microbiota ; *Kelp/microbiology ; *Seawater/microbiology ; *Nitrogen/metabolism ; *Temperature ; Nutrients ; Phaeophyceae/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Warming seawater temperatures and low dissolved inorganic nitrogen (DIN) levels are environmental stressors that affect the health and abundance of marine macroalgae and their microbiomes. Nereocystis luetkeana, a canopy-forming species of brown algae that forms critical habitat along the Pacific coast, has declined in regions impacted by these synergistic stressors. Little is known about how these environmental factors affect the microbiome of N. luetkeana, which could affect nutrient availability, vitamin production, and stress response for the host. We experimentally tested the interactive effects of three seawater temperatures (13°C, 16°C, 21°C) crossed with abundant and replete DIN levels on the diversity and composition of blade-associated microbiomes from two spatially separated kelp host populations. We hypothesised that kelp microbiomes exposed to high temperatures and low DIN would experience the lowest diversity. Contrary to our hypothesis, the highest temperature treatment resulted in the largest increase in microbial diversity, and microbiomes in all temperature treatments experienced a decrease in previously dominant taxa. Temperature had a larger effect than DIN on the kelp microbiome in all cases. The disruption to the kelp microbiome across all temperatures, especially at the highest temperature, suggests that the effects of warming on N. luetkeana extend to the microbiome.}, }
@article {pmid40075541, year = {2025}, author = {Papp-Rupar, M and Grace, ER and Korotania, N and Ciusa, ML and Jackson, RW and Rabiey, M}, title = {Impact of Phage Therapy on Pseudomonas syringae pv. syringae and Plant Microbiome Dynamics Through Coevolution and Field Experiments.}, journal = {Environmental microbiology}, volume = {27}, number = {3}, pages = {e70076}, doi = {10.1111/1462-2920.70076}, pmid = {40075541}, issn = {1462-2920}, support = {//The University of Warwick start-up fund/ ; BB/T010568/1//Plant Bacterial Diseases programme/ ; //JABBS Foundation/ ; //Applied Microbiology International/ ; //East Malling Trust/ ; //Worshipful Company of Fruiterers/ ; BB/S019669/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X019683/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //University of Birmingham/ ; }, mesh = {*Pseudomonas syringae/virology ; *Plant Diseases/microbiology ; *Microbiota ; *Plant Leaves/microbiology/virology ; Phage Therapy/methods ; Pseudomonas Phages/genetics/physiology ; Bacteriophages/genetics/physiology ; Prunus avium/microbiology/virology ; England ; Biological Coevolution ; }, abstract = {Bacteriophages (phages) are viruses that infect and lyse bacteria and have the potential for controlling bacterial diseases. Isolation of phages targeting the cherry pathogen Pseudomonas syringae pv. syringae (Pss) led to five distinct phage genotypes. Building on previous in vitro coevolution experiments, the coevolution of the five phages (individually and as a cocktail) with Pss on cherry leaves was conducted in glasshouse and field experiments. Phages effectively reduced Pss numbers on detached leaves, with no evidence of phage resistance emerging in the bacterial population. Field application of phages in a cherry orchard in Southeast England evaluated phage survival, viability and impact on bacterial populations and the microbial community. The bacterial population and phages persisted in the leaf and shoot environment as long as the bacterial host was present. In contrast to in vitro studies, the plant environment constrained the emergence of phage resistant Pss populations. Application of phage cocktail in the orchard did not affect the cherry leaf microbiome. These observations provide essential knowledge for using phage treatments to control bacterial diseases while minimising the impact on the plant microbiome, highlighting phages' potential to safely control bacterial diseases in trees.}, }
@article {pmid40075536, year = {2025}, author = {Zhang, Y and Peng, Y and Qu, X and Zhang, L and Wei, T and Wang, H and Guo, Z and Liu, W and Wang, X}, title = {On-orbit microbial succession patterns of the China Space Station during the construction period.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {73}, pmid = {40075536}, issn = {2049-2618}, mesh = {China ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; *Spacecraft ; Space Flight ; Microbiota/genetics ; Humans ; Astronauts ; }, abstract = {BACKGROUND: The China Space Station (CSS) modules feature many areas that are difficult to clean and thus susceptible to microbial outbreaks. A new sampling method utilizing an equivalent material sheet was applied to characterize the diversity of microbes that accumulated in inaccessible areas in orbit on the CSS. Equivalent material sheet is a membrane made of the same material as the wall of the module.<br><br>RESULTS: Fifty samples were collected from interior surfaces (work, sleeping, and sanitary areas) of the Tianhe core module and the Wentian and Mengtian experimental modules, covering three flights by the Shenzhou (SZ)-12 to SZ-14 astronaut crews from 2021 to 2022. The numbers of culturable bacteria and fungi that accumulated during the on-orbit periods of each flight ranged from 0 to 2.83&#x2009;&#xd7;&#x2009;10[9] colony-forming units/100 cm[2]. The number of bacteria detected by quantitative PCR (qPCR) ranged from 1.24&#x2009;&#xd7;&#x2009;10[5] to 2.59&#x2009;&#xd7;&#x2009;10[9] rRNA gene copies/100 cm[2], with an average viability of 65.08%. A total of 103 bacterial strains and 27 fungal strains were cultured and isolated. The dominant culturable microorganisms were mainly from the genera Bacillus, Staphylococcus, Aspergillus, Cladosporium, and Penicillium. High-throughput sequencing results showed that the predominant bacteria were Pseudomonas, Stenotrophomonas, Methylobacterium-Methylorubrum, Sphingomonas, Bacillus, Staphylococcus, and Nocardiopsis. The microbial diversity in each module varied significantly with sampling time and sampling area. In the early stage of CSS construction with the SZ-12 crew, the microbial species evenness in the modules was high; later, with the SZ-13 crew, Pseudomonas began to appear as the dominant microorganism. More than half (58.80%) of the bacteria on module surfaces originated from the human skin and oral environments. Lactobacillus was present in all areas of the three modules at all sampling times. The biomarker bacteria Stenotrophomonas sp., isolated from the work area in the Tianhe core module, are typically derived from plants. SourceTracker analysis indicated that most of the microbes in the orbiting CSS came from human bodies, and that microbial diversity was significantly altered with each crew change.<br><br>CONCLUSION: Future efforts at microbial prevention and control on orbit should emphasize the human and plant origins of microbes. Information on the microbial diversity in the condensate zone could be useful to guide the development of new strategies to prevent and control microbes during space flight. Video Abstract.}, }
@article {pmid40075274, year = {2025}, author = {Jeong, S and Tollison, T and Brochu, H and Chou, H and Yu, T and Baghaie, P and Yount, KS and Darville, T and Wiesenfeld, HC and Hillier, SL and Peng, X and O'Connell, CM}, title = {Diagnostic-avoiding Chlamydia trachomatis variants detected in cervical and endometrial specimens from women during 16S microbiome profiling.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {349}, pmid = {40075274}, issn = {1471-2334}, support = {U19 AI084024/AI/NIAID NIH HHS/United States ; U19 AI084024/AI/NIAID NIH HHS/United States ; U19 AI084024/AI/NIAID NIH HHS/United States ; U19 AI084024/AI/NIAID NIH HHS/United States ; U19 AI084024/AI/NIAID NIH HHS/United States ; U19 AI084024/AI/NIAID NIH HHS/United States ; U19 AI084024/AI/NIAID NIH HHS/United States ; U19 AI084024/AI/NIAID NIH HHS/United States ; U19 AI084024/AI/NIAID NIH HHS/United States ; U19 AI084024/AI/NIAID NIH HHS/United States ; U19 AI084024/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Female ; *Chlamydia trachomatis/genetics/isolation &amp; purification ; *Chlamydia Infections/diagnosis/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Cervix Uteri/microbiology ; *Microbiota/genetics ; Adult ; *DNA, Bacterial/genetics ; Endometrium/microbiology ; Gonorrhea/diagnosis/microbiology ; RNA, Ribosomal, 23S/genetics ; Neisseria gonorrhoeae/genetics/isolation &amp; purification ; Young Adult ; Pennsylvania ; }, abstract = {BACKGROUND: Performance of a 16S rRNA analysis of the cervicovaginal microbiome of 220 participants recruited into the T Cell Response against Chlamydia (TRAC) cohort between February 2011 and August 2014 in Allegheny County, Pennsylvania USA detected DNA encoding chlamydial 16S rRNA in samples from seven participants whose tests were negative for Chlamydia trachomatis (CT) and DNA encoding gonococcal 16S rRNA from five participants whose tests were negative for Neisseria gonorrhoeae (NG) infection with the Aptima Combo 2 assay (Hologic).<br><br>METHODS: We used targeted PCR amplification followed by sequencing to characterize the chlamydial 23S rRNA locus and qPCR to detect gonococcal DNA in residual diagnostic swab eluates or DNA used to generate 16S rRNA libraries.<br><br>RESULTS: Discrepant specimens that contained chlamydial DNA carried a diagnostic-avoidant, G1523A nucleotide polymorphism in the 23S rRNA locus identical to variants previously detected in Finland, Denmark, and the UK. PCR validation of gonococcal DNA was confirmed for all participants whose tests were negative, with stochastic effects consistent with infection levels close to the limit of detection by the diagnostic assay.<br><br>CONCLUSIONS: These data indicate that this probe-avoidant CT mutant was circulating in the northeastern US prior to its detection and characterization in 2019. Although infrequent, false negative tests could represent infection with probe-avoidant CT mutants. Additional research is needed to determine if there is a role for CT tests using alternate probes for symptomatic or exposed individuals suspected of infection with these mutant chlamydial strains.}, }
@article {pmid40075266, year = {2025}, author = {Cao, H and Xu, J and Wang, H and Yi, W and Yang, D and Yang, J and Sun, J and Wang, Y and Zhang, F and Yan, J and Li, D}, title = {Fecal microbiota transplantation mitigates postdieting weight regain in mice by modulating the gut-liver axis.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {135}, pmid = {40075266}, issn = {1471-2180}, support = {2023YFF1104305//National Key Research and Development Program of China/ ; 2022YFF1100601//National Key Research and Development Program of China/ ; K2023004//Key Research project of Health Commission of Jiangsu Province/ ; M2021055//Key Research project of Health Commission of Jiangsu Province/ ; Y2021001//Wuxi Science and Technology Bureau, "Taihu Light" Science and Technology Research program/ ; K20221026//Wuxi Science and Technology Bureau, "Taihu Light" Science and Technology Research program/ ; CXTD2021003//Key discipline construction program of Wuxi Commission of Health/ ; KX-23-B050//Soft Science Project of Wuxi Science and Technology Association/ ; KX-23-C196//Soft Science Project of Wuxi Science and Technology Association/ ; YJZ202305//Medical research projects in research-oriented hospitals of Affiliated Hospital of Jiangnan University/ ; HB2023062//"Shuangbai Talents" research program of Wuxi Commission of Health/ ; HB2023063//"Shuangbai Talents" research program of Wuxi Commission of Health/ ; HB2023061//"Shuangbai Talents" research program of Wuxi Commission of Health/ ; LCYJ202347//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; LCYJ202310//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; LCYJ202322//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; LCYJ202303//Clinical Research and translational medicine research program of Affiliated Hospital of Jiangnan University/ ; BK20210468//Natural Science Foundation of Jiangsu Province/ ; BK20210060//Natural Science Foundation of Jiangsu Province/ ; 82370809//National Natural Science Foundation of China/ ; 32101033//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; Mice ; *Weight Gain ; *Liver/metabolism ; Male ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; Mice, Inbred C57BL ; Feces/microbiology ; Dysbiosis/therapy/microbiology ; Fatty Acids, Volatile/metabolism ; Lipid Metabolism ; }, abstract = {BACKGROUND: Dysbiosis of the microbiome is strongly associated with weight rebound after dieting. However, the interactions between the host and microbiome and their relevance to the pathogenesis of post-diet weight rebound remain unclear.<br><br>PURPOSE: This study aimed to evaluate the effects of fecal microbiota transplantation (FMT) on post-diet weight regain and to investigate the underlying mechanisms by which FMT inhibits weight regain.<br><br>METHODS: FMT was administered once daily to mice for 5 weeks. Gas chromatography tandem mass spectrometry was employed to analyze short-chain fatty acid levels in serum, ultrahigh-performance liquid chromatography tandem mass spectrometry was utilized for analyzing hepatic lipid metabolites, and shotgun metagenomic sequencing was applied to examine the intestinal microbiome.<br><br>RESULTS: FMT reduced weight regain and prevented lipid accumulation in both liver and adipose tissue while also improving glucose intolerance in mice. Furthermore, FMT increased the abundance of Enterorhabdus caecimuris and decreased the abundances of Burkholderiales, Sutterellaceae, Turicimonas muris, Bacteroides stercorirosoris, and Acetivibrio ethanolgignens within the gut microbiota. Additionally, elevated propionic acid levels and significant alterations in hepatic lipid metabolites were observed following FMT administration.<br><br>CONCLUSIONS: Our findings demonstrate that FMT effectively mitigates post-diet weight regain and associated complications. These effects are mediated through interactions between the gut microbiota and the liver via the gut-propionic acid-liver axis.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid40075127, year = {2025}, author = {Cai, C and Zhang, Z and Alberti, G and Pereira, A and De Barbieri, F and García, C and Wine, E and Gana, JC}, title = {Early childhood adiposity, lifestyle and gut microbiome are linked to steatotic liver disease development in adolescents.}, journal = {International journal of obesity (2005)}, volume = {}, number = {}, pages = {}, pmid = {40075127}, issn = {1476-5497}, abstract = {BACKGROUND/OBJECTIVES: To examine the relationship between early childhood adiposity, adolescent lifestyles, gut microbiota and steatotic liver disease (SLD) development in adolescents using data from a prospective, longitudinal cohort study.<br><br>METHODS: We included 69 adolescents (14-17 years old) with SLD and 69 adolescents without SLD, matched for BMI-z scores, sex, and age, from the 13-year longitudinal cohort the "Growth and Obesity Cohort Study". Anthropometric data between the ages of 4 and 17 and lifestyle parameters (including diet and physical activity) at 14-17 years old were evaluated. Fecal samples were collected and microbiome composition and function were assessed using 16S ribosomal RNA amplicon sequencing.<br><br>RESULTS: Principal component analysis demonstrated dietary intake factors and childhood adiposity factors expanding the distribution variation between case and control groups, respectively. Lower odds of developing SLD during adolescence was associated with higher levels of daily fiber intake during adolescence (adjusted odds ratio&#x2009;=&#x2009;0.91) and lower childhood adiposity (triceps skinfold at 5 years of age, suprailiac skinfold at 8 and 11 years of age, and waist-to-hip ratio at age 5-9 years). SLD was associated with a lower abundance of specific microbial species, such as Bacteroides vulgatus, which was higher in the control group compared to the case group (control/case abundance ratio&#x2009;=&#x2009;18.71). B. vulgatus abundance also positively correlated with dietary fiber intake and inversely correlated with childhood adiposity.<br><br>CONCLUSIONS: Adiposity in early childhood and a low dietary fiber intake may contribute to the pathogenesis of SLD during adolescence, possibly through alterations to the intestinal microbiome; these findings could inform early disease markers and targets for intervention.}, }
@article {pmid40075091, year = {2025}, author = {Jeong, ES and Jung, HK and Choi, E and Yun, K and Lee, A and Kim, YS}, title = {Characterization of post-inflammatory irritable bowel syndrome animal model following acute colitis recovery.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8512}, pmid = {40075091}, issn = {2045-2322}, mesh = {Animals ; *Irritable Bowel Syndrome/microbiology/metabolism/pathology/physiopathology ; *Disease Models, Animal ; *Colitis/chemically induced/microbiology/metabolism/pathology ; Mice ; *Dextran Sulfate ; *Gastrointestinal Microbiome ; *Intestinal Mucosa/metabolism/pathology/microbiology ; Male ; Acute Disease ; Inflammation/metabolism/pathology ; Gastrointestinal Motility ; Permeability ; Mice, Inbred C57BL ; Colon/pathology/metabolism ; Cytokines/metabolism ; }, abstract = {Irritable bowel syndrome (IBS) is a prevalent disorder with an unclear pathophysiology. This study aimed to investigate the features of dextran sulfate sodium (DSS)-induced low-grade inflammation using murine models of acute severe colitis (acute model) and chronic mild repeated colitis (chronic model), with potential implications for IBS research. The acute model was induced with 3% DSS for 5 days, followed by a 12-week recovery period. The chronic model involved administration of 0.5% DSS for 5 days, followed by a 5-day resting period, repeated thrice. We conducted comparative analyses to assess inflammation severity, intestinal motility, permeability, visceral hypersensitivity, and microbiome composition. In the acute model, mild leukocyte infiltration was observed, colonic transit time shortened at 12 weeks (P < 0.001), occludin expression decreased (P = 0.041), inflammatory cytokines, and transient receptor potential vanilloid 1 was upregulated in colonic mucosa (P < 0.050). In the chronic model, only mild inflammatory changes were noted. Microbiota analysis in the acute model revealed differences in microbial abundance and compositions (P = 0.001). The acute model demonstrated low-grade inflammation that caused gut dysmotility, altered permeability, and increased visceral hypersensitivity with notable microbial composition changes, potentially relevant to IBS phenotypes.}, }
@article {pmid40075040, year = {2025}, author = {Jiang, Q and Wu, L and Wang, X and Gao, Z and Liu, X and Zhang, W and Xue, L and Yang, J and Chen, T and Chen, Y and Wang, B}, title = {Investigating Causal Links Between Gut Microbiota and Neurological Disorders via Genome-Wide Association Studies.}, journal = {Molecular neurobiology}, volume = {}, number = {}, pages = {}, pmid = {40075040}, issn = {1559-1182}, abstract = {Many reports have highlighted the involvement of the gut microbiome in the occurrence, progression, and outcomes of neurological disorders. However, current reports are somewhat chaotic, especially concerning whether the gut microbiota has a causal effect on various neurological diseases. Furthermore, whether there is a common mechanism involving gut microbial communities in these neurological disorders has not to be revealed. In this study, we leveraged data from the largest-scale genome-wide association study (GWAS) by the MiBioGen consortium, which includes genetic and microbial composition data from 18,340 individuals spanning 24 cohorts. We utilized single-nucleotide polymorphisms (SNPs) associated with the gut microbiome as instrumental variables (IVs) in Mendelian randomization (MR) analyses. These IVs were rigorously selected based on their genome-wide and locus-wide significance to ensure robust causal inference. Our study established robust associations between specific gut microbiota and various neurological disorders using MR. We systematically depicted the bacteria with causal relationships in all diseases, covering the levels of phylum, class, order, family, and genus. We identified 34 bacterial species as significant risk or protective factors across disorders, including two main phylum levels such as Firmicutes (22 species) and Proteobacteria (8 species), as well as Bacteroidetes (2 species), Actinobacteria (1 species), and Verrucomicrobiota (1 species). At the family level of bacteria, we found that Lachnospiraceae and Ruminococcaceae are the most related to these 11 diseases and they may play different roles in the same disease.}, }
@article {pmid40074999, year = {2025}, author = {Yan, Z and Guan, G and Jia, H and Li, H and Zhuoga, S and Zheng, S}, title = {The association between gut microbiota and accelerated aging and frailty: a Mendelian randomization study.}, journal = {Aging clinical and experimental research}, volume = {37}, number = {1}, pages = {82}, pmid = {40074999}, issn = {1720-8319}, support = {2020YFC2009000 and 2020YFC2009001//National Key R&amp;D Program of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Mendelian Randomization Analysis ; *Frailty/genetics/microbiology ; *Aging ; Genome-Wide Association Study ; Aged ; }, abstract = {BACKGROUND: The recent observational studies have unveiled the correlation between the composition and dynamic alterations of the gut microbiome and aging; however, the causal relationship remains uncertain.<br><br>AIMS: The objective of this study is to investigate the causal relationship between the gut microbiome and accelerated aging as well as frailty, from a genetic perspective.<br><br>METHODS: We obtained data on the gut microbiome, intrinsic epigenetic age acceleration, and Frailty Index from published large-scale genome-wide association studies. A two-sample Mendelian randomization analysis was conducted primarily using inverse variance weighting model. We utilized the MR-Egger intercept analysis, IVW method, the Cochran Q test, and the leave-one-out analysis to assess the robustness of the results.<br><br>RESULTS: IVW analysis indicated a potential association between Peptococcus (OR: 1.231, 95% CI 1.013-1.497, P&#x2009;=&#x2009;0.037), Dialister (OR: 1.447, 95% CI 1.078-1.941, P&#x2009;=&#x2009;0.014) and Subdoligranulum (OR: 1.538, 95% CI 1.047-2.257, P&#x2009;=&#x2009;0.028) with intrinsic epigenetic age acceleration; while Prevotella 7 (OR: 0.792, 95% CI 0.672-0.935, P&#x2009;=&#x2009;0.006) was associated with a potential protective effect. Allisonella (OR: 1.033, 95% CI 1.005-1.063, P&#x2009;=&#x2009;0.022), Howardella (OR: 1.026, 95% CI 1.002-1.050, P&#x2009;=&#x2009;0.031) and Eubacterium coprostanoligenes (OR: 1.037, 95% CI 1.001-1.073, P&#x2009;=&#x2009;0.042) were associated with an increased risk of frailty; conversely, Flavonifractor (OR: 0.954, 95% CI 0.920-0.990, P&#x2009;=&#x2009;0.012) and Victivallis (OR: 0.984, 95% CI 0.968-1.000, P&#x2009;=&#x2009;0.049) appeared to exhibit a potential protective effect against frailty.<br><br>CONCLUSION: The findings of this study provide further evidence for the genetic correlation between gut microbiota and accelerated aging as well as frailty, enhancing the understanding of the role of gut microbiota in aging-related processes. However, the underlying mechanisms and potential clinical applications require further investigation before any targeted interventions can be developed.}, }
@article {pmid40074935, year = {2025}, author = {Yan, Y and Satoh-Takayama, N}, title = {New perspectives on gastric disorders: the relationship between innate lymphoid cells and microbes in the stomach.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {82}, number = {1}, pages = {113}, pmid = {40074935}, issn = {1420-9071}, support = {21gm6310027h//the Japan Agency for Medical Research and Development Care Research for Evolutional Science Technology/ ; }, mesh = {Humans ; *Immunity, Innate ; *Lymphocytes/immunology ; *Gastric Mucosa/immunology/microbiology ; *Stomach Diseases/immunology/microbiology/pathology ; Animals ; Gastrointestinal Microbiome/immunology ; Helicobacter pylori/immunology ; Stomach/immunology/microbiology/pathology ; Helicobacter Infections/immunology/microbiology ; }, abstract = {A growing number of studies in recent years have revealed the changes in the gastric microbiota during the development of gastric diseases, breaking the stereotype that the stomach is hostile to microorganisms beyond H. pylori. After a decade of intensive research, the discovery of innate lymphoid cells (ILCs) has provided a new perspective on the immune response in many diseases. In the context of defense against infectious pathogens, the pre-existing innate defense mechanism of tissue-resident ILCs can rapidly recognize and respond to microbes to eliminate infection at the earliest stages. Here, we outline the basic function of ILCs in the gastric mucosa and in shaping the gastric microbiome. We discuss the interactions between the gastric microbiota and ILCs, explaining how the ILCs actively drive the immune response against bacterial pathogens that can lead to the development of the gastric disease.}, }
@article {pmid40074848, year = {2025}, author = {Xie, M and Yang, T and Liu, Q and Ning, Z and Feng, L and Min, X}, title = {The influence of Lactobacillus johnsonii on tumor growth and lymph node metastasis in papillary thyroid carcinoma.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {419}, pmid = {40074848}, issn = {2399-3642}, mesh = {*Thyroid Cancer, Papillary/pathology/microbiology/genetics ; Animals ; Humans ; *Thyroid Neoplasms/pathology/microbiology ; *Lymphatic Metastasis ; *Lactobacillus/genetics ; Mice ; *Mice, Nude ; Female ; *Cell Proliferation ; Male ; Cell Line, Tumor ; Middle Aged ; Cell Movement ; Mice, Inbred BALB C ; Adult ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Lymph node metastasis (LNM) is a key factor in the prognosis of papillary thyroid carcinoma (PTC). This study explores the effect of intratumoral bacteria on LNM in PTC. The intrathyroidal microbiome is analyzed in 55 PTC patients by 16S rRNA gene sequencing. The CCK8 and Transwell assays determine the impact of bacteria on the proliferation and migration abilities of PTC cells. Xenograft tumor and bacterial colonization experiments are carried out using nude mice. We show that Lactobacillus is significantly decreased in PTC lesions from patients with LNM. Lactobacillus johnsonii (L. johnsonii) suppresses the proliferation and migration capability of PTC cells in vitro and in vivo. Bacterial gut colonization of L. johnsonii increases its abundance in tumors and inhibits PTC growth and LNM. These findings suggest that L. johnsonii can be harnessed for the development of innovative therapeutic strategies for PTC.}, }
@article {pmid40074707, year = {2025}, author = {Jung, M and Lee, JY and Kim, S and Song, J and Jang, S and Shin, S and Lee, MH and Kim, MJ and Kim, J and Lee, HB and Kim, Y and Ahn, K and Kim, M and Kim, J}, title = {Altered diversity and composition of gut microbiota in Korean children with food allergy.}, journal = {Clinical and translational allergy}, volume = {15}, number = {3}, pages = {e70036}, doi = {10.1002/clt2.70036}, pmid = {40074707}, issn = {2045-7022}, support = {NRF-2021R1G1A1004372//National Research Foundation of Korea/ ; NRF-2023R1A2C1002740//National Research Foundation of Korea/ ; }, abstract = {BACKGROUND: This study aimed to comprehensively characterize the gut microbiome and identify individual and grouped gut microbes associated with food allergy (FA) using 16S rRNA gene sequencing.<br><br>METHODS: Fecal samples were collected from children with IgE-mediated FA and from sex- and age-matched controls. The V3-V4 variable regions of the 16S rRNA gene of the gut microbiome were profiled using next-generation sequencing (Illumina, USA). Bacterial species richness, intracommunity diversity, and intergroup dissimilarity were evaluated. Functional profiles were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) and the Minimal Set of Pathways (MinPath) algorithm.<br><br>RESULTS: Fecal samples were collected from children with IgE-mediated FA (n&#xa0;=&#xa0;66) and from sex- and age-matched controls (n&#xa0;=&#xa0;22). Gut microbiome richness (p&#xa0;<&#xa0;0.0001), intra-community diversity (p&#xa0;<&#xa0;0.0001), and inter-community diversity (p&#xa0;=&#xa0;0.0004) were higher in the healthy group than in the FA group. Patients with FA were enriched in Blautia, Fusicatenibacter, and Ruminococcus_g5 compared with healthy control individuals (all p&#xa0;<&#xa0;0.05). Healthy control individuals were significantly enriched in Oscillibacter and Ruminococcus compared with patients with FA (all p&#xa0;<&#xa0;0.05). Functional pathway analysis identified enrichment in pathways related to endoglucanase in healthy controls and the ATP-binding cassette (ABC) transport system in FA patients.<br><br>CONCLUSIONS: The gut microbiomes of patients with FA and healthy control individuals had different taxonomic abundances, and the microbiome richness and diversity of the bacterial flora of patients with FA were reduced compared with controls.}, }
@article {pmid40074704, year = {2025}, author = {Schwartz, J and Capistrano, K and Hussein, H and Hafedi, A and Shukla, D and Naqvi, A}, title = {Oral SARS-CoV-2 Infection and Risk for Long Covid.}, journal = {Reviews in medical virology}, volume = {35}, number = {2}, pages = {e70029}, doi = {10.1002/rmv.70029}, pmid = {40074704}, issn = {1099-1654}, support = {/NH/NIH HHS/United States ; R01DE027980//NIDCR/NIH/ ; R56DE033249//NIDCR/NIH/ ; R01EY033622//NEI/NIH/ ; }, mesh = {Humans ; *COVID-19/immunology/virology ; *SARS-CoV-2/immunology/physiology ; Post-Acute COVID-19 Syndrome ; Microbiota ; Dysbiosis ; Mouth Mucosa/virology/immunology/microbiology ; Virus Internalization ; Mouth Diseases/virology/microbiology/immunology ; Angiotensin-Converting Enzyme 2/metabolism ; }, abstract = {SARS-CoV-2 is an oral pathogen that infects and replicates in mucosal and salivary epithelial cells, contributing to oral post-acute sequelae COVID-19 (PASC) and other oral and non-oral pathologies. While pre-existing inflammatory oral diseases provides a conducive environment for the virus, acute infection and persistence of SARS-CoV-2 can also results in oral microbiome dysbiosis that further worsens poor oral mucosal health. Indeed, oral PASC includes periodontal diseases, dysgeusia, xerostomia, pharyngitis, oral keratoses, and pulpitis suggesting significant bacterial contributions to SARS-CoV-2 and oral tissue tropism. Dysbiotic microbiome-induced inflammation can promote viral entry via angiotensin-converting enzyme receptor-2 (ACE2), serine transmembrane TMPRSS2 and possibly other non-canonical pathways. Additionally, metabolites derived from a dysbiotic microbiome can alter the physiological and biochemical pathways related to the metabolism of lipids, carbohydrates, and amino acids. This may promote a pro-inflammatory microenvironment, leading to immune exhaustion, loss of tolerance, and susceptibility to a variety of oral pathogens, causing acute and later chronic inflammation. Microbial release of mimics of host metallopeptidases related to furin, ADAM17 (A disintegrin and metalloproteinase 17), and glycoprotein metabolites can further aid viral attachment to T cell immunoglobulin-like (TIMs), enhancing viral entry while simultaneously depressing oral mucosal immune resistance and clearance. Membrane reorganization characterised by neuroproteins, such as neuropilins, also functionally assists with SARS-CoV-2 entry and extends the pathogenesis of PASC from the oral cavity to the brain, gut, or other non-oral tissues. Thus, poor oral health, characterised by disrupted oral microbiomes can promote viral tropism, weaken antiviral resistance, and heightens susceptibility to SARS-CoV-2 infection. This immune dysfunction also increases the risk of additional viral infections, exacerbating oral conditions like periodontal and endodontic diseases. These persistent oral health issues can contribute to systemic inflammation, creating bidirectional effects between oral and non-oral tissues, potentially leading to Post-Acute Sequelae of COVID-19 (PASC).}, }
@article {pmid40074633, year = {2025}, author = {Le, PH and Yeh, YM and Chen, YC and Chen, CL and Tsou, YK and Chen, CC and Chiu, CT and Chiu, CH}, title = {Fecal microbiota transplantation for vancomycin-resistant Clostridium innocuum infection in inflammatory bowel disease: A pilot study evaluating safety and clinical and microbiota outcome.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jmii.2025.03.004}, pmid = {40074633}, issn = {1995-9133}, abstract = {BACKGROUND: Clostridium innocuum is a vancomycin-resistant pathobiome associated with poor clinical outcomes in inflammatory bowel disease (IBD). In ulcerative colitis (UC), it correlates with reduced remission rates, while in Crohn's disease (CD), it is linked to creeping fat formation and intestinal strictures. Notably, some patients experience refractory or recurrent C. innocuemailum infections despite metronidazole treatment. This study evaluates the safety and efficacy of single-dose fecal microbiota transplantation (FMT) in IBD patients with refractory or recurrent C. innocuum infections.<br><br>METHODS: We conducted a feasibility pilot study involving seven IBD patients (3 CD, 4 UC) with refractory (n&#xa0;=&#xa0;5) or recurrent (n&#xa0;=&#xa0;2) C. innocuum infections following metronidazole treatment. Patients underwent single-dose FMT and were monitored for six months.<br><br>RESULTS: No adverse events were recorded. All participants demonstrated improved disease activity post-FMT, as assessed by the Crohn's Disease Activity Index and Mayo Score. However, a mild increase in symptom severity was noted at six months. Follow-up cultures showed persistent C. innocuum infection in one patient and asymptomatic recurrence in another at three months. Alpha diversity of the gut microbiome increased post-FMT, and Bray-Curtis dissimilarity analysis revealed a microbiota composition more similar to that of the donor.<br><br>CONCLUSION: Single-dose FMT appears to be a safe and feasible therapeutic approach for refractory or recurrent C. innocuum infections in IBD patients, with potential benefits in disease activity and microbiome restoration. Further studies are warranted to optimize long-term outcomes.}, }
@article {pmid40074580, year = {2025}, author = {Shen, BA and Peterson, SB and Mougous, JD}, title = {Twists, turns and jumps: T6SS evolution within species.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.02.015}, pmid = {40074580}, issn = {1878-4380}, abstract = {The type VI secretion system mediates interbacterial antagonism between Gram-negative bacteria through delivery of toxic effector proteins. A recent comprehensive genomic analysis by Habich et al. reveals interesting features of the evolution of T6SSs and their corresponding effectors in Pseudomonas aeruginosa, raising questions about functional specialization of the system.}, }
@article {pmid40074579, year = {2025}, author = {Mukherjee, A and Han, L and Mukhopadhyay, S and Kopriva, S and Swarup, S}, title = {Sulfur traits in the plant microbiome: implications for sustainable agriculture.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.02.002}, pmid = {40074579}, issn = {1878-4380}, abstract = {Owing to its biochemical flexibility, sulfur (S) is uniquely poised to fulfill versatile roles in plant-microbe interactions - impacting their metabolism with significant consequences for plant health and the global S cycle. We present evidence that the diversity of S-metabolic genes in plant-associated microbiomes (phytobiomes) is underappreciated, and plant niches are hotspots of bacterial S-metabolism with implications for S emissions. Building upon emerging findings, we posit that coordination of S-metabolism between plants and phytobiomes is a common mechanism for plant-microbe homeostasis and agriculturally beneficial microbial services. Finally, we summarize strategies to harness S-metabolic traits of plants and phytobiomes to sustainably enhance agricultural productivity under the stresses associated with climate change.}, }
@article {pmid40074575, year = {2025}, author = {Raglin, SS and Kent, AD}, title = {Navigating nitrogen sustainability with microbiome-associated phenotypes.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2025.02.003}, pmid = {40074575}, issn = {1878-4372}, abstract = {Crop microbiomes promote plant health through various mechanisms, including nutrient provisioning. However, agriculture neglected the importance of these microbiome-associated phenotypes (MAPs) in conventional management approaches originating from the Green Revolution. Green Revolution innovations, such as nitrogen fertilizers and high-yielding germplasm, supported an increase in global crop yields. Yet these advances also led to many environmental issues, including disruptions in microbially mediated nitrogen transformations that have reduced reliance on microbiomes for sustainable nitrogen acquisition. Overcoming the challenges introduced by the Green Revolution requires a shift toward ecologically informed agronomic strategies that incorporate MAPs into breeding and management decisions. Agriculture in the Anthropocene needs to mindfully manage crop microbiomes to decouple agrochemical inputs from profitable yields, minimizing the environmental repercussions of modern agriculture.}, }
@article {pmid40074067, year = {2025}, author = {Pragasam, AK and Maurya, S and Jain, K and Pal, S and Raja, C and Yadav, R and Kumar, S and Purohit, A and Pradhan, D and Kajal, K and Talukdar, D and Singh, AN and Verma, J and Jana, P and Rawat, S and Kshetrapal, P and Krishna, A and Kumar, S and Bansal, VK and Das, B and Srikanth, CV and Garg, PK}, title = {Invasive Salmonella Typhimurium Colonizes Gallbladder and Contributes to Gallbladder Carcinogenesis through Activation of Host Epigenetic Modulator KDM6B.}, journal = {Cancer letters}, volume = {}, number = {}, pages = {217621}, doi = {10.1016/j.canlet.2025.217621}, pmid = {40074067}, issn = {1872-7980}, abstract = {Gallbladder stones alone do not explain the risk of gallbladder cancer (GBC) as the sole etiological factor. Chronic microbial infection, particularly Salmonella, has been implicated in GB carcinogenesis, but its causative role and the underlying mechanisms are largely unknown. We studied gut and gallbladder tissue microbiome through targeted metagenomics to identify pathogenic bacteria in GBC. Virulence and pathogenicity of identified Salmonella Typhimurium from GBC tissue were studied after culture by whole genome sequencing, phylogenetic analysis, mutational profiling, and pangenome analysis. Mechanistic studies for GBC carcinogenesis were carried out in a mouse model of gallstones and chronic Salmonella infection, a cellular model using GBC (NOZ) cell lines, and a xenograft tumor model. We found an increased abundance of Salmonella in the gut microbiome of patients with GBC and culturable S. Typhimurium from the gallbladder cancer tissue. Comparative genomics of S. Typhimurium isolated from the GBC tissue showed a high invasive index. S. Typhimurium isolates harbored horizontally acquired virulence functions in their accessory genome. Chronic S. Typhimurium infection caused chronic inflammation, pre-malignant changes, and tumor-promoting mechanisms in the mouse model with gallbladder stones with activation of the epigenetic modulator KDM6B both in the mouse model and human GBC. Inhibition of KDM6B reduced engrafted tumor size in SCID mice. Of the differentially regulated genes in human GBC tissue, ADAMTSL5, CX3CR1, and SPSB4 were also significantly dysregulated in NOZ cells infected with Salmonella. Chronic Salmonella infection contributes to gallbladder carcinogenesis through a host epigenetic mechanism involving KDM6B.}, }
@article {pmid40073753, year = {2025}, author = {Huang, L and Du, J and Ye, L and Zheng, Y and Liu, X and Huang, E and Le, J and Huang, X and Du, W and Liu, C and Chen, L}, title = {Species level and SNP profiling of skin microbiome improve the specificity in identifying forensic fluid and individual.}, journal = {Forensic science international. Genetics}, volume = {78}, number = {}, pages = {103256}, doi = {10.1016/j.fsigen.2025.103256}, pmid = {40073753}, issn = {1878-0326}, abstract = {Human skin possesses individual and body fluid-specific microbial signatures potentially useful for forensic identification. Previous studies mostly attribute individuals based on the relative abundance of microbiota at single time point, however fluctuations in taxonomy and phylogenetic structure may cause this to be unreliable. In this study, we assessed the skin microbiome of individuals at consecutive time-point from fingers, palm, arm and forehead sites using full-length 16S rRNA gene sequencing. At the species level, hand samples (fingers, palm, arm) differed significantly from forehead microbes. Additionally, skin flora of the present study differed significantly from the dominant species that have been reported for saliva, feces, and vaginal secretions samples. ANOSIM analysis of all skin samples showed that inter-individual differences were greater than intra-individual differences, yet accuracy of individual identification was only 52.5 %. At the microbial gene level, three machine learning models based on single nucleotide polymorphism (SNP) profiles of Cutibacterium acnes resulted in accurate classification of more than 97.5 % individuals. These results indicate that consideration of bacterial SNP profiling may provide new directions for forensic identification and may have potential applications in body fluid identification and individual identification in forensic.}, }
@article {pmid40073571, year = {2025}, author = {Deng, W and Zhang, X and Liu, W and Wang, X and Wang, Z and Liu, J and Zhai, W and Wang, J and Zhao, Z}, title = {Deciphering the effects of long-term exposure to conventional and biodegradable microplastics on the soil microbiome.}, journal = {Journal of hazardous materials}, volume = {491}, number = {}, pages = {137890}, doi = {10.1016/j.jhazmat.2025.137890}, pmid = {40073571}, issn = {1873-3336}, abstract = {Despite recent advances in the understanding of the impacts of microplastics (MPs) on the soil microbiome under short-term exposure, little information is known regarding the long-term ecological effects of MPs in soil, especially biodegradable MPs (BMPs). Here, we systematically compared the effects of four prevalent microplastics, including two conventional MPs (CMPs) and two BMPs, on the soil microbiome over short- and long-term exposure durations. The soil microbial community were not significantly affected by the MP addition under short-term exposure; however, the soil microbial composition was obviously impacted by MP exposure under long-term exposure, some MP-adapted microbes (e.g., the phyla Protobacteria and Actinobacteria) were enriched but the phyla Acidobacteriota declined. These results indicated that the effects of the MP exposure on the soil microbiome were time dependent. PERMANOVA analysis demonstrated that the exposure time played a more important role in the variation in soil microbiome than the polymer type. The soil microbes which were reshaped by MPs were specialized in genetic potential of lipid metabolism and xenobiotics degradation and metabolism and weakened in microbial genetic information process. The carbon metabolic capacity and nitrogen transformation of soil microbes were disturbed by MPs under long-term exposure. Compared with CMPs, many more MPs derivatives, such as dissolved organic matter and low molecular-weight oligomers, were released from BMPs during the long-term degradation process in soil; thus, BMPs had a stronger effect on the soil microbiome than CMPs under long-term exposure. This study underscores the potential risk of the replacement of conventional plastics with biodegradable plastics.}, }
@article {pmid40073514, year = {2025}, author = {Fortuna, V and Oliveira, GF and Xavier, LM and Oliveira, DV and Lima, JG and Oliveira, YS and Costa, BS and Jesus, GB and Yahouedehou, SCMA and Zanchin, EM and Meyer, JR and Meneses, JV and Gonçalves, MS and Bagnato, VS}, title = {Enhancing sickle cell leg ulcer healing with combined photodynamic and photobiomodulation therapies: A pilot experience.}, journal = {Journal of tissue viability}, volume = {34}, number = {2}, pages = {100879}, doi = {10.1016/j.jtv.2025.100879}, pmid = {40073514}, issn = {0965-206X}, abstract = {AIM: This study aimed to evaluate the safety and efficacy of combined photodynamic therapy (PDT) and photobiomodulation (PBM) in treating sickle cell leg ulcers (SCLUs), with a focus on pain reduction and enhanced healing.<br><br>MATERIALS AND METHODS: In this prospective, open-label, uncontrolled pilot study, ten SCD patients with 17 chronic leg ulcers received PDT and PBM treatments. Ulcer severity, pain levels, and microbiome changes were monitored, and clinical data were analyzed using appropriate statistical methods.<br><br>RESULTS: Among the treated ulcers, 64.7&#xa0;% (11 out of 17) showed significant healing, with 9 ulcers achieving complete closure. The average reduction in ulcer size was significant, with a median healing time of 123 days. Pain levels decreased significantly in 82.3&#xa0;% of treated ulcers (p&#xa0;<&#xa0;0.001), and a 75.4&#xa0;% reduction in bacterial load was observed, alongside increased microbiome diversity (p&#xa0;<&#xa0;0.05). Elevated levels of IL-6 and PSGL-1 were associated with non-healing ulcers, indicating their potential as prognostic biomarkers.<br><br>CONCLUSION: The combined PDT and PBM therapy proved to be effective and safe for SCLUs, offering significant improvements in healing and pain reduction. These findings suggest that integrating PDT and PBM into standard care protocols could enhance the management of SCLUs.}, }
@article {pmid40073325, year = {2025}, author = {Dunleavy, K and Camilleri, M and Raffals, L}, title = {Altered Bile Acids and Pouch Microbiota Composition in Patients With Chronic Pouchitis.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izaf005}, pmid = {40073325}, issn = {1536-4844}, }
@article {pmid40073212, year = {2025}, author = {Li, T and Tao, R and Yang, L and Wan, Z and Li, R and Wang, R}, title = {Upadacitinib outperforms dupilumab in restoring the fungal microbiome in atopic dermatitis.}, journal = {The British journal of dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1093/bjd/ljaf095}, pmid = {40073212}, issn = {1365-2133}, }
@article {pmid40072847, year = {2025}, author = {Nguyen, HD and Kim, WK}, title = {Disrupted microbial cross-feeding and altered L-phenylalanine consumption in people living with HIV.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {2}, pages = {}, doi = {10.1093/bib/bbaf111}, pmid = {40072847}, issn = {1477-4054}, support = {SCR_008167//Tulane National Primate Research Center/ ; P51OD011104//TNPRC P51 Base/ ; /NH/NIH HHS/United States ; }, mesh = {*Phenylalanine/metabolism ; Humans ; *HIV Infections/metabolism/microbiology ; Gastrointestinal Microbiome ; Case-Control Studies ; Bacteria/metabolism/classification/genetics ; Microbiota ; }, abstract = {This work aims to (1) identify microbial and metabolic alterations and (2) reveal a shift in phenylalanine production-consumption equilibrium in individuals with HIV. We conducted extensive searches in multiple databases [MEDLINE, Web of Science (including Cell Press, Oxford, HighWire, Science Direct, IOS Press, Springer Nature, PNAS, and Wiley), Google Scholar, and Embase] and selected two case-control 16S data sets (GenBank IDs: SRP039076 and EBI ID: ERP003611) for analysis. We assessed alpha and beta diversity, performed univariate tests on genus-level relative abundances, and identified significant microbiome features using random forest. We also utilized the MICOM model to simulate growth and metabolic exchanges within the microbiome, focusing on the Metabolite Exchange Score (MES) to determine key metabolic interactions. We found that L-phenylalanine had a higher MES in HIV-uninfected individuals compared with their infected counterparts. The flux of L-phenylalanine consumption was significantly lower in HIV-infected individuals compared with healthy controls, correlating with a decreased number of consuming species in the chronic HIV stage. Prevotella, Roseburia, and Catenibacterium were demonstrated as the most important microbial species involving an increase in L-phenylalanine production in HIV patients, whereas Bacteroides, Faecalibacterium, and Blautia contributed to a decrease in L-phenylalanine consumption. We also found significant alterations in both microbial diversity and metabolic exchanges in people living with HIV. Our findings shed light on why HIV-1 patients have elevated levels of phenylalanine. The impact on essential amino acids like L-phenylalanine underscores the effect of HIV on gut microbiome dynamics. Targeting the restoration of these interactions presents a potential therapeutic avenue for managing HIV-related dysbiosis.}, }
@article {pmid40072555, year = {2025}, author = {Shah, H and Patel, P and Nath, A and Shah, U and Sarkar, R}, title = {Role of human microbiota in facilitating the metastatic journey of cancer cells.}, journal = {Naunyn-Schmiedeberg's archives of pharmacology}, volume = {}, number = {}, pages = {}, pmid = {40072555}, issn = {1432-1912}, abstract = {Cancer continues to be the leading cause of mortality worldwide, with metastasis being the primary contributor to cancer-related deaths. Despite significant advancements in cancer therapies, metastasis remains a major challenge in effective cancer management. Metastasis, the process by which cancer cells spread from the primary tumor to distant organs, is a complex phenomenon influenced by multiple factors, including the human microbiota. The human body encompasses various microorganisms, comprising bacteria, viruses, fungi, and protozoa, collectively known as microbiota. In fact, the microbiota is more abundant than human cells, and its disruption, leading to an imbalance in host-microbiota interactions (dysbiosis), has been linked to various diseases, including cancer. Among all microbiota, bacteria are one of the key contributors to cancer progression. Bacteria and bacteria-derived components such as secondary metabolites, QSPs, and toxins play a pivotal role in the metastatic progression of cancers. This review explores the intricate relationship between the human microbiota and cancer progression, focusing on different bacterial species which have been implicated in tumorigenesis, immune evasion, and metastasis. The present review explores the role of the human microbiome, specifically of bacteria in promoting metastasis in different types of cancers, demonstrating its ability to impact both the spread of tumors and their underlying mechanisms. This review also highlights the therapeutic potential and challenges of microbiome-based interventions in combating metastatic cancers. By addressing these challenges and by integrating microbiome-targeted strategies into clinical cancer treatment could represent a transformative approach in the fight against metastasis.}, }
@article {pmid40072493, year = {2025}, author = {Venter, C and Groetch, M}, title = {Emerging concepts in introducing foods for food allergy prevention.}, journal = {Current opinion in clinical nutrition and metabolic care}, volume = {}, number = {}, pages = {}, doi = {10.1097/MCO.0000000000001126}, pmid = {40072493}, issn = {1473-6519}, abstract = {PURPOSE OF REVIEW: This review focuses on the latest information regarding the role of complementary feeding practices and food allergen introduction in the prevention of food allergies.<br><br>RECENT FINDINGS: Early introduction of food allergens for food allergy prevention is recommended by food allergy prevention guidelines and is supported by the latest randomized controlled trials. Diet diversity is recommended, supported by the latest studies from Asia. A European study indicated that diet diversity after the first year of life may still be important for food allergy prevention. The latest systematic reviews indicate there may be an association between ultra-processed food intake and food allergy development. Plant based foods and fiber play an important role in modulating the gut microbiome which has been associated with reduced food allergy outcomes. However, increased intake of food allergens within a diverse diet raises questions about excessive calorie and protein intake but can be managed by focusing on infant satiety cues.<br><br>SUMMARY: The latest studies clearly indicate and further supports that introduction of food allergies should not be delayed once complementary feeding is commenced. A diverse diet is recommended to further support the prevention of food allergies.}, }
@article {pmid40072466, year = {2025}, author = {Gu, T and Guo, R and Chen, L and Zong, Y and Tian, Y and Xu, W and Zeng, T and Lu, L}, title = {Multi-omics uncover acute stress vulnerability through gut-hypothalamic communication in ducks.}, journal = {British poultry science}, volume = {}, number = {}, pages = {1-10}, doi = {10.1080/00071668.2025.2454960}, pmid = {40072466}, issn = {1466-1799}, abstract = {1. The avian gut hosts a complex and dynamic microbial ecosystem, which is essential for regulating host organ function. However, the relationship between the gut microbiota and the hypothalamic axis in acute stress vulnerability in ducks remains unclear.2. This study investigated how the gut microbiota affects microbial metabolism and the host stress response by comparing hypothalamic neurotransmitter availability, microbial composition and co-metabolites generated by both the microbiota and hypothalamus in ducks exhibiting the lowest active avoidance (LAA) and highest active avoidance (HAA) behaviour.3. The HAA group experienced a significant increase in the availability of arginine, histidine, glutamine, norepinephrine, L-tyrosine and melatonin during acute stress in the hypothalamus, compared to that in the LAA group. The 16S rRNA sequencing revealed significant differences in the gut microbiota composition based on acute stress vulnerabilities.4. Both caecal and hypothalamic metabolomic analyses identified 71 metabolites altered in caecal content and 95 in the hypothalamus. There was significant enrichment in pathways such as the cGMP-PKG signalling, dopaminergic synapse and endocrine resistance.5. Correlation analyses demonstrated that certain co-metabolites, including 1,3-dicyclohexylurea, 1-deoxyvaleric acid, 2-amino-2-methyl-1,3-propanediol, 3-chloroaniline, methenamine, N4-acetylcytidine-triphosphate and traumatin, may play a role in the gut microbiota-hypothalamic axis.6. The results suggested that the gut microbiome influenced acute stress responses. This provided a basis for understanding gut-hypothalamic communication and its impact on behaviour in ducks.}, }
@article {pmid40072296, year = {2025}, author = {Logan, AC and Mishra, P and Prescott, SL}, title = {The Legalome: Microbiology, Omics and Criminal Justice.}, journal = {Microbial biotechnology}, volume = {18}, number = {3}, pages = {e70129}, doi = {10.1111/1751-7915.70129}, pmid = {40072296}, issn = {1751-7915}, mesh = {Humans ; *Criminal Law ; Microbiota ; United States ; Genomics ; Forensic Psychiatry ; Europe ; }, abstract = {Advances in neuromicrobiology and related omics technologies have reinforced the idea that unseen microbes play critical roles in human cognition and behaviour. Included in this research is evidence indicating that gut microbes, through direct and indirect pathways, can influence aggression, anger, irritability and antisocial behaviour. Moreover, gut microbes can manufacture chemicals that are known to compromise cognition. For example, recent court decisions in the United States and Europe acknowledge that gut microbes can produce high levels of ethanol, without consumption of alcohol by the defendants. The dismissal of driving while intoxicated charges in these cases-so-called auto-brewery syndrome-highlights the way in which microbiome knowledge will enhance the precision, objectivity and fairness of our legal systems. Here in this opinion essay, we introduce the concept of the 'legalome'-the application of microbiome and omics science to forensic psychiatry and criminal law. We argue that the rapid pace of microbial discoveries, including those that challenge ideas of free will and moral responsibility, will necessitate a reconsideration of traditional legal doctrines and justifications of retributive punishment. The implications extend beyond the courtroom, challenging us to reconsider how environmental factors-from diet to socioeconomic conditions-might shape preventative and rehabilitative efforts through their effects on the microbiome.}, }
@article {pmid40072112, year = {2025}, author = {Xu, M and Zhou, EY and Shi, H}, title = {Tryptophan and Its Metabolite Serotonin Impact Metabolic and Mental Disorders via the Brain-Gut-Microbiome Axis: A Focus on Sex Differences.}, journal = {Cells}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/cells14050384}, pmid = {40072112}, issn = {2073-4409}, support = {1R15CA274480-23A1/NH/NIH HHS/United States ; }, mesh = {Humans ; *Serotonin/metabolism ; *Tryptophan/metabolism ; *Gastrointestinal Microbiome/physiology ; *Sex Characteristics ; *Brain-Gut Axis/physiology ; Animals ; *Mental Disorders/metabolism/microbiology ; Brain/metabolism ; Metabolic Diseases/metabolism/microbiology ; Female ; Male ; }, abstract = {The crisis of metabolic and mental disorders continues to escalate worldwide. A growing body of research highlights the influence of tryptophan and its metabolites, such as serotonin, beyond their traditional roles in neural signaling. Serotonin acts as a key neurotransmitter within the brain-gut-microbiome axis, a critical bidirectional communication network affecting both metabolism and behavior. Emerging evidence suggests that the gut microbiome regulates brain function and behavior, particularly through microbial influences on tryptophan metabolism and the serotonergic system, both of which are essential for normal functioning. Additionally, sex differences exist in multiple aspects of serotonin-mediated modulation within the brain-gut-microbiome axis, affecting feeding and affective behaviors. This review summarizes the current knowledge from human and animal studies on the influence of tryptophan and its metabolite serotonin on metabolic and behavioral regulation involving the brain and gut microbiome, with a focus on sex differences and the role of sex hormones. We speculate that gut-derived tryptophan and serotonin play essential roles in the pathophysiology that modifies neural circuits, potentially contributing to eating and affective disorders. We propose the gut microbiome as an appealing therapeutic target for metabolic and affective disorders, emphasizing the importance of understanding sex differences in metabolic and behavioral regulation influenced by the brain-gut-microbiome axis. The therapeutic targeting of the gut microbiota and its metabolites may offer a viable strategy for treating serotonin-related disorders, such as eating and affective disorders, with potential differences in treatment efficacy between men and women. This review would promote research on sex differences in metabolic and behavioral regulation impacted by the brain-gut-microbiome axis.}, }
@article {pmid40072039, year = {2025}, author = {Roy, B and Cao, K and Singh, CO and Fang, X and Yang, H and Wei, D}, title = {Advances in gut microbiota-related treatment strategies for managing colorectal cancer in humans.}, journal = {Cancer biology &amp; medicine}, volume = {22}, number = {2}, pages = {}, doi = {10.20892/j.issn.2095-3941.2024.0263}, pmid = {40072039}, issn = {2095-3941}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/microbiology/therapy ; *Dysbiosis/microbiology ; Probiotics/therapeutic use ; }, abstract = {Colorectal cancer (CRC) is a major contributor to global cancer-related mortality with increasing incidence rates in both developed and developing regions. Therefore, CRC presents a significant challenge to global health. The development of innovative tools for enhancing early CRC screening and diagnosis, along with novel treatments and therapies for improved management, remains an urgent necessity. CRC is intricately associated with the gut microbiota, which is integral to food digestion, nutrient generation, drug metabolism, metabolite production, immune enhancement, endocrine regulation, neurogenesis modulation, and the maintenance of physiologic and psychological equilibrium. Dysbiosis or imbalances in the gut microbiome have been implicated in various disorders, including CRC. Emerging evidence highlights the critical role of the gut microbiome in CRC pathogenesis and treatment, which presents potential opportunities for early detection and diagnosis. Despite substantial advances in understanding the relationship between the gut microbiota and CRC, significant challenges persist. Gaining a deeper and more detailed understanding of the interactions between the human microbiota and cancer is essential to fully realize the potential of the microbiota in cancer management. Unlike genetic factors, the gut microbiome is subject to modification, offering a promising avenue for the development of CRC treatments and drug discovery. This review provides an overview of the interactions between the human gut microbiome and CRC, while examining prospects for precision management of CRC.}, }
@article {pmid40072031, year = {2025}, author = {Huang, YJ}, title = {The Microbiome in Asthma Heterogeneity: The Role of Multi-Omic Investigations.}, journal = {Immunological reviews}, volume = {330}, number = {1}, pages = {e70015}, doi = {10.1111/imr.70015}, pmid = {40072031}, issn = {1600-065X}, support = {U01TR004066/TR/NCATS NIH HHS/United States ; 75N92024D00012-0-759202400001-1/HL/NHLBI NIH HHS/United States ; }, mesh = {*Asthma/microbiology/immunology/etiology ; Humans ; *Microbiota/immunology ; Animals ; Biomarkers ; Genomics/methods ; Proteomics ; Metabolomics/methods ; Disease Susceptibility ; Metagenomics/methods ; Multiomics ; }, abstract = {Asthma is one of the most prevalent and extensively studied chronic respiratory conditions, yet the heterogeneity of asthma remains biologically puzzling. Established factors like exogenous exposures and treatment adherence contribute to variability in asthma risk and clinical outcomes. It is also clear that the endogenous factors of genetics and immune system response patterns play key roles in asthma. Despite significant existing knowledge in the above, divergent clinical trajectories and outcomes are still observed, even among individuals with similar risk profiles, biomarkers, and optimal medical management. This suggests uncaptured biological interactions that contribute to asthma's heterogeneity, for which the role of host microbiota has lately attracted much research attention. This review will highlight recent evidence in this area, focusing on bedside-to-bench investigations that have leveraged omic technologies to uncover microbiome links to asthma outcomes and immunobiology. Studies centered on the respiratory system and the use of multi-omics are noted in particular. These represent a new generation of reverse-translational investigations revealing potential functional crosstalk in host microbiomes that may drive phenotypic heterogeneity in chronic diseases like asthma. Multi-omic data offer a wide lens into ecosystem interactions within a host. This informs new hypotheses and experimental work to elucidate mechanistic pathways for unresolved asthma endotypes. Further incorporation of multi-omics into patient-centered investigations can yield new insights that hopefully lead to even more precise, microbiome-informed strategies to reduce asthma burden.}, }
@article {pmid40071861, year = {2025}, author = {Organski, AC and Rajwa, B and Reddivari, A and Jorgensen, JS and Cross, TL}, title = {Gut microbiome-driven regulation of sex hormone homeostasis: a potential neuroendocrine connection.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2476562}, doi = {10.1080/19490976.2025.2476562}, pmid = {40071861}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Mice ; *Homeostasis ; *Fecal Microbiota Transplantation ; Gonadal Steroid Hormones/metabolism/blood ; Mice, Inbred C57BL ; Germ-Free Life ; Bacteria/classification/metabolism/isolation &amp; purification/genetics ; Testosterone/blood/metabolism ; Testis/metabolism/microbiology ; Hypothalamo-Hypophyseal System/metabolism ; Feces/microbiology ; Neurosecretory Systems/metabolism ; }, abstract = {The gut microbiome is known to have a bidirectional relationship with sex hormone homeostasis; however, its role in mediating interactions between the primary regulatory axes of sex hormones and their productions is yet to be fully understood. We utilized both conventionally raised and gnotobiotic mouse models to investigate the regulatory role of the gut microbiome on the hypothalamic-pituitary-gonadal (HPG) axis. Male and female conventionally raised mice underwent surgical modifications as follows: (1) hormonally intact controls; (2) gonadectomized males and females; (3) gonadectomized males and females supplemented with testosterone and estrogen, respectively. Fecal samples from these mice were used to colonize sex-matched, intact, germ-free recipient mice through fecal microbiota transplant (FMT). Serum gonadotropins, gonadal sex hormones, cecal microbiota, and the serum global metabolome were assessed. FMT recipients of gonadectomized-associated microbiota showed lower circulating gonadotropin levels than recipients of intact-associated microbiota, opposite to that of FMT donors. FMT recipients of gonadectomized-associated microbiota also had greater testicular weights compared to recipients of intact-associated microbiota. The gut microbiota composition of recipient mice differed significantly based on the FMT received, with the male microbiota having a more concerted impact in response to changes in the HPG axis. Network analyses showed that multiple metabolically unrelated pathways may be involved in driving differences in serum metabolites due to sex and microbiome received in the recipient mice. In sum, our findings indicate that the gut microbiome responds to the HPG axis and subsequently modulates its feedback mechanisms. A deeper understanding of interactions between the gut microbiota and the neuroendocrine-gonadal system may contribute to the development of therapies for sexually dimorphic diseases.}, }
@article {pmid40071689, year = {2025}, author = {van Smoorenburg, MY and Remmerswaal, EBM and Segui-Perez, C and van Hamme, JL and Strijbis, K and Geijtenbeek, TBH}, title = {Vaginal Prevotella timonensis Bacteria Enhance HIV-1 Uptake and Differentially Affect Transmission by Distinct Primary Dendritic Cell Subsets.}, journal = {European journal of immunology}, volume = {55}, number = {3}, pages = {e202451192}, doi = {10.1002/eji.202451192}, pmid = {40071689}, issn = {1521-4141}, mesh = {*Dendritic Cells/immunology/microbiology/virology ; Female ; *HIV-1/immunology/physiology ; Humans ; *HIV Infections/immunology/transmission/microbiology ; *Prevotella/immunology ; *Vagina/microbiology/immunology/virology ; Vaginosis, Bacterial/immunology/microbiology ; Antigens, CD1/metabolism/immunology ; Cells, Cultured ; Adult ; Glycoproteins ; }, abstract = {Young females are at high risk of acquiring HIV-1 infections and an imbalance in the vaginal microbiome enhances susceptibility to HIV-1 infection. More insights into the underlying mechanisms could open up new strategies to prevent HIV-1 acquisition and dissemination. Here, we investigated the effect of anaerobic bacteria associated with bacterial vaginosis (BV) on HIV-1 transmission by two distinct dendritic cell (DC) subsets, that is, inflammatory monocyte-derived DCs (moDCs) and primary CD1c[+] DCs. Notably, in contrast to other BV-associated microbiota, Prevotella timonensis enhanced uptake of HIV-1 by both moDCs and CD1c[+] DCs and the increased uptake was independent of cellular HIV-1 (co-)receptors. Imaging flow cytometry analyses showed that HIV-1 did not co-localise with P. timonensis but was internalized into tetraspanin-positive compartments known to be involved in HIV-1 transmission. P. timonensis bacteria enhanced HIV-1 transmission by CD1c[+] DCs, but not by moDCs, and the enhanced transmission was independent of viral infection. Our study strongly suggests that mucosal DC subsets have distinct functions in BV-associated HIV-1 susceptibility, and underscores the importance of early diagnosis and targeted treatment of vaginal dysbiosis to reduce the risk of HIV-1 acquisition.}, }
@article {pmid40071418, year = {2025}, author = {Zimmermann, J and Schreiber, A and Heeringa, P and Te Velde-Keyzer, CA}, title = {Highlights from the plenary session: cellular and molecular mechanisms of disease (I).}, journal = {Rheumatology (Oxford, England)}, volume = {64}, number = {Supplement_1}, pages = {i85-i87}, doi = {10.1093/rheumatology/keae411}, pmid = {40071418}, issn = {1462-0332}, mesh = {Humans ; *Anti-Neutrophil Cytoplasmic Antibody-Associated Vasculitis/immunology/therapy ; *Gastrointestinal Microbiome/physiology ; Translational Research, Biomedical ; T-Lymphocytes, Regulatory/immunology ; Interleukin-17 ; }, abstract = {In this plenary session of the Vasculitis Workshop 2024, pioneering translational research on autoimmune vasculitis, particularly ANCA-associated vasculitis (AAV), was presented, highlighting advancements in our understanding of disease mechanisms and promising therapeutic prospects. Advances in elucidating molecular pathways, such as IL-17 and IFN-I, pave the way for specific treatments. Preclinical studies have revealed the gut microbiome's role in the pathogenesis of MPO-AAV and demonstrate the therapeutic potential of dietary interventions. Furthermore, research into the protective role of Tregs has shed light on potential new targets for therapeutic interventions. Innovative approaches, such as CAR-T cell therapy and Deoxy Mab DX-1/DX-3, show significant promise in mitigating AAV pathology. These advancements underscore the transformative potential of translational research. By enhancing our understanding of disease mechanisms, these findings pave the way for the development of personalized and effective therapies, ultimately enhancing patient outcomes.}, }
@article {pmid40071205, year = {2025}, author = {Park, J and Park, T}, title = {Composite quantile regression approach to batch effect correction in microbiome data.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1484183}, doi = {10.3389/fmicb.2025.1484183}, pmid = {40071205}, issn = {1664-302X}, abstract = {BACKGROUND: Batch effects refer to data variations that arise from non-biological factors such as experimental conditions, equipment, and external factors. These effects are considered significant issues in the analysis of biological data since they can compromise data consistency and distort actual biological differences, which can severely skew the results of downstream analyses.<br><br>METHOD: In this study, we introduce a new approach that comprehensively addresses two types of batch effects: "systematic batch effects" which are consistent across all samples in a batch, and "nonsystematic batch effects" which vary depending on the variability of operational taxonomic units (OTUs) within each sample in the same batch. To address systematic batch effects, we apply a negative binomial regression model and correct for consistent batch influences by excluding fixed batch effects. Additionally, to handle nonsystematic batch effects, we employ composite quantile regression. By adjusting the distribution of OTUs to be similar based on a reference batch selected using the Kruskal-Walis test method, we consider the variability at the OTU level.<br><br>RESULTS: The performance of the model is evaluated and compared with existing methods using PERMANOVA R-squared values, Principal Coordinates Analysis (PCoA) plots and Average Silhouette Coefficient calculated with diverse distance-based metrics. The model is applied to three real microbiome datasets: Metagenomic urine control data, Human Immunodeficiency Virus Re-analysis Consortium data, and Men and Women Offering Understanding of Throat HPV study data. The results demonstrate that the model effectively corrects for batch effects across all datasets.}, }
@article {pmid40071093, year = {2025}, author = {Fang, P and Yang, J and Zhang, H and Shuai, D and Li, M and Chen, L and Liu, L}, title = {Emerging roles of intratumoral microbiota: a key to novel cancer therapies.}, journal = {Frontiers in oncology}, volume = {15}, number = {}, pages = {1506577}, doi = {10.3389/fonc.2025.1506577}, pmid = {40071093}, issn = {2234-943X}, abstract = {Microorganisms, including bacteria, viruses, and fungi, have been found to play critical roles in tumor microenvironments. Due to their low biomass and other obstacles, the presence of intratumor microbes has been challenging to definitively establish. However, advances in biotechnology have enabled researchers to reveal the association between intratumor microbiota and cancer. Recent studies have shown that tumor tissues, once thought to be sterile, actually contain various microorganisms. Disrupted mucosal barriers and adjacent normal tissues are important sources of intratumor microbiota. Additionally, microbes can invade tumors by traveling through the bloodstream to the tumor site and infiltrating through damaged blood vessels. These intratumor microbiota may promote the initiation and progression of cancers by inducing genomic instability and mutations, affecting epigenetic modifications, activating oncogenic pathways, and promoting inflammatory responses. This review summarizes the latest advancements in this field, including techniques and methods for identifying and culturing intratumor microbiota, their potential sources, functions, and roles in the efficacy of immunotherapy. It explores the relationship between gut microbiota and intratumor microbiota in cancer patients, and whether altering gut microbiota might influence the characteristics of intratumor microbiota and the host immune microenvironment. Additionally, the review discusses the prospects and limitations of utilizing intratumor microbiota in antitumor immunotherapy.}, }
@article {pmid40070644, year = {2025}, author = {Flores, R and Calvo, PA and Antunes, C and Duarte, R and Lérias, G}, title = {Ruminococcus gnavus Bacteremia in a SARS-CoV-2 Patient With Diverticulosis.}, journal = {Cureus}, volume = {17}, number = {2}, pages = {e78784}, doi = {10.7759/cureus.78784}, pmid = {40070644}, issn = {2168-8184}, abstract = {Ruminococcus gnavus is a constituent of the human intestinal microbiota, found in the commensal flora of healthy individuals. Changes in the intestinal microflora associated with chronic conditions and immunosuppression promote the bacterial translocation of R. gnavus. We present a case of bacteremia due to R. gnavus in an elderly man with multiple comorbidities, including diverticular disease and moderate SARS-CoV-2 infection requiring corticosteroid therapy. He had a prolonged hospital stay and multiple infectious complications. According to the literature review in databases such as PubMed (the last search was conducted in August 2023), a total of 17 cases were described. The reported cases had in common gastrointestinal symptoms such as gastrointestinal bleeding, diverticular disease, ulcerative colitis, cholecystitis, gastrointestinal fistula, or infection due to an orthopedic prosthesis. There was also a case in a patient with hemato-oncological disease, previously treated with a cycle of corticosteroids. It was considered that, alongside the history of diverticular disease, the immunosuppression secondary to the corticosteroid therapy for the SARS-CoV-2 infection may have contributed to the imbalance of the intestinal microbiome, leading to the occurrence of bacteremia due to this commensal agent.}, }
@article {pmid40070156, year = {2025}, author = {Vilarrasa, J and Pereira Couto, C and Àlvarez, G and Carrió, N and Gil, J and Blanc, V and Nart, J}, title = {Microbiological, Inflammatory and Clinical Outcome of Citric Acid Passivated Definitive Abutments: Interim 12-Month Results From a Randomised Controlled Clinical Trial.}, journal = {Journal of clinical periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jcpe.14146}, pmid = {40070156}, issn = {1600-051X}, support = {//Klockner Implant System/ ; }, abstract = {AIM: To assess the efficacy of citric acid passivation on implant abutments by evaluating their impact on bacterial load, microbiome composition, inflammatory response, and clinical and radiographic outcomes compared with control abutments over a 12-month follow-up period.<br><br>METHODS: Implants were placed subcrestally in the posterior sextants and randomly assigned to receive a 2-mm high definitive abutment, either with citric acid passivation (CA group) or without (CTR group). Final restorations were delivered after 12&#x2009;weeks. Samples of the peri-implant crevicular fluid were collected at 3, 6 and 12&#x2009;months for microbiological and inflammatory analysis. Clinical and radiographic measurements were also performed at these intervals. The primary outcome was total bacterial quantification (log CFU/mL).<br><br>RESULTS: Data from 17 patients in the CA group and 16 in the CTR group were analysed. At 12&#x2009;months, there were no significant&#xa0;differences in total bacterial load between groups (p&#x2009;=&#x2009;0.689). The biofilm was predominantly composed of commensal bacterial genera in both groups throughout the study period. Although no significant differences were observed&#xa0;in the microbiome alpha- and beta-diversity (p&#x2009;>&#x2009;0.05), the microbiome within study time points showed an increased beta-diversity in the CA group at 12&#x2009;months (p&#x2009;=&#x2009;0.019). CA abutments also showed a higher differential abundance of peri-implant pathogenic bacterial genera at 12&#x2009;months. At the 6-month mark, the CA group exhibited a trend toward lower IL-1&#x3b2; levels compared with the CTR group (p&#x2009;=&#x2009;0.072). No significant differences were noted in other clinical or radiographic parameters.<br><br>CONCLUSIONS: Citric acid passivation of definitive abutments does not enhance the microbiological or inflammatory profiles in the short term. Further studies are needed to explore the potential benefits of citric acid passivation on implant abutments.<br><br>TRIAL REGISTRATION: Initially registered on clinicatrials.gov (NCT05592327).}, }
@article {pmid40069904, year = {2025}, author = {Aguado-Norese, C and Maldonado, JE and Hodar, C and Galvez, G and Palma, DE and Cambiazo, V and Gonzalez, M}, title = {Ironing out the conflicts: iron supplementation reduces negatives bacterial interactions in the rhizosphere of an Atacama-endemic perennial grass.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {29}, pmid = {40069904}, issn = {2524-6372}, support = {CN2021-044//Agencia Nacional de Investigaci&#xf3;n y Desarrollo (ANID)/ ; 1241424//ANID | Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico (FONDECYT)/ ; 1211893//ANID | Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico (FONDECYT)/ ; }, abstract = {BACKGROUND: In plants, root exudates selectively influence the growth of bacteria that colonize the rhizosphere. Bacterial communities associated with root systems are involved in macro and micronutrients cycling and organic matter transformation. In particular, iron is an essential micronutrient required for the proper functioning of iron-containing enzymes in processes such as photosynthesis, respiration, biomolecule synthesis, redox homeostasis, and cell growth in plants. However, the impact of changes of iron availability on the structure and set of ecological interactions taking place in the rhizosphere remains poorly understood. In this study, field experiments were conducted to compare the effects of iron supplementation (0.1 and 0.5 mM of FeSO4) on the assembly of the bacterial community of rhizosphere soil and bulk soil in a perennial grass present in the Andes steppe of Atacama Desert.<br><br>RESULTS: The results indicated that the difference in beta diversity between bulk soil and rhizosphere soil detected before supplementation did not persist after iron supplementation, in addition, co-occurrence networks showed a significant reduction in negative interactions among soil bacteria, mainly in rare taxa (<&#x2009;0.1% relative abundance).<br><br>CONCLUSIONS: These observations suggest that iron availability contributes to the differentiation between bulk soil and rhizosphere bacterial communities, a process that is linked to significant changes in the relative abundance of more abundant species (>&#x2009;0.1% relative abundance) and with a decrease in the negative interactions in both compartments after metal exposure. The differential effect of iron on the competition/cooperation ratio between bulk soils and the rhizosphere microbiome supports the hypothesis that the host limits the degree of cooperation that can be achieved by the bacterial community associated with an organ dedicated to nutrient absorption.}, }
@article {pmid40069800, year = {2025}, author = {Zhu, LT and Zhao, L and Zhu, Y and Xu, XL and Lin, JJ and Duan, YF and Long, L and Wu, YY and Xu, WJ and Chen, JY and Yin, YH and Obeten, AU and Huang, Q}, title = {Disruption and adaptation: infant gut microbiota's dynamic response to SARS-CoV-2 infection.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {72}, pmid = {40069800}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *COVID-19/microbiology ; Infant ; *SARS-CoV-2/genetics ; Adaptation, Physiological ; Longitudinal Studies ; Bacteria/classification/genetics ; }, abstract = {BACKGROUND: The responses of the infant gut microbiota to infection significantly disrupt the natural intrahost evolutionary processes of the microbiome. Here, we collected a 16-month longitudinal cohort of infant gut microbiomes affected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Then, we developed a multicriteria approach to identify core interaction network driving community dynamics under environmental disturbances, which we termed the Conserved Variated Interaction Group (CVIgroup).<br><br>RESULTS: The CVIgroup showed significant advantages on pinpointing a sparse set associated with the disturbances, as validated both our own and publicly available datasets. Leveraging the Oxford Nanopore Technology, we found this group facilitates the ecosystem's adaptation to environmental disruptions by enhancing the mobility of mobile genetic elements, including the reinforcement of the twin-arginine translocation pathway in response to increased virulence factors. Furthermore, the CVIgroup serves as an effective indicator of ecosystem health. The timescale for the gut microbiota's adaptation extends beyond 10&#xa0;months. Members of the CVIgroup, such as Bacteroides thetaiotaomicron and Faecalibacterium, exhibit varying degrees of genomic structural variants, which contribute to guiding the community toward a new stable state rather than returning to its original configuration.<br><br>CONCLUSIONS: Collectively, the CVIgroup offers a snapshot of the gut microbiota's adaptive response to environmental disturbances. The disruption and subsequent adaptation of the gut microbiota in infants after COVID-19 infection underscores the necessity of re-evaluating reference standards in the context of the post-pandemic era. Video Abstract.}, }
@article {pmid40069605, year = {2025}, author = {Zhang, H and Wang, Y and Luo, Z and Zhang, B and Lan, X and Xu, L and Li, X and Huang, Z and Bai, J and Hu, D}, title = {Gut microbiome reveals the trophic variation and significant adaption of three sympatric forest-dwelling ungulates on the eastern Qinghai-Xizang Plateau.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {128}, pmid = {40069605}, issn = {1471-2180}, support = {YC-20018//Zhangzhou Pientzehuang Pharmaceutical Co., Ltd./ ; 2023I0046//Supported by Science and Technology Planning Project of Fujian Province, China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; China ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Phylogeny ; Forests ; Metagenomics ; Sympatry ; Adaptation, Physiological ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Ruminants/microbiology ; }, abstract = {BACKGROUND: The gut microbiome of herbivorous mammals regulates numerous physiological processes, including digestion and energy metabolism. The complex stomach architecture of ruminants, in conjunction with the metabolic capabilities of their microbiota, confers a considerable adaptive advantage to these animals. Nevertheless, a significant gap persists in comparative studies on the variations in the gut microbiome among sympatric ruminants and their potential adaptive implications. Accordingly, in this study, 16S rRNA gene sequencing and metagenomic approaches were used to analyse the composition and functional attributes of the gut microbiome of sympatric Moschus chrysogaster, Capricornis sumatraensis, and Cervus albirostris inhabiting the eastern periphery of the Qinghai-Xizang Plateau.<br><br>RESULTS: The gut microbiome of C. albirostris exhibited a higher diversity than that of M. chrysogaster and C. sumatraensis, whereas those of M. chrysogaster and C. sumatraensis were similar. Although species-specific variations existed among the three mammalian microbiomes, the microbiomes of C. albirostris and C. sumatraensis were more similar, whereas that of M. chrysogaster was markedly distinct. Metagenomic analysis revealed a pattern of functional convergence in the gut microbiome of the three species, with the gut microbiome of C. albirostris exhibiting a pronounced emphasis on carbohydrate metabolism, significantly surpassing that of M. chrysogaster and C. sumatraensis. Compared to the other two species, the gut microbiome of C. sumatraensis presented significantly elevated levels of amino acids and energy metabolism, whereas that of M. chrysogaster presented an increased capacity for 3-hydroxyacyl- [acyl carrier protein]-dehydratase production.<br><br>CONCLUSION: These findings suggest that the gut microbiome of sympatric M. chrysogaster, C. sumatraensis, and C. albirostris tend to converge. Metabolic variations within their gut microbiome may result in differential food resource utilisation, potentially indicating significant nutritional and ecological trait characteristics for stable coexistence.}, }
@article {pmid40069468, year = {2025}, author = {Yang, Y and Meng, Y and Xu, Z and Zhang, Q and Li, M and Kong, F and Zhang, S and Li, X and Zhu, Y}, title = {Leveraging microbiome signatures to predict tumor immune microenvironment and prognosis of patients with endometrial carcinoma.}, journal = {Discover oncology}, volume = {16}, number = {1}, pages = {299}, pmid = {40069468}, issn = {2730-6011}, support = {20214Y0226//Shanghai Municipal Health Commission/ ; 2024CRTS045//Sunshine Clinical Research Incubator Program/ ; 2024CRTS017//Sunshine Clinical Research Incubator Program/ ; 2024CRTS015//Sunshine Clinical Research Incubator Program/ ; }, abstract = {Recent studies suggest that the human microbiome influence tumor development. Endometrial carcinoma (EC) is the sixth most common malignancy in women. Recent research has demonstrated the microbes play a critical role in the development and metastasis of EC. However, it remains unclear whether intratumoral microbes are associated with tumor microenvironment (TME) and prognosis of EC. In this study, we collected the EC microbiome data from cBioPortal and constructed a prognostic model based on Resident Microbiome of Endometrium (RME). We then examined the relationship between the RME score, immune cell infiltration, immunotherapy-related signature, and prognosis. The findings demonstrated the independent prognostic value of the RME score for EC. The group with low RME scores had higher enrichment of immune cells. Drug sensitivity analysis revealed that the RME score may serve as a potential predictor of chemotherapy efficacy. In conclusion, our research offers new perspectives on the relationships between tumor immunity and microbes.}, }
@article {pmid40069438, year = {2025}, author = {Park, M and Jung, J and Lee, JA and Lee, E and Lee, H and Eom, HS and Park, HJ}, title = {Understanding gut Microbiome changes in Korean children, adolescents, and young adults with hematologic malignancies.}, journal = {Annals of hematology}, volume = {}, number = {}, pages = {}, pmid = {40069438}, issn = {1432-0584}, support = {2011500-1//National Cancer Center, Korea/ ; }, abstract = {We investigated whether changes in the gut microbiome composition are associated with infections and immunologic complications during the treatment of Korean children, adolescents, and young adults (AYAs) with hematologic malignancies. We analyzed stool samples from 26 patients and 10 healthy siblings using 16 S rRNA gene sequencing. At diagnosis, patients exhibited a lower abundance of Lachnospiraceae and a higher abundance of Enterococcaceae than their healthy siblings. Both the Chao1 and Shannon diversity indices declined from diagnosis to the end of induction chemotherapy. Patients with fever during induction had a lower baseline microbial diversity and higher Ruminococcus g4 abundance than those without fever. The use of either meropenem or piperacillin/tazobactam during induction was correlated with reduced richness and altered composition of the gut microbiome after induction. The Chao index and beta diversity of stool samples significantly differed before conditioning when compared with those of healthy siblings. During allogeneic hematopoietic stem cell transplantation, both the Chao1 and Shannon diversity indices significantly decreased on day 14 but recovered by day 60. Our study highlights the role of gut microbiome diversity and compositional structure in influencing treatment outcomes in children and AYA with hematologic malignancies, providing the information required to improve the gut microbiome configuration and treatment outcomes.}, }
@article {pmid40069378, year = {2025}, author = {Gulyaeva, K and Nadinskaia, M and Maslennikov, R and Aleshina, Y and Goptar, I and Lukashev, A and Poluektova, E and Ivashkin, V}, title = {Gut microbiota analysis in cirrhosis and non-cirrhotic portal hypertension suggests that portal hypertension can be main factor of cirrhosis-specific dysbiosis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8394}, pmid = {40069378}, issn = {2045-2322}, support = {123021000156-7//Ministry of Health/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Male ; Female ; *Hypertension, Portal/microbiology ; *Liver Cirrhosis/microbiology/complications ; Middle Aged ; Cross-Sectional Studies ; *RNA, Ribosomal, 16S/genetics ; Adult ; Aged ; Feces/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Case-Control Studies ; }, abstract = {Gut dysbiosis plays an important role in cirrhosis, but the mechanism of its development was not established. The aim of the study was to test the hypothesis that portal hypertension can be the main factor in the development of gut dysbiosis in cirrhosis. This cross-sectional study included 25 patients with chronic non-cirrhotic portal hypertension due to extrahepatic portal vein obstruction after portal vein thrombosis (PVT) (NCPVT group), 29 cirrhotic patients without PVT (CirNoPVT), 15 cirrhotic patients with chronic PVT (CPVT), and 22 healthy controls. The fecal microbiota was assessed using 16S rRNA gene sequencing. The CirNoPVT and CPVT groups had largely similar differences in gut microbiota composition from the control group. Patients with NCPVT, as well as patients with cirrhosis, had a higher abundance of Streptococcus, Escherichia, Enterococcus, Enterobacteriaceae, Enterococcaceae, Streptococcaceae, Bacilli, Gammaproteobacteria, Proteobacteria, and a lower abundance of Roseburia, Faecalibacterium, Methanobrevibacter, Ruminococcaceae, Methanobacteriaceae, Clostridia, Methanobacteria, and Euryarchaeota as they were compared with healthy individuals. Patients with NCPVT had a higher abundance of Bifidobacterium, Bifidobacteriaceae, Actinobacteria, and a lower abundance of Gemmiger and Catenibacterium compared to healthy individuals, which was not observed in the cirrhosis groups. The abundance of Porphyromonadaceae with the genus Parabacteroides was reduced in both groups with PVT, but not in CirNoPVT. There were no significant differences in gut microbiota beta-diversity among the CirNoPVT, CPVT and NCPVT groups. All these groups had significant differences in beta-diversity from the control group. Portal hypertension seems be the main factor in the development of gut dysbiosis in cirrhosis.}, }
@article {pmid40069167, year = {2025}, author = {Katona, BW and Shukla, A and Hu, W and Nyul, T and Dudzik, C and Arvanitis, A and Clay, D and Dungan, M and Weber, M and Tu, V and Hao, F and Gan, S and Chau, L and Buchner, AM and Falk, GW and Jaffe, DL and Ginsberg, G and Palmer, SN and Zhan, X and Patterson, AD and Bittinger, K and Ni, J}, title = {Microbiota and metabolite-based prediction tool for colonic polyposis with and without a known genetic driver.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2474141}, doi = {10.1080/19490976.2025.2474141}, pmid = {40069167}, issn = {1949-0984}, mesh = {Humans ; Male ; Middle Aged ; Female ; *Gastrointestinal Microbiome ; Adult ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology/chemistry ; Adenomatous Polyposis Coli/microbiology/genetics ; Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Colonic Polyps/microbiology/genetics/pathology ; Aged ; Colon/microbiology/pathology/metabolism ; Metabolome ; }, abstract = {Despite extensive investigations into the microbiome and metabolome changes associated with colon polyps and colorectal cancer (CRC), the microbiome and metabolome profiles of individuals with colonic polyposis, including those with (Gene-pos) and without (Gene-neg) a known genetic driver, remain comparatively unexplored. Using colon biopsies, polyps, and stool from patients with Gene-pos adenomatous polyposis (N = 9), Gene-neg adenomatous polyposis (N = 18), and serrated polyposis syndrome (SPS, N = 11), we demonstrated through 16S rRNA sequencing that the mucosa-associated microbiota in individuals with colonic polyposis is representative of the microbiota associated with small polyps, and that both Gene-pos and SPS cohorts exhibit differential microbiota populations relative to Gene-neg polyposis cohorts. Furthermore, we used these differential microbiota taxa to perform linear discriminant analysis to differentiate Gene-neg subjects from Gene-pos and from SPS subjects with an accuracy of 89% and 93% respectively. Stool metabolites were quantified via [1]H NMR, revealing an increase in alanine in SPS subjects relative to non-polyposis subjects, and Partial Least Squares Discriminant Analysis (PLS-DA) analysis indicated that the proportion of leucine to tyrosine in fecal samples may be predictive of SPS. Use of these microbial and metabolomic signatures may allow for better diagnostric and risk-stratification tools for colonic polyposis patients and their families as well as promote development of microbiome-targeted approaches for polyp prevention.}, }
@article {pmid40069139, year = {2025}, author = {Vogtmann, E and Yano, Y and Zouiouich, S and Hua, X and Wan, Y and Purandare, V and Li, S and Dagnall, CL and Jones, K and Hicks, BD and Hutchinson, A and Caporaso, JG and Wheeler, W and Huang, WY and Freedman, ND and Sandler, DP and Beane Freeman, LE and Liao, LM and Gail, MH and Shi, J and Abnet, CC and Sinha, R}, title = {The human oral microbiome and risk of colorectal cancer within three prospective cohort studies in the United States.}, journal = {Cancer}, volume = {131}, number = {6}, pages = {e35802}, doi = {10.1002/cncr.35802}, pmid = {40069139}, issn = {1097-0142}, support = {/NH/NIH HHS/United States ; Z01-ES049030/ES/NIEHS NIH HHS/United States ; 1U24CA248454-01/CA/NCI NIH HHS/United States ; Z01-CP010119/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/epidemiology ; Male ; Female ; Prospective Studies ; Middle Aged ; United States/epidemiology ; Aged ; *Microbiota ; Mouth/microbiology ; Risk Factors ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Oral microbes detected in feces have been associated with colorectal cancer (CRC) in cross-sectional studies. This study investigated the prospective associations between the oral microbiome and incident CRC in the Agricultural Health Study (AHS), National Institutes of Health-AARP (NIH-AARP) Diet and Health Study, and Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial.<br><br>METHODS: Individuals with oral samples collected before incident CRC diagnoses were identified in the AHS (N&#xa0;=&#xa0;331), NIH-AARP (N&#xa0;=&#xa0;249), and PLCO (N&#xa0;=&#xa0;446) and compared with referent subcohorts (N&#xa0;=&#xa0;3431). The V4 region of the 16S ribosomal RNA gene was sequenced from oral wash DNA, and the data were processed with QIIME2. Hazard ratios (HRs) and 95% confidence intervals (CIs) for overall CRC and by anatomic subsite (i.e., proximal colon, distal colon, and rectum) were estimated with Cox proportional hazards models with adjustment for potential confounders by cohort and then meta-analyzed.<br><br>RESULTS: Overall, no associations were found between microbial characteristics and CRC risk. However, associations were observed with alpha and beta diversity indices and individual genera in analyses stratified by anatomic subsite. For instance, the presence of Olsenella was strongly positively associated with distal colon cancer risk (HR, 2.16; 95% CI, 1.59-2.95), whereas the presence of Prevotella 2 was positively associated with rectal cancer risk (HR, 1.68; 95% CI, 1.14-2.46).<br><br>CONCLUSIONS: This large study of the prospective association between the oral microbiome and CRC risk showed numerous site-specific associations, including multiple associations with distal colon and rectal cancer risk.}, }
@article {pmid40069023, year = {2025}, author = {Lechien, JR}, title = {Dysbiosis Patterns in Glottic and Laryngeal Cancers: A Systematic Review of Microbiome Alterations.}, journal = {Journal of voice : official journal of the Voice Foundation}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jvoice.2025.02.036}, pmid = {40069023}, issn = {1873-4588}, abstract = {BACKGROUND: This systematic review summarized current evidence regarding the role of upper aerodigestive tract microbiomes (UAM) in laryngeal squamous cell carcinoma (LSCC) development, progression, clinical, and oncological outcomes.<br><br>METHODS: Two investigators systematically search PubMed, Scopus, and Cochrane Library databases for studies investigating microbiome characteristics, mechanistic roles, and associations with clinical and oncological outcomes in LSCC according to the Preferred Reporting Items For A Systematic Review And Meta-analysis statements. The bias analysis was conducted with the methodological index for nonrandomized studies.<br><br>RESULTS: Ten studies were included, accounting for 491 LSCC patients. LSCC tissues demonstrated lower bacterial diversity compared with controls. Taxonomic analyses suggested an overrepresentation of Bacteroidetes (Prevotella) and Fusobacteriota (Fusobacterium) in LSCC, while Firmicutes (Stomatobaculum longum, Abiotrophia, Gemella, and&#xa0;Streptococcus) and Actinobacteria (Actinomyces, Corynebacterium, and&#xa0;Rothia mucilaginosa) were predominant in control tissues. Firmicutes demonstrated the largest compositional variation across studies, with 30.9%-63.6% abundance in LSCC compared with 13.9%-32% in controls. Two studies explored microbiome signatures: one for LSCC diagnosis and another for prognosis. Substantial methodological heterogeneity was observed across studies regarding confounding factor analysis, UAM assessment protocols, and control tissue selection.<br><br>CONCLUSION: The current literature supports potential distinct UAM signatures between LSCC and noncancerous tissues, with Bacteroidetes and Fusobacteriota enriched in LSCC tissues. Although emerging evidence supporting the key role of UAM in the development of LSCC, substantial methodological heterogeneity across studies necessitates standardized protocols for future investigations.}, }
@article {pmid40068937, year = {2025}, author = {Da-Anoy, J and Toyama, K and Jasnos, O and Wong, A and Gilmore, TD and Davies, SW}, title = {Microbial Depletion is Associated with Slower Cnidarian Regeneration.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icaf007}, pmid = {40068937}, issn = {1557-7023}, abstract = {Microbiomes play an important role in physiology and development in cnidarians, but how these communities influence tissue regeneration is poorly understood. Here, we examined the effects of antibiotic exposure on regeneration and microbial communities in two cnidarian models, the sea anemones Nematostella vectensis (non-symbiotic, hereafter, Nematostella) and Exaiptasia diaphana (symbiotic, hereafter, Aiptasia). Bisected animals were incubated in either sterile or antibiotic-treated artificial seawater for seven days and regeneration was monitored daily. After seven days, tentacle number and length were measured, and microbial communities were profiled using metabarcoding of the V4 region of the 16S rRNA. Microbiome disruption was observed under antibiotic treatment in both species, resulting in decreased microbial load and shifts in relative abundances of certain microbial taxa. Nematostella exhibited a greater reduction in microbial diversity and community shifts under antibiotic exposure, whereas Aiptasia showed only moderate changes in diversity. In both species, microbiome disruption was associated with slower regeneration rates and reduced tentacle number and length, suggesting a functional role for the microbiome in anemone regeneration. Our findings suggest that host-microbiome interactions in both symbiotic and aposymbiotic anemones are important for the maintenance of regenerative processes. These findings provide insight into how cnidarians and their microbiomes respond to environmental stressors, with implications for predicting cnidarian resilience in the context of emerging threats to the marine environment.}, }
@article {pmid40068788, year = {2025}, author = {Palm, CL and de Wit, S and Gorter, TM and Rienstra, M and Vos, MJ and Kema, IP and van der Ley, CP and Bakker, SJL and Bakker, BM and de Boer, RA and van Veldhuisen, DJ and Meijers, WC and Westenbrink, BD}, title = {Beyond the gut: Systemic levels of short-chain fatty acids are altered in patients with heart failure.}, journal = {International journal of cardiology}, volume = {}, number = {}, pages = {133124}, doi = {10.1016/j.ijcard.2025.133124}, pmid = {40068788}, issn = {1874-1754}, abstract = {BACKGROUND &amp; AIM: The gut microbiome produces short-chain fatty acids (SCFAs), which serve as a substantial energy source and provide a link between the microbiome and (cardiac) metabolism. It has been demonstrated that the composition of the microbiome is altered in patients with heart failure (HF), but whether circulating levels of SCFAs are altered in HF is unknown.<br><br>METHODS &amp; RESULTS: Serum concentrations of the SCFAs acetate, propionate, and butyrate were measured in 205 patients with HF and in 54 healthy controls, using isotope dilution liquid chromatography-tandem mass spectrometry. Of the patients with HF, 99 had HF with a reduced ejection fraction (HFrEF) and 106 had HF with mildly-reduced or preserved ejection fraction (HFmrEF/HFpEF). Healthy controls were age and sex matched to the HFrEF patients. Serum concentrations of acetate and propionate were significantly lower in patients with HF than in healthy controls, whereas butyrate levels were higher in patients with HF. Analyses by HF type revealed that acetate and propionate levels were lower in both HFrEF and HFpEF/HFmrEF patients in comparison to healthy controls. However, butyrate levels were observed to be lower in patients with HFmrEF/HFpEF in comparison to healthy controls, while they were higher in patients with HFrEF.<br><br>CONCLUSIONS: In patients with HF, serum levels of acetate and propionate are lower across the HF spectrum, whereas serum butyrate levels are elevated in HFrEF, but lower in HFmrEF/HFpEF. These alterations in SCFA profiles suggest a microbiome-driven metabolic dysregulation, which appears to differ between HF subtypes.}, }
@article {pmid40068681, year = {2025}, author = {Shiver, AL and Sun, J and Culver, R and Violette, A and Wynter, C and Nieckarz, M and Mattiello, SP and Sekhon, PK and Bottacini, F and Friess, L and Carlson, HK and Wong, DPGH and Higginbottom, S and Weglarz, M and Wang, W and Knapp, BD and Guiberson, E and Sanchez, J and Huang, PH and Garcia, PA and Buie, CR and Good, BH and DeFelice, B and Cava, F and Scaria, J and Sonnenburg, JL and Van Sinderen, D and Deutschbauer, AM and Huang, KC}, title = {Genome-scale resources in the infant gut symbiont Bifidobacterium breve reveal genetic determinants of colonization and host-microbe interactions.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2025.02.010}, pmid = {40068681}, issn = {1097-4172}, abstract = {Bifidobacteria represent a dominant constituent of human gut microbiomes during infancy, influencing nutrition, immune development, and resistance to infection. Despite interest in bifidobacteria as a live biotic therapy, our understanding of colonization, host-microbe interactions, and the health-promoting effects of bifidobacteria is limited. To address these major knowledge gaps, we used a large-scale genetic approach to create a mutant fitness compendium in Bifidobacterium breve. First, we generated a high-density randomly barcoded transposon insertion pool and used it to determine fitness requirements during colonization of germ-free mice and chickens with multiple diets and in response to hundreds of in vitro perturbations. Second, to enable mechanistic investigation, we constructed an ordered collection of insertion strains covering 1,462 genes. We leveraged these tools to reveal community- and diet-specific requirements for colonization and to connect the production of immunomodulatory molecules to growth benefits. These resources will catalyze future investigations of this important beneficial microbe.}, }
@article {pmid40068292, year = {2025}, author = {Liu, HX and Yang, MK and Li, YC and Liu, CX and Li, GP and Meng, XL and Pei, K and Wen, SY}, title = {Shenqi granules enhance recovery from cerebral ischemia-reperfusion injury by modulating tryptophan and tyrosine metabolism and activating NFE2L2/NRF2.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {140}, number = {}, pages = {156623}, doi = {10.1016/j.phymed.2025.156623}, pmid = {40068292}, issn = {1618-095X}, abstract = {BACKGROUND: Stroke is a multifaceted physiological event linked to imbalances in gut microbiota and disruptions in metabolic pathways. Traditional Chinese medicines, leveraging the gut-brain axis, have been shown to significantly ameliorate ischemic stroke. However, the specific role and molecular mechanism of Shenqi granules (SQF) in enhancing the recovery from ischemic stroke remain to be elucidated.<br><br>PURPOSE: This study aims to explore the therapeutic effects of SQF on rats with cerebral ischemia-reperfusion injury (CIRI) and its regulatory effects on the gut microbiota, providing a basis for the clinical rational use of drugs in ischemic stroke.<br><br>METHODS: The study conducted a comprehensive biological assessment of SQF's role in improving CIRI at the whole-animal level. Subsequently, Weighted Gene Co-expression Network Analysis (WGCNA) and network pharmacology analysis were used for component analysis and target prediction. Then, the therapeutic targets of SQF were further validated through molecular docking and molecular experiments. Finally, an integrated omics approach combining fecal untargeted metabolome and 16S rRNA sequencing was employed to state the anti-CIRI effects of SQF and its potential mechanisms.<br><br>RESULTS: SQF alleviates cerebral infarct volume and improves cognitive functions in MCAO rats. Network pharmacology analysis shows 20 potential active ingredients of SQF could target 13 target proteins. Further employing WGCNA, our study identified four key targets of SQF in the treatment of ischemic stroke. Based on molecular docking and molecular experiments, SQF improves CIRI by activating NFE2L2/NRF2. Serum metabolomics analysis identified six metabolites related to the tryptophan and tyrosine metabolic pathways, which interact with NFE2L2/NRF2 protein. Fecal metabolome and microbiome reveal that SQF's protective effect on CIRI is linked to the tryptophan metabolism and tyrosine metabolism and gut microbiome modulation. In particular, metabolites related to tryptophan and tyrosine metabolism, such as kynurenic acid and dopamine, may exert their protective effects by interacting with NFE2L2/NRF2.<br><br>CONCLUSION: This pioneering study unveils the therapeutic potential of SQF in addressing CIRI, highlighting the pivotal role of NFE2L2/NRF2 upregulation in its mechanism of action. Furthermore, SQF demonstrates its efficacy in restoring gut microbiota balance by modulating the metabolism of tryptophan and tyrosine in CIRI. By elucidating the intricate interplay among constituents, targets, metabolites, and gut microbiota, this research offers novel insights into the multifaceted mechanisms underlying SQF's therapeutic impact on CIRI.}, }
@article {pmid40068150, year = {2025}, author = {Li, G and Cheng, Y and Yang, X and Chai, Z and Mu, Z and Chao, H and Li, H and Qi, Y and Qi, L and Liu, J}, title = {Integrated gut microbiota and serum metabolomics reveal glyphosate-induced hepatic injury in mice.}, journal = {Human &amp; experimental toxicology}, volume = {44}, number = {}, pages = {9603271251326877}, doi = {10.1177/09603271251326877}, pmid = {40068150}, issn = {1477-0903}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Glyphosate ; *Chemical and Drug Induced Liver Injury/blood ; *Glycine/analogs &amp; derivatives/toxicity ; Mice ; Male ; *Herbicides/toxicity ; *Metabolomics ; Liver/drug effects/metabolism ; Pyrimidines/toxicity ; Pentose Phosphate Pathway/drug effects ; }, abstract = {IntroductionGlyphosate (GLP) is one of the most widely used herbicides in the world. However, its underlying effects on the liver remain unclear. This study aims to investigate the toxic effects and the gut microbiome- and serum metabolite-related mechanisms of GLP on the liver in mice.Methods16S rDNA sequencing and UPLC-Q-TOF-MS/MS were used to investigate the mechanisms of GLP toxicity in mice administered with 0, 50, 250 and 500 mg/kg/day GLP for 30 days.ResultsGLP induced hepatocyte edema and ballooning as well as inflammatory cell infiltration. Exposure to GLP resulted in increased levels of serum ALT, TBIL, DBIL, and GLU. Microbiota analysis at the phylum level demonstrated that the proportions of Patescibacteria decreased in the GLP-treated group. The genus-level analysis identified 11 different genera, with eight decreased and three increased in the GLP-exposed group. Metabolomics analysis of serum showed 42 differential metabolites between the GLP and control groups. The metabolic pathway enrichment analysis revealed that the pentose phosphate pathway (PPP) and pyrimidine metabolism were significantly activated. Spearman analysis showed that the changes in the differential metabolites of the PPP and pyrimidine metabolism and gut microbiota were strongly associated with the biochemical index.DiscussionIn conclusion, GLP exposure induces hepatic injury through alterations in the gut microbiome and metabolic pathways, particularly by activating the pentose phosphate pathway and pyrimidine metabolism.}, }
@article {pmid40068044, year = {2025}, author = {Xu, S and Yang, K and Qiu, J and Zhong, J and Xian, D}, title = {Bidirectional causal relationships between the skin microbiome and psoriasis: Insights from Mendelian randomization analysis.}, journal = {Medicine}, volume = {104}, number = {10}, pages = {e41736}, doi = {10.1097/MD.0000000000041736}, pmid = {40068044}, issn = {1536-5964}, support = {2023XGZX001//Based on the extraction of SARS-CoV-2 infected body organ tissues Construction of Basic Human Tissue Resource Library/ ; }, mesh = {*Psoriasis/microbiology ; Humans ; *Mendelian Randomization Analysis ; *Microbiota ; *Skin/microbiology ; Genome-Wide Association Study ; Risk Factors ; Female ; Male ; Germany/epidemiology ; }, abstract = {Psoriasis is a chronic inflammatory skin disease affecting 2% of the global population. Recent research suggests the skin microbiome plays a critical role in psoriasis. Skin microbiome data were obtained from the KORA FF4 study in Germany, and psoriasis data from FinnGen genome-wide association study summary statistics. Forward and reverse 2-sample Mendelian randomization (MR) analyses were conducted to assess causal relationships. Forward MR analysis identified several microbial features as risk factors for psoriasis, including the family Neisseriaceae in sebaceous skin (OR = 1.036, 95% CI: 1.010-1.062, P = .0054), ASV011 in dry skin (OR = 1.024, 95% CI: 1.000-1.048, P = .0490), and the order Clostridiales in moist skin (OR = 1.016, 95% CI: 1.000-1.032, P = .0449). Protective features included ASV016 (OR = 0.972, 95% CI: 0.949-0.994, P = .0136) and ASV053 (OR = 0.973, 95% CI: 0.954-0.992, P = .0054) in dry skin. Reverse MR analysis confirmed psoriasis as a significant risk factor for changes in the skin microbiome, with notable associations in the dry skin region for asv002 (OR = 1.266, 95% CI: 1.061-1.510, P = .027) and genus: Haemophilus (OR = 1.364, 95% CI: 1.065-1.746, P = .013). This study reveals bidirectional causal relationships between the skin microbiome and psoriasis, highlighting specific microbial features such as Neisseriaceae and Clostridiales as potential risk factors. Further research is needed to develop treatments that modulate the skin microbiome to improve psoriasis outcomes.}, }
@article {pmid40067836, year = {2025}, author = {Zhang, Q and Li, Y and Han, Y and Zhou, W and Li, X and Sun, J and Bai, W}, title = {Lactiplantibacillus plantarum FEED8 Biosynthesis of Pyranoanthocyanin (Cyanidin-3-glucoside-4-vinylcatechol) Improves Oxidative Stress and Inflammation of the Gut Microbiome in Cadmium-Exposed Mice.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c01093}, pmid = {40067836}, issn = {1520-5118}, abstract = {The study is to explore the biosynthesis of cyanidin-3-glucoside-4-vinylcatechol (C3G_VC) through Lactiplantibacillus plantarum-fermented caffeic acid and cyanidin-3-glucoside (C3G) extract (molar ratio = 1:30) in the model medium. C3G_VC was isolated and purified by a venusil ASB-C18 column with a medium-pressure liquid chromatography (MPLC) system. The chemical structure of C3G_VC was identified by high-performance liquid chromatography (HPLC), which showed the maximum absorption wavelength of 505.57 nm. This study showed that Cd exposure of mice induced liver damage, oxidative stress, and inflammation of the gut microbiome. Our findings demonstrated that C3G_VC intervention in Cd-exposed mice significantly mitigated oxidative stress injury by declining the malondialdehyde (MDA) level and increasing the activity of superoxide dismutase (SOD) and glutathione peroxidase (GSH-PX) in the liver, meanwhile alleviating liver injury by decreasing the bile acid (BA) level and accelerating the excretion of fecal BA. Moreover, the Cd_C3G_VC group showed elevated levels of mRNA expression of pro-inflammatory cytokines (IL6, IL1β, and TNF-α) and inhibited BA synthesis (CYP7A1) in Cd-exposed mice. The fermentation results in vitro showed that C3G_VC had a higher residue than that of cyanidin-3-glucoside. The 16S rRNA high-throughput sequencing disclosed that C3G_VC intervention in Cd-exposed mice significantly increased the abundance of Faecalibaculum and unidentified_Lachnospiraceae. It is noteworthy that the C3G_VC supplement increased the abundance of Akkermansia. Overall, this study demonstrated that C3G_VC intervention in Cd-exposed mice had the potential to decrease the occurrence of inflammatory and oxidative stress and maintain bile acid homeostasis by regulating gut microflora.}, }
@article {pmid40067818, year = {2025}, author = {Han, X and Song, K}, title = {TphPMF: A microbiome data imputation method using hierarchical Bayesian Probabilistic Matrix Factorization.}, journal = {PLoS computational biology}, volume = {21}, number = {3}, pages = {e1012858}, doi = {10.1371/journal.pcbi.1012858}, pmid = {40067818}, issn = {1553-7358}, abstract = {In microbiome research, data sparsity represents a prevalent and formidable challenge. Sparse data not only compromises the accuracy of statistical analyses but also conceals critical biological relationships, thereby undermining the reliability of the conclusions. To tackle this issue, we introduce a machine learning approach for microbiome data imputation, termed TphPMF. This technique leverages Probabilistic Matrix Factorization, incorporating phylogenetic relationships among microorganisms to establish Bayesian prior distributions. These priors facilitate posterior predictions of potential non-biological zeros. We demonstrate that TphPMF outperforms existing microbiome data imputation methods in accurately recovering missing taxon abundances. Furthermore, TphPMF enhances the efficacy of certain differential abundance analysis methods in detecting differentially abundant (DA) taxa, particularly showing advantages when used in conjunction with DESeq2-phyloseq. Additionally, TphPMF significantly improves the precision of cross-predicting disease conditions in microbiome datasets pertaining to type 2 diabetes and colorectal cancer.}, }
@article {pmid40067563, year = {2025}, author = {Martin, WJ and Mirmozaffari, Y and Cook, LM and Benaim, EH and Monk, AS and Armstrong, M and Vuncannon, J and Klatt-Cromwell, C and Ebert, CS and Thorp, BD and Senior, BA and Raz Yarkoni, T and Kimple, AJ}, title = {The Role of the Environment and Occupational Exposures in Chronic Rhinosinusitis.}, journal = {Current allergy and asthma reports}, volume = {25}, number = {1}, pages = {16}, pmid = {40067563}, issn = {1534-6315}, support = {P30ES010126//National Institute of Environmental Health Sciences of the National Institutes of Health/ ; }, mesh = {*Sinusitis/etiology/immunology ; Humans ; *Rhinitis/etiology/immunology/epidemiology ; *Occupational Exposure/adverse effects ; Chronic Disease ; *Environmental Exposure/adverse effects ; Microbiota/immunology ; Tobacco Smoke Pollution/adverse effects ; Air Pollutants/adverse effects ; Microplastics/adverse effects ; Rhinosinusitis ; }, abstract = {PURPOSE OF REVIEW: The purpose of the review is to summarize the current literature and evaluate how different environmental exposures may contribute to the development and course of chronic rhinosinusitis (CRS). The review aims to explore the relationship between host factors and environmental exposures in the pathogenesis of CRS.<br><br>RECENT FINDINGS: Recent studies have helped establish the role of air pollutants, tobacco smoke, occupational exposures, and microplastics in the pathogenesis of CRS. These exposures have been shown to cause epithelial dysfunction and promote inflammation through different mechanisms and to different degrees. The pathogenesis of CRS is complex and multifactorial, with environmental exposures playing a key role in its onset and exacerbation. Research indicates that pollutants can damage the sinonasal epithelial barrier and disrupt the microbiome, leading to increased inflammation. A deeper understanding of the mechanisms behind this inflammatory process and its link to environmental exposures could enhance strategies for preventing and treating CRS.}, }
@article {pmid40067381, year = {2025}, author = {Jung, Y and Cho, YS}, title = {Gut Microbiota Differences Among Patients with Burns with Varied Pruritus Responses: A Case Report.}, journal = {Journal of burn care &amp; research : official publication of the American Burn Association}, volume = {}, number = {}, pages = {}, doi = {10.1093/jbcr/iraf029}, pmid = {40067381}, issn = {1559-0488}, abstract = {Pruritus-a common symptom in patients with burns- impairs the quality of life and contributes to anxiety and depression. Although the mechanisms underlying post-burn pruritus remain unclear, gut microbiome dysbiosis may affect systemic inflammation and drug responsiveness. This study analyzed the gut microbiome composition of six male patients (40-50 years old) with burns and categorized them into three groups based on pruritus outcomes-non-pruritus (NP, did not receive antihistamine), responder (R, pruritus reduced with antihistamine treatment), and non-responder (NR, pruritus persisted despite antihistamine treatment). Fecal samples were collected at baseline (week 0) and after eight weeks. The NP and R groups exhibited enhanced alpha diversity, increased Firmicutes/Bacteroidota (F/B) ratios, and reduced Proteobacteria over time, indicating microbiome recovery. In contrast, the NR group exhibited inconsistent results, with case 5 demonstrating reduced diversity and increased F/B and Proteobacteria, whereas case 6 exhibited increased diversity and decreased F/B and Proteobacteria. Faecalibacterium was absent in the NR group, whereas the relative abundance of unclassified Lachnospiraceae increased. This study highlights the potential effects of dysbiosis on pruritus outcomes and drug responsiveness in patients with burns. Future studies with larger cohorts are necessary to assess these findings and explore microbiome-targeted therapies to enhance treatment outcomes.}, }
@article {pmid40067377, year = {2025}, author = {Kemp, JA and Ribeiro, M and Borges, NA and Cardozo, L and Fouque, D and Mafra, D}, title = {Dietary Intake and Gut Microbiome in Chronic Kidney Disease.}, journal = {Clinical journal of the American Society of Nephrology : CJASN}, volume = {}, number = {}, pages = {}, doi = {10.2215/CJN.0000000705}, pmid = {40067377}, issn = {1555-905X}, abstract = {Gut dysbiosis, characterized by an imbalance in the gut microbiota, has emerged as a potential factor influencing chronic kidney disease (CKD) progression. This condition plays a crucial role in the gut-kidney axis, where changes in microbial composition can contribute to systemic inflammation and uremic toxin production and ultimately exacerbate kidney damage. Understanding the dynamics of the gut-kidney axis provides new insights into potential therapeutic strategies to mitigate CKD progression. Diet is the primary driver of gut microbiota composition. Therefore, an approach emphasizing healthy nutritional patterns is recommended for improving overall health, cardiovascular disease, and profoundly altered metabolic patterns in CKD patients. Dietary modifications have been explored as therapeutic strategies targeting the microbiome to improve outcomes in CKD. An emerging therapeutic target is the production of dysmetabolites by the gut microbiota, which may help alleviate uremic and cardiovascular toxicity. Additionally, future research should broaden the scope to include other microorganisms, such as fungi, archaea, and viruses. This expanded focus will enable a more comprehensive understanding of the gut-kidney axis and pave the way for more personalized and effective treatment strategies for CKD patients. This review explores the role of lifestyle, particularly diet, in kidney health, highlights new gut microbiome therapies, and identifies research opportunities in CKD.}, }
@article {pmid40066981, year = {2025}, author = {Velaz, M and Santesteban, LG and Torres, N}, title = {Mycorrhizae and grapevines: the known unknowns of their interaction for wine growers´ challenges.}, journal = {Journal of experimental botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/jxb/eraf081}, pmid = {40066981}, issn = {1460-2431}, abstract = {Arbuscular mycorrhizal fungi (AMF) play an important role in grapevine production systems. However, little is known about how this relationship is achieved in the nursery and how soil management might modify it and its derived benefits. Here, we review the current knowledge on the establishment of grapevine-AMF relationships from the nursery to the field, the main factors that affect the effectiveness of the symbiosis, the potential role of AMF as biostimulants in grapevine production systems, and the future perspectives of their use in the current context of climate change. The process of establishing mycorrhizal symbiosis is complex, and the molecular dialogue between the plant roots and the fungus is still not yet fully understood. During vine plant production, rooting occurs in nurseries, where spontaneous symbiosis can be generated. The effectiveness of mycorrhizal symbiosis appears to depend not only on the identity of the fungus but also the diversity of the vine material and soil management. Finally, the use of AMF as biostimulants might be an effective strategy to face the new climatic scenario, but further research dealing with the application of AMF inocula and the protection of native cohorts should be conducted.}, }
@article {pmid40066530, year = {2025}, author = {Heidari, F and Heboyan, A and Rokaya, D and Fernandes, GVO and Heidari, M and Banakar, M and Zafar, MS}, title = {Postbiotics and Dental Caries: A Systematic Review.}, journal = {Clinical and experimental dental research}, volume = {11}, number = {1}, pages = {e70114}, doi = {10.1002/cre2.70114}, pmid = {40066530}, issn = {2057-4347}, support = {//The authors received no specific funding for this work./ ; }, mesh = {Humans ; *Dental Caries/prevention &amp; control/microbiology ; *Streptococcus mutans/drug effects ; *Biofilms/drug effects ; *Probiotics/administration &amp; dosage ; Lactobacillus ; Saliva/microbiology ; Randomized Controlled Trials as Topic ; }, abstract = {OBJECTIVE: This systematic review aimed to evaluate the current evidence regarding the impact of postbiotics on dental caries, focusing on the effectiveness of postbiotic interventions in caries prevention, mechanisms of action, optimal dosages, and administration protocols.<br><br>METHODS: A literature search was conducted across PubMed/MEDLINE, Scopus, Web of Science, and the Cochrane Library. Eligible studies included randomized controlled trials, quasi-experimental, observational, and in vitro studies. The selection followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. A qualitative synthesis was performed due to heterogeneity in study designs and outcomes.<br><br>RESULTS: Twenty-one studies were included (18 in vitro and three randomized controlled trials). Postbiotics derived from various Lactobacillus species demonstrated inhibitory effects on Streptococcus mutans growth, biofilm formation, and virulence gene expression. Proposed mechanisms include direct antimicrobial activity, inhibition of bacterial adhesion, disruption of biofilm formation, modulation of immune responses, and pH buffering. After postbiotic interventions, human trials showed reduced salivary S. mutans counts and increased salivary pH.<br><br>CONCLUSIONS: Postbiotics offer a promising novel approach to dental caries prevention by targeting cariogenic bacteria and modulating the oral microbiome through multiple mechanisms. Compared to probiotics, postbiotics present additional advantages, including enhanced safety, stability, and ease of incorporation into oral care products.}, }
@article {pmid40066462, year = {2025}, author = {Swain, SS and Nayak, S and Mishra, S and Ghana, M and Dash, D}, title = {Exploring the plant growth promoting attributes of pteridophyte-associated microbiome for agricultural sustainability.}, journal = {Physiology and molecular biology of plants : an international journal of functional plant biology}, volume = {31}, number = {2}, pages = {211-232}, pmid = {40066462}, issn = {0971-5894}, abstract = {Pteridophytes, encompassing ferns and fern allies, are integral components of terrestrial ecosystems worldwide. These vascular plants characterized by their spore-based reproduction, fulfil various ecological roles such as influencing biodiversity, soil stability, nutrient dynamics, and ecological succession. Similar to higher plants, pteridophytes too are known to have close symbiotic associations with a diverse array of microorganisms, including bacteria, fungi and actinomycetes. Exploring the microbial diversity in pteridophytes has prospects both in pure and applied research. Research on pteridophyte microbial communities have revealed their role in plant growth promotion, nutrient acquisition and tolerance against stresses. Besides, it would be interesting to unravel the microbial diversity associated with pteridophytes, which are the first vascular plants. Further, study of pteridophytes-associated microbes would also help in conservation programmes of these rare and endangered group of plants. In spite of the immense potential of pteridophyte microbiome, only few studies have been undertaken in this area, thereby creating a huge research gap. Hence, this review compiles pteridophyte microbiome research, and explores its prospects in agricultural sustainability. Our literature survey sheds light on the tremendous potential of pteridophyte-associated microbes as plant growth promoters and biocontrol agents for sustainable agriculture, which is highly relevant in the era of climate change.}, }
@article {pmid40066274, year = {2025}, author = {Karnwal, A and Jassim, AY and Mohammed, AA and Al-Tawaha, ARMS and Selvaraj, M and Malik, T}, title = {Addressing the global challenge of bacterial drug resistance: insights, strategies, and future directions.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1517772}, pmid = {40066274}, issn = {1664-302X}, abstract = {The COVID-19 pandemic underscored bacterial resistance as a critical global health issue, exacerbated by the increased use of antibiotics during the crisis. Notwithstanding the pandemic's prevalence, initiatives to address bacterial medication resistance have been inadequate. Although an overall drop in worldwide antibiotic consumption, total usage remains substantial, requiring rigorous regulatory measures and preventive activities to mitigate the emergence of resistance. Although National Action Plans (NAPs) have been implemented worldwide, significant disparities persist, particularly in low- and middle-income countries (LMICs). Settings such as farms, hospitals, wastewater treatment facilities, and agricultural environments include a significant presence of Antibiotic Resistant Bacteria (ARB) and antibiotic-resistance genes (ARG), promoting the propagation of resistance. Dietary modifications and probiotic supplementation have shown potential in reshaping gut microbiota and reducing antibiotic resistance gene prevalence. Combining antibiotics with adjuvants or bacteriophages may enhance treatment efficacy and mitigate resistance development. Novel therapeutic approaches, such as tailored antibiotics, monoclonal antibodies, vaccines, and nanoparticles, offer alternate ways of addressing resistance. In spite of advancements in next-generation sequencing and analytics, gaps persist in comprehending the role of gut microbiota in regulating antibiotic resistance. Effectively tackling antibiotic resistance requires robust policy interventions and regulatory measures targeting root causes while minimizing public health risks. This review provides information for developing strategies and protocols to prevent bacterial colonization, enhance gut microbiome resilience, and mitigate the spread of antibiotic resistance.}, }
@article {pmid40066155, year = {2025}, author = {Winder, C and Lodhia, A and Basso, M and Cohen Kadosh, K}, title = {Gut microbiome differences in individuals with PTSD compared to trauma-exposed controls: a systematic review.}, journal = {Frontiers in neuroscience}, volume = {19}, number = {}, pages = {1540180}, pmid = {40066155}, issn = {1662-4548}, abstract = {Post-traumatic stress disorder (PTSD) is a common mental health disorder that can occur following exposure to a traumatic event, and is characterized by symptoms including intrusive memories, dissociation, and nightmares. PTSD poses significant suffering on the individual and can reduce quality of life substantially, however, its mechanisms are not fully understood. It has also been associated with gut abnormalities, such as with irritable bowel syndrome, indicating possible involvement of the gut microbiome and gut-brain axis. Whereas previous research has implicated the gut microbiome and microbiome gut-brain axis in various mental health disorders, the relationship between gut microbiome function and PTSD is unclear. Specifically, little is known about whether specific gut microbiome compositions can increase the risk of developing PTSD, or, vice versa, act as a protective factor for the individual. This systematic review aims to synthesize the literature looking at gut microbiome differences between individuals with PTSD and trauma-exposed controls (TEC) while exploring potential risk and resilience factors for development of the disorder. Three studies met the inclusion criteria, and results showed that all studies found differences in gut microbial taxa between PTSD and TEC groups yet varied in their taxonomic level and type. One study found a significant difference in diversity between groups, reporting lower diversity in PTSD, and two studies found certain taxa to be correlated with PTSD symptom severity: Mitsuokella, Odoribacter, Catenibacterium and Olsenella genera, and Actinobacteria, Lentisphaerae and Verrucomicrobia phyla. This review has important implications for potential novel treatments for PTSD which target the gut microbiome, for example psychobiotic dietary interventions such as prebiotics and probiotics. It also informs our understanding of potential risk and resilience factors for the disorder, such as certain gut microbiome compositions being potentially protective or increasing susceptibility. More research is needed, as currently sample sizes are small and confounding variables (e.g., diet) are not always controlled for. Systematic review registration: The protocol was registered on PROSPERO, registration number: CRD42024530033.}, }
@article {pmid40066068, year = {2025}, author = {Ganesan, R and Thirumurugan, D and Vinayagam, S and Kim, DJ and Suk, KT and Iyer, M and Yadav, MK and HariKrishnaReddy, D and Parkash, J and Wander, A and Vellingiri, B}, title = {A critical review of microbiome-derived metabolic functions and translational research in liver diseases.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1488874}, pmid = {40066068}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Liver Diseases/microbiology/metabolism ; *Dysbiosis/microbiology ; *Fecal Microbiota Transplantation ; Animals ; *Translational Research, Biomedical ; *Probiotics/therapeutic use ; Liver/metabolism/microbiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Significant changes in gut microbial composition are associated with chronic liver disease. Using preclinical models, it has been demonstrated that ethanol/alcohol-induced liver disease is transmissible through fecal microbiota transplantation (FMT). So, the survival rate of people with severe alcoholic hepatitis got better, which suggests that changes in the makeup and function of gut microbiota play a role in metabolic liver disease. The leaky intestinal barrier plays a major role in influencing metabolic-related liver disease development through the gut microbiota. As a result, viable bacteria and microbial products can be transported to the liver, causing inflammation, contributing to hepatocyte death, and causing the fibrotic response. As metabolic-related liver disease starts and gets worse, gut dysbiosis is linked to changes in the immune system, the bile acid composition, and the metabolic function of the microbiota in the gut. Metabolic-related liver disease, as well as its self-perpetuation, will be demonstrated using data from preclinical and human studies. Further, we summarize how untargeted treatment approaches affect the gut microbiota in metabolic-related liver disease, including dietary changes, probiotics, antibiotics, and FMT. It discusses how targeted therapies can improve liver disease in various areas. These approaches may improve metabolic-related liver disease treatment options.}, }
@article {pmid40066066, year = {2025}, author = {Bai, J and Tian, Y and Lu, Y and Chen, Y and Yu, M and Gao, X}, title = {Differential effects of high-fat diet on salivary and gut microbiota.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1547555}, pmid = {40066066}, issn = {2235-2988}, mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; *Saliva/microbiology/metabolism ; *Mice, Inbred C57BL ; Male ; Mice ; *RNA, Ribosomal, 16S/genetics ; *Obesity/microbiology/metabolism ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; Disease Models, Animal ; Gas Chromatography-Mass Spectrometry ; }, abstract = {OBJECTIVES: Microorganisms contribute to the pathogenesis of obesity, while more studies focus on gut microbiome. However, the relationship between oral microbiota and obesity has yet to be elucidated. This study was designed to investigate the similarities and differences in the effects of a high-fat diet on salivary and gut microbiota through mouse experiments, exploring the hypothesis that oral microbial mechanisms may contribute to obesity.<br><br>METHODS: An obese mouse model was established in male C57BL/6J mice by feeding a high-fat diet, confirmed by body weight records and blood glucose tests. This study evaluated the physiological effects of the high-fat diet on mice. 16S rRNA sequencing technology was used to analyze changes in salivary and gut microbiota, and gas chromatography-mass spectrometry was employed to evaluate 17 short-chain and medium-chain fatty acids quantitatively.<br><br>RESULTS: The microbiota distribution in salivary was different between the high-fat diet (HFD) and normal chow diet (NCD) groups. At the genus level of salivary microbiota, Streptococcus and Escherichia were highly abundant in the HFD group. Rodentibacter and Turicibacter were more abundant in the NCD group. Regarding the gut microbiome, the diversity changes of gut microbiota are more significant than those of salivary microbiota. The HFD group had a significantly higher abundance of Kineothrix, Cryptobacteroides, and a lower abundance of CAG-485. Nine genera had consistent alterations in salivary and gut microbiota, among which Akkermansia, Lactobacillus, and Intestinimonas were significantly correlated with physiological indicators, and Muribaculum was significantly correlated with increased decanoic acid levels in the HFD group. The dysregulated nine genera were associated with significant upregulation of certain metabolic pathways of the HFD group, including the pentose phosphate, bacterial invasion of epithelial cells, and steroid biosynthesis pathways.<br><br>CONCLUSIONS: There are differences and similarities in the effects of HFD on salivary and gut microbiota. Certain genera of the oral-gut axis altered consistently by HFD may affect obesity through mechanisms involving metabolic pathways and inflammation.}, }
@article {pmid40065635, year = {2025}, author = {Maggitt, S and Cox, J and Dobson, K and McCann, J and Wickersham, TA and Drewery, ML}, title = {Intake, digestion, and rumen microbial impacts of black soldier fly larvae and frass provided as protein supplements to cattle consuming forage.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skaf077}, pmid = {40065635}, issn = {1525-3163}, abstract = {Insects reared in large-scale, commercial settings may be a sustainable alternative to conventional livestock feeds. Black soldier fly larvae (BSFL) has been researched as a potential protein supplement for cattle, but knowledge gaps remain in how BSFL affects rumen microbial populations. Further, frass and larval sheddings (FRS) are produced in greater quantities than larval biomass and are N rich but have not been investigated as feed. Accordingly, the objective of our study was to compare the effects of isonitrogenous levels of cottonseed meal (CSM), BSFL, and FRS on forage utilization responses and rumen microbial communities in cattle consuming low-quality forage. Angus steers (n=8; 240 ± 22.5 kg BW) with ad libitum access to low-quality forage (5.9% crude protein) were used in replicated 4 × 4 Latin squares. One of four treatments was provided daily: no supplemental protein (CON), CSM, partially defatted BSFL, or FRS all provided at 100 mg N/kg BW. There were four 16-d experimental periods which included an 8-d adaptation to treatments, 7-d measurement of intake and digestion, and 1-d for determination of ruminal fermentation and sampling of rumen content for determination of microbial populations. Rumen content samples were separated into liquid and solid fractions, extracted for genomic DNA, PCR amplified for the V3 to V4 region of the 16S rRNA gene, sequenced on a MiSeq platform, and analyzed using the QIIME2 pipeline. Protein supplementation increased forage organic matter (OM) intake and total digestible OM intake (TDOMI) relative to CON (P≤0.01). For TDOMI, there were differences (P≤0.03) between CSM (2.84 kg/d) and BSFL (3.07 kg/d) and CSM and FRS (3.05 kg/d). Treatment did not affect OM (P=0.82) or neutral detergent fiber (P=0.43) digestibility. Relative abundances of certain bacterial genera (i.e., Butyrvibrio, NK4A214, Prevotellacaeae UCG003, and Veillonellacaeae) were significantly affected by treatment in either the liquid or solid rumen fraction, but diversity indices, phyla, and dominant families were not affected. These data indicate that BSFL and FRS stimulate forage utilization to a similar or greater extent than a conventional protein supplement. The minor observed impacts on microbial community composition suggests no adverse effects on the rumen microbiome associated with supplementation of BSFL or FRS. Ultimately, BSFL and FRS may be suitable protein supplements for beef steers consuming low-quality forage.}, }
@article {pmid40065594, year = {2025}, author = {Sun, Y and Yu, YT and Castillo, XO and Anderson, R and Wang, M and Sun, Q and Tallmadge, R and Sams, K and Reboul, G and Zehr, J and Brown, J and Wang, X and Marra, N and Stanhope, B and Grenier, J and Pusterla, N and Divers, T and Mittel, L and Goodman, LB}, title = {Investigation of the Blood Microbiome in Horses With Fever of Unknown Origin.}, journal = {Veterinary medicine and science}, volume = {11}, number = {2}, pages = {e70272}, doi = {10.1002/vms3.70272}, pmid = {40065594}, issn = {2053-1095}, support = {//Harry M. Zweig Memorial Fund for Equine Research/ ; 1U18FD006993//US Food and Drug Administration's Veterinary Laboratory Investigation and Response Network/ ; 1U18FD006716//US Food and Drug Administration's Veterinary Laboratory Investigation and Response Network/ ; W81XWH-22-1-0891//Department of Defense/ ; }, mesh = {Horses ; Animals ; *Horse Diseases/microbiology/virology/blood/epidemiology ; Case-Control Studies ; *Fever of Unknown Origin/veterinary/microbiology/etiology ; Microbiota ; Male ; Female ; }, abstract = {BACKGROUND: Fever of unknown origin (FUO) without a respiratory component is a frequent clinical presentation in horses. Multiple pathogens, both tick-borne and enteric, can be involved as etiologic agents. An additional potential mechanism is intestinal barrier dysfunction.<br><br>OBJECTIVES: This case-control study aimed to detect and associate microbial taxa in blood with disease state.<br><br>STUDY DESIGN: Areas known for a high prevalence of tick-borne diseases in humans were chosen to survey horses with FUO, which was defined as fever of 101.5&#xb0;F or higher with no signs of respiratory illness or other recognisable diseases. Blood samples and clinical parameters were obtained from 52 FUO cases and also from matched controls from the same farms. An additional 23 febrile horses without matched controls were included.<br><br>METHODS: Broadly targeted polymerase chain reaction (PCR) amplification directed at conserved sequence regions of bacterial 16S rRNA, parasite 18S rRNA, coronavirus RdRp and parvovirus NS1 was performed, followed by deep sequencing. To control for contamination and identify taxa unique to the cases, metagenomic sequences from the controls were subtracted from those of the cases, and additional targeted molecular testing was performed. Sera were also tested for antibodies to equine coronavirus.<br><br>RESULTS: Over 60% of cases had intestinal microbial DNA circulating in the blood. Nineteen percent of cases were attributed to infection with Anaplasma phagocytophilum, of which two were subtyped as human-associated strains. A novel Erythroparvovirus was detected in two cases and two controls. Serum titres for equine coronavirus were elevated in some cases but not statistically different overall between the cases and controls.<br><br>MAIN LIMITATIONS: Not all pathogens are expected to circulate in blood, which was the sole focus of this study.<br><br>CONCLUSIONS: The presence of commensal gut microbes in blood of equine FUO cases is consistent with a compromised intestinal barrier, which is highlighted as a direction for future study.}, }
@article {pmid40065353, year = {2025}, author = {Liu, GS and Song, Y and Yan, JS and Chai, YJ and Zhao, YF and Ma, H}, title = {Identification of enterotype for patients with Alzheimer's disease.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {299}, pmid = {40065353}, issn = {1479-5876}, mesh = {*Alzheimer Disease/microbiology ; Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Aged ; *RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Feces/microbiology ; Case-Control Studies ; Neural Networks, Computer ; Aged, 80 and over ; }, abstract = {BACKGROUND: Alzheimer's disease (AD) is a progressive and chronic neurodegenerative disorder of the central nervous system, characterized by behavioral and dysexecutive deficits. Its pathogenesis is closely associated with the intestinal flora. This study aimed to explore the enterotypes in AD by identifying key bacteria through machine learning and species co-occurrence network analysis.<br><br>METHODS: The collection of fecal samples from AD patients was followed by 16&#xa0;S rRNA analysis using QIIME2. Enterotype clustering was conducted at the genus level, and deep neural network (DNN) classification models were developed for AD and healthy controls within each enterotype.<br><br>RESULTS: Analysis of three 16&#xa0;S rRNA gut microbiome datasets identified three distinct enterotypes: Escherichia_Shigella (ET-E), Faecalibacterium (ET-F), and Bacteroides (ET-B). The ET-E is mainly characterized by the absence of Akkermansia in AD group. The Akkermansia was significantly positively correlated with Eubacterium_coprostanoligenes_group and negatively correlated with biosynthesis and amino acid metabolism. The ET-F highly expressed Agathobacter, un_f__Lachnospiraceae, Lachnoclostridium, and low expressed Dorea in AD group. Among them, Agathobacter was significantly positively correlated with un_f__Lachnospiraceae, and un_f__Lachnospiraceae was significantly positively correlated with Lachnoclostridium. The Dorea was significantly negatively correlated with Lachnoclostridium. The AD from ET-B group had high expression of two beneficial bacteria, Butyricicoccus and Parabacteroides. The findings suggest that the ET-E enterotype may predispose individuals to AD, with Akkermansia identified as a potential risk factor. Conversely, the ET-B enterotype appears to be associated with milder symptoms, with Butyricicoccus and Parabacteroides potentially serving as protective factors. Therefore, a comprehensive understanding of the species characteristics and interactions within different enterotypes is essential for modulating the gut-brain axis and mitigating AD symptoms.}, }
@article {pmid40065181, year = {2025}, author = {Iliev, ID and Ananthakrishnan, AN and Guo, CJ}, title = {Microbiota in inflammatory bowel disease: mechanisms of disease and therapeutic opportunities.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {40065181}, issn = {1740-1534}, abstract = {Perturbations in the intestinal microbiome are strongly linked to the pathogenesis of inflammatory bowel disease (IBD). Bacteria, fungi and viruses all make up part of a complex multi-kingdom community colonizing the gastrointestinal tract, often referred to as the gut microbiome. They can exert various effects on the host that can contribute to an inflammatory state. Advances in screening, multiomics and experimental approaches have revealed insights into host-microbiota interactions in IBD and have identified numerous mechanisms through which the microbiota and its metabolites can exert a major influence on the gastrointestinal tract. Looking into the future, the microbiome and microbiota-associated processes will be likely to provide unparalleled opportunities for novel diagnostic, therapeutic and diet-inspired solutions for the management of IBD through harnessing rationally designed microbial communities, powerful bacterial and fungal metabolites, individually or in combination, to foster intestinal health. In this Review, we examine the current understanding of the cross-kingdom gut microbiome in IBD, focusing on bacterial and fungal components and metabolites. We examine therapeutic and diagnostic opportunities, the microbial metabolism, immunity, neuroimmunology and microbiome-inspired interventions to link mechanisms of disease and identify novel research and therapeutic opportunities for IBD.}, }
@article {pmid40065148, year = {2025}, author = {Hiratsuka, D and Matsuo, M and Kashiwabara, K and Inoue, M and Ishizawa, C and Iida, R and Fukui, Y and Aikawa, S and Hiraoka, T and Harada, M and Wada-Hiraike, O and Osuga, Y and Hirota, Y}, title = {Comparison of diagnostic tests for chronic endometritis and endometrial dysbiosis in recurrent implantation failure: Impact on pregnancy outcomes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8272}, pmid = {40065148}, issn = {2045-2322}, mesh = {Humans ; Female ; Pregnancy ; *Endometritis/microbiology/diagnosis ; *Dysbiosis/diagnosis/microbiology ; Adult ; *Endometrium/microbiology/pathology ; *Embryo Implantation ; *Pregnancy Outcome ; Chronic Disease ; Microbiota ; Hysteroscopy ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {Chronic endometritis (CE) and endometrial dysbiosis (ED) are major causes of recurrent implantation failure (RIF). CE is diagnosed via hysteroscopy or the endometrial CD138 test; ED is examined using endometrial microbiome testing with next-generation sequencing. ED is characterized by a reduction in Lactobacillus species. However, correlations between the results of the three tests and the efficacy of treatment against CE and ED in pregnancy outcomes remain unclear. We analyzed 73 patients with RIF who underwent all three tests (hysteroscopy, endometrial CD138 test, and endometrial microbiome test). Patients with CE received antibiotics, whereas those with ED received antibiotics and vaginal Lactobacillus probiotics. The incidences of CE diagnosed using hysteroscopy and the CD138 test were 56.2 and 49.3%, respectively, and the prevalence of ED was 53.4%. No correlations were observed among the test-positive individuals in these three tests. Among patients with ED, 88.9% had a post-treatment clinical pregnancy, a significantly higher rate than that in patients without ED (p = 0.021). Multivariate analysis demonstrated that ED was associated with clinical pregnancy (odds ratio (OR): 6.29, p = 0.031). In conclusion, the three tests detected different populations of patients with RIF. ED diagnosed using the endometrial microbiome test was associated with favorable pregnancy outcomes after testing.}, }
@article {pmid40065134, year = {2025}, author = {Jalil, A and Perino, A and Dong, Y and Imbach, J and Volet, C and Vico-Oton, E and Demagny, H and Plantade, L and Gallart-Ayala, H and Ivanisevic, J and Bernier-Latmani, R and Hapfelmeier, S and Schoonjans, K}, title = {Bile acid 7α-dehydroxylating bacteria accelerate injury-induced mucosal healing in the colon.}, journal = {EMBO molecular medicine}, volume = {}, number = {}, pages = {}, pmid = {40065134}, issn = {1757-4684}, support = {310030_189178/SNSF_/Swiss National Science Foundation/Switzerland ; CRSII5_180317/1/SNSF_/Swiss National Science Foundation/Switzerland ; CRSII5_180317/1/SNSF_/Swiss National Science Foundation/Switzerland ; CRSII5_180317/1/SNSF_/Swiss National Science Foundation/Switzerland ; }, abstract = {Host-microbiome communication is frequently perturbed in gut pathologies due to microbiome dysbiosis, leading to altered production of bacterial metabolites. Among these, 7α-dehydroxylated bile acids are notably diminished in inflammatory bowel disease patients. Herein, we investigated whether restoration of 7α-dehydroxylated bile acids levels by Clostridium scindens, a human-derived 7α-dehydroxylating bacterium, can reestablish intestinal epithelium homeostasis following colon injury. Gnotobiotic and conventional mice were subjected to chemically-induced experimental colitis following administration of Clostridium scindens. Colonization enhanced the production of 7α-dehydroxylated bile acids and conferred prophylactic and therapeutic protection against colon injury through epithelial regeneration and specification. Computational analysis of human datasets confirmed defects in intestinal cell renewal and differentiation in ulcerative colitis patients while expression of genes involved in those pathways showed a robust positive correlation with 7α-dehydroxylated bile acid levels. Clostridium scindens administration could therefore be a promising biotherapeutic strategy to foster mucosal healing following colon injury by restoring bile acid homeostasis.}, }
@article {pmid40064825, year = {2025}, author = {Richard, PI and Baltosser, WH and Williams, PH and He, Q}, title = {Phylogenetic analysis of microbial CP-lyase cluster genes for bioremediation of phosphonate.}, journal = {AMB Express}, volume = {15}, number = {1}, pages = {42}, pmid = {40064825}, issn = {2191-0855}, support = {80NSSC22M0043//Arkansas Space Grant Consortium/ ; }, abstract = {The ever-increasing use of phosphonates and their derivatives has resulted in the discharge of large quantities of these materials into the ecosystem, causing pollution and harmful shifts in microbiome composition. We conducted an extensive phylogenetic analysis to address this mounting problem and to help determine suitable microbes for bioremediation in specific environments. The 84 microorganisms included in our study span the gamut of species and occupied habitats. They degrade phosphonates by expressing an enzyme complex; CP-Lyase transcribed from 14 cistrons. Of the organisms studied, 12, 39, and 25 are singularly suitable for mostly freshwater, marine, or terrestrial habitats, respectively. Others adapted to multihabitats include Calothrix sp. PCC 7507 (both freshwater and marine habitats), Escherichia coli, Kaistia soli, Limoniibacter endophyticus, Marivita sp. and Virgibacillus dokdonensis (both marine and terrestrial habitats), Acidithiobacillus ferrooxidans (both freshwater and terrestrial habitats), with Paenibacillus contaminans suitable for freshwater, marine, and terrestrial habitats. All organisms were statistically rooted to glutathione peroxidase for phylogenetic perspective with tree topology dependent upon 50% or greater support. Clustered genes have been shown to have co-evolved based on striking nucleotide similarity and clade groupings within the tree topologies generated.}, }
@article {pmid40064239, year = {2025}, author = {Okunlola, FO and Okunlola, AR and Adetuyi, BO and Soliman, MES and Alexiou, A and Papadakis, M and Fawzy, MN and El-Saber Batiha, G}, title = {Beyond the Gut: Unraveling the Multifaceted Influence of Microbiome on Cardiovascular Health.}, journal = {Clinical nutrition ESPEN}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.clnesp.2025.03.002}, pmid = {40064239}, issn = {2405-4577}, abstract = {Cardiovascular disease is one of the leading causes of death worldwide. Even while receiving adequate pharmacological treatment for their hypertension, people are nonetheless at greater risk for cardiovascular disease. There is growing evidence that the gut microbiota may have major positive and negative effects on blood pressure and illnesses related with it as more study into this topic is conducted. Trimethylamine n-oxide (TMAO) and short-chain fatty acids (SCFA) are two major by-products of the gut microbiota. TMAO is involved in the formation of other coronary artery diseases, including atherosclerosis and hypertension, while SCFAs play an important role in controlling blood pressure. Numerous investigations have confirmed the established link between dietary salt intake and hypertension. Reducing sodium in the diet is linked to lower rates of cardiovascular disease morbidity and mortality as well as lower rates of blood pressure and hypertension. In both human and animal research, high salt diets increase local and systemic tissue inflammation and compromise gut architecture. Given that the gut microbiota constantly interacts with the immune system and is required for the correct maturation of immune cells, it is scientifically conceivable that it mediates the inflammatory response. This review highlights the therapeutic possibilities for focusing on intestinal microbiomes as well as the potential functions of the gut microbiota and its metabolites in the development of hypertension.}, }
@article {pmid40064231, year = {2025}, author = {Jia, Y and Huang, D and Lan, X and Sun, X and Lin, W and Sun, W and Wang, Y}, title = {Community structure and metabolic potentials of keystone taxa and their associated bacteriophages within rice root endophytic microbiome in response to metal(loid)s contamination.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {126028}, doi = {10.1016/j.envpol.2025.126028}, pmid = {40064231}, issn = {1873-6424}, abstract = {Heavy metal (HM) contamination of agricultural products is of global environmental concern as it directly threatened the food safety. Plant-associated microbiome, particularly endophytic microbiome, hold the potential for mitigating HM stress as well as promoting plant growth. The metabolic potentials of the endophytes, especially those under the HM stresses, have not been well addressed. Rice, a major staple food worldwide, is more vulnerable to HM contamination compared to other crops and therefore requires special attentions. Therefore, this study selected rice as the target plants. Geochemical analysis and amplicon sequencing were combined to characterize the rice root endophytic bacterial communities and identify keystone taxa in two HM-contaminated rice fields. Metagenomic analysis was employed to investigate the metabolic potentials of these keystone taxa. Burkholderiales and Rhizobiales were identified as predominant keystone taxa. The metagenome-assembled genome (MAG)s associated with these keystone populations suggested that they possessed diverse genetic potentials related to metal resistance and transformation (e.g., As resistance and cycling, V reduction, Cr efflux and reduction), and plant growth promotion (nitrogen fixation, phosphate solubilization, oxidative stress resistance, indole-3-acetic acid, and siderophore production). Moreover, bacteriophages encoding auxiliary metabolism genes (AMGs) associated with the HM resistance as well as nitrogen and phosphate acquisition were identified, suggesting that these phages may contribute to these crucial biogeochemical processes within rice roots. The current findings revealed the beneficial roles of rice endophytic keystone taxa and their associated bacteriophages within HM-contaminated rice root endophytic microbiome, which may provide valuable insights on future applications of employing root microbiome for safety management of agriculture productions.}, }
@article {pmid40064155, year = {2025}, author = {Cryan, JF}, title = {Microbiome and Brain Development: A Tale of Two Systems.}, journal = {Annals of nutrition &amp; metabolism}, volume = {}, number = {}, pages = {1-19}, doi = {10.1159/000544950}, pmid = {40064155}, issn = {1421-9697}, abstract = {BACKGROUND: For the past two decades there has been a growing appreciation of the role that the microbiota (the trillions of microorganisms within and on our bodies) plays as one of the key regulators of gut-brain function and has led to the appreciation of the importance of a distinct microbiota-gut-brain axis across the lifespan but especially during neurodevelopment.<br><br>SUMMARY: The gut microbiota and its relevant metabolites interact with the immune and the central nervous systems during critical temporal windows of development. These critical developmental windows perinatally (during the first 1000 days) are susceptible timepoints for insults that can endure long-lasting effects on the microbiota-gut-brain axis. Accumulating evidence shows that a variety of factors can impact the microbiota in early life including mode of birth delivery, antibiotic exposure, mode of nutritional provision, infection, stress as well as host genetics. Additionally, sex differences occur in response to microbial manipulations in early life although the underlying mechanisms underpinning such effects remains elusive. Animal models have been essential in delineating a role of the microbiome in neurodevelopmental disorders ranging from autism spectrum disorder to attention deficit hyperactivity disorder. This mechanistic perspective should be supplemented with more translational studies to evaluate the applicability of findings from animal models to human subjects.<br><br>KEY MESSAGES: Studies examining the translation of these effects from animal models to humans are currently ongoing with evidence for microbial modulation of neurocognitive development and neurodevelopmental risk increasing.}, }
@article {pmid40064088, year = {2025}, author = {Lehr, PP and Gschwendtner, S and Du, B and Rennenberg, H and Schloter, M and Zörb, C}, title = {Grapevines and trees: A biodiversity study of microbiomes in an established temperate agroforestry system.}, journal = {Journal of environmental management}, volume = {379}, number = {}, pages = {124882}, doi = {10.1016/j.jenvman.2025.124882}, pmid = {40064088}, issn = {1095-8630}, abstract = {Biodiversity is threatened particularly in perennial crop cultivation such as fruit trees or grapevines. If established, agroforestry has the potential to increase biodiversity by providing a higher habitat heterogeneity at the example of grapevine (Vitis vinifera L. cv. Riesling) cultivated together with oak or poplar trees for 12 years. Together with the rhizosphere microbiome, the root metabolome was quantified as an indicator of root exudation. Since the root metabolome does not fully align with the exudate metabolome, we are using the root metabolome as a proxy for the exudate metabolome. The results reveal that co-cultivation of grapevine with trees reduces the nutrient availability in the soil and changes the root metabolome of both, grapevine and trees with a more distinct effect of trees on grapevine than vice versa, particularly for oak. Apparently, root-to-root signalling takes place between trees and grapevine. Co-cultivation of grapevine and oak trees also enhanced the alpha diversity of the microbiome. Correlation analysis revealed strong positive correlations between distinct microbial families and metabolites enriched in the roots of Riesling. Thus, microbiome analyses support the view that root-to-root interaction in mixed cultivation of grapevine with trees is mediated by root exudation.}, }
@article {pmid40063888, year = {2025}, author = {Saraphol, B and Hinthong, W and Chienwichai, P and Pumipuntu, N and Reamtong, O and Srisook, T and Premsuriya, J}, title = {Analysis of the fecal microbiome and metabolome in dairy cows with different body condition scores.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0319461}, pmid = {40063888}, issn = {1932-6203}, mesh = {Animals ; Cattle ; *Feces/microbiology ; *Metabolome ; Female ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; }, abstract = {Holstein Friesian is the most popular breed of dairy cows worldwide due to its exceptional milk production capabilities. In dairy cow management, the body condition score (BCS) is a useful tool, serving as a reliable indicator of a cow's nutritional status and overall health. It is determined via a subjective visual and tactile assessment of fat cover and muscle mass. A low BCS is associated with decreased milk production and fertility. While genetic and nutritional factors have previously been associated with BCS, their effects are often moderate. In this study, we compared the fecal microbiome and the untargeted fecal metabolome of normal (BCS ≥ 3, n = 16) and thin (BCS < 3, n = 16) Holstein Friesian dairy cows. The 16S rRNA gene-based metagenomic analysis revealed that thin cows had significantly higher levels of Clostridiaceae, Erysipelotrichales, Erysipelotrichaceae, and Turicibacter, while normal cows had higher levels of Clostridiales_vadinBB60_group, UCG-010, Bacteroidaceae, Ruminococcaceae, Paludibacteraceae, Alistipes, and Bacteroides. The fecal metabolomic analysis showed that key signaling pathways, including the mechanistic target of rapamycin (mTOR), phosphatidylinositol 3-kinase (PI3K)-Akt, and AMP-activated protein kinase (AMPK) pathways, were enriched in thin cows. In addition, a significant correlation was observed between differential microbial taxa and metabolites. Notably, Clostridiaceae and Erysipelotrichaceae species are linked to inflammation, infectious diseases, and conditions such as ruminal acidosis. Additionally, the mTOR, PI3K-Akt, and AMPK pathways are known to be activated by both nutrient deficiencies and inflammation. We propose that, in addition to genetic and nutritional factors, gut microbiome dysbiosis may contribute to subclinical health conditions, such as chronic inflammation and acidosis, which indirectly affect the cow's BCS. These findings are guiding our ongoing research on the underlying health conditions in thin cows to better understand the role that the gut microbiome plays in the regulation of the body condition.}, }
@article {pmid40063791, year = {2025}, author = {Morrison, ML and Xue, KS and Rosenberg, NA}, title = {Quantifying compositional variability in microbial communities with FAVA.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {11}, pages = {e2413211122}, doi = {10.1073/pnas.2413211122}, pmid = {40063791}, issn = {1091-6490}, support = {R01 HG005855/HG/NHGRI NIH HHS/United States ; R21-AI168860//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Microbiota/genetics ; *Phylogeny ; Bacteria/genetics/classification/isolation &amp; purification ; Humans ; }, abstract = {Microbial communities vary across space, time, and individual hosts, generating a need for statistical methods capable of quantifying variability across multiple microbiome samples at once. To understand heterogeneity across microbiome samples from different host individuals, sampling times, spatial locations, or experimental replicates, we present FAVA (FST-based Assessment of Variability across vectors of relative Abundances), a framework for characterizing compositional variability across two or more microbiome samples. FAVA quantifies variability across many samples of taxonomic or functional relative abundances in a single index ranging between 0 and 1, equaling 0 when all samples are identical and 1 when each sample is entirely composed of a single taxon (and at least two distinct taxa are present across samples). Its definition relies on the population-genetic statistic FST, with samples playing the role of "populations" and taxa playing the role of "alleles." Its mathematical properties allow users to compare datasets with different numbers of samples and taxonomic categories. We introduce extensions that incorporate phylogenetic similarity among taxa and spatial or temporal distances between samples. We demonstrate FAVA in two examples. First, we use FAVA to measure how the taxonomic and functional variability of gastrointestinal microbiomes across individuals from seven ruminant species changes along the gastrointestinal tract. Second, we use FAVA to quantify the increase in temporal variability of gut microbiomes in healthy humans following an antibiotic course and to measure the duration of the antibiotic's influence on temporal microbiome variability. We have implemented this tool in an R package, FAVA, for use in pipelines for the analysis of microbial relative abundances.}, }
@article {pmid40063675, year = {2025}, author = {Chavarria, X and Park, HS and Oh, S and Kang, D and Choi, JH and Kim, M and Cho, YH and Yi, MH and Kim, JY}, title = {Using gut microbiome metagenomic hypervariable features for diabetes screening and typing through supervised machine learning.}, journal = {Microbial genomics}, volume = {11}, number = {3}, pages = {}, doi = {10.1099/mgen.0.001365}, pmid = {40063675}, issn = {2057-5858}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Supervised Machine Learning ; *Diabetes Mellitus, Type 1/microbiology ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Adult ; Bacteria/genetics/classification/isolation &amp; purification ; Metagenome ; Support Vector Machine ; Aged ; Algorithms ; }, abstract = {Diabetes mellitus is a complex metabolic disorder and one of the fastest-growing global public health concerns. The gut microbiota is implicated in the pathophysiology of various diseases, including diabetes. This study utilized 16S rRNA metagenomic data from a volunteer citizen science initiative to investigate microbial markers associated with diabetes status (positive or negative) and type (type 1 or type 2 diabetes mellitus) using supervised machine learning (ML) models. The diversity of the microbiome varied according to diabetes status and type. Differential microbial signatures between diabetes types and negative group revealed an increased presence of Brucellaceae, Ruminococcaceae, Clostridiaceae, Micrococcaceae, Barnesiellaceae and Fusobacteriaceae in subjects with diabetes type 1, and Veillonellaceae, Streptococcaceae and the order Gammaproteobacteria in subjects with diabetes type 2. The decision tree, elastic net, random forest (RF) and support vector machine with radial kernel ML algorithms were trained to screen and type diabetes based on microbial profiles of 76 subjects with type 1 diabetes, 366 subjects with type 2 diabetes and 250 subjects without diabetes. Using the 1000 most variable features, tree-based models were the highest-performing algorithms. The RF screening models achieved the best performance, with an average area under the receiver operating characteristic curve (AUC) of 0.76, although all models lacked sensitivity. Reducing the dataset to 500 features produced an AUC of 0.77 with sensitivity increasing by 74% from 0.46 to 0.80. Model performance improved for the classification of negative-status and type 2 diabetes. Diabetes type models performed best with 500 features, but the metric performed poorly across all model iterations. ML has the potential to facilitate early diagnosis of diabetes based on microbial profiles of the gut microbiome.}, }
@article {pmid40063530, year = {2025}, author = {Serbanescu, M and Lee, S and Li, F and Boppana, SH and Elebasy, M and White, JR and Mintz, CD}, title = {Effects of Perioperative Exposure on the Microbiome and Outcomes From an Immune Challenge in C57Bl/6 Adult Mice.}, journal = {Anesthesia and analgesia}, volume = {}, number = {}, pages = {}, doi = {10.1213/ANE.0000000000007467}, pmid = {40063530}, issn = {1526-7598}, abstract = {BACKGROUND: Previous work suggests that the gut microbiome can be disrupted by antibiotics, anesthetics, opiates, supplemental oxygen, or nutritional deprivation-all of which are common and potentially modifiable perioperative interventions that nearly all patients are exposed to in the setting of surgery. Gut microbial dysbiosis has been postulated to be a risk factor for poor surgical outcomes, but how perioperative care-independent of the surgical intervention-impacts the gut microbiome, and the potential consequences of this impact have not been directly investigated.<br><br>METHODS: We developed a perioperative exposure model (PEM) in C57Bl/6 mice to emulate the most common elements of perioperative medicine other than surgery, which included 12 hours of nutritional deprivation, 4 hours of volatile general anesthetic, 7 hours of supplemental oxygen, surgical antibiotics (cefazolin), and opioid pain medication (buprenorphine). Gut microbial dynamics and inferred metabolic changes were longitudinally assessed before-and at 3 time points after-PEM by 16S rRNA amplicon sequencing. We then used fecal microbial transplant in secondary abiotic mice to test if, compared to preexposure microbiota, day 3 post-PEM microbial communities affect the clinical response to immune challenge in an endotoxemia model.<br><br>RESULTS: We observed transient changes in microbiota structure and function after the PEM, including reduced biodiversity, loss of diverse commensals associated with health (including Lactobacillus, Roseburia, and Ruminococcus), and changes in microbiota-mediated amino acid metabolic pathways. Mice engrafted with day 3 post-PEM microbial communities demonstrated markedly reduced survival after endotoxemia compared to those bearing preexposure communities (7-day survival of ~20% vs ~70%, P = .0002).<br><br>CONCLUSIONS: These findings provide the first clear evidence that the combined effects of common perioperative factors, independent of surgery, cause gut microbial dysbiosis and alter the host response to inflammation in the postoperative period.}, }
@article {pmid40063366, year = {2025}, author = {Su, F and Su, M and Wei, W and Wu, J and Chen, L and Sun, X and Liu, M and Sun, S and Mao, R and Bourgonje, AR and Hu, S}, title = {Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel disease.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2476570}, doi = {10.1080/19490976.2025.2476570}, pmid = {40063366}, issn = {1949-0984}, mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Host Microbial Interactions ; *Dysbiosis/microbiology ; Animals ; Bacteria/metabolism/genetics/classification ; Genomics ; Metabolomics ; Proteomics ; Multiomics ; }, abstract = {Numerous studies have accelerated the knowledge expansion on the role of gut microbiota in inflammatory bowel disease (IBD). However, the precise mechanisms behind host-microbe cross-talk remain largely undefined, due to the complexity of the human intestinal ecosystem and multiple external factors. In this review, we introduce the interactome concept to systematically summarize how intestinal dysbiosis is involved in IBD pathogenesis in terms of microbial composition, functionality, genomic structure, transcriptional activity, and downstream proteins and metabolites. Meanwhile, this review also aims to present an updated overview of the relevant mechanisms, high-throughput multi-omics methodologies, different types of multi-omics cohort resources, and computational methods used to understand host-microbiota interactions in the context of IBD. Finally, we discuss the challenges pertaining to the integration of multi-omics data in order to reveal host-microbiota cross-talk and offer insights into relevant future research directions.}, }
@article {pmid40063073, year = {2025}, author = {Yasin, M and Zohoori, FV and Kumah, EA and Subramanian, M and Dean, P and Orr, CH}, title = {Effect of Fluoride on Gut Microbiota: A Systematic Review.}, journal = {Nutrition reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/nutrit/nuae202}, pmid = {40063073}, issn = {1753-4887}, support = {//Teesside University/ ; }, abstract = {CONTEXT: Fluoride can prevent dental caries by inhibiting demineralization and promoting remineralization of teeth while affecting the physiology of oral microbiota, thus inhibiting cellular enzymes. However, the effect of systemic fluoride on gut microbiota is unknown.<br><br>OBJECTIVE: To explore the impacts of systemic fluoride on gut microbiota composition and abundance and associated functions such as gene and metabolic regulation.<br><br>DATA SOURCES: A systematic database search was conducted of MEDLINE, Web of Science, Scopus, PubMed, CINAHL, and Embase to find articles on studies reporting the effects of fluoride on gut microbiota.<br><br>DATA EXTRACTION: Forty-nine studies were included (n&#x2009;=&#x2009;42 in animals, 4 of humans, 3 in vitro studies) after screening for title, abstract, and full text using Covidence to check against eligibility criteria. Data were extracted using Covidence and study quality was assessed using the Mixed Method Appraisal Tool by 2 reviewers independently.<br><br>DATA ANALYSIS: Two human studies of dental fluorosis and 1 of patients with breast cancer (intestinal fluorine-18 fluorodeoxyglucose uptake) showed significant differences in gut microbial composition, with increased relative abundance of Acidobacteria and Proteobacteria, and decreased abundance of Firmicutes and Bacteroidetes. An ex vivo study of human feces indicated that &#x2264;&#x2009;2&#x2009;mg L-1 NaF might boost "health-associated" taxa, but concentrations (&#x2265;&#x2009;10&#x2009;mg L-1 NaF) could increase the ratio of some unhealthy microbes after 24&#x2009;hours. The animal studies examined the effects of high fluoride doses in water and diet (50-1200 mg L-1 NaF) for long-term (1-6&#x2009;months) and short-term (6&#x2009;hours to 7&#x2009;days) exposure, with all showing a significant disturbance in the Firmicutes to Bacteroidota ratio.<br><br>CONCLUSION: In humans, high doses potentially may be detrimental to the microbiome, whereas &#x2264;&#x2009;2&#x2009;mg L-1 NaF had positive effects. Similarly, in animals, &#x2265;&#x2009;50&#x2009;mg L-1 NaF was unsafe, whereas &#x2264;&#x2009;25&#x2009;mg L-1 NaF had harmless effects.<br><br>PROSPERO registration No. CRD42022347357.}, }
@article {pmid40062854, year = {2025}, author = {Zhang, F and Luan, J and Suo, L and Wang, H and Zhao, Y and Sun, T and Ni, Y and Cao, H and Zou, X and Liu, B}, title = {Altered gut microbiota and metabolite profiles in community-acquired pneumonia: a metagenomic and metabolomic study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0263924}, doi = {10.1128/spectrum.02639-24}, pmid = {40062854}, issn = {2165-0497}, abstract = {UNLABELLED: Emerging evidence suggests that altered gut microbiota is linked to community-acquired pneumonia (CAP), but the potential mechanisms by which gut microbiota and its metabolites contribute to the development of CAP remain unclear. Fecal samples from 32 CAP patients and 36 healthy controls were analyzed through metagenomic sequencing and metabolomic profiling. The gut microbiota composition in CAP patients showed significant differences and lower diversity compared to healthy controls. Genera involved in short-chain fatty acid (SCFA) production, such as Faecalibacterium, Ruminococcus, and Eubacterium, as well as species like Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Eubacterium rectale, Prevotella copri, and Ruminococcus bromii, were significantly depleted in CAP patients. Bacterial co-occurrence network analysis revealed an over-representation of pro-inflammatory bacteria, which contributed to the core gut microbiome in CAP patients. Metabolomic analysis of fecal samples identified a distinct metabolic profile, with a notable increase in arachidonic acid, but a decrease in secondary bile acids, such as deoxycholic acid, lithocholic acid, and ursodeoxycholic acid, compared to healthy controls. Spearman correlation analysis between differential microbiota and bile acids showed that Faecalibacterium prausnitzii, Bifidobacterium adolescentis, Eubacterium rectale, and Prevotella copri were positively correlated with ursocholic acid, lithocholic acid, and ursodeoxycholic acid, respectively. Our results suggest that the reduction in secondary bile acids, insufficient production of SCFAs, and an overabundance of pro-inflammatory bacteria may contribute to metabolic inflammation in the body. These factors could play a key role in the pathogenesis of CAP, driven by gut microbiota alterations.<br><br>IMPORTANCE: This study presents a comprehensive metagenomic and metabolomic analysis of fecal samples from community-acquired pneumonia (CAP) patients, identifying key characteristics, such as decreased secondary bile acids, imbalanced short-chain fatty acid production, and increased pro-inflammatory bacteria. These findings provide valuable insights into the mechanisms linking gut microbiota alterations to CAP pathogenesis and suggest that targeting the gut microbiota could be a promising strategy for intervening in CAP.}, }
@article {pmid40062772, year = {2025}, author = {Connolly, JP and Kelly, L}, title = {The physical biogeography of Fusobacterium nucleatum in health and disease.}, journal = {mBio}, volume = {}, number = {}, pages = {e0298924}, doi = {10.1128/mbio.02989-24}, pmid = {40062772}, issn = {2150-7511}, abstract = {UNLABELLED: Fusobacterium nucleatum (Fn) is an oral commensal inhabiting the human gingival plaque that is rarely found in the gut. However, in colorectal cancer (CRC), Fn can be isolated from stool samples and detected in metagenomes. We hypothesized that ecological characteristics of the gut are altered by disease, enabling Fn to colonize. Multiple genomically distinct populations of Fn exist, but their ecological preferences are unstudied. We identified six well-separated populations in 133 Fn genomes and used simulated metagenomes to demonstrate sensitive detection of populations in human oral and gut metagenomes. In 9,560 samples from 11 studies, Fn population C2 animalis is elevated in gut metagenomes from CRC and Crohn's disease patients and is observed more frequently in CRC stool samples than in the gingiva. Polymorphum, the most prevalent gingival Fn population, is significantly increased in Crohn's stool samples; this effect was significantly stronger in male hosts than in female. We find polymorphum genomes are enriched for biosynthetic gene clusters and fluoride exporters, while C2 animalis are high in iron transporters. Fn populations thus associate with specific clinical and demographic phenotypes and harbor distinct functional features. Ecological differences in closely related groups of bacteria inform microbiome impacts on human health.<br><br>IMPORTANCE: Fusobacterium nucleatum is a bacterium normally found in the gingiva. F. nucleatum generally does not colonize the healthy gut, but is observed in approximately a third of colorectal cancer (CRC) patient guts. F. nucleatum's presence in the gut during CRC has been linked to worse prognosis and increased tumor proliferation. Here, we describe the population structure of F. nucleatum in oral and gut microbiomes. We report substantial diversity in gene carriage among six distinct populations of F. nucleatum and identify population disease and body-site preferences. We find the C2 animalis population is more common in the CRC gut than in the gingiva and is enriched for iron transporters, which support gut colonization in known pathogens. We find that C2 animalis is also enriched in Crohn's disease and type 2 diabetes, suggesting ecological commonalities between the three diseases. Our work shows that closely related bacteria can have different associations with human physiology.}, }
@article {pmid40062764, year = {2025}, author = {Watkins, E and Lin, J and Lingohr-Smith, M and Yong, C and Tangirala, K and Collins, K}, title = {Biological, Clinical, and Sociobehavioral Factors Associated with Disproportionate Burden of Bacterial Vaginosis in the United States: A Comprehensive Literature Review.}, journal = {Journal of women's health (2002)}, volume = {}, number = {}, pages = {}, doi = {10.1089/jwh.2024.0583}, pmid = {40062764}, issn = {1931-843X}, abstract = {Background: Bacterial vaginosis (BV), a common gynecological infection characterized by reduced lactic acid-producing bacteria and increased anerobic bacteria in the vaginal microbiome, is associated with adverse health outcomes. Methods: A PubMed search for English-language articles about BV in the USA and factors contributing to disparities in BV risk, with an emphasis on the role of the vaginal microbiome, published from August 2012 to August 2022, identified 760 articles. Results: Among the 52 articles meeting the prespecified criteria, BV prevalence varied among different populations and disproportionately impacted Black women (49-51%), Hispanic ethnicity (32-43%), and women of reproductive age (30%). Differences in microbial ecology and host genetics were important factors underlying these disparities. Colonization of BV-associated bacteria was more common in women of color than in non-Hispanic White women. Other factors linked with disproportionate burden included multiple/same-sex partners, obesity, immunosuppression, and C-section birth. Conclusions: BV prevalence was multifactorial, with some populations having higher prevalence rates and distinctive microbiome profiles that may predispose them to the condition. BV treatment and recurrence prevention were challenging due to the complex interplay of biological, clinical, and sociobehavioral factors. Understanding these disparate risk factors is critical to reducing BV burden.}, }
@article {pmid40062725, year = {2025}, author = {Galindo-Moreno, P and Gutierrez-Garrido, L and Duarte, J and Robles-Vera, I and Martin-Morales, N and O'Valle, F and Olaechea, A and Carrillo-Galvez, AB and Padial-Molina, M}, title = {Evolution in the Peri-Implant Oral Microbiome and Their Relationship to Long-Term Marginal Bone Loss: A Randomized Clinical Study.}, journal = {Clinical oral implants research}, volume = {}, number = {}, pages = {}, doi = {10.1111/clr.14426}, pmid = {40062725}, issn = {1600-0501}, support = {//Dentsply Sirona Iberia/ ; CTS-138//Junta de Andaluc&#xed;a/ ; CTS-164//Junta de Andaluc&#xed;a/ ; CTS-1028//Junta de Andaluc&#xed;a/ ; PID2020-116347RB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; //MIS Implants Technologies Ltd./ ; }, abstract = {OBJECTIVES: To analyze the clinical, radiographic, and microbiological changes around implants with a multiphosphonate-treated surface, prosthetically loaded with two different protocols after 5 years of functional loading.<br><br>MATERIAL AND METHODS: A randomized clinical trial was designed to initiate prosthetic loading over single dental implants after 8 (control) or 4&#x2009;weeks (test). Several variables were analyzed, including patients' level variables, intrasulcular biofilm, and marginal bone level at several time points, from 1 to 60&#x2009;months after loading.<br><br>RESULTS: A total of 23 patients attended the 5-year follow-up visit. No clinical variable changed over time, except mucosal thickness from dental impressions to prosthesis delivery. No significant radiographic differences were observed either over time or between groups. Microbiologically, there was a change in the microbiome from the constitution of the biological width to the final follow-up. Seven species changed significantly, with a significant increase in Porphyromonas gingivalis and Tannerella forsythia from 12 to 60&#x2009;months and a decrease in the other species. However, changes in the relative abundance of species over time, whether increasing or decreasing, did not show a correlation with marginal bone loss.<br><br>CONCLUSION: Implants with a multiphosphonate-treated surface showed no differences in clinical and radiographic variables after 5&#x2009;years of function, regardless of the prosthetic loading protocol used. From a microbiological point of view, although there was an evolution of the microbiome in the peri-implant sulcus towards Socransky's red circle pathogenic bacteria, no microorganism showed a significant correlation with the radiographic changes produced in the peri-implant bone over time.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT03059108.}, }
@article {pmid40062472, year = {2025}, author = {Keane, K and Stephens, M and Roizes, S and Xue, J and Liao, S and von der Weid, PY}, title = {The Spatiotemporal Development of Mesenteric Lymphatic Changes in the TNF[ΔARE/+] Mouse Model of Terminal Ileitis.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpgi.00334.2024}, pmid = {40062472}, issn = {1522-1547}, support = {623941//Crohn's and Colitis Canada (Crohn et Colite Canada)/ ; //Lymphedema Research and Education Program, Snyder Institute for Chronic Diseases, University of Calgary/ ; }, abstract = {Crohn's disease (CD) is a chronic inflammatory bowel disease which also encompasses significant alterations of the mesenteric lymphatic system. Whether these changes are a mere consequence of, or directly contribute to the inflammation is unknown. Here we characterized the spatial and temporal development of these events in the TNF[ΔARE/+] mouse, which develops CD-like ileitis and significant mesenteric lymphatic alterations. At 8-, 12-, 20-, and 28 weeks of age, specific pathogen-free (SPF), germ-free (GF) TNF[ΔARE/+] and WT mice were assessed for ileitis via myeloperoxidase activity (MPO) while mesenteric lymphatic alterations were assessed by confocal immunofluorescence imaging. Lymphatic alterations in the SPF TNF[ΔARE/+] occurred in a stepwise manner between 8 and 28 weeks of age beginning with the development of mesenteric lymphadenopathy at 8 weeks despite no significant ileitis. By 12 weeks ileal MPO significantly elevates concomitantly with lymphangiectasia of the mesenteric collecting lymphatic vessels (CLV) and clustering of CD45[+] immune cells around them. At 20 weeks, significant lymphangiogenesis of the initials (ILV) and tertiary lymphoid organs aligned along lymphatic collectors (CA-TLOs) had developed. At 28 weeks, lymphangiectasia, lymphangiogenesis, and CA-TLOs increased. However, 28-week-old GF TNF[ΔARE/+], while displaying no ileitis, presented with mesenteric lymphadenopathy, lymphangiectasia, and lymphangiogenesis but no immune cell clustering nor CA-TLOs. The TNF[ΔARE/+] mice develop terminal ileitis and lymphatic alterations in a stepwise manner beginning with MLN lymphadenopathy and ileal inflammation, followed by CLV dilation and lymphangiogenesis. These lymphatic alterations are exacerbated by the gut microbiome, with immune cell clustering and TLO formation being entirely dependent of its presence.}, }
@article {pmid40062463, year = {2025}, author = {Roth, BJ and Khooblall, P and Leelani, N and Suryavanshi, M and Shumaker, A and Werneburg, G and Miller, A and Bajic, P}, title = {Antimicrobial resistance and biofilm formation of penile prosthesis isolates: insights from in-vitro analysis.}, journal = {The journal of sexual medicine}, volume = {}, number = {}, pages = {}, doi = {10.1093/jsxmed/qdaf001}, pmid = {40062463}, issn = {1743-6109}, support = {//Coloplast Corporation/ ; }, abstract = {BACKGROUND: Inflatable penile prostheses (IPPs) have been shown to harbor biofilms in the presence and absence of infection despite exposure to various antimicrobials. Microbes persisting on IPPs following antibiotic exposure have not been adequately studied to assess biofilm formation capacity and antibiotic resistance.<br><br>AIM: In this study, we aimed to assess these properties of microbes obtained from explanted infected and non-infected IPPS using an in vitro model.<br><br>METHODS: 35 bacterial isolates were grown and tested against various single-agent or multiple agent antibiotic regimens including: bacitracin, cefaclor, cefazolin, gentamicin, levofloxacin, trimethoprim-sulfamethoxazole, tobramycin, vancomycin, piperacillin/tazobactam, gentamicin + piperacillin/tazobactam, gentamicin + cefazolin, and gentamicin + vancomycin. Zones of inhibition were averaged for each sample site and species. Statistics were analyzed with Holm's corrected, one-sample t-tests against a null hypothesis of 0. Isolates were also allowed to form biofilms in a 96-well polyvinyl plate and absorbance was tested at 570&#xa0;nm using a microplate reader.<br><br>OUTCOMES: Resistance was determined via clinical guidelines or previously established literature, and the mean and standard deviation of biofilm absorbance values were calculated and normalized to the optical density600 of the bacterial inoculum.<br><br>RESULTS: Every species tested was able to form robust biofilms with the exception of Staphylococcus warneri. As expected, most bacteria were resistant to common perioperative antimicrobial prophylaxis. Gentamicin dual therapy demonstrated somewhat greater efficacy.<br><br>STRENGTHS AND LIMITATIONS: This study examines a broad range of antimicrobials against clinically obtained bacterial isolates. However, not all species and antibiotics tested had standardized breakpoints, requiring the use of surrogate values from the literature. The microbes included in this study and their resistance genes are expectedly biased towards those that survived antibiotic exposure, and thus reflect the types of microbes which might "survive" in vivo exposure following revisional surgery.<br><br>CLINICAL TRANSLATION: Despite exposure to antimicrobials, bacteria isolated during penile prosthesis revision for both infected and non-infected cases exhibit biofilm forming capacity and extensive antibiotic resistance patterns in vitro. These microbes merit further investigation to understand when simple colonization vs re-infection might occur.<br><br>CONCLUSIONS: Although increasing evidence supports the concept that all IPPs harbor biofilms, even in the absence of infection, a deeper understanding of the characteristics of bacteria that survive revisional surgery is warranted. This study demonstrated extensive biofilm forming capabilities, and resistance patterns among bacteria isolated from both non-infected and infected IPP revision surgeries. Further investigation is warranted to determine why some devices become infected while others remain colonized but non-infected.}, }
@article {pmid40062406, year = {2025}, author = {Moutsoglou, D and Ramakrishnan, P and Vaughn, BP}, title = {Microbiota transplant therapy in inflammatory bowel disease: advances and mechanistic insights.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2477255}, doi = {10.1080/19490976.2025.2477255}, pmid = {40062406}, issn = {1949-0984}, mesh = {Humans ; *Inflammatory Bowel Diseases/therapy/microbiology/immunology ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Animals ; }, abstract = {Microbiota transplant therapy is an emerging therapy for inflammatory bowel disease, but factors influencing its efficacy and mechanism remain poorly understood. In this narrative review, we outline key elements affecting therapeutic outcomes, including donor factors (such as age and patient relationship), recipient factors, control selection, and elements impacting engraftment and its correlation with clinical response. We also examine potential mechanisms through inflammatory bowel disease trials, focusing on the interplay between the microbiota, host, and immune system. Finally, we briefly explore potential future directions for microbiota transplant therapy and promising emerging treatments.}, }
@article {pmid40062050, year = {2025}, author = {Almuntashiri, SA and Alsubaie, FF and Alotaybi, M}, title = {Plant-Based Diets and Their Role in Preventive Medicine: A Systematic Review of Evidence-Based Insights for Reducing Disease Risk.}, journal = {Cureus}, volume = {17}, number = {2}, pages = {e78629}, pmid = {40062050}, issn = {2168-8184}, abstract = {Plant-based diets have gained increasing attention for their potential role in preventive medicine, particularly in reducing the risk of chronic diseases such as type 2 diabetes, cardiovascular disease, obesity, and metabolic syndrome. This systematic review synthesizes evidence from 32 longitudinal studies to evaluate the impact of plant-based diets on disease prevention and health outcomes. The review identifies consistent patterns, including improved metabolic health, weight management, cardiovascular risk reduction, and positive effects on gut microbiome composition and inflammation. However, inconsistencies arise due to variability in diet definitions, mixed findings on specific outcomes, and heterogeneity in study populations. Critical gaps in the literature include the lack of long-term studies, limited mechanistic insights, underrepresentation of diverse populations, and a need for more rigorous intervention studies and personalized nutrition approaches. Identified research gaps highlight the need for long-term studies, deeper exploration of mechanistic pathways, and greater inclusivity of diverse populations. These insights underscore the significance of plant-based diets as a cornerstone of preventive medicine while emphasizing the necessity for targeted interventions and personalized approaches to maximize their benefits. The findings contribute to a growing body of evidence supporting the integration of plant-based dietary strategies into public health policies and clinical practices.}, }
@article {pmid40061946, year = {2025}, author = {Guan, Y and Cheng, H and Zhang, N and Cai, Y and Zhang, Q and Jiang, X and Wang, A and Zeng, H and Jia, B}, title = {The role of the esophageal and intestinal microbiome in gastroesophageal reflux disease: past, present, and future.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1558414}, pmid = {40061946}, issn = {1664-3224}, mesh = {Humans ; *Gastroesophageal Reflux/microbiology/immunology ; *Gastrointestinal Microbiome/immunology ; *Dysbiosis/immunology ; *Esophagus/microbiology/immunology ; Animals ; }, abstract = {Gastroesophageal reflux disease (GERD) is one of the common diseases of the digestive system, and its incidence is increasing year by year, in addition to its typical symptoms of acid reflux and heartburn affecting the quality of patients' survival. The pathogenesis of GERD has not yet been clarified. With the development of detection technology, microbiome have been studied in depth. Normal microbiome are symbiotic with the host and can assist the host to fulfill the roles of digestion and absorption, and promote the development of the host. Dysbiosis of the microbiome forms a new internal environment, under which it may affect the development of GERD from the perspectives of molecular mechanisms: microbial activation of Toll-like receptors, microbial stimulation of cyclooxygenase-2 expression, microbial stimulation of inducible nitrous oxide synthase, and activation of the NLRP3 inflammatory vesicle; immune mechanisms; and impact on the dynamics of the lower gastrointestinal tract. This review will explore the esophageal microbiome and intestinal microbiome characteristics of GERD and the mechanisms by which dysbiotic microbiome induces GERD.}, }
@article {pmid40061819, year = {2024}, author = {Ren, HY and Lv, Y and Ma, BN and Gao, C and Yuan, HM and Meng, HH and Cao, ZQ and Chen, YT and Zhang, YX and Zhang, YT and Liu, W and Fan, YP and Li, MH and Wu, YX and Feng, ZY and Zhang, XX and Luo, ZJ and Tang, QY and Wesselius, A and Chen, J and Luo, HX and ,  and Qin, QR and Chen, L and Yu, EY}, title = {Cohort Profile: TRacing Etiology of Non-communicable Diseases (TREND): Rationale, Progress and Perspective.}, journal = {Phenomics (Cham, Switzerland)}, volume = {4}, number = {6}, pages = {584-591}, pmid = {40061819}, issn = {2730-5848}, abstract = {UNLABELLED: The TRacing Etiology of Non-communicable Diseases (TREND) cohort is a prospective longitudinal cohort and biobank that is mainly based in Ma'anshan, Anhui Province, China. The primary aim of the study is to decipher comprehensive molecular characterization and deep phenotyping for a broad spectrum of chronic non-communicable diseases (NCDs), which focuses on providing mechanistic insights with diagnostic, prognostic and therapeutic implications. The recruitment was initiated in 2023 and is expected to complete in 2025 with 20,000 participants originated from urban and rural area. In the first phase, 3360 participants were recruited. Follow-up visits are scheduled annually and intervally for a total of 30 years. The cohort includes individuals aged over 18 years. Two participants with first-degree linkage were recruited from a household. The age distribution of recruited participants was stratified into four categories: 18-45, 45-55, 55-65, and ≥65 years, aligning with the population proportions of Ma'anshan. Meanwhile, the gender distribution was controlled by pairing men and women from the same household. Data collected at baseline includes socio-economic information, medical history, lifestyle and nutritional habits, anthropometrics, blood oxygen, electrocardiogram (ECG), heart sound, as well as blood, urine and feces tests results. Molecular profiling includes genome, proteome, metabolome, microbiome and extracellular vesicles -omics. Blood, urine and fecal samples are collected and stored at -80 °C in a storage facility for future research.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-024-00196-4.}, }
@article {pmid40061431, year = {2025}, author = {Alamri, A and Alhassan, M and Almutairi, AK and Jayaseeli, N and Berg, RP and Stensvold, CR and Andersen, LO and Nielsen, HV and AlKhater, SA}, title = {Airway Microbiota Profiles in Children With and Without Asthma: A Comparative Study.}, journal = {Journal of asthma and allergy}, volume = {18}, number = {}, pages = {349-361}, pmid = {40061431}, issn = {1178-6965}, abstract = {BACKGROUND: Asthma is a common chronic respiratory disease that affects children and adults and can have a serious impact on their quality of life. Factors contributing to the development of asthma and related exacerbations are multifactorial, with microbial communities colonizing the airways possibly playing a key role.<br><br>METHODS: The study included asthmatic (79) and healthy children (57) aged 5-16 years. Nasal and throat swabs were collected, and bacterial (16s rRNA) and fungal (18s rRNA) amplicon sequence analysis was performed. Diversity indices and the most abundant microbial genera were estimated accordingly.<br><br>RESULTS: At the level of the bacteriome in the nasal samples, the asthma group had significantly lower diversity than the control group (p = 0.02). However, the microbiota of the asthma cohort was more evenly distributed, and staphylococci were enriched in the control group. Throat samples collected from the asthma cohort revealed significantly lower diversity (p < 0.0001), with a significant difference in species composition between the two groups (p = 0.005). Enriched bacterial species were different within the asthma subgroups (controlled vs uncontrolled asthma). The fungal microbiome of the nasal and throat samples showed no difference in species richness between the two groups, however, a significant difference in beta diversity (species composition) was detected. The nasal samples from the control group were enriched with Malassezia species, while the asthma cases were enriched with Mucor species. On the other hand, throat specimens of the asthma group were found to be enriched with Candida and Saccharomyces.<br><br>CONCLUSION: Our findings suggest that asthmatic samples were less diverse than the control samples with certain microbial genera enriching some study groups. Addressing the biomarkers that influence the progression of asthma could lead to improved care for children suffering from severe asthmatic episodes, possibly by including targeted therapies and prevention strategies.}, }
@article {pmid40061321, year = {2025}, author = {Lamichhane, S and Dickens, AM and Buchacher, T and Lou, ET and Charron-Lamoureux, V and Kattelus, R and Karmacharya, P and Pinto da Silva, L and Kråkström, M and Rasool, O and Sen, P and Walker, C and Patan, A and Gentry, EC and Arzoomand, A and Lakshmikanth, T and Mikeš, J and Mebrahtu, A and Vatanen, T and Raffatellu, M and Zengler, K and Hyötyläinen, T and Xavier, RJ and Brodin, P and Lahesmaa, R and Dorrestein, PC and Knip, M and Orešič, M}, title = {Trajectories of microbiome-derived bile acids in early life - insights into the progression to islet autoimmunity.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.18.25322275}, pmid = {40061321}, abstract = {Recent studies reveal that gut microbes produce diverse bile acid conjugates, termed microbially conjugated bile acids (MCBAs). However, their regulation and health effects remain unclear. Here, we analyzed early-life MCBA patterns and their link to islet autoimmunity. We quantified 110 MCBAs in 303 stool samples collected longitudinally (3- 36 months) from children who developed one or more islet autoantibodies and controls who remained autoantibody-negative. Stool MCBAs showed distinct age-dependent trajectories and correlated with gut microbiome composition. Altered levels of ursodeoxycholic and deoxycholic acid conjugates were linked to islet autoimmunity as well as modulated monocyte activation in response to immunostimulatory lipopolysaccharide and Th17/Treg cell balance. These findings suggest MCBAs influence immune development and type 1 diabetes risk.}, }
@article {pmid40061054, year = {2025}, author = {Dixon, R and Egan, S and Payne, M and Mullally, C and Chapman, B}, title = {Bacterial transfer during sexual intercourse as a tool for forensic detection.}, journal = {iScience}, volume = {28}, number = {2}, pages = {111861}, pmid = {40061054}, issn = {2589-0042}, abstract = {In forensic science, detecting transfers of physical and biological material is critical for establishing evidence of criminal involvement. Unique bacterial signatures from the reproductive system transfer during unprotected penetrative intercourse offer a novel tool for criminal investigation. Here, we demonstrate this transfer using full-length 16S rRNA gene sequencing and discuss the impact of barrier contraceptives. These microbial signatures can potentially aid in sexual assault casework for perpetrator identification when human male DNA is absent.}, }
@article {pmid40060808, year = {2025}, author = {Gao, B and Shi, X and Zhao, M and Ren, F and Xu, W and Gao, N and Shan, J and Shen, W}, title = {Mixture Effects of Polystyrene Microplastics on the Gut Microbiota in C57BL/6 Mice.}, journal = {ACS omega}, volume = {10}, number = {8}, pages = {7597-7608}, pmid = {40060808}, issn = {2470-1343}, abstract = {Microplastics are plastic particles with sizes of less than 5 mm. The ubiquity of microplastics in the environment has raised serious public health concerns. Microplastics could disturb the composition of the gut microbiota due to both chemical composition and physical interactions, which might further influence the metabolism and immune function of the host. However, most of the exposure studies chose microplastics of specific sizes. In the natural environment, living organisms are exposed to a mixture of microplastics of various sizes. In this study, male C57BL/6 mice were exposed to polystyrene (PS) microplastics with different sizes, including microplastics with diameters of 0.05-0.1 μm (PS0.1 group, 100 ppb), 9-10 μm (PS10 group, 100 ppb), and microplastic mixtures of both 0.05-0.1 and 9-10 μm (PSMix group) at a total concentration of 100 ppb (50 ppb for each size). Mixture effects of microplastics were investigated on the composition of bacteria and fungi as well as functional metagenome and microbial genes encoding antibiotic resistance and virulence factors. We found that some bacteria, fungi, and microbial metabolic pathways were only altered in the PSMix group, not in the PS0.1 or PS10 group, suggesting the toxic effects of the microplastic mixture on the composition of fungi and bacteria, and the functional metagenome is different from the effects of microplastics at specific sizes. Meanwhile, altered genes encoding antibiotic resistance and virulence factors in the PSMix group were shared with the PS0.1 and PS10 groups, possibly due to functional redundancy. Our findings help improve the understanding of the toxic effects of the microplastic mixture on the gut microbiome.}, }
@article {pmid40060755, year = {2025}, author = {Yi, D and Li, T and Xiao, Y and Zhang, X and Hao, Q and Zhang, F and Qiu, T and Yang, G and Sun, X and Dong, Y and Wang, N}, title = {Fecal microbiota transplantation for the treatment of intestinal and extra-intestinal diseases: Mechanism basis, clinical application, and potential prospect.}, journal = {Bioengineering &amp; translational medicine}, volume = {10}, number = {2}, pages = {e10728}, pmid = {40060755}, issn = {2380-6761}, abstract = {To review the theoretical basis and therapeutic effects of fecal microbiota transplantation (FMT) in various diseases in animal experiments and clinical studies, as well as the limitations and current standards of FMT application. PubMed and Web of Science databases were searched for articles published only in English between 1975 and 2023 on reliable results of animal experiments and clinical treatment of FMT. The properties of the gut microbiota and its interactions with the host metabolism are critical to human health, and microbiome disturbance is closely associated with human intestinal and extra-intestinal diseases. Therefore, therapeutic tools targeting on the modulation of gut microbiota have attracted increasing attention, among which FMT represents the most widely studied intervention strategy. This review gathered and summarized application of FMT in intestinal diseases, metabolic diseases, hypertension, cancer, nervous system diseases and arthritis, and elaborated the beneficial effects that can be achieved by altering the microbiota with FMT and the mechanisms of action. In addition, the potential risks and side effects of FMT approach are discussed, as well as current efforts to standardize the development of FMT. Through a systemic review of the outcome and mechanism of FMT in the treatment of intestinal diseases and extra-intestinal diseases, we aimed to provide a theoretical basis for the construction of an optimized FMT framework, so as to better exert its application prospects.}, }
@article {pmid40060716, year = {2025}, author = {Zhao, Y and Yuan, X and Ran, W and Zhao, Z and Su, D and Song, Y}, title = {The Ecological Restoration Strategies in Terrestrial Ecosystems Were Reviewed: A New Trend Based on Soil Microbiomics.}, journal = {Ecology and evolution}, volume = {15}, number = {3}, pages = {e70994}, pmid = {40060716}, issn = {2045-7758}, abstract = {Soil microorganisms play a pivotal role in the biogeochemical cycle and serve as crucial indicators of ecological restoration in terrestrial ecosystems. The soil microbial community is regarded as a pivotal participant in environmental processes, offering both positive and negative feedback to diverse media within the ecosystem. This community can serve as a potential indicator in ecological monitoring and restoration processes. Consequently, an increasing number of scholars are directing their research towards the field of soil microbial ecology in diverse ecosystems and fragile areas, with the aim of elucidating the intricate interactions between microbes and vegetation. However, the implementation of soil microbiome in ecological restoration remains in the experimental stage due to the interference of extreme events and the complexity of governance measures. Consequently, a comprehensive evaluation of existing research is imperative. This review aims to address the ecological crises currently experienced by diverse terrestrial ecosystems and to provide a comprehensive overview of the specific practices of soil microorganisms in the context of ecological restoration. We also incorporate them into fragile habitats and identify urgent issues that need to be addressed in the ecological restoration process of fragile areas.}, }
@article {pmid40060518, year = {2025}, author = {Day, AW and Perez-Lozada, J and DiLeo, A and Blandino, K and Maguire, J and Kumamoto, CA}, title = {Candida albicans Colonization Modulates Murine Ethanol Consumption and Behavioral Responses Through Elevation of Serum Prostaglandin E 2 and Impact on the Striatal Dopamine System.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.25.640044}, pmid = {40060518}, issn = {2692-8205}, abstract = {UNLABELLED: Candida albicans is a commensal yeast that is a common component of the gastrointestinal (GI) microbiome of humans. C. albicans has been shown to bloom in the GI tract of individuals with alcohol use disorder (AUD) and can promote and increase the severity of alcoholic liver disease (ALD). However, the effects of C. albicans blooms on the host in the context of AUD or AUD-related phenotypes, such as ethanol preference, have been unstudied. In this work, we report a reduction in ethanol consumption and preference in mice colonized with C. albicans . C. albicans- colonized mice exhibited elevated levels of serum PGE 2 and reduced ethanol preference was reversed by injection with antagonists of PGE 2 receptors. Further, injection of mice with a PGE 2 derivative decreased their ethanol preference. These results show that PGE 2 acting on its receptors EP1 and EP2 drives reduced ethanol preference in C. albicans- colonized mice. We also showed altered transcription of dopamine receptors in the dorsal striatum of C. albicans- colonized mice and more rapid acquisition of ethanol conditioned taste aversion, suggesting alterations to reinforcement or aversion learning. Finally, C. albicans -colonized mice were more susceptible to ethanol-induced motor coordination impairment showing significant alterations to the behavioral effects of ethanol. This study identifies a member of the fungal microbiome that alters ethanol preference and demonstrates a role for PGE 2 signaling in these phenotypes.<br><br>IMPORTANCE: Candida albicans is a commensal yeast that is found in the gut of most individuals. C. albicans has been shown to contribute to alcoholic liver disease. Outside of this, the impact of intestinal fungi on alcohol-use disorder (AUD) had been unstudied. As AUD is a complex disorder characterized by high relapse rates, and there are only 3 FDA-approved therapies for the maintenance of abstinence, it is important to study novel AUD contributors to find new therapeutic targets. Here we show that an intestinal fungus, C. albicans , can alter mammalian ethanol consumption through an immune modulator, prostaglandin E 2 . The results highlight novel contributors to AUD-related phenotypes and further implicate the gut-brain axis in AUD. Future studies could lead to new therapeutic avenues for the treatment of AUD.}, }
@article {pmid40060402, year = {2025}, author = {McDermott, CR and Gao, Z and Mirmajlesi, AS and Ntim, C and Kimbark, K and Thomas, D and Mughal, Z and Zhang, XS and Zhou, X and Popov, D and Halchenko, A and Xing, J and Thakker-Varia, S and Alder, J and Millonig, JH and Samuels, BA and Blaser, MJ and DiCicco-Bloom, E}, title = {The 16p11.2 microdeletion influences how early-life microbiota perturbations affect hippocampal development and behavior throughout the lifespan.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.25.639888}, pmid = {40060402}, issn = {2692-8205}, abstract = {Neurodevelopmental disorders result from interactions between genetic predisposition and environmental risk factors, with infancy being the most vulnerable period. We designed a longitudinal study to determine how short-term antibiotic exposure during early postnatal life impacts the gut microbiome, neurodevelopment, and behavior, and whether these alterations were exacerbated by the neurodevelopmental disorder-associated 16p11.2 microdeletion (16pDel) mutation. The cephalosporin antibiotic, cefdinir, broadly altered the gut microbiome acutely, with persistent reductions in several Lachnospiraceae genera despite overall recovery. These alterations preceded long-term behavioral changes, including reduced juvenile sociability, compromised risk assessment, and deficits in associative learning. Remarkably, only cefdinir-exposed 16pDel mice had changes in hippocampal stem cell proliferation, subsequent adolescent cell numbers, and gene expression compared to other groups, demonstrating that genetic predisposition can modulate the effects of early-life antibiotic exposure on neurodevelopment. These alterations may be mediated by gastrointestinal disturbances, as cefdinir-exposed 16pDel males had increased intestinal permeability and shifted metabolite profiles including arginine biosynthesis and glycerophospholipid metabolism. Taken together, this study highlights how early-life microbial alterations affect behavior and reveals that genetic predisposition influences antibiotic-induced changes in hippocampal development. Further, these insights identify metabolic mechanisms as potential targets for intervention and may raise concerns regarding antibiotic use during infancy.}, }
@article {pmid40060387, year = {2025}, author = {Kim, M and Wang, J and Pilley, SE and Lu, RJ and Xu, A and Kim, Y and Liu, M and Fu, X and Booth, SL and Mullen, PJ and Benayoun, BA}, title = {Estropausal gut microbiota transplant improves measures of ovarian function in adult mice.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.05.03.592475}, pmid = {40060387}, issn = {2692-8205}, abstract = {Decline in ovarian function with age not only affects fertility but is also linked to a higher risk of age-related diseases in women (e.g . osteoporosis, dementia). Intriguingly, earlier menopause is linked to shorter lifespan; however, the underlying molecular mechanisms of ovarian aging are not well understood. Recent evidence suggests the gut microbiota may influence ovarian health. In this study, we characterized ovarian aging associated microbial profiles in mice and investigated the effect of the gut microbiome from young and estropausal female mice on ovarian health through fecal microbiota transplantation. We demonstrate that the ovarian transcriptome can be broadly remodeled after heterochronic microbiota transplantation, with a reduction in inflammation-related gene expression and trends consistent with transcriptional rejuvenation. Consistently, these mice exhibited enhanced ovarian health and increased fertility. Using metagenomics-based causal mediation analyses and serum untargeted metabolomics, we identified candidate microbial species and metabolites that may contribute to the observed effects of fecal microbiota transplantation. Our findings reveal a direct link between the gut microbiota and ovarian health.}, }
@article {pmid40060342, year = {2024}, author = {Koyyala, VPB and Kantharia, C and Darooka, N and Kumar, M and Ranjan, P and Anikhindi, S and Bansal, NK and Sharma, P and Bhalla, DVP and Kumar, M and Sharma, M and Abrol, D and Sahni, P and Ardhanari, R and Pradeep, R and Yadav, A and John, S and Rawat, S and Parikh, P and Selvasekar, C and Aggarwal, S}, title = {Inflammatory Bowel Disease and Colorectal Cancer: An Eternal Fire in a Beautiful Garden.}, journal = {South Asian journal of cancer}, volume = {13}, number = {4}, pages = {300-304}, pmid = {40060342}, issn = {2278-330X}, abstract = {Inflammatory bowel disease (IBD), encompassing Crohn's disease and ulcerative colitis, significantly increases the risk of colitis-associated cancer (CAC). Chronic inflammation, a key contributor to carcinogenesis, disrupts immune surveillance, induces deoxyribonucleic acid (DNA) damage, and alters genetic and epigenetic pathways. Molecular pathways such as STAT3, mTOR, and NF-κB drive CAC progression, while unique microbiome alterations-loss of Faecalibacterium prausnitzii and increases in Escherichia coli and Fusobacterium species-exacerbate the inflammatory milieu. CAC accounts for 2% of all colon cancers and up to 15% of IBD-related deaths. Risk correlates with IBD duration, increasing approximately 1% annually after the first decade. Surveillance via colonoscopy is crucial, with chromoendoscopy recommended for high-risk cases. Preventive drugs, including aminosalicylates, thiopurines, and biologics, offer modest benefits but lack conclusive evidence. Post-CAC diagnosis, immunosuppressants are discontinued in favor of corticosteroids, with 5-aminosalicylates continued as needed. The use of immune checkpoint inhibitors remains controversial due to exacerbation of colitis. Emerging insights into the gut microbiota's role in IBD and CAC may revolutionize prevention and management strategies. Advances in screening, surveillance, and therapeutic approaches have reduced CAC mortality, underscoring the importance of personalized medicine and ongoing research to address these complex conditions.}, }
@article {pmid40060340, year = {2024}, author = {Agrawal, M and Surendran, AK and Venkatesh, KK and Velammal, PNKP and Zope, S and Goel, A and Pathak, A and Mittal, M and K K, V and Vinakar, AS and Agrawal, D and Parikh, PM}, title = {Screening for Colorectal Carcinoma in India: Real-World Scenario, Pitfalls, and Solutions.}, journal = {South Asian journal of cancer}, volume = {13}, number = {4}, pages = {229-235}, pmid = {40060340}, issn = {2278-330X}, abstract = {INTRODUCTION: Noninvasive colorectal cancer (CRC) screening has introduced innovative blood- and stool-based biomarkers, improving early detection and enabling personalized solutions. Global and Indian adoption of CRC screening remains a public health challenge. This study evaluates the real-world utility of screening colonoscopy, as recommended by global guidelines.<br><br>METHODOLOGY: A survey based on the American Medical Association (AMA) guidelines was designed, setting 45+ years as the cutoff age for colonoscopy screening. A Google form was shared via social media application with health care professionals. Participation was voluntary, responses were collected over 30 days, and data were analyzed.<br><br>RESULTS: A total of 2,199 individuals' data were analyzed. Among these, 1,374 were eligible for screening colonoscopy, out of which only 7.14% (98/1,374) actually underwent the procedure.<br><br>CONCLUSION: Among various cancer programs, screening sigmoidoscopy has proved to improve both CRC-specific mortality and all-cause mortality. Unfortunately, its utilization is suboptimal, at best. Even among the highly educated medical community, the real-world utility was only in 7.14% of the eligible population. Barriers include invasive nature of intervention, need for appropriate bowel preparation, operator dependence, and small but significant risk of serious toxicity. An important method of increasing utility of screening colonoscopy is use of a test that can identify high-risk population, who can then be persuaded to undergo screening colonoscopy. This is the value of recently developed noninvasive blood- and stool-based tests, like Guardant Health's Shield. Being U.S. Food and Drug Administration (FDA) approved with specificity of 90% and sensitivity of 84%, it should be offered to all eligible persons who can afford it, thereby increasing colonoscopy use and potentially saving lives.}, }
@article {pmid40060328, year = {2025}, author = {Pietruska, A and Macklin, KS and Wang, X and Krehling, JT and Dormitorio, T and Hauck, R}, title = {Investigation of Intestinal Health in Broiler Chickens Following Salmonella Typhimurium and Coccidiosis Vaccination and Challenge with Salmonella Typhimurium.}, journal = {The journal of poultry science}, volume = {62}, number = {}, pages = {2025009}, pmid = {40060328}, issn = {1349-0486}, abstract = {Salmonella enterica and coccidia (Eimeria spp.) are important intestinal pathogens in broiler production. Salmonella has high zoonotic potential, and coccidia are responsible for large economic losses. Live vaccines reduce shedding of Salmonella and minimize the impact of coccidial infections on broiler performance. This study investigated the interaction between both vaccines on the intestinal health of broilers. The 2 × 2 experimental design included vaccination against Salmonella Typhimurium (ST) (no vaccination or vaccination on day 14) and vaccination against coccidiosis (no vaccination or vaccination on day 1). On day 28, all groups were challenged with a ST marker strain resistant to nalidixic acid. Re-isolation of ST from the liver and ceca on day 42 indicated higher susceptibility to systemic infection with ST in birds vaccinated against coccidiosis than that in unvaccinated birds. On day 42, cecal immunoglobulin A (IgA) levels against ST decreased in the group vaccinated against ST and coccidia compared to those in all other groups. IgG antibodies in the cecal contents significantly decreased in the group vaccinated against coccidiosis compared to that of the group vaccinated against ST. There was no difference in systemic IgG levels among groups. Analysis of the cecal microbiota revealed a significant difference in beta diversity on days 28 and 42 between the groups vaccinated against coccidiosis and unvaccinated groups. Functional pathway profiling showed increased activity of pathways associated with carbohydrate and arachidonic acid metabolism in the group vaccinated against ST compared to that in other groups. Gene expression of claudin 1, claudin 4, E-cadherin, β-catenin, and zonula occludens 2 in the cecal wall differed between the groups on days 28 and 42. These findings indicated the significant influence of ST and coccidiosis vaccines on the intestinal health of broilers; however, further studies are required to clarify the implications for health and performance.}, }
@article {pmid40060187, year = {2025}, author = {Cao, J and Ma, Y and Fu, J and Wang, Z and Zhao, Y and Zhong, N and Zhao, P}, title = {Bacillus atrophaeus DX-9 biocontrol against potato common scab involves significant changes in the soil microbiome and metabolome.}, journal = {aBIOTECH}, volume = {6}, number = {1}, pages = {33-49}, pmid = {40060187}, issn = {2662-1738}, abstract = {UNLABELLED: Potato common scab (CS) is a worldwide disease, caused by Streptomyces spp., and its presence reduces the market value of potatoes. A nontoxic and potentially effective approach in many control strategies is the use of antagonistic microbes as biocontrol agents. In this study, Bacillus atrophaeus DX-9 was isolated and assessed for its ability to protect against CS. Through integrated metagenomic and metabolomic analyses, changes in the soil microbial community structure and soil properties were analyzed to understand the effects of Bacillus atrophaeus DX-9 on CS. These studies revealed that DX-9 inoculation could significantly decrease CS disease rate, disease index, and the number of CS pathogens, along with an increase in soil N and P content. Our metagenomic assays identified 102 phyla and 1154 genera, and DX-9 inoculation increased the relative abundances of the phyla Pseudomonadota, Chloroflexota and Gemmatimonadota. Additionally, an increase in the relative abundance of genera, such as Bradyrhizobium, Agrobacterium, and Nitrobacter, were significantly and positively correlated with soil N and P. Metabolomic analysis revealed that DX-9 inoculation significantly increased the soil levels of phytolaccoside A, 7,8-dihydropteroic acid, novobiocin, and azafrin. These compounds were enriched in microbe pathway metabolites, including xenobiotic biodegradation and metabolism, biosynthesis of other secondary metabolites, and metabolism of cofactors and vitamins. In summary, the use of Bacillus atrophaeus DX-9 against potato CS offers an alternative biocontrol method that can improve both soil microbial community and properties. This study provides insight into the potential mechanisms by which microbial inoculants can control CS disease.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42994-025-00199-3.}, }
@article {pmid40060035, year = {2025}, author = {Seyedmoalemi, MA and Saied-Moallemi, Z}, title = {Association between periodontitis and Alzheimer's disease: A narrative review.}, journal = {IBRO neuroscience reports}, volume = {18}, number = {}, pages = {360-365}, pmid = {40060035}, issn = {2667-2421}, abstract = {Periodontitis is a chronic inflammatory disease that progressively damages the supporting structures of teeth, resulting in gum bleeding, inflammation, gum recession, and eventual tooth loss. Key factors, including poor oral hygiene, plaque accumulation, smoking, inadequate nutrition, and genetic predisposition, drive its development. Recent evidence underscores the potential role of periodontitis as a contributing factor to systemic diseases, including Alzheimer's disease (AD). AD is a neurodegenerative disorder marked by memory loss, cognitive decline, and brain inflammation. Emerging clinical and experimental studies indicate that these two conditions share overlapping risk factors and may be interconnected. One notable finding is the detection of specific periodontal pathogens, such as Porphyromonas gingivalis (P. gingivalis), in the brains of individuals with AD. This suggests a possible link between chronic oral infections and neurodegeneration. These pathogens are believed to exacerbate neuroinflammatory processes by activating microglia and promoting systemic inflammation, which is central to AD pathogenesis. Further research is needed to clarify the biological mechanisms underlying this association. Targeted interventions that address periodontitis, such as anti-inflammatory therapies or treatments targeting specific pathogens like P. gingivalis, could potentially mitigate its impact on the onset and progression of AD, offering a novel avenue for prevention and management strategies.}, }
@article {pmid40060029, year = {2025}, author = {Yan, C and Si, T and Zheng, W and Huang, L and Wen, L and Shen, H and Qu, M}, title = {Characteristics of Gut Microbiota and Plasma Metabolites in Patients with Post-Stroke Depression.}, journal = {Neuropsychiatric disease and treatment}, volume = {21}, number = {}, pages = {477-489}, pmid = {40060029}, issn = {1176-6328}, abstract = {PURPOSE: The changes in gut microbiota and plasma metabolites have been proposed to play a key role in post stroke depression (PSD), but clinical study based on combined omics is still in lack. This study aimed to investigate the characteristics of gut microbiota and plasma metabolites in patients 3 months after the onset of acute ischemic stroke (AIS), compare PSD and non-PSD groups, and explore possible diagnostic biomarkers.<br><br>PATIENTS AND METHODS: Seventy patients with stroke were included at 3 months after AIS onset. Plasma and fecal samples were collected. Gut microbiome was examined using 16S rRNA sequencing, and plasma metabolites were assessed via targeted liquid chromatography-mass spectrometry.<br><br>RESULTS: Of the 70 patients with ischemic stroke, 25 (35.71%) were diagnosed with PSD. At the genus level, patients with PSD had increased abundance of Parabacteroides, Pyramidobacter, Anaeroglobus, Haliangium, Staphylococcus, CAG-56, Shuttleworthia, and Epulopiscium, and decreased levels of the Eubacterium eligens group and Prevotella. In patients with PSD, 12 plasma metabolites were altered, with cortisol and pyroglutamic acid levels increased, while 2-phosphoglyceric acid, 3-phosphoglycerate, phosphorylcholine, tryptophan, caffeine, N-methylalanine, ornithine, serotonin, theophylline, and vanillic acid were decreased. Enriched metabolic pathways included glutathione, tryptophan, and caffeine metabolism. Furthermore, significant correlations were observed between gut microbial dysregulation and major plasma metabolite alterations. The areas under the curve values of gut microbiota, plasma metabolites, and the combined dataset for PSD diagnosis were 0.704, 0.875, and 0.940, respectively.<br><br>CONCLUSION: This study identified the characteristics of gut microbiota and plasma metabolites as well as a panel of combined biomarkers in 3-month PSD, possibly providing a new theoretical framework for diagnosis and treatment.}, }
@article {pmid40059472, year = {2025}, author = {Elahi, Z and Mokhtaryan, M and Mahmoodi, S and Shahroodian, S and Darbandi, T and Ghasemi, F and Ghanavati, R and Darbandi, A}, title = {All Properties of Infertility Microbiome in a Review Article.}, journal = {Journal of clinical laboratory analysis}, volume = {}, number = {}, pages = {e25158}, doi = {10.1002/jcla.25158}, pmid = {40059472}, issn = {1098-2825}, support = {4150//Behbahan Faculty of Medical Sciences/ ; }, abstract = {BACKGROUND: The microbiome is crucial for many physiological processes, including immunity, metabolism, and reproduction.<br><br>AIMS: This review aims to contribute to a detailed understanding of the microbiome of the genital tract, which can lead to better management of dysbiosis and reproductive disorders.<br><br>METHODS: Data from the four international information databases Medline, Scopus, Embase, and Google Scholar. The search strategy was based on the combination of the following terms: "microbiota," "microbiome," "microfilm," "microflora," "fertility," or "infertility."<br><br>RESULT: The advent of next-generation sequencing-based technologies during the last decade has revealed the presence of microbial communities in nearly every part of the human body, including the reproductive system. Several studies have shown significant differences between the microbiota of the vagina and endometrium, as well as other parts of the upper genital tract.<br><br>DISCUSSION: The human microbiome plays a critical role in determining a person's health state, and the microbiome of the genital tract may impact fertility potential before and after assisted reproductive treatments (ARTs).<br><br>CONCLUSION: To completely understand the role of the microbiome, future research should focus not only on the description of microbiota but also on the interaction between bacteria, the production of biofilms, and the interaction of microorganisms with human cells.}, }
@article {pmid40059439, year = {2025}, author = {Szaraz, D and Bohm, J and Cerulova, S and Bodokyova, L and Danek, Z and Machacek, C and Borilova Linhartova, P}, title = {Bacterial genera in the fluids from apical periodontitis-related radicular cysts: An observational study.}, journal = {International endodontic journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/iej.14220}, pmid = {40059439}, issn = {1365-2591}, support = {NU20-08- 00205//Ministerstvo Zdravotnictv&#xed; Cesk&#xe9; Republiky/ ; //Horizon 2020 Framework Programme/ ; 65269705//University Hospital Brno, Ministry of Health, Czech Republic - RVO/ ; }, abstract = {AIM: This study aimed to evaluate bacteriome profiles (diversity, composition and relative abundances of bacterial genera) of the fluids from apical periodontitis (AP)-related radicular cysts (RCs).<br><br>METHODOLOGY: This observational study included 29 patients with AP and RC with complete sample triplets (supragingival plaque, cryopulverized tooth and cystic fluid). The bacteriome profiles of each matrix as well as of negative controls (NCs) were examined using 16S rRNA amplicon sequencing.<br><br>RESULTS: Bacteriome profiles of cystic fluids differed from NCs in 79% of cases. The number of distinct amplicon sequence variants and Shannon index detected in cystic fluids and cryopulverized teeth were significantly lower than in paired supragingival plaque samples. Gram-negative genera and anaerobic genera were more abundant in cystic fluids than in paired cryopulverized teeth or their supragingival plaques. The relative abundances of the genera Prevotella_7/Prevotella, Fusobacterium and Porphyromonas were higher in cystic fluids than in paired cryopulverized teeth and NCs; their relative abundances dominated (>20%) in individual cystic fluids. Also, DNA from the genus Fretibacterium was significantly more commonly found in cryopulverized teeth and cystic fluids than in supragingival plaque samples. The relative abundances of this gram-negative bacterial genera in cryopulverized teeth differed from NCs; the difference from cystic fluids was borderline insignificant.<br><br>CONCLUSIONS: Although the alpha-diversity in the cystic fluids is much lower compared to supragingival plaques, most cystic fluids are not sterile. DNA from specific anaerobic gram-negative bacterial genera dominated the fluids from AP-related RCs.}, }
@article {pmid40059228, year = {2025}, author = {Thapa, A and Hasan, MR and Kabir, AH}, title = {Transcriptional reprogramming and microbiome dynamics in garden pea exposed to high pH stress during vegetative stage.}, journal = {Planta}, volume = {261}, number = {4}, pages = {83}, pmid = {40059228}, issn = {1432-2048}, support = {5SFAES-293007//College of Arts, Education, and Sciences, University of Louisiana Monroe/ ; }, mesh = {*Pisum sativum/microbiology/genetics/physiology ; Hydrogen-Ion Concentration ; *Microbiota/genetics ; *Symbiosis ; Stress, Physiological/genetics ; Soil/chemistry ; Gene Expression Regulation, Plant ; Soil Microbiology ; Plant Roots/microbiology/genetics ; }, abstract = {High soil pH induces the upregulation of genes involved in oxidative stress and nutrient transport, while the enrichment of beneficial microbes (Variovorax, Chaetomium, and Pseudomonas) highlights their potential role in promoting stress adaptation. High soil pH severely impacts plant growth and productivity, yet the transcriptomic changes and microbial dynamics underlying stress adaptation in garden pea (Pisum sativum ssp. hortense) remain unclear. This study demonstrates that high soil pH leads to stunted growth, reduced biomass, impaired photosynthesis, and nutrient status in garden pea. Further, disruption in key nitrogen-fixing bacteria (Rhizobium indicum, R. leguminosarum, and R. redzepovicii), along with the downregulation of NifA and NifD genes and upregulation of NifH in nodules highlights the critical role of micronutrient balance in legume-microbe symbiosis and a compensatory response to maintain nitrogen status. RNA seq analysis revealed extensive transcriptional reprogramming in roots, characterized by the upregulation of oxidative stress response genes (e.g., oxidoreductase and glutathione transferase activities, metal ion transporters) and the downregulation of genes related to ammonia-lyase activity and ion binding, reflecting broader disruptions in nutrient homeostasis. KEGG pathway analysis identified enrichment of MAPK signaling pathway, likely interacting with other pathways associated with stress tolerance, metabolic adjustment, and structural reorganization as part of adaptive responses to high pH. Root microbiome analysis showed significant enrichment of Variovorax, Shinella, and Chaetomium, suggesting host-driven recruitment under high pH stress. Stable genera, such as Pseudomonas, Novosphingobium, Mycobacterium, Herbaspirillum, and Paecilomyces, displayed resilience to stress conditions, potentially forming core microbiome components for adaptation to high pH. In a targeted study, inoculation of plants with an enriched microbiome, particularly C. globosum, under high pH conditions improved growth parameters and increased the abundance of Stenotrophomonas and Pseudomonas in the roots. It suggests that these bacterial genera may act as helper microbes to C. globosum, collectively promoting stress resilience in pea plants suffering from high pH. These findings provide a foundation for microbiome-aided breeding programs and the development of microbial consortia to enhance the adaptation of pea plants to high pH conditions.}, }
@article {pmid40059174, year = {2025}, author = {Jin, X and Cheng, AG and Chanin, RB and Yu, FB and Dimas, A and Jasper, M and Weakley, A and Yan, J and Bhatt, AS and Pollard, KS}, title = {Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {71}, pmid = {40059174}, issn = {2049-2618}, support = {1563159//National Science Foundation/ ; HL160862/HL/NHLBI NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Bacteria/genetics/classification/isolation &amp; purification ; *Bacterial Adhesion/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Animals ; Metagenome ; Mice ; Promoter Regions, Genetic ; Intestines/microbiology ; }, abstract = {BACKGROUND: Bacteria use invertible genetic elements known as invertons to generate heterogeneity among a population and adapt to new and changing environments. In human gut bacteria, invertons are often found near genes associated with cell surface modifications, suggesting key roles in modulating dynamic processes such as surface adhesion and intestinal colonization. However, comprehensive testing of this hypothesis across complex bacterial communities like the human gut microbiome remains challenging. Metagenomic sequencing holds promise for detecting inversions without isolation and culturing, but ambiguity in read alignment limits the accuracy of the resulting inverton predictions.<br><br>RESULTS: Here, we developed a customized bioinformatic workflow-PhaseFinderDC-to identify and track invertons in metagenomic data. Applying this method to a defined yet complex gut community (hCom2) across different growth environments over time using both in vitro and in vivo metagenomic samples, we detected invertons in most hCom2 strains. These include invertons whose orientation probabilities change over time and are statistically associated with environmental conditions. We used motif enrichment to identify putative inverton promoters and predict genes regulated by inverton flipping during intestinal colonization and surface adhesion. Analysis of inverton-proximal genes also revealed candidate invertases that may regulate flipping of specific invertons.<br><br>CONCLUSIONS: Collectively, these findings suggest that surface adhesion and intestinal colonization in complex gut communities directly modulate inverton dynamics, offering new insights into the genetic mechanisms underlying these processes. Video Abstract.}, }
@article {pmid40059170, year = {2025}, author = {Duan, Y and Xu, C and Wang, W and Wang, X and Xu, N and Zhong, J and Gong, W and Zheng, W and Wu, YH and Myers, A and Chu, L and Lu, Y and Delzell, E and Hsing, AW and Yu, M and He, W and Zhu, S}, title = {Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses.}, journal = {BMC medicine}, volume = {23}, number = {1}, pages = {146}, pmid = {40059170}, issn = {1741-7015}, support = {Grant No. 2022YFC2705303//the National Key R&amp;D Program of China/ ; Grant No. 2022YFC2705300//the National Key R&amp;D Program of China/ ; Grant No. 2024C03180//"Pioneer" and "Leading Goose" R&amp;D Program of Zhejiang/ ; }, mesh = {Humans ; Male ; *Gastrointestinal Microbiome ; *Obesity/microbiology ; Middle Aged ; *Siblings ; Adult ; *Smoking/adverse effects ; China/epidemiology ; Cohort Studies ; Body Mass Index ; RNA, Ribosomal, 16S/genetics ; Aged ; Female ; }, abstract = {BACKGROUND: Individuals who smoke tend to have a lower body mass index (BMI) but face an increased risk of obesity-related diseases. This study investigates this paradox from the perspective of gut microbiota.<br><br>METHODS: We conducted microbiome analyses to identify smoking-related microbial genera and created a smoking-related microbiota index (SMI) using 16S rRNA sequencing data from 4000 male participants in WELL-China cohort and Lanxi cohort. We employed logistic regression to explore the association between SMI and obesity indices derived from dual-energy X-ray absorptiometry. Cox regression analyses were conducted to explore the association of SMI with incident of obesity-related diseases. To further control for unmeasured familial confounders, sibling comparison analyses were conducted using between-within (BW) model.<br><br>RESULTS: The smoking-related microbiota index (SMI) showed a positive association with BMI and other obesity indices. Further analyses revealed that SMI is linked to obesity-related diseases, with hazard ratios (95% confidence intervals) of 1.97 (1.41-2.75) for incident diabetes, 1.31 (1.01-1.71) for major adverse cardiovascular events, and 1.70 (1.05-2.75) for obesity-related cancers. Results from sibling comparison analyses reinforced these findings.<br><br>CONCLUSIONS: While smoking may reduce weight through various mechanisms, alterations in gut microbiota related to smoking are associated with weight gain. Further research is required to determine if changes in the smoking-related microbiome contribute to weight gain following smoking cessation.}, }
@article {pmid40059138, year = {2025}, author = {Zhang, C and Zhong, B and Jiang, Q and Lu, W and Wu, H and Xing, Y and Wu, X and Zhang, Z and Zheng, Y and Li, P and Li, Z and Lin, Z and Chen, Y and Hong, C and Zhao, Z and Zhang, T and Liang, W and Zhang, Y and Zhang, C and Yuan, JX and Liu, C and Wang, J and Yang, K}, title = {Distinct airway mycobiome signature in patients with pulmonary hypertension and subgroups.}, journal = {BMC medicine}, volume = {23}, number = {1}, pages = {148}, pmid = {40059138}, issn = {1741-7015}, support = {82241012, 82270052, 82120108001, 82170065, 82170069, 82370063//National Natural Science Foundation of China/ ; 82241012, 82270052, 82120108001, 82170065, 82170069, 82370063//National Natural Science Foundation of China/ ; 82241012, 82270052, 82120108001, 82170065, 82170069, 82370063//National Natural Science Foundation of China/ ; 82241012, 82270052, 82120108001, 82170065, 82170069, 82370063//National Natural Science Foundation of China/ ; 2024ZD0528700//National Science and Technology Innovation 2030, Major Project- Research on Cancer, Cardiovascular, Respiratory and Metabolic Diseases/ ; }, mesh = {Humans ; Male ; Female ; Middle Aged ; *Mycobiome ; *Hypertension, Pulmonary/microbiology ; Adult ; Aged ; Fungi/classification/isolation &amp; purification ; Lung/microbiology ; }, abstract = {BACKGROUND: The association between lung microbiome and pulmonary hypertension (PH) remain unknown. This study aims to define the airway mycobiome signature and its potential correlation with clinical parameters of PH.<br><br>METHODS: Overall, 244 patients with PH and 120 healthy controls (CON) were recruited from three independent centers. The PH group was divided into subgroups not using antibiotics or corticosteroids (non-ANT/CORT), and those using ANT, CORT, or ANT&#x2009;+&#x2009;CORT within 1&#xa0;month, and clinical classification (Groups 1, 3, and 4), World Health Organization functional class (I-IV), and disease severity based on mean pulmonary artery pressure or pulmonary vascular resistance levels for in-depth comparison.<br><br>RESULTS: Distinct airway mycobiome profiles were observed in PH, CON, and PH subgroups. Linear discriminant analysis effect size analysis showed increased Purpureocillium, Issatchenkia, and Cyberlindnera and decreased Peroneutypa, Simplicillium, and Metarhizium in patients with PH (non-ANT/CORT, ANT, CORT, and ANT&#x2009;+&#x2009;CORT) than in CON. Receiver operating characteristic analysis indicated a strong prediction of the two fungal genera sets in distinguishing PH and its subgroups from CON. The two major fungal phyla, Ascomycota and Basidiomycota, correlated differently with major clinical factors. Increased connections among the top fungal phyla or genera were observed in the PH than in the CON group. Dominant enrichment (Purpureocillium, Issatchenkia, and Cyberlindnera) and diminishment (Peroneutypa, Simplicillium, and Metarhizium) of fungal genera consistently and strongly predicted PH without being influenced by different PH subgroups.<br><br>CONCLUSIONS: This study provides the first description of the unique airway mycobiome signature in PH and among different PH subgroups.}, }
@article {pmid40058902, year = {2025}, author = {Revelo-Romo, DM and Hurtado Gutiérrez, NH and Hidalgo Troya, A and Amaya-Gómez, CV and Flórez-Martínez, DH and Overmann, J and Villegas Torres, MF and González Barrios, AF}, title = {Omics approaches to explore the coffee fermentation microecosystem and its effects on cup quality.}, journal = {Food research international (Ottawa, Ont.)}, volume = {206}, number = {}, pages = {116035}, doi = {10.1016/j.foodres.2025.116035}, pmid = {40058902}, issn = {1873-7145}, mesh = {*Fermentation ; *Coffee/microbiology ; *Coffea/microbiology/chemistry/metabolism ; Microbiota ; Metagenomics/methods ; Seeds/microbiology/metabolism ; Food Handling/methods ; }, abstract = {The cultivation and postharvest processing of coffee constitute the basis of the subsistence and traditional culture for rural family-owned farms, as well as for the economic success of commercial enterprises in many coffee-producing countries worldwide. The quality of the final beverage is determined by a multitude of variables. A key post-harvest factor is the spontaneous fermentation of the coffee beans, conducted directly on the farm, to remove the mucilage that firmly adheres to the beans. The effect of this fermentation step on the aromatic profile of the coffee is not yet sufficiently understood. All of the above have drawn the attention of researchers on the application of various omics approaches to elucidate fermentation processes in more detail. These approaches have been used to study the fermentation of Arabica (Coffea arabica) beans, as this species is economically most important worldwide. It is known that Arabica mild coffee is obtained through the wet method, which involves fermenting depulped coffee beans using various strategies and then washing the fermented coffee with clean water. In contrast, the fermentation of Canephora coffee beans has been much less studied using omics technologies. This review highlights the trends and future research in coffee fermentation based on a scientometric analysis, supplemented by a traditional systematic literature review. It highlights the composition of the coffee fermentation microbiome, as elucidated by metagenomics applications, in light of several factors that can influence its structure. Additionally, it considers the metabolites associated with microbial metabolism that can influence the chemical composition of coffee beans and, consequently, the cup quality. In this way, this review evidences the promising path in understanding microbial functions in coffee fermentation and in particular in the development of microbial inocula and in the refinement of fermentation processes to improve coffee quality.}, }
@article {pmid40058892, year = {2025}, author = {Esmail, GA and Uriot, O and Mottawea, W and Denis, S and Sultan, S and Njoku, EN and Chiba, M and Tosh, S and Blanquet-Diot, S and Hammami, R}, title = {Western diet-based NutriCol medium: A high-pectin, low-inulin culture medium promoted gut microbiota stability and diversity in PolyFermS and M-ARCOL continuous in vitro models.}, journal = {Food research international (Ottawa, Ont.)}, volume = {206}, number = {}, pages = {115993}, doi = {10.1016/j.foodres.2025.115993}, pmid = {40058892}, issn = {1873-7145}, mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Inulin/metabolism ; *Fermentation ; *Diet, Western ; *Pectins ; *Colon/microbiology/metabolism ; Dietary Fiber/analysis ; Culture Media ; Feces/microbiology/chemistry ; Mannans ; Galactans/metabolism ; Models, Biological ; Fatty Acids, Volatile/metabolism/analysis ; }, abstract = {Optimizing fermentation media to accurately reflect the colonic environment remains a challenge in developing in vitro models that simulate the human colon. This study aimed to develop a fermentation medium, Nutritive Colonic (NutriCol), which mimics colonic chyme with fiber content reflective of a typical Western diet and compared to the widely used MacFarlane medium. MacFarlane/NutriCol media contained the following fiber (g/L): potato starch (5/0.1), pectin (2/5.6), xylan (2/4.4), arabinogalactan (2/1.8), guar gum (1/0.4), glucomannan (0/0.8), and inulin (1/0.2). The performance of NutriCol was evaluated using two in vitro models: PolyFermS, which simulates the human proximal colon, and M-ARCOL, which mimics both the lumen and mucosa of the human colon. In the PolyFermS model, findings revealed that NutriCol maintained microbiota α-diversity closer to the donor fecal samples and significantly higher than MacFarlane (Shannon's p ≤ 0.01; Simpson's p ≤ 0.001). In contrast, no significant differences in α-diversity were observed between NutriCol and MacFarlane in the M-ARCOL model, likely due to differences in model design and donor microbiome composition. Microbial community structure, assessed by Bray-Curtis distance and A Permutational multivariate analysis of variance (PERMANOVA), revealed significant variations between the two media in both models (PolyFermS: p = 0.02; M-ARCOL: p = 0.01). Additionally, NutriCol demonstrated a higher capacity to cultivate gut microbes, with increased ASV numbers compared to MacFarlane across PolyFermS and M-ARCOL. SCFAs production was influenced by media composition, individual microbiome structure, and the colonic model used. In the M-ARCOL, NutriCol significantly increased acetate (p = 0.0006) and butyrate (p = 0.02) levels compared to MacFarlane. While a similar trend was observed with the PolyFermS, the differences were not statistically significant (p > 0.05). This increase is attributed to the enrichment of SCFA-producing bacteria, such as Butyricicoccus, Lachnospira, Oscillospiraceae UCG-003, Clostridium butyricum, and Lachnospiraceae NK4A136-group. Additionally, NutriCol generated lower levels of intestinal gases (H2, O2, CO2, and CH4) than MacFarlane in the M-ARCOL model. In conclusion, our study demonstrates that NutriCol, a growth medium specifically designed to replicate the typical fiber content of a Western diet, supports gut microbiota diversity and structure better than the established MacFarlane medium. NutriCol's impact was model- and donor-dependent, enhancing microbiota diversity in PolyFermS, while promoting SCFA production and reducing gas levels in M-ARCOL.}, }
@article {pmid40058710, year = {2025}, author = {Bai, J and Gong, C and Hu, YJ and Bruner, DW and Torres, MA and Buchwald, ZS and Lin, JY}, title = {Skin Microbiome, Inflammation, and Skin Toxicities in Women with Breast Cancer Receiving Moderately Hypofractionated Radiation Therapy.}, journal = {International journal of radiation oncology, biology, physics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijrobp.2025.02.044}, pmid = {40058710}, issn = {1879-355X}, abstract = {PURPOSE: Up to 95% of women during and after radiation therapy (RT) for breast cancer have reported cutaneous toxicity. However, the biologic link between skin microbiome and skin toxicities from RT remains largely unknown. This study aimed to assess the associations of skin microbiome with clinician- and patient-reported skin toxicities and inflammatory markers in women with breast cancer receiving RT.<br><br>MATERIALS AND METHODS: A prospective, longitudinal study was conducted at a single institution. Thirty-two women with breast cancer undergoing moderately hypofractionated RT for 3-4 weeks after breast conserving surgery were enrolled and 30 of them were analyzed. 240 swabs for skin microbiome and 120 plasma samples collected pre-RT baseline (T1), week-1 of RT (T2), week-3 of RT (T3), and 3-months post-RT (T4), from the cancer-affected and contralateral healthy breasts. Skin microbiome specimens were processed using 16S V1-V3 sequencing.<br><br>RESULTS: Differences in skin microbiome of the treated breasts during RT (T2 and T3) were observed compared to the skin microbiome of pre-RT baseline breasts (T1) and contralateral, healthy breasts, with the affected breasts having an increased abundance of pathogenetic Finegoldia (p=0.001), Dermacoccus (p=0.01), and Variovorax (p=0.003) during RT. Longitudinal analysis showed that decreased Variovorax but increased Staphylococcus were associated with increased clinician-reported grade 2 pruritus (p=0.002) and dermatitis (p=0.012), and increased patient-reported moderate or severe darkened skin (p=0.002) and itchy skin (p=0.012). Additionally, the plasma IFN-&#x3b3; was associated with changes in skin microbiome in women with breast cancer undergoing RT.<br><br>CONCLUSIONS: This study shows changes in the skin microbiome during well-tolerated moderately hypofractionated breast RT. The skin microbiome return towards baseline appears to associate with improvement of clinician- and patient-reported skin toxicities post-treatment. While there were few high-grade toxicities observed among frequently prescribed courses of hypofractionated whole breast RT, changes in skin microibome may be of interest as further targets of symptomatic relief or intervention as ultrahypofractionated courses become more common.}, }
@article {pmid40058701, year = {2025}, author = {Wang, Y and Li, T and Dong, Z and Zhang, Q and Mi, J and Wang, Q and Lin, G and Ma, Q and Jia, R and Huang, S}, title = {Extracellular vesicles from Lactobacillus fermentum enhance intestinal barrier integrity and restore gut microbial homeostasis in experimental murine colitis.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tjnut.2025.03.001}, pmid = {40058701}, issn = {1541-6100}, abstract = {BACKGROUND: Lactobacillus fermentum (L. fermentum) has been shown to improve intestinal health and treat colitis; however, its precise efficacy and mechanisms in inflammatory bowel disease (IBD) remain unclear.<br><br>OBJECTIVES: This study aimed to evaluate whether L. fermentum and its metabolites, extracellular vesicles, and other components could modulate intestinal barrier function and gut microbiota to alleviate dextran sulfate sodium (DSS)-induced colitis in mice.<br><br>METHODS: Forty-eight mice were randomly assigned to six groups: Control (CON), DSS, L. fermentum + DSS group (LF + DSS), heat-inactivated L. fermentum + DSS group (LHF + DSS), L. fermentum supernatant solution + DSS group (LSF + DSS), and L. fermentum extracellular vesicles + DSS group (LEV + DSS). After a one-week acclimation, mice were gavaged daily for three weeks. Fresh cultures, including live (LF + DSS), heat-inactivated (LHF + DSS), supernatant (LSF + DSS), and extracellular vesicles (LEV + DSS), were prepared daily. During the final seven days, the control group received normal water, while the other groups received 3% DSS. Data were collected daily, followed by sample collection from the mice.<br><br>RESULTS: Herein, significant reductions (P < 0.05) in body weight changes, disease activity index (DAI), intestinal damage, and histology scores were observed in the treatment groups, especially LEV + DSS and LF + DSS. Additionally, compared with the DSS group, colonic mucus secretion, as well as claudin-1 and occludin expression, increased significantly (P < 0.05) in the LEV + DSS and LF + DSS groups, while proinflammatory cytokines interleukin (IL) -1&#x3b2; and tumor necrosis factor-&#x3b1; (TNF-&#x3b1;) decreased (P < 0.05) and IL-10 increased (P < 0.05) in the LEV + DSS group. L. fermentum and its components significantly regulated gut microbiota &#x3b1;-diversity and &#x3b2;-diversity, affecting overall composition. LEfSe analysis revealed an enrichment of beneficial bacteria including Prevotellaceae_UCG-001, Romboutsia, and Ruminococcus in the LF + DSS group, and Akkermansia, Odoribacter, and Marvinbryantia in the LEV + DSS group. Both L. fermentum and its extracellular vesicles significantly downregulated the gene expression of TNF-&#x3b1; and IL-1&#x3b2;, while upregulating the expression of IL-10, thereby contributing to the alleviation of colitis symptoms.<br><br>CONCLUSIONS: This study reveals that L. fermentum alleviates colitis through modulation of the gut microbiota and reinforcement of the intestinal mucosal barrier, with its extracellular vesicles potentially playing a key role in this regulatory process.}, }
@article {pmid40058670, year = {2025}, author = {Langgartner, D and Weimer, K and Brunner-Weisser, J and Winkler, R and Mannes, M and Huber-Lang, M and Sterrett, JD and Lowry, CA and Rohleder, N and Bajrami, B and Luippold, AH and Groß, A and Kestler, HA and Tost, H and Meyer-Lindenberg, A and Gündel, H and Jarczok, MN and Reber, SO}, title = {Pawsitive impact: How pet contact ameliorates adult inflammatory stress responses in individuals raised in an urban environment.}, journal = {Brain, behavior, and immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.bbi.2025.03.013}, pmid = {40058670}, issn = {1090-2139}, abstract = {BACKGROUND: Individuals raised in an urban environment (URBANs) show an exaggerated inflammatory response to the Trier Social Stress Test (TSST) compared with individuals raised in a rural environment. The underlying mechanisms are unclear but may relate to childhood animal contact. As an exaggerated immune (re)activity plays a causal role in the pathogenesis of stress-associated disorders, these findings might explain the higher prevalence of stress-associated disorders in urban vs. rural areas.<br><br>METHODS: We recruited physically and emotionally healthy male URBANs, raised in a city with more than 40,000 residents either in the absence (noPETs) or presence (PETs) of household pets. Participants were individually exposed to the TSST, and before and after the TSST, blood and saliva were collected for assessment of different stress-related parameters. An additional saliva sample before the TSST was collected for salivary microbiome analysis. Heart rate (HR) and HR variability (HRV) were recorded continuously. Mental and physical health status, early-life and perceived life stress, current animal contact, and subjective strain induced by TSST exposure were assessed using validated questionnaires.<br><br>RESULTS: Here we show that adult healthy male URBANs raised in the absence (noPETs) vs. presence (PETs) of household pets still reported less animal contact during adulthood and were characterized by deficits in their immunoregulatory and intestinal barrier function, which under basal conditions did not translate into a chronic low-grade inflammatory state. This was different under acute psychosocial stress conditions. Exposure to the TSST resulted in a facilitated mobilization of particularly neutrophil granulocytes in noPETs vs. PETs, accompanied by an enhanced pro- and compromised anti-inflammatory systemic stress response.<br><br>CONCLUSION: Together, the presence of pets seems to reduce the risk for URBANs to develop stress-associated disorders later in life (i.e., primary prevention) by facilitating immunoregulatory and barrier functions, in turn preventing an overshooting immune activation in response to acute stressors and chronic low-grade inflammation in response to repeated/chronic stressors.}, }
@article {pmid40058669, year = {2025}, author = {Sánchez, IM and Spielbauer, J and Heijtz, RD}, title = {Maternal peptidoglycan overexposure during late pregnancy alters neurodevelopment and behavior in juvenile offspring.}, journal = {Brain, behavior, and immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.bbi.2025.03.014}, pmid = {40058669}, issn = {1090-2139}, abstract = {Emerging evidence suggests that maternal gut microbiota-derived metabolites and components influence fetal brain development and subsequent neurodevelopment. This study investigates the effects of maternal overexposure to muramyl dipeptide (MDP)-a bacterial peptidoglycan (PGN) motif recognized by Nod2 receptors-on offspring neurodevelopment and behavior. Time-mated C57BL/6J female mice received MDP via drinking water from gestational days 16-19. Nod2 activation in amniotic fluid was assessed using a Nod2 cell-based reporter assay, showing a significant increase in males 24 h after MDP exposure. Gene expression analysis revealed upregulation of PGN transporters in fetal brains, with males showing higher levels of Slc15a1/PepT1, Slc15a2/PepT2, and Slc46a2. No changes in inflammatory or microglia-related markers were found. Behavioral assessments during the juvenile period revealed sex-specific effects: prenatally exposed males showed reduced social interaction, while females exhibited reduced novelty-induced locomotion and impaired social recognition. These behavioral changes were linked to altered expression of synaptic (Dlg4, Ppp1r9b, Darpp-32) and microglial (Trem-2, Cx3cr1) genes in the prefrontal cortex. Our findings underscore the sex-specific effects of maternal PGN overexposure on offspring neurodevelopment, highlighting the potential role of the maternal microbiome in the neurobiology of neurodevelopmental disorders, even in the absence of infection or robust inflammation.}, }
@article {pmid40058511, year = {2025}, author = {Zhou, G and Yang, Y and Leng, J and Chen, J and Zhou, H and Ming, R and Jiang, H}, title = {Gut Microbiota-Derived Deoxycholic Acid in Colorectal Cancer Therapy: Critical Considerations and An Extended Clinical Investigation Panorama Analysis.}, journal = {Pharmacological research}, volume = {}, number = {}, pages = {107683}, doi = {10.1016/j.phrs.2025.107683}, pmid = {40058511}, issn = {1096-1186}, }
@article {pmid40058438, year = {2025}, author = {Cai, Z and Zhang, M and Zhou, L and Xiong, Y and Wang, H and Chen, Y and Yuan, JB}, title = {Kai-Xin-San polysaccharides exert therapeutic effects on D-gal and Aβ25-35-induced AD rats by regulating gut microbiota and metabolic profile.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {141850}, doi = {10.1016/j.ijbiomac.2025.141850}, pmid = {40058438}, issn = {1879-0003}, abstract = {Metabolic abnormalities and gut microbiota imbalance are intricately linked to the onset and progression of Alzheimer's disease (AD). Kai-Xin-San (KXS) is a traditional herbal formula known for its therapeutic effects on AD. Our previous research indicated that Kai-Xin-San polysaccharide (KXS-P) exhibits a significant therapeutic impact on AD, but the precise mechanisms remain incompletely understood. In this study, untargeted fecal metabolomics and 16S rRNA gene sequencing were used to investigate the potential mechanisms by which KXS-P acts against AD. Key metabolites and gut microbial species were identified using multivariate analysis and a comprehensive examination of intestinal microecology. Our findings revealed that KXS-P improves lipid metabolism in AD rats by modulating a series of lipid molecules and bile acid levels. Additionally, KXS-P regulated gut microbiota composition and restored the symbiotic relationships within the gut microbiome. Notably, the anti-inflammatory effect of KXS-P may be related to its regulation of specific lipotypes levels and the abundance of Romboutsia, Bifidobacterium and Alloprevotella. KXS-P demonstrates the ability to alleviate symptoms of AD rats through multiple mechanisms: ① Improving lipid metabolism and maintaining lipid homeostasis; ② Reducing neuronal and inflammatory damage; ③ Regulating the composition and symbiotic relationships of gut microbiota to preserve intestinal microecological balance.}, }
@article {pmid40058281, year = {2025}, author = {Balaji, SK and Khuwaja, WM and Hossain, ML and Fernando, LGB and Dong, X}, title = {Neuroimmune interactions between itch neurons and skin microbes.}, journal = {Seminars in immunology}, volume = {78}, number = {}, pages = {101933}, doi = {10.1016/j.smim.2025.101933}, pmid = {40058281}, issn = {1096-3618}, abstract = {Itch is an unpleasant sensation that is encoded by specific sensory neurons called pruriceptors. Itch is associated with almost all skin diseases. Recent studies revealed that many itchy skin diseases are associated with microbiome dysbiosis. Pathogenic microbes secrete proteases and toxins to invade skin cells. Some microbial products can directly activate sensory neurons, while others activate the mammalian immune system and indirectly cause itch. In this review, we summarize the current knowledge on microbe-immune-neuron crosstalks and discuss their relevance in itchy skin diseases.}, }
@article {pmid40058066, year = {2025}, author = {Mu, X and Feng, L and Wang, Q and Li, H and Zhou, H and Yi, W and Sun, Y}, title = {Decreased gut microbiome-derived indole-3-propionic acid mediates the exacerbation of myocardial ischemia/reperfusion injury following depression via the brain-gut-heart axis.}, journal = {Redox biology}, volume = {81}, number = {}, pages = {103580}, doi = {10.1016/j.redox.2025.103580}, pmid = {40058066}, issn = {2213-2317}, abstract = {Despite the increasing recognition of the interplay between depression and cardiovascular disease (CVD), the precise mechanisms by which depression contributes to the pathogenesis of cardiovascular disease remain inadequately understood. The involvement of gut microbiota and their metabolites to health and disease susceptibility has been gaining increasing attention. In this study, it was found that depression exacerbated cardiac injury, impaired cardiac function (EF%: P < 0.01; FS%: P < 0.05), hindered long-term survival (P < 0.01), and intensified adverse cardiac remodeling (WGA: P < 0.01; MASSON: P < 0.0001) after myocardial ischemia/reperfusion (MI/R) in mice. Then we found that mice receiving microbiota transplants from chronic social defeat stress (CSDS) mice exhibited worse cardiac function (EF%: P < 0.01; FS%: P < 0.01) than those receiving microbiota transplants from non-CSDS mice after MI/R injury. Moreover, impaired tryptophan metabolism due to alterations in gut microbiota composition and structure was observed in the CSDS mice. Mechanistically, we analyzed the metabolomics of fecal and serum samples from CSDS mice and identified indole-3-propionic acid (IPA) as a protective agent for cardiomyocytes against ferroptosis after MI/R via NRF2/System xc-/GPX4 axis, played a role in mediating the detrimental influence of depression on MI/R. Our findings provide new insights into the role of the gut microbiota and IPA in depression and CVD, forming the basis of intervention strategies aimed at mitigating the deterioration of cardiac function following MI/R in patients experiencing depression.}, }
@article {pmid40057978, year = {2025}, author = {Jeevannavar, A and Florenza, J and Divne, AM and Tamminen, M and Bertilsson, S}, title = {Cellular heterogeneity in metabolism and associated microbiome of a non-model phytoflagellate.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf046}, pmid = {40057978}, issn = {1751-7370}, abstract = {Single-cell transcriptomics is a key tool for unravelling metabolism and tissue diversity in model organisms. Its potential for elucidating the ecological roles of microeukaryotes, especially non-model ones, remains largely unexplored. This study employed the Smart-seq2 protocol on Ochromonas triangulata, a microeukaryote lacking a reference genome, showcasing how transcriptional states align with two distinct growth phases: a fast-growing phase and a slow-growing phase. Besides the two expected expression clusters, each corresponding to either growth phase, a third transcriptional state was identified across both growth phases. Metabolic mapping revealed a boost of photosynthetic activity in the fast growth over the slow growth stage, as well as down-regulation trend in pathways associated with ribosome functioning, CO2 fixation, and carbohydrate catabolism characteristic of the third transcriptional state. In addition, carry-over rRNA reads recapitulated the taxonomic identity of the target while revealing distinct bacterial communities, in co-culture with the eukaryote, each associated with distinct transcriptional states. This study underscores single-cell transcriptomics as a powerful tool for characterizing metabolic states in microeukaryotes without a reference genome, offering insights into unknown physiological states and individual-level interactions with different bacterial taxa. This approach holds broad applicability to describe the ecological roles of environmental microeukaryotes, culture-free and reference-free, surpassing alternative methods like metagenomics or metatranscriptomics.}, }
@article {pmid40057969, year = {2025}, author = {Herrington, RTB and Ellenberger, DT and Rosenfeld, CS}, title = {Maternal probiotic supplementation and effects on the Fetal placenta.}, journal = {Biology of reproduction}, volume = {}, number = {}, pages = {}, doi = {10.1093/biolre/ioaf041}, pmid = {40057969}, issn = {1529-7268}, abstract = {Increasing number of pregnant women are consuming probiotics to promote their own health and that of their unborn fetus. Such supplements are presumed to be safe for pregnant mothers and their unborn offspring. For pregnant mothers, such bioactive compounds might lower the risk of constipation, diarrhea, other gastrointestinal conditions, pre-term birth, and prevent adverse pregnancy outcomes, including gestational diabetes mellitus (GDM) and depression/anxiety. More research is needed to examine potential safety of probiotic consumption during pregnancy and long-term health consequences to offspring. The conceptus can also be indirectly affected by maternal probiotic supplementation through microorganism production of bioactive compounds. The placenta is in direct communication with the underlying uterine tissue. Thus, compounds in the maternal blood can easily transfer across the placenta and impact this hormonally sensitive organ. Select studies suggest that disruptions to the maternal microbiome dramatically affects the placenta. In the current review, we will therefore consider the evidence to date of how maternal probiotic supplementation affects the placenta. Three potential mechanisms we will explore include the possibility that maternal probiotic supplementation might impact the putative placenta microbiome. The second potential mechanism we will consider is that maternal probiotic consumption alters bacterial-derived metabolites, including short-chained fatty acids, polyamines, Vitamin B9, and Vitamin B12. The third potential mechanism to be discussed is that such supplements affect maternal and placental immune responses. Before probiotics are promoted for healthy pregnant women and those with gestational disorders, more studies, including those examining the effects on the placenta, are essential.}, }
@article {pmid40057860, year = {2025}, author = {Lebtig, M and Peschel, A and Kretschmer, D}, title = {Role of Formyl Peptide Receptor 2 and Toll-Like Receptor 2 in Skin Barrier Function and Atopic Dermatitis.}, journal = {The Journal of investigative dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jid.2025.02.002}, pmid = {40057860}, issn = {1523-1747}, abstract = {The skin acts as a barrier against external threats and plays an important role in tissue repair. Skin cells, including keratinocytes, sense microbe-associated molecular pattern molecules released by members of the bacterial microbiome, and the cellular responses control central processes of skin homeostasis or inflammation. How the combination and amount of different microbe-associated molecular patterns modulate skin cell functions is not yet fully understood. Here, we review the current knowledge of the responses of skin cells to microbe-associated molecular patterns, focusing on Toll-like receptor 2 and formyl peptide receptor 2, two of the most important receptors for sensing the skin microbiome.}, }
@article {pmid40057813, year = {2025}, author = {Kong, F and Wang, S and Zhang, Y and Li, C and Dai, D and Guo, C and Wang, Y and Cao, Z and Yang, H and Bi, Y and Wang, W and Li, S}, title = {Rumen microbiome associates with postpartum ketosis development in dairy cows: a prospective nested case-control study.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {69}, pmid = {40057813}, issn = {2049-2618}, support = {32130100//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Cattle ; *Ketosis/veterinary ; Female ; *Rumen/microbiology ; *Postpartum Period ; Case-Control Studies ; *Gastrointestinal Microbiome ; *Cattle Diseases/microbiology ; *3-Hydroxybutyric Acid/blood ; Prospective Studies ; Bacteria/classification/isolation &amp; purification/genetics ; Propionates/metabolism/blood ; Energy Metabolism ; Microbiota ; }, abstract = {BACKGROUND: Approximately, one-third of dairy cows suffer from postpartum diseases. Ketosis is considered an important inducer of other postpartum diseases by disrupting energy metabolism. Although the rumen microbiome may be involved in the etiology of ketosis by supplying volatile fatty acids, the rumen environmental dynamics of ketosis cows are unclear. Using multi-omics, this study aimed to elucidate changes in the rumen microbiome during parturition of ketosis cows and the association between the rumen microbiome and host energy metabolism. The study included 810 rumen content samples and 789 serum samples from day - 21 and 21 relative to calving day from 61 ketosis cows and 84 healthy cows.<br><br>RESULTS: In ketosis cows, the rumen bacterial composition after parturition changed dramatically and needed a longer time to restore. The molar proportions of propionate were lower in ketosis cows than those in healthy cows on days 3 and 7 and negatively correlated with the serum &#x3b2;-hydroxybutyrate (BHBA) levels. The fermentation sub-pathway of propionate metabolism and partial glucogenic amino acid pathways were downregulated on day 3. Prevotella, UBA1066, and microbiota diversity indices regulate serum BHBA and glucose (GLU) levels via arginine, alanine, glycine, or propionate. Propionate administration to ketosis cows potentially decreased the serum BHBA concentration.<br><br>CONCLUSIONS: Collectively, we found rumen disruption happened after calving among ketosis cows, and insufficient glycogenic substrates, such as propionate, may be related to ketosis development. The study findings have implications for the relationship between rumen microbiome dynamics and host energy metabolism, which lays the foundation for the future rumen microbiome investigation for improving postpartum management in cows. Video Abstract.}, }
@article {pmid40057571, year = {2025}, author = {Adams, SE and Cawley, AK and Arnold, D and Hoptroff, MJ and Slomka, V and Matheson, JR and Marriott, RE and Gemmell, MR and Marsh, PD}, title = {A randomised, double-blind clinical study into the effect of zinc citrate trihydrate toothpaste on oral plaque microbiome ecology and function.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {8136}, pmid = {40057571}, issn = {2045-2322}, mesh = {Humans ; *Toothpastes/pharmacology/therapeutic use ; *Dental Plaque/microbiology ; Male ; Female ; Adult ; *Microbiota/drug effects ; Double-Blind Method ; Middle Aged ; Zinc Compounds/pharmacology/therapeutic use/administration &amp; dosage ; Young Adult ; Bacteria/classification/drug effects/genetics/isolation &amp; purification ; }, abstract = {The oral microbiome is a diverse community of microbes residing on all oral surfaces. A balanced oral microbiome is associated with good oral health, and disruption can result in imbalance associated with diseases including gingivitis and dental caries. It is important, therefore, to understand how daily use of oral hygiene products impacts the microbiome. Composition and activity of dental plaque microbiome from 115 participants was analysed after brushing with one of two toothpastes, one containing zinc citrate trihydrate and the other a control toothpaste, in a parallel design. Each participant brushed twice daily for 6-weeks, with samples collected at baseline, 2 and 6-weeks. Metataxonomic analysis demonstrated changes in bacterial communities with use of the zinc toothpaste compared to the control product at community and species level. Increases at the species level were observed for taxa from the genus Veillonella with decrease in a taxon from the genus Fusobacterium for the zinc toothpaste. Analysis of microbiome function based on predicted metagenomic and metatranscriptomic analysis show that use of the zinc toothpaste is associated with an in-vivo reduction in glycolysis, consistent with the mode of action of zinc and, increases in processes linked to gum-health (lysine biosynthesis), and to whole-body health (nitrate reduction). Our findings provide the first understanding of the beneficial modulation of microbiome composition and function by zinc-containing toothpaste in-vivo for oral care benefits.}, }
@article {pmid40057258, year = {2025}, author = {Ragone, P and Parodi, C and Tomasini, N and Ramos, F and Uncos, A and Brandán, CP}, title = {The interplay between Trypanosoma cruzi and the microbiome of Triatoma infestans: Implications for the host's immune response.}, journal = {Acta tropica}, volume = {}, number = {}, pages = {107577}, doi = {10.1016/j.actatropica.2025.107577}, pmid = {40057258}, issn = {1873-6254}, abstract = {The infection dynamics of Trypanosoma cruzi is shaped by the parasite's genetics and interactions with host and vector factors. While most studies in the area use axenic parasite cultures devoid of insect fecal components, this study is focused on the immune response and the parasite loads generated after the interaction of T. cruzi with feces from Triatoma infestans in a murine model. First, using metagenomics, we analyzed the microbiota of infected and uninfected feces. Illumina sequencing of the 16S rRNA gene (V3-V4 region) revealed a predominance of the genus Arsenophonus in infected feces and of Enterococcus in uninfected ones. C57BL/6J mice inoculated with T. cruzi infected feces, displayed distinct immune responses compared to those inoculated with culture-derived metacyclic trypomastigotes alone, with lower levels of pro-inflammatory cytokines (IFN-ɣ, TNF-α) and higher amounts of IL-10, suggesting a regulatory response. Besides, total anti-T. cruzi IgG levels remained similar among groups, but IgG1 and IgG2c were reduced in the T. cruzi infected feces group, indicating a balanced Th1/Th2 response. Notably, mice inoculated with T. cruzi infected feces demonstrated significantly reduced blood and muscle parasite loads, potentially limiting inflammation and parasite dissemination. These findings highlight the possible role of vector fecal microbiota in shaping immune responses and influencing disease outcomes during natural T. cruzi infections.}, }
@article {pmid40056347, year = {2025}, author = {Petit, P and Vuillerme, N}, title = {Global research trends on the human exposome: a bibliometric analysis (2005-2024).}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {40056347}, issn = {1614-7499}, support = {ANR-19-P3IA-0003//MIAI@Grenoble Alpes/ ; ANR-10-AIRT-05//Agence Nationale de la Recherche/ ; ANR-15-IDEX-02//Agence Nationale de la Recherche/ ; }, abstract = {Exposome represents one of the most pressing issues in the environmental science research field. However, a comprehensive summary of worldwide human exposome research is lacking. We aimed to explore the bibliometric characteristics of scientific publications on the human exposome. A bibliometric analysis of human exposome publications from 2005 to December 2024 was conducted using the Web of Science in accordance with PRISMA guidelines. Trends/hotspots were investigated with keyword frequency, co-occurrence, and thematic map. Sex disparities in terms of publications and citations were examined. From 2005 to 2024, 931 publications were published in 363 journals and written by 4529 authors from 72 countries. The number of publications tripled during the last 5 years. Publications written by females (51% as first authors and 34% as last authors) were cited fewer times (13,674) than publications written by males (22,361). Human exposome studies mainly focused on air pollution, metabolomics, chemicals (e.g., per- and polyfluoroalkyl substances (PFAS), endocrine-disrupting chemicals, pesticides), early-life exposure, biomarkers, microbiome, omics, cancer, and reproductive disorders. Social and built environment factors, occupational exposure, multi-exposure, digital exposure (e.g., screen use), climate change, and late-life exposure received less attention. Our results uncovered high-impact countries, institutions, journals, references, authors, and key human exposome research trends/hotspots. The use of digital exposome technologies (e.g., sensors, and wearables) and data science (e.g., artificial intelligence) has blossomed to overcome challenges and could provide valuable knowledge toward precision prevention. Exposome risk scores represent a promising research avenue.}, }
@article {pmid40056222, year = {2025}, author = {Addissouky, TA}, title = {Advancing frontiers in skin offensive odor management: from innovative diagnostics to cutting-edge treatments and emerging technologies.}, journal = {Archives of dermatological research}, volume = {317}, number = {1}, pages = {539}, pmid = {40056222}, issn = {1432-069X}, mesh = {Humans ; *Odorants ; *Volatile Organic Compounds ; *Microbiota ; *Sweat/chemistry ; Skin ; Gas Chromatography-Mass Spectrometry ; Electronic Nose ; High-Throughput Nucleotide Sequencing ; Quality of Life ; Probiotics/administration &amp; dosage ; Deodorants ; }, abstract = {Skin bromhidrosis, commonly referred to as body odor, is caused by the microbial breakdown of sweat, leading to the formation of volatile organic compounds (VOCs) that result in unpleasant odors. While body odor is a natural consequence of sweat production, excessive or persistent odor can significantly affect quality of life, causing social stigma and psychological distress. Traditional approaches to managing body odor, such as antiperspirants and deodorants, have limitations, necessitating the development of more advanced diagnostic tools and treatments. This review aims to explore recent advancements in the diagnosis and treatment of skin offensive odor, focusing on cutting-edge technologies and novel approaches. It highlights the interplay of the skin microbiome, sweat gland activity, and external factors in odor formation and investigates innovative solutions for long-term odor management. Emerging diagnostic techniques, such as electronic nose (E-nose) technology, gas chromatography-mass spectrometry (GC-MS), and next-generation sequencing (NGS), enable precise detection and analysis of odor-causing VOCs and microbial profiles. These tools facilitate a deeper understanding of the pathophysiology of odor production. Treatment innovations include nanotechnology-based antimicrobials (e.g., silver and zinc oxide nanoparticles), probiotic formulations for microbiome modulation, and odor-neutralizing compounds such as cyclodextrins and enzymatic neutralizers. Advanced delivery systems, including microneedle patches and nanoencapsulation, enable targeted, sustained release of active ingredients. Additionally, systemic approaches like oral probiotics and dietary interventions offer complementary strategies for managing body odor. The integration of novel diagnostics with innovative topical and systemic treatments offers promising avenues for more effective and personalized management of skin offensive odor. These advancements pave the way for improved quality of life for individuals affected by bromhidrosis, with potential for widespread application in personal care and medical contexts. Clinical trial number: Not applicable.}, }
@article {pmid40056186, year = {2025}, author = {Chen, XX and Ju, Q and Qiu, D and Zhou, Y and Wang, Y and Zhang, XX and Li, JG and Wang, M and Chang, N and Xu, XR and Zhang, YB and Zhao, T and Wang, K and Zhang, Y and Zhang, J}, title = {Microbial dysbiosis with tryptophan metabolites alteration in lower respiratory tract is associated with clinical responses to anti-PD-1 immunotherapy in advanced non-small cell lung cancer.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {74}, number = {4}, pages = {140}, pmid = {40056186}, issn = {1432-0851}, support = {82103446//National Natural Science Foundation of China/ ; 82273226//National Natural Science Foundation of China/ ; 82473215//National Natural Science Foundation of China/ ; 2020QNRC001//China Association for Science and Technology/ ; 2021LC2115//Fourth Military Medical University/ ; }, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/immunology/drug therapy/metabolism/therapy ; *Tryptophan/metabolism ; *Lung Neoplasms/immunology/drug therapy/therapy/metabolism ; *Dysbiosis/immunology ; Female ; Male ; Middle Aged ; Aged ; *Immunotherapy/methods ; *Immune Checkpoint Inhibitors/therapeutic use ; Microbiota/drug effects/immunology ; Programmed Cell Death 1 Receptor/antagonists &amp; inhibitors/metabolism ; Respiratory System/immunology/metabolism/microbiology ; Adult ; }, abstract = {Lower respiratory tract microbiome constitutes a unique immune microenvironment for advanced non-small cell lung cancer as one of dominant localized microbial components. However, there exists little knowledge on the associations between this regional microbiome and clinical responses to anti-PD-1 immunotherapy from clinical perspectives. Here, we equivalently collected bronchoalveolar lavage fluids from 56 advanced NSCLC participants treated with none (untreated, n = 28) or anti-PD-1 immunotherapy (treated, n = 28), which was further divided into responder (n = 17) and non-responder (n = 11) subgroups according to clinical responses, aiming to compare their microbial discrepancy by performing metagenomic sequencing and targeted metabolic alterations by tryptophan sequencing. Correspondingly, microbial diversities transformed significantly after receiving immunotherapeutic agents, where Gammaproteobacteria and Campylobacter enriched, but Escherichia, Streptococcus, Chlamydia, and Staphylococcus reduced at the genus level, differences of which failed to be achieved among subgroups with various clinical responses (responder or non-responder; LDA > 2, P < 0.05[*]). And the relative abundance of Staphylococcus and Streptomyces was escalated in response subgroup to anti-PD-1 immunotherapy by microbial compositional analysis (as relative abundance ≥ 3%, P < 0.05[*]), no significance of which was achieved among treated and untreated groups. In addition, relative abundances of bacterial tryptophan metabolites and its derivatives were also higher in the responder subgroup, distinctively being associated with divergent genera (VIP > 1, P < 0.05[*]). Our study revealed predictive performance of lower respiratory tract microbiome to antitumoral immunotherapy and further suggested that anti-PD-1 immunotherapy may alter lower respiratory tract microbiome composition and interact with its tryptophan metabolites to regulate therapeutic efficacy in advanced NSCLC, performing as potential biomarkers to prognosis and interventional strategies.}, }
@article {pmid40056175, year = {2025}, author = {de Fernandes, MG and Nascimento-Silva, G and Rozas, EE and Hardoim, CCP and Custódio, MR}, title = {From Sea to Freshwater: Shared and Unique Microbial Traits in Sponge Associated Prokaryotic Communities.}, journal = {Current microbiology}, volume = {82}, number = {4}, pages = {178}, pmid = {40056175}, issn = {1432-0991}, support = {88887465142/2019-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 2016/17189-7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2017/10157-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, mesh = {*Porifera/microbiology ; Animals ; *Microbiota ; *Fresh Water/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Seawater/microbiology ; *Phylogeny ; Symbiosis ; Ecosystem ; Archaea/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; }, abstract = {Despite their ecological significance and biotechnological potential, freshwater sponges remain relatively understudied compared to their marine counterparts. In special, the prokaryotic communities of species from isolated yet highly diverse ecosystems, such as the Amazon Rainforest, remain unknown, leaving an important part of the Porifera microbiome underexplored. Using high-throughput sequencing of the 16S rRNA gene, we unraveled the structure of the microbiota associated to the freshwater sponges Heteromeyenia cristalina and Metania reticulata for the first time. Their microbiome was compared with that of the haplosclerid marine sponges Amphimedon viridis and Haliclona melana; and the tetractinellid Cinachyrella alloclada. Our findings reveal not only a shared core microbiome between the freshwater and marine environments but also indicate functional redundancy in their communities, suggesting that certain microbial metabolic functions are conserved across diverse habitats. Comparisons between ecosystems also revealed that microbiomes of freshwater sponges can be richer and more diverse than those of marine species. Moreover, we compared the microbiome of adults and asexual reproduction structures (buds and gemmules) of sponges from both habitats, revealing a remarkable similarity between adults and their respective offsprings, indicating an important role of vertical transmission in this mode of reproduction. Our observations emphasize the dynamic interactions and the adaptability of the sponge-associated microbiota, providing insights into how these symbiotic associations were affected during the colonization of freshwater environments and shedding light into how symbiotic relationships are maintained throughout generations.}, }
@article {pmid40055814, year = {2025}, author = {Gao, W and Wang, G and Yuan, H and Chen, Y and Che, J and Cheng, Z and Chen, L and Zhang, L and Zhu, Y and Liu, X and Liu, A and Yang, Q and Cao, P and Qian, W and Huang, W and Schnabl, B and Yang, L and Chu, H}, title = {Gram-positive probiotics improves acetaminophen-induced hepatotoxicity by inhibiting leucine and Hippo-YAP pathway.}, journal = {Cell &amp; bioscience}, volume = {15}, number = {1}, pages = {32}, pmid = {40055814}, issn = {2045-3701}, support = {82470584//National Natural Science Foundation of China/ ; 82000561//National Natural Science Foundation of China/ ; 82270614//National Natural Science Foundation of China/ ; 81974078//National Natural Science Foundation of China/ ; 81570530//National Natural Science Foundation of China/ ; 2022YFA1305600//National Key R&amp;D Program of China/ ; 2023YFC2413804//National Key R&amp;D Program of China/ ; P30 DK120515/DK/NIDDK NIH HHS/United States ; }, abstract = {OBJECTIVES: Drug-induced liver injury (DILI) can be improved by modulating gut microbiota. We aimed to investigate a probiotic mixture comprising Bifidobacterium Longum, Streptococcus thermophilus, and Lactobacillus delbrueckii subspecies bulgaricus (BSL) in mitigating acetaminophen induced liver injury (AILI), and to elucidate the underlying mechanisms.<br><br>METHODS: Gut bacterial communities were analyzed in fecal samples from patients with DILI and healthy controls. Mice were pretreated with BSL or PBS for 10&#xa0;days, then subjected to a single dose of acetaminophen (300&#xa0;mg/kg) gavage and euthanized 24&#xa0;h later. Transcriptome sequencing, microbiome, and metabolome sequencing were performed on mouse samples, respectively.<br><br>RESULTS: Gut bacterial dysbiosis existed in DILI patients, with a decrease in Gram-positive bacteria and an increase in Gram-negative bacteria. A similar situation occurred in AILI mice. Pretreatment of BSL significantly improved APAP-induced disorders of gut bacteria and alleviated hepatic inflammation and necrosis. Transcriptome sequencing showed that BSL inhibited the hepatic damage pathways, such as Hippo and TGF-&#x3b2; signaling pathway. Metabolomic profiling revealed an obvious increase in oligopeptides containing branched-chain amino acids (BCAAs) in AILI mice, whereas these metabolites were significantly negatively correlated with the abundance of BSL, but positively with key genes of Hippo pathway. In vitro experiments showed that leucine exerted a dose-related exacerbation pattern on APAP-mediated hepatocellular injury. Mice supplemented with leucine resulted in the further overexpression of Yes-associated protein, an increase in oxidative stress, and a worsening of AILI.}, }
@article {pmid40056901, year = {2025}, author = {Kuziel, GA and Lozano, GL and Simian, C and Li, L and Manion, J and Stephen-Victor, E and Chatila, T and Dong, M and Weng, JK and Rakoff-Nahoum, S}, title = {Functional diversification of dietary plant small molecules by the gut microbiome.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2025.01.045}, pmid = {40056901}, issn = {1097-4172}, abstract = {Plants are composed of diverse secondary metabolites (PSMs), which are widely associated with human health. Whether and how the gut microbiome mediates such impacts of PSMs is poorly understood. Here, we show that discrete dietary and medicinal phenolic glycosides, abundant health-associated PSMs, are utilized by distinct members of the human gut microbiome. Within the Bacteroides, the predominant gram-negative bacteria of the Western human gut, we reveal a specialized multi-enzyme system dedicated to the processing of distinct glycosides based on structural differences in phenolic moieties. This Bacteroides metabolic system liberates chemically distinct aglycones with diverse biological functions, such as colonization resistance against the gut pathogen Clostridioides difficile via anti-microbial activation of polydatin to the stilbene resveratrol and intestinal homeostasis via activation of salicin to the immunoregulatory aglycone saligenin. Together, our results demonstrate generation of biological diversity of phenolic aglycone "effector" functions by a distinct gut-microbiome-encoded PSM-processing system.}, }
@article {pmid40056781, year = {2025}, author = {Chen, H and Li, J and Wu, Y and Li, Y and Zheng, S and Wu, Y and Xuan, R and Wu, L and Miao, J and Wang, Y and Tan, H and Zhou, J and Huang, J and Yan, X}, title = {Structural characteristics of intestinal microbiota of domestic ducks with different body sizes.}, journal = {Poultry science}, volume = {104}, number = {4}, pages = {104930}, doi = {10.1016/j.psj.2025.104930}, pmid = {40056781}, issn = {1525-3171}, abstract = {Domestic ducks are economically important agricultural animals, and their body size is a crucial economic trait. The intestinal flora plays a pivotal role in influencing body metabolism, growth, and development. Currently, no literature is available on the potential effect of the intestinal flora of domestic ducks on body size. This study used 16S rRNA sequencing technology to investigate the fecal microbiota of 229 individuals reared under identical feeding conditions. The findings revealed that partridge ducks with large body sizes (LBS) exhibited a higher level of intestinal microbial diversity than ducks with small body sizes (SBS). Notably, the gut microbiota composition of SBS displayed significantly elevated proportions of Streptococcus, Rothia, and Psychrobacter compared to their counterparts with LBS. Conversely, Lactobacillus was significantly more abundant in LBS. Jeotgalibaca and Psychrobacter were identified as key biomarkers of SBS, whereas Lactobacillus and Bacteroides were predominant biomarkers of LBS. Functional predictions based on intestinal microbiota indicated discernible differences among different body types, particularly evident in non- partridge ducks. The present study investigated the correlation between the intestinal microbiota and body size of domestic ducks, aiming to provide practical insights for the production management of domestic duck farming.}, }
@article {pmid39961369, year = {2025}, author = {Tomatsu, S and Abbott, SM and Attarian, H}, title = {Clinical Chronobiology: Circadian Rhythms in Health and Disease.}, journal = {Seminars in neurology}, volume = {}, number = {}, pages = {}, doi = {10.1055/a-2538-3259}, pmid = {39961369}, issn = {1098-9021}, abstract = {Circadian rhythms (CRs) are entrainable endogenous rhythms that respond to external stimuli and regulate physiological functions. The suprachiasmatic nucleus (SCN) in the hypothalamus is the mammalian master clock that synchronizes all other tissue-specific peripheral clocks, primarily through gamma-aminobutyric acid (GABA) and vasoactive intestinal polypeptide (VIP). The SCN follows Earth's 24-hour cycle by light entrainment through the retinohypothalamic tract. At the cellular level, the core clock genes CLOCK, BMAL1, PER1-PER3, CRY1, and CRY2 regulate CRs in a negative feedback loop. The circadian disruption of the sleep-wake cycle manifests in at least six distinct clinical conditions. These are the circadian rhythm sleep-wake disorders (CRSWDs). Their diagnosis is made by history, sleep diaries, and actigraphy. Treatment involves a combination of timed light exposure, melatonin/melatonin agonists, and behavioral interventions. In addition, CR disturbances and subsequent misalignment can increase the risk of a variety of illnesses. These include infertility and menstrual irregularities as well as diabetes, obesity, fatty liver disease, and other metabolic syndromes. In addition, a disruption in the gut microbiome creates a proinflammatory environment. CR disturbances increase the risk for mood disorders, hence the utility of light-based therapies in depression. People with neurodegenerative disorders demonstrate significant disturbances in their CRs, and in their sleep-wake cycles. Circadian realignment therapies can also help decrease the symptomatic burden of these disorders. Certain epilepsy syndromes, such as juvenile myoclonic epilepsy (JME), have a circadian pattern of seizures. Circadian disturbances in epilepsy can be both the consequence and cause for breakthrough seizures. The immune system has its own CR. Disturbances in these due to shift work, for instance, can increase the risk of infections. CR disturbances can also increase the risk of cancer by impacting DNA repair, apoptosis, immune surveillance, and cell cycle regulation. Moreover, the timing of chemotherapeutic agents has been shown to increase their therapeutic impact in certain cancers.}, }
@article {pmid40055808, year = {2025}, author = {Avershina, E and Qureshi, AI and Winther-Larsen, HC and Rounge, TB}, title = {Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {66}, pmid = {40055808}, issn = {2049-2618}, support = {2022067//Helse S&#xf8;r-&#xd8;st RHF/ ; }, mesh = {*Software ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Humans ; *Mycobiome ; *Fungi/genetics/classification/isolation &amp; purification ; *Metagenomics/methods ; Computational Biology/methods ; Ascomycota/genetics/classification/isolation &amp; purification ; Basidiomycota/genetics/isolation &amp; purification/classification ; Databases, Genetic ; }, abstract = {BACKGROUND: The mycobiome, representing the fungal component of microbial communities, is increasingly acknowledged as an integral part of the gut microbiome. However, research in this area remains relatively limited. The characterization of mycobiome taxa from metagenomic data is heavily reliant on the quality of the software and databases. In this study, we evaluated the feasibility of mycobiome profiling using existing bioinformatics tools on simulated fungal metagenomic data.<br><br>RESULTS: We identified seven tools claiming to perform taxonomic assignment of fungal shotgun metagenomic sequences. One of these was outdated and required substantial modifications of the code to be functional and was thus excluded. To evaluate the accuracy of identification and relative abundance of the remaining tools (Kraken2, MetaPhlAn4, EukDetect, FunOMIC, MiCoP, and HumanMycobiomeScan), we constructed 18 mock communities of varying species richness and abundance levels. The mock communities comprised up to 165 fungal species belonging to the phyla Ascomycota and Basidiomycota, commonly found in gut microbiomes. Of the tools, FunOMIC and HumanMycobiomeScan needed source code modifications to run. Notably, only one species, Candida orthopsilosis, was consistently identified by all tools across all communities where it was included. Increasing community richness improved precision of Kraken2 and the relative abundance accuracy of all tools on species, genus, and family levels. MetaPhlAn4 accurately identified all genera present in the communities and FunOMIC identified most species. The top three tools for overall accuracy in both identification and relative abundance estimation were EukDetect, MiCoP, and FunOMIC, respectively. Adding 90% and 99% bacterial background did not significantly impact these tools' performance. Among the whole genome reference tools (Kraken2, HMS, and MiCoP), MiCoP exhibited the highest accuracy when the same reference database was used.<br><br>CONCLUSION: Our survey of mycobiome-specific software revealed a very limited selection of such tools and their poor robustness due to error-prone software, along with a significant lack of comprehensive databases enabling characterization of the mycobiome. None of the implemented tools fully agreed on the mock community profiles. FunOMIC recognized most of the species, but EukDetect and MiCoP provided predictions that were closest to the correct compositions. The bacterial background did not impact these tools' performance. Video Abstract.}, }
@article {pmid40055708, year = {2025}, author = {Hall, LM and Ellis, JT and Stark, DJ}, title = {Diagnostic dilemma: application of real-time PCR assays for the detection of Dientamoeba fragilis in medical and veterinary specimens.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {94}, pmid = {40055708}, issn = {1756-3305}, mesh = {Animals ; *Real-Time Polymerase Chain Reaction/methods/veterinary ; *Dientamoeba/genetics/isolation &amp; purification ; Cattle ; Cats ; *Dientamoebiasis/diagnosis/parasitology ; Dogs ; Humans ; Dog Diseases/diagnosis/parasitology ; DNA, Protozoan/genetics ; Cattle Diseases/diagnosis/parasitology ; Reproducibility of Results ; Cat Diseases/diagnosis/parasitology ; Cross Reactions ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Real-time PCR (qPCR) diagnostics developed for use in human clinical settings have been implemented to identify new animal hosts of the gastrointestinal protozoan Dientamoeba fragilis. The gut microbiome varies between species; unrecognised cross-reactivity could occur when applying these assays to new animal hosts. The use of qPCR diagnostics was assessed for the identification of new animal hosts of the gastrointestinal protozoan Dientamoeba fragilis.<br><br>METHODS: Forty-nine cattle, 84 dogs, 39 cats and 254 humans were screened for D. fragilis using two qPCR assays: EasyScreen (Genetic Signatures) and a laboratory-based assay commonly used in Europe. The reliability of the identifications made by these assays were assessed using melt curve analysis of qPCR products, conventional PCR targeting the SSU rDNA sequencing and NGS amplicon sequencing of qPCR product.<br><br>RESULTS: PCR products from the D. fragilis identified in cattle had a 9&#xa0;&#xb0;C cooler melt curve than when detected in humans. This melt curve discrepancy, indicative of cross-reactivity with an unknown organism, was investigated further. DNA sequencing determined that Simplicimonas sp. was the genera responsible for this cross-reactivity in cattle specimens. Dientamoeba fragilis was not detected in either dogs or cats. There was a discrepancy in the number of positive samples detected using the two qPCR assays when applied to human samples. The EasyScreen assay detected 24 positive samples; the laboratory-based assay detected an additional 34 positive samples. Of the discrepant samples, 5 returned sequence data for D. fragilis, and 29 were unsupported (false) positive samples.<br><br>CONCLUSIONS: Analysis of the melt curve after the qPCR reaction is a valuable technique to help differentiate samples containing D. fragilis compared to cross-reactions with non-target organisms. The identification of new animal hosts requires further evidence from either microscopy or DNA sequencing to confirm the presence of D. fragilis. Additionally, to reduce the risk of false-positive results due to non-specific amplification, we recommend reducing the number of PCR cycles to less than 40. Based on these results, we consider the ramifications of this identified cross-reactivity to the known host species distribution of D. fragilis.}, }
@article {pmid40054656, year = {2025}, author = {Wu, HH and Leng, S and Eisenstat, DD and Sergi, C and Leng, R}, title = {Targeting p53 for Immune Modulation: Exploring Its Functions in Tumor Immunity and Inflammation.}, journal = {Cancer letters}, volume = {}, number = {}, pages = {217614}, doi = {10.1016/j.canlet.2025.217614}, pmid = {40054656}, issn = {1872-7980}, abstract = {p53, often referred to as the "guardian of the genome," is a critical regulator of cellular responses to stress. p53 plays a dual role in tumor suppression and immune regulation. In addition to its well-known functions of maintaining genomic stability and inducing apoptosis, p53 orchestrates a complex interaction between innate and adaptive immune responses. This involvement contributes to pathogen clearance, immune surveillance, and immunogenic cell death (ICD). This review explores the influence of p53 on immune dynamics, detailing its effects on macrophages, dendritic cells, natural killer cells (NK), T cells, and B cells. This review explains how mutations in p53 disrupt immune responses, promoting tumor immune evasion, and highlights its regulation of inflammatory cytokines and pattern recognition receptors. Furthermore, p53's role in ICD marks it as a key player in antitumor immunity, which has significant implications for cancer immunotherapy. The review also discusses the role of p53 in inflammation, autoimmune diseases, and chronic infections, revealing its dual function in promoting and suppressing inflammation through interactions with NF-κB signaling. Therapeutically, approaches that target p53, including wild-type p53 reactivation and combination therapies with immune checkpoint inhibitors, show considerable promise. Advances in high-throughput technologies, such as single-cell RNA sequencing and CRISPR screens, provide new insights into the immunological functions of p53, including its role in microbiome-immune interactions and immune senescence. This comprehensive review highlights the importance of incorporating immunological insights from p53 into innovative therapeutic strategies, addressing existing knowledge gaps, and paving the way for personalized medicine.}, }
@article {pmid40054557, year = {2025}, author = {Zhao, C and Peng, Y and Raza, MF and Wang, W and Zhang, Y and Chen, Y and Han, R and Guo, J and Huang, S and Li, W}, title = {A gut bacterial supplement for Asian honey bee (Apis cerana) enhances host tolerance to nitenpyram: Insight from microbiota-gut-brain axis.}, journal = {Environmental research}, volume = {274}, number = {}, pages = {121306}, doi = {10.1016/j.envres.2025.121306}, pmid = {40054557}, issn = {1096-0953}, abstract = {The widespread use of neonicotinoid pesticides has severely impacted honey bees, driving population declines. Gut microbiota are increasingly recognized for their role in mitigating pesticide toxicity. This study evaluated the ability of Gilliamella sp. G0441, a core microbiome member of the Asian honey bee (Apis cerana), to confer resistance to the toxicity of a neonicotinoid nitenpyram. Newly emerged Asian honey bees were first colonized with gut microbiota in the source colony, then divided into four treatments: SS (fed sucrose solution throughout), SN (fed sucrose solution, then exposed to nitenpyram), GS (fed Gilliamella, then sucrose solution), and GN (fed Gilliamella, then exposed to nitenpyram), and their responses-mortality, food consumption, body weight, and sucrose sensitivity-were assessed. The protective effects of Gilliamella administration on the host were further validated using a microbiota-free bee model. Gilliamella supplementation significantly mitigated nitenpyram-induced appetite suppression, weight loss, impaired learning, and gut microbiota disruption. Mechanistic analyses revealed that nitenpyram disrupted brain metabolism via the intestinal MAPK pathway, reducing ascorbate and aldarate metabolism. Prophylactic Gilliamella treatment reversed these effects, restored metabolic balance, and modulated esterase E4 expression, enhancing pesticide resistance. This study underscores Gilliamella's vital role in honey bee resilience to neonicotinoids, offering insights into the microbiota-gut-brain axis (MGBA) as a pathway for enhancing pesticide tolerance and ecological health.}, }
@article {pmid40054499, year = {2025}, author = {Luan, WW and Gu, HW and Qiu, D and Ding, X and Liu, PM and Hashimoto, K and Yang, JJ and Wang, XM}, title = {Repeated administration of esketamine ameliorates mechanical allodynia in mice with chemotherapy-induced peripheral neuropathy: A role of gut microbiota and metabolites.}, journal = {Neurochemistry international}, volume = {}, number = {}, pages = {105961}, doi = {10.1016/j.neuint.2025.105961}, pmid = {40054499}, issn = {1872-9754}, abstract = {Chemotherapy-induced peripheral neuropathy (CIPN) severely diminishes the quality of life for cancer survivors, yet effective treatments remain scarce. Esketamine, a commonly used anesthetic, has demonstrated neuroprotective effects by restoring gut microbiome dysbiosis. In this study, we investigated the impact of esketamine on nociceptive sensitivity in a mouse model of CIPN and explored the potential involvement of the gut microbiome. In mice treated with oxaliplatin, repeated esketamine doses (in contrast to a single dose) significantly improved the paw withdrawal threshold (PWT). Western blot and qPCR analyses further revealed that repeated esketamine administration markedly reduced microglial activation and neuroinflammation in the dorsal root ganglion (DRG), underscoring its potent anti-inflammatory properties. Moreover, fecal 16S rRNA analysis indicated that esketamine partially restored the abnormal gut microbiota composition (β-diversity). Plasma metabolome analysis showed that repeated esketamine treatment significantly lowered the elevated levels of 6H-indolo[2,3-b]quinoline and restored the reduced levels of (3-exo)-3-[3-methyl-5-(1-methylethyl)-4H-1,2,4-triazol-4-yl]-8-azabicyclo[3.2.1]octane observed in oxaliplatin-treated mice. In addition, fecal microbiota transplantation from esketamine-treated CIPN mice notably improved both the diminished PWT and DRG neuroinflammation in oxaliplatin-treated mice. Collectively, these findings suggest that repeated esketamine administration may alleviate mechanical allodynia in CIPN mice by modulating neuroinflammation, gut microbiota, and associated metabolites.}, }
@article {pmid40054447, year = {2025}, author = {Xiao, X and Zhao, W and Song, Z and Qi, Q and Wang, B and Zhu, J and Lin, J and Wang, J and Hu, A and Huang, S and Wang, Y and Chen, J and Fang, C and Ji, Q and Zhang, N and Meng, L and Wei, X and Chen, C and Cai, S and Chen, S and Ding, K and Li, D and Liu, S and Song, T and Tian, L and Zhang, H and Zhang, Y and Xu, S and Chen, J and Chen, H and Cen, Q and Jiang, F and Hu, G and Tang, C and Guo, W and Wang, X and Zhan, L and Fan, J and Wang, J and Zhou, C and Li, L and Lv, Z and Hu, Y and Lin, X and Mai, G and Luo, L and Yang, T and Wang, W and Kristiansen, K and Chen, L and Yang, H and Ni, M and Gu, Y and Mu, F and Yang, Y and Zhou, J and Wang, J and Zhang, WJ and Han, M and Xu, X and Liu, S}, title = {Microbial ecosystems and ecological driving forces in the deepest ocean sediments.}, journal = {Cell}, volume = {188}, number = {5}, pages = {1363-1377.e9}, doi = {10.1016/j.cell.2024.12.036}, pmid = {40054447}, issn = {1097-4172}, mesh = {*Geologic Sediments/microbiology/chemistry ; *Oceans and Seas ; *RNA, Ribosomal, 16S/genetics ; *Ecosystem ; Phylogeny ; Bacteria/genetics/classification/metabolism ; Microbiota/genetics ; Metagenome ; Metagenomics ; }, abstract = {Systematic exploration of the hadal zone, Earth's deepest oceanic realm, has historically faced technical limitations. Here, we collected 1,648 sediment samples at 6-11 km in the Mariana Trench, Yap Trench, and Philippine Basin for the Mariana Trench Environment and Ecology Research (MEER) project. Metagenomic and 16S rRNA gene amplicon sequencing generated the 92-Tbp MEER dataset, comprising 7,564 species (89.4% unreported), indicating high taxonomic novelty. Unlike in reported environments, neutral drift played a minimal role, while homogeneous selection (HoS, 50.5%) and dispersal limitation (DL, 43.8%) emerged as dominant ecological drivers. HoS favored streamlined genomes with key functions for hadal adaptation, e.g., aromatic compound utilization (oligotrophic adaptation) and antioxidation (high-pressure adaptation). Conversely, DL promoted versatile metabolism with larger genomes. These findings indicated that environmental factors drive the high taxonomic novelty in the hadal zone, advancing our understanding of the ecological mechanisms governing microbial ecosystems in such an extreme oceanic environment.}, }
@article {pmid40054445, year = {2025}, author = {Turjeman, S and Rozera, T and Elinav, E and Ianiro, G and Koren, O}, title = {From big data and experimental models to clinical trials: Iterative strategies in microbiome research.}, journal = {Cell}, volume = {188}, number = {5}, pages = {1178-1197}, doi = {10.1016/j.cell.2025.01.038}, pmid = {40054445}, issn = {1097-4172}, mesh = {*Microbiota ; Humans ; *Big Data ; Animals ; Clinical Trials as Topic ; Metagenomics/methods ; Metabolomics/methods ; }, abstract = {Microbiome research has expanded significantly in the last two decades, yet translating findings into clinical applications remains challenging. This perspective discusses the persistent issue of correlational studies in microbiome research and proposes an iterative method leveraging in silico, in vitro, ex vivo, and in vivo studies toward successful preclinical and clinical trials. The evolution of research methodologies, including the shift from small cohort studies to large-scale, multi-cohort, and even "meta-cohort" analyses, has been facilitated by advancements in sequencing technologies, providing researchers with tools to examine multiple health phenotypes within a single study. The integration of multi-omics approaches-such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics-provides a comprehensive understanding of host-microbe interactions and serves as a robust hypothesis generator for downstream in vitro and in vivo research. These hypotheses must then be rigorously tested, first with proof-of-concept experiments to clarify the causative effects of the microbiota, and then with the goal of deep mechanistic understanding. Only following these two phases can preclinical studies be conducted with the goal of translation into the clinic. We highlight the importance of combining traditional microbiological techniques with big-data approaches, underscoring the necessity of iterative experiments in diverse model systems to enhance the translational potential of microbiome research.}, }
@article {pmid40054249, year = {2025}, author = {Walling, LK and Gamache, MH and González-Pech, RA and Harwood, VJ and Ibrahim-Hashim, A and Jung, JH and Lewis, DB and Margres, MJ and McMinds, R and Rasheed, K and Reis, F and van Riemsdijk, I and Santiago-Alarcon, D and Sarmiento, C and Whelan, CJ and Zalamea, PC and Parkinson, JE and Richards, CL}, title = {Incorporating microbiome analyses can enhance conservation of threatened species and ecosystem functions.}, journal = {The Science of the total environment}, volume = {970}, number = {}, pages = {178826}, doi = {10.1016/j.scitotenv.2025.178826}, pmid = {40054249}, issn = {1879-1026}, abstract = {Conservation genomics is a rapidly growing subdiscipline of conservation biology that uses genome-wide information to inform management of biodiversity at all levels. Such efforts typically focus on species or systems of conservation interest, but rarely consider associated microbes. At least three major approaches have been used to study how microorganisms broadly contribute to conservation areas: (1) diversity surveys map out microbial species distribution patterns in a variety of hosts, natural environments or regions; (2) functional surveys associate microbial communities with factors of interest, such as host health, symbiotic interactions, environmental characteristics, ecosystem processes, and biological invasions; and (3) manipulative experiments examine the response of changes to microbial communities or determine the functional roles of specific microbes within hosts or communities by adding, removing, or genetically modifying microbes. In practice, multiple approaches are often applied simultaneously. The results from all three conservation genomics approaches can be used to help design practical interventions and improve management actions, some of which we highlight below. However, experimental manipulations allow for more robust causal inferences and should be the ultimate goal of future work. Here we discuss how further integration of microbial research of a host's microbiome and of free living microbes into conservation biology will be an essential advancement for conservation of charismatic organisms and ecosystem functions in light of ongoing global environmental change.}, }
@article {pmid40055466, year = {2025}, author = {Vaaben, TH and Lützhøft, DO and Koulouktsis, A and Dawoodi, IM and Stavnsbjerg, C and Kvich, L and Gögenur, I and Vazquez-Uribe, R and Sommer, MOA}, title = {Modulating tumor immunity using advanced microbiome therapeutics producing an indole metabolite.}, journal = {EMBO reports}, volume = {}, number = {}, pages = {}, pmid = {40055466}, issn = {1469-3178}, support = {NNF20CC0035580//Novo Nordisk Fonden (NNF)/ ; NNF17CO0028232//Novo Nordisk Fonden (NNF)/ ; NNF21OC0072832//Novo Nordisk Fonden (NNF)/ ; }, abstract = {The gut microbiome has emerged as a key player in modulating immune responses against cancer, suggesting that microbial interventions can enhance treatment outcomes. Indole metabolites produced by probiotic bacteria activate the aryl hydrocarbon receptor (AhR), a transcription factor important for immune cell regulation. Cancer patients with high plasma concentrations of these metabolites have shown improved survival. Building on these findings, we have engineered Escherichia coli Nissle 1917 to produce the AhR agonist indole-3-acetic acid. Delivery of indole-3-acetic acid by tumor-colonizing bacteria changes the tumor microenvironment in a murine model, significantly increasing levels of CXCL9 and IFN-γ and elevating tumor-infiltrating T-cell abundance and activation. Treatment with our engineered strain inhibits tumor growth, improves survival in syngeneic tumor models, and leads to long-lasting immunity in a tumor rechallenge experiment. Further investigation indicates that this immune modulation is driven by the direct activation of AhR by indole-3-acetic acid, leading to differential cytokine expression and a shift in immune cell composition within the tumor. This study highlights the importance of microbial metabolites in immune modulation and supports exploring microbiome-based therapies in oncology.}, }
@article {pmid40054578, year = {2025}, author = {Zeng, Y and Lu, X and Wang, M and Chen, R and Li, Q and Zhu, J and Su, Z and Lin, F}, title = {Endophyte Acrocalymma vagum establishes the holobiont with rice to attract beneficial microorganisms and promote disease resistance.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2025.03.008}, pmid = {40054578}, issn = {2090-1224}, abstract = {INTRODUCTION: Endophytic fungi are essential microorganisms in promoting plant health. However, the mechanism of endophytic fungi regulating root microbiota to enhance crop production and resistance remains unclear.<br><br>OBJECTIVES: We aimed i) to explore the microbial alteration driven by endophytic Acrocalymma vagum in developing crop yield and rice resistance; ii) to reveal the mechanism of root-released compound stimulated by A. vagum in recruiting benefit microbes.<br><br>METHODS: The microbiome was applied in a culture-dependent and culture-independent method to study the microbial communities of the A. vagum-rice holobiont using 16S rRNA and ITS gene metabarcoding. Non-target metabolome identified distinct metabolites responsible for community variations. Label-free proteomic analyses investigated the association between primary genes related to the holobiont formation. CRISPR/Cas9 technique and homologous recombination replacement were used to characterize the functions of putative genes.<br><br>RESULTS: A. vagum enhanced cultivated rice yield by 5.73&#x202f;&#xb1;&#x202f;1.76&#x202f;% and induced 83.24&#x202f;&#xb1;&#x202f;9.86&#x202f;% control efficiency against rice blast. We discovered that A. vagum simplified rice microbial structure based on co-occurrence networks, by lowering the proportion of potentially pathogenic predominant Burkholderia and driving rice to recruit beneficial Lactobacillus, Sarocladium and Nigrospora to promote rice growth with the increases of 44.41&#x202f;&#xb1;&#x202f;5.10&#x202f;% shoot height and 70.21&#x202f;&#xb1;&#x202f;9.57&#x202f;% shoot biomass. Moreover, the holobiont released coumaric and trans-ferulic acids to attract beneficial microbes. 206 rice proteins were notably up-regulated in the holobiont, particularly the OsPrxs. CRISPR/Cas9-edited mutants of OsPRX70 and OsPRX95 reduced the promotion effect of A. vagum on rice growth. Furthermore, the pathways of 39 overexpressed proteins in A. vagum were enriched in invading the host and inducing resistance. The knockouts of AvGH3, AvGH7, AvMFS1, and AvCBA transformed A. vagum role from endophyte to pathogen.<br><br>CONCLUSIONS: The A. vagum-rice holobiont releases recruitment signals and improves the rice community structure. We provide ecological and molecular evidence to confirm the mutualism of endophyte-plant-promoting growth and disease resistance.}, }
@article {pmid40054511, year = {2025}, author = {Yang, S and He, Y and Ma, Y and Wang, R and Wu, Y and Wu, W}, title = {Associations between the oral microbiome, number of teeth and frailty among American adults: A cross-sectional study from NHANES 2009-2012.}, journal = {Experimental gerontology}, volume = {}, number = {}, pages = {112727}, doi = {10.1016/j.exger.2025.112727}, pmid = {40054511}, issn = {1873-6815}, abstract = {BACKGROUND: The intricate interrelationship between oral health, the number of teeth, oral microbiota, and frailty remains largely unexplored in clinical research. This study aimed to investigate the interrelationship between oral microbiome, the number of teeth, and frailty.<br><br>METHODS: Data from 4518 participants in NHANES 2009-2012 were analyzed. Frailty was measured using the 48-item Frailty Index (FI), oral microbiota diversity through 16S rRNA sequencing, and tooth retention via clinical examination. Multivariable logistic regression and restricted cubic spline (RCS) evaluated associations between alpha diversity and frailty. Mediation analysis assessed tooth retention's role. Mortality associations were analyzed using Kaplan-Meier survival curves and Cox regression. Beta diversity was examined with PCoA and PERMANOVA.<br><br>RESULTS: The prevalence of frailty was 39.73&#x202f;%. Univariate analysis showed that alpha diversity indices except for the Simpson index were significantly lower in frailty, and after adjusted for confounders, observed ASVs (adjusted OR: 0.80 [0.73, 0.87], p&#x202f;<&#x202f;0.001), Faith's PD (adjusted OR: 0.81 [0.74, 0.88], p&#x202f;<&#x202f;0.001) and Shannon-Weiner index (adjusted OR: 0.88 [0.81, 0.95], p&#x202f;=&#x202f;0.002) were remained significantly associated with frailty. The reduced number of teeth partially mediated the relationship (for Faith's PD: &#x3b2;indirect&#x202f;=&#x202f;-0.001 [-0.003, 0.000], p&#x202f;=&#x202f;0.036, proportion: 8.33&#x202f;% [0.00&#x202f;%, 37.50&#x202f;%]; for Shannon-Weiner index, &#x3b2;indirect&#x202f;=&#x202f;-0.007 [-0.013, -0.002], p&#x202f;=&#x202f;0.007, Proportion&#x202f;=&#x202f;17.07&#x202f;% [3.39&#x202f;%, 65.00&#x202f;%]). Univariable Cox proportional hazard regression showed that all alpha diversity indices were significantly associated with all-cause mortality in frail population, and in multivariable analysis, Shannon-Weiner index (HR: 0.72 [0.55, 0.94], p&#x202f;=&#x202f;0.017) and Simpson index (HR: 0.71 [0.60, 0.83], p&#x202f;<&#x202f;0.001) remained statistically significant. PCoA showed that beta diversity was also significantly associated with frailty.<br><br>CONCLUSION: Lower oral microbiome diversity is associated with higher frailty and reduced survival. Tooth retention partially mediates this link, emphasizing the importance of oral health in mitigating frailty and promoting healthy aging.}, }
@article {pmid40054458, year = {2025}, author = {O'Riordan, KJ and Moloney, GM and Keane, L and Clarke, G and Cryan, JF}, title = {The gut microbiota-immune-brain axis: Therapeutic implications.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {101982}, doi = {10.1016/j.xcrm.2025.101982}, pmid = {40054458}, issn = {2666-3791}, abstract = {The microbiota-gut-brain axis has major implications for human health including gastrointestinal physiology, brain function, and behavior. The immune system represents a key pathway of communication along this axis with the microbiome implicated in neuroinflammation in health and disease. In this review, we discuss the mechanisms as to how the gut microbiota interacts with the brain, focusing on innate and adaptive immunity that are often disrupted in gut-brain axis disorders. We also consider the implications of these observations and how they can be advanced by interdisciplinary research. Leveraging an increased understanding of how these interactions regulate immunity has the potential to usher in a new era of precision neuropsychiatric clinical interventions for psychiatric, neurodevelopmental, and neurological disorders.}, }
@article {pmid40054278, year = {2025}, author = {Wang, YC and Wang, S and Lv, YH and Wang, JY and Yang, WX and Deng, Y and Ju, F and Wang, C}, title = {Diversity, influential factor, and communication network construction of quorum sensing bacteria in global wastewater treatment plants.}, journal = {Water research}, volume = {279}, number = {}, pages = {123437}, doi = {10.1016/j.watres.2025.123437}, pmid = {40054278}, issn = {1879-2448}, abstract = {Quorum sensing (QS) is widespread in the microbial world and mediates microbial relationships in communities. However, the existing knowledge is far from a full description of the complex communication-based microbial interactions in engineered ecosystems, i.e., wastewater treatment plants (WWTPs). Herein, we conducted a systematic analysis of the diversity and influential factors of the QS-related microflora through the collection of global 1186 activated sludge microbiome samples. We found that the richness of bacteria associated with the universal bacterial secondary messenger presented the highest in QS system, whereas the bacteria related to the degradation of N-Acyl-homoserine lactones occupied the main position in the quorum quenching system. The community turnover of QS microflora was found more likely to be dominated by the deterministic process, such as the dissolved oxygen and resource availability (the ratio of organic matter to microorganisms). Meanwhile, these QS microflora in turn have a profound impact on the functions of WWTPs, especially multilingual intelligencers involving various language systems, such as Nitrospira. By connecting the signal molecule synthesis and acceptance bacteria, we constructed a QS communication network, which can be a robust tool for initial investigation of signaling molecule-mediated microbial interactions. The above results were further integrated into an online access website, named Quorum Sensing Communication Network in Activated Sludge (QSCNAS) (https://www.qscnas.cn/), which allowed users to browse and capture possible QS-based interactions of target bacterium. This work contributes to the understanding of bacterial communication in WWTPs and provides a platform to help in developing potential regulation strategies.}, }
@article {pmid40054134, year = {2025}, author = {Jiang, T and Ren, J and Li, D and Luo, Y and Huang, Y and Gao, T and Yang, J and Yu, J and Liu, L and Yuan, H}, title = {Pseudomonas syringae exacerbates apple replant disease caused by Fusarium.}, journal = {Microbiological research}, volume = {296}, number = {}, pages = {128124}, doi = {10.1016/j.micres.2025.128124}, pmid = {40054134}, issn = {1618-0623}, abstract = {Apple replant disease (ARD) causes significant economic losses globally, including in China. Analyzing the causes of this replant disease from the perspective of rhizosphere microecology is therefore essential. In this study, we examined rhizosphere soils from apple trees subjected to continuous cropping. The mechanisms underlying ARD were elucidated through high-throughput sequencing of the soil microbiome, co-occurrence network analysis using NetShift, and correlation analyses. Core bacterial microbes were isolated, and their roles in altering the microecological environment were verified through reinoculation experiments. The results indicated that the disease indices for apple seedlings cultivated increased in continuously cropped soils. Bacterial diversity decreased in continuously cropped apple orchards for 10 years (R10) and 15 years (R15), but the relative abundance of Pseudomonas increased. In contrast, fungal diversity increased, with the relative abundance of Fusarium also increasing. As a dominant genus, Pseudomonas exhibited significant network variation after 10 years of consecutive cultivation, suggesting that this microorganism may play a key role in the occurrence of ARD. Moreover, the correlation analysis revealed, for the first time, that Pseudomonas is negatively correlated with bacterial diversity but positively correlated with the relative abundance of Fusarium, indicating a close relationship between Pseudomonas and Fusarium in continuously cropped soil. Four key Pseudomonas amplicon sequence variants (ASVs) strains were isolated from the continuously cropped rhizosphere soil of apple trees, and reinoculation experiments verified that introducing Pseudomonas exacerbated the occurrence of replant diseases in both strawberry and apple, with significantly higher disease indices compared to single Fusarium inoculation. The findings of this study provide new and timely insights into the mechanism underlying the occurrence of ARD.}, }
@article {pmid40053783, year = {2025}, author = {Ram, S and Corbin, M and 't Mannetje, A and Eng, A and Kvalsvig, A and Baker, MG and Douwes, J}, title = {Antibiotic Use In Utero and Early Life and Risk of Chronic Childhood Conditions in New Zealand: Protocol for a Data Linkage Retrospective Cohort Study.}, journal = {JMIR research protocols}, volume = {14}, number = {}, pages = {e66184}, doi = {10.2196/66184}, pmid = {40053783}, issn = {1929-0748}, mesh = {Humans ; Female ; Retrospective Studies ; *Anti-Bacterial Agents/adverse effects/therapeutic use ; Pregnancy ; *Prenatal Exposure Delayed Effects/epidemiology ; New Zealand/epidemiology ; Child, Preschool ; *Diabetes Mellitus, Type 1/drug therapy/epidemiology ; Infant ; Cohort Studies ; Chronic Disease/epidemiology ; Male ; Inflammatory Bowel Diseases/drug therapy/epidemiology ; Child ; Information Storage and Retrieval ; Attention Deficit Disorder with Hyperactivity/drug therapy/epidemiology ; Infant, Newborn ; }, abstract = {BACKGROUND: The incidence of many common chronic childhood conditions has increased globally in the past few decades, which has been suggested to be potentially attributed to antibiotic overuse leading to dysbiosis in the gut microbiome.<br><br>OBJECTIVE: This linkage study will assess the role of antibiotic use in utero and in early life in the development of type 1 diabetes (T1D), attention-deficit/hyperactive disorder (ADHD), and inflammatory bowel disease.<br><br>METHODS: The study design involves several retrospective cohort studies using linked administrative health and social data from Statistics New Zealand's Integrated Data Infrastructure. It uses data from all children who were born in New Zealand between October 2005 and December 2010 (N=334,204) and their mothers. Children's antibiotic use is identified for 4 time periods (at pregnancy, at &#x2264;1 year, at &#x2264;2 years, and at &#x2264;5 years), and the development of T1D, ADHD, and inflammatory bowel disease is measured from the end of the antibiotic use periods until death, emigration, or the end of the follow-up period (2021), whichever came first. Children who emigrated or died before the end of the antibiotic use period are excluded. Cox proportional hazards regression models are used while adjusting for a range of potential confounders.<br><br>RESULTS: As of September 2024, data linkage has been completed, involving the integration of antibiotic exposure and outcome variables for 315,789 children. Preliminary analyses show that both prenatal and early life antibiotic consumption is associated with T1D. Full analyses for all 3 outcomes will be completed by the end of 2025.<br><br>CONCLUSIONS: This series of linked cohort studies using detailed, complete, and systematically collected antibiotic prescription data will provide critical new knowledge regarding the role of antibiotics in the development of common chronic childhood conditions. Thus, this study has the potential to contribute to the development of primary prevention strategies through, for example, targeted changes in antibiotic use.<br><br>DERR1-10.2196/66184.}, }
@article {pmid40053776, year = {2025}, author = {Abu El Kheir-Mataria, W and Mahmoud Abdelraheem, O and Chun, S}, title = {Genetic, Socioecological, and Health Determinants of Extreme Longevity in Semi-Supercentenarians and Supercentenarians: Protocol for a Scoping Review.}, journal = {JMIR research protocols}, volume = {14}, number = {}, pages = {e63900}, doi = {10.2196/63900}, pmid = {40053776}, issn = {1929-0748}, mesh = {Humans ; *Longevity/genetics ; Aged, 80 and over ; Quality of Life ; Female ; Male ; }, abstract = {BACKGROUND: The study of supercentenarians (individuals aged 110 years or older) offers valuable insights into aging, longevity, and the factors contributing to exceptional lifespans. These individuals often exhibit extraordinary cognitive and physical performance, which can inform strategies to improve the health of the general population. Research on centenarians (individuals aged 100 years or older), semi-supercentenarians (individuals aged 105-109 years), and supercentenarians covers themes like genetic factors, microbiome, inflammation, diet, lifestyle, and psychological aspects. These studies often focus on various aspects of extreme longevity, using varied objectives and methodologies, highlighting the need for a comprehensive synthesis to map the breadth of research and identify gaps in understanding this demographic.<br><br>OBJECTIVE: This scoping review aims to map and synthesize existing evidence on the determinants of extreme longevity, focusing on individuals living beyond 105 years. This review seeks to categorize genetic factors associated with semi-supercentenarians and supercentenarians; explore the range of socioecological factors contributing to their longevity; and identify common themes such as health, functional capacity, cognition, mental health, behaviors, social support, quality of life, personality traits, environmental factors, and religiosity. Additionally, it aims to examine and describe the methodologies and assessment tools used in studies on extreme longevity and provide an overview of global demographic trends and patterns among supercentenarians, including geographic distribution, gender prevalence, and socioeconomic characteristics.<br><br>METHODS: This scoping review follows the PRISMA-P (Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols) 2015 guidelines and the Population, Exposure, and Outcome framework. It includes observational and interventional, quantitative and qualitative studies on supercentenarians and semi-supercentenarians. Data will be sourced from databases like Scopus, PubMed, ProQuest, PsycINFO, and The Cochrane Library. The selection process involves abstract and full-text screening by two independent reviewers, with data extraction focusing on study characteristics, participant demographics, interventions or exposures, and key findings. A thematic analysis will identify patterns across various themes.<br><br>RESULTS: As of October 2, 2024, five databases were searched, yielding 844 studies. After removing duplicates, 706 studies remained. Following the first and second screening stages, 135 studies were found to be eligible. The study is expected to be completed by the end of February 2025.<br><br>CONCLUSIONS: By synthesizing evidence, this study will understand the global scope of supercentenarians, describe the main themes of research interest, and identify gaps. The findings are expected to contribute significantly to the body of knowledge on longevity, informing future research and public health policies. This scoping review aims to enhance the understanding of factors promoting healthy aging and extreme longevity, benefiting broader public health initiatives.<br><br>TRIAL REGISTRATION: PROSPERO CRD42024512298; https://tinyurl.com/4cmux7h4.}, }
@article {pmid40053318, year = {2025}, author = {Nihalani, R and Zola, J and Aluru, S}, title = {Disambiguating a Soft Metagenomic Clustering.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {}, number = {}, pages = {}, doi = {10.1089/cmb.2024.0825}, pmid = {40053318}, issn = {1557-8666}, abstract = {Clustering is a popular technique used for analyzing amplicon sequencing data in metagenomics. Specifically, it is used to assign sequences (reads) to clusters, each cluster representing a species or a higher level taxonomic unit. Reads from multiple species often sharing subsequences, combined with lack of a perfect similarity measure, make it difficult to correctly assign reads to clusters. Thus, metagenomic clustering methods must either resort to ambiguity, or make the best available choice at each read assignment stage, which could lead to incorrect clusters and potentially cascading errors. In this article, we argue for first generating an ambiguous clustering and then resolving the ambiguities collectively by analyzing the ambiguous clusters. We propose a rigorous formulation of this problem and show that it is NP-Hard. We then propose an efficient heuristic to solve it in practice. We validate our approach on several synthetically generated datasets and two datasets consisting of 16S rDNA sequences from the microbiome of rat guts.}, }
@article {pmid40053288, year = {2025}, author = {Melese, K and Alemu, T and Desalegn, A}, title = {Probiotic effects of Lactobacillus reuteri and Pediococcus pentosaceus on growth performance, blood biochemistry, and antibody response in broiler chickens.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {40053288}, issn = {1678-4405}, support = {1/CX/CSRD VA/United States ; 2//Addis Ababa University/ ; }, abstract = {The gut microbiome, consisting of a diverse community of beneficial bacteria, supports broiler health and performance. This study aimed to assess the impact of probiotic lactic acid bacteria supplementation on growth performance, blood parameters, and antibody response in broiler chickens. The experiment involved 108 Cobb 500 breed chicks, which were allocated into three groups: T1 (received basal diets + L. reuteri at 1 × 10[8] CFU/mL), T2 (received basal diets + P. pentosaceus at 1 × 10[8] CFU/mL), and T3 (control group receiving only basal diets). The chicks were assigned to these groups randomly, following a completely randomized design. The results showed that the broiler groups supplemented with either L. reuteri or P. pentosaceus probiotics exhibited significant improvements (p < 0.05) in body weight, weight gain, and feed conversion ratio throughout the study. There were no significant differences (p > 0.05) in total protein and albumin levels. At the same time, cholesterol levels were lower in the L. reuteri and P. pentosaceus-treated groups compared to the control group. Furthermore, the hemagglutination inhibition titer of Newcastle disease was significantly (p < 0.05) higher in the groups supplemented with L. reuteri and P. pentosaceus. The study also found that the lymphoid organ weight/body weight ratio was significantly higher in the L. reuteri and P. pentosaceus groups. In conclusion, the oral administration of the probiotic strains L. reuteri DSM 20016T and P. pentosaceus DSM 20206 to broiler chickens improved growth performance, reduced blood cholesterol levels, and enhanced immune function. These findings indicate that these lactic acid bacteria could be beneficial as both immunomodulators and growth promoters in broiler production.}, }
@article {pmid40053245, year = {2025}, author = {Lukic, I and Ivkovic, S and Glavonic, E and Adzic, M and Mitic, M}, title = {Long-lasting Depressive Behavior of Adolescent Chronically Stressed Mice is Mediated by Gut Microbiota Dysbiosis.}, journal = {Molecular neurobiology}, volume = {}, number = {}, pages = {}, pmid = {40053245}, issn = {1559-1182}, abstract = {Depression is one of the most common mental disorders worldwide, and its prevalence sharply rises during adolescence. Adolescence is a particularly sensitive period to the effects of environmental stressors, which can cause persistent depressive behavior extending into adulthood. However, the studies assessing if changes in gut microbiota could be one of the mediators of long-term effects of adolescent stress are scarce. In the present study, we examined enduring effects of adolescent chronic unpredictable stress (CUS) on mice behavior along with alterations in their gut microbiome, by using 16 s rRNA gene sequencing and fecal microbiota transplantation (FMT). CUS mice, as well as naïve mice receiving FMT from stressed animals, showed long-lasting anxiety and depressive-like behavior extending into adulthood. The microbiota dysbiosis in adolescence was characterized by higher abundance of Alloprevotella and lower abundance of Paraprevotella, Parasutterella, Parabacteroides, and undefined genus Rikenellaceae_RC9_gut_group. On the contrary, microbiota dysbiosis in adulthood was characterized by higher abundance of Bacteroides, Enterorhabdus, Marvinbriantia, and Parabacteroides and lower abundance of Akkermansia, Odoribacter, and Rikenella. In particular, depressive-like behavior in adolescence was negatively correlated with Paraprevotella, while depressive-like behavior in adulthood was negatively correlated with Rikenella abundance, in both CUS and FMT mice. Therefore, the transfer of microbiota from mice stressed in adolescence is able to induce long-lasting depressive-like behavior in naïve mice, clearly showing the importance of gut microbiota dysbiosis in adolescence in shaping enduring depressive behavior. Moreover, our results indicate that changes in specific but different bacteria are related to depressive behavior in adolescence and in adulthood.}, }
@article {pmid40052570, year = {2025}, author = {Shen, M and Gao, S and Zhu, R and Wang, W and Gao, W and Tao, L and Chen, W and Zhu, X and Yang, Y and Xu, T and Zhao, T and Jiao, N and Zhi, M and Zhu, L}, title = {Multimodal Metagenomic Analysis Reveals Microbial InDels as Superior Biomarkers for Pediatric Crohn's Disease.}, journal = {Journal of Crohn's &amp; colitis}, volume = {}, number = {}, pages = {}, doi = {10.1093/ecco-jcc/jjaf039}, pmid = {40052570}, issn = {1876-4479}, abstract = {BACKGROUND AND AIMS: The gut microbiome is closely associated with pediatric Crohn's disease (CD), while the multidimensional microbial signature and their capabilities for distinguishing pediatric CD are underexplored. This study aims to characterize the microbial alterations in pediatric CD and develop a robust classification model.<br><br>METHODS: A total of 1,175 fecal metagenomic sequencing samples, predominantly from three cohorts of pediatric CD patients, were re-analyzed from raw sequencing data using uniform process pipelines to obtain multidimensional microbial alterations in pediatric CD, including taxonomic profiles, functional profiles, and multi-type genetic variants. Random forest algorithms were used to construct classification models after comparing multiple machine learning algorithms.<br><br>RESULTS: We found pediatric CD samples exhibited reduced microbial diversity and unique microbial characteristics. Pronounced abundance differences in 45 species and 1,357 KO genes. Particularly, Enterocloster bolteae emerged as a pivotal pediatric CD-associated species. Additionally, we identified a vast amount of microbial genetic variants linked to pediatric CD, including 192 structural variants, 1,256 insertions/deletions (InDels), and 3,567 single nucleotide variants, with a considerable portion of these variants occurred in non-genic regions. The InDel-based model outperformed other predictive models against multidimensional microbial signatures, achieving an AUC of 0.982. The robustness and disease specificity were further confirmed in an independent CD cohort (AUC=0.996) and five other microbiome-associated pediatric cohorts.<br><br>CONCLUSIONS: Our study provided a comprehensive landscape of microbial alterations in pediatric CD and introduced a highly effective diagnostic model rooted in microbial InDels, which contributes to the development of the non-invasive diagnostic tools and targeted therapies.}, }
@article {pmid40052450, year = {2025}, author = {Qian, Z and Chen, S and Liao, X and Xie, J and Xu, Y and Zhong, H and Ou, L and Zuo, X and Xu, X and Peng, J and Wu, J and Cai, S}, title = {Decreased intestinal abundance of Akkermansia muciniphila is associated with metabolic disorders among people living with HIV.}, journal = {Annals of medicine}, volume = {57}, number = {1}, pages = {2474730}, doi = {10.1080/07853890.2025.2474730}, pmid = {40052450}, issn = {1365-2060}, mesh = {Humans ; Male ; *HIV Infections/complications/microbiology ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; *Akkermansia ; *Non-alcoholic Fatty Liver Disease/microbiology/metabolism ; Prospective Studies ; Feces/microbiology ; Metagenomics/methods ; Hyperlipidemias/microbiology ; Metabolic Diseases/microbiology/epidemiology ; Verrucomicrobia/isolation &amp; purification ; Overweight/microbiology/complications ; }, abstract = {BACKGROUND: Previous studies have shown changes in gut microbiota after human immunodeficiency virus (HIV) infection, but there is limited research linking the gut microbiota of people living with HIV (PLWHIV) to metabolic diseases.<br><br>METHODS: A total of 103 PLWHIV were followed for 48&#x2009;weeks of anti-retroviral therapy (ART), with demographic and clinical data collected. Gut microbiome analysis was conducted using metagenomic sequencing of fecal samples from 12 individuals. Nonalcoholic fatty liver disease (NAFLD) was diagnosed based on controlled attenuation parameter (CAP) values of 238&#x2009;dB/m from liver fibro-scans. Participants were divided based on the presence of metabolic disorders, including NAFLD, overweight, and hyperlipidemia. Akkermansia abundance in stool samples was measured using RT-qPCR, and Pearson correlation and logistic regression were applied for analysis.<br><br>RESULTS: Metagenomic sequencing revealed a significant decline in gut Akkermansia abundance in PLWHIV with NAFLD. STAMP analysis of public datasets confirmed this decline after HIV infection, while KEGG pathway analysis identified enrichment of metabolism-related genes. A prospective cohort study with 103 PLWHIV followed for 48&#x2009;weeks validated these findings. Akkermansia abundance was significantly lower in participants with NAFLD, overweight, and hyperlipidemia at baseline, and it emerged as an independent predictor of NAFLD and overweight. Negative correlations were observed between Akkermansia abundance and both CAP values and body mass index (BMI) at baseline and at week 48. At the 48-week follow-up, Akkermansia remained a predictive marker for NAFLD.<br><br>CONCLUSIONS: Akkermansia abundance was reduced in PLWHIV with metabolic disorders and served as a predictive biomarker for NAFLD progression over 48&#x2009;weeks of ART.}, }
@article {pmid40051875, year = {2025}, author = {De Troyer, L and Audenaert, K and Ommeslag, S and Debode, J and De Gelder, L and De Zutter, N}, title = {The biocontrol agent Streptomyces rimosus subsp. rimosus tempers shifts in the wheat spicosphere microbiome induced by Fusarium Head Blight.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1540242}, pmid = {40051875}, issn = {1664-462X}, abstract = {INTRODUCTION: Fusarium Head Blight (FHB) is a major fungal disease in wheat caused by Fusarium graminearum, inducing severe yield losses. Biological control agents (BCAs) can be an effective and sustainable approach to mitigate this phytopathogen. In this study, Streptomyces rimosus subsp. rimosus LMG19352 was used as a BCA to mitigate F. graminearum on wheat ears. Moreover, we aimed to assess the impact of BCA inoculation on non-target microorganisms present on the wheat spikes. Therefore, we evaluated shifts in the fungal and bacterial spicosphere microbiome (i) over time from flowering to mid-grain filling stage and (ii) across inoculations with F. graminearum and/or S. rimosus subsp. rimosus LMG19352.<br><br>METHODS: FHB symptoms were determined by multispectral imaging, and Illumina MiSeq was used to amplify 16S V3-V4 rDNA for bacteria and ITS2 for fungi, whereafter a correlation network analysis was performed.<br><br>RESULTS: The biocontrol potential of S. rimosus subsp. rimosus LMG19352 against F. graminearum was confirmed, as FHB symptoms were significantly reduced. Based on the microbial abundances, S. rimosus subsp. rimosus LMG19352 compensated for shifts in the spicosphere microbiome community induced by FHB. These results were supported by a network analysis, revealing a more complex and stable microbiome in the presence of the BCA compared to the infected control.<br><br>DISCUSSION: To our knowledge, this study is the first to reveal the potential of a bacterial BCA to temper shifts in the wheat microbiome caused by a phytopathogen, and thereby acting as a promising BCA.}, }
@article {pmid40051835, year = {2025}, author = {Zhou, J and Sun, Z and Wang, X and Wang, S and Jiang, W and Tang, D and Xia, T and Xiao, F}, title = {Low-temperature cold plasma promotes wound healing by inhibiting skin inflammation and improving skin microbiome.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {13}, number = {}, pages = {1511259}, pmid = {40051835}, issn = {2296-4185}, abstract = {Wound healing includes four consecutive and overlapping stages of hemostasis, inflammation, proliferation, and remodeling. Factors such as aging, infection, and chronic diseases can lead to chronic wounds and delayed healing. Low-temperature cold plasma (LTCP) is an emerging physical therapy for wound healing, characterized by its safety, environmental friendliness, and ease of operation. This study utilized a self-developed LTCP device to investigate its biological effects and mechanisms on wound healing in adult and elderly mice. Histopathological studies found that LTCP significantly accelerated the healing rate of skin wounds in mice, with particularly pronounced effects in elderly mice. LTCP can markedly inhibit the expression of pro-inflammatory cytokines (TNF-α, IL-6, IL-1β) and senescence-associated secretory phenotype factors (MMP-3, MMP-9), while significantly increasing the expression of tissue repair-related factors, such as VEGF, bFGF, TGF-β, COL-I, and α-SMA. It also regulated the expression of genes related to cell proliferation and migration (Aqp5, Spint1), inflammation response (Nlrp3, Icam1), and angiogenesis (Ptx3, Thbs1), promoting cell proliferation and inhibit apoptosis. Furthermore, LTCP treatment reduced the relative abundance of harmful bacteria such as Delftia, Stenotrophomonas, Enterococcus, and Enterobacter in skin wounds, while increasing the relative abundance of beneficial bacteria such as Muribaculaceae, Acinetobacter, Lachnospiraceae NK4A136_group, and un_f__Lachnospiraceae, thereby improving the microbial community structure of skin wounds. These research findings are of significant implications for understanding the mechanism of skin wound healing, as well as for the treatment and clinical applications of skin wounds, especially aging skin.}, }
@article {pmid40051690, year = {2025}, author = {Waller, ME and Gutierrez, A and Ticer, TD and Glover, JS and Baatz, JE and Wagner, CL and Engevik, MA and Chetta, KE}, title = {Profiling the response of individual gut microbes to free fatty acids (FFAs) found in human milk.}, journal = {Journal of functional foods}, volume = {125}, number = {}, pages = {}, pmid = {40051690}, issn = {1756-4646}, support = {K01 DK123195/DK/NIDDK NIH HHS/United States ; KL2 TR001452/TR/NCATS NIH HHS/United States ; P30 DK123704/DK/NIDDK NIH HHS/United States ; UL1 TR001450/TR/NCATS NIH HHS/United States ; }, abstract = {Preterm infants have an immature intestinal environment featuring microbial dysbiosis. Human milk can improve the composition of the neonatal gut microbiome by supporting commensal species. Milk free fatty acids (FFAs) provide nutritional energy, participate in endogenous signaling, and exert antimicrobial effects. This study examined the growth of individual commensal and pathobiont microbes in response to unesterified unsaturated FFAs found in milk: oleic, linoleic, arachidonic, and docosahexaenoic acid. Select species of commensal and pathobiont genera (Bifidobacterium, Lactobacillus, Streptococcus, Staphylococcus, Enterococcus, Acinetobacter, Pseudomonas, Escherichia, and Klebsiella) were cultured with FFAs. The growth of all commensals, except for L. johnsonii, was significantly inhibited by the highest concentration (1 %) of all FFAs. L. johnsonii was only inhibited by arachidonic acid. In contrast, suppression of pathobionts in response to FFAs was less pronounced. Higher concentrations (0.1 %, 1 %) of docosahexaenoic acid significantly inhibited the growth of five of eight pathobionts. Meanwhile, for oleic, linoleic, and arachidonic acid, only two of eight pathobionts were significantly affected. Intriguingly, the effects for these FFAs were highly complex. For example, S. agalactiae growth was enhanced with 1 % oleic acid but suppressed at 0.01 %; however, the effects were directionally opposite for linoleic acid, i.e., suppressed at 1 % but enhanced at 0.01 %. Our genome analyses suggest that pathobiont survival may be related to the number of gene copies for fatty acid transporters. Overall, the effect of FFAs was dose-dependent and species-specific, where commensal growth was broadly inhibited while pathobionts were either unaffected or exhibited complex, bi-directional responses.}, }
@article {pmid40051624, year = {2025}, author = {De Martinis, ECP and Alves, VF and Pereira, MG and Andrade, LN and Abichabki, N and Abramova, A and Dannborg, M and Bengtsson-Palme, J}, title = {Applying 3D cultures and high-throughput technologies to study host-pathogen interactions.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1488699}, pmid = {40051624}, issn = {1664-3224}, mesh = {Humans ; *Host-Pathogen Interactions ; *Cell Culture Techniques, Three Dimensional/methods ; Animals ; High-Throughput Screening Assays/methods ; Microbiota ; High-Throughput Nucleotide Sequencing ; }, abstract = {Recent advances in cell culturing and DNA sequencing have dramatically altered the field of human microbiome research. Three-dimensional (3D) cell culture is an important tool in cell biology, in cancer research, and for studying host-microbe interactions, as it mimics the in vivo characteristics of the host environment in an in vitro system, providing reliable and reproducible models. This work provides an overview of the main 3D culture techniques applied to study interactions between host cells and pathogenic microorganisms, how these systems can be integrated with high-throughput molecular methods, and how multi-species model systems may pave the way forward to pinpoint interactions among host, beneficial microbes and pathogens.}, }
@article {pmid40051478, year = {2025}, author = {Park, H and Yeo, S and Lee, T and Han, Y and Ryu, CB and Huh, CS}, title = {Culture-based characterization of gut microbiota in inflammatory bowel disease.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1538620}, pmid = {40051478}, issn = {1664-302X}, abstract = {Inflammatory bowel disease (IBD) is characterized by disruptions in the gut microbiome. While most studies on gut dysbiosis in IBD rely on sequencing-based methods, we employed a streamlined culturomics approach to obtain a more comprehensive understanding of gut microbiota imbalance in patients with IBD that may not be captured by sequencing alone. A total of 367 bacteria were identified at the species level, including 211 species from ulcerative colitis patients, 164 species from Crohn's disease (CD) patients, and 263 species from healthy individuals. Consistent with our 16S rRNA gene amplicon sequencing results, a significant decrease in microbial diversity and a severe imbalance, especially in CD patients, were also observed in the culture-based analysis. Our culturomics approach provided additional insights, highlighting dysbiosis in unique anaerobic and Gram-negative species in CD patients. Moreover, species-level findings for Bifidobacterium and Enterobacterales emphasized specific species expansions in IBD patients. Notably, Mediterraneibacter gnavus, Thomasclavelia ramosa, Parabacteroides merdae, and Collinsella aerofaciens are of particular clinical interest due to their correlation with inflammatory biomarkers. This comprehensive analysis underscores the value of integrating a culture-based approach with a genome-based approach to provide complementary insights and therapeutic targets in IBD.}, }
@article {pmid40051134, year = {2025}, author = {Bi, O and Caballero-Lima, D and Sikkink, S and Westgate, G and Kauser, S and Elies, J and Thornton, MJ}, title = {Do Melanocytes Have a Role in Controlling Epidermal Bacterial Colonisation and the Skin Microbiome?.}, journal = {Experimental dermatology}, volume = {34}, number = {3}, pages = {e70071}, doi = {10.1111/exd.70071}, pmid = {40051134}, issn = {1600-0625}, support = {//Innovate UK/ ; }, mesh = {Humans ; *Melanocytes ; *Microbiota ; *Staphylococcus epidermidis ; *Keratinocytes/microbiology/immunology ; Corynebacterium ; Epidermis/microbiology/immunology ; Fibroblasts/microbiology ; Melanins/metabolism ; Propionibacteriaceae ; Skin/microbiology/immunology ; alpha-MSH/metabolism ; Cells, Cultured ; Immunity, Innate ; }, abstract = {In addition to producing melanin to protect epidermal keratinocytes against DNA damage, melanocytes may have important roles in strengthening innate immunity against pathogens. We have developed a functional, pigmented, human full-thickness 3D skin equivalent to determine whether the presence of melanocytes impacts epidermal bacterial growth and regulates the expression of genes involved in the immune response. We introduced primary epidermal melanocytes to construct a 3-cell full-thickness skin equivalent with primary dermal fibroblasts and epidermal keratinocytes. Immunohistochemistry verified the appropriate ratio and spatial organisation of melanocytes. Alpha-MSH induced melanogenesis, confirming an appropriate physiological response. We compared this 3-cell skin equivalent with the 2-cell version without melanocytes in response to inoculation with 3 species of bacteria: Staphylococcus epidermidis, Corynebacterium striatum, and Cutibacterium acnes. There was a significant decrease in the colonisation of bacteria in the skin equivalents containing functional melanocytes. There was increased expression of immune-response genes (S100A9, DEFB4A, IL-4R) following microorganism exposure; however, there were marked differences between the unpigmented and pigmented skin equivalents. This physiologically relevant human 3D-skin equivalent opens up new avenues for studying complex skin pigmentation disorders, melanoma, and UV damage, as well as the rapidly evolving field of the skin microbiome and the balance between commensal and pathogenic species.}, }
@article {pmid40051043, year = {2025}, author = {Cresci, GAM}, title = {Understanding how foods and enteral feedings influence the gut microbiome.}, journal = {Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1002/ncp.11285}, pmid = {40051043}, issn = {1941-2452}, support = {//This study funding was provided by a research grant from Nestl&#xe9; Health Science./ ; }, abstract = {The gut microbiome supports both gut and overall health. Diet is known to be one of the driving factors that influences the gut microbiome. The foods we eat, the dietary and nondietary components they contain, various food consumption patterns, and the ratio of nutrients consumed have been shown to impact gut microbiome composition and function. Studies indicate that many acute and chronic diseases are associated with alterations to the gut microbiome. There are many patients who rely on enteral tube feeding for their nutrition support. More recently, enteral tube feeding formulations of "real food" have become commercially available. However, little is known about how enteral tube feeding impacts the gut microbiome in patients requiring this specialized form of nutrition therapy. This review summarizes the existing evidence regarding the food sources of commonly consumed macronutrients and their impact on the gut microbiome. Also presented is what is known regarding "standard" and real food enteral formulations on the gut microbiome. Existing evidence is suggestive that real food enteral formulations positively impact the gut microbiome. Still, more research is needed on ready-to-feed formulations, particularly in patients with various clinical conditions, and how gut microbiome modulation impacts clinical outcomes.}, }
@article {pmid40050995, year = {2025}, author = {Garrigues, Q and Apper, E and Mercier, F and Rodiles, A and Rovere, N and Chastant, S and Mila, H}, title = {Composition of the fecal, vaginal and colostrum microbiotas of dams at parturition and their relationship with neonatal outcomes in dogs.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {23}, pmid = {40050995}, issn = {2524-4671}, abstract = {BACKGROUND: Microbial seeding in early life is critical for the host's short- and long-term health, and the mother is the first source of bacteria for the newborn. The objective of this study was to characterize the maternal fecal, vaginal, and colostral microbiotas in the canine species one day after parturition and to evaluate the relationship between the microbial profiles of 36 dams and the neonatal outcomes of 284 newborns.<br><br>RESULTS: The first part of the study revealed the presence of 2 fecal, 3 vaginal, and 2 colostral microbial clusters on the basis of the core microbiota of the dams. Among these three maternal microbiotas, only the vaginal microbiome was found to be associated with neonatal outcomes. Compared with those in the other clusters, females in Cluster 1, with the lowest stillbirth and neonatal mortality ratios, presented a greater abundance of Moraxellaceae in their vaginal microbiota; Cluster 2, with a greater abundance of Pasteurellaceae, mostly from the Haemophilus genus; and Cluster 3 (with the highest stillbirth and neonatal mortality ratios), a greater abundance of Enterobacteriaceae, mostly E. coli. Moreover, Cluster 3 dams presented significantly lower species richness according to the Shannon index than did dams from the other clusters.<br><br>CONCLUSIONS: This study underscores the strong association between maternal microbiota, particularly the vaginal microbiota, and newborn health. The results of this study call for further research to gain a deeper understanding of the optimal vaginal microbiota composition in canine species and the ways to modulate it to improve neonatal outcomes.}, }
@article {pmid40050994, year = {2025}, author = {Talat, A and Bashir, Y and Khalil, N and Brown, CL and Gupta, D and Khan, AU}, title = {Antimicrobial resistance transmission in the environmental settings through traditional and UV-enabled advanced wastewater treatment plants: a metagenomic insight.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {27}, pmid = {40050994}, issn = {2524-6372}, support = {BT/PR40148/BTIS/137/20/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, abstract = {BACKGROUND: Municipal wastewater treatment plants (WWTPs) are pivotal reservoirs for antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). Selective pressures from antibiotic residues, co-selection by heavy metals, and conducive environments sustain ARGs, fostering the emergence of ARB. While advancements in WWTP technology have enhanced the removal of inorganic and organic pollutants, assessing ARG and ARB content in treated water remains a gap. This metagenomic study meticulously examines the filtration efficiency of two distinct WWTPs-conventional (WWTPC) and advanced (WWTPA), operating on the same influent characteristics and located at Aligarh, India.<br><br>RESULTS: The dominance of Proteobacteria or Pseudomonadota, characterized the samples from both WWTPs and carried most ARGs. Acinetobacter johnsonii, a prevailing species, exhibited a diminishing trend with wastewater treatment, yet its persistence and association with antibiotic resistance underscore its adaptive resilience. The total ARG count was reduced in effluents, from 58 ARGs, representing 14 distinct classes of antibiotics in the influent to 46 and 21 in the effluents of WWTPC and WWTPA respectively. However, an overall surge in abundance, particularly influenced by genes such as qacL, blaOXA-900, and rsmA was observed. Numerous clinically significant ARGs, including those against aminoglycosides (AAC(6')-Ib9, APH(3'')-Ib, APH(6)-Id), macrolides (EreD, mphE, mphF, mphG, mphN, msrE), lincosamide (lnuG), sulfonamides (sul1, sul2), and beta-lactamases (blaNDM-1), persisted across both conventional and advanced treatment processes. The prevalence of mobile genetic elements and virulence factors in the effluents possess a high risk for ARG dissemination.<br><br>CONCLUSIONS: Advanced technologies are essential for effective ARG and ARB removal. A multidisciplinary approach focused on investigating the intricate association between ARGs, microbiome dynamics, MGEs, and VFs is required to identify robust indicators for filtration efficacy, contributing to optimized WWTP operations and combating ARG proliferation across sectors.}, }
@article {pmid40050988, year = {2025}, author = {Fujita, H and Yoshida, S and Suzuki, K and Toju, H}, title = {Alternative stable states of microbiome structure and soil ecosystem functions.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {28}, pmid = {40050988}, issn = {2524-6372}, support = {Fellowship//Japan Society for the Promotion of Science/ ; 20K06820//Japan Society for the Promotion of Science/ ; 20K20586//Japan Society for the Promotion of Science/ ; JPMJPR16Q6//Japan Science and Technology Agency/ ; RGP0029/2019//Human Frontier Science Program/ ; JPNP18016//New Energy and Industrial Technology Development Organization/ ; }, abstract = {BACKGROUND: Theory predicts that biological communities can have multiple stable states in terms of their species/taxonomic compositions. The presence of such alternative stable states has been examined in classic ecological studies on the communities of macro-organisms (e.g., distinction between forest and savanna vegetation types). Nonetheless, it remains an essential challenge to extend the target of the discussion on multistability from macro-organismal systems to highly species-rich microbial systems. Identifying alternative stable states of taxonomically diverse microbial communities is a crucial step for predicting and controlling microbiome processes in light of classic ecological studies on community stability.<br><br>RESULTS: By targeting soil microbiomes, we inferred the stability landscapes of community structure based on a mathematical framework of statistical physics. We compiled a dataset involving 11 archaeal, 332 bacterial, and 240 fungal families detected from >&#x2009;1,500 agroecosystem soil samples and applied the energy landscape analysis to estimate the stability/instability of observed taxonomic compositions. The statistical analysis suggested that both prokaryotic and fungal community structure could be classified into several stable states. We also found that the inferred alternative stable states differed greatly in their associations with crop disease prevalence in agroecosystems. We further inferred "tipping points", through which transitions between alternative stable states could occur.<br><br>CONCLUSION: Our results suggest that the structure of complex soil microbiomes can be categorized into alternative stable states, which potentially differ in ecosystem-level functioning. Such insights into the relationship between structure, stability, and functions of ecological communities will provide a basis for ecosystem restoration and the sustainable management of agroecosystems.}, }
@article {pmid40050917, year = {2025}, author = {Zou, B and Liu, S and Dong, C and Shen, H and Lv, Y and He, J and Li, X and Ruan, M and Huang, Z and Shu, S}, title = {Fecal microbiota transplantation restores gut microbiota diversity in children with active Crohn's disease: a prospective trial.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {288}, pmid = {40050917}, issn = {1479-5876}, mesh = {Humans ; *Crohn Disease/therapy/microbiology ; Child ; Female ; Male ; Prospective Studies ; *Gastrointestinal Microbiome ; *Fecal Microbiota Transplantation ; Adolescent ; Biodiversity ; Feces/microbiology ; Biomarkers/metabolism ; Treatment Outcome ; }, abstract = {BACKGROUND: Clinical data on oral fecal microbiota transplantation (FMT), a promising therapy for Crohn's disease (CD), are limited. Herein, we determined the short-term safety and feasibility of FMT for pediatric patients with active CD.<br><br>METHODS: In this open-label, parallel-group, single-center prospective trial, patients with active CD were treated with oral FMT capsules combined with partial enteral nutrition (PEN) (80%). The control group comprised pediatric patients with active CD treated with PEN (80%) and immunosuppressants. Thirty-three patients (11.6&#x2009;&#xb1;&#x2009;1.82&#xa0;years)-17 in the capsule and 16 in the control groups-were analyzed. Data regarding the adverse events, clinical reactions, intestinal microbiome composition, and biomarker parameters were collected and compared post-treatment.<br><br>RESULTS: At week 10, the clinical and endoscopic remission rates did not differ between the two groups. By week 10, the mean fecal calprotectin level, C-reactive protein level, erythrocyte sedimentation rate, simple endoscopic score for CD, and pediatric CD activity index decreased significantly in the capsule group (all P&#x2009;<&#x2009;0.05). The main adverse event was mild-to-moderate constipation. Core functional genera, Agathobacter, Akkermansia, Roseburia,&#xa0;Blautia, Subdoligranulum, and Faecalibacterium, were lacking pre-treatment. Post-treatment, the implantation rates of these core functional genera increased significantly, which positively correlated with the anti-inflammatory factor, interleukin (IL)-10, and negatively correlated with the pro-inflammatory factor, IL-6. The combination of these six functional genera distinguished healthy children from those with CD (area under the curve&#x2009;=&#x2009;0.96).<br><br>CONCLUSIONS: Oral FMT capsules combined with PEN (80%) could be an effective therapy for children with active CD. The six core functional genera identified here may be candidate biomarkers for identifying children with CD.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov, retrospectively registered, ID# NCT05321758, NCT05321745, date of registration: 2022-04-04.}, }
@article {pmid40050732, year = {2025}, author = {Kim, K and Won, S}, title = {Robust phylogenetic tree-based microbiome association test using repeatedly measured data for composition bias.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {75}, pmid = {40050732}, issn = {1471-2105}, support = {NRF-2021R1A5A1033157//National Research Foundation/ ; NRF-2023M3E5D3009803//National Research Foundation of Korea/ ; 2024ER210800//Korea National Institute of Health/ ; }, mesh = {*Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; Humans ; }, abstract = {BACKGROUND: The effects of microbiota on the host phenotypes can differ substantially depending on their age. Longitudinally measured microbiome data allow for the detection of the age modification effect and are useful for the detection of microorganisms related to the progression of disease whose identification change over time. Moreover, longitudinal analysis facilitates the estimation of the within-subject covariate effect, is robust to the between-subject confounders, and provides better evidence for the causal relationship than cross-sectional studies. However, this method of analysis is limited by compositional bias, and few statistical methods can estimate the effect of microbiota on host diseases with repeatedly measured 16S rRNA gene data. Herein, we propose mTMAT, which is applicable to longitudinal microbiome data and is robust to compositional bias.<br><br>RESULTS: mTMAT normalized the microbial abundance and utilized the ratio of the pooled abundance for association analysis. mTMAT is based on generalized estimating equations with a robust variance estimator and can be applied to repeatedly measured microbiome data. The robustness of mTMAT against compositional bias is underscored by its utilization of abundance ratios.<br><br>CONCLUSIONS: With extensive simulation studies, we showed that mTMAT is statistically relatively powerful and is robust to compositional bias. mTMAT enables detection of microbial taxa associated with host diseases using repeatedly measured 16S rRNA gene data and can provide deeper insights into bacterial pathology.}, }
@article {pmid40050684, year = {2025}, author = {Badar, A and Aqueel, R and Nawaz, A and Ijaz, UZ and Malik, KA}, title = {Microbiota transplantation for cotton leaf curl disease suppression-core microbiome and transcriptome dynamics.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {380}, pmid = {40050684}, issn = {2399-3642}, support = {BB/T010649/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {*Gossypium/microbiology/genetics ; *Plant Diseases/microbiology/prevention &amp; control ; *Microbiota ; *Transcriptome ; Disease Resistance/genetics ; Rhizosphere ; Gene Expression Regulation, Plant ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; }, abstract = {Microbiota transplantation is a strong tool for managing plant disease. This study investigates the effects of microbiota transplantation on Cotton Leaf Curl Disease (CLCuD) resistance in Gossypium hirsutum, a species with good fiber length but high susceptibility to biotic stresses. Using metabarcoding for V3-V4 16S rRNA gene amplicon, microbial fractions from both rhizosphere and phyllosphere of CLCuD-resistant species Gossypium arboreum, and susceptible cotton varieties are analyzed. Unique bacterial taxa have been identified associated with disease resistance. Interspecies and intraspecies microbiota transplantation is conducted, followed by CLCuD incidence assays. It is seen that rhizospheric microbiota transplantation from G. arboreum FDH228 significantly suppresses CLCuD in G. hirsutum varieties, outperforming exogenous salicylic acid application. While phyllospheric transplants also reduce disease incidence, they are less effective than rhizospheric transplants. Differential expression analysis DESeq2 is utilized to identify key bacterial genera correlated with CLCuD suppression, including Pseudoxanthomonas and Stenotrophomonas in the rhizosphere of G. arboreum FDH228. Functional pathway analysis reveals upregulation of stress response and metabolism in tolerant species. Transcriptomics reveals upregulation of genes involved in protein phosphorylation and stress response in interspecies rhizospheric microbiota transplants. This study highlights microbiota transplantation as a sustainable method for controlling CLCuD along with specific microbial and genetic mechanisms contributing to CLCuD resistance.}, }
@article {pmid40050613, year = {2025}, author = {Jimenez-Sanchez, M and Celiberto, LS and Yang, H and Sham, HP and Vallance, BA}, title = {The gut-skin axis: a bi-directional, microbiota-driven relationship with therapeutic potential.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2473524}, doi = {10.1080/19490976.2025.2473524}, pmid = {40050613}, issn = {1949-0984}, mesh = {Humans ; *Skin/microbiology ; *Gastrointestinal Microbiome/physiology ; Animals ; *Dysbiosis/microbiology ; Gastrointestinal Tract/microbiology ; Homeostasis ; Skin Diseases/microbiology/therapy ; }, abstract = {This review explores the emerging term "gut-skin axis" (GSA), describing the bidirectional signaling that occurs between the skin and the gastrointestinal tract under both homeostatic and disease conditions. Central to GSA communication are the gut and skin microbiota, the microbial communities that colonize these barrier surfaces. By influencing diverse host pathways, including innate immune, vitamin D receptor, and Aryl hydrocarbon receptor signaling, a balanced microbiota contributes to both tissue homeostasis and host defense. In contrast, microbiota imbalance, or dysbiosis at one site, can lead to local barrier dysfunction, resulting in the activation of signaling pathways that can disrupt tissue homeostasis at the other site, potentially leading to inflammatory skin conditions such as atopic dermatitis and psoriasis, or gut diseases like Inflammatory Bowel Disease. To date, most research on the GSA has examined the impact of the gut microbiota and diet on skin health, but recent studies show that exposing the skin to ultraviolet B-light can beneficially modulate both the gut microbiome and intestinal health. Thus, despite the traditional focus of clinicians and researchers on these organ systems as distinct, the GSA offers new opportunities to better understand the pathogenesis of cutaneous and gastrointestinal diseases and promote health at both sites.}, }
@article {pmid40050500, year = {2025}, author = {Dave, M and Tattar, R}, title = {Antimicrobial resistance genes in the oral microbiome.}, journal = {Evidence-based dentistry}, volume = {}, number = {}, pages = {}, pmid = {40050500}, issn = {1476-5446}, abstract = {A COMMENTARY ON: Sukumar S, Rahmanyar Z, El Jurf H Q et al. Mapping the oral resistome: a systematic review. J Med Microbiol 2024; https://doi.org/10.1099/jmm.0.001866 .<br><br>DESIGN: This systematic review, without meta-analysis, aimed to map the oral resistome by analysing clinical studies that detected bacterial antimicrobial resistance genes (ARGs) in the oral cavity using molecular techniques.<br><br>DATA SOURCES: The researchers used Medline, Embase, Web of Science, CINAHL and Scopus databases from January 2015 to August 2023.<br><br>STUDY SELECTION: This systematic review included cross-sectional or longitudinal clinical studies that detected ARGs using molecular techniques; specifically polymerase chain reaction (PCR) or next-generation sequencing (NGS) metagenomics&#xa0;for samples from the oral cavity (saliva, gingival biofilm, pulp, or oral mucosa). Studies were excluded if they were in vitro or animal studies, literature reviews and not focused on ARG detection.<br><br>DATA EXTRACTION AND SYNTHESIS: Five reviewers independently screened titles and abstracts based on inclusion criteria. Full-text reports were then independently assessed for eligibility by three reviewers. Extracted data encompassed publication details, sample size, country, molecular methods used, number of ARGs detected, participants' health status, antibiotic exposure, and sample location within the oral cavity.<br><br>RESULTS: Out of 580 initially identified studies, 15 met the inclusion criteria. These studies, published between 2015 and 2023 from 12 different countries, employed either PCR (n&#x2009;=&#x2009;10) or NGS metagenomics (n&#x2009;=&#x2009;5) to detect ARGs from a pool of 1486 participants (1 study did not report on the number of participants). PCR-based studies identified an average of 7 ARGs (range 1-20), while NGS studies identified an average of 34 ARGs (range 7-70). In total, 159 unique ARGs conferring resistance to 22 antibiotic classes were identified across six regions of the oral cavity. The supragingival biofilm and saliva exhibited the highest richness of ARGs, defined by the number of unique ARGs detected. Genes conferring resistance to 19 antibiotic classes were present in the supragingival biofilm. Notably, 49 ARGs, including tetracycline and macrolide resistance genes, were found across all sampled locations, indicating a widespread distribution within the oral cavity. Thirteen studies reported on bacterial species associated with ARGs. NGS studies identified a mean of 65 ARG-carrying bacterial species, compared to a mean of 4 species in PCR studies. Specifically, 25 ARG-carrying species were identified in PCR studies, while NGS studies identified 177 species. Four studies reported ARGs associated with streptococcal species implicated in distant-site infections such as infective endocarditis. ESKAPE pathogens (group of highly virulent multidrug-resistant bacteria) were detected with ARGs in various oral sites using both PCR and NGS methods. Comparisons between healthy and diseased states revealed that a healthy oral microbiome harbours a more diverse resistome at the antibiotic class level. The supragingival resistome demonstrated the richest composition in both health and disease, with tetracycline ARGs predominating in the supragingival and saliva resistomes in cases of dental caries.<br><br>CONCLUSIONS: The analysis of the oral resistome from these 15 studies identified three ARGs present in all sites of the oral cavity, suggesting the presence of a core resistome. NGS studies provided greater insights compared to PCR studies; however, the overall research base is limited. Further comprehensive studies are necessary to fully map the oral resistome.}, }
@article {pmid40050445, year = {2025}, author = {Akhi, R and Lavrinienko, A and Hakula, M and Tjäderhane, L and Hindström, R and Nissinen, A and Wang, C and Auvinen, J and Kullaa, AM and Ylöstalo, P and Salo, T and Kaikkonen, K and Koskimäki, JJ and Hörkkö, S}, title = {Oral microbiome diversity associates with carotid intima media thickness in middle-aged male subjects.}, journal = {Communications medicine}, volume = {5}, number = {1}, pages = {66}, pmid = {40050445}, issn = {2730-664X}, abstract = {BACKGROUND: Although there have been significant advancements in reducing the burden of cardiovascular disease (CVD) by modifying traditional CVD risk factors, substantial risks persist, particularly among male subjects who exhibit heightened susceptibility to atherosclerosis. In this context, we aim to study the link between oral microbiome and carotid intima media thickness (cIMT).<br><br>METHODS: The Northern Finland Birth Cohort of 1966 (mean age 46 years, n&#x2009;=&#x2009;869) underwent an extensive health examination, including the measurement of cIMT. The oral microbiome was also investigated using high-throughput 16S rRNA gene sequencing.<br><br>RESULTS: Here we show that oral microbiome diversity links with atherosclerosis risk factors, namely smoking, glycemic balance, low-grade inflammation, and periodontitis. After excluding CVD-influencing factors (n&#x2009;=&#x2009;339), oral microbiome genera (p&#x2009;=&#x2009;0.030), Shannon index (p&#x2009;=&#x2009;0.001), &#x3b2;-diversity Bray-Curtis (p&#x2009;<&#x2009;0.001), and Jaccard (p&#x2009;<&#x2009;0.001) are associated with cIMT in males, but not in the female sub-cohort. Furthermore, in the male sub-cohort (n&#x2009;=&#x2009;131), the genera Prevotella, Megasphaera, and Veillonella associate positively with cIMT, while Absconditabacteria, Capnocytophaga, Gemella, Fusobacterium, Neisseria, Aggregatibacter, Tannerella, Treponema, Cardiobacterium, and Bacteroidales associate inversely with cIMT. We examine the involvement of serum total immunoglobulins and antibodies to phosphorylcholine (PCho) and malondialdehyde-acetaldehyde LDL (MAA-LDL) with cIMT. Subjects with high cIMT have lower levels of serum total IgA (p&#x2009;=&#x2009;0.009), IgA to PCho (p&#x2009;=&#x2009;0.017), and IgG to PCho (p&#x2009;=&#x2009;0.008). The relative abundance of cIMT-associated genera correlates with serum IgA antibodies.<br><br>CONCLUSIONS: This middle-aged birth cohort study shows that male oral microbiome diversity links to cIMT, suggesting a potential sex-specific interaction between the oral microbiome and atherosclerosis.}, }
@article {pmid40050220, year = {2025}, author = {Huang, X and Zhao, W and Feng, R and Zhou, Y and Wang, J and Xiao, J and Li, L and Shan, X and Feng, Y and Ming, Y and Cao, J and Kang, X and Wu, L and Chen, H and Duan, X}, title = {Linking gut microbiome profiles and white matter integrity to social behavior in young autistic children: from the perspective of individual variation.}, journal = {Science bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.scib.2025.02.031}, pmid = {40050220}, issn = {2095-9281}, }
@article {pmid40049993, year = {2025}, author = {Sargison, ND and Chaudhry, U and Costa-Junior, L and Kutcher, JR and Li, K and Sargison, FA and Zahid, O}, title = {The diagnosis and vector potential of Ornithonyssus bacoti tropical rat mites in northern Europe.}, journal = {Veterinary parasitology, regional studies and reports}, volume = {58}, number = {}, pages = {101204}, doi = {10.1016/j.vprsr.2025.101204}, pmid = {40049993}, issn = {2405-9390}, mesh = {Animals ; *Mites/microbiology/physiology ; *Mite Infestations/veterinary/parasitology/diagnosis ; RNA, Ribosomal, 16S/genetics/analysis ; Europe ; Rodent Diseases/parasitology/diagnosis/microbiology/epidemiology ; Rats ; Male ; Female ; Microbiota ; }, abstract = {The mesostigmatid tropical rat mite, Ornithonyssus bacoti, is an important cause of disease in small rodents, and of gamasoidosis in humans when they come into contact with infestations. Most reports of O. bacoti infestations are from warmer parts of the Americas, southern Europe and Asia; and infection has only rarely been recorded in northern Europe. In 2021 and 2024, two separate cases of gamasoidosis were identified in student flats in the city of Edinburgh, UK. Further investigation highlighted the value of combining conventional morphological and 16S ribosomal DNA sequencing methods in establishing the species identity of the mites; hence confirming the diagnosis of gamasoidosis. The bacterial microbiome associated with the mites was explored by conventional culture and metabarcoding microbiome sequencing of the ribosomal16S v3-v4 hypervariable region. The results highlight the utility of the mixed approach; and show the presence of potentially pathogenic bacteria and recognised causes of opportunistic nosocomial infections, along with known mite gut and intracellular symbionts. The results indicate the potential for O. bacoti mites as vectors of bacterial infections. The clinical presentation of gamasoidosis is indistinguishable from non-specific arthropod-bite reactions; and the cause is seldom confirmed because the temporarily parasitic mites spend most of their time in the environment. The two confirmed index cases may, therefore, represent a more widespread emerging problem; putatively associated with an increase in urban rodent populations.}, }
@article {pmid40049951, year = {2025}, author = {Zhao, Y and Wang, P and Wang, D and Zhao, W and Wang, J and Ge, Z and Liu, Y and Zhao, X}, title = {Gut microbiota and metabolic profile affected by pectic domains during in vitro rat fecal fermentation: A comparative study between different glycans rich in pectic monosaccharides.}, journal = {Carbohydrate polymers}, volume = {356}, number = {}, pages = {123365}, doi = {10.1016/j.carbpol.2025.123365}, pmid = {40049951}, issn = {1879-1344}, mesh = {Animals ; *Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; *Pectins/metabolism ; *Fermentation ; Rats ; Male ; Galactans/metabolism/chemistry ; Monosaccharides/metabolism ; Xylans/metabolism ; Glucans/metabolism ; Polysaccharides/metabolism/chemistry ; Metabolome ; Rats, Sprague-Dawley ; Hexuronic Acids ; }, abstract = {This study aimed to investigate in vitro rat fecal fermentation behavior of pectic polymers and glycans that constitute typical pectic fragments, i.e. homogalacturonan (HG), arabinan (AB), arabinogalactan (AG), rhamnogalacturonan (RG), and xyloglucan (XG). Results showed that galacturonic acid proportion of HG (73.85 mol%) was the highest, followed by pectin (67.99 mol%), whereas arabinose (70.23 mol%) and galactose (86.22 mol%) enriched in AB and AG, respectively. Absolute quantitative microbiome revealed that Bacteroides showed dramatic growth in RG and AG; higher absolute abundances of Bifidobacterium (5.06E+09 and 3.36E+09 copies/g feces, respectively) were found in AB and XG; Escherichia Shigella, Enterococcus, and Klebsiella were inhibited after fermentation with pectin and HG by >95 %. Untargeted metabolomics indicated that the differential metabolite in AG and RG were 7-ketodeoxycholic acid and 9,10-epoxyoctadecanoic acid, respectively, both of which were positively related to arabinose and galactose (p < 0.001). Besides, another characteristic monosaccharide, rhamnose was positively correlated with succinic acid (p < 0.05), and Parvibacter (p < 0.001). Overall, this work help to understand the interactions among pectin structure, gut microbiota and metabolites, thereby guiding the targeted design of the nutrient-directed pectins in future personalized diets.}, }
@article {pmid40049897, year = {2025}, author = {Jiang, Y and Luo, J and Guo, X and Qiao, Y and Li, Y and Zhang, Y and Zhou, R and Vaculík, M and Li, T}, title = {Phyllosphere microbiome assists the hyperaccumulating plant in resisting heavy metal stress.}, journal = {Journal of environmental sciences (China)}, volume = {154}, number = {}, pages = {563-574}, doi = {10.1016/j.jes.2024.05.032}, pmid = {40049897}, issn = {1001-0742}, mesh = {*Metals, Heavy/metabolism/toxicity ; *Microbiota/drug effects ; *Soil Pollutants/metabolism/toxicity ; Sedum/metabolism/microbiology/drug effects ; Soil Microbiology ; Biodegradation, Environmental ; }, abstract = {Phyllosphere microbiome plays an irreplaceable role in maintaining plant health under stress, but its structure and functions in heavy metal-hyperaccumulating plants remain elusive. Here, the phyllosphere microbiome, inhabiting hyperaccumulating (HE) and non-hyperaccumulating ecotype (NHE) of Sedum alfredii grown in soils with varying heavy metal concentration, was characterized. Compared with NHE, the microbial community α-diversity was greater in HE. Core phyllosphere taxa with high relative abundance (>10 %), including Streptomyces and Nocardia (bacteria), Cladosporium and Acremonium (fungi), were significantly related to cadmium (Cd) and zinc (Zn) concentration and biomass of host plants. Moreover, microbial co-occurrence networks in HE exhibited greater complexity than those in NHE. Additionally, proportions of positive associations in HE bacterial networks increased with the rising heavy metal concentration, indicating a higher resistance of HE phyllosphere microbiome to heavy metal stress. Furthermore, in contrast to NHE, microbial community functions, primarily involved in heavy metal stress resistance, were more abundant in HE, in which microbiome assisted hosts to resist heavy metal stress better. Collectively, this study indicated that phyllosphere microbiome of the hyperaccumulator played an indispensable role in assisting hosts to resist heavy metal stress, and provided new insights into phyllosphere microbial application potential in phytoremediation.}, }
@article {pmid40049661, year = {2025}, author = {Yang, YP and Xu, LB and Lu, Y and Wang, J and Nie, YH and Sun, Q}, title = {Dynamic alterations in bacterial and fungal microbiome and inflammatory cytokines following SRV-8 infection in cynomolgus monkeys.}, journal = {Zoological research}, volume = {46}, number = {2}, pages = {325-338}, doi = {10.24272/j.issn.2095-8137.2024.278}, pmid = {40049661}, issn = {2095-8137}, mesh = {Animals ; *Cytokines/genetics/metabolism ; *Macaca fascicularis ; *Bacteria/classification/isolation &amp; purification/genetics ; Gastrointestinal Microbiome ; Monkey Diseases/microbiology/immunology ; Mycobiome/genetics ; Fungi/physiology ; }, abstract = {While viral infections can disturb the host gut microbiome, the dynamic alterations in microbial composition following infection remain poorly characterized. This study identified SRV-8-infected monkeys and classified them into five groups based on infection progression. 16S rRNA amplicon sequencing revealed significant alterations in the relative and inferred absolute abundance of bacterial genera UCG-002, Agathobacter, Coprococcus, and Holdemanella during the early stage of SRV-8 infection, coinciding with provirus formation. These microbial shifts were accompanied by functional modifications in bacterial communities at the same stage. In contrast, ITS amplicon sequencing indicated no significant differences in fungal composition between healthy wild-type and SRV-8-infected monkeys. Spearman correlation analyses demonstrated close interactions between intestinal bacteria and fungi following SRV-8 infection. Additionally, SRV-8 seropositive groups exhibited significantly elevated mRNA expression levels of pro-inflammatory (TNF-α, IFN-γ, IL-1β, and IL-6) and anti-inflammatory (IL-10) cytokine genes, highlighting close associations between inflammatory cytokines and immune responses. Overall, these findings provide a comprehensive characterization of bacterial and fungal microbiota dynamics and inflammatory cytokine responses associated with SRV-8 infection, clarifying the pathobiological mechanisms underlying SRV-8 infection from the perspective of the gut microbiome.}, }
@article {pmid40049555, year = {2025}, author = {Song, W and Huang, L}, title = {Targeting Tumor-Associated Microbiome: A New Aspect of Modulating Tumor Microenvironment for Cancer Therapy.}, journal = {Advanced drug delivery reviews}, volume = {}, number = {}, pages = {115554}, doi = {10.1016/j.addr.2025.115554}, pmid = {40049555}, issn = {1872-8294}, }
@article {pmid40049533, year = {2025}, author = {Zheng, Z and Xu, M and Xiao, K and Yu, K}, title = {Association between oral microbiome and depression: A population-based study.}, journal = {Journal of affective disorders}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jad.2025.03.018}, pmid = {40049533}, issn = {1573-2517}, abstract = {OBJECTIVE: Depression is a global mental health issue, particularly affecting adolescents and young adults. While the role of gut microbiota in depression has been extensively studied, the influence of the oral microbiome remains underexplored. Recent studies suggest that the oral microbiome may affect systemic and brain health through the oral-brain axis. This study aimed to investigate the relationship between oral microbiota diversity and depression using data from 6212 participants in the National Health and Nutrition Examination Survey (NHANES) 2009-2012.<br><br>METHODS: Oral microbiota diversity was assessed through oral rinse samples using 16S rRNA sequencing, focusing on &#x3b1;-diversity metrics (observed ASVs and Faith's phylogenetic diversity) and &#x3b2;-diversity measures. Depressive symptoms were evaluated with the Patient Health Questionnaire (PHQ-9) questionnaire. Weighted regression models were employed to assess associations between &#x3b1;-diversity and depression, while linear regression was used to examine the relationship between &#x3b1;-diversity and PHQ-9 scores. &#x3b2;-diversity differences were analyzed via permutational analysis of variance (PERMANOVA).<br><br>RESULTS: 10.04&#x202f;% of the participants were diagnosed with depression. Higher &#x3b1;-diversity in the oral microbiome was negatively correlated with depression: observed ASVs (OR: 0.713 [CI: 0.508-0.999], P&#x202f;=&#x202f;0.050) and Faith's phylogenetic diversity (OR: 0.584 [CI: 0.367-0.931], P&#x202f;=&#x202f;0.025). Linear regression indicated that greater &#x3b1;-diversity was associated with lower PHQ-9 scores, reflecting fewer depressive symptoms. Furthermore, &#x3b2;-diversity analysis revealed significant differences in the microbiome composition between depressed and non-depressed individuals.<br><br>CONCLUSION: Reduced oral microbiome diversity is associated with an increased risk and severity of depression. The study underscores the importance of exploring the oral-brain axis and highlights the need for further research into the mechanisms and therapeutic strategies targeting this relationship.}, }
@article {pmid40049396, year = {2025}, author = {Yoshimura, Y and Wakabayashi, H and Nagano, F and Matsumoto, A and Shimazu, S and Shiraishi, A and Kido, Y and Bise, T and Hamada, T and Yoneda, K and Maeda, K}, title = {Gut Microbiome Diversity is Associated with Muscle Mass, Strength and Quality in Post-Stroke Patients.}, journal = {Clinical nutrition ESPEN}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.clnesp.2025.02.027}, pmid = {40049396}, issn = {2405-4577}, abstract = {BACKGROUND: The gut microbiome has emerged as a potential influencer of muscle health; however, its role in hospitalized patients remains unclear. This study aimed to investigate the association between gut microbiome diversity and skeletal muscle mass, strength, and quality in hospitalized post-stroke patients.<br><br>METHODS: We conducted a cross-sectional study of post-stroke patients admitted to a rehabilitation facility. Gut microbiome diversity was assessed using 16S ribosomal ribonucleic acid (rRNA) gene sequencing, calculating Operational Taxonomic Unit (OTU) Richness, Faith's Phylogenetic Diversity (PD), and Shannon index. Muscle health was evaluated using skeletal muscle index (SMI) for muscle mass, handgrip strength (HGS) for muscle strength, and bioimpedance analysis-derived phase angle (PhA) for muscle quality. Multiple linear regression analyses were performed, adjusting for potential confounders.<br><br>RESULTS: A total of 156 patients (mean age 78.4 years; 55.7% male) were analyzed. OTU Richness showed significant positive associations with SMI (&#x3b2; = 0.197, p = 0.025), HGS (&#x3b2; = 0.180, p = 0.005), and PhA (&#x3b2; = 0.178, p = 0.022). The Shannon index was also positively associated with SMI (&#x3b2; = 0.120, p = 0.041), HGS (&#x3b2; = 0.140, p = 0.028), and PhA (&#x3b2; = 0.164, p = 0.032). Faith's PD did not demonstrate significant associations with muscle health parameters.<br><br>CONCLUSIONS: Higher gut microbiome diversity, assessed by OTU Richness and Shannon index, is associated with better muscle mass, strength, and quality in post-stroke patients. These findings suggest a potential role for gut microbiota in muscle health during stroke rehabilitation.}, }
@article {pmid40049183, year = {2025}, author = {Yu, K and Tenaglia, V and Chua, EG and Haines, R and Bahal, G and Nicol, MP and Bahal, RK}, title = {Interactions between bacteria in the human nasopharynx: a scoping review.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101062}, doi = {10.1016/j.lanmic.2024.101062}, pmid = {40049183}, issn = {2666-5247}, abstract = {Emerging evidence indicates that interactions between bacteria shape the nasopharyngeal microbiome and influence respiratory health. This Review uses the systematic scoping methodology to summarise 88 studies including observational and experimental studies, identifying key interactions between bacteria that colonise the human nasopharynx. A range of bacterial interactions were reported in the observational studies, including a variable association between Streptococcus pneumoniae and Haemophilus influenzae, a consistent positive association between S pneumoniae and Moraxella catarrhalis, and a consistent negative association between S pneumoniae and Staphylococcus aureus. Experimental studies largely validated the associations reported in the observational studies and provided insights into the mechanism and direction of interactions. In the context of respiratory health, non-pneumococcal alpha-haemolytic streptococci and the Gram-positive commensals Dolosigranulum and Corynebacterium inhibited respiratory pathogens such as H influenzae, S pneumoniae, M catarrhalis, and S aureus. These findings underscore how bacterial competition and coexistence shape the microbiome composition in this niche. This study has relevance for respiratory health and can be helpful for informing the design of potential microbiota-targeted therapies.}, }
@article {pmid40049043, year = {2025}, author = {Huang, JN and Gao, CC and Ren, HY and Wen, B and Wang, ZN and Gao, JZ and Chen, ZZ}, title = {Multi-omics association pattern between gut microbiota and host metabolism of a filter-feeding fish in situ exposed to microplastics.}, journal = {Environment international}, volume = {197}, number = {}, pages = {109360}, doi = {10.1016/j.envint.2025.109360}, pmid = {40049043}, issn = {1873-6750}, abstract = {Microplastics (MPs) are widespread in water environments and can affect gut microbiota and host metabolism of fish, but whether changes in host metabolism under MPs are mediated by gut microbiota remains unclear. Here, silver carp, a filter-feeding fish with important ecological functions, was in-situ exposure to environmentally relevant MPs. Multi-omics analysis and fecal microbiota transplantation were used to reveal the metabolic responses of carp along gut-liver-muscle axis. After three months of in situ exposure to MPs, community structure of gut microbiota of carp was reshaped, and five dominate phyla were significantly changed, including increased Cyanobacteria, Chloroflexi and Planctomycetota but decreased Firmicutes and Fusobacteriota. Weighted gene co-expression network analysis was further performed between these phyla and liver transcription spectrum, showing that the hub gene module contained up-regulated hppD, maiA and plg and activated ubiquinone and other terpenoid-quinone biosynthesis and phenylalanine metabolism. By fecal microbiota transplantation, the key gene module associated with core microbiota phyla of carp was verified in germ-free zebrafish. Interestingly, up-regulated hppD, maiA and plg and enriched phenylalanine metabolism were also observed in this module. Subsequently, metabolome performed in carp liver also shared activated phenylalanine metabolism, including increased trans-cinnamic acid and L-tyrosine. Furthermore, high-associated mapping showed that the differentially expressed metabolites (gamma-aminobutyric acid, ornithine and L-serine) related to amino acid metabolism in carp muscle were significantly accompanied with increased L-tyrosine in its liver. Overall, MPs exposure could change gut microbiome of silver carp and alter host metabolism especially amino acid metabolism along the gut-liver-muscle axis.}, }
@article {pmid40049002, year = {2025}, author = {Ching, XL and Samsol, S and Rusli, MU and Aqmal-Naser, M and Bidai, JA and Sonne, C and Wu, X and Ma, NL}, title = {Blood and cloacal microbiome profile of captive green turtles (Chelonia mydas) and hawksbill turtles (Eretmochelys imbricata): Water quality and conservation implications.}, journal = {Chemosphere}, volume = {375}, number = {}, pages = {144223}, doi = {10.1016/j.chemosphere.2025.144223}, pmid = {40049002}, issn = {1879-1298}, abstract = {In this study, we studied the environment factors such as plastics and heavy metals affecting the blood and cloacal microbiome of green (Chelonia mydas) and hawksbill (Eretmochelys imbricata) in captivity. By non-metric multidimensional scaling analysis, data has shown that the environment factors (p = 0.02), rather than species differences (p = 0.06), significantly influenced the composition of the cloacal microbiota of green and hawksbill turtles. The cloacal microbiota of both captive green and hawksbill turtles was dominated by several similar dominant phyla at differential abundance. Green turtles' cloacal microbiome was made up of 46% of Proteobacteria, 31% of Bacteroidota, 11% of Campylobacterota and 4% of Firmicutes, while the hawksbill turtles' cloacal microbiome was made up of 33% of Bacteroidota, 18% of Firmicutes, 17% of Proteobacteria, and 2% of Campylobacterota. Water conductivity, salinity, microplastic polymers (polycarbonate, polyethylene terephthalate, polystyrene), and copper are positively associated (p < 0.05) with blood urea nitrogen. Hematocrit and hemoglobin were found also negatively correlated (p < 0.05) with water pH, polyethylene terephthalate, iron, lead and zinc. The correlations established in this study shed light on the intricate interplay between water quality and the physiological responses of sea turtles. Recognizing these relationships is pivotal for monitoring and preserving the well-being of sea turtles in their natural habitats.}, }
@article {pmid40048957, year = {2025}, author = {Wu, H and Liu, J and Zhang, XH and Jin, S and Li, P and Liu, H and Zhao, L and Wang, J and Zhao, S and Tian, HD and Lai, JR and Hao, Y and Liu, GR and Hou, K and Yan, M and Liu, SL and Pang, D}, title = {The combination of flaxseed lignans and PD-1/ PD-L1 inhibitor inhibits breast cancer growth via modulating gut microbiome and host immunity.}, journal = {Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy}, volume = {80}, number = {}, pages = {101222}, doi = {10.1016/j.drup.2025.101222}, pmid = {40048957}, issn = {1532-2084}, abstract = {BACKGROUND: Patients with breast cancer (BC) who benefit from the PD-1/PD-L1 inhibitor (PDi) is limited, necessitating novel strategies to improve immunotherapy efficacy of BC. Here we aimed to investigate the inhibitory effects of flaxseed lignans (FL) on the biological behaviors of BC and evaluate the roles of FL in enhancing the anticancer effects of PDi.<br><br>METHODS: HPLC was used to detect the content of enterolactone (ENL), the bacterial transformation product of FL. Transcript sequencing was performed and identified CD38 as a downstream target gene of ENL. CD38-overexpressing cells were constructed and cell proliferation, colony formation, wound healing and transwell assays were used to assess the function of ENL/CD38 axis on BC cells in vitro. Multiplexed immunohistochemistry (mIHC) and CyTOF were used to detect the changes of the tumor immune microenvironment (TIM). 16S rDNA sequencing was used to explore the changes of gut microbiota in mice. A series of in vivo experiments were conducted to investigate the anticancer effects and mechanisms of FL and PDi.<br><br>RESULTS: FL was converted to ENL by gut microbiota and FL administration inhibited the progression of BC. ENL inhibited the malignant behaviors of BC by downregulating CD38, a key gene associated with immunosuppression and PD-1/PD-L1 blockade resistance. The mIHC assay revealed that FL administration enhanced CD3[+], CD4[+] and CD8[+] cells and reduced F4/80[+] cells in TIM. CyTOF confirmed the regulatory effects of FL and FL in combination with PDi (FLcPDi) on TIM. In addition, 16S rDNA analysis demonstrated that FLcPDi treatment significantly elevated the abundance of Akkermansia and, importantly, Akkermansia administration enhanced the response to PDi in mice treated with antibiotics.<br><br>CONCLUSIONS: The FL/ENL/CD38 axis inhibited BC progression. FL enhanced the anticancer effects of PDi by modulating gut microbiota and host immunity.}, }
@article {pmid40048944, year = {2025}, author = {Zhu, N and Cui, X and Leng, F and Lv, X and Wang, X and Guo, X and Luo, W and Wang, Y}, title = {Volatile organic compounds from medicinal plant Codonopsis radix: Unraveling rhizoplane microbiome interactions for accumulation of active components.}, journal = {Plant physiology and biochemistry : PPB}, volume = {222}, number = {}, pages = {109688}, doi = {10.1016/j.plaphy.2025.109688}, pmid = {40048944}, issn = {1873-2690}, abstract = {Plant roots emit a diverse array of volatile organic compounds (VOCs) to attract specific soil microorganisms, thereby promoting their growth and development. However, the mechanisms by which medicinal plants interact with surrounding microorganisms through VOCs to enhance their quality remain poorly understood. This study integrated microbiome, transcriptome, and metabolome analyses to investigate the VOCs that mediate interactions between rhizoplane microorganisms and Codonopsis radix plants. The research identified a total of 36 common VOCs in the roots of Codonopsis radix, with 2, 3, 5-trimethylpyrazine being the primary VOC responsible for the root's nutty flavor. Chemoheterotrophic microorganisms, including both saprophytes and arbuscular mycorrhizae, were found to be the dominant types in the rhizoplane. The rhizoplane microorganism Rugamonas was significantly positively correlated with naringin and 2-ethyl-3-methylpyrazine. Furthermore, VOCs were found to influence the accumulation of phenylpropane differential metabolites and the expression of genes involved in phenylpropane synthesis and metabolite accumulation by modulating the structure and diversity of rhizoplane microbial communities. Overall, this study provides valuable insights into the complex interactions between medicinal plants and microorganisms, as well as potential strategies for enhancing the quality of medicinal plants.}, }
@article {pmid40048904, year = {2025}, author = {Chen, L and Zhao, B and Zhang, M and Yan, Y and Nie, C and Yu, K and Tu, Z and Xia, Y}, title = {Micron-scale heterogeneity reduction leads to increased interspecies competition in thermophilic digestion microbiome.}, journal = {Water research}, volume = {279}, number = {}, pages = {123419}, doi = {10.1016/j.watres.2025.123419}, pmid = {40048904}, issn = {1879-2448}, abstract = {Microbial spatial heterogeneity is an important determinant of larger-scale community properties, whereas most studies neglect it and therefore only provide average information, potentially obscuring the signal of microbial interactions. Our study takes a step toward addressing this problem by characterizing the spatial heterogeneity of a microbiome with micron-scale resolution. Micron-scale single clusters (40-70 μm) were randomly collected from lab-scale anaerobic digestion (AD) biosystems, and a comparative analysis was performed to evaluate differences between mesophilic and thermophilic systems. Here we reveal a cascading effect from high-temperature selection to global microbial interactions. We observed that thermophilic communities exhibited less spatial heterogeneity than mesophilic communities, which we attribute to the considerable extinction of low-abundant species by high-temperature selection. Then, the low spatial heterogeneity and the high-temperature selection acting in conjunction resulted in a high proportion of competitive interactions in thermophilic communities. Unexpectedly, however, the thermophilic AD, characterized by lower micron-scale spatial heterogeneity, showed more efficient synergistic and syntrophic cooperations involving around Clostridiales, which significantly enhanced hydrolysis performance under thermophilic conditions. In addition, the fact that high temperatures favor slower growers, along with functional redundancy-related competitive advantage, led to the selection of more proficient methanogens in more competitive environments, which are also potentially associated with enhanced methanogenic performance. In summary, our findings underscore the significance of micron-scale resolution for revealing the microbial ecology in spatially structured environments.}, }
@article {pmid40048710, year = {2025}, author = {Zhou, Y and Hubscher, CH}, title = {Biomarker expression level changes within rectal gut-associated lymphoid tissues in spinal cord-injured rats.}, journal = {ImmunoHorizons}, volume = {9}, number = {4}, pages = {}, doi = {10.1093/immhor/vlaf002}, pmid = {40048710}, issn = {2573-7732}, support = {W81XWH-18-1-0675//Department of Defense Spinal Cord Injury Research Program/ ; 17-5//Kentucky Spinal Cord Head Injury Research Trust/ ; R01DK133195/NH/NIH HHS/United States ; }, mesh = {Animals ; Rats ; *Spinal Cord Injuries/metabolism/immunology ; *Biomarkers/metabolism ; *Lymphoid Tissue/immunology/metabolism ; *Rectum/microbiology/pathology/metabolism ; Female ; Rats, Sprague-Dawley ; Neurogenic Bowel/genetics/metabolism ; Gastrointestinal Microbiome/immunology ; Disease Models, Animal ; Intestinal Mucosa/metabolism/microbiology/immunology/pathology ; }, abstract = {Neurogenic bowel dysfunction (NBD) is common after spinal cord injury (SCI). Gut-associated lymphoid tissue (GALT), an organized structure within the mucosal immune system, is important for the maintenance of gut homeostasis and body health and serves as the first line barrier/defense against diet antigens, commensal microbiota, pathogens, and toxins in mucosal areas. The current study examined gene expression levels along six segments of anorectal tissue using real-time polymerase chain reaction (RT-PCR) in uninjured rats (28-day sham surgical controls) and at both 28- and 42-days post-T9 contusion injury. Consistent with our previous report of functional regional differences in the ano-rectum, we demonstrate the existence of GALTs located primarily within the segment at 3-4.5 cm from the rectal dentate line (termed rectal GALTs-rGALTs) in shams with upregulated gene expression levels of multiple biomarkers, including B cell and T cell-related genes, major histocompatibility complex (MHC) class II molecules, and germinal center (GC)-related genes, which was further confirmed by histologic examination. In the same rectal tissue segment following T9 SCI, inflammation-related genes were upregulated at 28 days post-injury (DPI) indicating that microbial infection and inflammation of rGALTs modified structure and function of rGALTs, while at 42 DPI rGALTs exhibited resolution of inflammation and impaired structure/function for extrafollicular B cell responses. Taken together, our data suggest that rGALTs exists in rat rectum for homeostasis of gut microbiota/barrier. SCI induces microbial infection and inflammation in rectal tissues containing rGALTs, which could contribute to development of SCI-related gut microbiome dysbiosis, NBD, and systemic diseases.}, }
@article {pmid40048707, year = {2025}, author = {Hernández-Verdin, I and Kirasic, E and Mokhtari, K and Barillot, N and Rincón de la Rosa, L and Sourdeau, E and Abada, Y and Le Tarff-Tavernier, M and Nichelli, L and Rozenblum, L and Kas, A and Mathon, B and Choquet, S and Houillier, C and Hoang-Xuan, K and Alentorn, A}, title = {Gut microbiome modulates the outcome in primary central nervous system lymphoma patients undergoing chemotherapy: an ancillary study from the BLOCAGE trial.}, journal = {Neuro-oncology}, volume = {}, number = {}, pages = {}, doi = {10.1093/neuonc/noaf059}, pmid = {40048707}, issn = {1523-5866}, abstract = {BACKGROUND: Primary central nervous system lymphoma (PCNSL) treatment relies on a high-dose methotrexate based chemotherapy (HD-MTX-based CT) regimen; however, whether there is a specific microbiota composition association with treatment response and clinical outcomes remains incompletely understood.<br><br>METHODS: We conducted a prospective study of PCNSL patients, included in the clinical trial NCT02313389 and the ancillary study NCT04253496 from 2020 to 2023, where patients were treated with first line HD-MTX-based polychemotherapy without a consolidation treatment. Stool (n=52), cerebrospinal fluid (CSF, n=52), and plasma samples (n=35) were collected before and/or after therapy initiation to perform metagenomic, flow cytometry, and metabolomic analyses. Plasma metabolomic data of 90 patients also included in the BLOCAGE clinical trial was subsequently used as a validation cohort.<br><br>RESULTS: Unsupervised clustering of microbial data identified two distinct gut microbial communities, differing in Parabacteroides distasonis abundance, which correlated with progression-free survival and overall survival in both uni- and multivariate analyses. Higher P. distasonis levels were linked to increased plasma betaine/valine metabolites and enhanced CD8 T cell infiltration in the CSF, suggesting a connection between gut microbiota and immune regulation. Stratifying the validation cohort by betaine/valine content confirmed these clinical associations.<br><br>CONCLUSIONS: Our findings suggest that gut microbiome communities modulate clinical outcomes in PCNSL patients undergoing standard treatment. Moreover, after future validation in external cohorts, the quantification of Parabacteroides distasonis could potentially provide a basis for patient stratification and guide personalized therapeutic strategies in the near future.}, }
@article {pmid40048584, year = {2025}, author = {Loublier, C and Costa, M and Taminiau, B and Lecoq, L and Daube, G and Amory, H and Cesarini, C}, title = {Longitudinal Changes in Fecal Microbiota During Hospitalization in Horses With Different Types of Colic.}, journal = {Journal of veterinary internal medicine}, volume = {39}, number = {2}, pages = {e70039}, doi = {10.1111/jvim.70039}, pmid = {40048584}, issn = {1939-1676}, support = {//Fonds Sp&#xe9;ciaux de Recherche (DYSBIOHORSIRS)/ ; //Fonds De La Recherche Scientifique - FNRS (Veterinary MD. Ph.D. VETE-CCD)/ ; }, mesh = {Animals ; Horses ; *Colic/veterinary/microbiology ; *Horse Diseases/microbiology ; *Feces/microbiology ; Male ; Female ; Prospective Studies ; Hospitalization ; Gastrointestinal Microbiome ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Research on fecal microbiota changes during hospitalization of horses with colic is emerging.<br><br>OBJECTIVES: Describe changes of the fecal microbiota during hospitalization of horses with colic caused by inflammatory (INFL), simple (SIMPLE), and strangulated (STR) obstructions, and investigate associations with survival.<br><br>ANIMALS: Twenty-three horses with colic: 9 in INFL, 5 in STR, and 9 in SIMPLE groups. Seventeen horses survived, and 6 were euthanized.<br><br>METHODS: Prospective observational study. Fecal samples were collected on admission (D1), on days 3 (D3) and 5 (D5). Bacterial taxonomy profiling was obtained by V1V3 16S amplicon sequencing. Data were compared using a 2-way permutational analysis of variance (PERMANOVA). Linear discriminant analysis Effect Size (LEfSE) analysis identified significant bacterial population differences, with significance set at p&#x2009;<&#x2009;0.05 and a linear discriminant analysis (LDA) cut-off >&#x2009;3.0.<br><br>RESULTS: Alpha diversity indices remained stable during hospitalization within each colic group. However, at D5, the INFL group had significantly higher richness (p&#x2009;<&#x2009;0.01) and diversity (Shannon, p&#x2009;<&#x2009;0.001 and Simpson, p&#x2009;<&#x2009;0.05) than other colic types. Beta diversity (Jaccard membership and Bray-Curtis indices) was significantly different in the INFL compared to SIMPLE and STR groups (both p&#x2009;<&#x2009;0.001) but not between SIMPLE and STR. Beta diversity membership analysis by analysis of molecular variance (AMOVA) indicated a significant difference between survivors and non-survivors within the INFL group (p&#x2009;<&#x2009;0.01). Increased relative abundances of Bacilliculturomica and Saccharofermentans were associated with survival.<br><br>CONCLUSIONS: Microbiota showed no significant variation over 5&#x2009;days of hospitalization. Colic type influenced fecal microbiota more than hospitalization duration. Specific bacterial populations may differ between survival and non-survival groups.}, }
@article {pmid40048569, year = {2025}, author = {Loy, M and Mahadevan, R and Mascarenhas, M and Walsh, L}, title = {Culinary Medicine.}, journal = {Pediatric annals}, volume = {54}, number = {3}, pages = {e83-e87}, doi = {10.3928/19382359-20250108-02}, pmid = {40048569}, issn = {1938-2359}, mesh = {Humans ; *Cooking ; Child ; }, abstract = {The use of food as medicine to treat illness and maintain health has ancient roots across various cultures. Despite significant scientific progress during the past 2 centuries linking diet, the microbiome, and overall health, modern challenges persist due to sociocultural factors, aggressive food marketing, and insufficient nutritional education. However, there is increasing support from health systems, insurers, nonprofits, philanthropic organizations, and government bodies to develop health policies that promote access to high-quality meals for disease prevention and management. Culinary medicine is now incorporated into undergraduate and postgraduate medical education through electives, certifications in culinary and lifestyle medicine, and continuing medical education conferences. There is substantial potential for culinary medicine to enhance patient care across diverse populations and settings, including individual consultations, group visits, schools, farms, and community gardens. Collaborative efforts among stakeholders can advance practical solutions to translate scientific knowledge into effective policy and practice. [Pediatr Ann. 2025;54(3):e83-e87.].}, }
@article {pmid40048434, year = {2025}, author = {Meka, AF and Bekele, GK and Abas, MK and Gemeda, MT}, title = {Exploring bioactive compound origins: Profiling gene cluster signatures related to biosynthesis in microbiomes of Sof Umer Cave, Ethiopia.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0315536}, doi = {10.1371/journal.pone.0315536}, pmid = {40048434}, issn = {1932-6203}, mesh = {*Multigene Family ; *Microbiota/genetics ; *Caves/microbiology ; Ethiopia ; Bacteria/genetics/metabolism/classification ; Soil Microbiology ; Secondary Metabolism/genetics ; }, abstract = {Sof Umer Cave is an unexplored extreme environment that hosts novel microbes and potential genetic resources. Microbiomes from caves have been genetically adapted to produce various bioactive metabolites, allowing them to survive and tolerate harsh conditions. However, the biosynthesis-related gene cluster signatures in the microbiomes of Sof Umer Cave have not been explored. Therefore, high-throughput shotgun sequencing was used to explore biosynthesis-related gene clusters (BGCs) in the microbiomes of Sof Umer Cave. The GeneAll DNA Soil Mini Kit was used to extract high-molecular-weight DNA from homogenized samples, and the purified DNA was sequenced using a NovaSeq PE150. According to the Micro-RN database, the most common microbial genera in Sof Umer Cave are Protobacteria, Actinobacteria, Verrucomicrobiota, and Cyanobacteria. The biosynthesis-related gene clusters were annotated and classified, and the BGCs were predicted using antiSMASH and NAPDOS1. A total of 460 putative regions of BGCs encoding a wide range of secondary metabolites were identified, including RiPP (47.82%), terpene (19.57%), NRPS (13.04%), hybrid (2.18%), and other newly annotated (10.87%) compounds. Additionally, the NAPDOS pipeline identified a calcium-dependent antibiotic gene cluster from Streptomyces coelicolor, an actinomycin gene cluster from Streptomyces chrysomallus, and a bleomycin gene cluster from Streptomyces verticillus. These findings highlight the untapped biosynthetic potential of the Sof Umer Cave microbiome, as well as its potential for the discovery of natural products.}, }
@article {pmid40047941, year = {2025}, author = {Koshy, NG and Rajan, SA and Anith, KN and Chitra, N and Soumya, VI and Scaria, TM and Beena, R}, title = {Beyond the pink: uncovering the secrets of pink pigmented facultative methylotrophs.}, journal = {Archives of microbiology}, volume = {207}, number = {4}, pages = {80}, pmid = {40047941}, issn = {1432-072X}, mesh = {*Methylobacterium/metabolism ; Plants/microbiology ; Microbiota/physiology ; Pigmentation ; Plant Development ; Agriculture/methods ; Ecosystem ; }, abstract = {Pink Pigmented Facultative Methylotrophs (PPFMs) belong to a diverse group of methylotrophic bacteria predominantly in the genus Methylobacterium, and are known for their beneficial interactions with plants. They can use single-carbon compounds, such as methanol, formate, formaldehyde and methyl amines as well as various multi-carbon substrates as sources of carbon and energy. PPFMs are characterized by their distinctive pink pigmentation and are commonly found in the phyllosphere, where they play a major role in promoting plant growth through various mechanisms; These mechanisms include the production of phytohormones, enhancing nutrient acquisition, mitigating abiotic stresses and providing biocontrol of phytopathogens. Due to their eco-friendly nature PPFMs are viewed as promising alternatives to synthetic fertilizers and pesticides in green agriculture. Furthermore, the ecological significance of PPFMs extends beyond their direct interactions with host plants. They also contribute to the resilience of ecosystems by participating in the cycling of nutrients in the environment. As the importance of the plant microbiome in agriculture becomes more recognized, the potential of PPFMs to support sustainable farming practices and contribute to environmental health is increasingly evident. This underscores their relevance in addressing global agricultural challenges.}, }
@article {pmid40047940, year = {2025}, author = {Chen, P and Liu, Q and Shi, H and Liu, Z and Yang, X}, title = {Choline metabolism disorder induced by Prevotella is a risk factor for endometrial cancer in women with polycystic ovary syndrome.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {285}, pmid = {40047940}, issn = {1573-4978}, support = {2023A1515110325//Guangdong Basic and Applied Basic Research Foundation/ ; 2023A1515012940//Guangdong Natural Science Foundation/ ; 23ptpy106//the Fundamental Research Funds for the Central Universities, Sun Yat-sen University/ ; }, mesh = {Humans ; Female ; *Polycystic Ovary Syndrome/microbiology/complications/metabolism ; *Endometrial Neoplasms/microbiology ; *Prevotella ; *Choline/metabolism ; Adult ; Risk Factors ; Microbiota ; Vagina/microbiology ; Dysbiosis/complications ; RNA, Ribosomal, 16S/genetics ; Lipid Metabolism ; Transcriptome/genetics ; }, abstract = {BACKGROUND: Polycystic ovary syndrome (PCOS) is an endocrine disorder associated with an increased risk of endometrial cancer, potentially mediated by vaginal microbiota dysbiosis and hormonal disturbances. This study investigates how hormonal imbalances in PCOS patients affect the vaginal microbiome and choline metabolism, thereby influencing endometrial cancer risk.<br><br>METHODS: In this observational study, 70 women were enrolled, including 36 with PCOS and 34 controls. We analyzed their vaginal microbiota, lipid metabolism, and endometrial transcriptome using 16S rRNA sequencing, untargeted lipidomics, and transcriptomic sequencing.<br><br>RESULTS: The PCOS group showed significant differences in vaginal microbiota composition, notably an increase in LPS-producing Prevotella spp. Functional analyses indicated activation of LPS biosynthesis and inflammatory signaling pathways. Lipidomics revealed disrupted choline metabolism, with alterations in phosphocholine and total choline levels. Transcriptomic data highlighted the up-regulation of inflammatory and metabolic dysregulation pathways.<br><br>CONCLUSIONS: Hormonal imbalances in PCOS contribute to significant changes in the vaginal microbiome and metabolic pathways, increasing the risk of endometrial cancer. These findings suggest potential therapeutic targets for reducing cancer risk in this population.}, }
@article {pmid40047510, year = {2025}, author = {Shuman, JHB and Lin, AS and Westland, MD and Bryant, KN and Fortier, GE and Piazuelo, MB and Reyzer, ML and Judd, AM and Tsui, T and McDonald, WH and McClain, MS and Schey, KL and Algood, HM and Cover, TL}, title = {Helicobacter pylori CagA and Cag type IV secretion system activity have key roles in triggering gastric transcriptional and proteomic alterations.}, journal = {Infection and immunity}, volume = {}, number = {}, pages = {e0059524}, doi = {10.1128/iai.00595-24}, pmid = {40047510}, issn = {1098-5522}, abstract = {Colonization of the human stomach with cag pathogenicity island (PAI)-positive Helicobacter pylori strains is associated with increased gastric cancer risk compared to colonization with cag PAI-negative strains. To evaluate the contributions of the Cag type IV secretion system (T4SS) and CagA (a secreted bacterial oncoprotein) to gastric molecular alterations relevant for carcinogenesis, we infected Mongolian gerbils with a Cag T4SS-positive wild-type (WT) H. pylori strain, one of two Cag T4SS mutant strains (∆cagT or ∆cagY), or a ∆cagA mutant for 12 weeks. Histologic staining revealed a biphasic distribution of gastric inflammation severity in WT-infected animals and minimal inflammation in animals infected with mutant strains. Atrophic gastritis (a premalignant condition), dysplasia, and gastric adenocarcinoma were only detected in WT-infected animals with high inflammation scores. Transcriptional profiling, liquid chromatography-tandem mass spectrometry analysis of micro-extracted tryptic peptides, and imaging mass spectrometry revealed more than a thousand molecular alterations in gastric tissues from WT-infected animals with high inflammation scores compared to uninfected tissues and few alterations in tissues from other groups of infected animals. Proteins with altered abundance in animals with severe Cag T4SS-induced inflammation mapped to multiple pathways, including the complement/coagulation cascade and proteasome pathway. Proteins exhibiting markedly increased abundance in tissues from H. pylori-infected animals with severe inflammation included calprotectin components, proteins involved in proteasome activation, polymeric immunoglobulin receptor (PIGR), interferon-inducible guanylate-binding protein (GBP2), lactoferrin, lysozyme, superoxide dismutase, and eosinophil peroxidase. These results demonstrate key roles for CagA and Cag T4SS activity in promoting gastric mucosal inflammation, transcriptional alterations, and proteomic alterations relevant to gastric carcinogenesis.IMPORTANCEHelicobacter pylori colonizes the stomachs of about half of humans worldwide, and its presence is the primary risk factor for the development of stomach cancer. H. pylori strains isolated from humans can be broadly classified into two groups based on whether they contain a chromosomal cag pathogenicity island, which encodes a secreted effector protein (CagA) and components of a type IV secretion system (T4SS). In experiments using a Mongolian gerbil model, we found that severe gastric inflammation and gastric transcriptional and proteomic alterations related to gastric cancer development were detected only in animals infected with a wild-type H. pylori strain containing CagA and an intact Cag T4SS. Mutant strains lacking CagA or Cag T4SS activity successfully colonized the stomach without inducing detectable pathologic host responses. These findings illustrate two different patterns of H. pylori-host interaction.}, }
@article {pmid40047509, year = {2025}, author = {London, LY and Lim, CH and Modliszewski, JL and Siddiqui, NY and Sysoeva, TA}, title = {Draft genomes of Klebsiella pneumoniae and Streptococcus anginosus strains found in the urine of the same female patient.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0131124}, doi = {10.1128/mra.01311-24}, pmid = {40047509}, issn = {2576-098X}, abstract = {Here, we report the draft genomes of Klebsiella pneumoniae 5008-1 and Streptococcus anginosus 5008-2 strains isolated from a catheterized urine sample obtained from an asymptomatic postmenopausal woman diagnosed with recurrent urinary tract infection and receiving vaginal estrogen cream.}, }
@article {pmid40047508, year = {2025}, author = {Mori, A and Kudoh, M and Kuboniwa, M and Rückert-Reed, C and Busche, T and Eisenhut, M and Fukusaki, E and Bräutigam, A and Laker, B}, title = {Closed genome sequence of Fretibacterium fastidiosum, a potential contributor to periodontal disease.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0000425}, doi = {10.1128/mra.00004-25}, pmid = {40047508}, issn = {2576-098X}, abstract = {Human oral microbiome consists of diverse bacteria. Not all oral bacteria are well characterized due to challenges in cultivation in vitro. In this study, we report the closed genome sequence of one of the recently identified oral bacteria, Fretibacterium fastidiosum.}, }
@article {pmid40047452, year = {2025}, author = {Hou, Z and Wang, M and Xu, H and Wang, M and Hannula, SE}, title = {Differential effects of pine wilt disease on root endosphere, rhizosphere, and soil microbiome of Korean white pine.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0232624}, doi = {10.1128/spectrum.02326-24}, pmid = {40047452}, issn = {2165-0497}, abstract = {Pine wilt disease (PWD), caused by pinewood nematodes, is highly destructive to pine forests in Asia and Europe, including Korean white pine (Pinus koraiensis). The microbiome in the needles and trunk of Pinus spp. are recognized to play key roles in resistance against PWD. However, the role of root and soil microbiomes in the resistance remains unclear. This study compares bacterial and fungal communities in the root endosphere, rhizosphere soil, and bulk soil of diseased versus healthy P. koraiensis. Results showed that PWD increased the α-diversity of fungi in rhizosphere soil but did not affect the microbial diversity in the root endosphere or bulk soil. The composition of bacterial and fungal communities in rhizosphere and bulk soils was significantly altered by PWD. Specifically, the relative abundance of Planctomycetes decreased, and the relative abundance of Tremellomycetes increased, while Agaricomycetes decreased in both rhizosphere and bulk soils after infestation with PWD, respectively. Relative abundances of Chloroflexi and Verrucomicrobia increased, while Proteobacteria decreased in bulk soil following PWD. Relative abundances of Leotiomycetes and Eurotiomycetes increased in the rhizosphere soil and bulk soil following PWD, respectively. Furthermore, with the host plant infestation by PWD, the relative abundance of ectomycorrhizal fungi decreases, while that of saprotrophic fungi increases in both rhizosphere and bulk soils. Our results revealed that PWD significantly affects the soil microbiomes of P. koraiensis, with varying impacts across different plant-soil compartments. This study provides insights into how root and soil microbiomes respond to PWD, enhancing our understanding of the disease's ecological consequences.IMPORTANCEThe belowground microbiome is often sensitive to infection of forest diseases and is also recognized as a potential reservoir for selection of microbial agents against PWD. Our study demonstrates that the dynamics of belowground microbiome following natural infection of PWD are compartment and taxa specific, with varying degrees of responses in both diversity and composition of bacterial or fungal communities across the root endosphere, rhizosphere soil, and bulk soil. The results highlight the importance of utilizing appropriate plant-soil compartments and microbial taxa to understand the ecological consequences of the destructive PWD.}, }
@article {pmid40047321, year = {2025}, author = {Liang, Z and Liang, Z and Hu, HW and Howell, K and Fang, Z and Zhang, P}, title = {Food substances alter gut resistome: Mechanisms, health impacts, and food components.}, journal = {Comprehensive reviews in food science and food safety}, volume = {24}, number = {2}, pages = {e70143}, doi = {10.1111/1541-4337.70143}, pmid = {40047321}, issn = {1541-4337}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; Phytochemicals/pharmacology ; Probiotics/pharmacology ; Animals ; Drug Resistance, Bacterial ; Functional Food ; Drug Resistance, Microbial ; Diet ; }, abstract = {Antibiotics are effective in treating bacterial infections, but their widespread use has spurred antibiotic resistance, which is linked closely with human disease. While dietary components are known to influence the gut microbiome, specific effects on the gut resistome-the collection of antibiotic-resistant genes in the gut-remain underexplored. This review outlines the mechanisms of antibiotic action and the development of resistance, emphasizing the connection between the gut resistome and human diseases such as metabolic disorders, cardiovascular disease, liver disease, and nervous system disorders. It also discusses the effects of diet habits and dietary components, including bioactive macronutrients, phytochemicals, and probiotics, on the composition of the gut resistome by enhancing antibiotic efficacy and potentially reducing resistance. This review highlights the emerging trend of increasing interest in functional foods aimed at targeting the gut resistome and a growing focus on bioactive plant compounds with the potential to modulate antibiotic resistance.}, }
@article {pmid40047190, year = {2025}, author = {Ríos-Osorio, N and Ladino, LG and Guerrero-Torres, M}, title = {Structure, biology, and function of peri-implant soft tissues in health and disease: a comprehensive review of the literature.}, journal = {Journal of periodontal &amp; implant science}, volume = {}, number = {}, pages = {}, doi = {10.5051/jpis.2402080104}, pmid = {40047190}, issn = {2093-2278}, abstract = {The morphogenesis of peri-implant soft tissues following surgical trauma, along with the nature, topography, and design of implant-prosthetic material surfaces, leads to peri-implant tissues that exhibit unique histological and morphological characteristics. It has been shown that mucosal phenotypes with a mucosal thickness of at least 2 mm and a keratinised mucosa width of at least 2 mm promote proper integration and a biological seal at the mucosa-implant interface. This seal prevents pathogen penetration, protects the underlying peri-implant bone, and reduces susceptibility to inflammatory peri-implant diseases (IPDs). Furthermore, even under ideal conditions, peri-implant soft tissues demonstrate less mechanical resistance, stability, and hermeticity compared to periodontal tissues. These deficiencies are directly associated with both the onset and progression of IPDs such as peri-implant mucositis (PM) and peri-implantitis (PI). Over recent decades, the prevalence of PM and PI has risen, making them the primary causes of implant failure. Given that the characteristics of peri-implant mucosa are closely linked to the progression of these diseases, a deep understanding of the biology of peri-implant soft tissues is crucial for developing strategies to either avoid or minimise the impact of IPDs on implant therapy outcomes. This comprehensive review of the literature aims to provide a precise and detailed description of the structure, biology, and function of peri-implant soft tissues, starting from their formation process and linking their morphogenic characteristics to the establishment and evolution of IPDs. Additionally, the composition of the microbiome and the most relevant anti/pro-inflammatory mediators involved in the development of IPDs are summarised.}, }
@article {pmid40047100, year = {2025}, author = {Nicol, MR and Olsem, CM}, title = {Hormones, microbes, and PrEP drugs in the female genital tract.}, journal = {Expert opinion on drug metabolism &amp; toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1080/17425255.2025.2476792}, pmid = {40047100}, issn = {1744-7607}, abstract = {INTRODUCTION: For HIV medications intended for HIV prevention, it is critical to achieve exposures in that will provide reliable protection to the FGT. The female genital tract (FGT) is a complex and heterogenous environment.<br><br>AREAS COVERED: We reviewed what is known about drug transport and metabolism specific to female genital tissues. We performed a literature search using key words in PubMed and Google Scholar on articles published inclusive of August 2024. We then discuss the impact of sex steroid hormones and vaginal microbiome on the genital tract pharmacology of drugs used for PrEP.<br><br>EXPERT OPINION: Better characterization of FGT pharmacology can improve PrEP options for women. Better models that can fully capture the complexities of the FGT to evaluate pharmacokinetic-pharmacodynamic relationships in the context of the complex microenvironment of the FGT will need to be developed and validated to move the field forward.}, }
@article {pmid40047092, year = {2025}, author = {Husain, N and Kumar, A and Anbazhagan, AN and Gill, RK and Dudeja, PK}, title = {Intestinal Luminal Anion Transporters and their Interplay with Gut Microbiome and Inflammation.}, journal = {American journal of physiology. Cell physiology}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpcell.00026.2025}, pmid = {40047092}, issn = {1522-1563}, support = {BX002011//U.S. Department of Veterans Affairs (VA)/ ; BX005862//U.S. Department of Veterans Affairs (VA)/ ; BX006626//U.S. Department of Veterans Affairs (VA)/ ; I01BX006177//U.S. Department of Veterans Affairs (VA)/ ; 1IK6BX005242//U.S. Department of Veterans Affairs (VA)/ ; R01DK54016//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; R56DK92441//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; }, abstract = {The intestine, as a critical interface between the external environment and the internal body, plays a central role in nutrient absorption, immune regulation, and maintaining homeostasis. The intestinal epithelium, composed of specialized epithelial cells, hosts apical anion transporters that primarily mediate the transport of chloride and bicarbonate ions, essential for maintaining electrolyte balance, pH homeostasis, and fluid absorption/secretion. Additionally, the intestine hosts a diverse population of gut microbiota that plays a pivotal role in various physiological processes including nutrient metabolism, immune regulation and maintenance of intestinal barrier integrity, all of which are critical for host gut homeostasis and health. The anion transporters and gut microbiome are intricately interconnected, where alterations in one can trigger changes in the other leading to compromised barrier integrity and increasing susceptibility to pathophysiological states including gut inflammation. This review focuses on the interplay of key apical anion transporters including Down Regulated in Adenoma (DRA, SLC26A3), Putative Anion Transporter-1 (PAT1, SLC26A6) and Cystic Fibrosis Transmembrane Conductance Regulator (CFTR, ABCC7) with the gut microbiome, barrier integrity and their relationship to gut inflammation.}, }
@article {pmid40047013, year = {2025}, author = {Alverdy, J}, title = {Unpacking the sepsis controversy.}, journal = {Trauma surgery &amp; acute care open}, volume = {10}, number = {1}, pages = {e001733}, pmid = {40047013}, issn = {2397-5776}, abstract = {Despite its many definitions and revisions, consensus statements and clinical guidelines, the term 'sepsis' continues to be referred to as a discrete clinical entity that is often claimed to be a direct cause of mortality. The assertion that sepsis can be defined as a 'life-threatening organ dysfunction caused by a dysregulated host response to infection,' has led to a field dominated by failed clinical trials informed by host-centered, pathogen-agnostic, animal experiments in which animal models do not recapitulate the clinical condition. The observations from the National Health Service from England that claim that 77.5% of sepsis deaths occur in those aged 75 years or older and those from the USA indicating that most patients dying of sepsis have also been diagnosed with 'hospice qualifying conditions,' seem to refute the assertion that sepsis is caused by, rather than associated with, a 'dysregulated host response.' This piece challenges the current conceptual framework that forms the basis of the sepsis definition. Here we posit that as a result of both its definition and the use of inappropriate animal models, ineffective clinical treatments continue to be pursued in this field.}, }
@article {pmid40046939, year = {2025}, author = {Prokopov, AY and Gazitaeva, ZI and Sidorina, AN and Peno-Mazzarino, L and Radionov, N and Drobintseva, AO and Kvetnoy, IM}, title = {Influence of Injectable Hyaluronic Gel System on Skin Microbiota, Skin Defense Mechanisms and Integrity (Ex vivo Study).}, journal = {Clinical, cosmetic and investigational dermatology}, volume = {18}, number = {}, pages = {459-473}, pmid = {40046939}, issn = {1178-7015}, abstract = {OBJECTIVE: The influence of injectable hyaluronic gels on skin's microbiota is unclear. As well, skin microbiota is a key factor modulating final effect of injectable gels. The ex-vivo study was aimed at alterations following hyaluronic acid injection into the dermis in non-sterile skin surface conditions.<br><br>METHODS: Ex vivo human skin explants in the presence or absence of either S. epidermidis or S. aureus, were treated with either control excipient (0.9% sodium chloride) or test product (Hyaluronic acid injectable S, HA-S). Bacterial analysis was performed, as well as skin structural integrity. Histological imaging and immunostaining analysis in the presence of skin markers: epidermal (CD1a, Toll-like receptor 2 (TLR2), Beta-defensin-3 (BD3), CCN1) and dermal (DC-SIGN, Decorin) were then performed.<br><br>RESULTS: The injection of control excipient E and test product P, both associated with bacterial deposits, induced similar noticeable increase of S. epidermidis growth over 4 days, but no noticeable effect on growth of S. aureus. The injection of control excipient, associated with bacterial deposits, showed epidermal and dermal alterations increased with time. It was observed significant increase of epidermal CD1a, TLR2, CCN1 and dermal DC-SIGN, Decorin on Day 2. The injection of test product, associated with bacterial deposits, in contrast to injection of control excipient, associated with bacterial deposits, induced very slight but significant improvement of epidermal viability as well as significant decrease of epidermal TLR2, BD3, CCN1 and dermal DC-SIGN on Day 2.<br><br>CONCLUSION: Our investigation showed that both intradermal injections, HA-based solution or control excipient, trigger short-term skin microbiota growth. We indicate strong influence of non-sterile skin surface conditions on human skin explant viability when skin barrier damaged by injection puncture and highlights differences of epidermal/dermal response depended on injected composition.}, }
@article {pmid40046910, year = {2024}, author = {Eslami, M and Naderian, R and Ahmadpour, A and Shushtari, A and Maleki, S and Mohammadian, P and Amiri, A and Janbazi, M and Memarian, M and Yousefi, B}, title = {Microbiome structure in healthy and pregnant women and importance of vaginal dysbiosis in spontaneous abortion.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1401610}, pmid = {40046910}, issn = {2235-2988}, mesh = {Humans ; Female ; *Vagina/microbiology ; Pregnancy ; *Dysbiosis/microbiology ; *Microbiota ; *Abortion, Spontaneous/microbiology ; Lactobacillus ; Pregnant People ; }, abstract = {The vaginal microbiome of healthy women is dominated by Lactobacillus spp. A variety of illnesses, such as vaginosis, sexually transmitted infections (STIs), failed implantation, premature birth (PTB), and preterm pre-labor membrane rupture, are brought on by an unbalanced microbiota. Pregnancy is associated with a decrease in the metabolic capacity of the vaginal resident microbiome, which is consistent with a change to a less complex Lactobacillus-dominated microbiome. Age, race, sexual intercourse, smoking, IUD, contraception, lifestyle, and diet all affect the makeup of the vaginal microbiome. Moreover, physiological events including menarche, the menstrual cycle, pregnancy, menopause, and other hormonal changes have an impact on the vaginal microbiome. The vaginal microbiome is significantly disrupted by the menstrual cycle, with significant changes toward a more varied microbiota occurring around menstruation. Several major factors maintain or disrupt the vaginal microbiome including ethnic group, menstruation cycle, and pregnancy which are discussed in this section. In the index pregnancy, the vaginal microbiota of women who had already given birth, or had just experienced an induced or spontaneous abortion, was qualitatively and quantitatively different from that of women who were having their first child. Early pregnancy vaginal microbiome depletion is a risk factor for early pregnancy miscarriage. Although, early pregnancy miscarriage is not always caused by a high bacterial diversity and quantity of lactobacilli. Lactobacillus protects against pathogens through the production of antibacterial compounds such as lactic acid and bacteriocins.}, }
@article {pmid40046742, year = {2025}, author = {Jiang, T and Du, P and Liu, D and Chen, H and Ma, Y and Hu, B and Li, J and Jiang, H and Li, X}, title = {Exploring the glucose-lowering and anti-inflammatory immune mechanism of artemether by AMPK/mTOR pathway and microbiome based on multi-omics.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1520439}, pmid = {40046742}, issn = {1663-9812}, abstract = {BACKGROUND: Diabetes mellitus (DM) is a metabolic disease with high morbidity, which significantly affects human life and health expenditures. Previous studies have demonstrated that artemether (ATM) has anti-diabetes and anti-inflammation activities, but its mechanism has not been fully elucidated. This research aimed to elucidate the impact of ATM on glucolipid metabolism in a type 2 diabetes mellitus (T2DM) model db/db mice and what kind of role the gut microbiota played, and explored the underlying mechanisms involved.<br><br>METHODS: C57BL/KsJ-db/db mice were treated with 80 and 160&#xa0;mg/kg of ATM for 8&#xa0;weeks, with metformin as a positive control.<br><br>RESULTS: ATM treatment (160&#xa0;mg/kg) observably ameliorated insulin resistance (IR), hyperglycemia, hyperlipemia and pathological injury in the liver and pancreas. In addition, ATM significantly decreased the expression of TNF-&#x3b1;, IL-1&#x3b2;, IL-6, NF-&#x3ba;B and IL-17A, and significantly increased the level of IL-10 in diabetic mice. 16S rRNA sequencing and targeted GC-MS metabolomics result indicated that ATM restored gut microbiota dysbiosis based on increasing beneficial bacteria Lactobacillus and reducing pathogenic bacteria Helicobacter and Prevotella leading to the accumulation of propionic and valeric acids and the reduction of lipopolysaccharides (LPS) release, intestinal inflammation and intestinal barrier damage. Network pharmacology and metabolomics identified the AMPK/mTOR pathway as the main signaling involved in ATM improves glucolipid metabolism and inflammation in T2DM. Western blotting results revealed that ATM suppressed the phosphorylation of mTOR, P38, P65, IKB&#x3b1; and IRS1 whlie increased the levels of p-AMPK, TLR4, and occludin in mice liver and colon.<br><br>CONCLUSION: Taken together, ATM may modulate the composition of gut microbiota, increasing the abundance of Lactobacillus, which in turn elevates the levels of SCFAs. The elevation of SCFAs, especially propionic acid, may activate the AMPK/mTOR pathway, leading to a decrease in the levels of TNF-&#x3b1;, IL-1&#x3b2;, IL-6, NF-&#x3ba;B, and IL-17A, while increasing the levels of IL-10, thereby alleviating the inflammatory state and improving glucolipid metabolic disorder in T2DM. These findings laid a theoretical foundation for the clinical application of ATM in T2DM.}, }
@article {pmid40046303, year = {2025}, author = {Ma, X and Zeng, X and Huang, Z and Li, G and Liu, R and Luo, R and Li, X and Ling, S and Wang, C and Gu, Y}, title = {Analysis of fungal microbiota diversity and potential pathogenic fungi in oral secretions and gut feces of captive giant pandas.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1522289}, pmid = {40046303}, issn = {1664-302X}, abstract = {BACKGROUND: Maintaining good oral and gut health is essential for the wellbeing of animals, and fungi are key components of the oral and gut microbiota. This study aims to explore the diversity and seasonal dynamics of oral and gut fungal communities in captive giant pandas, with a focus on their potential functional roles in health and digestion.<br><br>METHODS: In the study, we collected saliva and fecal samples from 60 captive giant pandas were collected in different seasons, oral and gut fungi were analyzed using internal transcribed spacer (ITS) amplicon sequencing. We used &#x3b1; and &#x3b2; diversity analyses to examine the differences in species diversity and composition among the different seasons. Furthermore, we validated the ITS amplicon sequencing results through fungal isolation and identification.<br><br>RESULTS: Analyses of &#x3b1; and &#x3b2; diversity revealed both the differences and similarities between the fungal communities in the oral and gut microbiomes of giant pandas. Ascomycota and Basidiomycota were predominant in both oral and gut groups, while the dominant genera in the four seasons were Cutaneotrichosporon, and unidentified_Chaetothyriales_sp. Additionally, Cladosporium and Candida were predominant in the oral and gut fungus, respectively, across all four seasons. Notably, fungal abundance and diversity in the oral microbiome were significantly higher than in the gut microbiome, a pattern observed throughout most seasons. Several potentially pathogenic fungi, such as Fusarium, Candida and Aspergillus, were detected in healthy giant pandas, with most showing increased abundance during winter. It is worth mentioning that we found a distinct bias in the functional communities of oral and gut fungi. The abundance of saprophytic fungi in the gut is relatively high, which may be related to their role in cellulose digestion.<br><br>CONCLUSION: The abundance and diversity of fungal communities in the oral cavity and gut of giant pandas exhibit significant seasonal variations. While the oral cavity hosts a higher abundance and diversity of fungi, the species composition of fungal community composition is similar to that of the intestines. The majority of gut fungi are likely derived from the oral cavity or diet, the significant seasonal variation in gut fungal community structure further suggests that long-term resident fungi may not be present in the gut.}, }
@article {pmid40046294, year = {2025}, author = {Han, H and Xiong, H and Liu, Z and Liu, X and Wang, H and Kou, J and Yi, D and Shi, Y and Wu, H and Qiao, J}, title = {Pasteurized Akkermansia muciniphila Timepie001 ameliorates DSS-induced ulcerative colitis in mice by alleviating intestinal injury and modulating gut microbiota.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1542522}, pmid = {40046294}, issn = {1664-302X}, abstract = {INTRODUCTION: Akkermansia muciniphila (A. muciniphila), known as a next-generation probiotic, has been widely recognized for its beneficial effects in various metabolic diseases. While there is not much research whether live or pasteurized A. muciniphila has different effects on intestinal health.<br><br>METHODS: In the present study, a strain of A. muciniphila was isolated from healthy individuals, with the live and pasteurized A. muciniphila named Timepie001 and Timepie001+, respectively. They were administered to dextran sulfate sodium-induced ulcerative colitis mice to investigate their influences on the host intestinal health.<br><br>RESULTS AND CONCLUSION: The results showed that prophylactic supplementation with live and pasteurized A. muciniphila alleviates ulcerative colitis symptoms by retarding weight loss, preserving intestinal tissue structure, modulating inflammatory cytokines (TNF-&#x3b1;, IL-1&#x3b2;), and enhance the colonic mucosal barrier by upregulating the expression of tight junction protein Claudin-1. Interestingly, pasteurized A. muciniphila has a better effect compared with live A. muciniphila. Moreover, pasteurized A. muciniphila can regulates the gut microbiome to maintain intestinal homeostasis. This provides theoretical support for the widespread application of postbiotics in the food industry.}, }
@article {pmid40046174, year = {2025}, author = {Kim, YJ and Ihrie, VM and Shi, P and Ihrie, MD and Womble, JT and Meares, AH and Granek, JA and Gunsch, CK and Ingram, JL}, title = {Glucagon-Like Peptide 1 Receptor (Glp1r) Deficiency Does Not Appreciably Alter Airway Inflammation or Gut-Lung Microbiome Axis in a Mouse Model of Obese Allergic Airways Disease and Bariatric Surgery.}, journal = {Journal of asthma and allergy}, volume = {18}, number = {}, pages = {285-305}, pmid = {40046174}, issn = {1178-6965}, abstract = {PURPOSE: High body mass index (≥30 kg/m[2]) is associated with asthma severity, and nearly 40% of asthma patients exhibit obesity. Furthermore, over 40% of patients with obesity and asthma that receive bariatric surgery no longer require asthma medication. Increased levels of glucagon-like peptide 1 (GLP-1) occur after bariatric surgery, and recent studies suggest that GLP-1 receptor (GLP-1R) signaling may regulate the gut microbiome and have anti-inflammatory properties in the lung. Thus, we hypothesized that increased GLP-1R signaling following metabolic surgery in obese and allergen-challenged mice leads to gut/lung microbiome alterations, which together contribute to improved features of allergic airways disease.<br><br>METHODS: Male and female Glp1r-deficient (Glp1r[-/-]) and replete (Glp1r[+/+]) mice were administered high fat diet (HFD) to induce obesity with simultaneous intranasal challenge with house dust mite (HDM) allergen to model allergic airway disease with appropriate controls. Mice on HFD received either no surgery, sham surgery, or vertical sleeve gastrectomy (VSG) on week 10 and were sacrificed on week 13. Data were collected with regard to fecal and lung tissue microbiome, lung histology, metabolic markers, and respiratory inflammation.<br><br>RESULTS: HFD led to metabolic imbalance characterized by lower GLP-1 and higher leptin levels, increased glucose intolerance, and alterations in gut microbiome composition. Prevalence of bacteria associated with short chain fatty acid (SCFA) production, namely Bifidobacterium, Lachnospiraceae UCG-001, and Parasutterella, was reduced in mice fed HFD and positively associated with serum GLP-1 levels. Intranasal HDM exposure induced airway inflammation. While Glp1r[-/-] genotype affected fecal microbiome beta diversity metrics, its effect was limited.<br><br>CONCLUSION: Herein, GLP-1R deficiency had surprisingly little effect on host gut and lung microbiomes and health, despite recent studies suggesting that GLP-1 receptor agonists are protective against lung inflammation.}, }
@article {pmid40045625, year = {2025}, author = {Fan, F and Chen, L and Sun, H and Liu, JJ and Yang, K and Gu, F}, title = {Longitudinal dynamics of plasma bile acids and its associations with physiological parameters and fecal microbiome during the transition period in dairy cows.}, journal = {Animal bioscience}, volume = {}, number = {}, pages = {}, doi = {10.5713/ab.24.0628}, pmid = {40045625}, issn = {2765-0189}, abstract = {OBJECTIVE: The aim of this study is to investigate the dynamic changes of plasma bile acids (BA) and their associations with physiological metabolisms and fecal microbiome in transitional dairy cows.<br><br>METHODS: Twenty multiparous dairy cows were selected, the blood and fecal samples were collected at d -21, -7, +7, and +21 relative to calving. The targeted metabolome and 16s rDNA gene sequencing were applied to detect BA profiles and fecal microbial composition, respectively.<br><br>RESULTS: Totally, 32 BA species including 9 primary BAs (PBA) and 23 secondary BAs (SBA) were identified. Most of the PBAs (7 out to 9) and SBAs (15 out to 23) exhibited significant increases postpartum compared to prepartum. Notably, ursodeoxycholic acid, taurocholic acid and 7-ketodeoxycholic acid showed higher importance. Correlation analysis showed the BAs concentrations positively correlated with the concentrations of aspartate aminotransferase, total antioxidant capacity, and glutathione peroxidase, but negatively correlated with the concentrations of triglyceride significantly. A decline in bacterial alpha diversity in postpartum and significantly different &#x3b2;-diversity were observed. Additionally, 30 significant different genera were identified over the transition period. Among these, six and eleven biomarkers such as Alistipes and Ruminococcaceae_UCG_014 were identified at +7d and +21d, respectively. Furthermore, the abundances of choloylglycine hydrolase and 7-alpha-hydroxysteroid dehydrogenase involved in SBA biosynthesis were significantly higher postpartum as determined by PICRUSt2 analysis over the transition period.<br><br>CONCLUSION: These findings underscore a significant surge in the demand for BAs for postpartum dairy cows and highlight the potential impact of BAs on bovine health. By shedding light on these metabolic dynamics, our study offers valuable insights into strategies for optimizing the nutrition and well-being of perinatal dairy cows.}, }
@article {pmid40045464, year = {2025}, author = {Schlicht, K and Pape, L and Rohmann, N and Knappe, C and Epe, J and Geisler, C and Pohlschneider, D and Brodesser, S and Kruse, L and Rohlfing, ME and Hartmann, K and Türk, K and Marquardt, J and Beckmann, J and von Schönfels, W and Beckmann, A and Wietzke-Braun, P and Schulte, DM and Hollstein, T and Demetrowitsch, T and Jensen-Kroll, J and Brix, F and Schreiber, S and Franke, A and Schwarz, K and Waschina, S and Laudes, M}, title = {Prediabetes and type 2 diabetes but not obesity are associated with alterations in bile acid related gut microbe-microbe and gut microbe-host community metabolism.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2474143}, doi = {10.1080/19490976.2025.2474143}, pmid = {40045464}, issn = {1949-0984}, mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/metabolism ; *Bile Acids and Salts/metabolism ; *Obesity/microbiology/metabolism ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; *Prediabetic State/microbiology/metabolism ; Female ; Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Adult ; Aged ; Taurine/metabolism ; }, abstract = {The interplay between bile acids (BAs) and metabolic diseases has gained importance in recent years, with a variety of studies investigating their relationship with diverging results. Therefore, in the present study we performed a detailed analysis of BA metabolism in 492 subjects with different metabolic phenotypes. Besides microbiomics and metabolomics this investigation included in silico analysis of community metabolism to examine metabolic interchange between different microbes as well as microbes and the human host. Our findings revealed distinct changes in the BA profiles of patients with diabetes and prediabetes, whereas obesity alone had no influence on circulating BAs. Impaired glycemic control led to increased circulating BAs, a shift toward more secondary BAs, and an increase in the ratio of glycine to taurine-conjugated BAs. Additional analyses revealed that the ratio of glycine to taurine conjugation demonstrated variations between the single BAs, cholic acid (CA), chenodeoxycholic acid (CDCA) and deoxycholic acid (DCA), regardless of the metabolic status, with CA having a higher fraction of taurine conjugation. Furthermore, we found that microbiome alterations are associated with BAs, independent of diabetes or obesity. Analysis of microbial community metabolism revealed differential relative pathway abundance in relation to diabetes, particularly those related to membrane and polyamine synthesis. Increased bacterial cross-feeding of polyamines, galactose, and D-arabinose also coincided with an increase in BA. Notably, our serum metabolome analysis mirrored several of the previously in silico predicted exchanged metabolites, especially amino acid metabolism. Therefore, targeting BA metabolism may be a future approach for the treatment of metabolic diseases, especially prediabetes and type 2 diabetes.}, }
@article {pmid40045434, year = {2025}, author = {Tan, Y and Matsuzaki, J and Saito, Y and Suzuki, H}, title = {Environmental factors in gastric carcinogenesis and preventive intervention strategies.}, journal = {Genes and environment : the official journal of the Japanese Environmental Mutagen Society}, volume = {47}, number = {1}, pages = {5}, pmid = {40045434}, issn = {1880-7046}, support = {23K24188//Grant-in-Aid for Scientific Research B/ ; 24K22342//Grant-in-Aid for Challenging Research (Exploratory)/ ; }, abstract = {Gastric cancer, a significant global health concern, arises from a complex interplay of genetic and environmental factors. Helicobacter pylori (H. pylori) infection is a major risk factor that can be mitigated through eradication strategies. Epstein-Barr virus (EBV) infection causes a distinct subtype of gastric cancer called EBV-associated gastric cancer. The gastric microbiome, a dynamic ecosystem, is also involved in carcinogenesis, particularly dysbiosis and specific bacterial species such as Streptococcus anginosus. Long-term use of proton pump inhibitors and potassium-competitive acid blockers also increases the risk of gastric cancer, whereas non-steroidal anti-inflammatory drugs including aspirin may have a protective effect. Smoking significantly increases the risk, and cessation can reduce it. Dietary factors such as high intake of salt, processed meats, and red meat may increase the risk, whereas a diet rich in fruits and vegetables may be protective. Extracellular vesicles, which are small membrane-bound structures released by cells, modulate the tumor microenvironment and may serve as biomarkers for risk stratification and as therapeutic targets in gastric cancer. This review highlights the multifaceted etiology of gastric cancer and its risk factors and emphasizes the importance of a multi-pronged approach to prevention including H. pylori eradication and modification of lifestyle factors, as well as the potential of microbiome-based and EV-based interventions. Further research is needed to refine risk stratification and to develop personalized prevention strategies.}, }
@article {pmid40045431, year = {2025}, author = {Morni, MA and William-Dee, J and Jinggong, ER and Al-Shuhada Sabaruddin, N and Azhar, NAA and Iman, MA and Larsen, PA and Seelan, JSS and Bilung, LM and Khan, FAA}, title = {Gut microbiome community profiling of Bornean bats with different feeding guilds.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {21}, pmid = {40045431}, issn = {2524-4671}, abstract = {Bats are extraordinary mammals. They have evolved to consume various dietary sources, such as insects, fruits, nectar, blood, and meat. This diversity has generated considerable interest in the scientific community, resulting in efforts to leverage bats as model organisms to study the correlation between diet and gut microbiome community. Although such studies now commonly use Next Generation Sequencing (NGS), similar studies are early in their development in Southeast Asia, especially in Malaysia, which harbours an incredibly diverse bat fauna. This study provides pioneering NGS metabarcoding information on Bornean bats. By using a high-throughput Nanopore-based 16S rRNA gene sequencing method, Bacillota, Pseudomonadota, and Campylobacterota were found in insectivorous bats and phytophagous bats. Both insectivorous and phytophagous groups harboured no dominant taxon (D = 0.076; D = 0.085). A comparative analysis of gut bacteria functional groups identified eight major groups in both phytophagous and insectivorous bats, with fermentation being the predominant group. The correlation network analysis revealed a negative correlation between the 'good bacteria' Lactobacillus and various pathogenic bacteria genera, such as Salmonella (-0.4124) and Yersinia (-0.4654), demonstrating its prebiotic characteristics. This study broadens our understanding of the bat gut microbiome from various diets, with emphasis on new data from Borneo.}, }
@article {pmid40045231, year = {2025}, author = {Agyapong, D and Propster, JR and Marks, J and Hocking, TD}, title = {Cross-validation for training and testing co-occurrence network inference algorithms.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {74}, pmid = {40045231}, issn = {1471-2105}, support = {2125088//National Science Foundation/ ; 2125088//National Science Foundation/ ; 2125088//National Science Foundation/ ; 2125088//National Science Foundation/ ; }, mesh = {*Algorithms ; *Microbiota ; Computational Biology/methods ; Bacteria/genetics/classification ; }, abstract = {BACKGROUND: Microorganisms are found in almost every environment, including soil, water, air and inside other organisms, such as animals and plants. While some microorganisms cause diseases, most of them help in biological processes such as decomposition, fermentation and nutrient cycling. Much research has been conducted on the study of microbial communities in various environments and how their interactions and relationships can provide insight into various diseases. Co-occurrence network inference algorithms help us understand the complex associations of micro-organisms, especially bacteria. Existing network inference algorithms employ techniques such as correlation, regularized linear regression, and conditional dependence, which have different hyper-parameters that determine the sparsity of the network. These complex microbial communities form intricate ecological networks that are fundamental to ecosystem functioning and host health. Understanding these networks is crucial for developing targeted interventions in both environmental and clinical settings. The emergence of high-throughput sequencing technologies has generated unprecedented amounts of microbiome data, necessitating robust computational methods for network inference and validation.<br><br>RESULTS: Previous methods for evaluating the quality of the inferred network include using external data, and network consistency across sub-samples, both of which have several drawbacks that limit their applicability in real microbiome composition data sets. We propose a novel cross-validation method to evaluate co-occurrence network inference algorithms, and new methods for applying existing algorithms to predict on test data. Our method demonstrates superior performance in handling compositional data and addressing the challenges of high dimensionality and sparsity inherent in real microbiome datasets. The proposed framework also provides robust estimates of network stability.<br><br>CONCLUSIONS: Our empirical study shows that the proposed cross-validation method is useful for hyper-parameter selection (training) and comparing the quality of inferred networks between different algorithms (testing). This advancement represents a significant step forward in microbiome network analysis, providing researchers with a reliable tool for understanding complex microbial interactions. The method's applicability extends beyond microbiome studies to other fields where network inference from high-dimensional compositional data is crucial, such as gene regulatory networks and ecological food webs. Our framework establishes a new standard for validation in network inference, potentially accelerating discoveries in microbial ecology and human health.}, }
@article {pmid40045185, year = {2025}, author = {Freund, L and Hung, C and Topacio, TM and Diamond, C and Fresquez, A and Lyons, TW and Aronson, EL}, title = {Diversity of sulfur cycling halophiles within the Salton Sea, California's largest lake.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {120}, pmid = {40045185}, issn = {1471-2180}, support = {NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; }, mesh = {California ; *Sulfur/metabolism ; *Microbiota ; *Lakes/microbiology ; *Seawater/microbiology/chemistry ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Seasons ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Biodiversity ; }, abstract = {BACKGROUND: Microorganisms are the biotic foundation for nutrient cycling across ecosystems, and their assembly is often based on the nutrient availability of their environment. Though previous research has explored the seasonal lake turnover and geochemical cycling within the Salton Sea, California's largest lake, the microbial community of this declining ecosystem has been largely overlooked. We collected seawater from a single location within the Salton Sea at 0 m, 3 m, 4 m, 5 m, 7 m, 9 m, 10 m, and 10.5 m depths in August 2021, December 2021, and April 2022.<br><br>RESULTS: We observed that the water column microbiome significantly varied by season (R[2]&#x2009;=&#x2009;0.59, P&#x2009;=&#x2009;0.003). Temperature (R[2]&#x2009;=&#x2009;0.27, P&#x2009;=&#x2009;0.004), dissolved organic matter (R[2]&#x2009;=&#x2009;0.13, P&#x2009;=&#x2009;0.004), and dissolved oxygen (R[2]&#x2009;=&#x2009;0.089, P&#x2009;=&#x2009;0.004) were significant drivers of seasonal changes in microbial composition. In addition, several halophilic mixotrophs and other extremotolerant bacteria were consistently identified in samples across depths and time points, though their relative abundances fluctuated by season. We found that while sulfur cycling genes were present in all metagenomes, their relative coverages fluctuated by pathway and season throughout the water column. Sulfur oxidation and incomplete sulfur oxidation pathways were conserved in the microbiome across seasons.<br><br>CONCLUSIONS: Our work demonstrates that the microbiome within the Salton Seawater has the capacity to metabolize sulfur species and utilize multiple trophic strategies, such as alternating between chemorganotrophy and chemolithoautrophy, to survive this harsh, fluctuating environment. Together, these results suggest that the Salton Sea microbiome is integral in the geochemical cycling of this ever-changing ecosystem and thus contributes to the seasonal dynamics of the Salton Sea. Further work is required to understand how these environmental bacteria are implicated relationship between the Salton Sea's sulfur cycle, dust proliferation, and respiratory distress experienced by the local population.}, }
@article {pmid40045177, year = {2025}, author = {Torshizi Esfahani, A and Zafarjafarzadeh, N and Vakili, F and Bizhanpour, A and Mashaollahi, A and Karimi Kordestani, B and Baratinamin, M and Mohammadpour, S}, title = {Gut Microbiome in Colorectal Cancer: Metagenomics from Bench to Bedside.}, journal = {JNCI cancer spectrum}, volume = {}, number = {}, pages = {}, doi = {10.1093/jncics/pkaf026}, pmid = {40045177}, issn = {2515-5091}, abstract = {Colorectal cancer (CRC) is a major global health challenge. Emerging research highlights the pivotal role of the gut microbiota in influencing CRC risk, progression, and treatment response. Metagenomic approaches, especially high-throughput shotgun sequencing, have provided unprecedented insights into the intricate connections between the gut microbiome and CRC. By enabling comprehensive taxonomic and functional profiling, metagenomics has revealed microbial signatures, activities, and biomarkers associated with colorectal tumorigenesis. Furthermore, metagenomics has shown a potential to guide patient stratification, predict treatment outcomes, and inform microbiome-targeted interventions. Despite remaining challenges in multi-omics data integration, taxonomic gaps, and validation across diverse cohorts, metagenomics has propelled our comprehension of the intricate gut microbiome-CRC interplay. This review underscores the clinical relevance of microbial signatures as potential diagnostic and prognostic tools in CRC. Furthermore, it discusses personalized treatment strategies guided by this omics' approaches.}, }
@article {pmid40044961, year = {2025}, author = {El-Baz, AM and El-Mahmoudy, AA and Saber, S and ElRakaiby, MT}, title = {The coadministration of Lactobacillus probiotic augments the antitumor effect of telmisartan in rats.}, journal = {AMB Express}, volume = {15}, number = {1}, pages = {38}, pmid = {40044961}, issn = {2191-0855}, abstract = {Colorectal cancer (CRC) is a prevalent disease with a high mortality rate and is significantly affected by microbial dysbiosis. Recent research suggests that modulation of the gut microbiome can have therapeutic benefits and that Angiotensin-II Type 1 Receptor (AT1R) can stimulate cell growth, angiogenesis, and resistance to apoptosis in various cancers. In this study, the adjunctive administration of Lactobacillus spp. and telmisartan, an AT1R blocker, was explored in the treatment of CRC. The effect of telmisartan and a mixture of probiotic species, Lactobacillus delbrueckii and Lactobacillus fermentum, was assessed on key biomarkers and selected gut microbiota taxa in 1,2-dimethylhydrazine-induced CRC in rats. Angiogenesis, inflammation, and apoptosis were assessed by measuring vascular endothelial growth factor (VEGF), carcinoembryonic antigen (CEA), Interleukin 6 (IL-6), and Annexin V levels, respectively. The relative abundance of selected gut microbial taxa, including Bacteroides spp., Clostridium spp., Clostridium coccoides, Ruminococcus spp., and Lactobacillus spp. was analyzed to determine the change in the microbial composition in the different experimental groups of the animal model. This study demonstrated that the unique combination therapy using a Lactobacillus mixture and telmisartan effectively reduced VEGF and IL-6 levels, indicating decreased angiogenesis and inflammation. Lactobacillus spp. co-administration with telmisartan boosted programmed cell death, reversed dysbiosis, improved histopathological outcomes, and reduced CEA levels. These findings offer a new perspective on the role of Lactobacillus spp. and telmisartan in CRC treatment. Further research on their adjunctive use and therapeutic potential are needed to enhance clinical efficacy.}, }
@article {pmid40044917, year = {2025}, author = {Štůsková, K and Vavřiník, A and Hakalová, E and Čechová, J and Gramaje, D and Eichmeier, A}, title = {Arbuscular mycorrhizal fungi strongly influence the endorhizosphere of grapevine rootstock with soil type as a key factor.}, journal = {Mycorrhiza}, volume = {35}, number = {2}, pages = {17}, pmid = {40044917}, issn = {1432-1890}, support = {CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; IGA-ZF/2022-ST2-004//Internal Grant Agency, Mendel university in Brno/ ; IGA-ZF/2022-ST2-004//Internal Grant Agency, Mendel university in Brno/ ; }, mesh = {*Mycorrhizae/physiology ; *Vitis/microbiology ; *Soil Microbiology ; *Soil/chemistry ; Czech Republic ; Plant Roots/microbiology ; Mycobiome ; Basidiomycota/genetics/physiology ; Rhizosphere ; Phosphorus/metabolism/analysis ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) play a crucial role in enhancing the health and productivity of host plants, including grapevine. By forming symbiotic relationships with plant roots, AMF significantly improve water uptake and nutrient absorption, particularly phosphorus (P) and nitrogen (N). This study evaluated the microbiome composition and AMF colonization in the grapevine endorhizosphere across five wine-growing sub-regions in the Czech Republic. In all five sub-regions, in terms of composition of the fungal microbiome, the phyla Ascomycetes and Basidiomycetes were most numerous. Additionally, the study confirmed that LSU primers are more sensitive than ITS primers for AMF sequencing. While the representation of the phylum Glomeromycetes ranged from 0.07% to 5.65% in the ITS library, it was significantly higher, ranging from 83.74% to 98.71%, in the LSU library. The most significant difference compared to other sub-regions was observed in the Slovácko sub-region, where the soil had a low pH, a different texture (sandy loam), reduced micronutrient concentration, and low organic matter. The application of chemical plant protection products to grapevines also could have played a significant role, with 49 applications recorded in the Slovácko sub-region during the three years preceding sample collection. In other sub-regions, chemical treatments were conducted only 19-26 times. These factors resulted in only trace amounts of AMF being detected in Slovácko. Furthermore, it was demonstrated that AMF positively influenced the phosphorus concentration in the soil and reduced the presence of certain fungal pathogens.}, }
@article {pmid40044209, year = {2025}, author = {Wang, X and Zhang, P and Lu, H and Luo, D and Yang, D and Li, K and Qiu, S and Zeng, H and Zeng, X}, title = {Risk prediction models for dental caries in children and adolescents: a systematic review and meta-analysis.}, journal = {BMJ open}, volume = {15}, number = {3}, pages = {e088253}, doi = {10.1136/bmjopen-2024-088253}, pmid = {40044209}, issn = {2044-6055}, mesh = {Humans ; *Dental Caries/epidemiology ; Child ; Adolescent ; Risk Assessment/methods ; }, abstract = {OBJECTIVE: This study aimed to systematically evaluate published predictive models for dental caries in children and adolescents.<br><br>DESIGN: A systematic review and meta-analysis of observational studies.<br><br>DATA SOURCES: Comprehensive searches were conducted in PubMed, Web of Science, Cochrane Library, Cumulative Index to Nursing and Allied Health Literature, Embase, China National Knowledge Infrastructure, Wanfang Database, China Science and Technology Journal Database (VIP) and SinoMed for relevant studies published up to 18 January 2024. The search focused on caries prediction models in children and adolescents.<br><br>ELIGIBILITY CRITERIA: Eligible studies included observational research (cohort, case-control and cross-sectional designs) that developed risk prediction models for dental caries in children and adolescents aged &#x2264;18 years. Each model was required to include a minimum of two predictors. Studies were excluded if they were not available in English or Chinese, primarily focused on oral microbiome modelling, or lacked essential details regarding study design, model construction or statistical analyses.<br><br>RESULTS: A total of 11 studies were included in the review. All models demonstrated a high risk of bias, primarily due to inappropriate statistical methods and unclear applicability resulting from insufficiently detailed presentations of the models. Logistic regression, random forests and support vector machines were the most commonly employed methods. Frequently used predictors included fluoride toothpaste use and brushing frequency. Reported area under the curve (AUC) values ranged from 0.57 to 0.91. A combined predictive model incorporating six caries predictors achieved an AUC of 0.79 (95% CI: 0.73 to 0.84).<br><br>CONCLUSIONS: Simplified predictive models for childhood caries showed moderate discriminatory performance but exhibited a high risk of bias, as assessed using the Prediction Model Risk of Bias Assessment Tool (PROBAST). Future research should adhere to PROBAST guidelines to minimise bias risk, focus on enhancing model quality, employ rigorous study designs and prioritise external validation to ensure reliable and generalisable clinical predictions.<br><br>PROSPERO REGISTRATION NUMBER: CRD42024523284.}, }
@article {pmid40044134, year = {2025}, author = {Lee, SY and Lee, SB and Kwon, GH and Song, SH and Park, JH and Kim, MJ and Eom, JA and Lee, KJ and Yoon, SJ and Park, H and Won, SM and Jeong, JJ and Oh, KK and Ham, YL and Baik, GH and Kim, DJ and Sharma, SP and Suk, KT}, title = {Synbiotic combination of fructooligosaccharides and probiotics ameliorates the metabolic dysfunction-associated steatotic liver disease.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {63}, number = {2}, pages = {e2411002}, doi = {10.71150/jm.2411002}, pmid = {40044134}, issn = {1976-3794}, support = {//Hallym University Research Fund/ ; 2020R1I1A3073530//National Research Foundation of Korea/ ; 2020R1A6A1A03043026//National Research Foundation of Korea/ ; //Ministry of Education, Science and Technology/ ; P0020622//Korea Institute for Advancement of Technology/ ; }, mesh = {*Synbiotics/administration &amp; dosage ; *Oligosaccharides/pharmacology ; *Probiotics/administration &amp; dosage/pharmacology/therapeutic use ; Animals ; *Liver/metabolism/drug effects/pathology ; Male ; Mice ; Prebiotics/administration &amp; dosage ; Mice, Inbred C57BL ; Disease Models, Animal ; Fatty Liver/metabolism ; Lipid Metabolism/drug effects ; }, abstract = {Synbiotics have become a new-age treatment tool for limiting the progression of metabolic dysfunction-associated steatotic liver disease; however, inclusive comparisons of various synbiotic treatments are still lacking. Here, we have explored and evaluated multiple synbiotic combinations incorporating three distinctive prebiotics, lactitol, lactulose and fructooligosaccharides. Of the synbiotic treatments evaluated, a combination of fructooligosaccharides and probiotics (FOS+Pro) exhibited superior protection against western diet-induced liver degeneration. This synbiotic (FOS+Pro) combination resulted in the lowest body weight gains, liver weights and liver/body weight ratios. The FOS+Pro synbiotic combination substantially alleviated liver histopathological markers and reduced serum AST and cholesterol levels. FOS+Pro ameliorated hepatic inflammation by lowering expression of proinflammatory markers including TNF-α, IL-1β, IL-6, and CCL2. FOS+Pro significantly improved steatosis by restricting the expression of lipid metabolic regulators (ACC1, FAS) and lipid transporters (CD36) in the liver. These findings are critical in suggesting that synbiotic treatments are capable of restraining western diet-induced metabolic dysfunction in the liver. Additionally, this study demonstrated that adding probiotic strains amplified the effectiveness of fructooligosaccharides but not all prebiotics.}, }
@article {pmid40044111, year = {2025}, author = {Pratikna, AM and Rivai, MI and Suswita, R and Putra, AE and Rachman, IA and Suchitra, A}, title = {The effect of tumor resection on intestinal microbiota dysbiosis in patients with right-sided colon cancer.}, journal = {Annals of coloproctology}, volume = {41}, number = {1}, pages = {47-56}, doi = {10.3393/ac.2024.00346.0049}, pmid = {40044111}, issn = {2287-9714}, abstract = {PURPOSE: This study aimed to determine the effect of tumor resection on dysbiosis of the intestinal microbiota in patients with right-sided colon cancer.<br><br>METHODS: This study utilized a longitudinal design to explore the outcomes of patients diagnosed with right-sided colon cancer who underwent surgical resection at Dr. M. Djamil General Hospital from July to December 2023. We excluded patients with a documented history of comorbidities, specifically those affecting the digestive system. To compare the microbiota (genus and phylum) between patients with right-sided colon cancer and the control group, we conducted bivariate analyses using the independent t-test or Mann-Whitney test. Furthermore, we employed the dependent t-test or Wilcoxon test to assess changes in the dysbiosis of the microbiota (genus and phylum) before and after resection. A P-value of <0.05 was considered statistically significant.<br><br>RESULTS: This study included a total of 21 patients diagnosed with right-sided colon cancer. In the control group, Bacteroidetes constituted the highest proportion of intestinal microbiota, accounting for 56.34%. Prior to tumor resection, the intestinal microbiota of patients exhibited Proteobacteria as the predominant phylum, representing 52.97%. Following tumor resection, Bacteroidetes remained the most prevalent, comprising 50.9% of the intestinal microbiota. Significant variations in the levels of Proteobacteria, Verrucomicrobia, and Cyanobacteria/Chloroplast were observed in the intestinal microbiota of patients with right-sided colorectal cancer before and after tumor excision (all P=0.001).<br><br>CONCLUSIONS: The microbiome of patients with right-sided colorectal cancer differed significantly from that of the control group. However, following tumor resection, the microbiome composition of these patients became more similar to that observed in the control group.}, }
@article {pmid40043878, year = {2025}, author = {Ma, Q and Zhou, Y and Parales, RE and Jiao, S and Ruan, Z and Li, L}, title = {Effects of herbicide mixtures on the diversity and composition of microbial community and nitrogen cycling function on agricultural soil: a field experiment in Northeast China.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {125965}, doi = {10.1016/j.envpol.2025.125965}, pmid = {40043878}, issn = {1873-6424}, abstract = {Herbicide mixtures application is a widespread and effective practice in modern agriculture; however, a knowledge gap exists regarding the potential ecotoxicological effects of herbicide mixtures in agricultural systems. Here, the effects of various doses of herbicide mixtures (atrazine, nicosulfuron, and mesotrione) under different varieties of maize cultivation on the structure and function of microbial communities and soil chemical parameters were clarified through field experiments. The results showed that the application of herbicide mixtures increased the bacterial and fungal community alpha diversity at jointing and maturity, indicating a prolonged effect of the herbicide mixtures. Moreover, herbicide mixtures alter the composition of bacterial and fungal communities, with sensitive taxa suppressed and herbicide-tolerant taxa enriched. The herbicide mixtures significantly reduced the abundances of Bacillus even at lower doses, but Penicillum was enriched. FAPROTAX analysis and quantitative PCR (qPCR) results showed that herbicide mixtures inhibited the soil nitrogen-cycle process and related genes AOA-amoA, AOB-amoA, and nifH at maize seedling stage. Moreover, network analysis showed that low concentrations of the herbicide mixtures increased bacterial interactions while high concentrations inhibited them, which indicated that the network complexity may be herbicide concentration dependent. A synthetic community (SynCom) consisting of six bacterial strains was established for the biodegradation of the herbicide mixtures based on the analysis of the bacterial network, which resulted in an increase in the degradation efficiency of nicosulfuron by 15.90%. Moreover, potted maize experiment showed that the addition of the SynCom alleviated the toxic effects of herbicide mixtures on the plants. In summary, this study provides a comprehensive perspective for assessing the ecological risk at taxonomic and functional levels and the biodegradation approach of herbicide mixtures residue on agricultural soils in Northeastern China.}, }
@article {pmid40043874, year = {2025}, author = {Gan, H and Jiang, Y and Wu, L and Zhu, B and Ji, D and Liu, J and Ding, Z and Ye, X}, title = {Long-term and low-dose exposure to triclosan induces POI phenotype in female offspring mice.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {125966}, doi = {10.1016/j.envpol.2025.125966}, pmid = {40043874}, issn = {1873-6424}, abstract = {Triclosan (TCS), a typical endocrine disruptor, is widely used as an antibacterial agent in consumer goods. However, there are few studies on the effects of long-term low-dose TCS exposure on ovarian function in F1 female mice. In this paper, F1 female mice were exposed to TCS (0-3000 μg/kg/day) from intrauterine to postnatal day (PND) 91 to investigate its effects on the ovary. The results revealed that the number of total follicles was decreased, while atretic follicles was increased after TCS exposure. At the hormonal level, the secretion of estradiol was reduced, while follicle-stimulating hormone and luteinizing hormone were increased after TCS exposure. Observation of vaginal smear showed that TCS disrupted the estrous cycle of F1 female mice, especially at the dose of 3000 μg/kg/day. Moreover, TCS promoted cell apoptosis by activating the p38-MAPK signaling pathway and oxidative stress in vitro. In addition, analysis of the fecal microbiome and serum metabolomics revealed that exposure to TCS may cause gut microbiota disruption and metabolic abnormalities in F1 female mice. In conclusion, long-term low-dose TCS exposure may induce primary ovarian insufficiency phenotype in F1 female mice via inducing cell apoptosis and disrupting gut microbiota and metabolism.}, }
@article {pmid40043859, year = {2025}, author = {Lu, F and Wei, J and Guan, D and Peng, Y and Song, J and Qian, F}, title = {16S rDNA sequencing reveal synergistic effects of silkworm feces and earthworms on nutrient-poor soil microbial community structure and function in Guangxi.}, journal = {Genomics}, volume = {}, number = {}, pages = {111025}, doi = {10.1016/j.ygeno.2025.111025}, pmid = {40043859}, issn = {1089-8646}, abstract = {This study evaluates the synergistic effects of silkworm feces and earthworms on nutrient-poor acidic red soils in Guangxi, China. Using 16S rDNA amplicon sequencing, soil samples from untreated fields, silkworm feces, earthworm gut contents, and soils treated with silkworm feces combined with three earthworm densities (50, 80, and 110 worms/kg) were compared. The earthworm gut microbiome increased in diversity in a density-dependent manner, while treated soils displayed enhanced microbial richness-with the 80 worms/kg treatment showing the highest diversity (605 genera). Random Forest analysis identified key bacterial genera, and co-occurrence networks pinpointed potential keystone taxa. PICRUSt2 predicted enrichment of pathways for xenobiotic biodegradation, carbohydrate metabolism, and secondary metabolite biosynthesis. These findings demonstrate that integrating silkworm feces with an optimal earthworm density improves soil microbial diversity and function, offering insights for sustainable organic waste management and soil health.}, }
@article {pmid40043768, year = {2025}, author = {Fernando, SC and Adams, S and Lakamp, A and Spangler, ML}, title = {Stochastic and deterministic factors that shape the rumen microbiome.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2024-25797}, pmid = {40043768}, issn = {1525-3198}, abstract = {At the heart of degradation of complex organic matter within the rumen are its microbes. These microbes can convert unusable organic matter into useable protein and energy sources and therefore can directly influence the animal's health, performance and utilization of feed. As such, understanding stochastic and deterministic factors that contribute toward rumen microbial assembly and persistence can provide valuable information into developing methods to improve animal health, performance, and nutrient utilization through microbiome modulation. In this review, we describe how ecological concepts such as colonization history, priority effects and historical contingency may influence rumen microbial community assembly and in turn impact community composition and function. Additionally, we discuss how such ecological concepts can be used to develop novel microbial community assembly strategies to develop rumen microbiomes with long-term benefits to the host ruminant. Finally, we discuss current knowledge gaps in rumen microbiome research associated with host-microbe interactions and microbial assembly and propose potential opportunities for future microbiome studies to improve the understanding of the rumen microbiome to improve animal health and productivity.}, }
@article {pmid40043758, year = {2025}, author = {Ghaffari, MH and Sauerwein, H and Sadri, H and Schuchardt, S and Martín-Tereso, J and Doelman, JH and Daniel, JB}, title = {Longitudinal characterization of the metabolome of dairy cows transitioning from one lactation to the next: Investigations in fecal samples.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-26273}, pmid = {40043758}, issn = {1525-3198}, abstract = {The fecal metabolome comprises metabolites that are excreted or not absorbed by the animal. This study examined the changes in the fecal metabolome of dairy cows from the end of one lactation period, through the dry period, and into the subsequent lactation. Twelve Holstein cows (BW = 745 ± 71 kg, BCS = 3.43 ± 0.66) were housed in a tie-stall barn from 7 wk before to 15 wk after parturition, with dry-off occurring approximately 6 wk before the expected calving date (mean dry-off time = 42 d). Fecal samples were taken at wk -7, -5, -1, +1, +5, +10, +15 relative to calving. Targeted metabolomics identified a total of 93 metabolites, including AA, biogenic amines, bile acids (BA), and acylcarnitines (AcylCN) and some phospholipids. Principal component analysis (PCA) revealed clear metabolic shifts that showed a clear separation between the samples from the dry period and the samples from the end, early and middle of lactation, indicating significant changes in the metabolic profiles in the feces. The transition from the dry period (wk -5, -1 relative to calving) to lactation (wk +1, +5, +10, +15, -7 relative to calving) is characterized by an increase in fecal AA and metabolites, such as Glu, Met, β-alanine, and methionine sulfoxide, reflecting a shift in nitrogen metabolism to support increased protein metabolism for milk production. Higher concentrations of polyamines, such as spermidine and putrescine, were observed postpartum, indicating increased cell growth and improved tissue regeneration. Elevated gamma-aminobutyric acid (GABA) levels during lactation indicate increased microbial activity driven by a nutrient-rich diet. Results showed significant adjustments in bile acid profiles as cows transitioned into lactation. Deoxycholic acid (DCA) remained the predominant BA in feces, reflecting ongoing microbial transformation, while glycine- and taurine-conjugated BA increased postpartum, suggesting improved enterohepatic circulation and lipid absorption. Fecal acylcarnitines showed dynamic shifts with elevated levels during late gestation, a decrease in the dry period, and an increase postpartum, indicating increased fatty acid oxidation to meet energy demands. Results showed that phosphatidylcholines decreased prepartum but increased after calving. This indicates shifts in lipid metabolism reflecting energy requirements in lactation and suggests that fecal lipid composition is an indicator of metabolic adaptations in dairy cows. In particular, PCA revealed cosiderable overlap in the fecal metabolite profiles of multiparous and primiparous cows, indicating similar metabolic profiles. This was also confirmed by volcano plots, which showed no significant differences in fecal metabolism between the 2 groups across different weeks relative to calving (wk -7, -5, -1, +1, +5, +10, +15). Overall, these results emphasize the complex interactions between dietary factors, liver and gastrointestinal function, and the gut microbiome in shaping the fecal metabolite profile of dairy cows. These results underscore the value of this data set in advancing the application of fecal metabolome profiling to investigate metabolic changes during critical transitions in the lactation cycle of dairy cows.}, }
@article {pmid40043731, year = {2025}, author = {Wang, M and Liu, YB and Tong, WM and Leung, WK and He, LL and Xu, X and Xu, D and Zhou, Q}, title = {Periodontitis History Shapes the Early Peri-Implant Microbiome Formation: A Metagenomic Analysis.}, journal = {Journal of clinical periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jcpe.14147}, pmid = {40043731}, issn = {1600-051X}, support = {32270188//National Natural Science Foundation of China/ ; 32070134//National Natural Science Foundation of China/ ; 2023-YBSF-162//Key Research and Development Program of Shaanxi Province, China/ ; //National Training Program of Innovation and Entrepreneurship for Undergraduates/ ; }, abstract = {AIM: This study aims to investigate the early alterations in microbiome construction and succession around dental implants in both periodontally healthy individuals and patients with a history of periodontitis during the first month after implant-crown placement.<br><br>MATERIALS AND METHODS: Ninety-five subgingival plaque samples were collected from 10 periodontally compromised patients (PCP) and nine periodontally healthy patients (PHP) at four time points with a 1-week interval and analysed using dynamic metagenomic analysis. The study compared the formation and temporal change in the peri-implant microbiome in the PCP and PHP groups during the first month after the implant crown placement. A two-year follow-up examination was conducted to assess the clinical outcomes of early peri-implant dysbiosis.<br><br>RESULTS: The results showed that PCP groups exhibited distinctively dysbiotic features in their peri-implant microbiome upon initial establishment, with an earlier and elevated emergence of periodontopathogens. This dysbiosis in the PCP group was associated with significantly higher modified sulcus bleeding index (mBI) scores compared with the PHP group. Neisseria was identified as a key driver of early peri-implant dysbiosis in patients with a periodontitis history.<br><br>CONCLUSIONS: This study established the first microbial link between periodontitis history and early peri-implant dysbiosis, highlighting the importance of early prevention strategies against peri-implant diseases in patients with a periodontitis history.}, }
@article {pmid40043672, year = {2025}, author = {Kiššová, Z and Mátis, G and Mackei, M and Tráj, P and Márton, RA and Horváth, DG and Tóthová, C and Mudroňová, D and Karaffová, V}, title = {Research note: utilizing a novel chicken ileal explant model to assess the efficacy of probiotic Limosilactobacillus reuteri CCM 9425 against Salmonella Enteritidis infection.}, journal = {Poultry science}, volume = {104}, number = {4}, pages = {104909}, doi = {10.1016/j.psj.2025.104909}, pmid = {40043672}, issn = {1525-3171}, abstract = {The establishment of a consistent ex vivo model of poultry gut tissue for the study of intestine-microbiome interactions remains still a significant challenge. In this study a pro-inflammatory response of chicken ileal explant cultures was observed after Salmonella enterica serotype Enteritidis infection reflected by up-regulation of IL-18, TNF-α, IL-1β mRNA expression and the levelof serum amyloid A (SAA) protein. In contrast, pre-treatment of ileal explants with probiotic strain Limosilactobacillus reuteri CCM 9425 was able to suppress the infection-induced up-regulation of IL-1β, IL-18 cytokines and the SAA protein. Moreover, the applied probiotics elevated the RNA level of the gene encoding the anti-inflammatory cytokine IL-10 in the probiotic group and the pre-treatment group. Using ileal explant cultures isolated from chicken offers a reliable model of the gut, for studiing the effects of microorganisms at the level of histological tissue structure, gene expression of selected markers and protein production. In summary, regarding our results the miniature chicken ileal explants exhibited appropriate innate immune responses following exposure to bacterial infection with Salmonella Enteritidis and Limosilactobacillus reuteri, furthermore, represents a suitable model for the study of host-pathogen interactions under ex vivo conditions.}, }
@article {pmid40043655, year = {2025}, author = {Cheng, X and Yan, Z and Li, Q and Schmitz, L and Yan, J and Ge, Y and Lan, Y and Zhao, Y and Wang, Y and Li, G and Liu, Y and Schneijderberg, M and Yang, L and Bian, H and van Dijk, ADJ and Qin, L and Cao, Q and Bisseling, T}, title = {Chinese chestnut did not induce negative plant soil feedback during centuries of growth.}, journal = {The Science of the total environment}, volume = {970}, number = {}, pages = {178883}, doi = {10.1016/j.scitotenv.2025.178883}, pmid = {40043655}, issn = {1879-1026}, abstract = {Certain tree species can reach ages of centuries, whereas lifespan of species like apple are markedly shorter. The latter is caused by negative plant-soil feedback that results in microbiome changes. We hypothesized that tree species with a long lifespan will be able to avoid such negative feedback and their root-associated microbiomes will be similar in trees of different ages. To test this, we used Chinese chestnut (Castanea mollissima) trees, ranging from 8 to 830 years old from a Ming orchard at the Great Wall. Their root-associated microbiomes were analysed by using meta-amplicon sequencing analysis. Their root-associated bacterial microbiomes were rather similar although based on linear regression models we cannot exclude that age has a weak correlation with microbiome compositions. When chestnut seedlings were grown for 3 months in soil associated with young or old trees, the plants were healthy and their growth was similar. This strongly supported that negative feedback had not occurred. Pseudomonas OTU1, a member of the core microbiome and representing >50 % of the rhizosphere community, strongly inhibited growth of chestnut pathogens and stimulated plant growth. Such properties of the microbiome, in combination with a high number of resistance genes can contribute to longevity of chestnut.}, }
@article {pmid40043583, year = {2025}, author = {Horill, S and Zhou, XK and Jin, W}, title = {Probiotics as a possible novel therapeutic option to mitigate perioperative neurocognitive disorders: A review exploring the latest research findings.}, journal = {Journal of clinical anesthesia}, volume = {103}, number = {}, pages = {111801}, doi = {10.1016/j.jclinane.2025.111801}, pmid = {40043583}, issn = {1873-4529}, abstract = {Perioperative neurocognitive disorders (PND) refer to a constellation of symptoms that primarily affect the elderly and typically manifest as common complications after exposure to surgery and anesthesia. PND is associated with high morbidity, mortality, and progression to neurodegenerative diseases, thus exerting significant financial strains on families as well as the healthcare system. Given that an ageing global population is an inevitable trend and, with the latest advances in the healthcare system, an ever-growing number of elderly people present for surgery and anesthesia, PND is of prominent concern. The two-way communication between the intestinal flora and the brain, also known as the microbiota-gut-brain axis, plays an important role in central nervous system development, and multiple studies have highlighted the influence exerted by gut microbiome in both health and disease. Pertinent studies have corroborated the fact that anesthesia and surgery disrupt the harmony of the gut ecology, which sets off a cascade of events that initiate neuroinflammation, eventually leading to PND. Probiotics, which are live microorganisms that promote the host's health, have been shown as a viable option to restore or minimise the disruption of gut flora. Evidence exists that probiotics exhibit immunomodulatory and anti-inflammatory benefits. Given the effectiveness of probiotics in reducing neuroinflammation, research has also focused on their impact on the development of PND. This review aims to compile the data from relevant clinical trials focusing on the influence of probiotics on PND to determine whether the derived findings might be applied for the prevention and treatment of PND.}, }
@article {pmid40043555, year = {2025}, author = {Darvishi, S and Donnachie, E and Uibel, PA and Flaskamp, M and Gasperi, C and Hapfelmeier, A and Hemmer, B}, title = {Antibiotic drug use in the five years preceding the diagnosis of multiple sclerosis.}, journal = {Multiple sclerosis and related disorders}, volume = {96}, number = {}, pages = {106366}, doi = {10.1016/j.msard.2025.106366}, pmid = {40043555}, issn = {2211-0356}, abstract = {BACKGROUND: Microbiota may play a role in autoimmune disease pathogenesis, including multiple sclerosis (MS). Antibiotic use disrupts the microbiome and may increase the risk of autoimmune diseases. We evaluated the relationship between MS diagnosis and antibiotic, antimycotic and antiviral drug use in the 5 years preceding diagnosis.<br><br>METHOD: Our population-based case-control study used German ambulatory claims data from 2012 to 2022. We defined cohorts of 13,053 MS patients, 22,898 Crohn's disease patients, and 15,037 matched controls without autoimmune diseases, aged 21-70. Logistic and Poisson regression models explored the relationship between MS diagnosis and antimicrobial usage. Two sub-analyses were performed: a separate analysis of patients with clinically isolated syndrome (CIS) and a sensitivity analysis of newly diagnosed MS patients without preceding neurological symptoms.<br><br>RESULTS: Patients with MS had higher exposure to antibiotic (Odd Ratio (OR) = 1.27, 95 % CI 1.21-1.33), antimycotic (OR = 1.27, 95 % CI 1.12-1.45), and antiviral drugs (OR = 1.28, 95 % CI 1.15-1.43) in the five years before diagnosis compared to patients with no autoimmune diseases. Similar findings were obtained for the CIS cohort and in the sensitivity analysis. Antibiotic use peaked 5 years before MS diagnosis, declining closer to diagnosis, while antiviral and antimycotic drug use showed the opposite. This effect was not observed in the sensitivity analysis and CIS cohorts. Antibiotic use was higher in Crohn's disease than in MS (OR = 0.86, 95 % CI 0.82-0.90), with no consistent differences in antimycotic and antiviral use.<br><br>CONCLUSIONS: The association and kinetic of antibiotic use before MS and CIS diagnosis supports the role of microbiota in MS pathogenesis and suggests antibiotic use to be related to the development of autoimmune diseases, including MS. Additional studies are warranted to clarify whether increased antibiotic use is part of the MS prodrome or a true risk factor for MS.}, }
@article {pmid40043439, year = {2025}, author = {Afsari, Y and Atabi, F and Aghelan, Z and Khazaie, H and Vakili, Z and Abtahi, SH and Rezaie Pouya, M}, title = {Serum levels of 1,3-β-D-glucan is correlated with NLRP3 inflammasome activation and insomnia severity in people with chronic insomnia disorder.}, journal = {Sleep medicine}, volume = {129}, number = {}, pages = {187-191}, doi = {10.1016/j.sleep.2025.02.046}, pmid = {40043439}, issn = {1878-5506}, abstract = {This study aimed to explore the correlation between serum levels 1,3-β-D-glucan as a biomarker for gut microbiome imbalance and NLRP3 inflammasome/IL-1β axis activation and insomnia severity in humans with chronic insomnia disorder (CID). Blood samples were collected from 20 people diagnosed with CID based on the Pittsburgh Sleep Quality Index (PSQI) and video-polysomnography and 20 healthy individuals based on PSQI. 1,3-β-D-glucan, IL-1β, and NLRP3 protein serum levels were assayed using enzyme-linked immunosorbent assay (ELISA). 1,3-β-D-glucan, IL-1β, and NLRP3 protein serum concentrations in the CID group were significantly higher than in the control group. Also, we observed a significant positive correlation between the serum levels of these three factors in the CID group and a significant positive correlation between 1,3-β-D-glucan and insomnia severity index. Our findings suggest that 1,3-β-D-glucan may indicate gut microbiome imbalance in people with CID and may play an important role in the pathogenesis of chronic insomnia by activating the NLRP3/IL-1β inflammasome pathway. These results highlight the potential for dual therapeutic strategies targeting gut microbiota modulation and NLRP3 inflammasome inhibition to disrupt the neuroinflammatory cascade driving chronic insomnia.}, }
@article {pmid40043274, year = {2025}, author = {Al, ET}, title = {FULL SUPPLEMENT: Exploring The Scalp Barrier and Microbiome In Diverse Dandruff Patients.}, journal = {Journal of drugs in dermatology : JDD}, volume = {24}, number = {3}, pages = {32730s1-32730s16}, doi = {10.36849/JDD.32730}, pmid = {40043274}, issn = {1545-9616}, mesh = {Humans ; *Dandruff/microbiology/drug therapy ; *Microbiota/drug effects ; *Scalp/microbiology ; Malassezia/isolation &amp; purification/drug effects ; Dysbiosis/microbiology ; Antifungal Agents/administration &amp; dosage/pharmacology ; }, abstract = {Although the exact pathophysiology of dandruff is still not completely decoded, current theories highlight the role of the microbiome on the skin surface in the patho-genesis. Several scalp microbiome studies from different populations have revealed the association of dandruff with bacterial and fungal dysbiosis. Another study comparing the major bacterial-fungal populations colonizing dandruff scalps in China and France suggests that targeting one par-ticular Malassezia species by antifungals instead of using broad-spectrum antifungals and rebalancing the dandruff scalp microbiota could be a common approach to improve dandruff condition.}, }
@article {pmid40043273, year = {2025}, author = {Bitton, A and Idkowiak-Baldys, J and Bouslimani, A and Chun Wang, EH and Paturi, J and Chen, Y and Clavaud, C and Baalbaki, N}, title = {INDIVIDUAL ARTICLE: A Clinical Evaluation of Scalp Barrier Function, Ceramide Levels, and Microbiome in Diverse Dandruff Patients.}, journal = {Journal of drugs in dermatology : JDD}, volume = {24}, number = {3}, pages = {32731s3-32731s14}, doi = {10.36849/JDD.32731}, pmid = {40043273}, issn = {1545-9616}, mesh = {Humans ; *Ceramides/metabolism/analysis ; *Dandruff/microbiology ; *Microbiota/physiology ; Male ; Female ; Adult ; Middle Aged ; *Scalp/microbiology ; Malassezia/isolation &amp; purification ; Young Adult ; Aged ; Water Loss, Insensible ; Epidermis/microbiology/metabolism ; }, abstract = {Dandruff is a common chronic scalp condition that affects approximately half the population irrespective of their origin. Dandruff scalps are characterized by flaking skin, pruritus, and minimal visible scalp inflammation. At the biological level, dandruff scalp presents a disruption of the barrier function supported by lower levels of ceramides in the stratum corneum and typically accompanied by altered microbiome diversity, including a higher abundance of Malassezia yeasts and exacerbated sebum peroxidation. This study evaluated the relationship between skin barrier integrity in association with epidermal ceramide profile, microbiome imbalance, and inflammatory markers in pathophysiology of dandruff in an ethnically diverse panel. Our results confirm a significant increase in TEWL and decrease in hydration along with an increase in erythema, dryness, flakiness, and itchiness in patients with dandruff vs normal scalps; and an elevation of IL1RA:IL1α ratio dependent on the severity of the dandruff, supporting the inflammatory association with dandruff. For the first time, a study shows that dandruff scalps have a significantly higher amount of short-chain ceramides and a significantly lower proportion of long-chain ceramides consistent with lower conformational ordering and, thus explaining a higher permeability of the skin contributing to barrier dysfunction. In addition, reduced phytosphingosine and dihydrosphingosine based ceramides (NP, AP, NDS) were also observed, supporting a weakened scalp barrier. In addition to an expected increase in Malassezia, especially Malassezia restricta, in dandruff scalp, an increase in Staphylococcus aureus and decrease in Malassezia globosa was also observed as compared to healthy scalp in the population analyzed. J Drugs Dermatol. 2025;24:3(Suppl 1):s3-14.}, }
@article {pmid40043268, year = {2025}, author = {A Okoye, G and Bui, H and Zadu, A and A Myles, I and S Byrd, A}, title = {The Multifaceted Effects of Berberine: Potential Uses in Dermatology.}, journal = {Journal of drugs in dermatology : JDD}, volume = {24}, number = {3}, pages = {298-301}, doi = {10.36849/JDD.8899}, pmid = {40043268}, issn = {1545-9616}, mesh = {Humans ; *Berberine/pharmacology/therapeutic use/administration &amp; dosage ; *Skin Diseases/drug therapy ; Antioxidants/pharmacology/administration &amp; dosage/therapeutic use ; Dermatologic Agents/therapeutic use/pharmacology/administration &amp; dosage ; Dermatology/methods/trends ; Gastrointestinal Microbiome/drug effects ; }, abstract = {Berberine is a natural alkaloid found in several plant species and has been utilized in traditional medicine for its antimicrobial, anti-inflammatory, and antioxidant properties. Berberine supplements are readily available over-the-counter in the United States. It has recently gained popularity on social media and is increasingly being used as complementary and alternative medicine. Berberine possesses a broad spectrum of pharmacological properties, which may be a result of its potent antioxidant properties and its regulatory effects on the gut microbiome. Acne, atopic dermatitis, pigmentary disorders, hidradenitis suppurativa, psoriasis, and skin aging are complex disorders, often requiring multifaceted treatment strategies. Berberine's broad mechanisms of action make it a promising candidate for the management of these conditions. This review explores the mechanisms of action of berberine and its clinical relevance in the management of dermatologic diseases. J Drugs Dermatol. 2025;24(3):298-301 doi:10.36849/JDD.8899.}, }
@article {pmid40043265, year = {2025}, author = {Whiting, C and Abdel Azim, S and Joly-Tonetti, N and Lachmann, N and Friedman, A}, title = {Effects on the Skin Microbiome by a Moisturizer Formulated for Eczema-Prone and Sensitive Skin.}, journal = {Journal of drugs in dermatology : JDD}, volume = {24}, number = {3}, pages = {275-280}, doi = {10.36849/JDD.8707}, pmid = {40043265}, issn = {1545-9616}, mesh = {Humans ; *Filaggrin Proteins ; *Microbiota/drug effects ; Female ; Adult ; *Skin Cream/administration &amp; dosage ; Male ; *Skin/microbiology/drug effects ; *Dermatitis, Atopic/microbiology/drug therapy ; Young Adult ; Plant Extracts/administration &amp; dosage/pharmacology ; Middle Aged ; Eczema/microbiology/drug therapy ; Administration, Cutaneous ; Dysbiosis/microbiology ; }, abstract = {BACKGROUND: Cutaneous dysbiosis contributes to the pathophysiology of atopic dermatitis and potentially that of sensitive skin; regulation of the bacterial communities through skincare products is an emerging management strategy. Previous studies have highlighted the utility of ingredients that function as prebiotics, are anti-inflammatory, and have barrier-repairing properties to help shift species richness and composition toward more eubiotic states.<br><br>METHODS: In a single-site open-label study, a moisturizer containing colloidal oatmeal, Ophiopogon japonicus root extract (AD-Resyl&amp;reg;, SILAB, France), and a patented filaggrin protein byproduct was evaluated for its effect on the bacterial communities of eczema-prone and sensitive skin (n=12). Skin swab samples from participants' cheeks were collected before and after applying the moisturizer twice daily for 21 days. Measures of alpha diversity (richness, Shannon diversity index) and beta diversity were calculated using paired, comparative analyses of sampled bacterial loads.<br><br>RESULTS: Bacterial species richness was significantly increased in 10 participants (P<0.05) without dysbiotic shifts in overall microbial composition.<br><br>CONCLUSION: These results support the use of a moisturizer containing anti-inflammatory and skin barrier-repairing ingredients for managing atopic dermatitis and add to our knowledge of the skin microbiome in sensitive skin. J Drugs Dermatol. 2025;24(3):275-280. doi:10.36849/JDD.8707.}, }
@article {pmid40042645, year = {2025}, author = {Rust, C and Asmal, L and O'Hare, M and Pretorius, E and Emsley, R and Seedat, S and Hemmings, S}, title = {Investigating the gut microbiome in schizophrenia cases versus controls: South Africa's version.}, journal = {Neurogenetics}, volume = {26}, number = {1}, pages = {34}, pmid = {40042645}, issn = {1364-6753}, support = {MRC-RFA-IFSP-01-2013/SHARED ROOTS//South African Medical Research Council/ ; MRC-RFA-IFSP-01-2013/SHARED ROOTS//South African Medical Research Council/ ; MRC-RFA-IFSP-01-2013/SHARED ROOTS//South African Medical Research Council/ ; MRC-RFA-IFSP-01-2013/SHARED ROOTS//South African Medical Research Council/ ; MRC-RFA-IFSP-01-2013/SHARED ROOTS//South African Medical Research Council/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Schizophrenia/microbiology ; South Africa/epidemiology ; Male ; Female ; Adult ; *RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Middle Aged ; Bacteria/genetics/classification ; Feces/microbiology ; }, abstract = {Schizophrenia (SCZ) is a chronic and severe mental disorder with a complex molecular aetiology. Emerging evidence indicates a potential association between the gut microbiome and the development of SCZ. Considering the under-representation of African populations in SCZ research, this study aimed to explore the association between the gut microbiome and SCZ within a South African cohort. Gut microbial DNA was obtained from 89 participants (n = 41 SCZ cases; n = 48 controls) and underwent 16S rRNA (V4) sequencing. Data preparation and taxa classification were performed with the DADA2 pipeline in R studio followed by diversity analysis using QIIME2. Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) was utilised to identify differentially abundant taxa. No statistically significant differences were observed between SCZ patients and controls in terms of alpha-diversity (Shannon q = 0.09; Simpson q = 0.174) or beta-diversity (p = 0.547). Five taxa, namely Prevotella (p = 0.037), Faecalibacterium (p = 0.032), Phascolarctobacterium (p = 0.002), Dialister (p = 0.043), and SMB53 (p = 0.012), were differentially abundant in cases compared to controls, but this observation did not survive correction for multiple testing. This exploratory study suggests a potential association between the relative abundance of Prevotella, Faecalibacterium, Phascolarctobacterium, Dialister, and SMB53 with SCZ case-control status. Given the lack of significance after correcting for multiple testing, these results should be interpreted with caution. Mechanistic studies in larger samples are warranted to confirm these findings and better understand the association between the gut microbiome and SCZ.}, }
@article {pmid40042519, year = {2025}, author = {Gonzalez, E and Sahar, T and Haddad, M and Toupin, S and Zioud, R and Zoabi, M and Waldman, LE and Leshinsky, ZT and Ben Sasson, M and Kumar, V and Marom, Y and Midbari, A and Brereton, NJ and Shir, Y and Minerbi, A}, title = {Altered gut microbiome composition and function in individuals with complex regional pain syndrome.}, journal = {Anesthesiology}, volume = {}, number = {}, pages = {}, doi = {10.1097/ALN.0000000000005435}, pmid = {40042519}, issn = {1528-1175}, abstract = {BACKGROUND: Complex regional pain syndrome (CRPS) is a chronic pain syndrome typically affecting a limb. It is characterized by severe spontaneous and evoked pain, along with vasomotor, autonomic, and motor signs and symptoms. Although dysregulation in several physiologic systems has been suggested in CRPS, including aberrant inflammatory and immune responses, vasomotor dysfunction, and nervous system changes, the pathophysiologic mechanisms underlying the syndrome remain elusive. Effective treatment options are also limited. Previous research has highlighted the role of the gut microbiome in chronic pain, prompting us to investigate the composition and function of the gut microbiome in CRPS.<br><br>METHODS: The gut microbiomes of individuals with CRPS to age-, gender- and ethnicity-matched pain-free control participants were compared using 16S rRNA gene amplification. To minimize environmental confounders, participants were recruited from two geographically independent regions. To explore potential changes in gut-bacteria-derived metabolites targeted metabolomic analysis of feces and plasma was performed. Finally, machine learning algorithms were trained to identify the gut microbiome composition specific to CRPS patients and were tested on a validation cohort.<br><br>RESULTS: In this study, differential abundance analysis revealed significant differences in several bacterial taxa when comparing 53 CRPS patients to 52 unrelated controls, including alterations in short-chain fatty acid (SCFA) metabolizing species. Targeted stool and plasma metabolite analysis confirmed differences in fecal and plasma SCFA levels between CRPS patients and controls. Notably, the microbiome composition alone allowed accurate classification of patients and controls in a geographically independent test cohort.<br><br>CONCLUSIONS: These findings highlight unique compositional and functional changes in the gut microbiome of individuals with CRPS, thus contributing to the growing body of evidence supporting the role of the gut microbiome in chronic pain syndromes. Furthermore, they pave the way for further studies elucidating the pathophysiology of CRPS and exploring new diagnostic aids and treatment modalities.}, }
@article {pmid40042420, year = {2025}, author = {Roseboom, TJ}, title = {[A child s first 1,000 days: its relevance to the oral care practice].}, journal = {Nederlands tijdschrift voor tandheelkunde}, volume = {132}, number = {3}, pages = {118-123}, doi = {10.5177/ntvt.2025.03.24122}, pmid = {40042420}, issn = {0028-2200}, mesh = {Humans ; Infant ; Child, Preschool ; *Oral Health ; Dental Caries/prevention &amp; control ; Infant, Newborn ; Oral Hygiene ; Feeding Behavior ; }, abstract = {Every human life begins as a single, fertilized egg-cell. During the first 1,000 days of life, this cell develops into a 2-year-old toddler. More milestones are reached in this period of life than in any other. All organs are formed, the metabolism is set up, the microbiome is formed, the child learns to eat and drink, develops eating habits, food preferences, and learns to walk and talk. The environment in which these developments take place is crucial to health in later life. The established structures and systems will last for life and will thus have a life-long influence on the individual s general health. Due to the regular check-ups they carry out and their expertise in the field of preventive medicine, oral care providers can make an important contribution during this unique window of opportunity. This article summarizes why the first 1,000 days are important, and describes how oral care providers can contribute. Together with parents (to be) and children, they can build healthy habits, help prevent caries, obesity, diabetes, cardiovascular disease and other chronic disorders, and be part of building the health of present and future generations.}, }
@article {pmid40042419, year = {2025}, author = {Zaura, E}, title = {[The microbiome and the first 1,000 days of life].}, journal = {Nederlands tijdschrift voor tandheelkunde}, volume = {132}, number = {3}, pages = {112-117}, doi = {10.5177/ntvt.2025.03.24064}, pmid = {40042419}, issn = {0028-2200}, mesh = {Humans ; Infant, Newborn ; Infant ; *Microbiota/physiology ; Female ; Pregnancy ; }, abstract = {A healthy human being lives in symbiosis with his microbes or microbiome. The first 1,000 days of life are crucial for developing a healthy and diverse microbiome. The development of a healthy microbiome begins as early as in the womb, where the training of the fetal immune cells begins. Next, the child s microbiome is influenced by the method of delivery during the birthing process. The largest and most important phase is the postnatal period. In this last phase, the child s environment, the behaviour and lifestyle of its caregivers, and the child itself are the main determinants of developing and maintaining a healthy microbiome.}, }
@article {pmid40042364, year = {2025}, author = {Wang, C and Yang, Y and Wang, N and Luan, A and Wang, H and Hu, C}, title = {Design and application of antimicrobial nanomaterials in the treatment of periodontitis.}, journal = {Nanomedicine (London, England)}, volume = {}, number = {}, pages = {1-17}, doi = {10.1080/17435889.2025.2469492}, pmid = {40042364}, issn = {1748-6963}, abstract = {Periodontitis is a chronic inflammatory disease induced by the microbiome, leading to the destruction of periodontal structures and potentially resulting in tooth loss. Using local drug delivery systems as an adjunctive therapy to scaling and root planning in periodontitis is a promising strategy. However, this administration method's effectiveness is constrained by the complexity of the periodontal environment. Nanomaterials have demonstrated significant potential in the antibacterial treatment of periodontitis, attributed to their controllable size, shape, and surface charge, high design flexibility, high reactivity, and high specific surface area. In this review, we summarize the complex periodontal microenvironment and the difficulties of local drug delivery in periodontitis, explicitly reviewing the application and design strategies of nanomaterials with unique properties in the distinct microenvironment of periodontitis. Furthermore, the review discusses the limitations of current research, proposes feasible solutions, and explores prospects for using nanomaterials in this context.}, }
@article {pmid40042343, year = {2025}, author = {Rodenes-Gavidia, A and Illescas, V and Martínez-Blanch, J and Chenoll, E and Moreno-Muñoz, JA and Jiménez López, J and Lamelas, A}, title = {Genome sequence of Lacticaseibacillus paracasei ORD 0998 (CECT 30660), a probiotic bacterium for women's health.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0084924}, doi = {10.1128/mra.00849-24}, pmid = {40042343}, issn = {2576-098X}, abstract = {Lacticaseibacillus paracasei is commonly isolated from dairy products and the microbiome of the human reproductive and gastrointestinal tract. We report the genome assembly of Lacticaseibacillus paracasei ORD 0998 (CECT 30660) with two contigs, having a size of 3,150,431 bp and a GC content of 46.33%.}, }
@article {pmid40042318, year = {2025}, author = {Sun, D and Liu, Y and Zhou, S and Meegaskumbura, M}, title = {Microbiome and climate: skin microbial diversity and community functions of Polypedates megacephalus (Anura: Rhacophoridae) associated with bioclimate.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0235824}, doi = {10.1128/spectrum.02358-24}, pmid = {40042318}, issn = {2165-0497}, abstract = {The microbiome inhabiting animal skin plays a crucial role in host fitness by influencing both the composition and function of microbial communities. Environmental factors, including climate, significantly impact microbial diversity and the functional attributes of these communities. However, it remains unclear how specific climatic factors affect amphibian skin microbial composition, community function, and the relationship between these two aspects. Understanding these effects is particularly important because amphibians are poikilotherms and, thus, more susceptible to temperature fluctuations. Here, we investigated the skin microbiome of the rhacophorid tree frog Polypedates megacephalus across different climatic regimes using 16S rRNA gene sequencing. Skin swab samples were collected from nine populations of P. megacephalus adults in the Guangxi region, China. The majority of the core microbiota were found to belong to the genus Pseudomonas. Our findings indicate that microbial community diversity, composition, and function are associated with changes in climatic conditions. Specifically, the taxonomic and functional diversity of the skin microbiome increased in response to higher climate variability, particularly in temperature fluctuations. Additionally, the functional traits of microbial communities changed in parallel with shifts in community diversity and composition. The significant correlations of the functional redundancy index with climatic factors suggest that environmental filtering driven by climate change impacts microbial community functional stability. These results highlight the critical influence of climatic factors on amphibian skin microbiomes and offer new insights into how microbial composition and function contribute to host adaptation in varying environmental conditions.IMPORTANCEThis study is important in understanding the association between climate variability, microbial diversity, and host adaptation in amphibians, which are particularly vulnerable to environmental changes due to their poikilothermic nature. Amphibians rely on their skin microbiome for key functions like disease resistance, yet little is known about how climate fluctuations impact these microbial communities. By analyzing the microbiome of Polypedates megacephalus across different climatic regimes, our analysis reveals that warmer climates could reduce the microbial diversity and community functional redundancy, indicating the functional stability of skin microbiome could be susceptible to climate variability, particularly in hosts adapted to relatively cooler conditions. These findings highlight the potential ecological consequences of climate change and emphasize the need to integrate microbiome health into amphibian conservation strategies.}, }
@article {pmid40042298, year = {2025}, author = {Kensiski, A and Gavzy, SJ and Wu, L and Mas, V and Ma, B and Bromberg, JS}, title = {Immunosuppressant imprecision: multidirectional effects on metabolism and microbiome.}, journal = {Clinical microbiology reviews}, volume = {}, number = {}, pages = {e0017824}, doi = {10.1128/cmr.00178-24}, pmid = {40042298}, issn = {1098-6618}, abstract = {SUMMARYTransplant recipients require lifelong, multimodal immunosuppression to prevent rejection by dampening alloreactive immunity. These treatments have long been known to lack antigen specificity. Despite empirically selected long-term immunosuppression regimens, most allografts succumb to alloimmune responses that result in chronic inflammation and scarring. Additionally, immunosuppressive medications themselves contribute to unintended intestinal dysbiosis and metabolic disorders. This review focuses on the effect of immunosuppressant treatments on alloimmunity, gut microbiome, and metabolism, with a particular emphasis on the effects on metabolic disorders. We also outline the shared and unique microbial and metabolic signatures produced by each immunosuppressant class, underlining their distinct impacts on immunity and metabolic homeostasis. These observations underscore the need for a holistic understanding of these drugs' on- and off-target effects to refine therapeutic strategies, enhance immunosuppression efficacy, and ultimately enhance graft and patient survival. By characterizing these complex interactions, strategies informed by the gut microbiome and host metabolism may offer a promising adjunctive approach to optimizing immunosuppressive regimens and promoting sustained graft acceptance.}, }
@article {pmid40042272, year = {2025}, author = {Murphree-Terry, M and Keith, JD and Oden, AM and Birket, SE}, title = {Spontaneous lung colonization in the cystic fibrosis rat model is linked to gastrointestinal obstruction.}, journal = {mBio}, volume = {}, number = {}, pages = {e0388324}, doi = {10.1128/mbio.03883-24}, pmid = {40042272}, issn = {2150-7511}, abstract = {Cystic fibrosis (CF) is a genetic disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, resulting in CFTR protein dysfunction. CFTR dysfunction has multi-organ consequences, leading to dehydrated mucus that is adherent to epithelia. In the lungs, this leads to recalcitrant infections with bacteria such as Pseudomonas aeruginosa. In the gut, mucus-laden feces can adhere to the intestines, resulting in distal intestinal obstruction syndrome (DIOS). There is limited information on how lung colonization and DIOS are correlated in people with CF (pwCF). In this novel work, we describe the development of spontaneous lung colonization of CF pathogens in young (<3 months old) CF rats, preceding the development of DIOS. Once DIOS is established, the lung microbiome becomes predominated by taxa also observed in the feces. Induced infection with P. aeruginosa in the CF rats reflects data found in pwCF, as once CF rats are infected, they retain a higher relative abundance of P. aeruginosa than their healthy agemates. Finally, we found that ivacaftor treatment favors a healthier gut microbiome in CF rats, decreasing the relative abundance of Escherichia coli. These results indicate that the CF rat model is recapitulative of human CF disease with the spontaneous lung colonization of traditional CF pathogens and maintenance of P. aeruginosa after induced infection. Furthermore, these results indicate a possible role for the gut-lung axis in lung colonization and DIOS in CF.IMPORTANCEThese data describe for the first time the development of spontaneous lung colonization in the cystic fibrosis (CF) rat model, a hallmark aspect of human CF disease. We also find that CF rats infected with Pseudomonas aeruginosa maintain higher relative abundance following chronic infection as compared to healthy rats, similar to those is seen in people with CF. Additionally, we describe the possible contribution of the gut-lung axis linking lung health with distal intestinal obstruction syndrome, a relationship largely unexplored in the context of CF.}, }
@article {pmid40042226, year = {2025}, author = {Ko, B and Son, J and In Won, J and Kang, BM and Choi, CW and Kim, R and Sung, JH}, title = {Gut microbe-skin axis on a chip for reproducing the inflammatory crosstalk.}, journal = {Lab on a chip}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4lc01010h}, pmid = {40042226}, issn = {1473-0189}, abstract = {The gut-skin axis has emerged as a crucial mediator of skin diseases, with mounting evidence highlighting the influence of gut microbiota on skin health. However, investigating these mechanisms has been hindered by the lack of experimental systems that enable direct study of gut microbiota-skin interactions. Here, we present the gut microbe-skin chip (GMS chip), a novel microfluidic platform designed to model microbiome-gut-skin axis interactions. The GMS chip allows the coculture of intestinal epithelial cells (Caco-2), human epidermal keratinocytes (HEKa), and gut microbes with fluidic connection mimicking the blood flow. We validated that the gut compartment, with a self-sustaining oxygen gradient, enabled coculturing gut bacteria such as Escherichia coli (E. coli) and Lactobacillus rhamnosus GG (LGG), and the skin cells properly differentiated in the chip in the presence of fluid flow. Disruption of intestinal epithelial integrity by dextran sodium sulfate (DSS) combined with lipopolysaccharides (LPS) selectively decreased skin cell viability while sparing gut cells. Notably, pretreatment with LGG showed a protective effect against the skin cell damage by enhancing the intestinal barrier function. The GMS chip effectively recapitulates the influence of gut microbiota on skin health, representing a pivotal step forward in studying gut-skin axis mechanisms and the role of the gut microbiome in skin diseases.}, }
@article {pmid40042189, year = {2025}, author = {Shao, X and Mi, X and Kuai, X and Zhou, D and Tai, Q and Lu, Y and Zhou, C and He, S}, title = {Microbial Butyrate Modified by Melatonin Alleviates Colon Inflammation by Inhibiting GPR109A/Caspase-1-Dependent Macrophage M1 Polarization.}, journal = {Journal of proteome research}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jproteome.4c00915}, pmid = {40042189}, issn = {1535-3907}, abstract = {Recurrent ulcerative colitis (UC) seriously affects the quality of life of patients. Melatonin affects the alteration of the gut microbiota and can effectively relieve inflammation-associated diseases. In the present study, we determined that melatonin effectively alleviated intestinal inflammation and delayed weight loss in mice. Analysis of ileocecal contents in mice via 16S-rRNA and GC-MS revealed that melatonin could elevate the diversity of the gut microbiota and the abundance of short-chain fatty acids producing bacteria and promote the secretion of butyrate. Subsequently, butyrate negatively regulates the NLRP3-mediated inflammatory signaling pathway to inhibit the secretion of proinflammatory mediators such as caspase-1 and IL-1β to restrict the further development of intestinal inflammation. The NLRP3 expression increased, and the GPR109A expression was reduced significantly in the intestinal tissues of active UC patients, which was also closely related to clinical indicators CRP and ESR closely. However, disrupting the gut microbiota with broad-spectrum antibiotics (ABX) blocks melatonin's role in reducing intestinal inflammation. Collectively, we indicate that melatonin arrests UC in mice by modulating the microbiome and the NLRP3/caspase-1 inflammatory signaling pathways to skew macrophage polarization, which may have potential implications in the development of new approaches to treat acute UC.}, }
@article {pmid40042044, year = {2025}, author = {Shen, Y and Choi, E and Kleinberg, S}, title = {Predicting Postprandial Glycemic Responses With Limited Data in Type 1 and Type 2 Diabetes.}, journal = {Journal of diabetes science and technology}, volume = {}, number = {}, pages = {19322968251321508}, doi = {10.1177/19322968251321508}, pmid = {40042044}, issn = {1932-2968}, abstract = {BACKGROUND: A core challenge in managing diabetes is predicting glycemic responses to meals. Prior work identified significant interindividual variation in responses and developed personalized forecasts. However, intraindividual variation is still not well understood, and the most accurate approaches require invasive microbiome data. We aimed to investigate (1) whether postprandial glycemic responses (PPGRs) can be predicted with limited data and (2) sources of intraindividual variation.<br><br>METHODS: We used data collected from 397 people with Type 1 Diabetes (T1DEXI) and 100 people with Type 2 Diabetes (ShanghaiT2DM) who wore continuous glucose monitors (CGMs) and logged meals. Using dietary, demographic, and temporal features, we predicted 2 hours PPGR, and peak 2 hours postprandial glucose rise (Glumax). We evaluated the contribution of food features (eg, macronutrients, food category) and use of personal training data and investigated intraindividual variability in responses.<br><br>RESULTS: We achieved comparable accuracy to prior work for PPGR (T1DEXI R = 0.61, ShanghaiT2DM R = 0.72) and Glumax (T1DEXI R = 0.64, ShanghaiT2DM R = 0.73), without using invasive data like microbiome. Including food category features led to higher accuracy than macronutrients alone. Analysis of glycemic responses to duplicate meals identified time of day (PPGR: T1DEXI P < .05 for lunch, ShanghaiT2DM P < .001 for lunch and dinner) and menstrual cycle (Glumax: P < .05 for perimenstrual) as sources of variability.<br><br>CONCLUSIONS: We demonstrate that in individuals with T1D and T2D, glycemic responses to meals can be predicted without personalized training data or invasive physiological data.}, }
@article {pmid40041888, year = {2025}, author = {Xu, Z and Zhang, L and Tang, Q and Yang, C and Ding, X and Wang, Z and Huang, R and Jiang, R and Maitz, J and Shi, H and Yan, X and Dong, M and Chen, J and Wang, Y}, title = {Unlocking the role of wound microbiome in diabetic, burn, and germ-free wound repair treated by natural and synthetic scaffolds.}, journal = {Acta pharmaceutica Sinica. B}, volume = {15}, number = {1}, pages = {611-626}, pmid = {40041888}, issn = {2211-3835}, abstract = {In current clinical practice, various dermal templates and skin substitutes are used to enhance wound healing. However, the role of wound commensal microbiome in regulating scaffold performance and the healing process remains unclear. In this study, we investigated the influence of both natural and synthetic scaffolds on the wound commensal microbiome and wound repair in three distinct models including diabetic wounds, burn injuries, and germ-free (GF) wounds. Remarkably, synthetic electrospun polycaprolactone (PCL) scaffolds were observed to positively promote microbiome diversity, leading to enhanced diabetic wound healing compared to the natural scaffolds Integra® (INT) and MatriDerm® (MAD). In contrast, both natural and synthetic scaffolds exhibited comparable effects on the diversity of the microbiome and the healing of burn injuries. In GF wounds with no detectable microorganisms, a reversed healing rate was noted showing natural scaffold (MAD) accelerated wound repair compared to the open or the synthetic scaffold (PCL) treatment. Furthermore, the response of the wound commensal microbiome to PCL scaffolds appears pivotal in promoting anti-inflammatory factors during diabetic wound healing. Our results emphasize that the wound commensal microbiome, mediated by different scaffolds plays an important role in the wound healing process.}, }
@article {pmid40041871, year = {2025}, author = {Dias, NW}, title = {Editorial: Understanding the female reproductive microbiome in livestock.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1570990}, doi = {10.3389/fmicb.2025.1570990}, pmid = {40041871}, issn = {1664-302X}, }
@article {pmid40041870, year = {2025}, author = {Kumar, S and Mukherjee, R and Gaur, P and Leal, &#xc9; and Lyu, X and Ahmad, S and Puri, P and Chang, CM and Raj, VS and Pandey, RP}, title = {Unveiling roles of beneficial gut bacteria and optimal diets for health.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1527755}, pmid = {40041870}, issn = {1664-302X}, abstract = {The gut microbiome plays a pivotal role in human health, influencing digestion, immunity, and disease prevention. Beneficial gut bacteria such as Akkermansia muciniphila, Adlercreutzia equolifaciens, and Christensenella minuta contribute to metabolic regulation and immune support through bioactive metabolites like short-chain fatty acids (SCFAs). Dietary patterns rich in prebiotics, fermented foods, and plant-based bioactive compounds, including polyphenols and flavonoids, promote microbiome diversity and stability. However, challenges such as individual variability, bioavailability, dietary adherence, and the dynamic nature of the gut microbiota remain significant. This review synthesizes current insights into gut bacteria's role in health, emphasizing the mechanisms by which dietary interventions modulate microbiota. Additionally, it highlights advancements in microbiome-targeted therapies and the transformative potential of personalized nutrition, leveraging microbiota profiling and artificial intelligence (AI) to develop tailored dietary strategies for optimizing gut health and mitigating chronic inflammatory disorders. Addressing these challenges requires a multidisciplinary approach that integrates scientific innovation, ethical frameworks, and practical implementation strategies.}, }
@article {pmid40041796, year = {2025}, author = {Bai, Y and Tang, Z and Peng, X and Huang, J and Sun, M and Liu, J and Peng, F}, title = {A new psychrophilic yeast of Kriegeriaceae (Kriegeriales) isolated from lichen in the Arctic, with the description of Licheniasvalbardensis gen. et sp. nov.}, journal = {MycoKeys}, volume = {114}, number = {}, pages = {95-113}, pmid = {40041796}, issn = {1314-4049}, abstract = {Yeasts are an important component of the microbiome in circumpolar regions that are characterized by unique environmental conditions. However, the taxonomy of yeasts remains largely unknown in high- and low-latitude regions. Curing a field survey of yeasts in the Svalbard Archipelago, Norway, a new yeast genus in Kriegeriales was isolated from dendritic lichens. Based on the phylogeny of multiple loci (ITS, LSU, SSU, rpb1, rpb2, tef1-α, and cytb), morphology, and physiological characteristics, the new genus Lichenia is proposed with the type species Licheniasvalbardensis. Additionally, 10 °C and 15 °C are the fastest growth temperatures of L.svalbardensis. It has low or no growth at temperatures above 20 °C, and there appears to be a morphogenetic transition from yeast to pseudohyphae or hyphae above 10 °C.}, }
@article {pmid40041703, year = {2025}, author = {Sato, Y}, title = {Rumen DNA virome in beef cattle reveals an unexplored diverse community with potential links to carcass traits.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf021}, pmid = {40041703}, issn = {2730-6151}, abstract = {Rumen deoxyribonucleic acid viruses that infect and replicate within bacteria and archaea are key modulators of the prokaryotic community. These viruses influence prokaryotic community abundance, composition, and function impacting host productivity and methane production. In this study, viral genomes were assembled from the rumen of 37 Japanese Black cattle using virus-like particle metagenome sequencing, providing insights into viral diversity, functional potential, and virus-host interactions. The relationship between the rumen deoxyribonucleic acid virome and carcass traits, particularly carcass weight and marbling, was also investigated. A total of 22 942 viral operational taxonomic units of medium-quality or higher (≥5 kb length and ≥ 50% completeness), referred to as Japanese Black Rumen Viral genomes, were reconstructed. Among these, 5973 putative novel genera were identified, significantly expanding the catalog of rumen viral genomes. Hosts were predicted for 2364 viral operational taxonomic units, including carbohydrate-degrading bacteria and methanogens. Additionally, 27 auxiliary metabolic genes were categorized as glycosyl hydrolases which are responsible for the degradation of cellulose, hemicellulose, and oligosaccharides, suggesting that rumen viruses may enhance the breakdown of complex carbohydrates during infection. Furthermore, the rumen virome differed considerably between high vs low carcass weight cattle and high vs low marbling cattle. Viruses associated with Methanobrevibacter were linked to higher carcass weight. This database and the insights from this study provide primary information for the development and improvement of beef production.}, }
@article {pmid40041522, year = {2025}, author = {Aryati, Y and Farastuti, E and Sholichah, L and Koesharyani, I and Gardenia, L and Septiningsih, E and Yamin, M and Oryzanti, P and Puspaningsih, D and Sugiani, D}, title = {Effects of honey saccharide supplementation on growth performance, amylase enzyme activity, gut microvilli, and microbiome in Cyprinus carpio.}, journal = {Veterinary world}, volume = {18}, number = {1}, pages = {228-237}, pmid = {40041522}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: Prebiotics, such as saccharides in honey, play a crucial role in improving gut microbiota, digestion, and immune function. This study evaluates the effects of Kapok flower honey saccharides on growth performance, digestive enzyme activity, intestinal morphology, and gut microbiota in common carp (Cyprinus carpio).<br><br>MATERIALS AND METHODS: A completely randomized design was implemented with four honey supplementation levels (0% control, 0.5%, 0.75%, and 1%) applied to juvenile C. carpio diets over 30 days. Growth performance, feed utilization, intestinal microvilli structure, gut microbiota, and amylase activity were analyzed using advanced techniques, including high performance liquid chromatography, scanning electron microscopy, and biochemical assays.<br><br>RESULTS: Kapok flower honey contains fructooligosaccharides (FOS, 14.76%) and inulin (6.6%). Supplementation at 1% significantly improved weight gain, feed conversion ratio, and specific growth rate. Amylase activity increased with honey supplementation, peaking at 24.13 &#xb1; 3.11 U g[-1] protein for the 1% group. Gut morphology analysis revealed longer, denser intestinal microvilli and higher perimeter ratios in honey-treated groups than controls. Microbiota analysis showed increased beneficial Bacillus spp. exclusively in the honey-supplemented groups.<br><br>CONCLUSION: Honey saccharides, particularly FOS and inulin, significantly enhance the growth performance, digestive enzyme activity, and gut health of common carp. Supplementation with 1% honey is optimal, improving feed efficiency and fostering beneficial gut microbiota. These findings highlight honey as a cost-effective, natural prebiotic for aquaculture.}, }
@article {pmid40041456, year = {2025}, author = {Farah, A and Paul, P and Khan, AS and Sarkar, A and Laws, S and Chaari, A}, title = {Targeting gut microbiota dysbiosis in inflammatory bowel disease: a systematic review of current evidence.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1435030}, pmid = {40041456}, issn = {2296-858X}, abstract = {INTRODUCTION: The dysbiosis of the gut microbiota has been identified as a central factor in the pathogenesis of inflammatory bowel disease (IBD), a chronic condition characterized by frequent recurrence and various adverse effects of traditional therapies. While treatments targeting the gut microbiota show promise, their efficacy in IBD management still requires extensive evaluation. Our systematic review analyzes recent studies to elucidate the advancements and challenges in treating IBD using microbial-based therapies.<br><br>METHODS: Through a comprehensive systematic review spanning key scientific databases-PubMed, Embase, Cochrane, Web of Science, Scopus, and Google Scholar-we scrutinized the impact of probiotics, prebiotics, synbiotics, and fecal microbiota transplantation (FMT) on individuals with IBD. Our detailed analysis covered study and participant demographics, along with seven key outcome measures: disease activity index, inflammatory markers, serum cytokines, microbiome composition, adverse effects, and the rates of remission and relapse.<br><br>RESULTS: From 6,080 initial search hits, we included 71 studies that assessed various interventions compared to placebo or standard medical therapy. Although there was notable variation in clinical results while assessing different outcomes, overall, probiotics, prebiotics, and synbiotics enhanced the success rates in inducing remission among IBD patients. Furthermore, we noted significant reductions in levels of pro-inflammatory markers and cytokines. Additionally, the requirement for steroids, hospitalization, and poor outcomes in endoscopic and histological scores were significantly reduced in individuals undergoing FMT.<br><br>CONCLUSION: Our investigation highlights the potential of targeting gut microbiota dysbiosis with microbial-based therapies in patients with IBD. We recommend conducting larger, placebo-controlled randomized trials with extended follow-up periods to thoroughly assess these treatments' clinical efficacy and safety before widespread recommendations for clinical application.}, }
@article {pmid40041148, year = {2025}, author = {Zheng, Q and Sun, T and Li, X and Zhu, L}, title = {Reproductive tract microbiome dysbiosis associated with gynecological diseases.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1519690}, pmid = {40041148}, issn = {2235-2988}, mesh = {Female ; Humans ; *Dysbiosis/microbiology ; *Genital Diseases, Female/microbiology ; *Microbiota ; Animals ; Endometriosis/microbiology ; Genitalia, Female/microbiology ; Probiotics ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Female health and the microbiota of the reproductive tract are closely associated. The research scope on reproductive tract microbiota extends from the vaginal to the upper reproductive tract and from infectious diseases to various benign and malignant gynecological and obstetrical diseases. The primary focus of this paper was to evaluate the most recent findings about the role of reproductive tract microbiota in gynecological diseases, including endometrial polyps, uterine fibroids, endometriosis, adenomyosis, endometrial hyperplasia, and endometrial carcinoma. Different stages of gynecological diseases have diverse microbiota in the female reproductive tract, and some specific bacteria may help the disease progress. For example, Fusobacterium may exacerbate endometriosis, while treatments that target microbiota, such as antibiotics, probiotics, and flora transplantation, showed some efficacy in the experiment. These findings indicate the wonderful prospect of this field. Additionally, we have discussed how microbiome research can improve our understanding of the interactions between reproductive tract microorganisms and hosts, aid in the screening and diagnosis of gynecological diseases, and direct the development of preventive and therapeutic strategies aimed at maintaining and restoring a healthy reproductive tract microbiota when combined with other technologies like transcriptome and proteome, in vitro cultured cells, and animal models.}, }
@article {pmid40040961, year = {2025}, author = {KavianFar, A and Taherkhani, H and Lanjanian, H and Aminnezhad, S and Ahmadi, A and Azimzadeh, S and Masoudi-Nejad, A}, title = {Keystone bacteria dynamics in chronic obstructive pulmonary disease (COPD): Towards differential diagnosis and probiotic candidates.}, journal = {Heliyon}, volume = {11}, number = {4}, pages = {e42719}, pmid = {40040961}, issn = {2405-8440}, abstract = {Preventing exacerbations in Chronic Obstructive Pulmonary Disease (COPD) is crucial due to the high mortality rate and the associated costs of hospitalization for patients during exacerbations. Despite the proven influence of the lung microbiome on disease control, the dynamics of bacterial communication in different stages of COPD remain unknown. This study aimed to propose a group of candidate bacteria for the differential diagnosis of different states of COPD based on the relative abundance correlation of bacteria in lung sputum samples. We compared microbiome data collected from 101 COPD patients in stable and exacerbation states, as well as 124 healthy controls from two separate general cohorts, to determine the major microbiome and keystone genera. To validate our findings, we utilized two additional distinct public datasets, each comprising 81 healthy subjects and 87 COPD patients in stable condition, exacerbation, and post-treatment phases. During COPD exacerbation, Porphyromonas, Clostridium, Moryella, and Megasphaera were identified as phenotype-specific keystone genera, while Prevotella, Streptococcus, Haemophilus, and Veillonella were consistently present across all datasets as core microbiome members. Changes in keystone genera during different COPD stages indicate rewiring of bacterial interactions, with increased keystone bacteria and network connectivity observed during dysbiosis and more severe COPD. Bifidobacterium showed probiotic potential, positively correlating with Lactobacillus during exacerbation, while Neisseria and Haemophilus increased in abundance, and negatively correlated with key probiotic bacteria. These findings indicate promising potential for the simultaneous use of Bifidobacterium along with Lactobacillus as a therapeutic candidate to prevent COPD exacerbations in lung health, underscoring the need for further research in future clinical studies.}, }
@article {pmid40040878, year = {2025}, author = {Abdulla, A and Sadida, HQ and Jerobin, J and Elfaki, I and Mir, R and Mirza, S and Singh, M and Macha, MA and Uddin, S and Fakhro, K and Bhat, AA and Akil, ASA}, title = {Unraveling molecular interconnections and identifying potential therapeutic targets of significance in obesity-cancer link.}, journal = {Journal of the National Cancer Center}, volume = {5}, number = {1}, pages = {8-27}, pmid = {40040878}, issn = {2667-0054}, abstract = {Obesity, a global health concern, is associated with severe health issues like type 2 diabetes, heart disease, and respiratory complications. It also increases the risk of various cancers, including melanoma, endometrial, prostate, pancreatic, esophageal adenocarcinoma, colorectal carcinoma, renal adenocarcinoma, and pre-and post-menopausal breast cancer. Obesity-induced cellular changes, such as impaired CD8[+] T cell function, dyslipidemia, hypercholesterolemia, insulin resistance, mild hyperglycemia, and fluctuating levels of leptin, resistin, adiponectin, and IL-6, contribute to cancer development by promoting inflammation and creating a tumor-promoting microenvironment rich in adipocytes. Adipocytes release leptin, a pro-inflammatory substance that stimulates cancer cell proliferation, inflammation, and invasion, altering the tumor cell metabolic pathway. Adiponectin, an insulin-sensitizing adipokine, is typically downregulated in obese individuals. It has antiproliferative, proapoptotic, and antiangiogenic properties, making it a potential cancer treatment. This narrative review offers a comprehensive examination of the molecular interconnections between obesity and cancer, drawing on an extensive, though non-systematic, survey of the recent literature. This approach allows us to integrate and synthesize findings from various studies, offering a cohesive perspective on emerging themes and potential therapeutic targets. The review explores the metabolic disturbances, cellular alterations, inflammatory responses, and shifts in the tumor microenvironment that contribute to the obesity-cancer link. Finally, it discusses potential therapeutic strategies aimed at disrupting these connections, offering valuable insights into future research directions and the development of targeted interventions.}, }
@article {pmid40040706, year = {2025}, author = {Abbas, Z and Tong, Y and Zhang, J and Sammad, A and Wang, J and Ahmad, B and Wei, X and Si, D and Zhang, R}, title = {Transcriptomics and microbiome insights reveal the protective mechanism of mulberry-derived postbiotics against inflammation in LPS-induced mice.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1536694}, pmid = {40040706}, issn = {1664-3224}, mesh = {Animals ; *Morus ; Mice ; *Lipopolysaccharides ; *Gastrointestinal Microbiome/drug effects ; *Inflammation/immunology ; *Transcriptome ; Gene Expression Profiling ; Male ; Disease Models, Animal ; Mice, Inbred C57BL ; Protein Interaction Maps ; }, abstract = {BACKGROUND: Natural food-derived bioactive compounds have garnered increasing attention for their potential to modulate immune responses and promote gut health. In particular, compounds like mulberry-derived postbiotics (MDP) may offer novel therapeutic strategies to address inflammation, a key driver of many metabolic disorders.<br><br>METHODOLOGY: This study examines the protective effects of MDP against inflammation in LPS-induced mice, using transcriptomic and microbiome analyses to explore underlying mechanisms.<br><br>RESULTS: MDP pretreatment alleviates LPSinduced villous atrophy and intestinal barrier damage, promoting recovery of intestinal morphology. Transcriptomic profiling revealed significant changes in gene expression, with 983 upregulated and 1220 downregulated genes in the NC vs LPS comparison, and 380 upregulated and 204 downregulated genes in the LPS vs LPS+MDP comparison. Enrichment analysis using GO and KEGG pathways revealed significant associations with transcriptional regulatory activity, and the NOD-like receptor signaling pathway among the differentially expressed genes. Protein-protein interaction analysis identified key genes involved in inflammation and immune regulation, with hub genes like IL6, CXCL10, and MYD88 in the LPS group and CD74, CIITA, and H2-AB1 in the MDP-treated group.<br><br>CONCLUSION: Microbiome analysis suggested MDP may also influence gut microbiota composition, supporting systemic immune regulation. These findings highlight MDP's potential as a food additive for immune modulation and gut health.}, }
@article {pmid40040609, year = {2025}, author = {Liu, FQ and An, ZY and Cui, LJ and Xiao, MY and Wu, YJ and Li, W and Zhang, BS and Yu, L and Feng, J and Liu, ZG and Feng, R and Jiang, ZX and Huang, RB and Jing, HM and Ren, JH and Zhu, XY and Cheng, YF and Li, YH and Zhou, HB and Gao, D and Liu, Y and Yu, F and Wang, X and Qiao, JL and Hu, DH and Wang, LL and Zang, MT and Chen, Q and Qu, QY and Zhou, JY and Li, ML and Chen, YX and Huang, QS and Fu, HX and Li, YY and Wang, QF and Huang, XJ and Zhang, XH and , }, title = {Correlation Between Fecal Microbiota and Corticosteroid Responsiveness in Primary Immune Thrombocytopenia: an Exploratory Study.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2410417}, doi = {10.1002/advs.202410417}, pmid = {40040609}, issn = {2198-3844}, support = {2023YFC2507803//Key Technologies Research and Development Program/ ; 82300149//National Natural Science Foundation of China/ ; 82130008//National Natural Science Foundation of China/ ; 82230004//National Natural Science Foundation of China/ ; 82350004//National Natural Science Foundation of China/ ; 82430006//National Natural Science Foundation of China/ ; 2024M761208//China Postdoctoral Science Foundation/ ; 2023ZB182//Department of Human Resources and Social Security of Jiangsu Province/ ; 2022-1-4082//Capital Health Research and Development of Special Fund/ ; 7242154//Natural Science Foundation of Beijing Municipality/ ; 7232188//Natural Science Foundation of Beijing Municipality/ ; 71003Y3035//Peking University Medicine/ ; }, abstract = {Corticosteroids (CSs) are the initial therapy for immune thrombocytopenia (ITP); however, their efficacy is not adequately predicted. As a novel biomarker, the composition of the gut microbiota is non-invasively tested and altered in patients with ITP. This study aims to develop a predictive model that leverages gut microbiome data to predict the CS response in patients with ITP within the initial four weeks of treatment. Metagenomic sequencing is performed on fecal samples from 212 patients with ITP, 152 of whom underwent CS treatment and follow-up. Predictive models are trained using six machine-learning algorithms, integrating clinical indices and gut microbiome data. The support vector machine (SVM) algorithm-based model has the highest accuracy (AUC = 0.80). This model utilized a comprehensive feature set that combined clinical data (including sex, age, duration, platelet count, and bleeding scales) with selected microbial species (including Bacteroides ovatus, Bacteroides xylanisolvens, and Parabacteroides gordonii), alpha diversities, KEGG pathways, and microbial modules. This study will provide new ideas for the prediction of clinical CS efficacy, enabling informed decision-making regarding the initiation of CS or personalized treatment in patients with ITP.}, }
@article {pmid40040568, year = {2025}, author = {Fatori, D and Shephard, E and Benette, D and Naspolini, NF and Guzman, GC and Wang, JYT and Tótolo, P and Mafra, AL and Isaias, C and Dos Santos, DP and Russo, FB and Kobayashi, G and Argeu, A and Teixeira, M and Mattiello-Sverzut, AC and Fernandes, MTB and Petian-Alonso, DC and Brentani, H and Scliar, M and Schüroff, PA and Zuccolo, P and Lerner, R and Geraldini, S and Euclydes, VLV and Matijasevich, A and de Campos, AC and de Carvalho, ACP and Fujita, A and Taddei, CR and Passos-Bueno, MR and Beltrão-Braga, P and Polanczyk, GV}, title = {Identifying biomarkers and trajectories of executive functions and language development in the first 3 years of life: Design, methods, and findings of the Germina cohort study.}, journal = {Development and psychopathology}, volume = {}, number = {}, pages = {1-11}, doi = {10.1017/S0954579425000069}, pmid = {40040568}, issn = {1469-2198}, abstract = {This paper reports the methods and preliminary findings of Germina, an ongoing cohort study to identify biomarkers and trajectories of executive functions and language development in the first 3 years of life. 557 mother-infant dyads (mean age of mothers 33.7 years, 65.2% white, 48.7% male infants) have undergone baseline and are currently collecting data for other timepoints. A linear regression was used to predict baseline Bayley-III using scores derived from data-driven sparse partial least squares utilizing a multiple holdout framework of 15 domains. Significant associations were found between socioeconomic/demographic characteristics (B = 0.29), epigenetics (B = 0.11), EEG theta (B = 0.14) and beta activity (B = 0.11), and microbiome functional pathways (B = 0.08) domains, and infant development measured by the Bayley-III at T1, suggesting potential interventions to prevent impairments.}, }
@article {pmid40040420, year = {2025}, author = {Díaz, GY and da Silva, VA and Kalantarnia, F and Scheck, K and Tschofen, SA and Tuffs, SW and Willerth, SM}, title = {Using Three-Dimensional Bioprinting to Generate Realistic Models of Wound Healing.}, journal = {Advances in wound care}, volume = {}, number = {}, pages = {}, doi = {10.1089/wound.2024.0138}, pmid = {40040420}, issn = {2162-1918}, abstract = {Significance: The skin serves as the primary defense against external stimuli, making it vulnerable to damage. Injuries can cause a dysregulated environment, resulting in chronic inflammation and inhibition of cell proliferation and migration, which delays recovery. Innovative approaches, such as three-dimensional (3D) bioprinting, can foster a controlled healing environment by promoting synergy between the skin microbiome and cells. Recent Advances: Traditional approaches to wound healing have focused on fostering an environment conducive to the interplay between cells, extracellular proteins, and growth factors. 3D bioprinting, a manufacturing technology with applications in tissue engineering, deposits biomaterial-based bioink containing living cells to fabricate custom-designed tissue scaffolds in a layer-by-layer fashion. This process controls the architecture and composition of a construct, producing multilayered and complex structures such as skin. Critical Issues: The selection of biomaterials for scaffolds has been a challenge when 3D skin tissue engineering. While prioritizing mechanical properties, current biomaterials often lack the ability to interact with environmental stimuli such as pH, temperature, or oxygen levels. Employing smart biomaterials that integrate bioactive molecules and adapt to external conditions could overcome these limitations. This innovation would enable scaffolds to create a sustainable wound-healing environment, fostering microbiome balance, reducing inflammation, and facilitating cellular recovery and tissue restoration, addressing critical gaps in existing wound care solutions. Future Directions: Novel bioink formulations for skin injury recovery are focused on improving long-term cell viability, proliferation, vascularization, and immune integration. Efficient recovery of the skin microbiome using bioactive molecules has the potential to create microenriched environments that support the recovery of the skin microbiome and restore immune regulation. This promising direction for future research aims to improve patient outcomes in wound care.}, }
@article {pmid40039328, year = {2024}, author = {Pillai, N and Nanduri, B and Rothrock, MJ and Chen, Z and Ramkumar, M}, title = {Bayesian-Guided Generation of Synthetic Microbiomes with Minimized Pathogenicity.}, journal = {Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference}, volume = {2024}, number = {}, pages = {1-7}, doi = {10.1109/EMBC53108.2024.10782111}, pmid = {40039328}, issn = {2694-0604}, mesh = {*Bayes Theorem ; *Microbiota ; Humans ; }, abstract = {Synthetic microbiomes offer new possibilities for modulating microbiota, to address the barriers in multidtug resistance (MDR) research. We present a Bayesian optimization approach to enable efficient searching over the space of synthetic microbiome variants to identify candidates predictive of reduced MDR. Microbiome datasets were encoded into a low-dimensional latent space using autoencoders. Sampling from this space allowed generation of synthetic microbiome signatures. Bayesian optimization was then implemented to select variants for biological screening to maximize identification of designs with restricted MDR pathogens based on minimal samples. Four acquisition functions were evaluated: expected improvement, upper confidence bound, Thompson sampling, and probability of improvement. Based on each strategy, synthetic samples were prioritized according to their MDR detection. Expected improvement, upper confidence bound, and probability of improvement consistently produced synthetic microbiome candidates with significantly fewer searches than Thompson sampling. By combining deep latent space mapping and Bayesian learning for efficient guided screening, this study demonstrated the feasibility of creating bespoke synthetic microbiomes with customized MDR profiles.}, }
@article {pmid40039168, year = {2024}, author = {Sudi, SD and Kolli, T and Porras, AM}, title = {Investigating the Impact of a Gut metabolite on Valvular Interstitial Cell Activation.}, journal = {Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference}, volume = {2024}, number = {}, pages = {1-4}, doi = {10.1109/EMBC53108.2024.10782721}, pmid = {40039168}, issn = {2694-0604}, mesh = {Animals ; *Methylamines/pharmacology/metabolism ; Swine ; *Aortic Valve/metabolism/pathology/cytology ; Female ; Male ; Calcinosis/metabolism ; Aortic Valve Stenosis/metabolism ; Gastrointestinal Microbiome ; }, abstract = {Calcified Aortic Valve Disease (CAVD) affects up to 13% of the U.S. population and is linked to diet-induced changes in metabolism. Recent studies suggest that the gut metabolite trimethyl amine oxide (TMAO) may be a biomarker for atherosclerosis. Given the shared risk factors between atherosclerosis and CAVD, we hypothesize that TMAO may contribute to CAVD by activating the primary cell type in the valve, valve interstitial cells (VIC). VICs are usually found in a quiescent phenotype in healthy valves; however, VICs isolated from porcine aortic valves exhibit spontaneous activation in traditional culture. Thus, to study VIC activation induced by exposure to TMAO, we first applied our lab-engineered protocol to generate quiescent VICs (qVICs). TMAO treatment led to qVIC activation, demonstrated by increased αSMA expression, proliferation, and angiogenic cytokine secretion after 3 days in culture. The response to TMAO was not sex-specific with both male and female VICs responding to treatment with this metabolite. These results demonstrate that TMAO, a gut microbiome-derived metabolite, promotes the activation of quiescent VICs toward a myofibroblastic phenotype in vitro, potentially contributing to the initiation of CAVD. Overall, these findings underscore the significance of host-microbe interactions in the progression of cardiovascular disease.}, }
@article {pmid40038838, year = {2025}, author = {Thiruppathy, D and Moyne, O and Marotz, C and Williams, M and Navarro, P and Zaramela, L and Zengler, K}, title = {Absolute quantification of the living skin microbiome overcomes relic-DNA bias and reveals specific patterns across volunteers.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {65}, pmid = {40038838}, issn = {2049-2618}, support = {S10 OD026929/NH/NIH HHS/United States ; S10 OD026929/NH/NIH HHS/United States ; }, mesh = {Humans ; *Skin/microbiology ; *Microbiota/genetics ; *DNA, Bacterial/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Bacterial Load ; Healthy Volunteers ; Adult ; Female ; Male ; }, abstract = {BACKGROUND: As the first line of defense against external pathogens, the skin and its resident microbiota are responsible for protection and eubiosis. Innovations in DNA sequencing have significantly increased our knowledge of the skin microbiome. However, current characterizations do not discriminate between DNA from live cells and remnant DNA from dead organisms (relic DNA), resulting in a combined readout of all microorganisms that were and are currently present on the skin rather than the actual living population of the microbiome. Additionally, most methods lack the capability for absolute quantification of the microbial load on the skin, complicating the extrapolation of clinically relevant information.<br><br>RESULTS: Here, we integrated relic-DNA depletion with shotgun metagenomics and bacterial load determination to quantify live bacterial cell abundances across different skin sites. Though we discovered up to 90% of microbial DNA from the skin to be relic DNA, we saw no significant effect of this on the relative abundances of taxa determined by shotgun sequencing. Relic-DNA depletion prior to sequencing strengthened underlying patterns between microbiomes across volunteers and reduced intraindividual similarity. We determined the absolute abundance and the fraction of population alive for several common skin taxa across body sites and found taxa-specific differential abundance of live bacteria across regions to be different from estimates generated by total DNA (live&#x2009;+&#x2009;dead) sequencing.<br><br>CONCLUSIONS: Our results reveal the significant bias relic DNA has on the quantification of low biomass samples like the skin. The reduced intraindividual similarity across samples following relic-DNA depletion highlights the bias introduced by traditional (total DNA) sequencing in diversity comparisons across samples. The divergent levels of cell viability measured across different skin sites, along with the inconsistencies in taxa differential abundance determined by total vs live cell DNA sequencing, suggest an important hypothesis for certain sites being susceptible to pathogen infection. Overall, our study demonstrates a characterization of the skin microbiome that overcomes relic-DNA bias to provide a baseline for live microbiota that will further improve mechanistic studies of infection, disease progression, and the design of therapies for the skin. Video Abstract.}, }
@article {pmid40038576, year = {2025}, author = {Jiang, K and Pang, X and Li, W and Xu, X and Yang, Y and Shang, C and Gao, X}, title = {Interbacterial warfare in the human gut: insights from Bacteroidales' perspective.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2473522}, doi = {10.1080/19490976.2025.2473522}, pmid = {40038576}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bacteroidetes/physiology/genetics ; Microbial Interactions/physiology ; Gastrointestinal Tract/microbiology ; Antibiosis/physiology ; Animals ; }, abstract = {Competition and cooperation are fundamental to the stability and evolution of ecological communities. The human gut microbiota, a dense and complex microbial ecosystem, plays a critical role in the host's health and disease, with competitive interactions being particularly significant. As a dominant and extensively studied group in the human gut, Bacteroidales serves as a successful model system for understanding these intricate dynamic processes. This review summarizes recent advances in our understanding of the intricate antagonism mechanisms among gut Bacteroidales at the biochemical or molecular-genetic levels, focusing on interference and exploitation competition. We also discuss unresolved questions and suggest strategies for studying the competitive mechanisms of Bacteroidales. The review presented here offers valuable insights into the molecular basis of bacterial antagonism in the human gut and may inform strategies for manipulating the microbiome to benefit human health.}, }
@article {pmid40038319, year = {2025}, author = {Chen, H and Qi, T and Guo, S and Zhang, X and Zhan, M and Liu, S and Yin, Y and Guo, Y and Zhang, Y and Zhao, C and Wang, X and Wang, H}, title = {Publisher Correction: Integrating respiratory microbiome and host immune response through machine learning for respiratory tract infection diagnosis.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {39}, doi = {10.1038/s41522-025-00658-1}, pmid = {40038319}, issn = {2055-5008}, }
@article {pmid40038317, year = {2025}, author = {Kim, HS and Lee, JY and Whon, TW and Bae, JW}, title = {Assembly and maturation of calf gut microbiome from neonate to post-puberty.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {376}, pmid = {40038317}, issn = {2052-4463}, support = {22213MFDS537//Ministry of Food and Drug Safety (MFDS)/ ; RS-2023-00227274//National Research Foundation of Korea (NRF)/ ; 2020R1A2C3012797//National Research Foundation of Korea (NRF)/ ; RS-2021-NR061913//National Research Foundation of Korea (NRF)/ ; KE2401-1-1//World Institute of Kimchi (WIK)/ ; }, mesh = {Animals ; Cattle/microbiology ; *Gastrointestinal Microbiome ; *RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Rumen/microbiology ; Animals, Newborn ; }, abstract = {With the help of rumen bacteria, ruminants can feed on indigestible plant materials and produce over 70% of their energy as fatty acids. However, during lactation, ruminants exhibit characteristics of monogastric animals due to an undeveloped rumen; therefore, understanding gut microbiome changes in growing calves is essential. Our understanding of the gut microbiome in growing calves remains limited in large populations with the same diet, breed, and period. Here, we describe 16S rRNA gene amplicon sequencing data from 420 faecal samples, 20 rumen contents, 17 small intestine contents, and 18 large intestine contents collected from 57 healthy, antibiotic-free Korean beef cattle from neonatal to post-pubertal age. Eight 16S rRNA gene amplicon datasets from the host diet samples were obtained. Approximately 148 million raw reads, averaging 153,352 ± 96,050 (mean ± SD) reads per sample, and 51,596 unique amplicon sequence variants (381-368 per sample) were identified in the 483 samples. These shareable datasets can be reused by researchers to assess gut microbiome-related functions in growing calves and improve ruminant production and health.}, }
@article {pmid40038315, year = {2025}, author = {Chen, Y and Chen, S and Tao, J and Li, M and Wang, W and Chen, M and Fang, X and Kong, L and Wang, Y and Pereira, O and Zhang, C}, title = {Multi-omic stock of surface ocean microbiome built by monthly, weekly and daily sampling in Dapeng Bay, China.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {378}, pmid = {40038315}, issn = {2052-4463}, support = {32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; RCBS20221008093229035//Shenzhen Science and Technology Innovation Commission/ ; 92351301//&#xc9;cole Nationale d'Ing&#xe9;nieurs de Saint-Etienne (National Engineering School of Saint-&#xc9;tienne)/ ; }, mesh = {China ; *Microbiota ; *Archaea/genetics ; *Bacteria/genetics/classification ; *Bays ; Seawater/microbiology ; Metagenome ; Multiomics ; }, abstract = {The coastal ocean is the dynamic interface where terrestrial, atmospheric, and marine systems converge, acting as a hotspot for microbial activity, which underpins the intricate web of carbon and nitrogen cycling. Dapeng Bay, a typical semi-enclosed bay along the southern coastline of China, is strongly influenced by monsoon climates and human activities. Despite its ecological importance, long-term observations and investigations into the microbial community structure in this region are notably lacking. To address this gap, we conducted a two-year continuous sampling from May 2021 to June 2023 to explore shifts in nearshore surface microbial communities and assess the long-term effects of environmental stressors. This study presents comprehensive amplicon, metagenomic, and metatranscriptomic information. We identified 3,600 amplicon sequence variants and recovered 1,216 high-quality metagenome-assembled MAGs, representing 17 bacterial and 3 archaeal phyla. Additionally, 587 MAGs were correlated with transcriptional activity, comprising 539 bacterial and 48 archaeal populations. This dataset is anticipated to provide a multi-dimensional perspective, enhancing our understanding of the complexity, dynamics, and adaptability of microbial communities in coastal environments.}, }
@article {pmid40038269, year = {2025}, author = {Lee, JW and Lee, KA and Jang, IH and Nam, K and Kim, SH and Kyung, M and Cho, KC and Lee, JH and You, H and Kim, EK and Koh, YH and Lee, H and Park, J and Hwang, SY and Chung, YW and Ryu, CM and Kwon, Y and Roh, SH and Ryu, JH and Lee, WJ}, title = {Microbiome-emitted scents activate olfactory neuron-independent airway-gut-brain axis to promote host growth in Drosophila.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2199}, pmid = {40038269}, issn = {2041-1723}, support = {RS-2024-00345184//National Research Foundation of Korea (NRF)/ ; RS-2022-NR067345//National Research Foundation of Korea (NRF)/ ; }, mesh = {Animals ; *Drosophila melanogaster/microbiology/growth &amp; development ; *Microbiota ; *Drosophila Proteins/metabolism/genetics ; *Olfactory Receptor Neurons/metabolism ; Brain-Gut Axis/physiology ; Signal Transduction ; Smell/physiology ; Odorants ; Brain/metabolism/growth &amp; development ; Trachea/microbiology/metabolism ; Drosophila/microbiology ; }, abstract = {While it is now accepted that the microbiome has strong impacts on animal growth promotion, the exact mechanism has remained elusive. Here we show that microbiome-emitted scents contain volatile somatotrophic factors (VSFs), which promote host growth in an olfaction-independent manner in Drosophila. We found that inhaled VSFs are readily sensed by olfactory receptor 42b non-neuronally expressed in subsets of tracheal airway cells, enteroendocrine cells, and enterocytes. Olfaction-independent sensing of VSFs activates the airway-gut-brain axis by regulating Hippo, FGF and insulin-like growth factor signaling pathways, which are required for airway branching, organ oxygenation and body growth. We found that a mutant microbiome that did not produce (2R,3R)-2,3-butanediol failed to activate the airway-gut-brain axis for host growth. Importantly, forced inhalation of (2R,3R)-2,3-butanediol completely reversed these defects. Our discovery of contact-independent and olfaction-independent airborne interactions between host and microbiome provides a novel perspective on the role of the airway-gut-brain axis in microbiome-controlled host development.}, }
@article {pmid40038204, year = {2025}, author = {Stout, J and Austin, K and Bonnes, S and DuBroff, J and Muratore, A}, title = {Celiac Disease and Gluten Cross-Contact: How Much is too Much?.}, journal = {Current nutrition reports}, volume = {14}, number = {1}, pages = {41}, pmid = {40038204}, issn = {2161-3311}, mesh = {*Celiac Disease/diet therapy ; Humans ; *Glutens/adverse effects ; *Diet, Gluten-Free ; *Intestine, Small ; Gastrointestinal Microbiome ; Quality of Life ; }, abstract = {PURPOSE OF REVIEW: This review aimed to examine the variability in the susceptibility of the small intestine to injury when exposed to gluten among patients with celiac disease, particularly in the context of gluten cross-contact. It sought to address whether clinicians could recommend individualized gluten exposure levels based on current research to improve patient outcomes and quality of life, given the difficulties of maintaining a strict gluten-free diet.<br><br>RECENT FINDINGS: While some evidence suggests variability in small intestine susceptibility to injury, no current studies offer a reliable method for clinicians to stratify patients or recommend safe gluten levels. Research points to possible roles of the microbiome and immune responses in susceptibility to injury, though no definitive conclusions have been made. There is insufficient evidence to safely recommend varying gluten thresholds for celiac patients. While factors like the microbiome and cytokine responses may influence the small intestine's susceptibility to injury when exposed to gluten, the recommendation of a strict gluten-free diet remains the best approach until more conclusive research emerges. Future studies may help tailor dietary advice and improve quality of life for individuals with celiac disease.}, }
@article {pmid40038157, year = {2025}, author = {Prescott, J and Keyser, AJ and Litwin, P and Dunbar, MD and McClelland, R and Ruple, A and Ernst, H and Butler, BL and Kauffman, M and Avery, A and Harrison, BR and Partida-Aguilar, M and McCoy, BM and Slikas, E and Greenier, AK and Muller, E and Algavi, YM and Bamberger, T and Creevy, KE and ,  and Borenstein, E and Snyder-Mackler, N and Promislow, DEL}, title = {Rationale and design of the Dog Aging Project precision cohort: a multi-omic resource for longitudinal research in geroscience.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {40038157}, issn = {2509-2723}, support = {AG057377/AG/NIA NIH HHS/United States ; USDA/ARS 58-8050-9-004//U.S. Department of Agriculture/ ; }, abstract = {A significant challenge in multi-omic geroscience research is the collection of high quality, fit-for-purpose biospecimens from a diverse and well-characterized study population with sufficient sample size to detect age-related changes in physiological biomarkers. The Dog Aging Project designed the precision cohort to study the mechanisms underlying age-related change in the metabolome, microbiome, and epigenome in companion dogs, an emerging model system for translational geroscience research. One thousand dog-owner pairs were recruited into cohort strata based on life stage, sex, size, and geography. We designed and built a novel implementation of the REDCap electronic data capture system to manage study participants, logistics, and biospecimen and survey data collection in a secure online platform. In collaboration with primary care veterinarians, we collected and processed blood, urine, fecal, and hair samples from 976 dogs. The resulting data include complete blood count, chemistry profile, immunophenotyping by flow cytometry, metabolite quantification, fecal microbiome characterization, epigenomic profile, urinalysis, and associated metadata characterizing sample conditions at collection and during lab processing. The project, which has already begun collecting second- and third-year samples from precision cohort dogs, demonstrates that scientifically useful biospecimens can be collected from a geographically dispersed population through collaboration with private veterinary clinics and downstream labs. The data collection infrastructure developed for the precision cohort can be leveraged for future studies. Most important, the Dog Aging Project is an open data project. We encourage researchers around the world to apply for data access and utilize this rich, constantly growing dataset in their own work.}, }
@article {pmid40037974, year = {2025}, author = {Zattoni, F and Novara, G and Dal Moro, F and Tandogdu, Z}, title = {Prostate Biopsy: The Transperineal Approach is Better!.}, journal = {European urology focus}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.euf.2025.02.011}, pmid = {40037974}, issn = {2405-4569}, abstract = {Transperineal prostate biopsy offers advantages over transrectal biopsy in terms of cancer detection in specific prostate areas, potential use of larger-gauge needles for tissue sampling, a lower risk of severe infectious complications such as sepsis, and lower use of antibiotic prophylaxis, aligning with antibiotic stewardship policies and reducing the risk of antimicrobial resistance and gut microbiome changes.}, }
@article {pmid40037972, year = {2025}, author = {Zattoni, F and Novara, G and Dal Moro, F and Tandogdu, Z}, title = {Prostate Biopsy: The Transperineal Approach Is Better!.}, journal = {European urology focus}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.euf.2025.02.014}, pmid = {40037972}, issn = {2405-4569}, abstract = {Transperineal prostate biopsy offers advantages over transrectal biopsy in terms of cancer detection in specific prostate areas, potential use of larger-gauge needles for tissue sampling, a lower risk of severe infectious complications such as sepsis, and lower use of antibiotic prophylaxis, aligning with antibiotic stewardship policies and reducing the risk of antimicrobial resistance and gut microbiome changes.}, }
@article {pmid40037901, year = {2025}, author = {Williamson, E and Hill, K and Hogendoorn, K and Eisenhofer, R}, title = {The bacterial community associated with the solitary resin bee Megachile tosticauda throughout its life cycle.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf023}, pmid = {40037901}, issn = {1574-6941}, abstract = {Unlike in eusocial bees where the identity, acquisition and function of symbiotic microbes is well understood, little is known about the relationships formed between solitary bees and bacteria. Assessing the potential role of microbes in solitary bee health is important, especially in the face of global bee declines. Early evidence suggests solitary bee microbiomes differ between bee species and development stages, but the reported bacteria are often indistinguishable from environmental taxa. Here, we use metabarcoding of the 16S rRNA gene to characterise the bacterial communities associated with solitary resin bee Megachile tosticauda. We describe the microbiome at different lifecycle stages, and within pollen provisions, and investigate indirect inheritance from nesting substrate upon eclosion. The microbiome of adult M. tosticauda was consistent between samples, and the bacterial composition of larval pollen supplies changed with progressing larval development. In wild adults and pollen provisions, the genus Acinetobacter - a common nectar associate - dominated the communities. In prepupae and frass Tyzzerella dominated, a genus that has been found in a number of other immature bee systems. Intriguingly, while wild adults did not harbour Tyzzerella, all bees that had newly emerged from the nest did. The combined observations show that M. tosticauda acquire their bacterial community from the environment, and Tyzzerella may represent a beneficial symbiont for mature brood.}, }
@article {pmid40037603, year = {2025}, author = {Farrer, EC and Kulick, NK and Birnbaum, C and Halbrook, S and Bumby, CR and Willis, C}, title = {Environmental and host plant effects on taxonomic and phylogenetic diversity of root fungal endophytes.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf030}, pmid = {40037603}, issn = {1574-6968}, abstract = {Nearly all plants are colonized by fungal endophytes, and a growing body of work shows that both environment and host species shape plant-associated fungal communities. However, few studies place their work in a phylogenetic context to understand endophyte community assembly through an evolutionary lens. Here we investigated environmental and host effects on root endophyte assemblages in coastal Louisiana marshes. We isolated and sequenced culturable fungal endophytes from roots of three-four dominant plant species from each of three sites of varying salinity. We assessed taxonomic diversity and composition as well as phylogenetic diversity (mean phylogenetic distance, MPD) and phylogenetic composition (based on MPD). When we analyzed plant hosts present across the entire gradient, we found that the effect of environment on phylogenetic diversity (as measured by MPD) was host dependent and suggested phylogenetic clustering in some circumstances. We found that both environment and host plant affected taxonomic composition of fungal endophytes, but only host plant affected phylogenetic composition; suggesting different host plants selected for fungal taxa drawn from distinct phylogenetic clades whereas environmental assemblages were drawn from similar clades. Our study demonstrates that including phylogenetic, as well as taxonomic, community metrics can provide a deeper understanding of community assembly in endophytes.}, }
@article {pmid40037574, year = {2025}, author = {Gu, Y and Yan, W and Chen, Y and Liu, S and Sun, L and Zhang, Z and Lei, P and Wang, R and Li, S and Banerjee, S and Friman, VP and Xu, H}, title = {Plant growth-promotion triggered by extracellular polymer is associated with facilitation of bacterial cross-feeding networks of the rhizosphere.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf040}, pmid = {40037574}, issn = {1751-7370}, abstract = {Despite the critical role rhizosphere microbiomes play in plant growth, manipulating microbial communities for improved plant productivity remains challenging. One reason for this is the lack of knowledge on how complex substrates secreted in the microbiome ultimately shape the microbe-microbe and plant-microbe interaction in relation to plant growth. One such complex substrate is poly-γ-glutamic acid, which is a microbially derived extracellular polymer. While it has previously been linked with plant growth-promotion, the underlying mechanisms are not well understood. Here we show that this compound benefits plants by fostering cross-feeding networks between rhizosphere bacteria. We first experimentally demonstrate that poly-γ-glutamic acid application increases potassium bioavailability for tomato plants by driving a shift in the rhizosphere bacterial community composition. Specifically, application of poly-γ-glutamic acid increased the relative abundance of Pseudomonas nitroreducens L16 and Pseudomonas monteilii L20 bacteria which both promoted tomato potassium assimilation by secreting potassium-solubilizing pyruvic acid and potassium-chelating siderophores, respectively. Although either Pseudomonas strain could not metabolize poly-γ-glutamic acid directly, the application of poly-γ-glutamic acid promoted the growth of Bacillus species, which in turn produced metabolites that could promote the growth of both P. nitroreducens L16 and P. monteilii L20. Moreover, the P. monteilii L20 produced 3-hydroxycapric acid, which could promote the growth of P. nitroreducens L16, resulting in commensal cross-feeding interaction between plant growth-promoting bacteria. Together, these results show that poly-γ-glutamic acid plays a crucial role in driving plant growth-promotion via bacterial cross-feeding networks, highlighting the opportunity for using microbially derived, complex substrates as catalysts to increase agricultural productivity.}, }
@article {pmid40037564, year = {2025}, author = {Miller, SJ and Zhang, F and Taylor, S and Woodman, R and Shoubridge, AP and Papanicolas, LE and Rogers, GB}, title = {Oropharyngeal Staphylococcus aureus is linked to higher mortality in long-term aged care residents.}, journal = {Age and ageing}, volume = {54}, number = {3}, pages = {}, doi = {10.1093/ageing/afaf042}, pmid = {40037564}, issn = {1468-2834}, support = {//Australian Medical Research Future Fund/ ; GNT1152268//Australian Department of Health/ ; //Australian Department of Health/ ; GNT119378//National Health and Medical Research Council/ ; //Matthew Flinders Professorial Fellowship/ ; GNT2008625//NHMRC Emerging Leadership/ ; }, mesh = {Humans ; Male ; Female ; *Staphylococcal Infections/mortality/microbiology/diagnosis ; Aged, 80 and over ; Aged ; *Staphylococcus aureus/isolation &amp; purification ; *Oropharynx/microbiology ; *Homes for the Aged/statistics &amp; numerical data ; Risk Factors ; South Australia/epidemiology ; Nursing Homes/statistics &amp; numerical data ; Age Factors ; Long-Term Care/statistics &amp; numerical data ; Carrier State/microbiology/diagnosis ; Time Factors ; Metagenomics ; Microbiota ; Comorbidity ; Cause of Death ; Risk Assessment ; Methicillin-Resistant Staphylococcus aureus/isolation &amp; purification ; }, abstract = {BACKGROUND: Biological ageing, healthcare interactions, and pharmaceutical and environmental exposures in later life alter the characteristics of the oropharyngeal (OP) microbiome. These changes, including an increased susceptibility to colonisation by pathobiont species, have been linked with diverse health outcomes.<br><br>OBJECTIVES: To investigate the relationship between OP microbiome characteristics and all-cause mortality in long-term aged care residents.<br><br>METHODS: OP swabs were collected from 190 residents of five aged care facilities in South Australia. Microbiota composition was assessed by shotgun metagenomics and related to health outcomes during a 12-month follow-up period. OP carriage of Staphylococcus aureus and methicillin resistance was confirmed by qPCR.<br><br>RESULTS: OP carriage of S. aureus was identified in 13 (6.8%) residents. Detection of S. aureus was significantly associated with an increased risk of mortality (adjusted HR [95% CI]: 9.7 [3.8-24.9], P&#x2009;<&#x2009;.0001), compared with non-carriers, independent of methicillin resistance. Staphylococcus aureus carriage demonstrated a stronger association with mortality risk than the total number of comorbidities at the univariate level (S. aureus HR [95% CI]: 7.2 [3.4-15.5], P&#x2009;<&#x2009;.0001 vs. comorbidity count HR [95% CI]: 1.1 [1.0-1.3], P&#x2009;=&#x2009;.03), and remained significant after multivariable adjustment. Staphylococcus aureus detection was significantly associated with total number of comorbidities (adjusted OR [95% CI]: 1.4 [1.0-2.0], P&#x2009;=&#x2009;.04).<br><br>CONCLUSION: OP S. aureus carriage predicts all-cause mortality in long-term aged care. We speculate that S. aureus carriage represents a marker of general health, including prior healthcare exposures. OP S. aureus carriage could contribute to estimations of general health in older individuals and thereby inform care strategies.}, }
@article {pmid40037530, year = {2025}, author = {Koceva, H and Amiratashani, M and Akbarimoghaddam, P and Hoffmann, B and Zhurgenbayeva, G and Gresnigt, MS and Marcelino, VR and Eggeling, C and Figge, MT and Amorim, MJ and Mosig, AS}, title = {Deciphering respiratory viral infections by harnessing organ-on-chip technology to explore the gut-lung axis.}, journal = {Open biology}, volume = {15}, number = {3}, pages = {240231}, doi = {10.1098/rsob.240231}, pmid = {40037530}, issn = {2046-2441}, support = {//BMBF/ ; //Leibniz Center for Photonics/ ; //FSU/ ; //European Research Council (ERC)/ ; //European Union/ ; //Innovative Medicines Initiative/ ; //EFPIA/ ; //DFG, German Research Foundation/ ; //DFG/ ; //Germany&#xb4;s Excellence Strategy/ ; //Australian Research Council/ ; //Deutsche Forschungsgemeinschaft/ ; //M-M-M/ ; //Microverse Imaging Center/ ; }, mesh = {Humans ; *Lung/virology/microbiology ; *Respiratory Tract Infections/virology/microbiology ; Lab-On-A-Chip Devices ; SARS-CoV-2/physiology ; COVID-19/virology ; Animals ; Microbiota ; Gastrointestinal Microbiome ; }, abstract = {The lung microbiome has recently gained attention for potentially affecting respiratory viral infections, including influenza A virus, respiratory syncytial virus (RSV) and SARS-CoV-2. We will discuss the complexities of the lung microenvironment in the context of viral infections and the use of organ-on-chip (OoC) models in replicating the respiratory tract milieu to aid in understanding the role of temporary microbial colonization. Leveraging the innovative capabilities of OoC, particularly through integrating gut and lung models, opens new avenues to understand the mechanisms linking inter-organ crosstalk and respiratory infections. We will discuss technical aspects of OoC lung models, ranging from the selection of cell substrates for extracellular matrix mimicry, mechanical strain, breathing mechanisms and air-liquid interface to the integration of immune cells and use of microscopy tools for algorithm-based image analysis and systems biology to study viral infection in vitro. OoC offers exciting new options to study viral infections across host species and to investigate human cellular physiology at a personalized level. This review bridges the gap between complex biological phenomena and the technical prowess of OoC models, providing a comprehensive roadmap for researchers in the field.}, }
@article {pmid40037519, year = {2025}, author = {Jawale, N and Shenberger, J and Rodriguez, R and Shetty, AK and Garg, PM}, title = {The non-bacterial infant microbiome and necrotizing enterocolitis.}, journal = {American journal of perinatology}, volume = {}, number = {}, pages = {}, doi = {10.1055/a-2549-6551}, pmid = {40037519}, issn = {1098-8785}, support = {U54GM115428/GM/NIGMS NIH HHS/United States ; }, abstract = {Necrotizing enterocolitis (NEC) is among the most devastating neonatal illnesses of premature infants. Although it is a disease of multifactorial etiology associated with bacterial dysbiosis, several reports of viral and some fungal infections associated with NEC have been published. Despite the abundance of viruses - primarily bacteriophages, and 'virus-like particles' in the normal infant gut flora, there is limited understanding of the contribution of these elements to newborn gut health and disease. This article aims to review existing evidence on normal newborn virome and mycobiome development, and present insights into the complex inter kingdom interactions between gut bacteria, viruses and fungi in the intestinal ecosystem, exploring their potential role in predisposing the preterm infant to NEC.}, }
@article {pmid40037494, year = {2025}, author = {Sorbara, NT and Black, AKA and Bearne, SL}, title = {Bulky substrates of isoleucine 2-epimerase: α-Neopentylglycine and NV-5138.}, journal = {Bioorganic &amp; medicinal chemistry letters}, volume = {}, number = {}, pages = {130160}, doi = {10.1016/j.bmcl.2025.130160}, pmid = {40037494}, issn = {1464-3405}, abstract = {Isoleucine 2-epimerase from Lactobacillus buchneri (LbIleE) catalyzes the pyridoxal 5'-phosphate-dependent, reversible, racemization or epimerization of nonpolar amino acids at the C-2 position. The integral role of the enzyme in the biosynthesis of branched-chain d-amino acids makes it a potential target for the development of antimicrobial agents. Probing the hydrophobic active-site pocket with a series of alkyl boronic acids, we show that the hydrophobic pocket accommodates the neopentyl group with enhanced binding affinity relative to the sec-butyl group. Subsequently, we show that LbIleE catalyzes the racemization of l- and d-α-neopentylglycine, exhibiting binding affinities for these substrates 6- and 24-fold greater than those for l-Ile and d-allo-Ile, but with catalytic efficiencies (kcat/Km) reduced 46- and 27-fold, respectively. NV-5138 is a ligand of the leucine-binding site of Sestrin2, which activates the mechanistic target of rapamycin complex1 (mTORC1) and is structurally similar to α-neopentylglycine. Our demonstration that LbIleE catalyzes the racemization of l-NV-5138 (kcat/Km = 2.2 ± 0.2 s[-1] M[-1]), along with the fact that L. buchneri can be present in the human gut microbiome, suggests that formation of d-NV-5138 could occur in humans when l-NV-5138 is used as a pharmacological intervention for depression.}, }
@article {pmid40037471, year = {2025}, author = {Iban-Arias, R and Portela, ASD and Masieri, S and Radu, A and Yang, EJ and Chen, LC and Gordon, T and Pasinetti, GM}, title = {Role of acute exposure to environmental stressors in the gut-brain-periphery axis in the presence of cognitive resilience.}, journal = {Biochimica et biophysica acta. Molecular basis of disease}, volume = {}, number = {}, pages = {167760}, doi = {10.1016/j.bbadis.2025.167760}, pmid = {40037471}, issn = {1879-260X}, abstract = {Climate change-induced environmental stressors, including ambient particulate matter (PM2.5) and extreme heat stress (HS), pose serious health risks, particularly for neurodegenerative diseases. PM2.5 exacerbates cardiovascular and neurodegenerative conditions, while HS increases mortality and worsens air pollution. Combined exposure may amplify these effects, especially in vulnerable populations at risk for Alzheimer's disease (AD). In our experimental study using a mouse model of early-onset Alzheimer's disease (EOAD), we explored the combined effects of extreme weather conditions, particularly exposure to ambient PM2.5 and HS. Our research indicated that even short, repeated exposure to these environmental stressors disrupts brain energy metabolism and mitochondrial respiratory functions, which we found to be associated with altered hippocampal synaptic functions. Additionally, we find that key mechanisms associated with impaired intestinal permeability and gut dysbiosis are affected, supporting the hypothesis that exposure to climate change communication may also disrupt the gut-brain axis, as in part evidenced in our study by peripheral changes in immune and inflammatory signaling. Moreover, despite significant disruptions in metabolic and immune-inflammatory pathways, we observed no acceleration of cognitive decline in the young asymptomatic EOAD mice subjected to short, repeated exposure to extreme heat and environmental PM2.5. These findings highlight the potential role of climate change in promoting risk factors like neuroinflammation and gut-brain axis dysfunction due to gut microbiome dysbiosis in the onset and progression of AD, particularly in asymptomatic individuals at risk for developing the condition.}, }
@article {pmid40037444, year = {2025}, author = {Zhang, L and Li, G and Li, S and Zhou, Y and Zhao, M and Su, L and Liu, X and Yang, X and Zhao, Y}, title = {Overexpressing mannose-binding Lectin (NTL) protein affects sugarcane physiological status and increase its resistance to aphids (Ceratovacuna langigera).}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {141636}, doi = {10.1016/j.ijbiomac.2025.141636}, pmid = {40037444}, issn = {1879-0003}, abstract = {Narcissus tazetta Lectin (NTL) is a mannose-binding protein, known for its resistance to aphid (Ceratovacuna langigera). However, the mechanism underlying NTL-enhanced plant resistance to aphid remains elusive. Here, we produced NTL-overexpressing (NTL-OE) sugarcane lines that showed strong resistance to aphid. Overexpression of NTL gene led to reduction of total soluble sugar content, sucrose content, fructose content, soluble protein content, and most amino acid levels in sugarcane sap. Transcriptomic analysis and pathway annotation revealed significant role of plant hormone signal transduction, amino acid metabolism, photosynthesis-related pathways, and carbohydrate metabolism. Association analysis of the transcriptome and microbiome of NTL-OE plant fed aphids showed the significance of Christensenellaceae family in sugar-related metabolic regulation and Buchnera in amino acid-related metabolic regulation, which corroborated the essential role of sugars and amino acids in aphid survival. Correlation analysis between NTL-overexpressing sugarcane and aphid transcriptome discovered gene modules related to plant hormone signaling, amino acid metabolism, photosynthesis-related pathways, and sugar metabolism. Taken together, sugars and amino acids that were impacted by NTL protein overexpression in sugarcane sap were suggested to be critical for fed aphids' survival. Notably, HSP70 gene was up-regulated in both NTL-OE sugarcane and fed aphids that requires further investigation. This study suggested the role of NTL protein in plant resistance to aphids, offering new insights for mechanisms underlying NTL-enhanced plant resistance.}, }
@article {pmid40037353, year = {2025}, author = {Tian, S and Kim, MS and Zhao, J and Heber, K and Hao, F and Koslicki, D and Tian, S and Singh, V and Patterson, AD and Bisanz, JE}, title = {A designed synthetic microbiota provides insight to community function in Clostridioides difficile resistance.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2025.02.007}, pmid = {40037353}, issn = {1934-6069}, abstract = {Clostridioides difficile, a major cause of antibiotic-associated diarrhea, is suppressed by the gut microbiome, but the precise mechanisms are not fully described. Through a meta-analysis of 12 human studies, we designed a synthetic fecal microbiota transplant (sFMT1) by reconstructing microbial networks negatively associated with C. difficile colonization. This lab-built 37-strain consortium formed a functional community suppressing C. difficile in vitro and in animal models. Using sFMT1 as a tractable model system, we find that bile acid 7α-dehydroxylation is not a determinant of sFMT1 efficacy while one strain performing Stickland fermentation-a pathway of competitive nutrient utilization-is both necessary and sufficient for the suppression of C. difficile, replicating the efficacy of a human fecal transplant in a gnotobiotic mouse model. Our data illustrate the significance of nutrient competition in suppression of C. difficile and a generalizable approach to interrogating complex community function through robust methods to leverage publicly available sequencing data.}, }
@article {pmid40037329, year = {2025}, author = {Van Gerwen, OT and Aaron, KJ and Kay, ES and Siwakoti, K and Pontius, A and Richter, S and Sherman, ZA and Graves, KJ and Tamhane, A and Elnaggar, JH and Luo, M and Toh, E and Nelson, DE and Van Wagoner, NJ and Taylor, CM and Muzny, CA}, title = {The Impact of Testosterone Therapy on the Vaginal Microbiota of Transgender Men and Non-Binary People: A Prospective Study.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiaf114}, pmid = {40037329}, issn = {1537-6613}, abstract = {BACKGROUND: Understanding the impact of testosterone on the vaginal microbiota of transgender men (TGM) and non-binary people assigned female sex at birth over time is imperative as vaginal dysbiosis and incident bacterial vaginosis (iBV) may cause bothersome genital symptoms and increase HIV/STI acquisition risk. We investigated shifts in the composition of the vaginal microbiota over time in TGM initiating testosterone for gender-affirming hormone therapy, including development of vaginal dysbiosis and iBV.<br><br>METHODS: Participants ages &#x2265;18 years, assigned female sex at birth and reporting TGM or non-binary identity, interested in starting injectable testosterone, demonstrating optimal vaginal microbiota, with no current STI(s) were enrolled. Participants self-collected daily vaginal specimens for 7 days prior to testosterone initiation and 90 days thereafter for vaginal Gram staining and 16S rRNA gene sequencing. Episodes of vaginal dysbiosis and iBV were defined as Nugent scores &#x2265;4 or &#x2265;7, respectively, each for &#x2265;2 consecutive days.<br><br>RESULTS: Between February 2022-November 2023, 9 participants enrolled, 89% (8/9) developed &#x2265;1 episode(s) of vaginal dysbiosis after testosterone initiation, and 56% (5/9) developed iBV. Among those who developed iBV, most did so between days 20-40 after testosterone initiation. Community state type (CST) I was found most often in participants who did not develop iBV and CST IV-B most often in participants who developed iBV. Sexual activity and menses also appeared to influence the development of iBV.<br><br>CONCLUSION: The majority of participants developed vaginal dysbiosis including iBV.. Additional studies with larger sample sizes are needed to further elucidate how testosterone impacts the vaginal microbiota.}, }
@article {pmid40037297, year = {2025}, author = {Chao, J and Coleman, RA and Keating, DJ and Martin, AM}, title = {Gut Microbiome Regulation of Gut Hormone Secretion.}, journal = {Endocrinology}, volume = {166}, number = {4}, pages = {}, doi = {10.1210/endocr/bqaf004}, pmid = {40037297}, issn = {1945-7170}, support = {DE220100403//Alyce Martin from the Australian Research Council/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Enteroendocrine Cells/metabolism ; Animals ; Gastrointestinal Hormones/metabolism ; }, abstract = {The gut microbiome, comprising bacteria, viruses, fungi, and bacteriophages, is one of the largest microbial ecosystems in the human body and plays a crucial role in various physiological processes. This review explores the interaction between the gut microbiome and enteroendocrine cells (EECs), specialized hormone-secreting cells within the intestinal epithelium. EECs, which constitute less than 1% of intestinal epithelial cells, are key regulators of gut-brain communication, energy metabolism, gut motility, and satiety. Recent evidence shows that gut microbiota directly influence EEC function, maturation, and hormone secretion. For instance, commensal bacteria regulate the production of hormones like glucagon-like peptide 1 and peptide YY by modulating gene expression and vesicle cycling in EE cells. Additionally, metabolites such as short-chain fatty acids, derived from microbial fermentation, play a central role in regulating EEC signaling pathways that affect metabolism, gut motility, and immune responses. Furthermore, the interplay between gut microbiota, EECs, and metabolic diseases, such as obesity and diabetes, is examined, emphasizing the microbiome's dual role in promoting health and contributing to disease states. This intricate relationship between the gut microbiome and EECs offers new insights into potential therapeutic strategies for metabolic and gut disorders.}, }
@article {pmid40037293, year = {2025}, author = {Delherbe, NA and Gomez, O and Plominsky, AM and Oliver, A and Manzanera, M and Kalyuzhnaya, MG}, title = {Atmospheric methane consumption in arid ecosystems acts as a reverse chimney and is accelerated by plant-methanotroph biomes.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf026}, pmid = {40037293}, issn = {1751-7370}, abstract = {Drylands cover one-third of the Earth's surface and are one of the largest terrestrial sinks for methane. Understanding the structure-function interplay between members of arid biomes can provide critical insights into mechanisms of resilience toward anthropogenic and climate-change-driven environmental stressors-water scarcity, heatwaves, and increased atmospheric greenhouse gases. This study integrates in situ measurements with culture-independent and enrichment-based investigations of methane-consuming microbiomes inhabiting soil in the Anza-Borrego Desert, a model arid ecosystem in Southern California, United States. The atmospheric methane consumption ranged between 2.26 to 12.73 μmol m2 h-1, peaking during the daytime at vegetated sites. Metagenomic studies revealed similar soil-microbiome compositions at vegetated and unvegetated sites, with Methylocaldum being the major methanotrophic clade. Eighty-four metagenome-assembled genomes were recovered, six represented by methanotrophic bacteria (three Methylocaldum, two Methylobacter, and uncultivated Methylococcaceae). The prevalence of copper-containing methane monooxygenases in metagenomic datasets suggests a diverse potential for methane oxidation in canonical methanotrophs and uncultivated Gammaproteobacteria. Five pure cultures of methanotrophic bacteria were obtained, including four Methylocaldum. Genomic analysis of Methylocaldum isolates and metagenome-assembled genomes revealed the presence of multiple stand-alone methane monooxygenase subunit C paralogs, which may have functions beyond methane oxidation. Furthermore, these methanotrophs have genetic signatures typically linked to symbiotic interactions with plants, including tryptophan synthesis and indole-3-acetic acid production. Based on in situ fluxes and soil microbiome compositions, we propose the existence of arid-soil reverse chimneys, an empowered methane sink represented by yet-to-be-defined cooperation between desert vegetation and methane-consuming microbiomes.}, }
@article {pmid40037197, year = {2025}, author = {Abelouah, MR and Idbella, M and Nouj, N and Ben-Haddad, M and Hajji, S and Ouheddou, M and Ourouh, J and Iacomino, G and El Haouti, R and Barra, I and Oualid, JA and Bonanomi, G and Banni, M and Alla, AA}, title = {Marine plastic exposure triggers rapid recruitment of plastic-degrading bacteria and accelerates polymer-specific transformations.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137724}, doi = {10.1016/j.jhazmat.2025.137724}, pmid = {40037197}, issn = {1873-3336}, abstract = {Plastic pollution in marine ecosystems is a growing concern, yet the degradation behavior of different plastic types and their interactions with microbial communities remain poorly understood. This study investigated the degradation kinetics and microbial colonization of four widely used plastic materials, surgical masks (most made of PP), PET bottles, PS foam, and PP cups, over 40 days of seawater exposure in the Central Atlantic of Morocco. Mass loss measurement revealed distinct degradation patterns, with PS foam showing the highest mass loss (13 %), followed by PET bottles (5 %), likely due to environmental stressors that promote mechanical fragmentation. Surgical masks and PP cups exhibited minimal degradation, retaining nearly all their original mass, as well as limited extent of biodegradation. Fourier Transform Infrared Spectroscopy (FTIR) and X-ray Diffraction (XRD) analyses showed the formation of oxidative functional groups on PP cups and significant structural changes in PS foam and PET, particularly in their crystalline structures, correlating with their higher mass reduction rates. SEM/EDX biofilm imaging confirmed extensive microbial colonization, particularly on PS and PET surfaces. Using 16S rRNA metabarcoding, we identified a striking enrichment of Exiguobacterium, followed by Pseudomonas, Acinetobacter and Bacillus genera, containing reported plastic degrading strains, which were strongly correlated with the accelerated breakdown of plastics. However, its role in accelerating plastic breakdown in this study remains unclear and may warrant further investigation. Co-occurrence network analysis revealed a progressive shift in microbial community structure, evolving from highly interconnected networks at day 0 to more specialized, modular clusters by day 40, dominated by Proteobacteria and Firmicutes. Atomic Absorption Spectrometry (AAS) demonstrated significant heavy metal accumulation on plastic surfaces, potentially influencing microbial colonization and activity. While the observed fragmentation of PS foam and PET highlights the susceptibility of certain plastics to environmental stressors, this study also positions microbial colonization as a potential contributor to plastic surface changes, providing novel insights into the interplay between microbial communities and plastic degradation in marine environments.}, }
@article {pmid40037099, year = {2025}, author = {Badra, M and Freudenthal, J and Dumack, K}, title = {Sludge retention time in anaerobic digestion affects Archaea by a cascade through microeukaryotes.}, journal = {Water research}, volume = {278}, number = {}, pages = {123371}, doi = {10.1016/j.watres.2025.123371}, pmid = {40037099}, issn = {1879-2448}, abstract = {Anaerobic digestion is a crucial process for treating organic waste, such as wastewater sludge, agricultural residues and food waste. While the influence of physicochemical parameters on the prokaryotic community composition in anaerobic digesters has been extensively characterized, the role of biotic interactions in shaping the prokaryotic communities remains poorly understood. This study addresses this knowledge gap by analyzing the complete active microbiome of nine full-scale anaerobic digesters. Our findings reveal that eukaryotes, consisting primarily of protists and fungi, account for approximately 40 % of RNA sequence reads alongside dominant Archaea, indicating their substantial role in the digestion process. Our results suggest that the chosen sludge retention time during anaerobic digestion indirectly affects the archaeal community composition and thus treatment efficacy by cascading through eukaryotes, highlighting their integral role in the system. This study highlights the critical role of eukaryotes in regulating prokaryotic communities and their indirect contribution to the optimization of anaerobic digestion efficiency.}, }
@article {pmid40037080, year = {2025}, author = {Lv, M and Shi, W and Xu, J and He, S and Wang, L and Li, M and Ma, L and Wang, J and Nie, F and Xu, B and Han, Y and Zhou, B and Gao, Z}, title = {Exposure to thiazole pesticides disrupts pathogens and undermines keystone status of rare taxa within bacterial ecological networks.}, journal = {Ecotoxicology and environmental safety}, volume = {292}, number = {}, pages = {117983}, doi = {10.1016/j.ecoenv.2025.117983}, pmid = {40037080}, issn = {1090-2414}, abstract = {Considering the sensitivity of rare microbial taxa to environmental disturbances and their critical roles in ecosystems, it is essential to investigate how soil microbial communities (particularly rare microbes) respond to pesticide exposure. In this study, we found that thiazole pesticides significantly reduced the severity of potato common scab and effectively disrupted the pathogen's cell membrane integrity. Notably, hierarchical partitioning analysis indicated that the rare microbial taxa in potato geocaulosphere soil constitute key clusters influencing disease incidence. Within bacterial molecular ecological networks, nodes corresponding to these rare taxa generally exhibited higher degrees compared to those of more abundant taxa. However, pesticide exposure reduced the number of keystone nodes and substantially weakened the hub status of rare bacterial taxa in these networks. These findings suggest that, although thiazole pesticides effectively eradicate pathogens, they may also pose a non-negligible potential risk to rare taxa in agricultural ecosystems.}, }
@article {pmid40037072, year = {2025}, author = {Meng, JX and Li, MH and Wang, XY and Li, S and Zhang, Y and Ni, HB and Ma, H and Liu, R and Yan, JC and Li, XM and Sun, YZ and Yang, X and Zhang, XX}, title = {Temporal variability in the diversity, function and resistome landscapes in the gut microbiome of broilers.}, journal = {Ecotoxicology and environmental safety}, volume = {292}, number = {}, pages = {117976}, doi = {10.1016/j.ecoenv.2025.117976}, pmid = {40037072}, issn = {1090-2414}, abstract = {Understanding the dynamic and stability of gut microbiota over the course of production cycle of broiler chicken can help identify microbial features that associate with better health and productivity. In the present study, we profile the changes in the composition and stability of gut microbiota of commercially raised broilers at nine distinct time points using shotgun metagenomics and culturomics approaches. We demonstrate, within the first week post-hatching, a rapid decline in relative abundance of 122 pioneer microbial species including Bacteroides fragilis, Lachnospira eligens and Ruminococcus gnavus, accompanied by a substantial decrease in both microbial richness and diversity. This was followed by a gradual increase and stabilization in the microbial diversity and population structure that persisted until the broilers reached the marketing age. Throughout the production cycle, key bacterial families such as Lachnospiraceae, Bacteroidaceae, and Ruminococcaceae were identified. However, significant shifts at the lower taxonomic levels occurred at different production stages, influencing the functional capacities and resistance profiles of the microbiota. During the rapid growth phase, enzymes crucial to vitamin and amino acid metabolism dominated, whereas enzymes associated with carbohydrate and energy metabolism were notably more abundant during the fattening stage. Many predicted antibiotic resistance genes were detected in association with typical commensal bacterial species in the gut microbiota, indicating a sustained resistance of the gut microbiota to antibiotic classes such as aminoglycosides and tetracyclines, which persist even in the absence of antibiotic selection pressure. Our research carries important implications for the management and health surveillance of broiler production.}, }
@article {pmid40037066, year = {2025}, author = {Wahab, A and Batool, F and Abdi, G and Muhammad, M and Ullah, S and Zaman, W}, title = {Role of plant growth-promoting rhizobacteria in sustainable agriculture: Addressing environmental and biological challenges.}, journal = {Journal of plant physiology}, volume = {307}, number = {}, pages = {154455}, doi = {10.1016/j.jplph.2025.154455}, pmid = {40037066}, issn = {1618-1328}, abstract = {This review underscores the importance of plant growth-promoting rhizobacteria (PGPR), fostering sustainability to address various environmental and biological issues. PGPR helps crops withstand salinity, nutrient deficiencies, and drought stress while tackling agricultural threats. Sustainable agriculture has emerged as a response to the social and economic problems farming practices face. Plants encounter obstacles from biotic stressors such as bacteria, viruses, nematodes, arachnids, and weeds that impede their growth. Furthermore, PGPR enhances plant growth through improved nutrient absorption and defense against pests. Bacillus subtilis utilizes indirect methods to combat diseases and protect plants from various diseases and pests. Additionally, PGPR acts as a bio-fertilizer that mitigates drought stress effects on crops in various regions worldwide. This review proposes strategies to boost productivity and improve bio-inoculant efficiency under real-world conditions. PGPR demonstrates its role in combating threats by influencing plant defense mechanisms, initiating systemic resistance responses, and regulating gene expression related to pathogen detection and defense signaling pathways. It maintains a balanced root microbiome by suppressing harmful microbial proliferation while promoting beneficial microbial interactions. Despite the challenges posed by technology and ethical considerations surrounding their modification, integrating PGPR into farming methods holds promise for sustainable agriculture. Given the increasing impact of climate change, PGPR plays a crucial role in improving crop resilience, enhancing soil quality, and reducing dependence on synthetic agricultural inputs.}, }
@article {pmid40037004, year = {2025}, author = {Nuñez, P and Martinez-Boggio, G and Casellas, J and Varona, L and Peñagaricano, F and Ibáñez-Escriche, N}, title = {Applying recursive modelling to assess the role of the host genome and the gut microbiome on feed efficiency in pigs.}, journal = {Animal : an international journal of animal bioscience}, volume = {19}, number = {3}, pages = {101453}, doi = {10.1016/j.animal.2025.101453}, pmid = {40037004}, issn = {1751-732X}, abstract = {The gut microbiome plays an important role in the performance and health of swine by providing essential nutrients and supporting the immune system. Recent studies have demonstrated that the gut microbiome can explain part of the variation observed in growth, health, and meat quality. Feed efficiency is crucial in swine production, as feed cost account for more than 60% of total production costs. This study aimed to assess the relationships between the host genome, gut microbiome, and feed efficiency in Iberian pigs raised under intensive conditions. The specific objectives were to assess the mediating effects of the gut microbiome on feed efficiency and to estimate the direct and total heritability of feed efficiency. The data set included the feed conversion ratio (FCR) and residual feed intake (RFI) from 587 Iberian pigs, as well as the 16S rRNA gut microbial abundance from 151 of those pigs raised in a nucleus of selection. We reparametrised variance components from standard bivariate mixed models into recursive models to disentangle the microbiome's mediating effect on feed efficiency. In our models, the host genome has direct effects on both the phenotype (G→P) and the gut microbiome (G→M). Additionally, there is an indirect effect of the host genome on the phenotype mediated by the microbiome (G→M→P). We identified a total of 14 taxa with relevant effects on FCR and 16 taxa with relevant effects on RFI. We categorised the gut microbiome into groups for potential practical application in pig farming. The gut microbes with relevant causal effects and low heritability can be manipulated through management interventions, while those microbes with relevant causal effects and moderate heritability can be targeted through selective breeding. Our findings indicate that incorporating microbiome data leads to a reduction in total heritability for both FCR and RFI. This study provides new insights into the link between the gut microbiome and feed efficiency, presenting practical methods to target microbes that can be influenced through selective breeding or management interventions.}, }
@article {pmid40036964, year = {2025}, author = {Jyoti, J and Hütt, MT}, title = {Evaluating changes in attractor sets under small network perturbations to infer reliable microbial interaction networks from abundance patterns.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf095}, pmid = {40036964}, issn = {1367-4811}, abstract = {MOTIVATION: Inferring microbial interaction networks from microbiome data is a core task of computational ecology. An avenue of research to create reliable inference methods is based on a stylized view of microbiome data, starting from the assumption that the presences and absences of microbiomes, rather than the quantitative abundances, are informative about the underlying interaction network. With this starting point, inference algorithms can be based on the notion of attractors (asymptotic states) in Boolean networks. Boolean network framework offers a computationally efficient method to tackle this problem. However, often existing algorithms operating under a Boolean network assumption, fail to provide networks that can reproduce the complete set of initial attractors (abundance patterns). Therefore, there is a need for network inference algorithms capable of reproducing the initial stable states of the system.<br><br>RESULTS: We study the change of attractors in Boolean threshold dynamics on signed undirected graphs under small changes in network architecture and show, how to leverage these relationships to enhance network inference algorithms. As an illustration of this algorithmic approach, we analyze microbial abundance patterns from stool samples of humans with inflammatory bowel disease (IBD), with colorectal cancer and from healthy individuals to study differences between the interaction networks of the three conditions. The method reveals strong diversity in IBD interaction networks. The networks are first partially deduced by an earlier inference method called ESABO, then we apply the new algorithm developed here, EDAME, to this result to generate a network that comes nearest to satisfying the original attractors.<br><br>AVAILABILITY: Implementation code is freely available at https://github.com/Jojo6297/edame.git.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid40036950, year = {2025}, author = {de Luca Silva, B and Cendoroglo, MS and Colleoni, GWB}, title = {Gut Microbiota and Metabolic Biomarkers Associated With Longevity.}, journal = {Nutrition reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/nutrit/nuaf027}, pmid = {40036950}, issn = {1753-4887}, abstract = {The dynamic balance between pro- and anti-inflammatory networks decreases as individuals age, and intestinal dysbiosis can initiate and maintain low-grade systemic inflammation. Interactions between the microbiota and humans occur from the beginning of life and, in general, the diversity of microbiota decreases with aging. The microbiome produces different metabolites with systemic effects, including immune system regulation. This understanding will be useful in controlling inflammation and preventing metabolic changes. Therefore, this review aims to identify the main metabolites synthesized by the intestinal microbiota to be used as biomarkers associated with longevity. This is a narrative review using scientific articles published in the last 10 years in the following databases: PubMed, Scielo, and Lilacs, using the Boolean operators "and" or "or." For this review, we identified 5 articles. The main metabolites described in the literature to date are organic acids, bile acids (BAs), short-chain fatty acids, branched-chain amino acids, trimethylamine N-oxide (TMAO), and derivatives of tryptophan and indole. Among these, the only ones not yet well characterized in studies on longevity were BAs and TMAO. Glutamate and p-cresol were also highlighted in the literature, with a negative association with longevity. The others showed an association, mostly positive, and can be used as potential biomarkers correlated with healthy aging and, if better studied, as targets for intervention to promote health and well-being.}, }
@article {pmid40036939, year = {2025}, author = {Mallick, K and Khodve, G and Ruwatia, R and Banerjee, S}, title = {Gut microbes: Therapeutic Target for neuropsychiatric disorders.}, journal = {Journal of psychiatric research}, volume = {184}, number = {}, pages = {27-38}, doi = {10.1016/j.jpsychires.2025.02.031}, pmid = {40036939}, issn = {1879-1379}, abstract = {Neuropsychiatric diseases encompass a range of mental and neurological disorders that have a significant and far-reaching effect on an individual's quality of life. These conditions affect not only the mental status but also the physical well-being of individuals, which leads to weakened immune systems and other diseases. Emerging research underscores a significant connection between the gut microbiome and neuropsychiatric diseases, suggesting that microbial communities within the gastrointestinal tract may influence brain function and mental health. Gut dysbiosis is caused by various factors, including stress, diet, inappropriate usage of antibiotics, infections, and so on, all of which can disrupt numerous pathways, resulting in abnormal neurotransmitter signaling, inflammation, and impaired brain function. Similarly, various neuropsychiatric diseases can disrupt the specific microbiome in the gut, leading to gut dysbiosis, often impairing memory and cognitive function. The growing evidence supporting the role of gut dysbiosis in neuropsychiatric disorders has opened up new avenues for therapeutic interventions. Modulating the gut microbiome through strategies such as probiotics, prebiotics, or fecal microbiota transplantation has shown promising results in various studies of neuropsychiatric disorders. However, further research is needed to fully elucidate the mechanisms involved in gut dysbiosis-associated brain changes to develop effective and personalized treatment strategies for neuropsychiatric diseases.}, }
@article {pmid40036891, year = {2025}, author = {Prajapati, SK and Jain, S and Yadav, H}, title = {Age-Related Cognitive Decline and Dementia: Interface of Microbiome-Immune-Neuronal Interactions.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {}, number = {}, pages = {}, doi = {10.1093/gerona/glaf038}, pmid = {40036891}, issn = {1758-535X}, abstract = {The microbiome plays a critical role in both promoting human health and contributing to diseases. Multiple emerging evidence shows that it contributes to aging and cognitive decline; however, the mechanisms are not fully understood. Changes in the microbiome and immune system occur with age, and immune functions are one of the key mechanisms linking the microbiome to the brain. Disrupted immunological balance may lead to neuroinflammation and blood-brain barrier dysfunction, contributing to cognitive decline. However, comprehensive knowledge regarding the types of microbiome and immune interactions influencing neuronal and cognitive health in aging remains largely unknown. This review presents evidence about the types of microbiome alterations associated with healthy versus unhealthy aging and how they interact with immune cells linked to neuronal and cognitive functions. It also explores whether and how microbiome modulators like probiotics, prebiotics, and postbiotics can be potential interventions to help preserve cognitive function in older adults.}, }
@article {pmid40036783, year = {2025}, author = {Hartwig, RP and Santangeli, M and Würsig, H and Martín Roldán, M and Yim, B and Lippold, E and Tasca, A and Oburger, E and Tarkka, M and Vetterlein, D and Bienert, P and Blagodatskaya, E and Smalla, K and Hause, B and Wimmer, MA}, title = {Drought response of the maize plant-soil-microbiome system is influenced by plant size and presence of root hairs.}, journal = {Annals of botany}, volume = {}, number = {}, pages = {}, doi = {10.1093/aob/mcaf033}, pmid = {40036783}, issn = {1095-8290}, abstract = {BACKGROUND AND AIMS: We have abundant knowledge on drought responses of plants or soil microorganisms individually. However, there is a severe lack of knowledge regarding interactions in the plant-soil-microbiome continuum, and specifically root-soil interface traits including the role of root hairs. Here, we investigated how water limitation propagates in a plant-soil-microbiome system upon stopping irrigation. We used two Zea mays genotypes (rth3 and its isogenic wildtype B73), differing in root hair formation, to elucidate the effect of rhizosphere extension under water limitation.<br><br>METHODS: For 22 days, WT and rth3 were grown in a climate chamber, with irrigation stopped for drought treatment during the last 7 days. Daily measurements included soil water status, plant evapotranspiration and gas exchange. At harvest, root exudates, shoot relative water content, osmolality and nutrients, root morphological traits and transcriptomics, and soil microbial &#x3b2;-diversity and enzyme activity were determined.<br><br>KEY RESULTS: In line with a larger plant size, drought stress developed more rapidly and the number of differentially expressed genes was higher in the WT compared to rth3. Under water limitation, root exudation rates increased and soil enzyme activities decreased more strongly in the WT rhizosphere. In both genotypes, water level significantly altered microbial &#x3b2;-diversity in the bulk soil, particularly affecting fungi more than bacteria/archaea. The genotype affected only bacteria/archaea and was more pronounced in rhizosphere than in bulk soil.<br><br>CONCLUSIONS: This interdisciplinary study assessed how a short drought stress manifested in a plant-soil-microbiome system. Water limitation altered microbial (fungal) diversity more distant from the root surface. Genotype-specific stress-induced increases in exudation rates modified microbial activity in root proximity, possibly pointing to root hair functions under water limitation. Less intense drought responses of rth3 were confirmed at all levels of investigation and may be due at least in part to its smaller plant size.}, }
@article {pmid40036749, year = {2025}, author = {Soge, OO and Thibault, CS and Cannon, CA and McLaughlin, SE and Menza, TW and Dombrowski, JC and Fang, FC and Golden, MR}, title = {Potential Impact of Doxycycline Post-Exposure Prophylaxis on Tetracycline Resistance in Neisseria gonorrhoeae and Colonization with Tetracycline-Resistant Staphylococcus aureus and Group A Streptococcus.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciaf089}, pmid = {40036749}, issn = {1537-6591}, abstract = {BACKGROUND: Doxycycline post-exposure prophylaxis (doxy PEP) is increasingly used among men who have sex with men (MSM). Its impact on antimicrobial resistance and the microbiome is uncertain.<br><br>METHODS: We used Neisseria gonorrhoeae (NG) surveillance data from King County, WA and joinpoint regression to investigate trends in NG-tetracycline resistance (tetR), 2017-2024 and, among sexual health clinic (SHC) patients, evaluated the association of NG-tetR with doxy PEP use. We evaluated nasopharyngeal colonization with Staphylococcus aureus and Group A Streptococcus (GAS) 703 MSM SHC patients, August 2023-July 2024.<br><br>RESULTS: Among 2,312 MSM with NG, tetR was stable 2017 to quarter 1 (Q1) 2023 (mean=27%) and thereafter rose to 70% in Q2 2024 (p<0.0001). (King County released doxy PEP guidelines in Q2 2023.) NG with high-level (HL) tetR increased Q1 2021 to Q2 2024 (2% to 65%) (p<0.0001). Taking >3 doses of doxy PEP/month was associated with both tetR and HL tetR (p&#x2264;0.01 for both), though any use of doxy PEP was not associated with tetR or HL tetR. S. aureus colonization was less common among doxy PEP users than non-users (27% vs. 36%, p=0.02), but colonization with both tetracycline-resistant S. aureus and GAS were more common among doxy PEP users than non-users (18% vs. 8%, p<0.0001 and 9% vs. 4%, p=0.008, respectively).<br><br>CONCLUSIONS: TetR in NG rapidly increased from 2021 to 2024, and most NG among King County MSM now have HL tetR. Doxy PEP use is associated with colonization with GAS and tetracycline-resistant S. aureus, suggesting that doxy PEP impacts off-target bacteria.}, }
@article {pmid40036691, year = {2025}, author = {Gao, Y and Luo, H and Lyu, H and Yang, H and Yousuf, S and Huang, S and Liu, YX}, title = {Benchmarking short-read metagenomics tools for removing host contamination.}, journal = {GigaScience}, volume = {14}, number = {}, pages = {}, doi = {10.1093/gigascience/giaf004}, pmid = {40036691}, issn = {2047-217X}, support = {2024M753580//China Postdoctoral Science Foundation/ ; U23A20148//National Natural Science Foundation of China/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; }, mesh = {*Metagenomics/methods ; *Benchmarking ; Microbiota/genetics ; Humans ; DNA Contamination ; Metagenome ; Software ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; Reproducibility of Results ; }, abstract = {BACKGROUND: The rapid evolution of metagenomic sequencing technology offers remarkable opportunities to explore the intricate roles of microbiome in host health and disease, as well as to uncover the unknown structure and functions of microbial communities. However, the swift accumulation of metagenomic data poses substantial challenges for data analysis. Contamination from host DNA can substantially compromise result accuracy and increase additional computational resources by including nontarget sequences.<br><br>RESULTS: In this study, we assessed the impact of computational host DNA decontamination on downstream analyses, highlighting its importance in producing accurate results efficiently. We also evaluated the performance of conventional tools like KneadData, Bowtie2, BWA, KMCP, Kraken2, and KrakenUniq, each offering unique advantages for different applications. Furthermore, we highlighted the importance of an accurate host reference genome, noting that its absence negatively affected the decontamination performance across all tools.<br><br>CONCLUSIONS: Our findings underscore the need for careful selection of decontamination tools and reference genomes to enhance the accuracy of metagenomic analyses. These insights provide valuable guidance for improving the reliability and reproducibility of microbiome research.}, }
@article {pmid40036370, year = {2025}, author = {Duysburgh, C and Nicolas, C and Van den Broeck, M and Lloret, F and Monginoux, P and Rème, C and Marzorati, M}, title = {A specific blend of prebiotics and postbiotics improved gut microbiome of dogs with soft stools in the in vitro Simulator of the Canine Intestinal Microbial Ecosystem (SCIME).}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skaf056}, pmid = {40036370}, issn = {1525-3163}, abstract = {The Simulator of the Canine Intestinal Microbial Ecosystem (SCIME) allows for the study of long-term effects of food, supplements, or ingredients on the canine gut microbiome in a simulated proximal and distal colon. This model has been used to evaluate the impact of repeated administration of a test product blend composed of a mixture of baobab fruit pulp, acacia gum, heat-killed Lactobacillus helveticus HA-122, and specific fractions of selected inactivated yeast strains (including Saccharomyces cerevisiae AQP 12260 and AQP 12988 and Cyberlindnera jadinii AQP 12549), on the activity and composition of the gut microbiome of canine donors with soft stools. The SCIME colonic reactors were inoculated with fecal material from 3 different canine donors. After two days of stabilization, the 8-day parallel control/treatment period was initiated; reactors were fed with SCIME nutritional medium with or without test product. Changes in microbial metabolic activity were assessed by measuring levels of acetate, propionate, butyrate, lactate, branched short-chain fatty acids, and ammonium. Changes in microbial community composition were assessed using 16S-targeted Illumina sequencing. Overall, test product supplementation resulted in increased saccharolytic fermentation, as evidenced by increases in the health-promoting bacterial metabolites as propionate (donor-dependent), acetate and butyrate (donor-dependent) as well as increased abundances of several saccharolytic fermenting microbes, including Bifidobacterium. Conversely, proteolytic bacteria like Proteobacteria were reduced with test product compared to control. Repeated supplementation with the test product was therefore able to induce - in vitro - a positive modulation of the microbiome originated from dogs with soft stools.}, }
@article {pmid40036343, year = {2025}, author = {Nisha, FA and Horne, SM and Prüß, BM}, title = {Azospirillum brasilense and cytidine enhance lateral roots of peas.}, journal = {FEMS microbiology letters}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnaf025}, pmid = {40036343}, issn = {1574-6968}, abstract = {Azospirillum brasilense is a plant growth beneficial rhizobacteria (PGPR) that is used as inoculant to enhance root architecture in grassland and crop plants. The intent of our study was to develop A. brasilense into a pro-biotic inoculant for peas and supplement with a seedling exudate compound, to be used together or separately. As an initial characterization of the association of A. brasilense with pea roots, we performed several pea growth experiments. Azospirillum brasilense Sp7T increased the lengths of the five longest lateral roots from each plant by 63.6% and the top 10 lateral roots across fourteen plants by 30%, an effect that was abolished in an rpoN mutant and a ΔcheA1/cheA4 mutant. Azospirillum brasilense Cd increased the number of lateral roots by 76%. We detected colonization by this PGPR within the epiphytic root microbiome. To identify a pea seedling exudate compound capable of enhancing lateral pea roots, we tested 15 such compounds. Cytidine was the only one that increased the number of lateral roots, by ∼2 fold, an effect that did not require A. brasilense. We conclude that both A. brasilense and cytidine might be suitable as supplements to enhance lateral roots of pea plants.}, }
@article {pmid40035906, year = {2025}, author = {Wang, H and Baba, Y and Hara, Y and Toihata, T and Kosumi, K and Harada, K and Iwatsuki, M and Miyamoto, Y and Baba, H}, title = {The Relationship Between Gut Microbiome Bifidobacterium and Anti-tumor Immune Responses in Esophageal Squamous Cell Carcinoma.}, journal = {Annals of surgical oncology}, volume = {}, number = {}, pages = {}, pmid = {40035906}, issn = {1534-4681}, support = {17H04273//Japan Society for the Promotion of Science/ ; 17K19702//Japan Society for the Promotion of Science/ ; 17KK0195//Japan Society for the Promotion of Science/ ; }, abstract = {BACKGROUND: The Bifidobacterium genus is a prominent bacterial population in the gastrointestinal tract. Previous findings suggest that Bifidobacterium is linked to tumor suppression in mouse models of melanoma. Additionally, when combined with the programmed death-ligand 1 (PD-L1) antibody, it can enhance anti-tumor treatment by increasing tumor-specific T-cell responses and promoting infiltration of antigen-specific T cells into tumors. However, there is a lack of studies on Bifidobacterium in esophageal squamous cell carcinoma (ESCC). This study aimed to investigate the potential impact of Bifidobacterium on this cancer type.<br><br>METHODS: We examined 213 samples from ESCC patients who underwent tumor resection. The presence of Bifidobacterium was confirmed using quantitative polymerase chain reaction and fluorescent in situ hybridization (FISH). Patient overall survival (OS) was analyzed with Bifidobacterium positivity. Tumor-infiltrating lymphocytes (TILs) were evaluated via hematoxylin and eosin stains, and immunohistochemistry was used to assess programmed death-1 (PD-1), PD-L1, cluster of differentiation 8 (CD8), and forkhead box P3 (FOXP3) expression. Nutritional status was evaluated via computed tomography scans.<br><br>RESULTS: Bifidobacterium positivity showed no correlation with patient OS or TIL levels; however, Bifidobacterium positivity in normal tissue was associated with lower FOXP3 levels, suggesting a potential role in upregulating anti-tumor immune responses. Patients with Bifidobacterium present in peritumor normal tissue exhibited better skeletal muscle area and volume. Conversely, Bifidobacterium positivity in tumor tissue was associated with poorer prognostic nutrition index values, likely due to decreased albumin levels.<br><br>CONCLUSION: Bifidobacterium can induce the upregulated anti-tumor immune response and is more prevalent in cases with good nutritional status.}, }
@article {pmid40035853, year = {2025}, author = {Yao, X and Chen, Y and Li, Y and Mo, J and Liu, X and Wang, P and Jia, D and Li, H and Guo, C}, title = {Chrysin ameliorates dextran sulfate-induced ulcerative colitis in mice by modulating inflammation and gut microbiota.}, journal = {International journal of colorectal disease}, volume = {40}, number = {1}, pages = {57}, pmid = {40035853}, issn = {1432-1262}, support = {CSTB2023NSCQ-MSX0784//General Projects of Chongqing Natural Science Foundation/ ; }, mesh = {Animals ; *Flavonoids/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Colitis, Ulcerative/drug therapy/chemically induced/pathology/microbiology ; *Dextran Sulfate ; Mice ; Colon/pathology/drug effects/microbiology ; Tumor Necrosis Factor-alpha/metabolism/blood ; Mice, Inbred C57BL ; Inflammation/drug therapy/pathology ; Male ; Metabolomics ; Signal Transduction/drug effects ; NF-kappa B/metabolism ; Disease Models, Animal ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) encompasses chronic inflammation of the colon and rectum, posing significant health challenges. Previous studies have shown potential therapeutic effects of natural compounds on IBD. Chrysin, a naturally occurring flavonoid, has been suggested to modulate inflammatory pathways and gut microbiota, but its comprehensive impact on ulcerative colitis remains inadequately explored.<br><br>METHODS: This study employed a dextran sulfate sodium (DSS)-induced ulcerative colitis model in mice to investigate the effects of Chrysin. Using network pharmacology, we identified key signaling pathways potentially influenced by Chrysin. Experimental approaches included measuring disease activity index scores, serum levels of TNF-&#x3b1;, and assessing colon damage histologically. Transcriptomic and microbiome analyses were conducted to examine changes in gene expression and gut bacterial populations, respectively. Additionally, metabolomic profiling was used to identify alterations in colon metabolites.<br><br>RESULTS: Chrysin treatment significantly mitigated weight loss and reduced disease activity index scores in DSS-induced mice. There was a notable decrease in serum TNF-&#x3b1; levels and less histological damage in the colon. Transcriptomic analysis revealed significant alterations in gene expression within the NF-&#x3ba;B and IL-17 signaling pathways. Microbiome analysis showed significant shifts in the populations of Bacteroidetes and Firmicutes. Metabolomics analysis identified changes in 298 colon metabolites, implicating several essential metabolic pathways.<br><br>CONCLUSIONS: The findings suggest that Chrysin exerts a dual-action therapeutic effect on ulcerative colitis by reducing inflammation and modulating the gut microbiota. These multifaceted impacts highlight Chrysin's potential utility as a novel therapeutic agent in the clinical management of IBD, offering valuable insights into its mechanisms of action and paving the way for future clinical trials.}, }
@article {pmid40035787, year = {2025}, author = {Tappauf, N and Lamers, Y and Sham, HP and Piper, HG}, title = {Multiomics profiling and parenteral nutrition weaning in pediatric patients with intestinal failure: A longitudinal cohort study.}, journal = {JPEN. Journal of parenteral and enteral nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1002/jpen.2742}, pmid = {40035787}, issn = {1941-2444}, support = {//This study was funded through a 2021-2022 Healthy Starts Catalyst Grant, awarded by the BC Children's Hospital Research Institute in Vancouver, Canada./ ; }, abstract = {BACKGROUND: Intestinal failure (IF) is a life-limiting condition that includes a variety of intestinal pathologies. Currently, there are few clinical biomarkers that reflect intestinal function or a patient's potential to wean off parenteral nutrition (PN), making it difficult to predict the clinical trajectory. By associating gut microbiome taxonomic and functional features and blood analytes with the proportion of daily energy delivered via PN-a proxy for intestinal function-our study aimed to discover potential predictors of intestinal function and PN weaning potential.<br><br>METHODS: In this longitudinal multiomics cohort study, we followed 18 pediatric patients with IF and PN support for &#x2264;1.5 years. Fecal and stoma samples were analyzed using metagenomic shotgun sequencing to assess bacterial taxonomy and function and internal transcribed spacer 2 ribosomal RNA sequencing to characterize the fungal community. Targeted metabolomics was used to quantify 257 blood analytes. Linear mixed models were used to analyze the associations of PN dependence with microbiome features and blood analytes.<br><br>RESULTS: The bacterial and fungal taxonomic composition exhibited substantial interpatient and intrapatient variability, with no link to PN dependence. In contrast, bacterial functional analysis revealed 63 MetaCyc pathways significantly associated with PN dependence. Additionally, 32 blood analytes were associated with PN dependence.<br><br>CONCLUSION: In this exploratory study, we found that functional microbiome features and blood metabolomic profiles-particularly urea cycle metabolites, creatinine, asparagine, and tryptophan-derived metabolites-show promise for predicting intestinal function. Furthermore, they may have therapeutic implications for promoting intestinal adaptation. Confirmatory trials with larger sample sizes are needed to validate these findings.}, }
@article {pmid40035727, year = {2025}, author = {Ouyang, P and Qi, J and Tong, B and Li, Y and Cao, J and Wang, L and Niu, T and Qi, X}, title = {Butyrate Ameliorates Graves' Orbitopathy Through Regulating Orbital Fibroblast Phenotypes and Gut Microbiota.}, journal = {Investigative ophthalmology &amp; visual science}, volume = {66}, number = {3}, pages = {5}, doi = {10.1167/iovs.66.3.5}, pmid = {40035727}, issn = {1552-5783}, mesh = {*Graves Ophthalmopathy/drug therapy/microbiology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Fibroblasts/drug effects/metabolism/pathology ; Mice ; Humans ; *Disease Models, Animal ; *Butyrates/pharmacology ; *Orbit ; Cells, Cultured ; Phenotype ; Mice, Inbred C57BL ; Adipogenesis/drug effects ; Male ; Female ; }, abstract = {PURPOSE: Graves' orbitopathy (GO), the common extrathyroidal complication of Graves' disease (GD), is characterized by orbital fibroblast stimulation, adipogenesis, and hyaluronan production. Recently, gut microbiota and its metabolites have garnered attention for their possible involvement in GO.<br><br>METHODS: This study utilized an animal model of GO and examined the effects of butyrate treatment on orbital fibroblast cells and gut microbiota. Ex vivo experiments were performed using orbital fibroblasts derived from healthy patients' and patients' with GO orbital tissue to evaluate vitality, activation, and adipogenesis in response to butyrate treatment. Gut microbiota diversity was also analyzed in butyrate-treated and untreated GO mice.<br><br>RESULTS: In human orbital fibroblasts, butyrate treatment dramatically decreased the vitality of GO-derived fibroblasts without harming normal fibroblasts. Butyrate prevented activation and fibrotic processes induced by transforming growth factor beta 1 (TGF-&#x3b2;1) in GO and normal fibroblasts. Additionally, butyrate reduced lipid droplet formation and downregulated lipogenic markers in GO and normal orbital fibroblasts, inhibiting adipogenesis. In the GO mouse model, butyrate therapy improved orbital histological abnormalities and normalized serum thyroid hormone and antibody levels. The intestinal microbiome of butyrate-treated GO mice also changed significantly, with a reduction in certain bacteria (Bifidobacterium, GCA-900066575, and Parabacteroides) and an increase in others (Bacteroides and Rikenellaceae_RC9).<br><br>CONCLUSIONS: Butyrate ameliorates several of the symptoms of GO, lowering GO orbital fibroblast viability, adipogenesis, and TGF-&#x3b2;1-induced fibrosis without damaging normal fibroblasts. Butyrate normalizes thyroid function in a GO mouse model, improves histopathological alterations, and transforms gut microbiota populations, proving its potential in treating GO through the gut-thyroid axis.}, }
@article {pmid40035564, year = {2025}, author = {Xu, L and Li, X and Chen, L and Ma, H and Wang, Y and Liu, W and Liao, A and Tan, L and Gao, X and Xiao, W and Yang, H and Ji, G and Qiu, Y}, title = {Gut microbiome and plasma metabolome alterations in ileostomy and after closure of ileostomy.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0119124}, doi = {10.1128/spectrum.01191-24}, pmid = {40035564}, issn = {2165-0497}, abstract = {UNLABELLED: A temporary loop ileostomy is a routine procedure for protecting the anastomosis in patients undergoing radical resection of rectal cancer. Fecal diversion by a diverting ileostomy may induce microbiota dysbiosis in the defunctioned colon; however, data on temporal and spatial microbiome and metabolome changes in these patients are sparse. Thirty patients who underwent ileostomy closure were enrolled. Fecal and plasma samples were collected successively before ileostomy closure, at the first postoperative defecation, and 1 month postoperatively. The 16S rRNA gene sequencing was used to assess changes in gut microbes, and metabolic components in the plasma were analyzed using global untargeted metabolomics. Advanced data analysis methods were used to examine the differences and correlations between flora and metabolites. The gut microbiota in the ileostomy effluent and defunctioned colon had lesser species diversity and richness, with an abundance of aerobic, gram-negative, and potentially pathogenic bacteria. After the intestinal continuity was restored with routine meal feeding, the gut microbes recovered to a standard composition within 1 month. Moreover, xanthine, traumatic acid, L-glutamine, and norepinephrine levels increased markedly in patients with ileostoma. The ileostomy closure reversed the ileostomy-associated metabolic alterations, including an increased abundance of L-leucine, creatine, and 2-ketobutyric acid. Furthermore, Agathobacter and Peptostreptococcus were most closely associated with the reconstruction of postoperative gut microbes. We described a spatiotemporal map of the intestinal microbial ecological reconstruction and metabolic recovery before and after ileostomy reversal for perioperative intervention in patients with ileostomy closure surgery.<br><br>IMPORTANCE: In this paper, the changes in the intestinal microbiome and plasma metabolome before and after temporary ileostomy were reported for the first time, and the dynamic changes in intestinal contents were described. At the same time, the key bacterial genera involved in the reestablishment of microflora after the restoration of intestinal continuity were found, and the key relationship between them and plasma metabolites was also found. More importantly, we found that patients with ileal fistula may be at risk of metabolic imbalance and that this particular metabolic state may potentially affect the course of tumor treatment. Finally, the samples in this study were obtained in their natural state and can be easily applied to the clinic to avoid unnecessary invasive examinations.}, }
@article {pmid40035299, year = {2025}, author = {Kováčik, A and Vraníková, B and Čáp, R}, title = {What should we know about the skin as an application site for (not only) dermo-cosmetic products?.}, journal = {Ceska a Slovenska farmacie : casopis Ceske farmaceuticke spolecnosti a Slovenske farmaceuticke spolecnosti}, volume = {73}, number = {2}, pages = {88-92}, doi = {10.36290/csf.2024.014}, pmid = {40035299}, issn = {1210-7816}, mesh = {Humans ; *Cosmetics/chemistry ; *Skin/chemistry ; Administration, Cutaneous ; }, abstract = {What should we know about the skin as an application site for (not only) dermo-cosmetic products? The human skin can undoubtedly be regarded as the largest organ of the human body. This multi-layered selectively permeable tissue protects internal organs and other tissues from damage and is in direct contact with the surrounding environment. Part of this environment includes various substances, medicinal preparations, medical devices, and cosmetics. This article highlights selected facts regarding human skin's structure, significance, and role in local/topical product application. In addition to the overall condition of the skin (healthy vs. diseased), the structure of epidermis/stratum corneum and the pH of the skin surface are key factors influencing the effectiveness of (not only) cosmetic products applied to the skin.}, }
@article {pmid40034816, year = {2024}, author = {Liu, Z and Jiang, A and Ma, D and Liu, D and Han, X and Zhao, M and Zhou, C and Tan, Z}, title = {The impact of rumen microbial composition on apparent digestibility, rumen fermentation and metabolism in Sanhe cows and Holstein cows of different parities under identical dietary conditions.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1463209}, pmid = {40034816}, issn = {2297-1769}, abstract = {Previous studies have discussed the association between serum metabolism and lactation performance among Sanhe and Holstein cows of different parities and found that the metabolic profiles of these two breeds vary differently with parity. Since the rumen is the central organ for nutrient absorption and production transformation in dairy cows, it remains unknown whether the differences observed under the same dietary conditions are related to the structure of the rumen microbiome. This study measured the apparent digestibility and rumen fermentation parameters of Sanhe cows (S1/S2/S3/S4) and Holstein cows (H1/H2/H3/H4) across four parities and generated a comprehensive rumen microbiome dataset using high-throughput sequencing technology. Significant differences in dry matter digestibility (p = 0.001) and ammonia nitrogen (p = 0.024) were observed among the S groups, with higher trends of various VFA contents in S1 (0.05 < p < 0.1). The H group showed significant differences in crude protein digestibility (p = 0.001), higher isovaleric acid content in H1 (p = 0.002), and the lowest acetate to propionate ratio (p = 0.002) in H3. Metagenomic sequencing results indicated consistency between rumen microbiome patterns and metabolic changes, with S1 distinctly different from S2/S3/S4, and H1 and H2 different from H3 and H4. The species composition of the rumen microbiome was similar between Sanhe and Holstein cows, but differences in abundance were noted. Rhizophagus <glomeromycetes>, Neocallimastix, and Piromyces were more abundant in S1, H1, and H2, and pathways such as autophagy-animal, plant-pathogen interaction, and endocytosis were significantly enriched in these parities. Multiparous Sanhe cows had higher abundances of ATP-binding cassette transporters pathways. Additionally, CAZymes such as GH84 and GH37 were significantly associated with differential physiological indicators and milk traits. In conclusion, this study reveals the complex relationship between rumen microbiota and metabolic characteristics in Sanhe and Holstein cows of different parities, indicating that changes in the structure of the rumen microbiome may be key factors affecting lactation performance and metabolic differences in dairy cows.}, }
@article {pmid40034791, year = {2025}, author = {Li, R and Okoro, PC and Zillikens, MC and Vasan, RS and Sahni, S and Rivadeneira, F and Kiel, DP and Medina-Gomez, C}, title = {The association of gut microbiome composition with musculoskeletal features in middle-aged and older adults: a two-cohort joint study.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.19.25322523}, pmid = {40034791}, abstract = {BACKGROUND: Bones and muscles are connected anatomically, and functionally. Preliminary evidence has shown the gut microbiome influences the aging process of bone and muscle in animal studies. However, such evidence in humans is still scarce. This study aimed to assess the microbiome-bone and microbiome-muscle associations in two cohorts of community-dwelling older adults.<br><br>METHODS: We leveraged information from two large population-based cohorts, i.e., the Rotterdam Study (mean age 62.7 &#xb1; 5.6 years; n=1,249) and the Framingham Heart Study (mean age 55.2 &#xb1; 9.1 years; n=1,227). For individuals included in this study, gut microbiome 16S rRNA sequencing, musculoskeletal phenotyping derived from DXA images, lifestyle and socioeconomic data, and medication records were available. Per cohort, the 16S rRNA sequencing data, derived from stool, were processed with the DADA2 pipeline and taxonomies were assigned using the SILVA reference database. In addition, the microbiome functional potential was obtained with PICRUSt2. Further, we investigated the association between the human gut microbiome (alpha diversity, genera and predicted functional pathways) and appendicular lean mass (ALM), femoral neck bone mineral density (FN-BMD) and trabecular bone score (TBS) using multilinear regression models controlling for multiple confounders, and performed a joint analysis from both cohorts. Sex-stratified analyses were also conducted.<br><br>RESULTS: The gut microbiome alpha diversity was not associated with either tested phenotype after accounting for multiple-testing (P>1.67e-02). In the joint analysis, lower abundance of Oscillibacter (beta= -.51, 95%CI [-0.74, -.29]), Anaerotruncus (beta=-0.41, 95%CI [-0.61, - 0.21]), Eisenbergiella (beta=-0.39, 95%CI [-0.59, -.19]) and higher abundance of Agathobacter (beta=0.40, 95%CI [0.20, 0.60]) were associated with higher ALM (P<2.0e-04). Lower abundance of Anaerotruncus (beta=-0.32, 95%CI [-0.45, -.19]), Hungatella (beta=-0.26, 95%CI [-0.38, -.15]) and Clostridiales bacterium DTU089 (beta=-0.37, 95%CI [-0.55, -.19]) was associated with higher ALM only in females (P< 2.0e-04). Moreover, the biotin biosynthesis II pathway was positively associated with ALM (beta=0.44, 95% CI [0.24, 0.64]) (P<1.90e-04) in females while no associations were observed in males. We did not observe any robust association of bone traits with gut microbiome features.<br><br>CONCLUSION: Our results indicate that specific genera are associated with ALM in middle-aged and older adults and these associations can present in a sex-specific manner. Overall, our study suggests that the gut microbiome is linked to muscle aging in middle-aged and older adults. However, larger sample sizes are still needed to underpin the specific microbiome features involved.}, }
@article {pmid40034756, year = {2025}, author = {Flammer, ER and Christopher, MW and Powers, ER and Broncucia, H and Steck, AK and Gitelman, SE and Garrett, TJ and Ismail, HM}, title = {Exploring Microbiota-Associated Metabolites in Twins Discordant for Type 1 Diabetes.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.20.25322611}, pmid = {40034756}, abstract = {OBJECTIVE: Identify microbial and microbiota-associated metabolites in monozygotic (MZ) and dizygotic (DZ) twins discordant for type 1 diabetes (T1D) to gain insight into potential environmental factors that may influence T1D.<br><br>RESEARCH DESIGN AND METHODS: Serum samples from 39 twins discordant for T1D were analyzed using a semi-targeted metabolomics approach via liquid chromatography-high-resolution tandem mass spectrometry (LC-HRMS/MS). Statistical analyses identified significant metabolites (p < 0.1) within three groups: All twins (combined group), MZ twins, and DZ twins.<br><br>RESULTS: Thirteen metabolites were identified as significant. 3-indoxyl sulfate and 5-hydroxyindole were significantly reduced in T1D individuals across all groups. Carnitine was reduced, and threonine, muramic acid, and 2-oxobutyric acid were significantly elevated in both All and MZ groups. Allantoin was significantly reduced and 3-methylhistidine was significantly elevated in All and DZ groups.<br><br>CONCLUSIONS: Metabolite dysregulation associated with gut dysbiosis was observed. However, further validation of our findings in a larger cohort is needed.<br><br>ARTICLE HIGHLIGHTS: Why did we undertake this study? We believed this cohort of twins discordant for type 1 diabetes (T1D) would allow for control over genetic variability to examine environmental factors.What is the specific question(s) we wanted to answer? We aimed to identify differences in microbial and microbiota-associated metabolites in twins discordant for T1D to examine the effect of the gut microbiome on T1D.What did we find? Thirteen metabolites were identified as significantly different.What are the implications of our findings? Our results show the dysregulation of several microbial metabolites in twin pairs, suggesting that the gut microbiome plays a role in the pathogenesis of T1D.}, }
@article {pmid40034689, year = {2025}, author = {Arakelyan, NA and Kupriyanova, DA and Vasilevska, J and Rogaev, EI}, title = {Sexual dimorphism in immunity and longevity among the oldest old.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1525948}, pmid = {40034689}, issn = {1664-3224}, mesh = {Humans ; *Longevity/immunology ; *Sex Characteristics ; Female ; Male ; *Gastrointestinal Microbiome/immunology ; Aged, 80 and over ; Aging/immunology ; Immune System/immunology ; Immunity ; Sex Factors ; }, abstract = {Human longevity is a sex-biased process in which sex chromosomes and sex-specific immunity may play a crucial role in the health and lifespan disparities between men and women. Generally, women have a higher life expectancy than men, exhibiting lower infection rates for a broad range of pathogens, which results in a higher prevalence of female centenarians compared to males. Investigation of the immunological changes that occur during the process of healthy aging, while taking into account the differences between sexes, can significantly enhance our understanding of the mechanisms that underlie longevity. In this review, we aim to summarize the current knowledge on sexual dimorphism in the human immune system and gut microbiome during aging, with a particular focus on centenarians, based exclusively on human data.}, }
@article {pmid40034670, year = {2025}, author = {Adair, MG and Tolley, KA and van Vuuren, BJ and da Silva, JM}, title = {Anthropogenic reverberations on the gut microbiome of dwarf chameleons (Bradypodion).}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18811}, pmid = {40034670}, issn = {2167-8359}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics/physiology ; *RNA, Ribosomal, 16S/genetics ; *Lizards/microbiology ; Feces/microbiology ; Ecosystem ; Bacteria/genetics/classification/isolation &amp; purification ; }, abstract = {Exploration of the microbiome has been referred to as a final frontier in biological research. This is due to its precedence for generating insights on the holistic functioning of organismal biology by exploring the interactions between hosts and their associated symbiotic organisms. The microbiomes of many vertebrate groups still require exploration to advance current knowledge and fill previous knowledge gaps. This study generated initial descriptions of the bacterial microbiomes of three species of dwarf chameleon (Bradypodion) from the 16S rRNA gene region targeting the V3 and V4 hypervariable regions. This led to the successful identification of 1,073 and 4,502 independent amplicon sequence variants from buccal swab and faecal material samples, respectively. This newly acquired information is intended as a baseline for future work incorporating holobiont information. The diversity of microbial taxa suggests that the total dwarf chameleon microbiome is similar to other squamates investigated to date, as well as chelonians (Testudines). Microbial frequency differences were noted in comparison to crocodilians (Archosauria) and mammalian groups. Furthermore, this study aimed to examine the influence of habitat transformation on the composition of the microbiome in dwarf chameleons as each of the study species occupy both urban and natural habitats. Given that most urban habitats are highly transformed, the expectation was that microbial assemblages of the gastro-intestinal tracts of all three Bradypodion species would show significant differences between populations (i.e., natural, or urban). It was found, however, that the level of effect was contingent on species: B. melanocephalum populations showed noticeable microbiome differences between urban and natural populations; B. thamnobates showed variations in microbial community dispersions between populations; and B. setaroi showed no significant microbiome differences based on diversity metrics although some frequency differences, in microbiome composition, were observed between populations. We suggest that the magnitude of difference between the habitats occupied by the populations is a factor, given the apparent disparity between the natural and urban habitats for B. melanocephalum as compared to the other two species.}, }
@article {pmid40034495, year = {2025}, author = {Zhao, SY and Meng, YL and Yang, ZH and Li, BL and Li, YY and Han, H and Liu, L and Duan, PF and Chen, ZJ}, title = {Rhizosphere microbiome metagenomics in PGPR-mediated alleviation of combined stress from polypropylene microplastics and Cd in hybrid Pennisetum.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1549043}, pmid = {40034495}, issn = {1664-302X}, abstract = {The simultaneous presence of microplastics (MPs) and heavy metals in soil may result in heightened toxicity, causing more significant adverse effects on plant growth. Plant growth-promoting rhizobacteria (PGPR) have demonstrated significant capacities in alleviating the toxic stress caused by the combined pollution of heavy metals and other contaminants. However, research on the impacts and processes of PGPR in alleviating stress induced by the combined pollution from MPs and heavy metals is still insufficient. This study involved a pot experiment to evaluate the ability of PGPR to mitigate stress induced by the combined pollution from polypropylene microplastic (PP MPs) particles of different sizes (6.5 μm and 830 μm) and the heavy metal cadmium (Cd) in the bioenergy plant hybrid Pennisetum. Moreover, metagenomic analysis was used to examine the effects of PGPR on the rhizospheric microbial community and function. The cocontamination of PP and Cd affected the growth of the hybrid Pennisetum differently depending on the size of the MPs particles, with the aboveground and underground lengths of the 6.5 μm PP + Cd experimental group being smaller than those of the 830 μm PP + Cd group. The PGPRs (Bacillus sp. Y-35, Bacillus sp. Y-62, Bacillus sp. Y-S, and Enterobacter sp. Y-V) successfully alleviated the stress caused by the combined pollution of PP and Cd, resulting in increases of 8.24 and 42.21% in the plant height and dry weight, respectively. The metagenomic studies indicated that the cocontamination of PP and Cd, along with PGPR inoculation, altered the composition of the rhizospheric bacterial community, leading to changes in microbial diversity indices and the composition of dominant groups such as Pseudomonadota, Actinomycetota, and Acidobacteriota. The functional analysis revealed that the main functional groups involved glucose metabolism, energy metabolism, signal transduction, and nucleotide metabolism. The MPs particle size and different PGPR significantly affected functions such as the pentose phosphate pathway, benzoate degradation, and amide biosynthesis. This study provides essential data and scientific evidence on the ecotoxicological effects of simultaneous contamination by MPs and heavy metals, as well as insights into potential bioremediation methods.}, }
@article {pmid40034459, year = {2025}, author = {Xiong, L and Zhang, Z and Dong, S and Lin, T and Yue, X and Chen, F and Guan, W and Zhang, S}, title = {Maternal consumption of glycerol monolaurate optimizes milk fatty acid profile and enhances piglet gut health in association with G protein-coupled receptor 84 (GPR84) activation.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {20}, number = {}, pages = {387-403}, pmid = {40034459}, issn = {2405-6383}, abstract = {This study evaluated the effect of maternal glycerol monolaurate (GML) supplementation during late gestation and lactation on sow reproductive performance, transfer of immunity and redox status, milk fat and fatty acid profile, and fecal microbiota. Eighty multiparous sows (Landrace × Large white) were randomly allocated to two treatment groups (with or without 1000 mg/kg GML) with 40 replicates per treatment. The feeding experiment lasted from d 85 of gestation (G85) to d 23 of lactation (L23). The samples were collected on d 1 (L1) and 21 (L21) of lactation. Our results showed that maternal GML supplementation significantly increased litter weight (P = 0.002), average daily gain of piglets (P = 0.048), and sow average daily feed intake (P = 0.032). Compared with CON group, the concentrations of lauric acid (C12:0; P = 0.022), C16:0 (P = 0.001), and total saturated fatty acids (P = 0.006) in colostrum as well as C12:0 in L21 milk (P = 0.001) were higher in GML group. Besides, the concentrations of immunoglobulin A (IgA) and IgG in colostrum as well as sow and piglet plasma, the total antioxidant capacity and superoxide dismutase activity in sow colostrum were also significantly higher in the GML group (P < 0.05). Microbiome results showed that GML addition increased fecal microbial alpha diversity as well as the relative abundances of short chain fatty acids producing bacteria Ruminococcaceae and Parabacteroides; and decreased the harmful Proteobacteria of sows (P < 0.05). The Spearman analysis showed that the microbial biomarkers Prevotellaceae, Ruminococcaceae, and Parabacteroides were positively correlated with IgA and IgG of sow plasma and milk (P < 0.05). Besides, maternal GML addition up-regulated the relative protein expressions of proliferating cell nuclear antigen, cyclin D1, G protein-coupled receptor 84 (GPR84) and phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt) pathway in the duodenum and jejunum of piglets. Collectively, current findings suggested that maternal GML supplementation enhanced piglet growth during lactation, which might be associated with improving milk fat and lauric acid contents, microbiota derived immunoglobulins transfer, and gut health through potential involvement of GPR84 and PI3K/Akt signaling pathway.}, }
@article {pmid40034457, year = {2025}, author = {Gebeyew, K and Mi, H and Du, R and Gao, M and Diba, D and Tang, S and He, Z and Tan, Z}, title = {Wheat straw and alfalfa hay alone or combined in a high-concentrate diet alters microbial-host interaction in the rumen of lambs.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {20}, number = {}, pages = {444-457}, pmid = {40034457}, issn = {2405-6383}, abstract = {The inclusion of various forages in a normal forage-to-concentrate ratio has widely been reported to reveal the changes that occur in the foregut tissues. However, the mechanism by which the wheat straw, alfalfa hay, or both alter the orchestrated crosstalk of microbiome and host-transcriptome in the rumen of lambs fed a high-concentrate diet is elusive. Sixty-three Hulunbuir lambs were randomly allotted to 3 dietary groups, and each dietary group had 3 pens with 7 lambs. The lambs were fed high-concentrate diets (70%) supplemented with either 30% wheat straw (30S), a mixture of 15% alfalfa hay and 15% wheat straw (30M), or 30% alfalfa hay (30A) over a 2-week adaptation period and a 12-week formal trial. Compared with the 30S and 30A groups, the 30M group had greater (P < 0.05) levels of plasma glucagon-like peptide (GLP-2), interleukin-2 (IL-2). Humoral immunity showed a tendency to increase in the 30M group, as evidenced by the greater levels of plasma immunoglobulins (Ig) A and IgG (P > 0.05). The 16S rRNA result showed that the abundance of Lachnospiraceae (NK3A20 group and unclassified), Olsenella, Shuttleworthia, and Succiniclasticum were enriched in the 30M group. Meanwhile, the abundances of Ruminococcaceae NK4A214 and prevetolla_7 were enriched in 30S and 30A, respectively. The RNA-seq identified 35 shared differentially expressed genes (DEGs) between the "30S vs. 30M" and "30S vs. 30A," enriched in lipid metabolism pathways, including glycerophospholipid and arachidonic acid metabolism. The weighted gene co-expression network analysis results revealed that the expression of genes in the darkred (194 genes) and darkgreen (134 genes) modules showed a strong positive correlation with phenotypic traits and bacterial genera, respectively. The genes in the darkgreen module were involved in carbohydrate, lipid, and amino acid metabolism and showed a wide range of associations with Prevotella_7, Shuttleworthia, and Succiniclasticum, indicating that ruminal microbes might act as a vital driver in the microbiome-host interaction, likely through fermentation of end-products or metabolites. In conclusion, the results indicate that microbiome enrichment in response to feeding wheat straw and alfalfa hay might drive microbiome-host crosstalk to regulate rumen function in lambs fed a high-concentrate diet.}, }
@article {pmid40034456, year = {2025}, author = {Tang, M and Wu, Y and Olnood, CG and Gao, Y and Wang, F and Zhang, Z and Peng, C and Zhou, X and Huang, C and Xiong, X and Yin, Y}, title = {Effects of peroxidized lipids on intestinal morphology, antioxidant capacity and gut microbiome in piglets.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {20}, number = {}, pages = {430-443}, pmid = {40034456}, issn = {2405-6383}, abstract = {This study investigated the effect of peroxidized lipids on piglets' growth performance, intestinal morphology, inflammatory reactions, oxidative stress in the liver, duodenum, jejunum, ileum, and colon, and ileal microbiota. Twenty piglets (Duroc × [Landrace × Yorkshire]; age = 21 d old, BW = 6.5 ± 1 kg) were randomly assigned to two groups with 10 replicates per group and one piglet per replicate. The control group was fed 6% fresh soybean oil and the peroxidized soybean oil (PSO) group fed 6% PSO. The experimental feeding period lasted 24 d. The study found no impact on ADFI, ADG and gain to feed ratio (P > 0.05). However, the PSO group increased the diarrhea index and the serum levels of lactate dehydrogenase triglycerides, cholesterol, low-density lipoprotein cholesterol, and high-density lipoprotein cholesterol (P < 0.05), along with decreased concentrations of alanine aminotransferase and blood urea nitrogen (P < 0.05). For oxidative enzymes, PSO increased the concentration of F2-isoprostane in urine (P = 0.032), malondialdehyde (MDA) in the duodenum (P = 0.001) and jejunum (P = 0.004), decreased thiobarbituric acid reactive substances (TBARS) in the liver (P = 0.001) but increased TBARS in duodenum (P = 0.001), and carbonylated proteins in the duodenum (P = 0.003). For antioxidant enzymes, PSO decreased superoxide dismutase (SOD) in the liver (P = 0.001), colon (P = 0.002), and jejunum (P = 0.015), along with glutathione peroxidase (GSH-Px) in the liver (P = 0.008) and NAD(P)H:quinone oxidoreductase 1 (NQO1) in ileum (P = 0.001). For inflammatory reactions, PSO increased interleukin (IL)-1β concentrations in the duodenum and colon, and IL-10 in the jejunum, while decreasing IL-4 concentration in the duodenum (P < 0.05). For intestinal morphology and ileal microbiota, PSO increased ileal crypt depth, while decreasing the crypt-to-villus ratio (P < 0.05). Peroxidized soybean oil increased the relative abundance of Prevotella, Clostridium_sensu_stricto_1, Clostridium_sensu_stricto_6, Pasteurella and Klebsiella (P < 0.05). In conclusion, this study revealed that PSO worsened diarrhea, increasing the ileal crypt depth and the relative abundance of harmful microbiota, and induced oxidative stress and inflammation in the intestines and liver, primarily in the jejunum and ileum.}, }
@article {pmid40034366, year = {2024}, author = {Al-Abbas, NS and Shaer, NA}, title = {Gut microbiome synthesizes important core metabolites to prevent cognitive decline and mitigate onset and progression of Alzheimer's disease.}, journal = {Journal of Alzheimer's disease reports}, volume = {8}, number = {1}, pages = {1705-1721}, pmid = {40034366}, issn = {2542-4823}, abstract = {BACKGROUND: This study explores how gut metabolites, produced through bacterial metabolism in the gut, influence neurological conditions like Alzheimer's disease (AD). Key metabolites such as succinate and short-chain fatty acids signal through the autonomic nervous system and can cross the blood-brain barrier, impacting central nervous system functions.<br><br>OBJECTIVE: The aim is to examine the role of the gut microbiota in compensating for metabolic deficiencies in AD. By analyzing wild-type (WT) and APP/PS1 mice, the study investigates how the microbiome affects key metabolic processes and whether it can slow AD progression.<br><br>METHODS: High-throughput sequencing data from the gut microbiomes of APP/PS1 transgenic AD model mice and age-matched WT C57BL/6 male mice were analyzed for microbial and metabolite profiles.<br><br>RESULTS: Alpha and beta diversity analyses showed differences in microbial composition between groups. Partial least squares discriminant analysis and Anosim confirmed distinct microbiome profiles in WT and APP/PS1 mice. At the genus level, Vescimonas was more abundant in WT mice, while Odoribacter, Lacrimispora, Helicobacter, Bacteroides, and Alloprevotella were more prevalent in APP/PS1 mice.<br><br>CONCLUSIONS: While taxonomic differences did not directly link specific microorganisms to AD, functional analysis identified key metabolites-acetyl-CoA, glucose, succinate, lipids, choline, and acetylcholine-that may alleviate energy deficits and synaptic dysfunction. This study suggests that the microbiome may help compensate for AD-related impairments, opening avenues for microbiome-based therapies.}, }
@article {pmid40034229, year = {2025}, author = {Zeng, Y and Wu, Q and Guo, M and Teng, F and Jiang, C and Chen, J and Tan, X and Zeng, C and Long, Y and Law, BY and Xu, Y}, title = {Gut microbiota-derived imidazole propionate: an emerging target for the prevention and treatment of cardiometabolic diseases.}, journal = {Frontiers in endocrinology}, volume = {16}, number = {}, pages = {1409119}, pmid = {40034229}, issn = {1664-2392}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Imidazoles/therapeutic use ; *Cardiovascular Diseases/prevention &amp; control ; Animals ; Diabetes Mellitus, Type 2/microbiology/metabolism ; Metabolic Diseases/prevention &amp; control/microbiology ; }, abstract = {Despite significant advancements in prevention and treatment, cardiometabolic diseases continue to pose a high burden of incidence and mortality. The chronic progression of these diseases necessitates the identification of early and complementary therapeutic targets to elucidate and mitigate residual risks in patient care. The gut microbiota acts as a sentinel between internal and external environments, transmitting modified risks associated with these factors to the host. Imidazole propionate (ImP), a histidine metabolite originating from the gut microbiota, gained attention after being found to impair glucose tolerance and insulin signaling several years ago. Epidemiological studies over the past five years have demonstrated a robust correlation between ImP and an increased risk of onset of type 2 diabetes (T2D) and obesity, exacerbation of kidney traits in chronic kidney disease (CKD), progression of atherosclerotic plaques, and elevated mortality rates in heart failure (HF). These findings suggest that ImP may serve as a pivotal target for the prevention and treatment of cardiometabolic diseases. Mechanistic insights have uncovered associations between ImP and insulin resistance, impaired glucose metabolism, chronic inflammation, and intestinal barrier damage. This review provides a comprehensive summary of the current evidence regarding the association between ImP and cardiometabolic impairment, highlighting its potential in advancing personalized approaches to disease prevention and management, and exploring the intricate interplay of diet, gut microbiota, and ImP in cardiovascular metabolic impairment. Overall, this review offers valuable insights into the multifaceted roles of ImP in cardiometabolic diseases, identifies current knowledge gaps, and discusses future research directions.}, }
@article {pmid40034136, year = {2025}, author = {Lee, KH and Coull, BA and Majumder, S and Riviere, PJ and Welch, JLM and Starr, JR}, title = {A Bayesian Multivariate Spatial Point Pattern Model: Application to Oral Microbiome FISH Image Data.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {40034136}, issn = {2331-8422}, abstract = {Advances in cellular imaging technologies, especially those based on fluorescence in situ hybridization (FISH) now allow detailed visualization of the spatial organization of human or bacterial cells. Quantifying this spatial organization is crucial for understanding the function of multicellular tissues or biofilms, with implications for human health and disease. To address the need for better methods to achieve such quantification, we propose a flexible multivariate point process model that characterizes and estimates complex spatial interactions among multiple cell types. The proposed Bayesian framework is appealing due to its unified estimation process and the ability to directly quantify uncertainty in key estimates of interest, such as those of inter-type correlation and the proportion of variance due to inter-type relationships. To ensure stable and interpretable estimation, we consider shrinkage priors for coefficients associated with latent processes. Model selection and comparison are conducted by using a deviance information criterion designed for models with latent variables, effectively balancing the risk of overfitting with that of oversimplifying key quantities. Furthermore, we develop a hierarchical modeling approach to integrate multiple image-specific estimates from a given subject, allowing inference at both the global and subject-specific levels. We apply the proposed method to microbial biofilm image data from the human tongue dorsum and find that specific taxon pairs, such as Streptococcus mitis-Streptococcus salivarius and Streptococcus mitis-Veillonella, exhibit strong positive spatial correlations, while others, such as Actinomyces-Rothia, show slight negative correlations. For most of the taxa, a substantial portion of spatial variance can be attributed to inter-taxon relationships.}, }
@article {pmid40034134, year = {2025}, author = {Wang, S and Wikle, CK and Micheas, AC and Welch, JLM and Starr, JR and Lee, KH}, title = {Inference for Log-Gaussian Cox Point Processes using Bayesian Deep Learning: Application to Human Oral Microbiome Image Data.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {40034134}, issn = {2331-8422}, abstract = {It is common in nature to see aggregation of objects in space. Exploring the mechanism associated with the locations of such clustered observations can be essential to understanding the phenomenon, such as the source of spatial heterogeneity, or comparison to other event generating processes in the same domain. Log-Gaussian Cox processes (LGCPs) represent an important class of models for quantifying aggregation in a spatial point pattern. However, implementing likelihood-based Bayesian inference for such models presents many computational challenges, particularly in high dimensions. In this paper, we propose a novel likelihood-free inference approach for LGCPs using the recently developed BayesFlow approach, where invertible neural networks are employed to approximate the posterior distribution of the parameters of interest. BayesFlow is a neural simulation-based method based on "amortized" posterior estimation. That is, after an initial training procedure, fast feed-forward operations allow rapid posterior inference for any data within the same model family. Comprehensive numerical studies validate the reliability of the framework and show that BayesFlow achieves substantial computational gain in repeated application, especially for two-dimensional LGCPs. We demonstrate the utility and robustness of the method by applying it to two distinct oral microbial biofilm images.}, }
@article {pmid40034118, year = {2025}, author = {Chin, KTC and Yiu, JHC and Cheung, KW and Yuen, LC and Wong, WY and Cai, J and Cheung, SWM and Li, RHW and Woo, CW}, title = {Flagellin in blood and Bifidobacterium pseudocatenulatum in gut are associated with live birth upon IVF-frozen embryo transfer.}, journal = {iScience}, volume = {28}, number = {2}, pages = {111933}, pmid = {40034118}, issn = {2589-0042}, abstract = {The role of gut microbiota in live birth attainment upon in vitro fertilization (IVF) remains unclear. We recruited 67 women, evaluated bacterial constituents in the serum, and analyzed the gut microbiota composition and functions prior to an IVF-frozen embryo transfer (FET). A higher serum flagellin level, residues from flagellated bacteria, was observed in women without live birth after FET. Twelve species showed significant differences in abundance between with and without live birth groups, of which Roseburia inulinivorans and Bifidobacterium pseudocatenulatum were the most important to predict live birth outcome. R. inulinivorans abundances were higher among women with high flagellin levels. The cystathionine β-synthase activity in B. pseudocatenulatum, which may play roles in gut integrity, was a critical factor in the negative correlation with serum flagellin and MCP1 levels. The presence of bacterial residues in the circulation may elicit systemic inflammation and decrease the chances of attaining live birth after FET.}, }
@article {pmid40034103, year = {2025}, author = {Vecin, N and Balukoff, NC and Yaghi, M and Gonzalez, T and Sawaya, AP and Strbo, N and Tomic-Canic, M and Lev-Tov, H and Pastar, I}, title = {Hidradenitis Suppurativa Tunnels: Unveiling a Unique Disease Entity.}, journal = {JID innovations : skin science from molecules to population health}, volume = {5}, number = {3}, pages = {100350}, pmid = {40034103}, issn = {2667-0267}, abstract = {Hidradenitis suppurativa tunnel structures lined with epithelium within the dermis are unique features of advanced disease stages that significantly impair patients' QOL. The presence of hidradenitis suppurativa tunnels is associated with a decreased likelihood of achieving a clinical response, even when receiving biological therapy. The cellular and molecular mechanisms underlying tunnel formation and pathology are only partially understood, which hampers the development of more effective targeted therapies. Tunnels create a unique microenvironment that drives a vicious cycle of hidradenitis suppurativa inflammation, with tunnel keratinocytes exhibiting an activated phenotype characterized by distinct gene expression signatures. In this review, we summarize the current literature and discuss aspects of the pathophysiology of tunnels, including the role of hair follicle epidermal stem cells in tunnel formation, potential role of fibroblast-mediated epithelial-mesenchymal transition, role of dermal papilla fibroblasts, and aberrant proinflammatory repair response contributing to the observed fibrosis and scarring. Finally, tunnel structures are characterized by unique microbial dysbiosis and an overabundance of Gram-negative anaerobes that are not targeted by current therapeutics. In addition to outlining the possible mechanisms of tunnel formation, we provide perspectives on the translation of current knowledge into more effective treatment approaches for patients with hidradenitis suppurativa tunnels.}, }
@article {pmid40033428, year = {2025}, author = {Saigh, BH}, title = {Breastfeeding duration and neurodevelopment: insights into autism spectrum disorders and weaning practices.}, journal = {Journal of health, population, and nutrition}, volume = {44}, number = {1}, pages = {62}, pmid = {40033428}, issn = {2072-1315}, mesh = {Humans ; *Breast Feeding ; *Autism Spectrum Disorder ; *Weaning ; *Child Development ; Infant ; Female ; Time Factors ; Male ; Infant, Newborn ; }, abstract = {This paper examines the complex relationship between breastfeeding duration and the incidence of autism spectrum disorders (ASDs), focusing on identifying the most beneficial weaning period and its subsequent effects on child development. Breastfeeding is widely recognized for its role in promoting early health, strengthening the immune system, and supporting neurodevelopment. However, the debate over its optimal duration persists. Integrating insights from current scientific studies with interpretations of Qur'anic teachings, this study advocates for a breastfeeding duration of 21 months. This duration balances the benefits of extended breastfeeding with potential risks associated with prolonged exposure, reflecting both ancient wisdom and contemporary evidence. Key findings suggest that breastfeeding may play a preventive role in mitigating ASD symptoms and enhancing neurodevelopment through mechanisms such as immune regulation, microbiome diversity, and hormonal pathways. These insights underline the need for further specialized research to explore the long-term impacts of breastfeeding on ASD-related outcomes.}, }
@article {pmid40033386, year = {2025}, author = {Kodikara, S and Lê Cao, KA}, title = {Microbial network inference for longitudinal microbiome studies with LUPINE.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {64}, pmid = {40033386}, issn = {2049-2618}, support = {GNT1159458//National Health and Medical Research Council/ ; }, mesh = {Longitudinal Studies ; Humans ; *Microbiota ; Animals ; Mice ; Microbial Interactions/physiology ; Least-Squares Analysis ; Computer Simulation ; Bacteria/classification/genetics ; }, abstract = {BACKGROUND: The microbiome is a complex ecosystem of interdependent taxa that has traditionally been studied through cross-sectional studies. However, longitudinal microbiome studies are becoming increasingly popular. These studies enable researchers to infer taxa associations towards the understanding of coexistence, competition, and collaboration between microbes across time. Traditional metrics for association analysis, such as correlation, are limited due to the data characteristics of microbiome data (sparse, compositional, multivariate). Several network inference methods have been proposed, but have been largely unexplored in a longitudinal setting.<br><br>RESULTS: We introduce LUPINE (LongitUdinal modelling with Partial least squares regression for NEtwork inference), a novel approach that leverages on conditional independence and low-dimensional data representation. This method is specifically designed to handle scenarios with small sample sizes and small number of time points. LUPINE is the first method of its kind to infer microbial networks across time, while considering information from all past time points and is thus able to capture dynamic microbial interactions that evolve over time. We validate LUPINE and its variant, LUPINE_single (for single time point analysis) in simulated data and four case studies, where we highlight LUPINE's ability to identify relevant taxa in each study context, across different experimental designs (mouse and human studies, with or without interventions, and short or long time courses). To detect changes in the networks across time and groups or in response to external disturbances, we used different metrics to compare the inferred networks.<br><br>CONCLUSIONS: LUPINE is a simple yet innovative network inference methodology that is suitable for, but not limited to, analysing longitudinal microbiome data. The R code and data are publicly available for readers interested in applying these new methods to their studies. Video Abstract.}, }
@article {pmid40033326, year = {2025}, author = {Zhang, L and Cai, Y and Li, L and Hu, J and Jia, C and Kuang, X and Zhou, Y and Lan, Z and Liu, C and Jiang, F and Sun, N and Zeng, N}, title = {Analysis of global trends and hotspots of skin microbiome in acne: a bibliometric perspective.}, journal = {BioData mining}, volume = {18}, number = {1}, pages = {19}, pmid = {40033326}, issn = {1756-0381}, support = {HZ2023-No.233//Zunyi Foundation for Development of Science and Technology/ ; gzwkj2024-362//Science and Technology Project Fund of the Health Commission of Guizhou Province/ ; }, abstract = {BACKGROUND: Acne is a chronic inflammatory condition affecting the hair follicles and sebaceous glands. Recent research has revealed significant advances in the study of the acne skin microbiome. Systematic analysis of research trends and hotspots in the acne skin microbiome is lacking. This study utilized bibliometric methods to conduct in-depth research on the recognition structure of the acne skin microbiome, identifying hot trends and emerging topics.<br><br>METHODS: We performed a topic search to retrieve articles about skin microbiome in acne from the Web of Science Core Collection. Bibliometric research was conducted using CiteSpace, VOSviewer, and R language.<br><br>RESULTS: This study analyzed 757 articles from 1362 institutions in 68 countries, the United States leading the research efforts. Notably, Brigitte Dr&#xe9;no from the University of Nantes emerged as the most prolific author in this field, with 19 papers and 334 co-citations. The research output on the skin microbiome of acne continues to increase, with Experimental Dermatology being the journal with the highest number of published articles. The primary focus is investigating the skin microbiome's mechanisms in acne development and exploring treatment strategies. These findings have important implications for developing microbiome-targeted therapies, which could provide new, personalized treatment options for patients with acne. Emerging research hotspots include skincare, gut microbiome, and treatment.<br><br>CONCLUSION: The study's findings indicate a thriving research interest in the skin microbiome and its relationship to acne, focusing on acne treatment through the regulation of the skin microbiome balance. Currently, the development of skincare products targeting the regulation of the skin microbiome represents a research hotspot, reflecting the transition from basic scientific research to clinical practice.}, }
@article {pmid40033186, year = {2025}, author = {Yu, J and Liu, C and Wang, D and Wan, P and Cheng, L and Yan, X}, title = {Integrated microbiome and metabolome analysis reveals altered gut microbial communities and metabolite profiles in dairy cows with subclinical mastitis.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {115}, pmid = {40033186}, issn = {1471-2180}, support = {No.2023BBB058//Key Research and Development Program of Hubei Province/ ; }, mesh = {Animals ; Cattle ; Female ; *Gastrointestinal Microbiome ; *Mastitis, Bovine/microbiology ; *Metabolome ; *Feces/microbiology ; *Bacteria/classification/isolation &amp; purification/genetics/metabolism ; *RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology/veterinary ; Metabolomics/methods ; }, abstract = {BACKGROUND: Dairy cow mastitis is a common and prevalent disease arose by various complicated pathogeny, which poses serious threat to the health of cows, safety of dairy product and economic benefits for pastures. Due to the high stealthiness and long incubation period, subclinical mastitis (SM) of cows causes enormous economic losses. Besides the infection by exogenous pathogenic microorganisms, previous studies demonstrated that gastrointestinal microbial dysbiosis is one of the crucial causes for occurrence and development of mastitis based on the theory of entero-mammary axis. Whereas, limited researches have been conducted on potential pathological metabolic mechanisms underlying the relationship between gut microbiota and SM in cows.<br><br>RESULTS: The differences in blood parameters, gut microbiome, plasma and fecal metabolome between healthy and SM cows were compared by performing 16&#xa0;S rDNA sequencing and non-targeted metabolomic analysis in the current study. The content of total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), and activity of catalase (CAT), total antioxidant capacity(T-AOC) were significantly decreased, while malondialdehyde (MDA) concentration was dramatically increased in serum of SM cows in comparison with healthy cows. The gut of cows with SM harbored more abundant Cyanobacteria, Proteobacteria, Succinivibrio and Lactobacillus_iners. Moreover, the abundance of Paraprevotella, Coprococcus, Succiniclasticum, Desulfovibrio and Bifidobacterium_pseudolongum were observably reduced in the gut of SM cows. Furthermore, higher abundance of pro-inflammatory metabolites were observed in feces (9(S)-HPODE, 25-hydroxycholesterol, dodecanedioic acid, etc.) and plasma (9-hydroxy-10,12-octadecadienoic acid, 13,14-dihydro PGF1&#x3b1;, 5,6-dehydro arachidonic acid, myristic acid, histamine, etc.) of SM cows. The abundance of certain metabolites with anti-inflammatory and antioxidant properties (mandelic acid, gamma-tocotrienol, deoxycholic acid, etc.) were notably decreased in feces or plasma of cows with SM.<br><br>CONCLUSIONS: The intestinal microbial composition and metabolic profiles of healthy and SM cows were significantly distinct, that were characterized by decreased abundance of intestinal symbiotic bacteria, potential probiotics and anti-inflammatory, antioxidant compounds, along with increased abundance of potential pro-inflammatory bacteria, lipid metabolites, and the occurrence of oxidative stress in cows suffered from SM. The results of this study further enriched our understanding of the correlations between gut microbiota and metabolic profiles and SM, which provided insight into the formulation of management strategies for SM in cows.}, }
@article {pmid40033182, year = {2025}, author = {Driuchina, A and Isola, V and Hulmi, JJ and Salmi, VM and Hintikka, J and Ahtiainen, JP and Pekkala, S}, title = {Unveiling the impact of competition weight loss on gut microbiota: alterations in diversity, composition, and predicted metabolic functions.}, journal = {Journal of the International Society of Sports Nutrition}, volume = {22}, number = {1}, pages = {2474561}, doi = {10.1080/15502783.2025.2474561}, pmid = {40033182}, issn = {1550-2783}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Male ; *Weight Loss/physiology ; *Feces/microbiology ; Young Adult ; Adult ; Cytokines/metabolism/blood ; Female ; Body Composition ; Caloric Restriction ; Sports Nutritional Physiological Phenomena ; Exercise/physiology ; Chemokines/metabolism ; Athletes ; }, abstract = {BACKGROUND: Competitive sports and sports nutrition, popular among amateur athletes aiming for a lean physique, have limited research on gut microbiota.<br><br>METHODS: We conducted a 46-week study to analyze the consequences of fat loss and diet restrictions in 23 fitness athletes who prepared for a physique competition. Body composition, dietary intakes, serum cytokines and chemokines, and fecal samples were analyzed.<br><br>RESULTS: Fat loss through caloric restriction and aerobic exercise led to an increased phylogenetic diversity of gut microbiota and changes in the composition of gut microbiota, with Faecalibacterium, Lachnospiraceae, Bacteroides, and Intestinimonas showing altered abundances. Fat loss also changed the predicted microbial functions responsible for the metabolism of carbohydrates and amino acids. Consumption of energy, carbohydrates, fiber, vitamins and minerals, and various fatty acids decreased during the preparation for the competition, which was partly associated with changes in gut microbiota. Several cytokine levels decreased (IL1a, IL1b, IL10, and TFN&#x3b1;), and certain chemokine levels increased (GROa and RANTES). During the 23-week regain period after the competition, gut microbiota showed signs of recovery, with increased diversity compared to pre- and post-competition measurements. Most taxonomic changes returned to their baseline levels after the regain period.<br><br>CONCLUSIONS: The study highlights the dynamic nature of gut microbiota and its response to fat loss and regain in non-obese fitness/physique competitors and provides novel insights into how competitive sports and sports nutrition can influence the gut ecosystem.}, }
@article {pmid40033140, year = {2025}, author = {Thakur, BK and Malaise, Y and Choudhury, SR and Neustaeter, A and Turpin, W and Streutker, C and Copeland, J and Wong, EOY and Navarre, WW and Guttman, DS and Jobin, C and Croitoru, K and Martin, A}, title = {Dietary fibre counters the oncogenic potential of colibactin-producing Escherichia coli in colorectal cancer.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40033140}, issn = {2058-5276}, support = {PJT-173501//Gouvernement du Canada | Instituts de Recherche en Sant&#xe9; du Canada | CIHR Skin Research Training Centre (Skin Research Training Centre)/ ; }, abstract = {Diet, microbiome, inflammation and host genetics have been linked to colorectal cancer development; however, it is not clear whether and how these factors interact to promote carcinogenesis. Here we used Il10[-/-] mice colonized with bacteria previously associated with colorectal cancer: enterotoxigenic Bacteroides fragilis, Helicobacter hepaticus or colibactin-producing (polyketide synthase-positive (pks[+])) Escherichia coli and fed either a low-carbohydrate (LC) diet deficient in soluble fibre, a high-fat and high-sugar diet, or a normal chow diet. Colonic polyposis was increased in mice colonized with pks[+] E. coli and fed the LC diet. Mechanistically, mucosal inflammation was increased in the LC-diet-fed mice, leading to diminished colonic PPAR-γ signalling and increased luminal nitrate levels. This promoted both pks[+] E. coli growth and colibactin-induced DNA damage. PPAR-γ agonists or supplementation with dietary soluble fibre in the form of inulin reverted inflammatory and polyposis phenotypes. The pks[+] E. coli also induced more polyps in mismatch-repair-deficient mice by inducing a senescence-associated secretory phenotype. Moreover, oncogenic effects were further potentiated by inflammatory triggers in the mismatch-repair-deficient model. These data reveal that diet and host genetics influence the oncogenic potential of a common bacterium.}, }
@article {pmid40033063, year = {2025}, author = {Metwaly, A and Kriaa, A and Hassani, Z and Carraturo, F and Druart, C and ,  and Arnauts, K and Wilmes, P and Walter, J and Rosshart, S and Desai, MS and Dore, J and Blottiere, HM and Maguin, E and Haller, D}, title = {A Consensus Statement on establishing causality, therapeutic applications and the use of preclinical models in microbiome research.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, pmid = {40033063}, issn = {1759-5053}, abstract = {The gut microbiome comprises trillions of microorganisms and profoundly influences human health by modulating metabolism, immune responses and neuronal functions. Disruption in gut microbiome composition is implicated in various inflammatory conditions, metabolic disorders and neurodegenerative diseases. However, determining the underlying mechanisms and establishing cause and effect is extremely difficult. Preclinical models offer crucial insights into the role of the gut microbiome in diseases and help identify potential therapeutic interventions. The Human Microbiome Action Consortium initiated a Delphi survey to assess the utility of preclinical models, including animal and cell-based models, in elucidating the causal role of the gut microbiome in these diseases. The Delphi survey aimed to address the complexity of selecting appropriate preclinical models to investigate disease causality and to study host-microbiome interactions effectively. We adopted a structured approach encompassing a literature review, expert workshops and the Delphi questionnaire to gather insights from a diverse range of stakeholders. Experts were requested to evaluate the strengths, limitations, and suitability of these models in addressing the causal relationship between the gut microbiome and disease pathogenesis. The resulting consensus statements and recommendations provide valuable insights for selecting preclinical models in future studies of gut microbiome-related diseases.}, }
@article {pmid40032901, year = {2025}, author = {Brar, G and Ngor, L and McFrederick, QS and Torson, AS and Rajamohan, A and Rinehart, J and Singh, P and Bowsher, JH}, title = {High abundance of lactobacilli in the gut microbiome of honey bees during winter.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {7409}, pmid = {40032901}, issn = {2045-2322}, mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome ; *Lactobacillus/genetics/isolation &amp; purification ; *Seasons ; *RNA, Ribosomal, 16S/genetics ; }, abstract = {Honey bee gut microbiota play specific roles in promoting host growth and physiology by regulating the immune system, behavior, metabolism, and neurological processes. While the gut microbiota of honey bee queens, workers, and larvae has been extensively studied, less is known about the composition of gut microbiota in the winter worker bees. This study investigates the dynamics of the gut microbiota in overwintering adult worker bees, focusing on two commercial bee strains: Bolton™ bees and Mann Lake™ bees. These Apis mellifera strains were investigated under different storage conditions (indoor storage at 6 °C and outdoor storage in natural conditions) during the winter months (October, November, and December). Utilizing 16S rRNA gene amplicon sequencing, we characterized the microbial composition of the whole gut. We observed the Lactobacilli dominated in all the overwintering honey bee guts with a significantly higher abundance of unclassified Lactobacillus species in November, while Lactobacillus apis showed significantly higher abundance in October. Bolton bees exhibited significantly higher abundance levels of Bartonella (denoted as uncultured) and Bifidobacterium, along with an unexpected presence of Wolbachia. In contrast, Mann Lake bees demonstrated an increased abundance of Commensalibacter. Our results suggest that Shannon diversity is influenced by the month rather than by the bee strain or storage conditions. We also found significant differences in Bray Curtis diversity index by month. Overall, taxonomical abundance was not affected by whether the hives were stored outside or in constant temperature indoor storage. However, various bacterial species showed differences in abundance across different months, with slight variations observed between bee strains. Given the potential benefits of the honey bee gut microbiome for health and nutrition, our data suggests that the genus Lactobacillus may play a significant role in bee health during winter and overwintering storage.}, }
@article {pmid40032755, year = {2025}, author = {Singh, A and Chauhan, R and Prasad, R and Agrawal, AA and Sah, P and Goel, A}, title = {Unveiling the potential of bioslurry and biogenic ZnO nanoparticles formulation as significant bionanofertilizer by ameliorating rhizospheric microbiome of Vigna radiata.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {40032755}, issn = {1618-1905}, abstract = {Advancements in nanotechnology, particularly the use of bionanofertilizers, show promise for sustainable agriculture by enhancing soil health and reducing reliance on conventional fertilizers. This study explored the impact of a bioslurry and biogenic zinc oxide (ZnO) nanoparticle formulation on microbial diversity in the rhizosphere of Vigna radiata (mung bean) using 16S rRNA sequencing. High-quality reads from both untreated and treated soil samples revealed a dominance of Archaea, though its proportion was reduced in the treated sample (66% in untreated, 58% in treated). The treated soil showed an increased abundance of beneficial bacterial phyla, including Acidobacteria (+ 6%), Actinobacteria (+ 2%), and Firmicutes (+ 2%). Notably, Acidobacteria-6 and Chloroacidobacteria, essential for nutrient cycling, were enriched in treated soil. Alpha diversity (Chao1 and Shannon indices) was lower in treated samples, indicating selective enhancement of beneficial microbes. Functional analyses like Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) and Statistical Analysis of Taxonomic and Functional Profiles (STAMP) analysis highlighted increased pathways related to motility, chemotaxis, and metabolic processes in the treated soil. These findings suggest that ZnO NPs and bioslurry treatment at 250 ppm improves soil microbial composition and functional attributes, supporting its potential as a bionanofertilizer for soil health restoration and enhanced plant growth.}, }
@article {pmid40032666, year = {2025}, author = {Guggeis, MA and Harris, DM and Welz, L and Rosenstiel, P and Aden, K}, title = {Microbiota-derived metabolites in inflammatory bowel disease.}, journal = {Seminars in immunopathology}, volume = {47}, number = {1}, pages = {19}, pmid = {40032666}, issn = {1863-2300}, support = {iTREAT//BMBF/ ; 01ZX1915A//BMBF/ ; 01ZX2215//BMBF/ ; RU5042//Deutsche Forschungsgemeinschaft/ ; RU5042//Deutsche Forschungsgemeinschaft/ ; ExC2167//Deutsche Forschungsgemeinschaft/ ; CRC 1182 C2//Deutsche Forschungsgemeinschaft/ ; 2020_EKCS.11//Else Kr&#xf6;ner-Fresenius-Stiftung/ ; miGut Health//H2020 European Research Council/ ; }, mesh = {Humans ; *Inflammatory Bowel Diseases/metabolism/etiology/microbiology/immunology ; *Gastrointestinal Microbiome/immunology ; Animals ; *Metabolome ; Metabolomics/methods ; Disease Susceptibility ; Dysbiosis ; Biomarkers ; Immunomodulation ; }, abstract = {Understanding the role of the gut microbiota in the pathogenesis of inflammatory bowel diseases (IBD) has been an area of intense research over the past decades. Patients with IBD exhibit alterations in their microbial composition compared to healthy controls. However, studies focusing solely on taxonomic analyses have struggled to deliver replicable findings across cohorts regarding which microbial species drive the distinct patterns in IBD. The focus of research has therefore shifted to studying the functionality of gut microbes, especially by investigating their effector molecules involved in the immunomodulatory functions of the microbiota, namely metabolites. Metabolic profiles are altered in IBD, and several metabolites have been shown to play a causative role in shaping immune functions in animal models. Therefore, understanding the complex communication between the microbiota, metabolites, and the host bears great potential to unlock new biomarkers for diagnosis, disease course and therapy response as well as novel therapeutic options in the treatment of IBD. In this review, we primarily focus on promising classes of metabolites which are thought to exert beneficial effects and are generally decreased in IBD. Though results from human trials are promising, they have not so far provided a large-scale break-through in IBD-therapy improvement. We therefore propose tailored personalized supplementation of microbiota and metabolites based on multi-omics analysis which accounts for the individual microbial and metabolic profiles in IBD patients rather than one-size-fits-all approaches.}, }
@article {pmid40032486, year = {2025}, author = {Dong, L and Lou, W and Wang, J}, title = {β-Carotene-loaded cationic nanoparticles ameliorate MASLD via modulating lipid homeostasis and gut microbiome.}, journal = {Food research international (Ottawa, Ont.)}, volume = {205}, number = {}, pages = {115816}, doi = {10.1016/j.foodres.2025.115816}, pmid = {40032486}, issn = {1873-7145}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *beta Carotene/pharmacology ; *Nanoparticles/chemistry ; Mice ; *Lipid Metabolism/drug effects ; Homeostasis ; Male ; Mice, Inbred C57BL ; Cations ; Fatty Liver/drug therapy/metabolism ; Disease Models, Animal ; Insulin Resistance ; }, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is, increasingly, a major threat to human health, yet without any approved drug. β-carotene (BC) contributes to alleviating several metabolic diseases. However, the bioavailability of BC is hindered by hydrophobicity and environmental sensitivity. Herein, we explore the utilization of cationic lipid-assisted nanoparticles to achieve efficient delivery of BC. In the MASLD model, NP-BC ameliorated the development of metabolic disorders, insulin resistance, inflammatory injury and hepatic steatosis. Transcriptomic analysis showed that NP-BA rectifies various pathways involved in steatosis development by inhibiting the PI3K/AKT/mTOR pathway and PPARγ gene expression. Meanwhile, NP-BC also reshaped the composition of gut microbiota in MASLD mice by reducing the Firmicutes/Bacteroidetes ratio and increasing the abundance of beneficial bacteria. Taken together, our study demonstrates that NP-BC can improve MASLD and may be a promising candidate for treating MASLD.}, }
@article {pmid40032457, year = {2025}, author = {Ge, D and Zheng, L and Liu, L and Chen, X and Zhou, J and Ge, H and Guo, L and Hua, H and Wang, R and Zhang, L}, title = {The dynamics impact of phlorizin on gut microbiota and metabolites in an in vitro fermentation model.}, journal = {Food research international (Ottawa, Ont.)}, volume = {205}, number = {}, pages = {115930}, doi = {10.1016/j.foodres.2025.115930}, pmid = {40032457}, issn = {1873-7145}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Fermentation ; *Rats, Sprague-Dawley ; *Feces/microbiology ; Mice ; Rats ; *Phlorhizin/pharmacology/metabolism ; Male ; RNA, Ribosomal, 16S/genetics ; Fatty Acids, Volatile/metabolism ; Lactobacillus johnsonii/metabolism ; Lactobacillus/metabolism/drug effects ; }, abstract = {The multiple beneficial effects, but low bioavailability of phlorizin (PHZ) have sparked discussion about its role in interaction with the gut microbiota. In this study, the effects of PHZ on the fecal microbiota animals of different origins were investigated using an in vitro fermentation model. In the fermentation system of PHZ using SD rat feces, the dynamic variations of the bacterial profile, SCFAs, and organic acids were detected using 16S rRNA gene sequencing, GC-MS, and LC-MS/MS. The results showed that PHZ treatment significantly increased the phylum Bacteroidota and transiently reduced Firmicutes at 6 h. At the genus level, PHZ consistently increased the abundance of Lactobacillus (especially Lactobacillus johnsonii), significantly decreased the abundance of Ligilactobacillus and Limosilactobacillus, and temporarily suppressed Streptococcus after 12 h. Similarly, in the fermentation system using db/db mouse feces, PHZ enriched the abundance of Lactobacillus and Lactobacillus johnsonii. Monoculture of Lactobacillus johnsonii ATCC 33200 showed that PHZ could directly stimulate its growth. Meanwhile, we found that PHZ could significantly increase the production of butyric, isobutyric, isovaleric, valeric, and caproic acids. Organic acid analysis showed an increasing trend in succinic acid and a significant reduction in L-malic acid in the post-PHZ group. Correlation analysis revealed that the abundance of Lactobacillus positively correlated with the concentration of SCFAs and succinic acid, while negatively correlated with L-malic acid. These findings suggest that PHZ may regulate intestinal balance by promoting Lactobacillus johnsonii growth and modulating SCFA and specific organic acid levels. Our study highlights that natural polyphenol PHZ has a health-promoting potential by modulating gut microbiota.}, }
@article {pmid40032396, year = {2025}, author = {Zimmermann, P and Kurth, S and Giannoukos, S and Stocker, M and Bokulich, NA}, title = {NapBiome trial: Targeting gut microbiota to improve sleep rhythm and developmental and behavioural outcomes in early childhood in a birth cohort in Switzerland - a study protocol.}, journal = {BMJ open}, volume = {15}, number = {3}, pages = {e092938}, doi = {10.1136/bmjopen-2024-092938}, pmid = {40032396}, issn = {2044-6055}, mesh = {Humans ; *Gastrointestinal Microbiome ; Switzerland ; Infant ; Infant, Newborn ; *Sleep/physiology ; Double-Blind Method ; Child Development ; Infant, Premature ; Child, Preschool ; Brain-Gut Axis ; Female ; Randomized Controlled Trials as Topic ; Male ; Probiotics/therapeutic use ; Multicenter Studies as Topic ; }, abstract = {INTRODUCTION: The gut-brain axis plays a crucial role in the regulation and development of psychological and physical processes. The first year of life is a critical period for the development of the gut microbiome, which parallels important milestones in establishing sleep rhythm and brain development. Growing evidence suggests that the gut microbiome influences sleep, cognition and early neurodevelopment. For term-born and preterm-born infants, difficulties in sleep regulation may have consequences on health. Identifying effective interventions on the gut-brain axis in early life is likely to have long-term implications for the health and development of at-risk infants.<br><br>METHODS AND ANALYSES: In this multicentre, four-group, double-blinded, placebo (PLC)-controlled randomised trial with a factorial design, 120 preterm-born and 260 term-born infants will be included. The study will investigate whether the administration of daily synbiotics or PLC for a duration of 3&#x2009;months improves sleep patterns and neurodevelopmental outcomes up to 2 years of age. The trial will also: (1) determine the association between gut microbiota, sleep patterns and health outcomes in children up to 2 years of age; and (2) leverage the interactions between gut microbiota, brain and sleep to develop new intervention strategies for at-risk infants.<br><br>ETHICS AND DISSEMINATION: The NapBiome trial has received ethical approval by the Committee of Northwestern and Central Switzerland and Canton Vaud, Switzerland (#2024-01681). Outcomes will be disseminated through publication and will be presented at scientific conferences. Metagenomic data will be shared through the European Nucleotide Archive.<br><br>TRIAL REGISTRATION NUMBER: The US National Institutes of Health NCT06396689.}, }
@article {pmid40032061, year = {2025}, author = {Burden, E and Seyoum, Y and Evans, JP and Thomas, W and Kitson, J and Batten, T and Patel, R and van der Giezen, M and Smith, C}, title = {Mapping the Microbial Landscape and Variations Based on Biological Sex, Age and Biopsy Location in the Shoulder Skin Microbiome.}, journal = {Journal of shoulder and elbow surgery}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jse.2025.01.044}, pmid = {40032061}, issn = {1532-6500}, abstract = {BACKGROUND: The organisms responsible for periprosthetic joint infections (PJI) of the shoulder are often skin pathogens originating from the patient's own skin flora at the time of surgery. Understanding the normal skin flora around the shoulder is an important step to identify the range of organisms that could be responsible for PJI, and ensure optimization of culture mediums to identify them. This study aimed to provide the first description of the shoulder skin microbiome using high-throughput next-generation sequencing methodology, and explore variations by age, biological sex and biopsy location.<br><br>METHODS: Patients undergoing arthroscopic surgery were approached for informed consent to have punch biopsies taken from anterior, lateral and posterior arthroscopy portal sites. DNA extraction was undertaken followed by Illumina sequencing, focusing on the V3-V4 regions of the 16S rRNA gene. Amplicon sequence variants (ASV) were generated using Deblur workflow and used for taxonomic assignment. Variation in the microbiota community based on age, biological sex and biopsy location was assessed through alpha and beta diversity metric calculations using phyloseq R package.<br><br>RESULT: Sixty-two patients (24 female, 38 male) aged 18 to 80 were recruited, resulting in 186 punch biopsy samples for analysis. Following removal of low-prevalence taxa, 606 ASVs were aggregated at genus level resulting in 214 genera across 13 phyla. The top 20 most abundant genera accounted for 73.5% of the overall sequence count. Cutibacterium was the most abundant genus within the study population, followed by Ralstonia, Staphylococcus, Bacteroides and Streptococcus. Significant differences were observed in beta diversity metrics when comparing by biological sex, which accounted for 3.9%-5.3% of variation in the microbial community, but not age or biopsy location. Males displayed a greater proportion of Gram-positive and aerobic bacteria while females exhibited a greater proportion of Gram-negative and stress tolerant bacteria.<br><br>CONCLUSION: This is the first study to look specifically at the microbiome of the cutaneous shoulder and describe the most abundant genera and compositional differences based on age, biological sex and biopsy location. Biological sex was the only host co-variant studied which reached significance in explaining microbiota variation. The top 20 most abundant genera, accounting for 74% of the overall sequence count, would be isolated with standard microbiological culture. As such this study does not highlight a need to change current culture investigation practice for shoulder PJI, but serves as an important catalogue of skin commensals around the operative site in shoulder surgery.}, }
@article {pmid40032028, year = {2025}, author = {Ismaiah, MJ and Kwan Lo, EK and Chen, C and Shing-Jie Tsui, J and Johnson-Hill, WA and Felicianna,  and Zhang, F and Matthew Leung, HK and Oger, C and Durand, T and Chung-Yung Lee, J and El-Nezami, H}, title = {Alpha-aminobutyric acid administration suppressed visceral obesity and modulated hepatic oxidized PUFA metabolism via gut microbiota modulation.}, journal = {Free radical biology &amp; medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.freeradbiomed.2025.02.029}, pmid = {40032028}, issn = {1873-4596}, abstract = {BACKGROUND: High-fat diet (HFD) is associated with visceral obesity due to disruption in the lipid metabolism and gut dysbiosis. These symptoms may contribute to hepatic steatosis and the formation of oxidized polyunsaturated fatty acids (PUFAs). Alpha-aminobutyric acid (ABA) is an amino-acid derived metabolite, and its concentration has been correlated with several metabolic conditions and gut microbiome diversity while its direct effects on visceral obesity, lipid metabolism and the gut microbiota are not well understood. This study was designed to investigate the effect of physiological dose of ABA on diet-induced visceral obesity and lipid metabolism dysregulation by examining the fatty acids and oxidized PUFAs profile in the liver as well as the gut microbiota.<br><br>RESULTS: ABA administration reduced visceral obesity by 28% and lessened adipocyte hypertrophy. The expression of liver Cd36 was lowered by more than 50% as well as the saturated and monounsaturated FA concentration. Notably, the desaturation index for C16 and C18 FAs that are correlated with adiposity were reduced. The concentration of several DHA-derived oxidized PUFAs were also enhanced. Faecal metagenomics sequencing revealed enriched abundance of Leptogranulimonas caecicola and Bacteroides sp. ZJ-18 and were positively correlated with several DHA- and ALA-derived oxidized PUFAs in ABA group.<br><br>CONCLUSION: Our study revealed the modulatory effect of physiological dose of ABA on attenuating visceral obesity, reducing hepatic steatosis, and promoting the production of anti-inflammatory oxidized PUFAs that were potentially mediated by the gut microbiota.}, }
@article {pmid40031897, year = {2025}, author = {Loupy, KM and Dawud, LM and Zambrano, CA and Lee, T and Heinze, JD and Elsayed, AI and Hassell, JE and D'Angelo, HM and Frank, MG and Maier, SF and Brenner, LA and Lowry, CA}, title = {Effects of oral administration of the probiotic Lactobacillus rhamnosus GG on the proteomic profiles of cerebrospinal fluid and immunoregulatory signaling in the hippocampus of adult male rats.}, journal = {Neuroimmunomodulation}, volume = {}, number = {}, pages = {1-35}, doi = {10.1159/000544842}, pmid = {40031897}, issn = {1423-0216}, abstract = {INTRODUCTION: The microbiome-gut-brain axis, by modulating bidirectional immune, metabolic, and neural signaling pathways in the host, has emerged as a target for the prevention and treatment of psychiatric and neurological disorders. Oral administration of the probiotic bacterium Lactobacillus rhamnosus GG (LGG; ATCC 53103) exhibits anti-inflammatory effects, although the precise mechanisms by which LGG benefits host physiology and behavior are not known. The goal of this study was to explore the general effects of LGG on the cerebrospinal fluid (CSF) proteome and a biological signature of anti-inflammatory signaling in the central nervous system (CNS) of undisturbed, adult male rats.<br><br>METHODS: Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics were conducted using CSF samples collected after 21 days of oral treatment with live LGG (3.34 x 107 colony-forming units (CFU)/mL in the drinking water (resulting in an estimated delivery of ~1.17 x 109 CFU/day/rat) or water vehicle. Gene enrichment analysis (using DAVID, v. 6.8) and protein-protein interactions (using STRING, v. 11) were used to explore physiological network changes in CSF. Real time reverse transcription polymerase chain reaction (real time RT-PCR) was performed to assess gene expression changes of anti-inflammatory cytokines in the hippocampus. Genes associated with anti-inflammatory signaling that were analyzed included Il10, Tgfb1, Il4, and IL-4-responsive genes, Cd200, Cd200r1, and Mrc1 (Cd206).<br><br>RESULTS: Oral LGG administration altered the abundance of CSF proteins, increasing the abundance of five proteins (cochlin, NPTXR, reelin, Sez6l, and VPS13C) and decreasing the abundance of two proteins (CPQ, IGFBP-7) in the CSF. Simultaneously, LGG increased the expression of Il10 mRNA, encoding the anti-inflammatory cytokine interleukin 10, in the hippocampus.<br><br>CONCLUSION: Oral LGG altered the abundance of CSF proteins associated with extracellular scaffolding, synaptic plasticity, and glutamatergic signaling. These data are consistent with the hypothesis that oral administration of LGG may improve memory and cognition, and may promote a physiological resilience to neurodegenerative disease, by increasing glutamatergic signaling and promoting an anti-inflammatory environment in the brain.}, }
@article {pmid40031421, year = {2025}, author = {Wang, B and Guo, Y and Li, X and Dong, C and Sha, H and Li, H and Zhao, Z and Li, T}, title = {Phytostabilization potential and microbial response to the reclamation of native Cynodon dactylon in spoil heaps from a multiple-metal mining site in Southwest China.}, journal = {Journal of environmental management}, volume = {378}, number = {}, pages = {124758}, doi = {10.1016/j.jenvman.2025.124758}, pmid = {40031421}, issn = {1095-8630}, abstract = {Phytocapping offers a sustainable approach for managing exposed tailings by mitigating pollutant spread and enhancing phytoremediation. This study investigates the potential of Bermudagrass (Cynodon dactylon) as a pioneering plant for rehabilitating tailings from an open-pit lead-zinc mine in Southwest China. Our findings demonstrate that Bermudagrass significantly improved soil quality and multifunctionality compared to adjacent bare tailings. Soil improvements included increases in organic matter (107%), total and available nitrogen (50% and 110%, respectively), available phosphorus (170%), and soil enzyme activities, including β-glucosidase (170%), sucrase (1729%), alkaline phosphatase (3722%), and acid phosphatase (168%). The reclamation process also promoted microbial community succession, altering community composition, improving microbial diversity, and enhancing bacterial biomass from (0.89 ± 0.54) × 10[15] to (9.06 ± 3.25) × 10[15] copies/g in rhizosphere soils. Greenhouse experiments further confirmed Bermudagrass's resilience to cadmium (Cd), with both mining and non-mining ecotypes thriving in tailing soils and Cd[2+] hydroponic solutions (up to 44.5 μM) without evident phytotoxicity. Bermudagrass roots exhibited exceptional Cd accumulation (bioconcentration factor: 181-1006) while minimizing Cd translocation to shoots (translocation factor: <0.13). Inoculation with Funneliformis mosseae, a restored root-mutually symbiotic fungus, further mitigated Cd-induced phytotoxicity and enhanced plant growth. These findings highlight Bermudagrass as a promising pioneer species for phytostabilization in severely contaminated mining environments, with its rhizosphere microbiome playing a critical role in facilitating ecosystem restoration. Sustainable plant establishment in mine waste rock requires concurrent development of belowground fertility and healthy rhizospheric soil. Ultimately, successful revegetation depends on integrated above and belowground development to achieve long-term ecological restoration.}, }
@article {pmid40031410, year = {2025}, author = {Schwaiger, G and Matt, M and Bromann, S and Clauß, M and Elsner, M and Seidel, M}, title = {Rapid quantification of Legionella in agricultural air purification systems from fattening pig houses with culture-independent methods.}, journal = {International journal of hygiene and environmental health}, volume = {266}, number = {}, pages = {114547}, doi = {10.1016/j.ijheh.2025.114547}, pmid = {40031410}, issn = {1618-131X}, abstract = {Fattening pig houses often utilize biological agricultural exhaust air purification systems (APS) that employ an active microbiome to degrade nitrogen. Consequently, disinfection cannot be applied, and a neutral pH value must be maintained. However, the biofilm in biotrickling filters and a higher temperature can potentially facilitate the growth of Legionella spp. To investigate the occurrence of Legionella spp. or even the pathogen Legionella pneumophila in these systems, traditional cultivation methods proved impractical due to overgrowth and long turnaround times from sampling in the field to results in the laboratory. Therefore, innovative concepts for rapid and cultivation-independent analysis of Legionella spp. are highly demanded. In this study, two rapid analysis methods were applied using a standard addition qPCR method for the detection of L. pneumophila Sg1 and Legionella spp. as well as flow cytometry coupled with immunomagnetic separation (IMS-FCM) for the detection of viable L. pneumophila. Three APS were monitored over a period of more than a year during summer, winter, and intermediate seasons. While cultivation failed to quantify any Legionella spp., the standard addition qPCR quantified 230 to 9500 Legionella spp. cells per m[3] in air passing through the APS (clean gas). In process water that is used for circulating washing of the APS a high occurrence of 10[4] to 2.9 × 10[5]Legionella spp. cells/mL was measured. By IMS-FCM it was confirmed that viable L. pneumophila in concentrations higher than 100 cells/mL for process water and higher than 100 cells/m[3] in clean gas were found in all seasons. In contrast, Legionella spp. or L. pneumophila were rarely found in air directly from the barn (raw gas). We see no risk coming from the closed barn itself but there is a health risk, because the contamination of viable L. pneumophila in process water is not efficiently reduced in clean gas.}, }
@article {pmid40030297, year = {2024}, author = {Cui, Z and Wu, Y and Zhang, QH and Wang, SG and Guo, ZH}, title = {NPENN: A Noise Perturbation Ensemble Neural Network for Microbiome Disease Phenotype Prediction.}, journal = {IEEE journal of biomedical and health informatics}, volume = {PP}, number = {}, pages = {}, doi = {10.1109/JBHI.2024.3507789}, pmid = {40030297}, issn = {2168-2208}, abstract = {With advances in microbiomics, the crucial role of microbes in disease progression is increasingly recognized. However, predicting disease phenotypes using microbiome data remains challenging due to data complexity, heterogeneity, and limited model generalization. Current methods often depend on specific datasets and are vulnerable to adversarial attacks. To address these issues, this paper introduces a novel Noise Perturbation Ensemble Neural Network model (NPENN), which combines noise mechanisms with Gradient Boosting (GB) techniques for robust neural network ensemble learning. NPENN, validated on multiple microbiome datasets, shows superior accuracy and generalization compared to traditional methods, effectively handling data complexity and variability. This approach enhances model robustness and feature learning by integrating GB prior knowledge. Additionally, the study explores microbial community roles in various diseases, providing insights into disease mechanisms and potential biomarkers for personalized precision diagnosis and treatment strategies.}, }
@article {pmid40030030, year = {2025}, author = {Ghimire, S and Lehman, PC and Aguilar Meza, LS and Shahi, SK and Hoang, J and Olalde, H and Paullus, M and Cherwin, C and Wang, K and Gill, C and Cho, T and Mangalam, AK}, title = {Specific microbial ratio in the gut microbiome is associated with multiple sclerosis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {10}, pages = {e2413953122}, doi = {10.1073/pnas.2413953122}, pmid = {40030030}, issn = {1091-6490}, support = {R01AI137075//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1I01CX002212//U.S. Department of Veterans Affairs (VA)/ ; P30 ES005605/ES/NIEHS NIH HHS/United States ; T32AI007260//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {*Gastrointestinal Microbiome ; *Multiple Sclerosis/microbiology ; Animals ; Humans ; Mice ; Female ; *Dysbiosis/microbiology ; *Feces/microbiology ; Male ; Akkermansia ; Adult ; Encephalomyelitis, Autoimmune, Experimental/microbiology ; Middle Aged ; Bifidobacterium ; Prevotella/isolation &amp; purification ; Mice, Inbred C57BL ; Case-Control Studies ; }, abstract = {Gut microbiota dysbiosis is associated with multiple sclerosis (MS), but the causal relationship between specific gut bacteria and MS pathogenesis remains poorly understood. Therefore, we profiled the stool microbiome of people with MS (PwMS) and healthy controls (HC) using shotgun metagenomic sequencing. PwMS showed a distinct microbiome compared to HC, with Prevotella copri (PC) and Blautia species as drivers of microbial communities in HC and PwMS, respectively. Administration of MS-driving Blautia species (Blautia wexlerae; BW) to mice resulted in increased levels of gut inflammatory markers and altered microbiota with increased capacity to induce proinflammatory cytokines. Utilizing experimental autoimmune encephalomyelitis (EAE), an animal model of MS, we identified a lower gut Bifidobacterium to Akkermansia ratio as a hallmark of the disease. BW-administered mice also showed a lower Bifidobacterium to Akkermansia ratio pre-EAE induction which correlated with increased disease severity post-EAE induction. The importance of the Bifidobacterium to Akkermansia ratio at the species level, lower Bifidobacterium adolescentis to Akkermansia muciniphila (BA:AM), was validated in our MS cohort and a large International Multiple Sclerosis Microbiome Study. Thus, our findings highlight the BA:AM ratio as a potential gut microbial marker in PwMS, opening avenues for microbiome-based diagnosis, prognosis, and therapy in MS.}, }
@article {pmid40030005, year = {2025}, author = {Darwin, A and Xie, J and Smith, M}, title = {Antibiotic Use: Impact on the Microbiome and Cellular Therapy Outcomes.}, journal = {Blood advances}, volume = {}, number = {}, pages = {}, doi = {10.1182/bloodadvances.2024013809}, pmid = {40030005}, issn = {2473-9537}, abstract = {Antibiotics disrupt the delicate balance of bacteria, fungi, and viruses in the human microbiome. Growing evidence indicates a significant relationship between the intestinal microbiome and cellular therapy, which aligns with the established influence of the microbiome on immune responses. When examining the link between cellular therapy and the microbiome, it is essential to understand how disruptions in the microbiome-especially those caused by antibiotics-affect these therapies. Here, we discuss the impact of antibiotics on the intestinal microbiome, cellular therapy outcomes, and associated toxicities, particularly in the context of hematopoietic cell transplantation and chimeric antigen receptor T-cell therapy. Furthermore, we examine the mechanisms through which antibiotics affect cellular therapy, the future implications of this knowledge, and the areas that warrant further investigation.}, }
@article {pmid40029899, year = {2025}, author = {Venado, RE and Wilker, J and Pankievicz, VCS and Infante, V and MacIntyre, A and Wolf, ESA and Vela, S and Robbins, F and Fernandes-Júnior, PI and Vermerris, W and Ané, JM}, title = {Mucilage produced by aerial roots hosts diazotrophs that provide nitrogen in Sorghum bicolor.}, journal = {PLoS biology}, volume = {23}, number = {3}, pages = {e3003037}, doi = {10.1371/journal.pbio.3003037}, pmid = {40029899}, issn = {1545-7885}, abstract = {Sorghum (Sorghum bicolor) is an important food, feed, and fodder crop worldwide and is gaining popularity as an energy crop due to its high potential for biomass production. Some sorghum accessions develop many aerial roots and produce an abundant carbohydrate-rich mucilage after rain. This aerial root mucilage is similar to that observed in landraces of maize (Zea mays) from southern Mexico, which have been previously shown to host diazotrophs. In this study, we characterized the aerial root development of several sorghum accessions and the impact of humidity on this trait. We conducted a microbiome study of the aerial root mucilage of maize and sorghum and isolated numerous diazotrophs from field sorghum mucilage. We observed that the prevailing phyla in the mucilage were Pseudomonadota, Bacteroidota, and Bacillota. However, bacterial abundances varied based on the genotype and the location. Using acetylene reduction, 15N2 gas feeding, and 15N isotope dilution assays, we confirmed that these sorghum accessions can acquire about 40% of their nitrogen from the atmosphere through these associations on aerial roots. Nitrogen fixation in sorghum aerial root mucilage offers a promising avenue to reduce reliance on synthetic fertilizers and promote sustainable agricultural practices for food, feed, fodder, and bioenergy production.}, }
@article {pmid40029705, year = {2025}, author = {Hong, J and Xue, W and Wang, T}, title = {Emergence of alternative stable states in microbial communities undergoing horizontal gene transfer.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, doi = {10.7554/eLife.99593}, pmid = {40029705}, issn = {2050-084X}, support = {12401660//National Natural Science Foundation of China/ ; HSE499011086//Shenzhen Institue of Synthetic Biology Scientific Research Program/ ; }, mesh = {*Gene Transfer, Horizontal ; *Microbiota/genetics ; Bacteria/genetics ; Models, Theoretical ; Microbial Interactions/genetics ; Interspersed Repetitive Sequences/genetics ; Ecosystem ; }, abstract = {Microbial communities living in the same environment often display alternative stable states, each characterized by a unique composition of species. Understanding the origin and determinants of microbiome multistability has broad implications in environments, human health, and microbiome engineering. However, despite its conceptual importance, how multistability emerges in complex communities remains largely unknown. Here, we focused on the role of horizontal gene transfer (HGT), one important aspect mostly overlooked in previous studies, on the stability landscape of microbial populations. Combining mathematical modeling and numerical simulations, we demonstrate that, when mobile genetic elements (MGEs) only affect bacterial growth rates, increasing HGT rate in general promotes multistability of complex microbiota. We further extend our analysis to scenarios where HGT changes interspecies interactions, microbial communities are subjected to strong environmental selections and microbes live in metacommunities consisting of multiple local habitats. We also discuss the role of different mechanisms, including interspecies interaction strength, the growth rate effects of MGEs, MGE epistasis and microbial death rates in shaping the multistability of microbial communities undergoing HGT. These results reveal how different dynamic processes collectively shape community multistability and diversity. Our results provide key insights for the predictive control and engineering of complex microbiota.}, }
@article {pmid40029616, year = {2025}, author = {Ding, J and Zhu, J and Zhou, H and Yang, K and Qin, C and Zhang, Y and Han, C and Yang, L and He, C and Xu, K and Zheng, Y and Luo, H and Chen, K and Zhou, W and Jiang, S and Liu, J and Zhu, W and Niu, Q and Zhou, Z and Wang, S and Yu, S and Huang, Q and Meng, H}, title = {The host susceptibility/resistance-related genes and gut microbial characteristics in Salmonella pullorum-infected chickens.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0039224}, doi = {10.1128/spectrum.00392-24}, pmid = {40029616}, issn = {2165-0497}, abstract = {Pullorum disease is a bacterial disease caused by Salmonella pullorum in chickens, which is characterized by gastrointestinal infection and diarrhea. In traditional perspectives, research on pullorum disease primarily focused on clinical symptoms, epidemiological characteristics, and the pathogenic sites. This study, however, approaches the subject from the standpoint of host genetic basis and gut microbiota. For the positive and negative offspring chicks, which are the offspring of positive roosters and hens and negative roosters and hens, respectively, we conducted whole-genome association analysis and identified 195 SNPs and 79 significant InDels on the host genome that were associated with susceptibility/resistance to pullorum disease. A total of 77 genes were annotated, among which MYH7, ATP2A3, and CACNA1S exhibited variations in the exons. After infection with S. pullorum, the diversity and community structure of the gut microbiota in the chicken also underwent significant changes. Lactobacillus, Escherichia_Shigella, and Klebsiella were dominant bacteria in the dead negative offspring chicks with significantly higher abundance compared to the survival negative offspring chicks. These significant changes in host genome and bacterial abundance suggest that they may be associated with the susceptibility/resistance of pullorum disease.IMPORTANCEPullorum disease can be transmitted vertically and horizontally. Population purification and antibiotic treatment are the main methods for preventing and treating this disease, but they are associated with issues, such as high cost, poor accuracy, bacterial resistance, and overused antibiotics. In traditional perspectives, research on pullorum disease primarily focused on clinical symptoms, epidemiological characteristics, and the pathogenic sites. This study, however, approaches the subject from the standpoint of host genetic basis and gut microbiota. Using the genome-wide association analysis and microbiome comparison analysis, with chicken death and survival following Salmonella pullorum infection as phenotypes, we identified significant genetic variations (e.g., MYH7, ATP2A3, and CACNA1S) and gut microbiota (e.g., Lactobacillus, Escherichia_Shigella, Bacillus, and Enterococcus_cecorum) that may relate to susceptibility/resistance of pullorum disease. These results indicate that the infection of chickens with S. pullorum and the achievement of vertical transmission may be related to the host genome and gut microbiota.}, }
@article {pmid40029447, year = {2025}, author = {Qiu, C and Shi, Y and Huang, X and Chen, Z}, title = {Impact of Probiotics on Enzyme Activities, Intestinal Microbial Remodeling, and Metabolic Pathways in American Shad (Alosa sapidissima) at High Temperatures.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {27}, number = {2}, pages = {58}, pmid = {40029447}, issn = {1436-2236}, support = {2022-02-08-00-12-F01180//Shanghai Agriculture Applied Technology Development Program/ ; 13DZ2251800//Shanghai Yangtze Estuary Main Economic Aquatic Animal Artificial Breeding Engineering Technology Research Center/ ; G201860//Shanghai Leading Agricultural Talent Program/ ; }, mesh = {*Probiotics/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Metabolic Networks and Pathways ; *Lactococcus lactis/metabolism ; Hot Temperature ; Gene Expression Profiling ; Transcriptome ; Liver/metabolism ; }, abstract = {High temperature restricts the survival and growth of aquatic organisms. Probiotics have significant potential for mitigating the negative effects of temperature stress on fish. In this study, the American shad (Alosa sapidissima), a temperature-sensitive freshwater fish, was selected as the experimental paradigm to dissect the underlying mechanisms governing the interactions between the host and its microbiome, with a particular focus on the impact exerted by the probiotic Lactococcus lactis within a high-temperature setting. We evaluated the effects of probiotics on the growth and biochemistry of A. sapidissima by measuring relevant parameters and enzyme activities and conducted an integrated microbiome-transcriptome analysis to assess the impacts on the gut microbiota and uncover probiotic-regulated metabolic pathways. The findings of our research indicated that probiotics had beneficial effects on growth; the activities of enzymes such as LPS, T-SOD, and GSH-PX; and the gut microbial composition. Furthermore, the configuration of the intestinal microbiota underwent a transformation, as evidenced by the increased relative prevalence of bacteria with potential beneficial properties, including Bacillus, Lactococcus, and Clostridium. Liver transcriptomic analysis revealed 586 differentially expressed genes (DEGs). The expression of immune-related genes (nfil3-2, il17d, and leap2) and lipid metabolism-related genes (pla2g3 and sc5d) was strongly upregulated. KEGG enrichment analysis revealed that the DEGs were predominantly clustered within metabolic pathways such as circadian rhythm and fatty acid degradation. This study revealed that probiotics enhanced intestinal bacterial diversity and eased stress by regulating the circadian rhythm, immunity, and lipid metabolism under high-temperature conditions. This study provides a reference for the use of probiotics in A. sapidissima at high temperatures.}, }
@article {pmid40029433, year = {2025}, author = {Yijia, Z and Li, X and Ma, L and Wang, S and Du, H and Wu, Y and Yu, J and Xiang, Y and Xiong, D and Shan, H and Wang, Y and Wang, Z and Hao, J and Wang, J}, title = {Identification of intratumoral microbiome-driven immune modulation and therapeutic implications in diffuse large B-cell lymphoma.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {74}, number = {4}, pages = {131}, pmid = {40029433}, issn = {1432-0851}, support = {2022D01E72//Xinjiang Uygur Autonomous Region Distinguished Young Scientists Fund Project/ ; 2022TSYCCX0027//Xinjiang Uygur Autonomous Region Youth Science and Technology Top Talent Project-Youth Science and Technology Innova-tion Talent Training Program/ ; }, mesh = {Humans ; *Lymphoma, Large B-Cell, Diffuse/immunology/microbiology/therapy/genetics ; *Microbiota/immunology ; *Tumor Microenvironment/immunology ; Prognosis ; Transcriptome ; Immunomodulation ; }, abstract = {OBJECTIVE: Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of non-Hodgkin lymphoma, with significant clinical heterogeneity. Recent studies suggest that the intratumoral microbiome may influence the tumor microenvironment, affecting patient prognosis and therapeutic responses. This study aims to identify microbiome-related subtypes in DLBCL and assess their impact on prognosis, immune infiltration, and therapeutic sensitivity.<br><br>METHODS: Transcriptomic and microbiome data from 48 DLBCL patients were obtained from public databases. Consensus clustering was used to classify patients into distinct microbiome-related subtypes. Functional enrichment analysis, immune infiltration assessments, and single-cell RNA sequencing were performed to explore the biological characteristics of these subtypes. Drug sensitivity predictions were made using the OncoPredict tool. Hub genes' expression and biological function were validated and inferred in cell lines and independent cohorts of DLBCL.<br><br>RESULTS: Two distinct microbiome-related subtypes were identified. Patients in Cluster 1 exhibited significantly better overall survival (P&#x2009;<&#x2009;0.05), with higher immune infiltration of regulatory T cells and M0 macrophages compared to Cluster 2, which was associated with poorer outcomes. Functional enrichment analysis revealed that genes in Cluster 1 were involved in immune regulatory pathways, including cytokine-cytokine receptor interactions and chemokine signaling, suggesting enhanced anti-tumor immune responses. In contrast, genes in Cluster 2 were enriched in immunosuppressive pathways, contributing to a less favorable prognosis. Single-cell RNA sequencing analysis revealed significant heterogeneity in immune cell populations within the tumor microenvironment. B cells exhibited the most notable heterogeneity, as indicated by stemness and differentiation potential scoring. Intercellular communication analysis demonstrated that B cells played a key role in immune cell interactions, with significant differences observed in MIF signaling between B-cell subgroups. Pseudo-time analysis further revealed distinct differentiation trajectories of B cells, highlighting their potential heterogeneity across different immune environments. Metabolic pathway analysis showed significant differences in the average expression levels of metabolic pathways among B-cell subgroups, suggesting functional specialization. Furthermore, interaction analysis between core genes involved in B-cell differentiation and microbiome-driven differentially expressed genes identified nine common genes (GSTM5, LURAP1, LINC02802, MAB21L3, C2CD4D, MMEL1, TSPAN2, and CITED4), which were found to play critical roles in B-cell differentiation and were influenced by the intratumoral microbiome. DLBCL cell lines and clinical cohorts validated that MMEL1 and CITED4 with important biologically function in DLBCL cell survival and subtype classification.<br><br>CONCLUSIONS: This study demonstrates the prognostic significance of the intratumoral microbiome in DLBCL, identifying distinct microbiome-related subtypes that impact immune infiltration, metabolic activity, and therapeutic responses. The findings provide insights into the immune heterogeneity within the tumor microenvironment, focusing on B cells and their differentiation dynamics. These results lay the foundation for microbiome-based prognostic biomarkers and personalized treatment approaches, ultimately aiming to enhance patient outcomes in DLBCL.}, }
@article {pmid40029218, year = {2025}, author = {Zhao, S and Cao, H and Sun, F and Xu, M and Wang, X and Jiang, J and Luo, L and Zeng, L}, title = {Investigating the modulatory effects of Pu-erh tea on the gut microbiota in ameliorating hyperuricemia induced by circadian rhythm disruption.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4fo05659k}, pmid = {40029218}, issn = {2042-650X}, abstract = {Circadian rhythm disruption (CRD) can induce a variety of metabolic disorders. Our previous laboratory studies have shown that Pu-erh tea could alleviate CRD-induced syndromes, including obesity, intestinal dysfunction, and tryptophan metabolism disorders. However, its potential protective mechanism against CRD-induced hyperuricaemia remains unclear. In this work, we found that polyphenols of Pu-erh tea were significantly released in the stage of intestinal digestion, which might promote their interaction with gut microbes. Through animal experiments, C57BL6/J mice were given water or different doses of Pu-erh tea for 60 days, followed by a 90-day CRD, the lifestyle of modern individuals who frequently stay up late. Our results indicated that CRD mice exhibited high serum uric acid levels and gut microbiota disorders. Pu-erh tea intake significantly reshaped the gut microbiome, especially increasing the abundance of Bifidobacterium, Akkermansia and Faecalibaculum, and increased the production of short-chain fatty acids (SCFAs), especially acetic acid, which restored the function of the intestinal barrier. This improvement further regulated oxidative stress pathways (NRF2/HO-1), reduced systemic inflammatory response (IL-6, IL-1β, and TNF-α), restored hepatic function (SOD, MOD, CAT, and GSH) and modulated the activity of enzymes related to UA metabolism in the liver (XOD and ADA). Finally, Pu-erh tea intake promoted the excretion of UA and reduced the levels of UA and xanthine in the serum. Moreover, the results of antibiotic experiments showed that the UA improvement effect of Pu-erh tea depended on the existence of the gut microbiota. Collectively, Pu-erh tea intake has the potential to prevent CRD-induced hyperuricaemia by reshaping the gut microbiota.}, }
@article {pmid40028961, year = {2025}, author = {Girodon, L and Hauet, P}, title = {[Gut microbiome, a new tool for Alzheimer diagnosis].}, journal = {Medecine sciences : M/S}, volume = {41}, number = {2}, pages = {195-197}, doi = {10.1051/medsci/2025019}, pmid = {40028961}, issn = {1958-5381}, }
@article {pmid40028773, year = {2025}, author = {Śliwa-Dominiak, J and Czechowska, K and Blanco, A and Sielatycka, K and Radaczyńska, M and Skonieczna-Żydecka, K and Marlicz, W and Łoniewski, I}, title = {Flow Cytometry in Microbiology: A Review of the Current State in Microbiome Research, Probiotics, and Industrial Manufacturing.}, journal = {Cytometry. Part A : the journal of the International Society for Analytical Cytology}, volume = {}, number = {}, pages = {}, doi = {10.1002/cyto.a.24920}, pmid = {40028773}, issn = {1552-4930}, abstract = {Flow cytometry (FC) is a versatile and powerful tool in microbiology, enabling precise analysis of single cells for a variety of applications, including the detection and quantification of bacteria, viruses, fungi, as well as algae, phytoplankton, and parasites. Its utility in assessing cell viability, metabolic activity, immune responses, and pathogen-host interactions makes it indispensable in both research and diagnostics. The analysis of microbiota (community of microorganisms) and microbiome (collective genomes of the microorganisms) has become essential for understanding the intricate role of microbial communities in health, disease, and physiological functions. FC offers a promising complement, providing rapid, cost-effective, and dynamic profiling of microbial communities, with the added ability to isolate and sort bacterial populations for further analysis. In the probiotic industry, FC facilitates fast, affordable, and versatile analyses, helping assess both probiotics and postbiotics. It also supports the study of bacterial viability under stress conditions, including gastric acid and bile, improving insight into probiotic survival and adhesion to the intestinal mucosa. Additionally, the integration of Machine Learning in microbiology research has transformative potential, improving data analysis and supporting advances in personalized medicine and probiotic formulations. Despite the need for further standardization, FC continues to evolve as a key tool in modern microbiology and clinical diagnostics.}, }
@article {pmid40028749, year = {2025}, author = {Salahi, A and Abd El-Ghany, WA}, title = {A Spotlight on Archaea in Humans, Livestock and Poultry: A Review.}, journal = {Veterinary medicine and science}, volume = {11}, number = {2}, pages = {e70263}, doi = {10.1002/vms3.70263}, pmid = {40028749}, issn = {2053-1095}, mesh = {Animals ; *Archaea/physiology ; Humans ; *Poultry ; Livestock ; Gastrointestinal Microbiome ; }, abstract = {The microbiota includes prokaryotes (archaea and bacteria) and eukaryotes. Archaea are single-celled prokaryotes and essential part of gut microbiome. Researches on archaea in ruminants and humans are more than mono-gastric. The low abundance of archaea in the gut depends on the method used (metagenomics or meta-transcriptomic) and age of people or poultry. The lack of complete recognition of archaea is due to their small number and method of identifying them (16S rRNA gene primers). The uses of archaea include analytical kit, reduce oil pollution, archaeosomes or drugs production, vaccines agents, lipid carriers in the pharmaceutical industry and molybdenum extraction in the nuclear industry. The nutritional functions of methanogenic archaea including feed utilization (ruminants) and efficiency, hydrogen reducing (human), fat deposition and enhancement of energy harvesting in mice, CAZymes genes, cecal fermentation, syntrophic potential, carotenoid source and improved transit time and appetite and SCFAs production. Archaea acting as antibiotics (produce archaeocins, sulfolobicins and halocin KPS1) and as probiotics (archaeobiotics) can reduce TMAU (trimethylaminuria) disease, cardiovascular diseases (CVDs), and atherosclerosis, brain abscess, cancer, colorectal cancer, inflammatory bowel disease (IBD), constipation, obesity, food allergies, asthma and anti-inflammation which can be prevented by using archaea, and other functions include energy homeostasis, heat shock protein (HSP) production and reducing aging.}, }
@article {pmid40028723, year = {2025}, author = {Choi, H and Kwak, MJ and Choi, Y and Kang, AN and Mun, D and Eor, JY and Park, MR and Oh, S and Kim, Y}, title = {Extracellular vesicles of Limosilactobacillus fermentum SLAM216 ameliorate skin symptoms of atopic dermatitis by regulating gut microbiome on serotonin metabolism.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2474256}, doi = {10.1080/19490976.2025.2474256}, pmid = {40028723}, issn = {1949-0984}, mesh = {*Dermatitis, Atopic/microbiology/metabolism ; Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Extracellular Vesicles/metabolism/chemistry ; *Skin/microbiology/metabolism ; *Limosilactobacillus fermentum/physiology/metabolism ; *Serotonin/metabolism ; Probiotics/pharmacology/administration &amp; dosage ; Humans ; Disease Models, Animal ; Female ; Male ; }, abstract = {Atopic dermatitis (AD) is a globally prevalent chronic inflammatory skin disorder. Its pathogenesis remains incompletely understood, resulting in considerable therapeutic challenges. Recent studies have highlighted the significance of the interaction between AD and gut microbiome. In this study, we investigated the effects of probiotic-derived extracellular vesicles on AD. Initially, we isolated and characterized extracellular vesicles from Limosilactobacillus fermentum SLAM 216 (LF216EV) and characterized their composition through multi-omics analysis. Gene ontology (GO) and pathway analysis classified LF216EV proteins into biological processes, molecular functions, and cellular components. Importantly, specific abundance in linoleic, oleic, palmitic, sebacic, and stearic acids indicating upregulated fatty acid metabolism were observed by metabolomic analysis. Furthermore, featured lipid profiling including AcylGlcADG and ceramide were observed in LF216EV. Importantly, in an atopic dermatitis-like cell model induced by TNFα/IFNγ, LF216EV significantly modulated the expression of immune regulatory genes (TSLP, TNFα, IL-6, IL-1β, and MDC), indicating its potential functionality in atopic dermatitis. LF216EV alleviated AD-like phenotypes, such as redness, scaling/dryness, and excoriation, induced by DNCB. Histopathological analysis revealed that LF216EV decreased epidermal thickness and mast cell infiltration in the dermis. Furthermore, LF216EV administration reduced mouse scratching and depression-related behaviors, with a faster onset than the classical treatment with dexamethasone. In the quantitative real-time polymerase chain reaction (qRT-PCR) analysis, we observed a significant increase in the expression levels of htrb2c, sert, and tph-1, genes associated with serotonin, in the skin and gut of the LF216EV-treated group, along with a significant increase in the total serum serotonin levels. Gut microbiome analysis of the LF216EV-treated group revealed an altered gut microbiota profile. Correlation analysis revealed that the genera Limosilactobacillus and Desulfovibrio were associated with differences in the intestinal metabolites, including serotonin. Our findings demonstrate that LF216EV mitigates AD-like symptoms by promoting serotonin synthesis through the modulation of gut microbiota and metabolome composition.}, }
@article {pmid40028318, year = {2025}, author = {Chen, L and Xie, L and Wang, L and Zhan, X and Zhuo, Z and Jiang, S and Miao, L and Zhang, X and Zheng, W and Liu, TM and He, J and Liu, Y}, title = {Patchoulene epoxide mitigates colitis and hepatic damage induced by dextran sulfate sodium by regulating the colonic microbiota and purine metabolism.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1509114}, pmid = {40028318}, issn = {1664-3224}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Dextran Sulfate ; Mice ; *Colon/pathology/drug effects/metabolism/microbiology ; *Sesquiterpenes/pharmacology/therapeutic use ; Male ; Disease Models, Animal ; Purines ; Liver/metabolism/drug effects/pathology ; Mice, Inbred C57BL ; Colitis, Ulcerative/chemically induced/drug therapy/metabolism/microbiology ; Colitis/chemically induced/metabolism/microbiology/drug therapy ; Chemical and Drug Induced Liver Injury/metabolism/prevention &amp; control/drug therapy ; }, abstract = {INTRODUCTION: Ulcerative colitis (UC) is often characterized by dysbiosis of the colonic microbiota and metabolic disturbances, which can lead to liver damage. Patchoulene epoxide (PAO), a tricyclic sesquiterpene derived from the aged essential oil of Pogostemonis Herba, is known for its anti-inflammatory and ulcer-healing properties. However, its dual protective role against UC and liver injury remains largely unexplored. This study aims to elucidate the protective effect and underlying mechanism of PAO against dextran sulfate sodium (DSS)-induced UC and liver injury in mice.<br><br>METHODS: Colitis and liver injury in mice were induced by adding 3% DSS to their drinking water continuously for 7 days, and PAO at the doses of 20 and 40 mg/kg was administered orally to mice daily from the first day until the experimental endpoint. Stool consistency scores, blood stool scores, and body weights were recorded weekly. Disease activity index (DAI) was determined before necropsy, where colon and liver tissues were collected for biochemical analyses. Additionally, the fecal microbiome and its metabolites of treated mice were characterized using 16S rRNA amplicon sequencing and metabolomics.<br><br>RESULTS: PAO significantly reduced the disease activity index and mitigated colonic atrophy in UC mice. It also improved colonic and hepatic pathological changes by safeguarding tight and adherens junctions, and suppressing the generation of pro-inflammatory cytokines and lipopolysaccharide. These beneficial effects were attributed to PAO's capability to regulate the colonic microbiota and metabolic processes. PAO was found to enhance the diversity of the colonic microbiota and to shift the microbial balance in UC mice. Specifically, it restored the microbiota from an Akkermansia-dominated state, characteristic of UC, to a healthier Muribaculaceae-dominated composition. Furthermore, PAO corrected the colon metabolic disturbance in UC mice by modulating the purine metabolism, notably increasing the abundance of deoxyadenosine, adenosine and guanine in UC mice.<br><br>CONCLUSIONS: The therapeutic effect of PAO on UC and liver injury was mainly attributed to its regulation of colonic microbiota and purine metabolism. These insights emphasize the overall therapeutic benefits of PAO in treating UC and liver injury.}, }
@article {pmid40028156, year = {2025}, author = {Budden, KF and Romani, L}, title = {Editorial: Lung microbiome in health and disease.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1565849}, pmid = {40028156}, issn = {1663-9812}, }
@article {pmid40027896, year = {2025}, author = {Boima, V and Agyekum, AB and Ganatra, K and Agyekum, F and Kwakyi, E and Inusah, J and Ametefe, EN and Adu, D}, title = {Advances in kidney disease: pathogenesis and therapeutic targets.}, journal = {Frontiers in medicine}, volume = {12}, number = {}, pages = {1526090}, pmid = {40027896}, issn = {2296-858X}, abstract = {Chronic kidney disease (CKD) is a global public health issue characterized by progressive loss of kidney function, of which end-stage kidney disease (ESKD) is the last stage. The global increase in the prevalence of CKD is linked to the increasing prevalence of traditional risk factors, including obesity, hypertension, and diabetes mellitus, as well as metabolic factors, particularly insulin resistance, dyslipidemia, and hyperuricemia. Mortality and comorbidities, such as cardiovascular complications, rise steadily as kidney function deteriorates. Patients who progress to ESKD require long-term kidney replacement therapy, such as transplantation or hemodialysis/peritoneal dialysis. It is currently understood that a crucial aspect of CKD involves persistent, low-grade inflammation. In addition, increased oxidative and metabolic stress, endothelial dysfunction, vascular calcification from poor calcium and phosphate metabolism, and difficulties with coagulation are some of the complex molecular pathways underlying CKD-related and ESKD-related issues. Novel mechanisms, such as microbiome dysbiosis and apolipoprotein L1 gene mutation, have improved our understanding of kidney disease mechanisms. High kidney disease risk of Africa has been linked to APOL1 high-risk alleles. The 3-fold increased risk of ESKD in African Americans compared to European Americans is currently mainly attributed to variants in the APOL1 gene in the chromosome 22q12 locus. Additionally, the role of new therapies such as SGLT2 inhibitors, mineralocorticoid receptor antagonists, and APOL1 channel function inhibitors offers new therapeutic targets in slowing down the progression of chronic kidney disease. This review describes recent molecular mechanisms underlying CKD and emerging therapeutic targets.}, }
@article {pmid40027880, year = {2024}, author = {Onaivi, ES}, title = {Editorial: 8th biennial international drug and alcohol research society conference 2022.}, journal = {Advances in drug and alcohol research}, volume = {4}, number = {}, pages = {13706}, pmid = {40027880}, issn = {2674-0001}, }
@article {pmid40027830, year = {2025}, author = {Lubin, JB and Planet, PJ and Silverman, MA}, title = {Microbial succession at weaning is guided by microbial metabolism of host glycans.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.20.639370}, pmid = {40027830}, issn = {2692-8205}, abstract = {The weaning transition from a milk-based to a solid-food diet supports critical developmental changes to the intestinal microbiome and immune system. However, the specific microbial and host features that influence microbial succession at weaning are not well understood. Here, we developed a simple approach to investigate the complex dynamics of microbial succession during weaning by co-housing gnotobiotic mice colonized with the defined pre-weaning community PedsCom and the adult-derived consortium OMM12. As expected, co-housing PedsCom mice with OMM12 recapitulated microbial succession at weaning and induced immune system maturation in PedsCom mice. Unexpectedly, we found that the OMM12 microbes with the highest host glycan utilization profiles were the most adept colonizers of PedsCom mice. Genomic analysis confirmed that PedsCom is deficient in the carbohydrate-active enzymes responsible for degrading host-derived glycans, including mucins, compared to adult-derived consortia. We validated a role for glycan utilization in vivo by demonstrating that the mucus-degrading commensal microbe Akkermansia muciniphila critically depends on the metabolism of mucin glycans for colonization of PedsCom mice. These findings highlight the importance of host-derived glycans in shaping microbial communities during the weaning transition and suggest host glycans as novel targets to modulate intestinal microbial populations, introduce beneficial probiotics, and enhance immune system development during weaning.}, }
@article {pmid40027785, year = {2025}, author = {Blackmer-Raynolds, L and Sampson, MM and Kozlov, A and Yang, A and Lipson, L and Hamilton, AM and Kelly, SD and Chopra, P and Chang, J and Sloan, SA and Sampson, TR}, title = {Indigenous gut microbes modulate neural cell state and neurodegenerative disease susceptibility.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.17.638718}, pmid = {40027785}, issn = {2692-8205}, abstract = {UNLABELLED: The native microbiome influences a plethora of host processes, including neurological function. However, its impacts on diverse brain cell types remains poorly understood. Here, we performed single nucleus RNA sequencing on hippocampi from wildtype, germ-free mice and reveal the microbiome-dependent transcriptional landscape across all major neural cell types. We found conserved impacts on key adaptive immune and neurodegenerative transcriptional pathways, underscoring the microbiome's contributions to disease-relevant processes. Mono-colonization with select indigenous microbes identified species-specific effects on the transcriptional state of brain myeloid cells. Colonization by Escherichia coli induced a distinct adaptive immune and neurogenerative disease-associated cell state, suggesting increased disease susceptibility. Indeed, E. coli exposure in the 5xFAD mouse model resulted in exacerbated cognitive decline and amyloid pathology, demonstrating its sufficiency to worsen Alzheimer's disease-relevant outcomes. Together, these results emphasize the broad, species-specific, microbiome-dependent consequences on neurological transcriptional state and highlight the capacity of specific microbes to modulate disease susceptibility.<br><br>HIGHLIGHTS: The microbiome impacts the transcriptional landscape of all major brain cell types.Discrete microbes specifically modulate resident myeloid cell status. Gut E. coli triggers dynamic transcriptional responses across neural cell types. Exposure to E. coli exacerbates behavioral and cellular pathologies in 5xFAD mice.}, }
@article {pmid40027751, year = {2025}, author = {Fei, T and Donovan, V and Funnell, T and Baichoo, M and Waters, NR and Paredes, J and Dai, A and Castro, F and Haber, J and Gradissimo, A and Raj, SS and Lesokhin, AM and Shah, UA and van den Brink, MRM and Peled, JU}, title = {Correlating High-dimensional longitudinal microbial features with time-varying outcomes with FLORAL.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.17.638558}, pmid = {40027751}, issn = {2692-8205}, abstract = {Correlating time-dependent patient characteristics and matched microbiome samples can be helpful to identify biomarkers in longitudinal microbiome studies. Existing approaches typically repeat a pre-specified modeling approach for all taxonomic features, followed by a multiple testing adjustment step for false discovery rate (FDR) control. In this work, we develop an alternative strategy of using logratio penalized generalized estimating equations, which directly models the longitudinal patient characteristic of interest as the outcome variable and treats microbial features as high-dimensional compositional covariates. A cross validation procedure is developed for variable selection and model selection among different working cor-relation structures. In extensive simulations, the proposed method achieved superior sensitivity over the state-of-the-art methods with robustly controlled FDR. In the analyses of correlating longitudinal dietary intake and microbial features from matched samples of cancer patients, the proposed method effectively identified gut health indicators and clinically relevant microbial markers, showing robust utilities in real-world applications. The method is implemented under the open-source R package FLORAL , which is available at (https://vdblab.github.io/FLORAL/).}, }
@article {pmid40027723, year = {2025}, author = {Bowie, KR and Fischer, J and Karstens, L}, title = {Differences in cell-associated and cell-free microbial DNA in blood.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.13.638214}, pmid = {40027723}, issn = {2692-8205}, abstract = {UNLABELLED: In the absence of infection, blood has previously been understood to be free of microbes. However, with advances in sequencing technology this notion has been challenged, prompting new investigations into microbial DNA within the blood of both healthy and diseased individuals. To comprehensively survey microbial DNA in blood, we separated blood into fractions (plasma, red blood cells, and buffy coat) and assessed if the microbial-DNA is cell-free by the addition of DNase to a subset of each fraction. We measured 16S rRNA gene copy number with digital droplet PCR and identified the taxonomic origin of the microbial DNA with synthetic full-length 16S rRNA gene sequencing. As a use case, we examine microbial DNA from the blood of 5 men without prostate cancer (PC), 5 men with low-grade PC, and 5 men with high-grade PC. Our study demonstrates that the majority of microbial DNA is cell-free, indicating that it is not representative of proliferating microbes. Our analyses also revealed buffy coat had the lowest number of 16S rRNA gene copies yet highest number of genera of the fractions (median 23.3 copies/µL and 10 genera) and thus may be a useful fraction to study moving forward. Additionally, microbial DNA in blood may have utility as a biomarker, as we detected disease-associated compositional differences in the plasma and buffy coat fractions. This study lays the groundwork for rigorously studying microbial DNA in blood, however larger studies are needed to confirm our disease-association findings.<br><br>IMPORTANCE: The concept of a "blood microbiome" has sparked debate in recent years, with questions about whether microbes truly exist in circulation. This study provides a crucial evaluation of the fractions of blood and their capacity to harbor microbial DNA, offering important context for prior and future research. By using DNase to differentiate between cell-associated and cell-free microbial DNA, we show that while microbial DNA is present in blood, it is sparse and heterogenous. These findings highlight the need for rigorous study design that carefully considers both positive and negative controls, as well as the specific blood fractions being examined.}, }
@article {pmid40027556, year = {2025}, author = {Zhao, CF}, title = {Association between Helicobacter pylori infection and metabolic dysfunction-associated steatohepatitis: From an analysis of a population-based study.}, journal = {World journal of hepatology}, volume = {17}, number = {2}, pages = {102734}, pmid = {40027556}, issn = {1948-5182}, abstract = {The growing global burden of metabolic dysfunction-associated steatohepatitis (MASH) demands a deeper understanding of its underlying mechanisms and risk factors. Recent studies, such as the large population-based case-control analysis by Abdel-Razeq et al, suggest a significant association between Helicobacter pylori (H. pylori) infection and an increased risk of developing MASH. This study provides compelling data supporting this association, even after adjusting for confounders such as obesity, diabetes, and hyperlipidemia. However, the complexity of this relationship remains unresolved, requiring further investigation into the biological, genetic, and environmental pathways that connect these two conditions. This article critically reviews the study's findings and identifies its limitations, offering innovative research directions for the future. Key areas of focus include integrating genomic and microbiome analyses, exploring the impact of H. pylori eradication on MASH progression, studying molecular mechanisms at the intersection of infection and liver disease, and developing personalized therapeutic strategies.}, }
@article {pmid40027489, year = {2025}, author = {Bai, D and Chen, T and Xun, J and Ma, C and Luo, H and Yang, H and Cao, C and Cao, X and Cui, J and Deng, YP and Deng, Z and Dong, W and Dong, W and Du, J and Fang, Q and Fang, W and Fang, Y and Fu, F and Fu, M and Fu, YT and Gao, H and Ge, J and Gong, Q and Gu, L and Guo, P and Guo, Y and Hai, T and Liu, H and He, J and He, ZY and Hou, H and Huang, C and Ji, S and Jiang, C and Jiang, GL and Jiang, L and Jin, LN and Kan, Y and Kang, D and Kou, J and Lam, KL and Li, C and Li, C and Li, F and Li, L and Li, M and Li, X and Li, Y and Li, ZT and Liang, J and Lin, Y and Liu, C and Liu, D and Liu, F and Liu, J and Liu, T and Liu, T and Liu, X and Liu, Y and Liu, B and Liu, M and Lou, W and Luan, Y and Luo, Y and Lv, H and Ma, T and Mai, Z and Mo, J and Niu, D and Pan, Z and Qi, H and Shi, Z and Song, C and Sun, F and Sun, Y and Tian, S and Wan, X and Wang, G and Wang, H and Wang, H and Wang, H and Wang, J and Wang, J and Wang, K and Wang, L and Wang, SK and Wang, X and Wang, Y and Xiao, Z and Xing, H and Xu, Y and Yan, SY and Yang, L and Yang, S and Yang, Y and Yao, X and Yousuf, S and Yu, H and Lei, Y and Yuan, Z and Zeng, M and Zhang, C and Zhang, C and Zhang, H and Zhang, J and Zhang, N and Zhang, T and Zhang, YB and Zhang, Y and Zhang, Z and Zhou, M and Zhou, Y and Zhu, C and Zhu, L and Zhu, Y and Zhu, Z and Zou, H and Zuo, A and Dong, W and Wen, T and Chen, S and Li, G and Gao, Y and Liu, YX}, title = {EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research.}, journal = {iMeta}, volume = {4}, number = {1}, pages = {e70001}, pmid = {40027489}, issn = {2770-596X}, abstract = {Shotgun metagenomics has become a pivotal technology in microbiome research, enabling in-depth analysis of microbial communities at both the high-resolution taxonomic and functional levels. This approach provides valuable insights of microbial diversity, interactions, and their roles in health and disease. However, the complexity of data processing and the need for reproducibility pose significant challenges to researchers. To address these challenges, we developed EasyMetagenome, a user-friendly pipeline that supports multiple analysis methods, including quality control and host removal, read-based, assembly-based, and binning, along with advanced genome analysis. The pipeline also features customizable settings, comprehensive data visualizations, and detailed parameter explanations, ensuring its adaptability across a wide range of data scenarios. Looking forward, we aim to refine the pipeline by addressing host contamination issues, optimizing workflows for third-generation sequencing data, and integrating emerging technologies like deep learning and network analysis, to further enhance microbiome insights and data accuracy. EasyMetageonome is freely available at https://github.com/YongxinLiu/EasyMetagenome.}, }
@article {pmid40027485, year = {2025}, author = {Liu, Y and Li, H and Sun, T and Sun, G and Jiang, B and Liu, M and Wang, Q and Li, T and Cao, J and Zhao, L and Xiao, F and Zhao, F and Cui, H}, title = {Gut microbiome and metabolome characteristics of patients with cholesterol gallstones suggest the preventive potential of prebiotics.}, journal = {iMeta}, volume = {4}, number = {1}, pages = {e70000}, pmid = {40027485}, issn = {2770-596X}, abstract = {Cholesterol gallstones (CGS) still lack effective noninvasive treatment. The etiology of experimentally proven cholesterol stones remains underexplored. This cross-sectional study aims to comprehensively evaluate potential biomarkers in patients with gallstones and assess the effects of microbiome-targeted interventions in mice. Microbiome taxonomic profiling was conducted on 191 samples via V3-V4 16S rRNA sequencing. Next, 60 samples (30 age- and sex-matched CGS patients and 30 controls) were selected for metagenomic sequencing and fecal metabolite profiling via liquid chromatography-mass spectrometry. Microbiome and metabolite characterizations were performed to identify potential biomarkers for CGS. Eight-week-old male C57BL/6J mice were given a lithogenic diet for 8 weeks to promote gallstone development. The causal relationship was examined through monocolonization in antibiotics-treated mice. The effects of short-chain fatty acids such as sodium butyrate, sodium acetate (NaA), sodium propionate, and fructooligosaccharides (FOS) on lithogenic diet-induced gallstones were investigated in mice. Gut microbiota and metabolites exhibited distinct characteristics, and selected biomarkers demonstrated good diagnostic performance in distinguishing CGS patients from healthy controls. Multi-omics data indicated associations between CGS and pathways involving butanoate and propanoate metabolism, fatty acid biosynthesis and degradation pathways, taurine and hypotaurine metabolism, and glyoxylate and dicarboxylate metabolism. The incidence of gallstones was significantly higher in the Clostridium glycyrrhizinilyticum group compared to the control group in mice. The grade of experimental gallstones in control mice was significantly higher than in mice treated with NaA and FOS. FOS could completely inhibit the formation of gallstones in mice. This study characterized gut microbiome and metabolome alterations in CGS. C. glycyrrhizinilyticum contributed to gallstone formation in mice. Supplementing with FOS could serve as a potential approach for managing CGS by altering the composition and functionality of gut microbiota.}, }
@article {pmid40027484, year = {2025}, author = {Liu, L and Zhou, Q and Xu, T and Deng, Q and Sun, Y and Fu, J and Chen, M and Chen, X and Ma, Z and Dong, Q and Ma, B and Jiao, Y and Zhou, Y and Wu, T and Zou, H and Shi, J and Wang, Y and Sheng, Y and Tang, L and Zheng, C and Wu, W and Ma, W and Sun, W and Hu, S and Zhou, H and He, Y and Kong, X and Chen, L}, title = {Non-differential gut microbes contribute to hypertension and its severity through co-abundances: A multi-regional prospective cohort study.}, journal = {iMeta}, volume = {4}, number = {1}, pages = {e268}, pmid = {40027484}, issn = {2770-596X}, abstract = {Microbial dysbiosis, characterized by an imbalanced microbial community structure and function, has been linked to hypertension. While prior research has primarily focused on differential abundances, our study highlights the role of non-differential microbes in hypertension. We propose that non-differential microbes contribute to hypertension through their ecological interactions, as defined by co-abundances (pairs of microbes exhibiting correlated abundance patterns). Using gut microbiome data from the Guangdong Gut Microbiome Project, which includes 2355 hypertensive and 4644 non-hypertensive participants across 14 regions, we identified replicable hypertension-related microbial interactions. Notably, most co-abundances involved non-differential microbes, which were found to correlate with both hypertension severity and hypertension-related microbial metabolic pathways. These findings emphasize the importance of microbial interactions in hypertension pathogenesis and propose a novel perspective for microbiome-based therapeutic strategies.}, }
@article {pmid40027479, year = {2025}, author = {Shi, Y and Chen, Z and Fang, T and Chen, X and Deng, Y and Qin, H and Lian, M and Shen, J and Zong, Y and Chu, H and Hoebinger, C and Guo, H and Yuan, Z and Zheng, J and Zhou, Y and Pan, Y and Mendes, BG and Lang, S and Hendrikx, T and Zeng, S and Cao, H and Yang, L and Chen, L and Chen, P and Dai, L and Wang, H and Yin, S and Zhu, S and Ma, X and Schnabl, B and Chen, H and Duan, Y}, title = {Gut microbiota in treating inflammatory digestive diseases: Current challenges and therapeutic opportunities.}, journal = {iMeta}, volume = {4}, number = {1}, pages = {e265}, pmid = {40027479}, issn = {2770-596X}, abstract = {Accumulating evidence indicates that the gut microbiota is intricately involved in the initiation and progression of human diseases, forming a multidirectional regulatory axis centered on intestinal microbiota. This article illustrates the challenges in exploring the role of the gut microbiota in inflammatory digestive diseases, such as metabolic dysfunction-associated steatotic liver disease (MASLD) and inflammatory bowel disease (IBD), and summarizes the existing microbiome-focused treatment strategies (probiotics, prebiotics, symbiotics, fecal microbiota transplantation, and bacteriophages therapy), emerging technologies (gut microbiome-on-a-chip and artificial intelligence), as well as possible future research directions. Taken together, these therapeutic strategies and technologies present both opportunities and challenges, which require researchers and clinicians to test the rationality and feasibility of various therapeutic modalities in continuous practice.}, }
@article {pmid40027478, year = {2025}, author = {Bai, D and Ma, C and Xun, J and Luo, H and Yang, H and Lyu, H and Zhu, Z and Gai, A and Yousuf, S and Peng, K and Xu, S and Gao, Y and Wang, Y and Liu, YX}, title = {MicrobiomeStatPlots: Microbiome statistics plotting gallery for meta-omics and bioinformatics.}, journal = {iMeta}, volume = {4}, number = {1}, pages = {e70002}, pmid = {40027478}, issn = {2770-596X}, abstract = {The rapid growth of microbiome research has generated an unprecedented amount of multi-omics data, presenting challenges in data analysis and visualization. To address these issues, we present MicrobiomeStatPlots, a comprehensive platform offering streamlined, reproducible tools for microbiome data analysis and visualization. This platform integrates essential bioinformatics workflows with multi-omics pipelines and provides 82 distinct visualization cases for interpreting microbiome datasets. By incorporating basic tutorials and advanced R-based visualization strategies, MicrobiomeStatPlots enhances accessibility and usability for researchers. Users can customize plots, contribute to the platform's expansion, and access a wealth of bioinformatics knowledge freely on GitHub (https://github.com/YongxinLiu/MicrobiomeStatPlot). Future plans include extending support for metabolomics, viromics, and metatranscriptomics, along with seamless integration of visualization tools into omics workflows. MicrobiomeStatPlots bridges gaps in microbiome data analysis and visualization, paving the way for more efficient, impactful microbiome research.}, }
@article {pmid40027466, year = {2025}, author = {Ho, T and Elma, &#xd6; and Kocanda, L and Brain, K and Lam, T and Kanhere, T and Dong, HJ}, title = {The brain-gut axis and chronic pain: mechanisms and therapeutic opportunities.}, journal = {Frontiers in neuroscience}, volume = {19}, number = {}, pages = {1545997}, pmid = {40027466}, issn = {1662-4548}, abstract = {The brain-gut axis (BGA) is emerging as a critical mediator in chronic pain, involving bidirectional communication between the central nervous system and the gastrointestinal system. The "Pain Matrix" is associated with microbial dysbiosis, vagus nerve dysfunction, and hypothalamic-pituitary-adrenal (HPA) axis dysregulation, driving neuroinflammation and central sensitization. Key mechanisms include microbial diversity loss, leaky gut, and altered neuroactive signaling via short-chain fatty acids (SCFAs) and vagal pathways. This narrative review explores the intricate interplay between BGA mechanisms and chronic pain, highlighting therapeutic opportunities such as restoring dysbiosis, modulating vagus nerve activity, and regulating endocrine pathways. These interventions target inflammation, autonomic balance, and stress/reward pathway modulation, offering a promising path toward integrative pain management. Further research is required to validate these strategies and improve patient outcomes.}, }
@article {pmid40027450, year = {2025}, author = {Yousuf, B and Mottawea, W and Esmail, GA and Nazemof, N and Bouhlel, NE and Njoku, E and Li, Y and Zhang, X and Minic, Z and Hammami, R}, title = {Multi-omics unveils strain-specific neuroactive metabolite production linked to inflammation modulation by Bacteroides and their extracellular vesicles.}, journal = {Current research in microbial sciences}, volume = {8}, number = {}, pages = {100358}, pmid = {40027450}, issn = {2666-5174}, abstract = {Bacteroides species are key members of the human gut microbiome and play crucial roles in gut ecology, metabolism, and host-microbe interactions. This study investigated the strain-specific production of neuroactive metabolites by 18 Bacteroidetes (12 Bacteroides, 4 Phocaeicola, and 2 Parabacteroides) using multi-omics approaches. Genomic analysis revealed a significant potential for producing GABA, tryptophan, tyrosine, and histidine metabolism-linked neuroactive compounds. Using untargeted and targeted metabolomics, we identified key neurotransmitter-related or precursor metabolites, including GABA, l-tryptophan, 5-HTP, normelatonin, kynurenic acid, l-tyrosine, and norepinephrine, in a strain- and media-specific manner, with GABA (1-2 mM) being the most abundant. Additionally, extracellular vesicles (EVs) produced by Bacteroides harbor multiple neuroactive metabolites, mainly GABA, and related key enzymes. We used CRISPR/Cas12a-based gene engineering to create a knockout mutant lacking the glutamate decarboxylase gene (gadB) to demonstrate the specific contribution of Bacteroides finegoldii-derived GABA in modulating intestinal homeostasis. Cell-free supernatants from wild-type (WT, GABA+) and ΔgadB (GABA-) provided GABA-independent reinforcement of epithelial membrane integrity in LPS-treated Caco-2/HT29-MTX co-cultures. EVs from WT and ΔgadB attenuated inflammatory immune response of LPS-treated RAW264.7 macrophages, with reduced pro-inflammatory cytokines (IL-1β and IL-6), downregulation of TNF-α, and upregulation of IL-10 and TGF-β. GABA production by B. finegoldii had a limited impact on gut barrier integrity but a significant role in modulating inflammation. This study is the first to demonstrate the presence of a myriad of neuroactive metabolites produced by Bacteroides species in a strain- and media-specific manner in supernatant and EVs, with GABA being the most dominant metabolite and influencing immune responses.}, }
@article {pmid40027422, year = {2025}, author = {Quevedo-Caraballo, S and Álvarez-Pérez, S}, title = {The Role of Phenotypic Plasticity and Within-Environment Trait Variability in the Assembly of the Nectar Microbiome and Plant-Microbe-Animal Interactions.}, journal = {Ecology and evolution}, volume = {15}, number = {3}, pages = {e71059}, pmid = {40027422}, issn = {2045-7758}, abstract = {The study of the rules that govern the relationship between phenotypic plasticity, genetic structure, and ecological success has traditionally focused on animals, plants, and a few model microbial species, whereas non-model microorganisms have received much less attention in this regard. The floral nectar of angiosperms is an ephemeral, island-like habitat for different highly adapted yeasts and bacteria. The growth of microorganisms in floral nectar depends on their ability to efficiently use the available nutrients and tolerate challenging physicochemical conditions, including high osmotic pressures, unbalanced carbon-to-nitrogen ratios, and the presence of diverse defensive compounds of plant origin. The production of alternative phenotypic states in response to environmental cues (i.e., phenotypic plasticity) or independently from these (within-environment trait variability) might be particularly relevant in floral nectar, in which rapid growth is needed for population persistence and to improve the chance of animal-mediated dispersal. In this article, we use the nectar microbiome as an example to encourage further research on the causes and ecological consequences of phenotypic plasticity and within-environment trait variability of microbes. We review previous work on the mechanisms and potential ecological significance of the phenotypic plasticity and within-environment trait variability displayed by nectar yeasts and bacteria. Additionally, we provide an overview of some topics that require further attention, including potential trade-offs between different traits that are relevant for adaptation to dynamic nectar environments and the direct and indirect effects of phenotypic variability on the fitness of plants, flower-visiting animals, and other nectar microbes. We conclude that further research on the causes and ecological consequences of phenotypic plasticity and within-environment trait variability of microbes is essential to get a better understanding of community assembly and the establishment of ecological interactions in floral nectar and other similar highly dynamic and strongly selective microbial habitats.}, }
@article {pmid40027415, year = {2025}, author = {Chu, D and Zhang, H and Shang, Z and Liu, N and Fu, H and Yuan, S}, title = {Gut Microecology of Four Sympatric Desert Rodents Varies by Diet.}, journal = {Ecology and evolution}, volume = {15}, number = {3}, pages = {e70992}, pmid = {40027415}, issn = {2045-7758}, abstract = {The gut microbiome can be one pathway by which a host rapidly acclimates and adapts to its ecological environment. Exploring how the microbiome has evolved to differ between hosts with different diets provides insights into the profound interactions between hosts and microbes within these systems. In this study, we used DNA metabarcoding techniques and macrogenomic prediction techniques to study the gut microbes of four desert rodent species with different feeding strategies in the same habitat. One species is herbivorous (Spermophilus alashanicu)s, one is granivorous (Phodopus roborovskii), another is omnivorous (Dipus sagitta), and the last (Orientallactaga sibirica) has a diet with a relatively high proportion of insects. Diets rich in plants and insects can be challenging to digest due to the abundance of indigestible fiber and stable chitin, respectively. Out of the species studied, the herbivorous Spermophilus alashanicus has the highest density of UCG-005 genes and the highest predicted abundance of genes related to digestive complexity. The composition of Phodopus roborovskii's microbiome has the highest variation between individuals, yet Phodopus roborovskii has the highest predicted abundance of genes associated with simple sugars-reflecting this species' potential adaptability to the starch within plant seeds and its constraints brought about by its smaller body size. The most insectivorous species, Orientallactaga sibirica, exhibits the highest predicted abundance of genes related to chitin degradation. This study has enhanced our understanding of the gut microbiota in the intestines of rodents as they adapt to various dietary strategies.}, }
@article {pmid40026503, year = {2025}, author = {Guers, JJ and Heffernan, KS and Campbell, SC}, title = {Getting to the Heart of the Matter: Exploring the Intersection of Cardiovascular Disease, Sex and Race and How Exercise, and Gut Microbiota Influence these Relationships.}, journal = {Reviews in cardiovascular medicine}, volume = {26}, number = {2}, pages = {26430}, pmid = {40026503}, issn = {2153-8174}, abstract = {Cardiovascular disease (CVD) is the leading cause of death worldwide, with physical inactivity being a known contributor to the global rates of CVD incidence. CVD incidence, however, is not uniform with recognized sex differences as well and racial and ethnic differences. Furthermore, gut microbiota have been associated with CVD, sex, and race/ethnicity. Researchers have begun to examine the interplay of these complicated yet interrelated topics. This review will present evidence that CVD (risk and development), and gut microbiota are distinct between the sexes and racial/ethnic groups, which appear to be influenced by acculturation, discrimination, stress, and lifestyle factors like exercise. Furthermore, this review will address the beneficial impacts of exercise on the cardiovascular system and will provide recommendations for future research in the field.}, }
@article {pmid40026365, year = {2025}, author = {Lu, Y and Li, Z and Xu, R and Xu, Y and Zhang, W and Zhang, Y and Fang, Z and Pan, C and Wang, X}, title = {Impact of fracture fixation surgery on cognitive function and the gut microbiota in mice with a history of stroke.}, journal = {Open life sciences}, volume = {20}, number = {1}, pages = {20221061}, pmid = {40026365}, issn = {2391-5412}, abstract = {Perioperative cognitive dysfunction is a common complication in stroke patients undergoing secondary surgeries. This study investigated the effects of tibial fracture internal fixation (TFIF) surgery on cognitive function and the gut microbiota in mice with a history of stroke. Using the middle cerebral artery occlusion method to induce stroke, we assessed cognitive function via the fear conditioning test and analyzed the gut microbiota through 16S rRNA sequencing. Compared with those in the normal and stroke groups, the cognitive function of the mice in the stroke group that underwent TFIF surgery was significantly impaired. Gut microbiota analysis revealed significant changes in beta diversity, but not in alpha diversity, in these mice. Additionally, TFIF surgery increased microglial activation and IL-1β and lipopolysaccharide (LPS) levels in the brain while reducing α-defensin levels and increasing IL-1β and LPS levels in the colon. These results suggest that TFIF surgery exacerbates cognitive impairment in stroke mice, possibly through alterations in the gut microbiota that impair intestinal defense and promote inflammation. This study highlights the critical role of the gut microbiome in cognitive function and perioperative outcomes, offering insights into potential therapeutic strategies for perioperative cognitive dysfunction in stroke patients.}, }
@article {pmid40026331, year = {2025}, author = {Wang, Y and Chen, T and Shi, Z and Dong, L and Li, M and Peng, B and Li, Q and Pan, R and Xiao, S and Yang, Q and Jiang, N and Liu, X and Hu, Q and Chen, Y}, title = {Ginsenoside Reshapes Intestinal Microecology to Alleviate Microgravity Stress.}, journal = {Drug design, development and therapy}, volume = {19}, number = {}, pages = {1289-1303}, pmid = {40026331}, issn = {1177-8881}, mesh = {Animals ; Rats ; *Gastrointestinal Microbiome/drug effects ; Male ; *Ginsenosides/pharmacology/administration &amp; dosage ; *Rats, Sprague-Dawley ; *Weightlessness ; Intestines/drug effects ; Panax/chemistry ; Hindlimb Suspension ; Weightlessness Simulation ; }, abstract = {BACKGROUND: During medium- to long-duration spaceflights, real-time microgravity can increase the health risks of astronauts. In particular, the disruption of intestinal homeostasis is closely related to other health problems, and it is necessary to monitor related treatment strategies. Ginseng is a well-known Chinese herbal medicine often used to maintain health. Ginseng total saponins (GTSs), which are the bioactive components of ginseng, have been reported to regulate immune homeostasis, anti-inflammation, and anti-oxidation. This study focused on the regulation of GTSs in intestinal homeostasis imbalance caused by microgravity.<br><br>METHODS: A hindlimb suspension (HLS) rat model was established to evaluate the intestinal protective effects of GTSs. Differentially expressed genes (DEGs) were screened using RNA-Seq. RT-PCR was performed to further focus and verify these results. The gut microbiome composition was examined based on 16S rRNA gene amplicon sequencing, and the short-chain fatty acids produced were further analyzed.<br><br>RESULTS: We found that GTSs intervention effectively improved the intestinal injury caused by simulated weightlessness, including reducing the pathological damage, increasing the expression of tight junction proteins and reducing the levels of inflammatory factors. Moreover, GTSs treatment significantly restored the levels of intestinal immunity-related genes and remodeled the gut microbiota. In particular, GTSs significantly increased the abundance of short-chain fatty acid metabolism-related bacteria, thereby increasing the level of propionic acid, butyric acid, isobutyric acid.<br><br>CONCLUSION: Our results revealed that GTSs improved intestinal microecological disorders and impaired immune function caused by the weightlessness simulation. The underlying mechanism may be related to the "intestinal immune -microbiota-metabolic" pathway. These findings provide a theoretical basis for the precise design and development of GTSs for space-health products.}, }
@article {pmid40026233, year = {2025}, author = {Green, EH and Kotrannavar, SR and Rutherford, ME and Lunnemann, HM and Kaur, H and Heiser, CN and Ding, H and Simmons, AJ and Liu, X and Lacy, DB and Washington, MK and Shrubsole, MJ and Liu, Q and Lau, KS and Sears, CL and Coffey, RJ and Drewes, JL and Markham, NO}, title = {Multiomic spatial atlas shows deleted in malignant brain tumors 1 (DMBT1) glycoprotein is lost in colonic dysplasia.}, journal = {The Journal of pathology}, volume = {}, number = {}, pages = {}, doi = {10.1002/path.6406}, pmid = {40026233}, issn = {1096-9896}, support = {P30CA068485/CA/NCI NIH HHS/United States ; P50CA236733/CA/NCI NIH HHS/United States ; R00CA230192/CA/NCI NIH HHS/United States ; BX002943//Veterans Administration Medical Center/ ; BX005699//Veterans Administration Medical Center/ ; P30DK058404/DK/NIDDK NIH HHS/United States ; }, abstract = {Colorectal cancer (CRC) is responsible for over 900,000 annual deaths worldwide. Emerging evidence supports pro-carcinogenic bacteria in the colonic microbiome are at least promotional in CRC development and may be causal. We previously showed toxigenic C. difficile from human CRC-associated bacterial biofilms accelerates tumorigenesis in Apc[Min/+] mice, both in specific pathogen-free mice and in gnotobiotic mice colonized with a defined consortium of bacteria. To further understand host-microbe interactions during colonic tumorigenesis, we combined single-cell RNA-sequencing (scRNA-seq), spatial transcriptomics, and immunofluorescence to define the molecular spatial organization of colonic dysplasia in our consortium model with or without C. difficile. Our data show a striking bipartite regulation of Deleted in Malignant Brain Tumors 1 (DMBT1) in the inflamed versus dysplastic colon. From scRNA-seq, differential gene expression analysis of normal absorptive colonocytes at 2 weeks postinoculation showed DMBT1 upregulated by C. difficile compared to colonocytes from mice without C. difficile exposure. In contrast, our spatial transcriptomic analysis showed DMBT1 dramatically downregulated in dysplastic foci compared with normal-adjacent tissue. We further integrated our datasets to generate custom colonic dysplasia scores and ligand-receptor mapping. Validation with immunofluorescence showed DMBT1 protein downregulated in dysplastic foci from three mouse models of colonic tumorigenesis and in adenomatous dysplasia from human samples. Finally, we used mouse and human organoids to implicate WNT signaling in the downregulation of DMBT1 mRNA and protein. Together, our data reveal cell type-specific regulation of DMBT1, a potential mechanistic link between bacteria and colonic tumorigenesis. Published 2025. This article is a U.S. Government work and is in the public domain in the USA. The Journal of Pathology published by John Wiley &amp; Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.}, }
@article {pmid40026151, year = {2025}, author = {Jena, PK and Wakita, D and Gomez, AC and Carvalho, TT and Atici, AE and Aubuchon, E and Narayanan, M and Lee, Y and Fishbein, MC and Takasato, Y and Kurashima, Y and Kiyono, H and Cani, PD and de Vos, WM and Underhill, DM and Devkota, S and Chen, S and Shimada, K and Crother, TR and Arditi, M and Noval Rivas, M}, title = {Intestinal Microbiota Contributes to the Development of Cardiovascular Inflammation and Vasculitis in Mice.}, journal = {Circulation research}, volume = {}, number = {}, pages = {}, doi = {10.1161/CIRCRESAHA.124.325079}, pmid = {40026151}, issn = {1524-4571}, abstract = {BACKGROUND: Alterations in the intestinal microbiota contribute to the pathogenesis of various cardiovascular disorders, but how they affect the development of Kawasaki disease, an acute pediatric vasculitis, remains unclear. Here, using a murine model mimicking Kawasaki disease vasculitis, we assessed the contribution of the intestinal microbiota to the development of vascular inflammation.<br><br>METHODS AND RESULTS: We report that depleting the gut microbiota reduces the development of cardiovascular inflammation in a murine model mimicking Kawasaki disease vasculitis. The development of cardiovascular lesions was associated with alterations in the intestinal microbiota composition and, notably, a decreased abundance of Akkermansia muciniphila and Faecalibacterium prausnitzii. Oral supplementation with either of these live or pasteurized individual bacteria or with short-chain fatty acids produced by them attenuated cardiovascular inflammation, as reflected by decreased local immune cell infiltrations. Treatment with Amuc_1100, the TLR-2 signaling outer membrane protein from Akkermansia muciniphila, also reduced the severity of vascular inflammation.<br><br>CONCLUSIONS: This study reveals an underappreciated gut microbiota-cardiovascular inflammation axis in Kawasaki disease vasculitis pathogenesis and identifies specific intestinal commensals that regulate vasculitis in mice by producing metabolites or via extracellular proteins capable of enhancing and supporting gut barrier function.}, }
@article {pmid40026117, year = {2025}, author = {Lindsell, HB and Williams, NC and Magistro, D and Corsetti, M and Walton, GE and Hunter, KA}, title = {Could the Therapeutic Effect of Physical Activity on Irritable Bowel Syndrome Be Mediated Through Changes to the Gut Microbiome? A Narrative and Hypothesis Generating Review.}, journal = {Neurogastroenterology and motility}, volume = {}, number = {}, pages = {e70004}, doi = {10.1111/nmo.70004}, pmid = {40026117}, issn = {1365-2982}, abstract = {BACKGROUND: Irritable bowel syndrome (IBS) is one of the most prevalent gastrointestinal (GI) disorders worldwide. Defined as a disorder of gut-brain interaction, its pathophysiology is still not completely clear. Consequently, current treatments primarily target symptoms rather than addressing the cause of the condition. The gut microbiome is increasingly acknowledged as central to IBS pathophysiology and, thus, may have therapeutic potential. Several national treatment guidelines recommend increasing physical activity for IBS management.<br><br>AIMS: This review summarises the evidence about the relationship between physical activity, IBS symptoms, and the gut microbiome, investigating the hypothesis that physical activity's therapeutic effects on IBS may be explained via modulation of the gut microbiome.<br><br>RESULTS: This review revealed that routine exercise was associated with a 15%-66% reduction in symptom severity and up to 41% enhanced QoL in IBS participants, and modulates the gut microbiome in healthy controls.<br><br>DISCUSSION: This review generates the hypothesis that routine physical activity may favorably alter gut microbiome composition in IBS to improve IBS symptomology. While a plausible hypothesis, research needs to confirm whether gut microbiome modulation is involved in physical activity associated IBS symptom relief.<br><br>CONCLUSION: Furthermore, the establishment of the most effective mode, duration, and intensity of physical activity for each sex and IBS-subtype is needed, with patient input during this process crucial to successfully translate science into practice.}, }
@article {pmid40025569, year = {2025}, author = {Lan, F and Wang, X and Zhou, Q and Li, X and Jin, J and Zhang, W and Wen, C and Wu, G and Li, G and Yan, Y and Yang, N and Sun, C}, title = {Deciphering the coordinated roles of the host genome, duodenal mucosal genes, and microbiota in regulating complex traits in chickens.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {62}, pmid = {40025569}, issn = {2049-2618}, support = {31930105//National Natural Science Foundation of China/ ; 2021YFD1300600//National Key Research and Development Program of China/ ; CARS-40//China Agriculture Research Systems/ ; 00109015//2115 Talent Development Program of China Agricultural University/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome/genetics ; *Duodenum/microbiology ; *Intestinal Mucosa/microbiology/metabolism ; Female ; Transcriptome ; Bacteria/genetics/classification ; Humans ; Phenotype ; Genome ; }, abstract = {BACKGROUND: The complex interactions between host genetics and the gut microbiome are well documented. However, the specific impacts of gene expression patterns and microbial composition on each other remain to be further explored.<br><br>RESULTS: Here, we investigated this complex interplay in a sizable population of 705 hens, employing integrative analyses to examine the relationships among the host genome, mucosal gene expression, and gut microbiota. Specific microbial taxa, such as the cecal family Christensenellaceae, which showed a heritability of 0.365, were strongly correlated with host genomic variants. We proposed a novel concept of regulatability (r b 2), which was derived from h[2], to quantify the cumulative effects of gene expression on the given phenotypes. The duodenal mucosal transcriptome emerged as a potent influencer of duodenal microbial taxa, with much higher r b 2 values (0.17&#x2009;&#xb1;&#x2009;0.01, mean&#x2009;&#xb1;&#x2009;SE) than h[2] values (0.02&#x2009;&#xb1;&#x2009;0.00). A comparative analysis of chickens and humans revealed similar average microbiability values of genes (0.18 vs. 0.20) and significant differences in average r b 2 values of microbes (0.17 vs. 0.04). Besides, cis (h cis 2) and trans heritability (h trans 2) were estimated to assess the effects of genetic variations inside and outside the cis window of the gene on its expression. Higher h trans 2 values than h cis 2 values and a greater prevalence of trans-regulated genes than cis-regulated genes underscored the significant role of loci outside the cis window in shaping gene expression levels. Furthermore, our exploration of the regulatory effects of duodenal mucosal genes and the microbiota on 18 complex traits enhanced our understanding of the regulatory mechanisms, in which the CHST14 gene and its regulatory relationships with Lactobacillus salivarius jointly facilitated the deposition of abdominal fat by modulating the concentration of bile salt hydrolase, and further triglycerides, total cholesterol, and free fatty acids absorption and metabolism.<br><br>CONCLUSIONS: Our findings highlighted a novel concept of r b 2 to quantify the phenotypic variance attributed to gene expression and emphasize the superior role of intestinal mucosal gene expressions over host genomic variations in elucidating host&#x2012;microbe interactions for complex traits. This understanding could assist in devising strategies to modulate host-microbe interactions, ultimately improving economic traits in chickens.}, }
@article {pmid40025538, year = {2025}, author = {Liu, T and Xu, J and Chen, X and Ren, J and He, J and Wang, Y and Cao, Y and Guan, LL and Yao, J and Wu, S}, title = {Ruminal-buccal microbiota transmission and their diagnostic roles in subacute rumen acidosis in dairy goats.}, journal = {Journal of animal science and biotechnology}, volume = {16}, number = {1}, pages = {32}, pmid = {40025538}, issn = {1674-9782}, support = {2023YFE0111800//National Key Research and Development Program for International Science and Technology Innovation Cooperation between Governments/ ; 2024//Shaanxi Province's San Qin Talent Attraction Program for Regional Youth Talents/ ; }, abstract = {BACKGROUND: Subacute rumen acidosis (SARA) is a common metabolic disorder in ruminants that disrupts the rumen microbiome and animal health, but diagnosis is challenging due to subtle symptoms and invasive testing requirements. This study explores the potential of the buccal (oral) microbiome as a diagnostic indicator for SARA, hypothesizing an interaction with the rumen microbiome.<br><br>RESULTS: The study involved 47 dairy goats, including 11 on a control diet and 36 on high-concentrate diets with increasing rumen-degradable starch. Animals were grouped based on dietary exposure and ruminal pH: Control, Low-RDS Tolerance/SARA (LRDST/LRDSS), and High-RDS Tolerance/SARA (HRDST/HRDSS). Transcriptomics of rumen epithelium showed heightened inflammatory pathway gene expression in SARA-susceptible goats compared to controls and tolerant groups. Alpha diversity of ruminal bacteria showed lower Shannon diversity in HRDSS goats compared to HRDST whereas buccal bacteria displayed significantly lower Chao1 diversity in LRDSS goats compared to HRDST. Beta diversity analyses revealed distinct patterns between SARA-affected goats and healthy controls in both ruminal and buccal microbiomes. Prevotellaceae_UCG-003 emerged as a candidate biomarker, with reduced abundance in SARA-susceptible goats in both rumen and buccal samples. Machine learning classifiers achieved high accuracy in distinguishing SARA-susceptible goats using this genus (rumen AUC&#x2009;=&#x2009;0.807; buccal AUC&#x2009;=&#x2009;0.779). Source tracking analysis illustrated diminished cross-population of bacteria from the buccal to rumen (2.86% to 0.25%) and vice versa (8.59% to 1.17%), signifying compromised microbial interchange in SARA-affected goats. A microbiota transplant experiment verified SARA microbiota's ability to induce pH decline, escalate inflammation-related gene expression (MAPK10, IL17B, FOSB, SPP1), disrupt microbial transfer, and reduce Prevotellaceae_UCG-003 in recipients.<br><br>CONCLUSION: Our findings highlight SARA's dual impact on ruminal and buccal microbiota, exacerbating epithelial inflammation gene expression. Shifts in the buccal microbiome, specifically reductions in Prevotellaceae_UCG-003, mirror ruminal changes and can be influenced by inter-compartmental bacterial transmission, thereby offering a non-invasive diagnostic approach for SARA.}, }
@article {pmid40025157, year = {2025}, author = {Baraniuk, JN}, title = {Cerebrospinal fluid metabolomics, lipidomics and serine pathway dysfunction in myalgic encephalomyelitis/chronic fatigue syndroome (ME/CFS).}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {7381}, pmid = {40025157}, issn = {2045-2322}, support = {R01NS085131/NS/NINDS NIH HHS/United States ; W81XWH-15-1-0679//Congressionally Directed Medical Research Programs/ ; }, mesh = {Humans ; Female ; Male ; *Serine/metabolism/cerebrospinal fluid ; *Fatigue Syndrome, Chronic/cerebrospinal fluid/metabolism ; Adult ; *Metabolomics/methods ; Middle Aged ; Lipidomics/methods ; Exercise/physiology ; Metabolic Networks and Pathways ; }, abstract = {We proposed that cerebrospinal fluid would provide objective evidence for disrupted brain metabolism in myalgic encephalomyelitis/chronic fatigue syndroome (ME/CFS). The concept of postexertional malaise (PEM) with disabling symptom exacerbation after limited exertion that does not respond to rest is a diagnostic criterion for ME/CFS. We proposed that submaximal exercise provocation would cause additional metabolic perturbations. The metabolomic and lipidomic constituents of cerebrospinal fluid from separate nonexercise and postexercise cohorts of ME/CFS and sedentary control subjects were contrasted using targeted mass spectrometry (Biocrates) and frequentist multivariate general linear regression analysis with diagnosis, exercise, gender, age and body mass index as independent variables. ME/CFS diagnosis was associated with elevated serine but reduced 5-methyltetrahydrofolate (5MTHF). One carbon pathways were disrupted. Methylation of glycine led to elevated sarcosine but further methylation to dimethylglycine and choline was decreased. Creatine and purine intermediates were elevated. Transaconitate from the tricarboxylic acid cycle was elevated in ME/CFS along with essential aromatic amino acids, lysine, purine, pyrimidine and microbiome metabolites. Serine is a precursor of phospholipids and sphingomyelins that were also elevated in ME/CFS. Exercise led to consumption of lipids in ME/CFS and controls while metabolites were consumed in ME/CFS but generated in controls. The findings differ from prior hypometabolic findings in ME/CFS plasma. The novel findings generate new hypotheses regarding serine-folate-glycine one carbon and serine-phospholipid metabolism, elevation of end products of catabolic pathways, shifts in folate, thiamine and other vitamins with exercise, and changes in sphingomyelins that may indicate myelin and white matter dysfunction in ME/CFS.}, }
@article {pmid40025082, year = {2025}, author = {Regmi, R and Anderson, J and Burgess, L and Mangelson, H and Liachko, I and Vadakattu, G}, title = {Shotgun and Hi-C Sequencing Datasets for Binning Wheat Rhizosphere Microbiome.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {367}, pmid = {40025082}, issn = {2052-4463}, mesh = {*Triticum/microbiology ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; Metagenome ; Metagenomics ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing ; Archaea/genetics ; South Australia ; }, abstract = {Binning is a crucial process in metagenomics studies, where sequenced reads are combined to form longer contigs and assigned to individual genomes. Conventional methods, such as shotgun binning, rely on similarity measurements and abundance profiles across multiple samples. However, cost constraints for sequencing and limited sample collection capacity hinder their effectiveness. High-throughput chromosome conformation capture (Hi-C), a DNA proximity ligation technique, has been adapted to accurately bin metagenome-assembled genomes (MAGs) from a single sample, addressing challenges like chimeric MAGs. In this study, we generated over 190 Gb of metagenomic data from wheat rhizospheres grown in two highly calcareous soils of South Australian region and compared conventional and Hi-C binning methods. Two shotgun metagenomes and Hi-C libraries were generated, assembling 1089 shotgun MAGs across 39 bacterial and one archaeal taxon, including 94 Hi-C based bins. Binning performed using only short read sequences was prone to high contamination, while the addition of Hi-C binning improved MAG quality and identified mobile element-host-infection interaction. This dataset provides important tools for studying microbial communities in wheat rhizosphere soils.}, }
@article {pmid40024940, year = {2025}, author = {Xiao, Y and Zhang, Y and Deng, S and Yang, X and Yao, X}, title = {Immune and Non-immune Interactions in the Pathogenesis of Androgenetic Alopecia.}, journal = {Clinical reviews in allergy &amp; immunology}, volume = {68}, number = {1}, pages = {22}, pmid = {40024940}, issn = {1559-0267}, support = {No.2022-I2M-C&amp;T-B-096, No.2021-I2M-1-059//CAMS Innovation Fund for Medical Sciences/ ; 82103735, 82373489, 82273542, 82304023//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Alopecia/immunology/etiology ; Animals ; *Oxidative Stress ; *Hair Follicle/immunology/metabolism ; Male ; Androgens/metabolism ; Microbiota/immunology ; Genetic Predisposition to Disease ; Dysbiosis/immunology ; Disease Susceptibility ; Disease Models, Animal ; }, abstract = {Androgenetic alopecia (AGA), a leading cause of progressive hair loss, affects up to 50% of males aged 50 years, causing significant psychological burden. Current treatments, such as anti-androgen drugs and minoxidil, show heterogeneous effects, even with long-term application. Meanwhile, the large-scale adoption of other adjuvant therapies has been slow, partly due to insufficient mechanistic evidence. A major barrier to developing better treatment for AGA is the incomplete understanding of its pathogenesis. The predominant academic consensus is that AGA is caused by abnormal expression of androgens and their receptors in individuals with a genetic predisposition. Emerging evidence suggests the contributing role of factors such as immune responses, oxidative stress, and microbiome changes, which were not previously given due consideration. Immune-mediated inflammation and oxidative stress disrupt hair follicles' function and damage the perifollicular niche, while scalp dysbiosis influences local metabolism and destabilizes the local microenvironment. These interconnected mechanisms collectively contribute to AGA pathogenesis. These additional aspects enhance our current understanding and confound the conventional paradigm, bridging the gap in developing holistic solutions for AGA. In this review, we gather existing evidence to discuss various etiopathogenetic factors involved in AGA and their possible interconnections, aiming to lay the groundwork for the future identification of therapeutic targets and drug development. Additionally, we summarize the advantages and disadvantages of AGA research models, ranging from cells and tissues to animals, to provide a solid basis for more effective mechanistic studies.}, }
@article {pmid40024881, year = {2025}, author = {Stapleton, AL and Kimple, A and Goralski, JL and Beswick, DM and Gupta, A and Li, DA and Branstetter, BF and Nouraie, SM and Shaffer, AD and Senior, B and Zemke, AC}, title = {Elexacaftor-Tezacaftor-Ivacaftor Improves Sinonasal Outcomes in Young Children With Cystic Fibrosis.}, journal = {International forum of allergy &amp; rhinology}, volume = {}, number = {}, pages = {e23555}, doi = {10.1002/alr.23555}, pmid = {40024881}, issn = {2042-6984}, support = {ZEMKE19A0//Cystic Fibrosis Foundation/ ; UL1-TR-001857//University of Pittsburgh/ ; }, abstract = {BACKGROUND: Severe chronic rhinosinusitis (CRS) is a near universal manifestation of cystic fibrosis. Elexacaftor/tezacaftor/ivacaftor (ETI) is an oral, small molecule, highly effective Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) corrector-potentiator drug. In people with cystic fibrosis age > 12 years, ETI improves sinonasal symptoms, endoscopy findings, polyp size, and radiologic findings. This study evaluates changes in CRS in children ages 6-12 years newly started on ETI.<br><br>METHODS: This was a prospective, three center, pre-post study of 11 children age 6-11 years newly started on ETI. Study endpoints included the SN-5 sinonasal health survey, Sniffin' Kids olfaction test, a sinus computerized tomography (CT) scan, and nasal endoscopy with mucus sampling for full-length 16S rRNA sequencing microbiome analysis. Study visits were conducted before ETI and at a median of 9 months after treatment initiation.<br><br>RESULTS: ETI lead to improvement in symptoms, endoscopy scores and radiologic findings of CRS. Olfaction was below normal at baseline and did not improve. The sinonasal microbiome was dominated by typically commensal organisms before and after treatment for most participants. Additionally, Staphylococcus aureus was found in five participants at baseline and six participants on treatment.<br><br>CONCLUSIONS: ETI improves sinonasal symptoms and endoscopy findings in children 6-11 years of age. Olfaction did not improve with ETI treatment in this age group, suggesting that olfactory dysfunction associated with CF is established early in life. This younger cohort of pediatric patients presented with abundant Staphylococcus aureus and only very rare Pseudomonas aeruginosa at baseline or after treatment.}, }
@article {pmid40024747, year = {2025}, author = {Pan, X and Xiu, Y and Huang, S and Lai, J and Wang, X and Cao, X and Jiang, L}, title = {A Compound Nutritional Supplement Relieving the Core Symptoms of Autism Rats.}, journal = {Journal of nutritional science and vitaminology}, volume = {71}, number = {1}, pages = {34-45}, doi = {10.3177/jnsv.71.34}, pmid = {40024747}, issn = {1881-7742}, mesh = {Animals ; *Dietary Supplements ; *Gastrointestinal Microbiome/drug effects ; *Autistic Disorder/diet therapy ; Female ; Rats ; Pregnancy ; *Vitamins/pharmacology ; Disease Models, Animal ; Male ; Behavior, Animal/drug effects ; Minerals ; Valproic Acid ; Rats, Sprague-Dawley ; Bifidobacterium ; Brain/drug effects ; }, abstract = {Autism, with a global morbidity of approximately 0.6% annually, significantly burdens on families and society. A predominant characteristic among autistic children is intestinal dysfunction, generating nutrient absorption issues. This often causes vitamin and mineral deficiencies, which significantly impacts neurological development. To address this, we have developed a comprehensive nutritional supplement containing compound vitamins, minerals, and gut bacteria. The aim of this study is to investigate the behavioral effects of this supplement on autism rats. The supplement formulated in this study encompasses compound vitamins, minerals, and intestinal bacteria. The autism offspring model (VPA model) was established through intraperitoneal injection of sodium valproate into pregnant rats. Behavioral assessments, gastrointestinal microbiota analysis, and brain development evaluations were conducted to assess the effects of the supplement on VPA offspring rats. A nutritional supplement enriched with vitamins (VB6, VB12, VC, VD, folic acid), minerals (calcium, magnesium), and bifidobacteria was prepared. Open field experiments demonstrated a 3-mo supplementation intervention effectively alleviated anxiety symptoms and enhanced curiosity levels in VPA offspring. The bead embedding experiment revealed the supplementation significantly improved stereotypical behaviors in VPA offspring. The nesting experiment showed a 3-mo supplementation intervention effectively enhanced cognitive abilities in VPA offspring rats. The three-box social experiment demonstrated the supplementation improved social novelty and tendency in VPA offspring. Analysis of gastrointestinal microbiota revealed the supplementation modulated the gut microbiome, promoting better nutrient absorption and overall health. Our findings suggest the comprehensive nutritional supplement, containing compound vitamins, minerals, and gut bacteria, effectively alleviates core symptoms of autism in rats. This study provides valuable insights into the potency of nutritional interventions in improving the quality of life for autistic individuals. Future research is warranted to further explore the mechanisms underlying these observed benefits and to assess the long-term effects of this supplement in larger clinical trials.}, }
@article {pmid40024586, year = {2025}, author = {Wang, T and Bao, MY and Xiao, GX and Wang, Z and Zhou, NN and Wei, H and Qiao, F and Du, ZY and Zhang, ML}, title = {The defatted black soldier fly meal (Hermetia illucens) improved the pathogen resistance and gut health of Nile Tilapia (Oreochromis niloticus).}, journal = {Fish &amp; shellfish immunology}, volume = {}, number = {}, pages = {110242}, doi = {10.1016/j.fsi.2025.110242}, pmid = {40024586}, issn = {1095-9947}, abstract = {As a novel protein source, the black soldier fly (Hermetia illucens) possesses the potential to enhance fish health due to its high protein content, essential amino acids, and bioactive compounds, but the mechanisms by which defatted black soldier fly meal affects fish health remain unclear. This study aimed to evaluate the effects of partially replacing soybean meal (SM) with defatted black soldier fly larvae meal on the pathogen resistance of juvenile Nile tilapia (Oreochromis niloticus) and to explore the underlying mechanisms. Defatted black soldier fly (Hermetia illucens) meal was used to replace 0% (CON), 15% (H15), 30% (H30), 45% (H45), and 60% (H60) of soybean meal in the diets, which were fed to Nile tilapia for 8 weeks. At the second week of the experiment, an unexpected infection was observed in the Nile tilapia, with subsequent isolation and identification confirming the pathogen as Aeromonas veronii. The results showed that defatted black soldier fly meal improved the survival rate and reduced the intestinal inflammation of Nile tilapia in H60 group compared to CON group (P < 0.05). Periodic acid-Schiff (PAS) staining of the gut indicated that a 60 % replacement of soybean meal with defatted black soldier fly meal significantly increased the number of goblet cells in the intestine (P < 0.05) and upregulated the expression level of mucin 2 (muc2) (P < 0.05). Throughout the experiment period, the survival rate in the defatted black soldier fly meal groups was higher than that in the soybean meal group, with the H60 group exhibiting the most significant improvement. In addition, defatted black soldier fly meal exhibited a promotion effect on goblet cell numbers, mucin production and mucin secretion with a dose dependent manner (P < 0.05). To identify the possible mechanism by which defatted black soldier fly meal enhanced goblet cell numbers, gut microbiome and metabolomics were conducted. The results showed that the defatted black soldier fly meal altered the composition of intestinal microbiota and increased the content of L-tyrosine in the H60 group. The effects of L-tyrosine were further identified in LS174T cells, and the results showed that L-tyrosine upregulated the expression levels of muc2 and SAM pointed domain-containing Ets transcription factor (spdef) (P < 0.05). In conclusion, the defatted black soldier fly meal improves gut health and enhances pathogen resistance, ultimately leading to the increased survival rates of Nile tilapia when exposed to A. veronii.}, }
@article {pmid40024538, year = {2025}, author = {Sliti, A and Kim, RH and Lee, D and Shin, JH}, title = {Whole Genome Sequencing and In Silico Analysis of the Safety and Probiotic Features of Lacticaseibacillus paracasei FMT2 Isolated from Fecal Microbiota Transplantation (FMT) Capsules.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {107405}, doi = {10.1016/j.micpath.2025.107405}, pmid = {40024538}, issn = {1096-1208}, abstract = {Lacticaseibacillus paracasei is widely used as a probiotic supplement and food additive in the medicinal and food industries. However, its application requires careful evaluation of safety traits associated with probiotic pathogenesis, including the transfer of antibiotic-resistance genes, the presence of virulence and pathogenicity factors, and the potential disruptions of the gut microbiome and immune system. In this study, we conducted whole genome sequencing (WGS) of L. paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules and performed genome annotation to assess its probiotic and safety attributes. Our comparative genomic analysis assessed this novel strain's genetic attributes and functional diversity and unraveled its evolutionary relationships with other L. paracasei strains. The assembly yielded three contigs: one corresponding to the chromosome and two corresponding to plasmids. Genome annotation revealed the presence of 2,838 DNA-coding sequences (CDS), 78 ribosomal RNAs (rRNAs), 60 transfer RNAs (tRNAs), three non-coding RNAs (ncRNAs), and 126 pseudogenes. The strain lacked antibiotic resistance genes and pathogenicity factors. Two intact prophages, one Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) region, and three antimicrobial peptide gene clusters were identified, highlighting the genomic stability and antimicrobial potential of the strain. Furthermore, genes linked to probiotic functions, such as mucosal colonization, stress resistance, and biofilm formation, were characterized. The pan-genome analysis identified 3,358 orthologous clusters, including 1,775 single-copy clusters, across all L. paracasei strains. Notably, L. paracasei FMT2 contained many unique singleton genes, potentially contributing to its distinctive probiotic properties. Our findings confirm the potential of L. paracasei FMT2 for food and therapeutic applications based on its probiotic profile and safety.}, }
@article {pmid40024121, year = {2025}, author = {Woo, SY and Park, SB and Lee, SY and Sul, WJ and Chun, HS}, title = {Mycotoxin and microbiome profiling for aflatoxin control in the Korean traditional fermented soybean paste Doenjang.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137777}, doi = {10.1016/j.jhazmat.2025.137777}, pmid = {40024121}, issn = {1873-3336}, abstract = {Mycotoxin contamination is an important concern in producing traditional fermented soybean paste, though no effective control strategy has been developed. This study investigated the mycotoxin profiles of the intermediate (fermented soybean brick, known as "Meju" in South Korea) and final soybean paste products ("Doenjang") to identify major contaminants and describe microbial diversity with the mycotoxins. Profiling of 323 Meju and Doenjang samples revealed severe aflatoxin (AF) contamination. Metagenomic analysis revealed that the species richness and phylogenetic diversity were significantly higher in AF-free than in AF-contaminated Meju and Doenjang. Certain Aspergillus and Penicillium species were more abundant in AF-free than in AF-contaminated Meju and Doenjang. To control AF levels, we developed a novel mycotoxin-reduction approach that preserves the indigenous microbiome by backslopping fermentation of Meju in both Aspergillus-dominant and Penicillium-dominant modes. Both treatments reduced AF levels by > 95 % at a backslopping rate of > 2.5 %. Our results suggested that backslopping fermentation can effectively reduce AF contamination in traditional soybean fermentation, maintaining food safety standards and artisanal practices.}, }
@article {pmid40024004, year = {2025}, author = {Otzen, DE and Peña-Díaz, S and Widmann, J and Daugberg, AOH and Zhang, Z and Jiang, Y and Mittal, C and Dueholm, MKD and Louros, N and Wang, H and Javed, I}, title = {Interactions between pathological and functional amyloid: A match made in Heaven or Hell?.}, journal = {Molecular aspects of medicine}, volume = {103}, number = {}, pages = {101351}, doi = {10.1016/j.mam.2025.101351}, pmid = {40024004}, issn = {1872-9452}, abstract = {The amyloid state of proteins occurs in many different contexts in Nature and in modern society, ranging from the pathological kind (neurodegenerative diseases and amyloidosis) via man-made forms (food processing and - to a much smaller extent - protein biologics) to functional versions (bacterial biofilm, peptide hormones and signal transmission). These classes all come together in the human body which endogenously produces amyloidogenic protein able to form pathological human amyloid (PaHA), hosts a microbiome which continuously makes functional bacterial amyloid (FuBA) and ingests food which can contain amyloid. This can have grave consequences, given that PaHA can spread throughout the body in a "hand-me-down" fashion from cell to cell through small amyloid fragments, which can kick-start growth of new amyloid wherever they encounter monomeric amyloid precursors. Amyloid proteins can also self- and cross-seed across dissimilar peptide sequences. While it is very unlikely that ingested amyloid plays a role in this crosstalk, FuBA-PaHA interactions are increasingly implicated in vivo amyloid propagation. We are now in a position to understand the structural and bioinformatic basis for this cross-talk, thanks to the very recently obtained atomic-level structures of the two major FuBAs CsgA (E. coli) and FapC (Pseudomonas). While there are many reports of homology-driven heterotypic interactions between different PaHA, the human proteome does not harbor significant homology to CsgA and FapC. Yet we and others have uncovered significant cross-stimulation (and in some cases inhibition) of FuBA and PaHA both in vitro and in vivo, which we here rationalize based on structure and sequence. These interactions have important consequences for the transmission and development of neurodegenerative diseases, not least because FuBA and PaHA can come into contact via the gut-brain interface, recurrent infections with microbes and potentially even through invasive biofilm in the brain. Whether FuBA and PaHA first interact in the gut or the brain, they can both stimulate and block each other's aggregation as well as trigger inflammatory responses. The microbiome may also affect amyloidogenesis in other ways, e.g. through their own chaperones which recognize and block growth of both PaHA and FuBA as we show both experimentally and computationally. Heterotypic interactions between and within PaHA and FuBA both in vitro and in vivo are a vital part of the amyloid phenomenon and constitute a vibrant and exciting frontier for future research.}, }
@article {pmid40023843, year = {2025}, author = {Golomb, SM and Guldner, IH and Aleksandrovic, E and Fross, SR and Liu, X and Diao, L and Liang, K and Wu, J and Wang, Q and Lopez, JA and Zhang, S}, title = {Temporal dynamics of immune cell transcriptomics in brain metastasis progression influenced by gut microbiome dysbiosis.}, journal = {Cell reports}, volume = {44}, number = {3}, pages = {115356}, doi = {10.1016/j.celrep.2025.115356}, pmid = {40023843}, issn = {2211-1247}, abstract = {Interactions between metastatic cancer cells and the brain microenvironment regulate brain metastasis (BrMet) progression. Central nervous system (CNS)-native and peripheral immune cells influence the BrMet immune landscape, but the dynamics and factors modulating this microenvironment remain unclear. As the gut microbiome impacts CNS and peripheral immune activity, we investigated its role in regulating immune response dynamics throughout BrMet stages. Antibiotic-induced (ABX) gut dysbiosis significantly increased BrMet burden versus controls but was equalized with fecal matter transplantation, highlighting microbiome diversity as a regulator of BrMet. Single-cell sequencing revealed a highly dynamic immune landscape during BrMet progression in both conditions. However, the timing of the monocyte inflammatory response was altered. Microglia displayed an elevated activation signature in late-stage metastasis in ABX-treated mice. T cell and microglia perturbation revealed involvement of these cell types in modulating BrMet under gut dysbiosis. These data indicate profound effects on immune response dynamics imposed by gut dysbiosis across BrMet progression.}, }
@article {pmid40023841, year = {2025}, author = {Pérez Escriva, P and Correia Tavares Bernardino, C and Letellier, E}, title = {De-coding the complex role of microbial metabolites in cancer.}, journal = {Cell reports}, volume = {44}, number = {3}, pages = {115358}, doi = {10.1016/j.celrep.2025.115358}, pmid = {40023841}, issn = {2211-1247}, abstract = {The human microbiome, an intricate ecosystem of trillions of microbes residing across various body sites, significantly influences cancer, a leading cause of morbidity and mortality worldwide. Recent studies have illuminated the microbiome's pivotal role in cancer development, either through direct cellular interactions or by secreting bioactive compounds such as metabolites. Microbial metabolites contribute to cancer initiation through mechanisms such as DNA damage, epithelial barrier dysfunction, and chronic inflammation. Furthermore, microbial metabolites exert dual roles on cancer progression and response to therapy by modulating cellular metabolism, gene expression, and signaling pathways. Understanding these complex interactions is vital for devising new therapeutic strategies. This review highlights microbial metabolites as promising targets for cancer prevention and treatment, emphasizing their impact on therapy responses and underscoring the need for further research into their roles in metastasis and therapy resistance.}, }
@article {pmid40023840, year = {2025}, author = {Goel, A and Shete, O and Goswami, S and Samal, A and C B, L and Kedia, S and Ahuja, V and O'Toole, PW and Shanahan, F and Ghosh, TS}, title = {Toward a health-associated core keystone index for the human gut microbiome.}, journal = {Cell reports}, volume = {44}, number = {3}, pages = {115378}, doi = {10.1016/j.celrep.2025.115378}, pmid = {40023840}, issn = {2211-1247}, abstract = {A robust index of gut microbiome taxa encompassing their association with host health and microbiome resilience would be valuable for development and optimization of microbiome-based therapeutics. Here we present a single ranked order for 201 taxa, the Health-Associated Core Keystone (HACK) index, derived using their association strengths with prevalence/community association in non-diseased subjects, longitudinal stability, and host health. The index was derived based on 127 discovery cohorts and 14 validation datasets (cumulatively encompassing 45,424 gut microbiomes, subject age >18 years, representing 42 countries, 28 disease categories, and 10,021 longitudinal samples). We show that this index is reproducible regardless of microbiome profiling strategies and cohort lifestyle. Specific consortia of high HACK index taxa respond positively to Mediterranean diet interventions and reflect immune checkpoint inhibitor responsiveness and associated with specific functional profiles at the genome level. The availability of HACK indices provides a rational basis for comparing microbiomes and facilitating selection and design of microbiome-based therapeutics.}, }
@article {pmid40023688, year = {2025}, author = {Carra, D and Maas, SCE and Seoane, JA and Alonso-Curbelo, D}, title = {Exposomal determinants of non-genetic plasticity in tumor initiation.}, journal = {Trends in cancer}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.trecan.2025.01.010}, pmid = {40023688}, issn = {2405-8025}, abstract = {The classical view of cancer as a genetically driven disease has been challenged by recent findings of oncogenic mutations in phenotypically healthy tissues, refocusing attention on non-genetic mechanisms of tumor initiation. In this context, gene-environment interactions take the stage, with recent studies showing how they unleash and redirect cellular and tissue plasticity towards protumorigenic states in response to the exposome, the ensemble of environmental factors impinging on tissue homeostasis. We conceptualize tumor-initiating plasticity as a phenotype-transforming force acting at three levels: cell-intrinsic, focusing on mutant epithelial cells' responses to environmental variation; reprogramming of non-neoplastic cells of the host, leading to protumor micro- and macroenvironments; and microbiome ecosystem dynamics. This perspective highlights cell, tissue, and organismal plasticity mechanisms underlying tumor initiation that are shaped by the exposome, and how their functional investigation may provide new opportunities to prevent, detect, and intercept cancer-promoting plasticity.}, }
@article {pmid40023621, year = {2025}, author = {Johnson, CE and Naik, HB}, title = {Microbiome Perturbations in Hidradenitis Suppurativa.}, journal = {Dermatologic clinics}, volume = {43}, number = {2}, pages = {193-202}, doi = {10.1016/j.det.2024.12.005}, pmid = {40023621}, issn = {1558-0520}, mesh = {*Hidradenitis Suppurativa/microbiology ; Humans ; *Gastrointestinal Microbiome/physiology ; *Skin/microbiology ; *Microbiota ; Dysbiosis ; }, abstract = {Skin and gut microbiome perturbations may play a role in hidradenitis suppurativa (HS) pathogenesis. Emerging microbiome research has established the complex roles of the skin and gut microbiomes in health maintenance and disease. Perturbations in the HS skin microbiome have been shown to correlate with HS disease severity. HS gut microbiome characterization studies point to a trend in decreased microbial diversity associated with HS. Future research efforts examining microbiome perturbations and their functional implications longitudinally and in the setting of interventions are needed to build on this foundational knowledge.}, }
@article {pmid40023579, year = {2025}, author = {Gu, TJ and Cai, J and Auster, A and Torres, E and Zhang, D and Khojasteh, SC and Wang, S}, title = {In vitro metabolism of targeted covalent inhibitors and their thiol conjugates by gut microbiome from rats, mice, and humans.}, journal = {Drug metabolism and disposition: the biological fate of chemicals}, volume = {53}, number = {2}, pages = {100027}, doi = {10.1016/j.dmd.2024.100027}, pmid = {40023579}, issn = {1521-009X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; Rats ; Humans ; Mice ; *Sulfhydryl Compounds/metabolism ; Male ; Feces/microbiology ; Acrylamides/metabolism/pharmacology ; Rats, Sprague-Dawley ; Female ; }, abstract = {Targeted covalent inhibitor (TCI) represents a noncanonical class of small molecules that function via "inactivating" the target protein through the formation of drug-protein adducts. The electrophilic groups (warheads) embedded in the TCIs are essential for their activity while also being recognized as sites susceptible to metabolism by various enzymes and endogenous nucleophiles. Given the growing knowledge of gut microbiome-mediated drug metabolism and its impact on drug absorption, distribution, metabolism, and excretion, the fate of the reactive warhead-containing TCIs in the gut warrants further understanding. In this study, we selected unsubstituted terminal acrylamides (ibrutinib, sotorasib, and divarasib), β-substituted acrylamides (afatinib, neratinib, and dacomitinib), an α-substituted acrylamide (adagrasib), an alkynamide (acalabrutinib), and a salicylaldehyde (voxelotor) to investigate. An anaerobic in vitro approach was utilized using both fecal slurry and feces-outgrown bacteria from rats, mice, and humans. The results showed that double bond reduction was the major metabolism captured for terminal acrylamides, but the activity decreases significantly when α or β substitutions are present; acalabrutinib was stable; and voxelotor was efficiently reduced to a benzyl alcohol metabolite. Synthesized TCI-GSH adducts can be efficiently hydrolyzed sequentially to cysteine adducts, which are rather stable from further microbiome modifications. There were no apparent species differences between rats, mice, and humans qualitatively, while the reductase activity observed was generally higher in the human gut microbiome. This study provides insights into both enzymatic and nonenzymatic reactions of TCIs and their thiol conjugates in the gut environment, which can be translated to the understanding of their absorption, distribution, metabolism, and excretion behavior during drug development. SIGNIFICANCE STATEMENT: Understanding the gut microbiome metabolism of targeted covalent inhibitors and their thiol conjugates will help interpret absorption, distribution, metabolism, and excretion studies for new targeted covalent inhibitors in delineating that from human metabolism, predicting clearance pathways, and assessing the impact on absorption/reabsorption. The species difference information can inform proper preclinical species for better human translation in overall drug behavior. The experimental conditions developed from this work can also be adapted to study gut microbiome metabolism in general across different species.}, }
@article {pmid40023429, year = {2025}, author = {Sagheer, U and Shu, J and Yu, H and Ren, X and Haroon, K and Majeed, U and Xu, C and Zhang, F and Xie, H and Li, Z}, title = {Protein glycopatterns for natural regulation of microbiota in lung adenocarcinoma.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {141542}, doi = {10.1016/j.ijbiomac.2025.141542}, pmid = {40023429}, issn = {1879-0003}, abstract = {Despite medical advancements, lung cancer remains a leading cause of mortality, necessitating a deeper understanding. Recent studies show that protein glycopatterns and lung microbiome are crucial in lung cancer development, but their relationship in adenocarcinoma remains unexplored. Therefore, this study evaluated protein glycopatterns and microbial changes between lung adenocarcinoma (n = 70) and paracancerous tissues (n = 70) through lectin microarrays and 16S rDNA sequencing. Further, we explored the impact of protein glycopatterns against a decreased abundant microbiota using extracted glycoproteins reflecting high expression protein glycopatterns observed in lung adenocarcinoma tissues. The results demonstrated a significant up-regulation of protein glycopatterns in tumor tissues, including WGA binding to multivalent Sia/(GlcNAc)n (P = 0.0078) and Jacalin binding to T/Tn antigens (P = 0.0313). Meanwhile, two bacterial species of the genus Sphingomonas showed a significant decrease (P < 0.01) in adenocarcinoma as compared to paracancerous tissue. Interestingly, adhesion assay results showed glycoproteins (25-100 μg/mL) with multivalent Sia and (GlcNAc)n structures extracted by WGA-magnetic particle conjugates significantly reduce (P < 0.0001) Sphingomonas mucosissima adhesion and toxicity to lung cancer cells (A-549). The findings indicated that protein glycopatterns could inhibit cancer-instigating oncomicrobes to intercept cancer progression, offering insights into molecular mechanisms driving disease progression and aiding to develop new treatment strategies.}, }
@article {pmid40023356, year = {2025}, author = {Das, M and Kiruthiga, C and Shafreen, RB and Nachammai, KT and Selvaraj, C and Langeswaran, K}, title = {Harnessing the Human Microbiome and its Impact on Immuno-Oncology and Nanotechnology for Next-Generation Cancer Therapies.}, journal = {European journal of pharmacology}, volume = {}, number = {}, pages = {177436}, doi = {10.1016/j.ejphar.2025.177436}, pmid = {40023356}, issn = {1879-0712}, abstract = {The integration of microbiome research and nanotechnology represents a significant advancement in immuno-oncology, potentially improving the effectiveness of cancer immunotherapies. Recent studies highlight the influential role of the human microbiome in modulating immune responses, presenting new opportunities to enhance immune checkpoint inhibitors (ICIs) and other cancer therapies. Nanotechnology offers precise drug delivery and immune modulation capabilities, minimizing off-target effects while maximizing therapeutic outcomes. This review consolidates current knowledge on the interactions between the microbiome and the immune system, emphasizing the microbiome's impact on ICIs, and explores the incorporation of nanotechnology in cancer treatment strategies. Additionally, it provides a forward-looking perspective on the synergistic potential of microbiome modulation and nanotechnology to overcome existing challenges in immuno-oncology. This integrated approach may enhance the personalization and effectiveness of next-generation cancer treatments, paving the way for transformative patient care.}, }
@article {pmid40023344, year = {2025}, author = {Gao, S and Wang, X and Xu, Q and Li, R and Yao, L and Zhang, A and Zhou, Q and Xiao, Z and Li, S and Meng, X and Wu, J and Qin, L}, title = {Total Sanghuangporus vaninii extract inhibits hepatocyte ferroptosis and intestinal microbiota disturbance to attenuate liver fibrosis in mice.}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {119571}, doi = {10.1016/j.jep.2025.119571}, pmid = {40023344}, issn = {1872-7573}, abstract = {Sanghuangporus, the dried fruiting body of Sanghuangporus vaninii (Ljub) L.W.Zhou et Y.C.Dai. As the main species of Sanghuang, it has been well-known and used commonly as a traditional medicinal and edible macrofungi for thousands of years in many countries, including China, Korea and Japan. Although it has good hepatoprotective activity, its potential efficacy and mechanism on liver fibrosis remain elusive.<br><br>AIM OF THE STUDY: Total Sanghuangporus vaninii extract (TSH) was prepared by ethanol extraction to investigate its chemical components and to conduct an initial assessment of its efficacy and underlying mechanism in a murine model of liver fibrosis.<br><br>MATERIALS AND METHODS: The chemical components of TSH were initially analyzed by UHPLC-Q-Orbitrap HRMS. To elucidate the effects of TSH, an in vivo model of fibrosis was established in mice using carbon tetrachloride (CCl4), followed by assessments of serum liver function and histopathological analysis. Besides, indicators related to liver fibrosis, hepatic stellate cells (HSCs) activation, inflammation response and ferroptosis related indicators were detected by western blotting, immunohistochemistry and real-time quantitative PCR (RT-qPCR) analysis. Additionally, the 16S rDNA sequencing and untargeted metabolomics analysis of intestinal microbiota were employed to investigating the role of TSH in gut microbiome. In vitro, the human hepatocyte line L02 was stimulated with erastin and treated with or without TSH to elucidate its underlying mechanism.<br><br>RESULTS: The administration of TSH significantly improved serum indicators of liver injury in CCl4-induced fibrosis mice, reduced HSCs activation and collagen deposition, while inhibiting the expressions of transforming growth factor-&#x3b2;1(TGF-&#x3b2;1)/Smad signaling pathway. Notably, TSH treatment attenuated hepatocyte ferroptosis and lipid peroxidation both in vivo and in vitro, as evidenced by a marked decrease in liver iron and malondialdehyde (MDA) contents. In particular, TSH was demonstrated to activate the nuclear factor erythroid 2-related factor 2 (Nrf2)-glutathione peroxidase 4 (GPX4) signaling pathway, thereby protecting hepatocytes from ferroptosis with a particular enhancement of Nrf2 nuclear transcription. Furthermore, TSH influenced gut microbiota composition and ameliorated intestinal metabolic disorders. The increased abundance of Parasutterella and Olsenellas due to TSH treatment was significantly positively correlated with elevated phosphatidylcholines involved in linoleic acid metabolism, and negatively correlated with the reduction of fatty acyls. And the enrichment of intestinal linoleic acid metabolism presented a negative correlation in the reduction of liver fibrosis biomarkers.<br><br>CONCLUSIONS: Our findings indicate that the TSH treatment exerts a significantly protective effect on CCl4-induced mice by ameliorating hepatic injury and ferroptosis damage, inhibiting HSCs activation and collagen deposition, and remodeling gut microbiota homeostasis and metabolic imbalance. Notably, TSH attenuated hepatocyte ferroptosis in liver fibrosis and exhibited upregulation of the Nrf2-GPX4 signaling pathway. Furthermore, TSH could enrich the abundance of Parasutterella and Olsenellas, which may contribute to intestinal linoleic acid metabolism, thereby contributing to the reduction of liver fibrosis damage. Our study provides more effective and unreported evidence of TSH in anti-fibrosis activity.}, }
@article {pmid40023320, year = {2025}, author = {Petracco, G and Faimann, I and Reichmann, F}, title = {Inflammatory bowel disease and neuropsychiatric disorders: Mechanisms and emerging therapeutics targeting the microbiota-gut-brain axis.}, journal = {Pharmacology &amp; therapeutics}, volume = {}, number = {}, pages = {108831}, doi = {10.1016/j.pharmthera.2025.108831}, pmid = {40023320}, issn = {1879-016X}, abstract = {Crohn's disease (CD) and ulcerative colitis (UC) are the two major entities of inflammatory bowel disease (IBD). These disorders are known for their relapsing disease course and severe gastrointestinal symptoms including pain, diarrhoea and bloody stool. Accumulating evidence suggests that IBD is not only restricted to the gastrointestinal tract and that disease processes are able to reach distant organs including the brain. In fact, up to 35 % of IBD patients also suffer from neuropsychiatric disorders such as generalized anxiety disorder and major depressive disorder. Emerging research in this area indicates that in many cases these neuropsychiatric disorders are a secondary condition as a consequence of the disturbed communication between the gut and the brain via the microbiota-gut-brain axis. In this review, we summarise the current knowledge on IBD-associated neuropsychiatric disorders. We examine the role of different pathways of the microbiota-gut-brain axis in the development of CNS disorders highlighting altered neural, immunological, humoral and microbial communication. Finally, we discuss emerging therapies targeting the microbiota-gut-brain axis to alleviate IBD and neuropsychiatric symptoms including faecal microbiota transplantation, psychobiotics, microbial metabolites and vagus nerve stimulation.}, }
@article {pmid40023240, year = {2025}, author = {Diesbourg, EE and Kidd, KA and Perrotta, BG}, title = {Effects of municipal wastewater effluents on the invertebrate microbiomes of an aquatic-riparian food web.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {125948}, doi = {10.1016/j.envpol.2025.125948}, pmid = {40023240}, issn = {1873-6424}, abstract = {Municipal wastewater effluents (MWWEs) contain antimicrobials and other contaminants that can alter the microbiomes of exposed aquatic animals, potentially negatively impacting host health. Contaminants and nutrients from MWWEs may be transferred across the aquatic - riparian boundary by aquatic insects, potentially altering the microbiomes of both prey and consumers. We evaluated host microbiome compositions of several taxa of freshwater larval and adult insects and riparian spiders at sites upstream and downstream of three wastewater treatment plants. Host microbiome compositions were analyzed by sequencing the 16S rRNA gene and MWWE exposure was assessed using stable carbon (δ[13]C) and nitrogen (δ[15]N) isotopes and effluent-associated bacteria. Most downstream insects and riparian spiders were enriched in δ[13]C and δ[15]N, indicating exposure to MWWEs and transfer of MWWE-derived nutrients to riparian consumers. Within sites, insect microbiomes varied after metamorphosis with a greater proportion of endosymbionts and effluent-associated bacteria and decreased alpha diversity in adults, and the microbiomes of Tetragnathidae spiders were dominated by endosymbionts (mainly Rickettsia and Wolbachia) compared to all other taxa. Downstream, Larval caddisfly (Hydropsychidae) microbiomes had a significantly lower proportion of endosymbionts (Rickettsia) and higher diversity, and Araneidae spiders also had higher diversity. However, there were no significant downstream changes in endosymbiont proportions or alpha diversity of larval and adult chironomids, larval and adult mayflies, larval stoneflies, or Tetragnathidae spiders. Most downstream invertebrates (except larval Chironomidae, adult Diptera, and Tetragnathidae spiders) had altered beta diversity (community compositions); however, host taxonomy explained more of the variation in microbiome composition than site or the interaction between them did. Overall, MWWE bacteria and nutrients were incorporated into most insect larvae and retained throughout metamorphosis, however there were taxa-dependent alterations in downstream insect microbiomes and minimal microbiome alterations to their riparian spider predators.}, }
@article {pmid40022890, year = {2025}, author = {Patankar, S and Gorde, A and Patankar, S and Raje, R and Devanpally, C and Ausekar, P and Patil, G and Chitale, S}, title = {A prospective, randomized, open label, parallel group, comparative clinical trial to evaluate the safety and efficacy of combination of herbal oral capsule and rectal medication to improve gut health of type 2 diabetic patients having chronic kidney disease (CKD).}, journal = {Journal of Ayurveda and integrative medicine}, volume = {16}, number = {2}, pages = {100992}, doi = {10.1016/j.jaim.2024.100992}, pmid = {40022890}, issn = {0975-9476}, abstract = {BACKGROUND: Chronic kidney disease (CKD) is a major health concern globally, with more than 850 million people suffering from it. Several studies have been carried out to reduce inflammation in CKD patients; and to study the relationship between gut microbiota and inflammation.<br><br>OBJECTIVE: The effect of herbal formulations to improve the gut flora and reduce inflammation has not been studied earlier. The study aims to evaluate effect of herbal formulation combined with standard of care (SOC) treatment compared to SOC.<br><br>METHODS: A prospective, randomized, parallel group clinical trial was planned on 90 patients split equally into standard of care (SOC) with herbal treatment (IP) and only SOC groups. The change in the abdominal pain score, percent change in the pathogenic and non-pathogenic microbiome were the key endpoints of interest. The safety assessment was in terms of adverse events, changes in hematological and biochemical parameters.<br><br>RESULTS: The demographic and other patient characteristics showed statistically non-significant differences between two groups. On day 90, the median abdominal score in SOC&#xa0;+&#xa0;IP group (2.00) was significantly lower than that of SOC group (3.00) (p&#xa0;=&#xa0;0.002). The quality of life score improved significantly in SOC&#xa0;+&#xa0;IP group (p&#xa0;<&#xa0;0.001), unlike SOC group. There was significant reduction in pathogenic microbes in SOC&#xa0;+&#xa0;IP group; however, the reduction in non-pathogenic microbes was non-significant in this group. The adverse events (AEs) were in mild form, and the proportion of patients with AEs differed non-significantly between two groups.<br><br>CONCLUSION: The IP supplementation along with SOC significantly improved the GUT micro flora, and improved the overall quality of life of CKD patients. This treatment combination can be practiced for effective patient management.}, }
@article {pmid40022799, year = {2025}, author = {Temovska, M and Hegner, R and Ortiz-Ardila, AE and Usack, JG and Angenent, LT}, title = {Lactate production from lactose-rich wastewater: A comparative study on reactor configurations to maximize conversion rates and efficiencies.}, journal = {Water research}, volume = {278}, number = {}, pages = {123365}, doi = {10.1016/j.watres.2025.123365}, pmid = {40022799}, issn = {1879-2448}, abstract = {About 90 % of global lactate production is derived from bacterial fermentation of sugars via pure homofermentative cultures in batch mode. Acid whey, which is a lactose-rich wastewater from the yogurt industry, can be used as an alternative substrate for commercial lactate production. Operating reactor microbiomes reduces the lactate production costs by circumventing sterilization, while continuous operation with biomass retention achieves higher productivity at shorter production times. To find the best reactor configuration with biomass retention for lactate production from acid whey, we operated three different reactor configurations: (1) an upflow anaerobic sludge blanket (UASB) reactor; (2) an anaerobic filter reactor (AFR); and (3) an anaerobic continuously stirred tank reactor (CSTR) with a hollow-fiber membrane module. We operated at different hydraulic retention times (HRTs) to find the optimum production parameters at a temperature of 50 °C and a pH of 5.0. We did not use an inoculum but enriched the endogenous D-lactate-producing Lactobacillus spp. that later dominated the reactor microbiomes (> 90 % relative abundance). Undissociated lactic acid concentrations of more than 60 mmol C L[-1] inhibited the microbiomes. We alleviated the inhibition effect by shortening the HRT to 0.6 days and using diluted acid-whey substrate (1.67-fold dilution) to achieve almost complete conversion of the acid-whey sugars to lactate. At the 0.6-day HRT, the AFR and CSTR performed better than the UASB reactor due to their better cell retention abilities. During the period between Day 365-384, we experienced an error in the pH control of the CSTR system during which the pH value dropped to 4.3. After this pH-error period, the lactose and galactose-into-lactate (LG-into-LA) conversion efficiency for the CSTR considerably improved and surpassed the AFR. We achieved the highest lactate conversion rate of 1256 ± 46.3 mmol C L[-1] d[-1] (1.57 ± 0.06 g L[-1] h[-1]) at a LG-into-LA conversion efficiency of 82.2 ± 3.4 % (in mmol C), with a yield of 0.85 ± 0.02 mmol C mmol C[-1] (product per consumed substrate) for the CSTR.}, }
@article {pmid40022791, year = {2025}, author = {Shukla, A and Sharma, C and Malik, MZ and Singh, AK and Aditya, AK and Mago, P and Shalimar,  and Ray, AK}, title = {Deciphering the tripartite interaction of urbanized environment, gut microbiome and cardio-metabolic disease.}, journal = {Journal of environmental management}, volume = {377}, number = {}, pages = {124693}, doi = {10.1016/j.jenvman.2025.124693}, pmid = {40022791}, issn = {1095-8630}, abstract = {The world is experiencing a sudden surge in urban population, especially in developing Asian and African countries. Consequently, the global burden of cardio-metabolic disease (CMD) is also rising owing to gut microbiome dysbiosis due to urbanization factors such as mode of birth, breastfeeding, diet, environmental pollutants, and soil exposure. Dysbiotic gut microbiome indicated by altered Firmicutes to Bacteroides ratio and loss of beneficial short-chain fatty acids-producing bacteria such as Prevotella, and Ruminococcus may disrupt host-intestinal homeostasis by altering host immune response, gut barrier integrity, and microbial metabolism through altered T-regulatory cells/T-helper cells balance, activation of pattern recognition receptors and toll-like receptors, decreased mucus production, elevated level of trimethylamine-oxide and primary bile acids. This leads to a pro-inflammatory gut characterized by increased pro-inflammatory cytokines such as tumour necrosis factor-α, interleukin-2, Interferon-ϒ and elevated levels of metabolites or metabolic endotoxemia due to leaky gut formation. These pathophysiological characteristics are associated with an increased risk of cardio-metabolic disease. This review aims to comprehensively elucidate the effect of urbanization on gut microbiome-driven cardio-metabolic disease. Additionally, it discusses targeting the gut microbiome and its associated pathways via strategies such as diet and lifestyle modulation, probiotics, prebiotics intake, etc., for the prevention and treatment of disease which can potentially be integrated into clinical and professional healthcare settings.}, }
@article {pmid40023874, year = {2024}, author = {Yakubova, II and Ostrianko, V and Skrypnyk, Y and Volovodovskiy, R}, title = {Extrinsic black staining of teeth: a review.}, journal = {Wiadomosci lekarskie (Warsaw, Poland : 1960)}, volume = {78}, number = {1}, pages = {210-215}, doi = {10.36740/WLek/197130}, pmid = {40023874}, issn = {0043-5147}, mesh = {Humans ; Child ; *Dental Plaque/microbiology ; *Dental Caries/prevention &amp; control ; Tooth Discoloration/etiology ; Risk Factors ; Child, Preschool ; Prevalence ; }, abstract = {OBJECTIVE: Aim: Discovering of the prevalence, causes and consequences of the Extrinsic black staining(EBS) of teeth in pediatric population.<br><br>PATIENTS AND METHODS: Materials and Methods: Upon completion of the scientific search, the review included 47 scientific articles from the electronic databases, reference lists of articles, and selected textbooks in the time interval from 1976 to 2023.<br><br>CONCLUSION: Conclusions: The results show that EBS is a possible protective factor against early childhood caries. Dental plaque and gut microbiome may be related to EBS in the temporary dentition. The literature suggests a decreased caries prevalence in the presence of EBS which associated with low incidence of caries in children. The nature of the black pigmentation is suggested to be a form of bacterial plaque with an insoluble ferric salt. Tabaco smoke, food and antibiotics that can be also a risk factors for EBS. There are some clinical and localization features that dentist have to pay attention for. Many diseases of various systems and organs are directly related to black plaque. With this review, we wanted to encourage dentists to identify the problem in childhood and collaborate in a multidisciplinary team to improve treatment efficiency and speed up the selection of the right tactics for the most person-centered approach to avoid worsening the problem in adulthood.}, }
@article {pmid40023235, year = {2025}, author = {Fang, J and Yin, B and Wang, X and Pan, K and Wang, WX}, title = {Clamworm bioturbation reduces mercury methylation through alteration of methylator composition in sediment.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {371}, number = {}, pages = {125947}, doi = {10.1016/j.envpol.2025.125947}, pmid = {40023235}, issn = {1873-6424}, abstract = {Coastal sediment has been recognized as a hotspot of mercury (Hg) methylation and acts as an important reservoir for Hg-methylating microbes. The bioturbation behaviors of benthic organisms can significantly influence sediment properties and potentially affect the mobility and availability of contaminants within the sediment. However, the effects of bioturbation on Hg speciation and disposition in sediment have not been well addressed. This study investigated the influence of clamworm activities on the Hg-methylation process and the composition of methylators in sediment. The results showed that the presence of clamworms greatly suppressed the growth of Hg-methylators and led to a significant decrease in the production rate of methylmercury (MeHg) (from 0.61 to 0.36 ng g[-1] dw d[-1]). Metagenomic results indicate that bioturbation significantly decreased the abundance and diversity of putative Hg methylators and altered the dominant contributors to Hg methylation process. Furthermore, clamworm activities influenced the metabolic traits of Hg methylators and shifted the community toward greater oxygen tolerance. Overall, bioturbation by clamworms suppressed the Hg methylation process and increased the abundance of eco-friendly microbiome, which ultimately contributed to making the sedimentary ecosystem more diverse and resilient. These findings highlight the vital role of bioturbation in mitigating MeHg contamination in sediment and provide a deeper understanding of Hg-methylating microbes and the Hg cycling processes in coastal environments.}, }
@article {pmid40022646, year = {2025}, author = {O'Halloran, KD}, title = {The gut microbiota: an amazing technicolour dream coat or the emperor's new clothes?.}, journal = {The Journal of physiology}, volume = {}, number = {}, pages = {}, doi = {10.1113/JP288465}, pmid = {40022646}, issn = {1469-7793}, }
@article {pmid40022397, year = {2025}, author = {Dai, J and Wang, W and He, F and Yu, X and Liu, Z and Wang, Y and Zou, D}, title = {Discovery of anti-inflammatory molecules from Dendrobium officinale based on activity labelled molecular networking and its alleviation effect on ulcerative colitis.}, journal = {Food research international (Ottawa, Ont.)}, volume = {203}, number = {}, pages = {115888}, doi = {10.1016/j.foodres.2025.115888}, pmid = {40022397}, issn = {1873-7145}, mesh = {*Dendrobium/chemistry ; *Colitis, Ulcerative/drug therapy/metabolism ; Animals ; *Anti-Inflammatory Agents/pharmacology ; Mice ; *Plant Extracts/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Male ; Signal Transduction/drug effects ; Mice, Inbred C57BL ; Intestinal Mucosa/metabolism/drug effects ; }, abstract = {The present study aimed to discover anti-inflammatory molecules from Dendrobium officinale using mass spectrometry-based molecular networking technology and evaluate its therapeutic potential against ulcerative colitis (UC). We employed activity-labeled molecular networking (ALMN) to identify anti-inflammatory molecules from D. officinale extracts. From 3700 metabolite molecules, five top anti-inflammatory molecules were prioritized and isovitexin was further selected to validate its alleviation effect on a mouse model of DSS-induced UC. Mechanistically, isovitexin was found to restore intestinal epithelial barrier function and modulate autophagy via suppression of the PI3K/AKT signaling pathway. Additionally, isovitexin treatment altered the diversity and composition of the gut microbiota, enriching beneficial bacteria and reducing pathogenic bacteria. This was accompanied by changes in short-chain fatty acid levels, particularly the increase of butyric and valeric acids. Our study provided insights into the pharmacological actions of D. officinale and highlighted isovitexin as a novel candidate for UC treatment.}, }
@article {pmid40022351, year = {2025}, author = {Wang, X and Li, P and Chen, X and Cui, W and Ni, S and Xu, H and Xu, Y and Cai, K and Zhou, H and Xu, B}, title = {Integrated microbiome and metabolomics analysis of spoilage characteristics of modified atmosphere packaged pork.}, journal = {Food research international (Ottawa, Ont.)}, volume = {203}, number = {}, pages = {115827}, doi = {10.1016/j.foodres.2025.115827}, pmid = {40022351}, issn = {1873-7145}, mesh = {*Metabolomics ; *Microbiota ; *Food Packaging/methods ; Animals ; Swine ; *Food Microbiology ; *Bacteria/metabolism/classification/growth &amp; development ; Food Storage/methods ; Pork Meat/microbiology/analysis ; Refrigeration ; Pseudomonas/metabolism/growth &amp; development ; Brochothrix/metabolism/growth &amp; development ; Food Preservation/methods ; High-Throughput Nucleotide Sequencing ; Red Meat/microbiology/analysis ; }, abstract = {The interactions between pork microbial communities and metabolites in modified atmosphere packaged (MAP) storage remain unclear. This study exposed the core microbial communities and metabolite profiles during refrigerated pork storage under MAP and illuminated the relationship between them by high-throughput sequencing and non-targeted metabolomics to comprehend the spoilage mechanism induced by microbial activity in MAP pork during storage. The results showed that Pseudomonas and Serratia were the predominant spoilage bacteria in the preliminary stages of refrigerated pork, while Brochothrix gradually dominated in the final stages of storage. 76 differential metabolites were identified from 822 metabolites, consisting of small-molecule metabolites including glycerophospholipids, bitter amino acids, amines, and nucleotides. The metabolic pathways involved in these metabolites were 10 metabolic pathways inclusive of purine metabolism, nucleotide metabolism, and glycerophospholipid metabolism. Correlation results revealed that bacterial genera like Pseudomonas, Brochothrix, Stenotrophomonas, Acinetobacter, and Aeromonas were significantly correlated with metabolites such as lipids, organic acids and nucleotides. These findings enhance our understanding of the spoilage mechanism of refrigerated pork stored in MAP.}, }
@article {pmid40022097, year = {2025}, author = {Ferneyhough, B and Roddis, M and Millington, S and Quirk, J and Clements, C and West, S and Schilizzi, R and Fischer, MD and Parkinson, NJ}, title = {A highly accurate nanopore-based sequencing workflow for culture and PCR-free microbial metagenomic profiling of urogenital samples.}, journal = {BMC urology}, volume = {25}, number = {1}, pages = {41}, pmid = {40022097}, issn = {1471-2490}, mesh = {Humans ; Female ; Male ; *Metagenomics/methods ; *Microbiota/genetics ; Nanopore Sequencing/methods ; Vagina/microbiology ; Workflow ; Urogenital System/microbiology ; }, abstract = {BACKGROUND: The application of molecular sequencing methods for microbiome profiling of biological samples are largely restricted to research use. However, they require significant resources such as time and cost and can suffer from amplification biases that may hamper interpretation of complex systems. These issues are also a barrier to adoption as standard clinical tools in, for example, diagnosis of urogenital infections. We report a new method that utilises third generation long-read nanopore sequencing to produce fast, accurate and fully quantitated metagenomic microbiome profiles. Here, as proof of principle, we apply this methodology to reassess the healthy urogenital microbiomes of asymptomatic female and male samples.<br><br>RESULTS: We show that our method is capable of accurately and reproducibly detecting both levels and composition of a synthetic mixture of ten species comprising known amounts of hard to lyse gram-positive bacteria, gram-negative bacteria and yeast. When applied to urogenital samples, we confirm previous observations that the female asymptomatic vaginal and urinary microbiomes are predominated by Gardnerella spp. or one of several Lactobacillus species (L. crispatus, L. gasseri, L. iners or L. jensenii) that conform to previously defined community state types. We show the tight relationship between vaginal and urinary populations of the same individual at both species and strain level, provide evidence for the previously observed dynamic nature of these microbiomes over a menstrual cycle and compare biomass and complexity of male and female urobiomes.<br><br>CONCLUSIONS: We set out to develop an unbiased, amplification and culture-free, fully quantitative metagenomic microbiome profiling tool. Our initial observations suggest our method represents a viable alternative to existing molecular research tools employed in the analysis of complex microbiomes.}, }
@article {pmid40022019, year = {2025}, author = {Zhang, H and Li, Y and Li, L}, title = {Blood metabolites reflect the effect of gut microbiota on differentiated thyroid cancer: a Mendelian randomization analysis.}, journal = {BMC cancer}, volume = {25}, number = {1}, pages = {368}, pmid = {40022019}, issn = {1471-2407}, support = {ZYGD23016//West China Hospital, Sichuan University/ ; }, mesh = {Humans ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics ; *Thyroid Neoplasms/blood/microbiology/genetics ; *Genome-Wide Association Study ; Thyroid Cancer, Papillary/blood/genetics/microbiology ; Bayes Theorem ; Bifidobacterium longum/genetics ; Metabolic Networks and Pathways/genetics ; Bacteroides/genetics ; Sphingomyelins/blood ; Adenocarcinoma, Follicular ; }, abstract = {BACKGROUND: Studies have linked gut microbiome and differentiated thyroid cancer (DTC). However, their causal relationships and potential mediating factors have not been well defined. Our study investigated the causal relationships between the gut microbiome, papillary thyroid cancer (PTC) and follicular thyroid cancer (FTC), as well as the mediating effect of potential blood metabolites, using genetic approaches.<br><br>METHODS: Leveraging the summary statistics of gut microbial taxa, blood metabolites, PTC and FTC from the largest genome-wide association studies (GWAS) to date, we applied the bidirectional and mediation Mendelian randomization (MR) design. The multivariable MR approach based on Bayesian model averaging (MR-BMA) was used to prioritize the most likely causal taxa. Furthermore, metabolic pathway analysis was performed via the web-based Metaconflict 4.0.<br><br>RESULTS: After sensitivity analyses, we identified 4 taxa, 19 blood metabolites, and 5 gut bacterial pathways were causally associated with PTC. Similarly, 3 taxa, 31 blood metabolites, and 3 gut bacterial pathways were found to be causally associated with FTC, with 2 blood metabolites exhibiting bidirectional causal relationships. Metabolic pathway analysis revealed 8 significant pathways in PTC and FTC. MR-BMA analysis pinpointed species Bifidobacterium longum as the primary causal taxon for PTC and genus Bacteroides for FTC. The mediation MR analysis showed that sphingomyelin (d18:2/23:0, d18:1/23:1, d17:1/24:1) and 2-hydroxysebacate mediated the causal effects of specific gut microbiota on PTC and FTC, respectively.<br><br>CONCLUSION: The study suggested a causal relationship between several gut microbial taxa and DTC, and that specific blood metabolites might mediate this relationship.}, }
@article {pmid40021286, year = {2025}, author = {Lee, S and Wischmeyer, PE and Mintz, CD and Serbanescu, MA}, title = {Recent Insights into the Evolving Role of the Gut Microbiome in Critical Care.}, journal = {Critical care clinics}, volume = {41}, number = {2}, pages = {379-396}, doi = {10.1016/j.ccc.2024.11.002}, pmid = {40021286}, issn = {1557-8232}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Critical Care/methods ; *Critical Illness ; Intensive Care Units ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {This review explores the evolving understanding of gut microbiota's role in critical illness, focusing on how acute illness and exposures in intensive care unit (ICU) environment negatively impact the gut microbiota and the implications of these changes on host responses in critically-ill patients. Focusing on recent findings from clinical and preclinical studies, we discuss the effects of inflammation, enteral nutrient deprivation, and antibiotics on gut microbial dynamics. This review aims to enhance comprehension of microbial dynamics in the ICU and their implications for clinical outcomes and therapeutic strategies.}, }
@article {pmid40022204, year = {2025}, author = {Debray, R and Dickson, CC and Webb, SE and Archie, EA and Tung, J}, title = {Shared environments complicate the use of strain-resolved metagenomics to infer microbiome transmission.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {59}, pmid = {40022204}, issn = {2049-2618}, support = {R01AG071684/NH/NIH HHS/United States ; R01AG071684/NH/NIH HHS/United States ; R61AG078470//National Science Foundation/ ; R61AG078470//National Science Foundation/ ; }, mesh = {Animals ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; *Fecal Microbiota Transplantation ; Humans ; Papio/microbiology ; Feces/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; }, abstract = {BACKGROUND: In humans and other social animals, social partners have more similar microbiomes than expected by chance, suggesting that social contact transfers microorganisms. Yet, social microbiome transmission can be difficult to identify based on compositional data alone. To overcome this challenge, recent studies have used information about microbial strain sharing (i.e., the shared presence of highly similar microbial sequences) to infer transmission. However, the degree to which strain sharing is influenced by shared traits and environments among social partners, rather than transmission per se, is not well understood.<br><br>RESULTS: Here, we first use a fecal microbiota transplant dataset to show that strain sharing can recapitulate true transmission networks under ideal settings when donor-recipient pairs are unambiguous and recipients are sampled shortly after transmission. In contrast, in gut metagenomes from a wild baboon population, we find that demographic and environmental factors can override signals of strain sharing among social partners.<br><br>CONCLUSIONS: We conclude that strain-level analyses provide useful information about microbiome similarity, but other facets of study design, especially longitudinal sampling and careful consideration of host characteristics, are essential for inferring the underlying mechanisms of strain sharing and resolving true social transmission network. Video Abstract.}, }
@article {pmid40021924, year = {2025}, author = {Neu, J and Stewart, CJ}, title = {Neonatal microbiome in the multiomics era: development and its impact on long-term health.}, journal = {Pediatric research}, volume = {}, number = {}, pages = {}, pmid = {40021924}, issn = {1530-0447}, abstract = {The neonatal microbiome has been the focus of considerable research over the past two decades and studies have added fascinating information in terms of early microbial patterns and how these relate to various disease processes. One difficulty with the interpretation of these relationships is that such data is associative and provides little in terms of proof of causality or the underpinning mechanisms. Integrating microbiome data with other omics such as the proteome, inflammatory mediators, and the metabolome is an emerging approach to address this gap. Here we discuss these omics, their integration, and how they can be applied to improve our understanding, treatment, and prevention of disease. IMPACT: This review introduces the concept of multiomics in neonatology and how emerging technologies can be integrated improve understanding, treatment, and prevention of disease. We highlight considerations for performing multiomic research in neonates and the need for validation in separate cohorts and/or relevant model systems. We summarise how the use of multiomics is expanding and lay out steps to bring this to the clinic to enable precision medicine.}, }
@article {pmid40021789, year = {2025}, author = {Ishihara, C and Sako, M and Tsutsumi, K and Fujii, N and Hashimoto, D and Sato, A and Ichiba, Y and Chikazawa, T and Kakizawa, Y and Nishinaga, E and Uchiyama, A}, title = {Involvement of propionate, citrulline, homoserine, and succinate in oral microbiome metabolite-driven periodontal disease progression.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {7149}, pmid = {40021789}, issn = {2045-2322}, mesh = {Humans ; *Periodontal Diseases/microbiology/metabolism ; *Microbiota ; Female ; Male ; *Succinic Acid/metabolism ; *Citrulline/metabolism ; Adult ; *Propionates/metabolism ; Middle Aged ; Disease Progression ; Mouth/microbiology ; Gingiva/microbiology/metabolism ; Bacteria/metabolism/classification ; }, abstract = {Dysbiosis of the oral microbiome has been implicated in the onset and progression of periodontal diseases. An altered oral microbiome can significantly affect the concentration and composition ratio of bacterial-derived metabolites, thereby contributing to disease development. However, there is limited research on the role of metabolites derived from the oral microbiota. This study aimed to identify specific bacteria-derived metabolites and their contributions to pathogenicity. Mouth-rinsed water was collected from 24 patients with periodontal disease and 22 healthy individuals. We conducted a correlation analysis between periodontal disease-associated bacteria and metabolites present in mouth-rinsed water. We evaluated the effects of these metabolites on human gingival epithelial cells analysis of oral bacteria culture supernatants confirmed the origin of these metabolites. We identified 20 metabolites associated with bacteria that are significantly more prevalent in periodontal disease. Notably, propionate, succinate, citrulline, and homoserine-metabolites derived from the oral microbiome-were identified as being associated with periodontal disease. These results suggested that metabolites derived from the oral microbiota are involved in periodontal disease.}, }
@article {pmid40021742, year = {2025}, author = {Deng, D and Zhao, L and Song, H and Wang, H and Cao, H and Cui, H and Zhou, Y and Cui, R}, title = {Microbiome analysis of gut microbiota in patients with colorectal polyps and healthy individuals.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {7126}, pmid = {40021742}, issn = {2045-2322}, support = {JDKW-2022-0030//Natural science research project of Jiading District, Shanghai/ ; JDKW-2023-0051//Natural science research project of Jiading District, Shanghai/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; *Colonic Polyps/microbiology ; *RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Aged ; Case-Control Studies ; Adult ; Bacteria/classification/genetics/isolation &amp; purification ; Prospective Studies ; Colorectal Neoplasms/microbiology ; }, abstract = {Colorectal polyps serve as the primary precursors for colorectal cancer. A close relationship has been observed between colorectal polyps and gut microbiota. However, the composition and role of the microbiome associated with tubular adenoma are not well understood. In this study, we prospectively evaluated alterations in gut microbiota among patients with colorectal polyps. A total of 60 subjects were enrolled in this study, including 30 patients with colorectal polyps (CP group) and 30 healthy controls (control group). The 16S rRNA sequencing was employed to characterize the gut microbiome in fecal samples. The results revealed that the beta diversity of the gut microbiota in the CP group significantly differs from that of the control group (p = 0.001). At the phylum level, the relative abundance of Bacteroides, Fusobacteria, and Proteobacteria was higher in the CP group compared to the control group (p < 0.05), whereas the relative abundance of Actinobacteria was higher in the control group in comparison to the CP group (p < 0.05). At the genus level, the abundance of Bacteroides increased in the CP group (p < 0.05), while Bifidobacterium declined in the CP group (p < 0.05). At the species level, the abundance of Clostridium perfringens, unidentified_Bacteroides, unidentified_Dorea, Escherichia coli, Clostridium ramosum, and Ruminococcus gnavus was higher (p < 0.05), whereas the abundance of Bifidobacterium adolescentis, unclassified_Bifidobacterium, Bifidobacterium longum, Faecalibacterium prausnitzii, and unidentified_Bifidobacterium is lower in CP group compared to the control group (p < 0.05). There was a structural imbalance in the composition of intestinal colonization flora for CP patients, characterized by a decrease in beneficial bacteria and an increase in harmful bacteria. Escherichia, Shigella, and Bacteroides may serve as promising biomarkers for early detection of colorectal polyps.}, }
@article {pmid40021386, year = {2025}, author = {Moyo, GT and Tepekule, B and Katsidzira, L and Blaser, MJ and Metcalf, CJE}, title = {Getting ahead of human-associated microbial decline in Africa: the urgency of sampling in light of epidemiological transition.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.01.004}, pmid = {40021386}, issn = {1878-4380}, abstract = {Evidence is growing that human-associated early-life microbial diversity modulates health over the long term, via effects in the infant termed 'immune and metabolic education'. Documenting high microbial diversity contexts, such as in Africa, thus, has rich potential for understanding this aspect of the landscape of health. Yet, change on the continent is occurring rapidly, and microbial communities are shifting as behaviors and diets are altered, and antibiotic use expands; we may be losing the opportunity to obtain relevant data. After introducing what is known about the effects of early life microbial diversity on late life health, we provide an overview of what is known of the current, and expected future, trajectory of human-associated microbial diversity in Africa, introducing data on the core drivers. We argue that critical insights may be lost if better understanding of infant microbial communities in Africa is not obtained soon.}, }
@article {pmid40020893, year = {2025}, author = {Weng, S and Zheng, J and Lin, Y and Fang, H and Ko, CY}, title = {Therapeutic effects of amisulpride in male schizophrenics: Role of short-chain fatty acids and gene expression changes.}, journal = {Physiology &amp; behavior}, volume = {}, number = {}, pages = {114864}, doi = {10.1016/j.physbeh.2025.114864}, pmid = {40020893}, issn = {1873-507X}, abstract = {Schizophrenia (SCZ) is a complex disorder characterized by acute symptom exacerbations. Amisulpride, an antipsychotic, has shown effects beyond its primary neurochemical actions, suggesting an influence on the gut microbiome, cytokine modulation, and short-chain fatty acid (SCFA) metabolism. This study aims to investigate these broader effects by examining changes in serum SCFA levels and gene expression profiles in peripheral blood mononuclear cells (PBMCs) following amisulpride treatment. Patients with SCZ undergoing a four-week amisulpride regimen were enrolled. Serum SCFA levels were quantified by gas chromatography, and gene expression profiling was performed in PBMCs using real-time quantitative polymerase chain reaction to assess treatment-associated changes. Results revealed that treatment with amisulpride resulted in a significant increase in serum acetate levels. Gene expression analysis revealed upregulation of G-protein coupled receptor 109a (GPR109a), histone deacetylase 1 (HDAC1), G-protein coupled receptor 43 (GPR43), Toll-like receptor 2 (TLR2), soluble CD14 (sCD14), and N-methyl-D-aspartate receptor (NMDAR), while Toll-like receptor 4 (TLR4) and pregnane X receptor (PXR) were downregulated. These findings suggest that amisulpride may modulate acetate metabolism and immune signaling pathways in SCZ, potentially contributing to anti-inflammatory effects and neuroimmune regulation. The observed increase in acetate, a key microbial metabolite, and the altered expression of immune-related genes suggest a possible link between metabolic shifts and immunomodulatory responses in SCZ pathophysiology. However, direct evidence linking these changes to gut-brain axis mechanisms remains insufficient. Further research is needed to elucidate the therapeutic implications of these metabolic and immunological alterations and their potential role in symptom modulation.}, }
@article {pmid40020572, year = {2025}, author = {Dean, LE and Wang, H and Li, X and Fitzjerrells, RL and Valenzuela, AE and Neier, K and LaSalle, JM and Mangalam, A and Lein, PJ and Lehmler, HJ}, title = {Identification of polychlorinated biphenyls (PCBs) and PCB metabolites associated with changes in the gut microbiome of female mice exposed to an environmental PCB mixture.}, journal = {Journal of hazardous materials}, volume = {489}, number = {}, pages = {137688}, doi = {10.1016/j.jhazmat.2025.137688}, pmid = {40020572}, issn = {1873-3336}, abstract = {Polychlorinated biphenyls (PCBs) are neurotoxic hazardous materials that may cause toxicity via the gut-liver-brain axis. This study investigated PCB × microbiome interactions in adult female mice exposed orally to an environmental PCB mixture. Female mice (6-week-old) were exposed daily for 7 weeks to peanut butter containing 0, 0.1, 1, or 6 mg/kg/day of PCBs. Twenty hours after the final exposure, the cecal content was collected to characterize the microbiome composition and predicted function. PCB and its metabolites in feces were analyzed using gas chromatography-tandem mass spectrometry (GC-MS/MS), while cecal content was assessed with liquid chromatography-high resolution mass spectrometry (LC-HRMS). PCB exposure influenced the abundance of microbial taxa and predicted functions within the cecal content. Complex PCB and metabolite mixtures were detected in the gastrointestinal tract. Network analysis revealed associations between specific parent PCBs and metabolites with changes in the abundance of bacteria in the gastrointestinal tract. These findings demonstrate that individual PCBs and their metabolites significantly influence the abundance of specific bacteria in the gastrointestinal tract following oral PCB exposure. These findings inform further research targeting the microbiome to attenuate the adverse health outcomes of PCB exposure.}, }
@article {pmid40020530, year = {2025}, author = {Xu, K and Corona-Avila, I and Frutos, MD and Núñez-Sánchez, M&#xc1; and Makhanasa, D and Shah, PV and Guzman, G and Ramos-Molina, B and Priyadarshini, M and Khan, MW}, title = {Hepatic HKDC1 deletion alleviates western diet-induced MASH in mice.}, journal = {Biochimica et biophysica acta. Molecular basis of disease}, volume = {1871}, number = {4}, pages = {167746}, doi = {10.1016/j.bbadis.2025.167746}, pmid = {40020530}, issn = {1879-260X}, abstract = {The global prevalence of Metabolic Dysfunction-Associated Steatohepatitis (MASH) has been rising sharply, closely mirroring the increasing rates of obesity and metabolic syndrome. MASH exhibits a strong sexual dimorphism where females are affected with more severe forms after menopause. Hexokinase domain-containing protein 1 (HKDC1) has recently been recognized for its role in liver diseases, where its expression is minimal under normal conditions but significantly increases in response to metabolic stressors like obesity and liver injury. This selective upregulation suggests HKDC1's potential specialization in hepatic glucose and lipid dysregulation, linking it closely to the progression of MASH. This study aims to clarify the role of HKDC1 in Western diet-induced MASH in female mice by examining its impact on hepatic glucose and lipid metabolism, offering insights into its potential as a therapeutic target and addressing the need for sex-specific research in liver disease. This study reveals that HKDC1 expression is elevated in obese women with MASH and correlates with liver pathology. In a mouse model, liver-specific HKDC1 knockout (HKDC1[LKO]) protected against Western diet-induced obesity, glucose intolerance, and MASH features, including steatosis, inflammation, and fibrosis. Transcriptomic analysis showed that HKDC1 deletion reduced pro-inflammatory and pro-fibrotic gene expression, while gut microbiome analysis indicated a shift toward MASH-protective bacteria. These findings suggest that HKDC1 may exacerbate MASH progression through its role in metabolic and inflammatory pathways, making it a potential therapeutic target.}, }
@article {pmid40020294, year = {2025}, author = {Zhao, Y and Li, L and Tan, J and Zhao, H and Wang, Y and Zhang, A and Jiang, L}, title = {Metagenomic insights into the inhibitory effect of phytochemical supplementation on antibiotic resistance genes and virulence factors in the rumen of transition dairy cows.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137717}, doi = {10.1016/j.jhazmat.2025.137717}, pmid = {40020294}, issn = {1873-3336}, abstract = {Antimicrobial resistance (AMR) is a major global health concern, with the rumen microbiota of dairy cows serving as an important reservoir for antibiotic resistance genes (ARGs) and virulence factors (VFs). This study explores the impact of dietary phytochemical supplementation on the rumen resistome and virulome of transition dairy cows using metagenomic sequencing. Naringin supplementation reduced the abundance of ARGs by up to 9.0 % and VFs by up to 7.2 % during the transition period, as indicated by metagenomic analysis (P < 0.05). Clinically high-risk ARGs, including those conferring resistance to beta-lactams (mecA), tetracyclines (tetM, tetO), and aminoglycosides (rmtF), were notably downregulated (P < 0.05). Virulence factors associated with adherence, secretion systems, and toxins were also significantly decreased (P < 0.05). Naringin altered the microbial community structure, particularly reducing the abundance of Proteobacteria, a key phylum harboring ARGs and VFs. Despite inducing increased ARG-VF network complexity, naringin supplementation promoted a less pathogenic microbiome with reduced resistance potential. These findings demonstrate the potential of naringin as a natural dietary strategy to mitigate AMR by reducing the risk of ARG and VF dissemination into the environment, while supporting rumen microbiota stability in transition dairy cows.}, }
@article {pmid40020666, year = {2025}, author = {Salido, RA and Zhao, HN and McDonald, D and Mannochio-Russo, H and Zuffa, S and Oles, RE and Aron, AT and El Abiead, Y and Farmer, S and González, A and Martino, C and Mohanty, I and Parker, CW and Patel, L and Portal Gomes, PW and Schmid, R and Schwartz, T and Zhu, J and Barratt, MR and Rubins, KH and Chu, H and Karouia, F and Venkateswaran, K and Dorrestein, PC and Knight, R}, title = {The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2025.01.039}, pmid = {40020666}, issn = {1097-4172}, abstract = {Space habitation provides unique challenges in built environments isolated from Earth. We produced a 3D map of the microbes and metabolites throughout the United States Orbital Segment (USOS) of the International Space Station (ISS) with 803 samples collected during space flight, including controls. We find that the use of each of the nine sampled modules within the ISS strongly drives the microbiology and chemistry of the habitat. Relating the microbiology to other Earth habitats, we find that, as with human microbiota, built environment microbiota also align naturally along an axis of industrialization, with the ISS providing an extreme example of an industrialized environment. We demonstrate the utility of culture-independent sequencing for microbial risk monitoring, especially as the location of sequencing moves to space. The resulting resource of chemistry and microbiology in the space-built environment will guide long-term efforts to maintain human health in space for longer durations.}, }
@article {pmid40020409, year = {2025}, author = {Seyoum, MM and Assumpcao, ALFV and Caputi, V and Ashwell, CM and Honaker, CF and Daniels, KM and Lyte, M and Siegel, PB and Taylor, RL and Lyte, JM}, title = {Multigenerational selection for high or low antibody response to sheep red blood cells modulates the chicken cecal microbiome and its relationship to the immune and serotonergic systems.}, journal = {Poultry science}, volume = {104}, number = {4}, pages = {104943}, doi = {10.1016/j.psj.2025.104943}, pmid = {40020409}, issn = {1525-3171}, abstract = {The chicken cecal microbiome has an important role in regulating immune function, health, resilience to foodborne pathogen carriage, and myriad other factors important in poultry production. However, in chickens, the effects of long-term immune modulation through selective breeding on gut microbiome composition and function remain understudied. The present study aimed to investigate how the multigenerational selection of chickens for high (HAS) or low (LAS) antibody response to sheep red blood cells (SRBC) influences cecal microbiome diversity, community composition, and functional capacity across different ages. Data from both lines and sexes were obtained in generation 49 at 293 days of age and in generation 50 at 28 and 56 days of age. The LAS chickens exhibited greater microbial diversity and abundance, particularly at 56 days (p < 0.05), than HAS. Microbial community composition also varied between the two lines, with age and line influencing microbiome structure across developmental stages and sexes (p < 0.05). Functional profiling revealed that metabolic activity of the LAS microbiome was different compared to the HAS microbiome, with pathways enriched in L-tryptophan biosynthesis, as well as carbon metabolism and degradation processes, suggesting that selection on the humoral immune system fostered alterations in microbial functional capacity. Correlation and co-occurrence analyses with serotonin, 5-hydroxyindoleacetic acid, IgA, and IgY revealed associations between microbial taxa and the neuroendocrine-immune axis, particularly in LAS (p < 0.05), including bacterial taxa known to be involved in serotonergic signaling, such as Clostridia, and immunoglobulin concentrations, including Oscillospiraceae. Overall, these results show that long-term selection for differential antibody responses has lasting impacts on cecal microbiome diversity, community structure, and functional potential. This study provides insights into the evolutionary relationship between the cecal microbiome and its relation to the chicken neuroendocrine-immune axis. Together, the findings of this study suggest specific bacterial taxa adapted to the chicken may be leveraged to affect host humoral immune and serotonergic systems to potentially bolster gut health and increase foodborne pathogen resistance.}, }
@article {pmid40020154, year = {2025}, author = {Hincher, MR and Carleton, JP and Wheeler, SJ and DelCogliano, M and Mathis, K and Tabima, JF}, title = {Ubiquity and diversity of Basidiobolus across amphibian species inhabiting an urbanization gradient.}, journal = {Mycologia}, volume = {}, number = {}, pages = {1-13}, doi = {10.1080/00275514.2025.2455909}, pmid = {40020154}, issn = {1557-2536}, abstract = {The role of microfungal species in the environment is wide and well documented, especially in terms of symbiosis. Nonetheless, microfungal species are usually overseen and vastly understudied. One example of these understudied microfungal groups is the genus Basidiobolus, an ecologically diverse zoopagomycete genus found within vertebrate gastrointestinal systems, a saprobe across leaf litter, or as an opportunistic pathogen of immunocompromised humans. Studies of Basidiobolus diversity and distribution have been focused mostly on non-urbanized areas of subtropical regions, but there is a recent paucity of studies on this genus in temperate and densely human populated areas. Here, we present insights into the ubiquity and diversity of Basidiobolus species associated with amphibian species that live in the Worcester waterway system, a system of connecting streams and ponds that originate in pristine, protected wild management areas, and the highly urbanized downtown area of Worcester, Massachusetts. Our results show the ubiquitous presence of Basidiobolus across the gastrointestinal tract samples of amphibians spanning diverse species and habitats, including conservation areas, urban watersheds, and rural ecosystems. Our study reveals that multiple individuals and species of Basidiobolus coexist within a single host, suggesting complex interactions within amphibian gut microbiomes. Finally, we present possible novel diversity in the genus, indicating that further studies should be focused on understanding the species richness, genetic diversity, and ecological roles and associations of this interesting fungal group.}, }
@article {pmid40019912, year = {2025}, author = {Ryan, N and O'Mahony, S and Leahy-Warren, P and Philpott, L and Mulcahy, H}, title = {The impact of perinatal maternal stress on the maternal and infant gut and human milk microbiomes: A scoping review.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0318237}, doi = {10.1371/journal.pone.0318237}, pmid = {40019912}, issn = {1932-6203}, mesh = {Humans ; *Milk, Human/microbiology ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; *Stress, Psychological/microbiology ; Infant ; Infant, Newborn ; }, abstract = {BACKGROUND: Perinatal maternal stress, which includes both psychological and physiological stress experienced by healthy women during pregnancy and the postpartum period, is becoming increasingly prevalent. Infant early exposure to adverse environments such as perinatal stress has been shown to increase the long-term risk to metabolic, immunologic and neurobehavioral disorders. Evidence suggests that the human microbiome facilitates the transmission of maternal factors to infants via the vaginal, gut, and human milk microbiomes. The colonization of aberrant microorganisms in the mother's microbiome, influenced by the microbiome-brain-gut axis, may be transferred to infants during a critical early developmental period. This transfer may predispose infants to a more inflammatory-prone microbiome which is associated with dysregulated metabolic process leading to adverse health outcomes. Given the prevalence and potential impact of perinatal stress on maternal and infant health, with no systematic mapping or review of the data to date, the aim of this scoping review is to gather evidence on the relationship between perinatal maternal stress, and the human milk, maternal, and infant gut microbiomes.<br><br>METHODS: This is an exploratory mapping scoping review, guided by the Joanna Briggs Institute's methodology along with use of the Prisma Scr reporting guideline. A comprehensive search was conducted using the following databases, CINAHL Complete; MEDLINE; PsycINFO, Web of Science and Scopus with a protocol registered with Open Science Framework DOI 10.17605/OSF.IO/5SRMV.<br><br>RESULTS: After screening 1145 papers there were 7 paper that met the inclusion criteria. Statistically significant associations were found in five of the studies which identify higher abundance of potentially pathogenic bacteria such as Erwinia, Serratia, T mayombie, Bacteroides with higher maternal stress, and lower levels of stress linked to potentially beneficial bacteria such Lactococcus, Lactobacillus, Akkermansia. However, one study presents conflicting results where it was reported that higher maternal stress was linked to the prevalence of more beneficial bacteria.<br><br>CONCLUSION: This review suggests that maternal stress does have an impact on the alteration of abundance and diversity of influential bacteria in the gut microbiome, however, it can affect colonisation in different ways. These bacterial changes have the capacity to influence long term health and disease. The review analyses data collection tools and methods, offers potential reasons for these findings as well as suggestions for future research.}, }
@article {pmid40019745, year = {2025}, author = {Older, CE and Goodman, PM and Reifers, JG and Yamamoto, FY}, title = {Differences in the bacterial communities along the intestinal tract of juvenile channel (Ictalurus punctatus) and hybrid (I. punctatus × I. furcatus) catfish.}, journal = {Physiological genomics}, volume = {}, number = {}, pages = {}, doi = {10.1152/physiolgenomics.00008.2025}, pmid = {40019745}, issn = {1531-2267}, support = {6066-10600-001-000-D//U.S. Department of Agriculture (USDA)/ ; 6066-31320-007-00-D//U.S. Department of Agriculture (USDA)/ ; }, abstract = {Hybrid catfish (Ictalurus punctatus × I. furcatus) is the preferred catfish for United States aquaculture due to heterosis exhibited in many production traits. Improvements in fry production protocols have enabled widespread adoption of these hybrids, with producers using management practices optimized for channel catfish. Research to consider differences, outside of production traits, which may exist between hybrids and their parent species is lacking. Utilizing management practices specifically designed for hybrids may improve production efficiency. The gut microbiome plays critical roles in host development and health, and thus is relevant to production. In the present study, the microbiota in the anterior, middle, and posterior segments of the intestinal tract were compared between channel and hybrid catfish using high-throughput 16S rRNA sequencing. Bacterial community structure was different between channels and hybrids across all intestinal segments (p<0.05), despite a lack of difference in community diversity. Cetobacterium spp. were found in higher abundances in the middle intestinal segment of hybrids compared to channels (q=0.02), and found to have a trend of increasing abundance with increasingly distal segments in both channels and hybrids (q<0.05). Vibrio spp., a low abundance taxon, was similarly found in higher abundances in the anterior segment of hybrids. These results provide evidence of differences in the gut microbiomes of channels and hybrids and insight into the bacterial communities along the catfish intestinal tract. Additional research will be valuable in understanding why differences between channel and hybrid catfish exist and how they may contribute to variation in gut microbiome-related production traits.}, }
@article {pmid40019271, year = {2025}, author = {Milani, C and Longhi, G and Alessandri, G and Fontana, F and Viglioli, M and Tarracchini, C and Mancabelli, L and Lugli, GA and Petraro, S and Argentini, C and Anzalone, R and Viappiani, A and Carli, E and Vacondio, F and van Sinderen, D and Turroni, F and Mor, M and Ventura, M}, title = {Functional modulation of the human gut microbiome by bacteria vehicled by cheese.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0018025}, doi = {10.1128/aem.00180-25}, pmid = {40019271}, issn = {1098-5336}, abstract = {Since cheese is one of the most commonly and globally consumed fermented foods, scientific investigations in recent decades have focused on determining the impact of this dairy product on human health and well-being. However, the modulatory effect exerted by the autochthonous cheese microbial community on the taxonomic composition and associated functional potential of the gut microbiota of human is still far from being fully dissected or understood. Here, through the use of an in vitro human gut-simulating cultivation model in combination with multi-omics approaches, we have shown that minor rather than dominant bacterial players of the cheese microbiota are responsible for gut microbiota modulation of cheese consumers. These include taxa from the genera Enterococcus, Bacillus, Clostridium, and Hafnia. Indeed, they contribute to expand the functional potential of the intestinal microbial ecosystem by introducing genes responsible for the production of metabolites with relevant biological activity, including genes involved in the synthesis of vitamins, short-chain fatty acids, and amino acids. Furthermore, tracing of cheese microbiota-associated bacterial strains in fecal samples from cheese consumers provided evidence of horizontal transmission events, enabling the detection of particular bacterial strains transferred from cheese to humans. Moreover, transcriptomic and metabolomic analyses of a horizontally transmitted (cheese-to-consumer) bacterial strain, i.e., Hafnia paralvei T10, cultivated in a human gut environment-simulating medium, confirmed the concept that cheese-derived bacteria may expand the functional arsenal of the consumer's gut microbiota. This highlights the functional and biologically relevant contributions of food microbes acquired through cheese consumption on the human health.IMPORTANCEDiet is universally recognized as the primary factor influencing and modulating the human intestinal microbiota both taxonomically and functionally. In this context, cheese, being a fermented food with its own microbiota, serves not only as a source of nourishment for humans, but also as a source of nutrients for the consumer's gut microbiota. Additionally, it may act as a vehicle for autochthonous food-associated microorganisms which undergo transfer from cheese to the consumer, potentially influencing host gut health. The current study highlights not only that cheese microbiota-associated bacteria can be traced in the human gut microbiota, but also that they may expand the functional repertoire of the human gut microbiota, with potentially significant implications for human health.}, }
@article {pmid40019226, year = {2025}, author = {Hu, W and Wang, Y and Han, J and Zhang, W and Chen, J and Li, X and Wang, L}, title = {Microfluidic organ-on-a-chip models for the gut-liver axis: from structural mimicry to functional insights.}, journal = {Biomaterials science}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4bm01273a}, pmid = {40019226}, issn = {2047-4849}, abstract = {The gut-liver axis plays a crucial role in maintaining metabolic balance and overall human health. It orchestrates various processes, such as blood flow, nutrient transfer, metabolite processing, and immune cell communication between the two organs. Traditional methods, such as animal models and two-dimensional (2D) cell cultures, are insufficient in fully replicating the intricate functions of the gut-liver axis. The emergence of microfluidic technology has revolutionized this field, facilitating the development of organ-on-a-chip (OOC) systems. These systems are capable of mimicking the complex structures and dynamic environments of the gut and liver in vitro and incorporating sensors for real-time monitoring. In this article, we review the latest progress in gut-on-a-chip (GOC) and liver-on-a-chip (LOC) systems, as well as the integrated gut-liver-on-a-chip (GLOC) models. Our focus lies in the simulation of physiological parameters, three-dimensional (3D) structural mimicry, microbiome integration, and multicellular co-culture. All these aspects are essential for constructing accurate in vitro models of the gut and liver. Furthermore, we explore the current applications of OOC technology in the study of the gut and liver, including its use in disease modeling, toxicity testing, and drug screening. Finally, we discuss the challenges that remain and outline potential future directions for advancing GOC and LOC development in vitro.}, }
@article {pmid40018800, year = {2025}, author = {Ye, Y and Jiang, P and Aasmul-Olsen, K and Akıllıoğlu, HG and Bjørnshave, A and Bechshøft, MR and Lund, MN and Sangild, PT and Bering, SB and Khakimov, B}, title = {Effects of Skim Milk Whey-Derived Proteins on Plasma, Urine, and Gut Metabolites in Preterm Piglets as a Model for Infants.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e70007}, doi = {10.1002/mnfr.70007}, pmid = {40018800}, issn = {1613-4133}, support = {//Arla Foods Ingredients Group P/S, University of Copenhagen, the Ministry of Food, Agriculture and Fisheries of Denmark./ ; }, abstract = {This study investigates the metabolic impact of skim milk whey-derived protein concentrate (SPC) for infant formula, including its heat-treated (HT-SPC) and stored (HTS-SPC) variants, on the plasma, urine, and gut metabolites of newborn piglets, compared to conventional whey protein concentrate (WPC). Preterm piglets were fed formula containing WPC, SPC, HT-SPC, or HT-SPC, HTS-SPC for 5 days. Metabolomic analysis of plasma, urine, and colon content was performed using 1H NMR. Relative to WPC, SPC mainly affected colon content metabolites, increasing 19 metabolites in the colon and tyrosine in plasma, while decreasing pyruvate in colon content and glycine in plasma. Heat-treatment and storage of SPC led to increased metabolite concentrations in colon contents and urine. Notably, significant correlations between gut metabolites and abundant gut bacteria genes were observed only in the SPC-fed pigs. SPC induced higher branched chain amino acid concentrations in the gut, but had minimal effects on plasma and urinary metabolites, likely due to differences in dietary proteins and in microbiota metabolism. While the clinical effects of SPC-induced gut branched chain amino acids remain unclear, the results from our study suggest that SPC-based infant formula is metabolically safe for sensitive newborns, comparable to WPC-based formulas.}, }
@article {pmid40018705, year = {2025}, author = {Beale, DJ and Nguyen, TV and Dyall, T and van de Kamp, J and Bissett, A and Hewitt, L and Small, AH}, title = {Use of fecal microbiome to understand the impact of housing conditions on metabolic stress responses in farmed saltwater crocodiles (Crocodylus porosus).}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1496946}, pmid = {40018705}, issn = {2297-1769}, abstract = {INTRODUCTION: Understanding the impact of housing conditions on the stress responses in farmed saltwater crocodiles (Crocodylus porosus) is crucial for optimizing welfare and management practices.<br><br>METHODS: This study employed a multi-omics methodology, combining targeted and untargeted LC-MS for metabolite, lipid, and hormone profiling with 16S rRNA gene sequencing for microbiome analysis, to compare stress responses and changes in fecal samples of crocodiles housed in single versus group pens. Metabolic responses to a startle test were evaluated through multivariate analysis, and changes post-stress were examined.<br><br>RESULTS: A total of 564 metabolic features were identified. Of these, 15 metabolites were linked to the cortisol biosynthesis pathway. Metabolite origin analysis showed that 128 metabolites originated from the host, 151 from the microbiota, and 400 remained unmatched. No significant differences in fecal corticosterone levels were observed between single and group pens. However, metabolic profiling revealed distinct differences in stress responses: single pen crocodiles exhibited downregulation of certain compounds and upregulation of others, affecting pyrimidine and purine metabolism pathways when compared to grouped pen crocodiles, linked to altering energy associated induced stress. Additionally, fecal microbiome analysis indicated increased Firmicutes:Bacteroides (F:B) ratio in group-housed animals, suggesting greater stress.<br><br>DISCUSSION: The study highlights that while traditional stress indicators like corticosterone levels may not differ significantly between housing conditions, metabolic and microbiome analyses provide deeper insights into stress responses. Single pens are associated with less metabolic disruption and potentially better health outcomes compared to group pens. These findings underscore the value of fecal microbiome and metabolomics in assessing animal welfare in farmed crocodiles.}, }
@article {pmid40018491, year = {2025}, author = {Shaikh, RG and Dey, A and Singh, VP and Khandagle, A and M, B and Naik, S and Hasan, A}, title = {Understanding the Impact of the Gut Microbiome on Mental Health: A Systematic Review.}, journal = {Cureus}, volume = {17}, number = {1}, pages = {e78100}, pmid = {40018491}, issn = {2168-8184}, abstract = {Mental health is a serious issue, with mental health disorders affecting millions of people globally. Gut microbiota has received considerable attention because of its potential role in the pathogenesis of mental health disorders. This systematic review synthesized 15 studies exploring the effects of the gut microbiome on depression, anxiety, schizophrenia, and bipolar disorder, with qualitative and quantitative insights. The studies were conducted in different countries and employed various methods including 16S rRNA sequencing and metagenomic analysis with sample sizes varying from 50 to 600. Some of the key findings were that depression was associated with reduced microbial diversity and high levels of Firmicutes, and anxiety was associated with low levels of short-chain fatty acid (SCFA)-producing bacteria and high levels of Proteobacteria. Schizophrenia was related to endotoxemia and a reduction in the Lactobacillus count whereas bipolar disorder displayed a shift in the Firmicutes/Bacteroidetes ratio. Of interest, probiotics and dietary changes were as effective as drug treatment leading to symptom alleviation in many patients. It was found that depression was linked to less diverse gut bacteria while anxiety was associated with an increase in inflammatory bacteria. People with bipolar disorder were also found to have different gut bacteria patterns. This review also emphasizes the importance of the gut microbiota in the pathophysiology of mental disorders and the promising value of targeting microbiomes in pharmacological treatment approaches.}, }
@article {pmid40018030, year = {2025}, author = {Vanhove, MPM and Koblmüller, S and Fernandes, JMO and Hahn, C and Plusquin, M and Kmentová, N}, title = {Cichlid fishes are promising underutilized models to investigate helminth-host-microbiome interactions.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1527184}, pmid = {40018030}, issn = {1664-3224}, mesh = {Animals ; *Helminths/immunology ; *Cichlids/immunology/microbiology/parasitology ; *Host-Parasite Interactions/immunology ; Microbiota/immunology ; Humans ; Helminthiasis/immunology/parasitology/microbiology ; Disease Models, Animal ; Fish Diseases/immunology/parasitology/microbiology ; Host Microbial Interactions/immunology ; Gastrointestinal Microbiome/immunology ; Helminthiasis, Animal/immunology/epidemiology/parasitology ; }, abstract = {The "Old Friends Hypothesis" suggests insufficient exposure to symbionts hinders immune development, contributing to increased immune-related diseases in the Global North. The microbiome is often the focus; helminths, potentially also offering health benefits, lack attention. Infection and effect of helminths are influenced and perhaps determined by micro-organisms. Mechanisms behind parasite-microbiome interactions are poorly understood, despite implications on host health. These interactions are typically studied for single helminth species in laboratory animal models, overlooking helminth diversity. Reviewing research on relationships between helminth and microbial diversity yielded 27 publications; most focused on human or other mammalian hosts, relying on natural exposure rather than experimental helminth inoculation. Only about half investigated host health outcomes. Remaining knowledge gaps warrant considering additional candidate model systems. Given the high helminthiasis burden and species diversity of helminths, we propose seeking models in the Global South, where a considerable proportion of research on diversity aspects of helminth-microbiome interactions took place. Low availability of genomic resources for helminths in the Global South, however, necessitates more integrative helminthological research efforts. Given substantial similarities in immune systems, several fishes are models for human health/disease. More effort could be done to establish this for cichlids, whose representatives in the African Great Lakes provide a well-delineated, closed natural system relevant to human health in view of fish-borne zoonoses and other water-borne parasites. A good baseline exists for these cichlids' genomics, parasitology, and microbiology. We suggest exploring African Great Lake cichlids as model hosts for interactions between microbial diversity, helminth diversity, and host health.}, }
@article {pmid40017817, year = {2025}, author = {Rotevatn, A&#xd8; and Eagan, TM and Tangedal, S and Husebø, GR and Ostridge, K and Nielsen, R}, title = {Gut microbiota in chronic obstructive pulmonary disease varies by CT-verified emphysema status.}, journal = {European clinical respiratory journal}, volume = {12}, number = {1}, pages = {2470499}, pmid = {40017817}, issn = {2001-8525}, abstract = {BACKGROUND AND AIM: The association of the gut microbiota to chronic obstructive pulmonary disease (COPD) phenotypes is underexplored. We aimed to compare stool samples from patients with COPD and subjects without COPD and relate findings to emphysema status, exacerbation rate, blood eosinophil levels, symptom score, and lung function.<br><br>METHODS: We report findings from a single-centre case-control study with 62 current and former smoking patients with COPD and 49 subjects without COPD. DNA was extracted from stool samples, and the V3V4-region of the bacterial 16S-rRNA gene was sequenced. Emphysema was defined based on thoracic computed tomography (CT thorax) low attenuating areas &#x2265;/<10% at threshold -950 and -910&#xa0;hounsfield units, respectively. Differential abundance of taxa was evaluated using Analysis of Composition of Microbes with Bias Correction (ANCOM-BC). Beta diversity was compared using a distance-based permanova-test.<br><br>RESULTS: The genus Veillonella was decreased and a genus belonging to class Clostridia was increased in COPD compared with controls without COPD. The composition of microbes (beta diversity) differed in emphysema compared to controls, and 27 genera were differentially abundant in emphysema vs. controls. Nine of these genera belonged to the family Lachnospiraceae. Lung function, blood counts and COPD assessment test score correlated with several genera's relative abundance. Of the genera showing significant correlation to lung function, nine belonged to the family Lachnospiraceae.<br><br>CONCLUSION: The gut microbiota in COPD differs from that in healthy individuals, even more so in emphysema. In particular, future studies should look into the mechanisms and therapeutic potential of dysbiosis affecting the family Lachnospiraceae.}, }
@article {pmid40017683, year = {2024}, author = {Jakonyte, A and Pliavga, V and Juodzbalys, G}, title = {A Comprehensive Analysis of the Association between Thyroid Dysfunctions and Periodontal Health: Systematic Review.}, journal = {Journal of oral &amp; maxillofacial research}, volume = {15}, number = {4}, pages = {e1}, pmid = {40017683}, issn = {2029-283X}, abstract = {OBJECTIVES: The purpose of this systematic literature review was to establish a correlation between thyroid dysfunctions and periodontium health.<br><br>MATERIAL AND METHODS: The systematic review was conducted according to PRISMA statement. An electronic search was performed using MEDLINE (PubMed) and Google Scholar databases using a combination of keywords "hypothyroidism", "hypothyroidism", "thyroid", "thyroid dysfunction" and "periodontitis". The research covered the period from January 1, 2019 and July 1, 2024, included studies written in English, conducted in humans.<br><br>RESULTS: The results showed that hyperthyroidism can be associated with a higher prevalence of periodontitis due to decreased oral microbiome diversity, serum thyroid-stimulating hormone levels, increased periodontal pocket depth, clinical attachment loss and interleukin-6. Hyperparathyroidism after parathyroidectomy may lead to a slightly higher risk of tooth extraction in the first two years afterward because decreasing lamina dura, increasing periodontal ligament width. And hypothyroidism negatively affects the homeostasis of calcium and phosphorus in the oral fluid and can change the composition of bone minerals.<br><br>CONCLUSIONS: Hyperthyroidism increases the risk of periodontitis by promoting deeper periodontal pockets, reducing oral microbiome diversity, altering alveolar bone structure and elevating inflammatory markers like interleukin-6, which are linked to disease progression. Hypothyroidism worsens periodontal disease by disrupting calcium-phosphorus balance and causing alveolar bone changes, especially in young individuals. Both conditions affect periodontal homeostasis, emphasizing the bidirectional relationship between endocrine and periodontal health. Dentists should monitor thyroid dysfunction, as managing thyroid levels may improve periodontal treatment.}, }
@article {pmid40017507, year = {2025}, author = {Kim, YR and Choi, TR and Jo, SH and Song, WS and Kim, T and Kim, MG and Baek, JH and Kwon, SY and Choi, BG and Seo, SW and Jang, CS and Yang, YH and Kim, YG}, title = {Deciphering the anti-obesity mechanisms of pharmabiotic probiotics through advanced multiomics analysis.}, journal = {iScience}, volume = {28}, number = {2}, pages = {111890}, pmid = {40017507}, issn = {2589-0042}, abstract = {Probiotics with "pharmabiotic" properties are increasingly recognized as effective tools for combating obesity by altering gut microbiota and reducing body fat. However, the molecular mechanisms underlying their anti-obesity effects remain largely unexplored due to the absence of a universal methodology. Herein, we developed a multiomics-based strategy to elucidate how probiotics reduce lipid production in adipocytes. Our initial investigation assessed the impact of probiotics at defined adipocyte differentiation stages. Leveraging these insights, we performed comprehensive multiomics analyses at key intervals to identify the suppression mechanisms of lipid formation. Lactobacillus reuteri, specifically, targets early differentiation stages, inhibits branched-chain amino acid catabolism, and reduces lipid accumulation in adipocytes by suppressing Krüppel-like factor 5. Concurrently, enhanced hypoxia-inducible factor 1 expression impedes adipogenesis by downregulating lipin-1 expression. This study not only demonstrates the effectiveness of our approach in revealing complex host-microbe interactions but also significantly advances probiotic therapeutic development, offering promising avenues for obesity management.}, }
@article {pmid40017273, year = {2025}, author = {Thatrimontrichai, A and Praditaukrit, M and Maneenil, G and Dissaneevate, S and Singkhamanan, K and Surachat, K}, title = {Characterization of gut microbiota in very low birth weight infants with versus without bronchopulmonary dysplasia.}, journal = {Clinical and experimental pediatrics}, volume = {}, number = {}, pages = {}, doi = {10.3345/cep.2024.01718}, pmid = {40017273}, issn = {2713-4148}, abstract = {BACKGROUND: Gut-lung crosstalk is a pathway involving interactions between the gastrointestinal, respiratory, and immune systems. The immune responses of the gut and lungs are intricately linked, and previous studies demonstrated that the gut microbiota can influence systemic immune responses in the respiratory system as well as bronchopulmonary dysplasia (BPD).<br><br>PURPOSE: To analyze the composition of the gut microbiota in very low birth weight infants with versus without BPD.<br><br>METHODS: Secondary data from a previous randomized controlled trial were analyzed. Microbiomes were analyzed using QIIME 2 software. Gut microbiota diversity and abundance were compared between groups.<br><br>RESULTS: Fifty-one neonates were classified into the BPD (n=24) and non-BPD (n=27) groups, between which no differences were noted in the alpha and beta diversities of the gut microbiota. In both groups, Proteobacteria, Gammaproteobacteria, and Klebsiella were the predominant phyla, class, and genus in gut microbiota, respectively. Enterococcus, Acinetobacter, Elizabethkingia, Clostridium sensu stricto 1, Bacteroides, Streptococcus, and Serratia were more abundant, whereas Klebsiella, Faecalibacterium, Escherichia-Shigella, Enterobacter, Bifidobacterium, Veillonella, Staphylococcus, and Enterobacteriaceae were less abundant in the BPD versus non-BPD group. Faecalibacterium, Roseburia, Clostridium, Eubacterium, and Coprococcus were significantly more abundant in the non-BPD versus BPD group.<br><br>CONCLUSION: The alpha and beta diversities of the gut microbiota did not differ significantly between the BPD and non-BPD groups. However, in terms of relative abundance, the presence of common respiratory pathogens was notable in the BPD group. Conversely, the non-BPD group had a significantly higher prevalence of anaerobic taxa known for their capacity to produce butyrate, a key component of postbiotics. Clinical Trial Registration: This trial was prospectively registered at Thai Clinical Trials (https://www.thaiclinicaltrials.org/export/pdf/TCTR20180306002; first posted registration: March 6, 2018).}, }
@article {pmid40016867, year = {2025}, author = {L'Orphelin, JM and Dompmartin, A and Dréno, B}, title = {The Skin Microbiome: A New Key Player in Melanoma, From Onset to Metastatic Stage.}, journal = {Pigment cell &amp; melanoma research}, volume = {38}, number = {2}, pages = {e13224}, doi = {10.1111/pcmr.13224}, pmid = {40016867}, issn = {1755-148X}, mesh = {Humans ; *Melanoma/microbiology/pathology/therapy ; *Microbiota ; *Skin/microbiology/pathology/radiation effects ; *Skin Neoplasms/microbiology/pathology ; Ultraviolet Rays ; Neoplasm Metastasis ; Animals ; }, abstract = {The skin microbiome plays a crucial role in maintaining skin health, defending the body against harmful pathogens, and interacting with melanoma. The composition of the skin microbiome can be affected by factors like age, gender, ethnicity, lifestyle, diet, and UV exposure. Certain bacteria like Staphylococcus and Veillonella are important for wound healing, while Cutibacterium acnes can play a role in dermatoses. UV radiation alters the skin microbiome, originates a "UV-resistome" and can lead to skin cancer initiation. Specifically, Staphylococcus epidermidis has shown protective effects against skin cancer, whereas Cutibacterium acnes can induce apoptosis in melanocytes postirradiation. The microbiome also interacts with melanoma treatment, affecting responses to immune checkpoint inhibitors. Strategies like bacteriotherapy, involving the manipulation of the gut microbiome but also the skin microbiome (with the gut-skin axis or through topical treatment) could improve treatment outcomes and show promise in melanoma therapy. Understanding the complex interplay between the skin microbiome, UV exposure, and melanoma development is crucial for developing personalized therapeutic approaches. Investigation into the skin microbiome and its potential role in melanoma progression continues to be an exciting area of research with implications for future therapeutic interventions.}, }
@article {pmid40016766, year = {2025}, author = {Son, SJ and Lee, DY and Roh, HW and Ly, M and Kolobaric, A and Aizenstein, H and Andreescu, C and Jašarević, E and Pascoal, TA and Ferreira, PCL and Bellaver, B and Cho, YH and Hong, S and Nam, YJ and Park, B and Kim, N and Choi, JW and Cheong, JY and Kim, YK and Shin, TS and Kang, CS and Kwon, CO and Yoon, SY and Hong, CH and Karim, HT}, title = {Brain age mediates gut microbiome dysbiosis-related cognition in older adults.}, journal = {Alzheimer's research &amp; therapy}, volume = {17}, number = {1}, pages = {52}, pmid = {40016766}, issn = {1758-9193}, support = {HR21C1003//Korea Health Industry Development Institute/Republic of Korea ; HR21C1003//Korea Health Industry Development Institute/Republic of Korea ; HR22C1734//Korea Health Industry Development Institute/Republic of Korea ; HR22C1734//Korea Health Industry Development Institute/Republic of Korea ; HR22C1734//Korea Health Industry Development Institute/Republic of Korea ; HR22C1734//Korea Health Industry Development Institute/Republic of Korea ; 6637-303//Korea Disease Control and Prevention Agency/ ; 6637-303//Korea Disease Control and Prevention Agency/ ; 6637-303//Korea Disease Control and Prevention Agency/ ; RS-2019-NR040055//National Research Foundation of Korea/ ; RS-2024-00339665//Korea Dementia Research Project through the Korea Dementia Research Center (KDRC)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology ; Male ; Female ; Aged ; *Brain/microbiology/diagnostic imaging ; *Cognition/physiology ; *Magnetic Resonance Imaging ; Cognitive Dysfunction/microbiology ; Aging/physiology ; Middle Aged ; Aged, 80 and over ; }, abstract = {BACKGROUND: Recent studies have focused on improving our understanding of gut microbiome dysbiosis and its impact on cognitive function. However, the relationship between gut microbiome composition, accelerated brain atrophy, and cognitive function has not yet been fully explored.<br><br>METHODS: We recruited 292 participants from South Korean memory clinics to undergo brain magnetic resonance imaging, clinical assessments, and collected stool samples. We employed a pretrained brain age model- a measure associated with neurodegeneration. Using cluster analysis, we categorized individuals based on their microbiome profiles and examined the correlations with brain age, Mental State Examination (MMSE) scores, and the Clinical Dementia Rating Sum of Box (CDR-SB).<br><br>RESULTS: Two clusters were identified in the microbiota at the phylum level that showed significant differences on a few microbiotas phylum. Greater gut microbiome dysbiosis was associated with worse cognitive function including MMSE and CDR-SB; this effect was partially mediated by greater brain age even when accounting for chronological age, sex, and education.<br><br>CONCLUSIONS: Our findings indicate that brain age mediates the link between gut microbiome dysbiosis and cognitive performance. These insights suggest potential interventions targeting the gut microbiome to alleviate age-related cognitive decline.}, }
@article {pmid40016738, year = {2025}, author = {Chen, X and Wang, B and Al Mamun, A and Du, K and Wang, S and Hu, Q and Chen, X and Lu, Y and Du, A and Wu, Y and Shao, J and Wang, S and Jiang, C and Zhou, K and Hu, S and Xiao, J}, title = {Pectin-Zein-IPA nanoparticles promote functional recovery and alleviate neuroinflammation after spinal cord injury.}, journal = {Journal of nanobiotechnology}, volume = {23}, number = {1}, pages = {152}, pmid = {40016738}, issn = {1477-3155}, support = {82172428//National Natural Science Foundation of China/ ; }, mesh = {*Spinal Cord Injuries/drug therapy ; Animals ; *Pectins/chemistry/pharmacology ; *Nanoparticles/chemistry ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Recovery of Function/drug effects ; *Zein/chemistry/pharmacology ; Indoles/pharmacology/chemistry ; Neuroinflammatory Diseases/drug therapy ; Rats, Sprague-Dawley ; Male ; Oxidative Stress/drug effects ; Female ; }, abstract = {INTRODUCTION: Spinal cord injury (SCI) impairs the balance of gut microbiomes, which further aggravates inflammation in the injured areas and inhibits axonal regeneration. The intestinal microbiome plays an important role in SCI and regulating intestinal microbiome promotes SCI repair. However, current studies have shown that indole-3 propionate (IPA), a metabolite of gut bacteria, can promote axonal regeneration. However, the short half-life of IPA limits its effectiveness. Gut microbiota plays a role in the progression of SCI, but the studies about diet regulates intestinal flora metabolites to improve SCI are still limited and lack guiding significance.<br><br>RESULTS: The results showed that Pectin-Zein-IPA NPs treatment improves motor function recovery, inhibits the activation of oxidative stress, enhances axonal regeneration and activates AKT/Nrf-2 signaling pathway following SCI. Further analysis showed that Pec-Zein-IPA NPs treatment reduced the intestinal flora metabolite accumulation of L-methionine, and alleviated neuroinflammation by improving autophagy and inhibiting pyroptosis. Pec-Zein-IPA may reduced neuroinflammation after SCI by decreasing the abundance of Clostridia-UCG-014, Clostridia-vadinBB60-group, Shewanella (positively correlated with L-Methionine) and increasing the abundance of Parasutterella (negatively correlated with L-Methionine).<br><br>CONCLUSIONS: Our findings provide a strategy for oral drug research in SCI. The results suggest that Pectin-Zein-IPA NPs have potential advantages for treatment and management of SCI. Reducing L-methionine intake may help reduce neuroinflammation after SCI.}, }
@article {pmid40016684, year = {2025}, author = {Thongsepee, N and Amonyingcharoen, S and Chamod, P and Himakhun, W and Sangpairoj, K and Martviset, P and Chantree, P and Sornchuer, P}, title = {Modulatory effects of Kratom extract on the gut microbiota of rats: implications for health.}, journal = {BMC complementary medicine and therapies}, volume = {25}, number = {1}, pages = {85}, pmid = {40016684}, issn = {2662-7671}, support = {2-19/2566//Faculty of Medicine, Thammasat University, Thailand/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Male ; *Plant Extracts/pharmacology ; Rats ; *Rats, Wistar ; *Mitragyna ; Feces/microbiology ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Kratom (Mitragyna speciosa), a plant native to Southeast Asia, is commonly used as a supplement for fatigue, pain relief, mood enhancement, and euphoria. Kratom extract exhibits diverse pharmacological properties, including antioxidant, anti-inflammatory, and gastrointestinal effects, with studies showing its ability to modulate gut microbiota and stimulate beneficial bacteria growth. Given these properties, kratom treatment may produce significant effects in a rat model, warranting further investigation.<br><br>METHODS: Male Wistar rats were administered kratom extract orally on a daily basis for 28 days. Fresh fecal samples were collected and analyzed for changes in gut microbiome composition using 16S rRNA sequencing. Hematological parameters and lipid profiles were also measured to evaluate any systemic effects.<br><br>RESULTS: The administration of kratom extract did not significantly affect hematological parameters or lipid profiles. However, notable changes were observed in gut microbiota composition, with significant increases in specific bacteria such as Candidatus Stoquefichus and Prevotellaceae UCG-001, and a decrease in Corynebacterium. LEfSe and cladogram analyses corroborated the higher prevalence of Candidatus Stoquefichus, Prevotellaceae UCG-001, and Erysipelatoclostridiaceae in the kratom treatment group compared to controls.<br><br>CONCLUSIONS: Kratom extract significantly alters gut microbiome composition in rats, promoting beneficial bacteria while also elevating certain taxa associated with negative health outcomes. These mixed effects highlight the need for further research on the long-term implications of kratom use for gut health and its broader health consequences, as well as potential therapeutic applications.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid40016656, year = {2025}, author = {Koslovsky, MD}, title = {Analyzing microbiome data with taxonomic misclassification using a zero-inflated Dirichlet-multinomial model.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {69}, pmid = {40016656}, issn = {1471-2105}, support = {DMS-2245492//National Science Foundation/ ; }, mesh = {Humans ; *Microbiota/genetics ; Gastrointestinal Microbiome/genetics ; Child ; Obesity/microbiology ; }, abstract = {The human microbiome is the collection of microorganisms living on and inside of our bodies. A major aim of microbiome research is understanding the role microbial communities play in human health with the goal of designing personalized interventions that modulate the microbiome to treat or prevent disease. Microbiome data are challenging to analyze due to their high-dimensionality, overdispersion, and zero-inflation. Analysis is further complicated by the steps taken to collect and process microbiome samples. For example, sequencing instruments have a fixed capacity for the total number of reads delivered. It is therefore essential to treat microbial samples as compositional. Another complicating factor of modeling microbiome data is that taxa counts are subject to measurement error introduced at various stages of the measurement protocol. Advances in sequencing technology and preprocessing pipelines coupled with our growing knowledge of the human microbiome have reduced, but not eliminated, measurement error. Ignoring measurement error during analysis, though common in practice, can then lead to biased inference and curb reproducibility. We propose a Dirichlet-multinomial modeling framework for microbiome data with excess zeros and potential taxonomic misclassification. We demonstrate how accommodating taxonomic misclassification improves estimation performance and investigate differences in gut microbial composition between healthy and obese children.}, }
@article {pmid40016229, year = {2025}, author = {Chang, J and Costa, OYA and Sun, Y and Wang, J and Tian, L and Shi, S and Wang, E and Ji, L and Wang, C and Pang, Y and Yao, Z and Ye, L and Zhang, J and Chen, H and Cai, Y and Chen, D and Song, Z and Rong, J and Raaijmakers, JM and Tian, C and Kuramae, EE}, title = {Domesticated rice alters the rhizosphere microbiome, reducing nitrogen fixation and increasing nitrous oxide emissions.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {2038}, pmid = {40016229}, issn = {2041-1723}, mesh = {*Oryza/microbiology/metabolism ; *Nitrous Oxide/metabolism ; *Rhizosphere ; *Microbiota/genetics ; *Soil Microbiology ; *Nitrogen Fixation ; *Plant Roots/microbiology/metabolism ; Domestication ; Metagenomics ; Soil/chemistry ; Nitrogenase/metabolism/genetics ; Nitrogen/metabolism ; Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Agriculture/methods ; }, abstract = {Crop domestication has revolutionized food production but increased agriculture's reliance on fertilizers and pesticides. We investigate differences in the rhizosphere microbiome functions of wild and domesticated rice, focusing on nitrogen (N) cycling genes. Shotgun metagenomics and real-time PCR reveal a higher abundance of N-fixing genes in the wild rice rhizosphere microbiomes. Validation through transplanting rhizosphere microbiome suspensions shows the highest nitrogenase activity in soils with wild rice suspensions, regardless of planted rice type. Domesticated rice, however, exhibits an increased number of genes associated with nitrous oxide (N2O) production. Measurements of N2O emissions in soils with wild and domesticated rice are significantly higher in soil with domesticated rice compared to wild rice. Comparative root metabolomics between wild and domesticated rice further show that wild rice root exudates positively correlate with the frequency and abundance of microbial N-fixing genes, as indicated by metagenomic and qPCR, respectively. To confirm, we add wild and domesticated rice root metabolites to black soil, and qPCR shows that wild rice exudates maximize microbial N-fixing gene abundances and nitrogenase activity. Collectively, these findings suggest that rice domestication negatively impacts N-fixing bacteria and enriches bacteria that produce the greenhouse gas N2O, highlighting the environmental trade-offs associated with crop domestication.}, }
@article {pmid40016228, year = {2025}, author = {Florence, L and Tomlinson, S and Freestone, M and Morgan, JW and Wood, JL and Truong, C}, title = {A curated soil fungal dataset to advance fungal ecology and conservation research in Australia and Antarctica.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {353}, pmid = {40016228}, issn = {2052-4463}, mesh = {Australia ; *Soil Microbiology ; *Fungi/genetics/classification ; Antarctic Regions ; *Biodiversity ; DNA Barcoding, Taxonomic ; Conservation of Natural Resources ; Ecosystem ; }, abstract = {DNA metabarcoding has played a pivotal role in advancing our understanding of the diversity and function of soil-inhabiting fungi. The Australian Microbiome Initiative has produced an extensive soil fungal metabarcoding dataset of more than 2000 plots across a breadth of ecosystems in Australia and Antarctica. Sequence data requires rigorous approaches for the integration of species occurrences into biodiversity platforms, addressing biases due to false positives or overinflated diversity estimates, among others. To tackle such biases, we conducted a rigorous analysis of the fungal dataset following best practices in fungal metabarcoding and integrated it with over 100 predictor variables to fast-track data exploration. We carefully validated our methodology based on studies conducted on historical versions of the dataset. Our approach generated robust information on Australian soil fungi that can be leveraged by end-users interested in biodiversity, biogeography, and conservation. This novel resource will unlock new frontiers in soil fungal research within the Southern Hemisphere and beyond.}, }
@article {pmid40016033, year = {2025}, author = {Zhang, J and Fu, J and Duan, C and Chen, M and Wu, W and Chen, X and Ma, W and Zhou, H and He, Y and Cao, P}, title = {Identifying reproducible biomarkers for microbiome association studies requires thousands of sample sizes.}, journal = {Science bulletin}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.scib.2025.02.022}, pmid = {40016033}, issn = {2095-9281}, }
@article {pmid40015964, year = {2025}, author = {Nguyen, HVM and Cabello, E and Dyer, D and Fender, C and Garcia-Jaramillo, M and Hord, NG and Austad, S and Richardson, A and Unnikrishnan, A}, title = {Age, sex, and mitochondrial-haplotype influence gut microbiome composition and metabolites in a genetically diverse rat model.}, journal = {Aging}, volume = {null}, number = {}, pages = {}, doi = {10.18632/aging.206211}, pmid = {40015964}, issn = {1945-4589}, abstract = {We evaluated the impact of sex and mitochondrial-haplotype on the age-related changes in the fecal gut microbiome of the genetically heterogeneous rodent model, the OKC-HET[B/W] rat. The age-related changes in the microbiome differed markedly between male and female rats. Five microbial species changed significantly with age in male rats compared to nine microbial species in female rats. Only three of these microbes changed with age in both male and female rats. The mitochondrial-haplotype of the rats also affected how aging altered the microbiome. Interestingly, most of the microbial species that changed significantly with age were mitochondrial-haplotype and sex specific, i.e., changing in one sex and not the other. We also discovered that sex and mitochondrial-haplotype significantly affected the age-related variations in content of fecal short-chain fatty acids and plasma metabolites that influence or are regulated by the microbiome, e.g., tryptophan derived metabolites and bile acids. This study demonstrates that the host's sex plays a significant role in how the gut microbiome evolves with age, even within a genetically diverse background. Importantly, this is the first study to show that the mitochondrial-haplotype of a host impacts the age-related changes in the microbiome.}, }
@article {pmid40015812, year = {2025}, author = {Chauhan, G and Rieder, F}, title = {The Pathogenesis of Inflammatory Bowel Diseases.}, journal = {The Surgical clinics of North America}, volume = {105}, number = {2}, pages = {201-215}, doi = {10.1016/j.suc.2024.10.008}, pmid = {40015812}, issn = {1558-3171}, mesh = {Humans ; *Inflammatory Bowel Diseases/etiology/immunology/genetics ; Immunity, Innate ; Gastrointestinal Microbiome/immunology/physiology ; Adaptive Immunity ; }, abstract = {Inflammatory bowel diseases (IBDs) are relapsing, remitting inflammatory diseases of the intestinal tract. Familial aggregation and genome-wide association studies revealed susceptibility variants that point toward a combination of innate immune and adaptive immune dysregulation that in concert with environmental factors, such as our microbiome, can initiate and perpetuate inflammation. Innate immune perturbations include functional abnormalities in the intestinal barrier, endoplasmic reticulum stress, and abnormal recognition of microbes. Adaptive immune changes include dysregulation of cytokines, regulatory T cells, and leukocyte migration. IBD is linked with an abnormal wound-healing response leading to fibrosis. This article summarizes key pathogenic mechanisms in the pathogenesis of IBDs.}, }
@article {pmid40015702, year = {2025}, author = {Liu, T and Li, GY and Huang, ZW and Bu, XW and Ma, JJ and Duan, N and Wang, WM and Wang, X}, title = {[Study on the invasion of Prevotella intermedia in tissues during carcinogenesis of oral mucosa].}, journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology}, volume = {60}, number = {3}, pages = {211-222}, doi = {10.3760/cma.j.cn112144-20241212-00476}, pmid = {40015702}, issn = {1002-0098}, support = {202305034//The Project of Nanjing Bureau of Science and Technology/ ; 0223A207//"2015" Cultivation Program for Reserve Talents for Academic Leaders of Nanjing Stomatological School, Medical School of Nanjing University/ ; 0222C116//"3456" Cultivation Program for Junior Talents of Nanjing Stomatological School, Medical School of Nanjing University/ ; }, abstract = {Objective: To explore the differences in bacterial communities within tissues during the process of oral mucosal carcinogenesis, and analyze the relationship between the high-abundance species Prevotella intermedia (Pi) and the occurrence and development of oral mucosal carcinogenesis. Methods: Fresh tissue samples were collected from patients diagnosed with oral leukoplakia (OLK), oral squamous cell carcinoma (OSCC), and healthy controls (HC) at Nanjing Stomatological Hospital from January 2022 to November 2024, following strict inclusion criteria. Bacterial DNA was extracted from these specimens, and the 2bRAD sequencing for microbiome (2bRAD-M) was employed to analyze and compare the α and β diversity, as well as the community composition of bacteria within tissues, aiming to identify specifically expressed bacteria. Subsequently, paraffin-embedded clinical specimens were collected: 15 cases in the OLK group (including 4 cases of simple hyperplasia, 6 cases of mild dysplasia, and 5 cases of moderate to severe dysplasia), 12 cases in the OSCC group, and 5 cases in the HC group. A 4-nitroquinoline n-oxide (4NQO)-induced OLK progression mouse model was also constructed. Mice were randomly divided into three groups using a random number table, with six in each group. The negative control group was given distilled water to drink; Group 1 was given distilled water containing 4NQO to drink until week 12, while Group 2 was given distilled water containing 4NQO to drink until week 22. After the mice were sacrificed, their tongue tissue were collected and fixed. Fluorescence in situ hybridization (FISH) with specific probes was used to validate the presence of Pi in human and mouse tissue sections, analyzing the correlation between histopathological grading and the invasion depth of Pi. Results: The 2bRAD-M microbial analysis revealed that the relative abundance of Pi in OSCC tissues (10.80%) was significantly higher than in the HC group (0.50%) (P=0.001) and OLK group (0.70%) (P=0.002). FISH probe detection showed that the fluorescence intensity of Pi in human OSCC tissues (125.00±25.13) was higher than in the HC group (11.40±25.49), simple hyperplasia OLK (11.75±23.50), and mild dysplasia OLK (26.83±29.51) groups, with statistically significant differences respectively (P=0.002, P=0.003, P=0.005). However, there was no significant difference compared to moderate to severe dysplasia OLK (47.40±26.88) (P=0.210). The fluorescence area of Pi in human OSCC tissues (9 255.00±2 048.00) was significantly larger than in the HC group (18.00±40.25), simple hyperplasia OLK group (27.00±54.00), mild dysplasia (76.00±95.19), and moderate to severe dysplasia (1 628.00±1 265.00) groups, with highly significant differences (P<0.001). There was a significant correlation between the invasive depth of Pi and the degree of histopathological grading (P<0.001). In mice, the fluorescence intensity of Pi in OSCC tissues (119.00±8.54) was significantly higher than in the HC group (8.17±20.00) (P<0.01), but showed no significant difference compared with the OLK group (34.33±28.28) (P>0.05). The fluorescence area of Pi in mice OSCC tissues (9 971.0±2 807.0) was significantly larger than in the HC group (37.83±92.67) and the OLK group (451.6±780.1) (P=0.006, P=0.043). There is a significant correlation between the depth of invasion of Pi and the degree of histopathological grading (P<0.001). Conclusions: This study suggests that Pi in oral mucosal tissue may be a potential biomarker for early detection of OSCC and play an important role in the carcinogenesis process of oral mucosa.}, }
@article {pmid40015656, year = {2025}, author = {Felicianna,  and Lo, EKK and Chen, C and Ismaiah, MJ and Zhang, F and Leung, HKM and El-Nezami, H}, title = {Alpha-aminobutyric Acid Ameliorates Diet-induced Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) Progression in Mice via Enhancing AMPK/SIRT1 Pathway and Modulating the Gut-Liver Axis.}, journal = {The Journal of nutritional biochemistry}, volume = {}, number = {}, pages = {109885}, doi = {10.1016/j.jnutbio.2025.109885}, pmid = {40015656}, issn = {1873-4847}, abstract = {Alpha-aminobutyric acid (ABA) is a non-proteinogenic amino acid, a metabolite which could be generated from the metabolism of methionine, threonine, serine and glycine or as a gut-microbiome-derived metabolite. Changes in ABA levels have been embroiled in metabolic dysfunction-associated steatotic liver disease (MASLD) intervention studies, but their relation to MASLD pathogenesis remains unclear. Hence, this present study aimed to investigate the effect of oral ABA supplementation on the progression of a high fat/high cholesterol diet (HFD) induced MASLD mice model. ABA was found to remodel the gut microbiome composition and ameliorate MASLD parameters in HFD-fed mice. ABA mitigated HFD-induced gain in liver weight, hepatic steatosis, insulin resistance, serum and hepatic triglyceride levels, and liver cholesterol levels. Modulation of lipid metabolism was observed in the liver, in which expression of proteins and/or genes involved in de novo lipogenesis were suppressed, while those involved in fatty acid oxidation and autophagy were upregulated together with cellular antioxidant capacity, in addition to the enhancement of the AMPK/SIRT1 pathway. ABA reshaped the gut composition by enriching nine bacterial species, including Helicobacter hepaticus, Desulfovibrio sp. G11, Parabacteroides distasonis, and Bacteroides fragilis, while diminishing the abundance of 16 species, which included four Helicobacter species. KEGG pathway analysis of microbial functions found that ABA impeded secondary bile acid biosynthesis - which was reflected in the faecal BA composition analysis. Notably, ABA also inhibited ileal FXR-Fgf15 signalling, allowing for increased hepatic Cyp7a1 expression to eliminate cholesterol buildup in the liver. Overall, our findings indicate that ABA could be used as a promising therapeutic approach for the intervention of MASLD.}, }
@article {pmid40015438, year = {2025}, author = {Guo, Q and Zhai, W and Guo, H and Liang, Y and Li, P and Wang, N and Liu, X and Zhou, Z and Wang, P and Liu, D}, title = {Insights of the coexisting fertilizers enhance metolachlor persistence in soil: perspectives from mobility, metabolism, and microbiome.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {125918}, doi = {10.1016/j.envpol.2025.125918}, pmid = {40015438}, issn = {1873-6424}, abstract = {Coexistence of fertilizers and pesticides in farmlands may alter the biodegradation of the latter. Herein, the effects of fertilizers, namely urea (N), superphosphate (P), potassium sulfate (K), compound fertilizers (NPK), chicken manure (CM), rice husk ash (PA) on the environmental behaviors of metolachlor (MET) are investigated. The sorption of MET is reduced by N and NPK at 1 mg/g (nitrogen content) but enhanced by CM and PA at 10 mg/g in soil. Meanwhile, these fertilizers inhibit the biodegradation of MET and prolonged its half-life to > 3 times in soil, which microbial-mediated effect was verified via sterilized soil. To explore the profiles of fertilizer-domesticated microbes, correlation analysis reveals that the abundances of nine potential MET-degrading genera are reduced by the fertilizers, further inhibiting the metabolic pathways of MET ["MET oxanilic acid (MOA)" and "ethane sulfonic acid (ESA)" pathways], thus enhancing the persistence of MET in soil. In summary, excessive nitrogen fertilizers may increase the soil risks associated with MET residues, whereas CM and PA reduce the risk via immobilization of MET and inhibition of its metabolic transformation.}, }
@article {pmid40015429, year = {2025}, author = {Wani, SM and Chesti, A and Rehman, S and Chandra Nautiyal, V and Bhat, IA and Ahmad, I}, title = {Repurposing and reusing aquaculture wastes through a biosecure microfloc technology.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121214}, doi = {10.1016/j.envres.2025.121214}, pmid = {40015429}, issn = {1096-0953}, abstract = {Intensive aquaculture waste management is a significant challenge in the aquaculture industry, often contributing to environmental issues. Intensive aquacultural techniques demand new strategies and alternatives aimed to achieving sustainability. Repurposing and reusing wastes through innovative technologies can mitigate their negative impact. Biofloc technology (BFT) or bio-colloidal technology is based on the concept of aquaculture waste utilization by heterotrophic microbial biomass and presents a biosecure and sustainable solution. The dynamics of BFT are shaped by ecological interactions like commensalism, competition, and predation, forming a trophic micro-network consisting of rotifers, ciliates, heterotrophic bacteria, and microalgae. Metagenomic studies showed dominance of microbial communities within the biofloc, such as Cyanobacteria, Nitrosomonas, Proteobacteria, Bacteroidetes, Pseudomonadota, Rhodobacteraceae and Bacillus species that play a crucial role in the mineralization and bioremediation of waste. These microbes also help to break down hazardous toxic compounds into non-toxic, beneficial nutrients, which are subsequently utilized as food by fish and shellfish. Also by recycling waste reduces pollution, improves water quality, and enhances the efficiency of aquaculture system. With increasing incidences of microbial diseases and growing expenses for energy, biosecurity with BFT seems, by all means a sustainable production method for aquaculture. The incorporation of biosecure biofloc technology into aquaculture practices enhances environmental sustainability while optimizing resource use, creating more eco-friendly and cost-effective systems. This review highlights key aspects such as the microbial dynamics, role of metagenomics in identifying the bacterial communities, bioremediation of aquaculture waste, biosecurity concerns, and the biocontrol of pathogenic microbes across various biofloc systems.}, }
@article {pmid40015320, year = {2025}, author = {Abi-Aad, SJ and Lovell, M and Khalaf, R and Sokol, RJ}, title = {PATHOGENESIS AND MANAGEMENT OF INTESTINAL FAILURE-ASSOCIATED LIVER DISEASE.}, journal = {Seminars in liver disease}, volume = {}, number = {}, pages = {}, doi = {10.1055/a-2545-7370}, pmid = {40015320}, issn = {1098-8971}, abstract = {Long-term parenteral nutrition (PN) has considerably improved the management of intestinal failure (IF) in children and adults, particularly those with short bowel syndrome; however, it carries a significant risk of hepatotoxicity, specifically intestinal failure-associated liver disease (IFALD), also known as PN-associated liver disease (PNALD). This review provides an update on the latest understanding of IFALD pathogenesis, emerging therapies, and ongoing challenges in management of this complication. A number of factors are associated with development of IFALD. PN lipid emulsions, phytosterol exposure, bacterial dysbiosis, an altered gut-liver axis and episodes of sepsis disrupt bile acid homeostasis and promote liver inflammation in the active phase of IFALD, favoring the development of PN-associated cholestasis (PNAC), and the more chronic form of steatohepatitis with fibrosis. Based on identification of pathophysiological pathways, potential therapies are being studied in preclinical and clinical trials including lipid emulsion modifications; targeted therapies such as FXR and LRH-1 agonists, tumor necrosis factor inhibitors, glucagon-like peptide-2 analogs; microbiome modulation; and supplementation with choline and antioxidants. In conclusion, the pathogenesis of IFALD is complex, and PN dependence and liver injury remain challenging, particularly in patients with IF who cannot advance to enteral nutrition and be weaned off PN.}, }
@article {pmid40015251, year = {2025}, author = {Zuffa, S and Charron-Lamoureux, V and Brennan, C and Ambre, M and Knight, R and Dorrestein, PC}, title = {Human Untargeted Metabolomics in High-Throughput Gut Microbiome Research: Ethanol vs Methanol.}, journal = {Analytical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.analchem.4c05142}, pmid = {40015251}, issn = {1520-6882}, abstract = {Untargeted metabolomics is frequently performed on human fecal samples in conjunction with sequencing to unravel the gut microbiome functionality. As sample collection efforts are rapidly expanding, with individuals often collecting specimens at home, metabolomics experiments should adapt to accommodate the safety and needs of bulk off-site collections and improve high throughput. Here, we show that a 95% ethanol, safe to be shipped and handled, extraction part of the Matrix Method pipeline recovers comparable amounts of metabolites as a validated 50% methanol extraction, preserving metabolic profile differences between investigated subjects. Additionally, we show that the fecal metabolome remains relatively stable when stored in 95% ethanol for up to 1 week at room temperature. Finally, we suggest a metabolomics data analysis workflow based on robust centered log ratio transformation, which removes the variance introduced by possible different sample weights and concentrations, allowing for reliable and integration-ready untargeted metabolomics experiments in gut microbiome research.}, }
@article {pmid40015179, year = {2025}, author = {Patra, D and Dev, G and Hand, TW and Overacre-Delgoffe, A}, title = {Friends close, enemies closer: the complex role of the microbiome in antitumor immunity.}, journal = {Current opinion in immunology}, volume = {93}, number = {}, pages = {102537}, doi = {10.1016/j.coi.2025.102537}, pmid = {40015179}, issn = {1879-0372}, abstract = {Immunotherapy has achieved remarkable advances in cancer treatment by harnessing the immune system to combat tumors, yet its effectiveness remains inconsistent across patients and tumor types. The microbiota, a diverse assemblage of microorganisms residing at host barrier surfaces, is pivotal in shaping immune responses. This review explores the direct and indirect mechanisms via which the microbiota modulates antitumor immune responses both locally within the tumor microenvironment and systemically by affecting distant tumors. We discuss recent findings linking microbiota-derived metabolites and microbiota-derived antigens with antitumor immunity and immunotherapy response. Additionally, we discuss recent advances in microbiome-based therapies, including fecal microbiota transplantation. We propose the use and development of new analytical techniques to further characterize the complex functions and interactions between the microbiome and immune system. To conclude, we outline recommendations for future research and therapeutic approaches to leverage the microbiome to improve current immunotherapies.}, }
@article {pmid40015092, year = {2025}, author = {Shi, T and Liu, Z and Hu, Q and Yang, ST and Liu, J and Jing, L}, title = {Periphyton as a nature-based solution for remediation of degraded Zoige alpine wetlands: Process, effects and evaluation.}, journal = {Journal of environmental management}, volume = {377}, number = {}, pages = {124647}, doi = {10.1016/j.jenvman.2025.124647}, pmid = {40015092}, issn = {1095-8630}, abstract = {Alpine wetlands are crucial yet fragile ecosystems, with the Zoige alpine wetlands experiencing severe degradation. However, hydrological recovery alone has proven insufficient to restore essential wetland functions and may exacerbate degradation, particularly in nutrient cycling and microbial communities. This highlighting an urgent need for nature-based solutions. Periphyton, which could thrive in plateau and regulate nutrients, presents a promising approach. This study explored the potential of locally sourced periphyton to remediate degraded alpine wetlands, assessing its effects and mechanisms. The results demonstrated that periphyton could create an environment with stable pH and electrical conductivity. More importantly, it enhanced nutrient fixation and bioavailability by increasing the activities of β-glucosidase, urease, and alkaline phosphatase, especially in the surface soil of alpine wetlands. It could be explained by microbiome analysis that periphyton boosted bacterial activity in the soil and improved the stability and complexity of soil bacterial communities. Specifically, periphyton promoted enzyme synthesis, metabolic function, and nutrient circulation at the functional gene level, and Pseudomonas, Bacteroidetes, and Acidobacteria played critical roles in the remediation process. Most importantly, periphyton primarily regulated nutrients within the soil rather than directly introducing them to promote plant growth, with coverage exceeding 280 g/m[2], yielding optimal physiological and reproductive states for alpine wetland plants. This study provided a potential nature-based solution for the remediation of degraded alpine wetlands.}, }
@article {pmid40015080, year = {2025}, author = {Ren, X and Liu, C and Yue, Y and Sun, S and Zhao, L and Tao, C and Wang, B and Xiong, W and Shen, Z and Li, R and Shen, Q}, title = {Exploring the potential role of soil protists in predicting banana health.}, journal = {Microbiological research}, volume = {295}, number = {}, pages = {128109}, doi = {10.1016/j.micres.2025.128109}, pmid = {40015080}, issn = {1618-0623}, abstract = {Fusarium wilt is increasingly threatening banana production around the world. Investigating soil microbial communities associated with healthy and diseased banana plants is the first step to understand the potential mechanisms involved in the disease suppression. Previous research has confirmed plant-beneficial bacterial and fungal communities are key determinants of banana health. However, to what extent protists, a key component of the soil microbiome, are linked to banana health on a large scale remains largely unknown. Here, we collected soil samples from healthy and diseased plants suffering from Fusarium wilt in multiple banana plantations within China and Laos, and examined holistic soil microbial communities including bacteria, fungi and protists using high-throughput sequencing. We explored the linkage between protists and Fusarium oxysporum and investigated the effects of biotic and abiotic factors on protists. Results showed the relative abundance of Fusarium oxysporum can be highly predicted by protists. Specifically, predatory protists revealed a negative correlation with F. oxysporum, which was confirmed in pot experiments. We found the putative plant growth-promoting bacteria, positively correlated with predatory protists, were also negatively correlated with F. oxysporum. In addition, both soil abiotic factors (i.e., soil pH and ammonia nitrogen) and biotic factors (soil bacteria) played crucial roles in determining predatory protists. We highlighted that soil predatory protists might contribute to banana health via directly inhibiting soil-borne pathogens or indirectly enriching plant beneficial bacteria.}, }
@article {pmid40014853, year = {2025}, author = {Lee, C and Zaheer, R and Thomas, K and Poulin-Laprade, D and Talbot, G and Diarra, M and Van Domselaar, G and Zovoilis, A and McAllister, TA}, title = {Comparative Metagenomics Reveals Limited Differences in Antimicrobial Resistance Gene Abundance Across Conventional and Natural Livestock Production Systems.}, journal = {Canadian journal of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1139/cjm-2024-0191}, pmid = {40014853}, issn = {1480-3275}, abstract = {The livestock industry has been a source of concern in terms of antimicrobial resistance (AMR) development and spread, especially from a One Health perspective. Raising livestock without antimicrobials, so called natural (NAT) production is an increasingly popular practice. This study used metagenomics to compare this practice to conventional (CONV) antimicrobial use (AMU) on the microbiome and resistome in the feces of beef cattle and swine and the cecal contents of broiler chickens. In cattle, Bacteroidetes, Euryarchaeota, and Spirochaetes were more abundant (q < 0.01) in CONV than NAT systems, with no differences (q > 0.05) in bacterial profiles in either swine or chickens. Classes of antimicrobial resistant genes (ARG) were not impacted regardless of AMU in any of the livestock species. However, many tetracycline resistance genes were more abundant in CONV as compared to NAT swine (q < 0.05), but this difference was not observed in cattle or chickens. This study confirmed that elimination of AMU does not necessarily result in an immediate decline in the abundance or diversity of ARGs within a single livestock production cycle.}, }
@article {pmid40014846, year = {2025}, author = {Mora, J and Olson, M and Rocks, SS and Zahn, G}, title = {Watershed urbanization alters aquatic plant mycobiomes through the loss of rare taxa.}, journal = {Mycologia}, volume = {}, number = {}, pages = {1-11}, doi = {10.1080/00275514.2025.2462525}, pmid = {40014846}, issn = {1557-2536}, abstract = {Urban expansion, projected to triple globally from 2000 to 2030, significantly impacts biodiversity and ecosystem processes, including those of microbial communities. Microbes are key drivers of many ecosystem processes and affect the fitness and resilience of plants and animals, but research on the biotic effects of urbanization has focused primarily on macroorganisms. This study investigates host-associated fungal communities in the pollution-tolerant aquatic plant Ranunculus aquatilis along an urbanization gradient in the Provo River, Utah, USA, a rapidly urbanizing region. We collected plant and adjacent water samples from 10 locations along the river, spanning from rural to urbanized areas within a single watershed, and conducted DNA amplicon sequencing to characterize fungal community composition. Our results show a significant decline in fungal alpha diversity correlated with increased urbanization metrics such as impervious surface area and developed land cover. Specifically, fungal richness and Shannon diversity decreased as urbanization intensified, driven primarily by a reduction in rare taxa. Despite a stable core microbiome dominated by a few taxa, the overall community structure varied significantly along the urbanization gradient, with notable shifts in dominant fungal taxa. Contrary to expectations, no detectable levels of heavy metals were found in water samples at any location, suggesting that other urbanization-related factors, potentially including organic pollutants or plant stress responses, influence fungal endophyte communities. Our findings underscore the need for further investigation into the mechanisms driving these patterns, particularly the roles of organic pollution, nutrient loads, and plant stress. As global urbanized watershed area grows, the fate of aquatic plant life is tied to their fungal community. Understanding these interactions is crucial for predicting the impacts of continued urbanization on freshwater ecosystems.}, }
@article {pmid40014569, year = {2025}, author = {Cheng, X and Li, Z and Zhu, J and Wang, J and Huang, R and Yu, LW and Lin, S and Forman, S and Gromilina, E and Puri, S and Patel, P and Bahramian, M and Tan, J and Hojaiji, H and Jelinek, D and Voisin, L and Yu, KB and Zhang, A and Ho, C and Lei, L and Coller, HA and Hsiao, EY and Reyes, BL and Matsumoto, JH and Lu, DC and Liu, C and Milla, C and Davis, RW and Emaminejad, S}, title = {Tandem metabolic reaction-based sensors unlock in vivo metabolomics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {9}, pages = {e2425526122}, doi = {10.1073/pnas.2425526122}, pmid = {40014569}, issn = {1091-6490}, support = {5R21DK128711-02//HHS | National Institutes of Health (NIH)/ ; R35GM138241//HHS | National Institutes of Health (NIH)/ ; R01DA047637//HHS | NIH | National Institute on Drug Abuse (NIDA)/ ; UH3NS119772//HHS | NIH | National Institute of Neurological Disorders and Stroke (NINDS)/ ; R01NS115537//HHS | National Institutes of Health (NIH)/ ; N/A//Elisabeth K. Harris Foundation Trust/ ; }, mesh = {*Metabolomics/methods ; Humans ; Nanotubes, Carbon/chemistry ; Metabolic Networks and Pathways ; Biosensing Techniques/methods ; Gastrointestinal Microbiome/physiology ; Electrodes ; Sweat/metabolism/chemistry ; Animals ; Electrochemical Techniques/methods/instrumentation ; Brain/metabolism ; }, abstract = {Mimicking metabolic pathways on electrodes enables in vivo metabolite monitoring for decoding metabolism. Conventional in vivo sensors cannot accommodate underlying complex reactions involving multiple enzymes and cofactors, addressing only a fraction of enzymatic reactions for few metabolites. We devised a single-wall-carbon-nanotube-electrode architecture supporting tandem metabolic pathway-like reactions linkable to oxidoreductase-based electrochemical analysis, making a vast majority of metabolites detectable in vivo. This architecture robustly integrates cofactors, self-mediates reactions at maximum enzyme capacity, and facilitates metabolite intermediation/detection and interference inactivation through multifunctional enzymatic use. Accordingly, we developed sensors targeting 12 metabolites, with 100-fold-enhanced signal-to-noise ratio and days-long stability. Leveraging these sensors, we monitored trace endogenous metabolites in sweat/saliva for noninvasive health monitoring, and a bacterial metabolite in the brain, marking a key milestone for unraveling gut microbiota-brain axis dynamics.}, }
@article {pmid40014232, year = {2025}, author = {Anastasiou, IA and Kounatidis, D and Vallianou, NG and Skourtis, A and Dimitriou, K and Tzivaki, I and Tsioulos, G and Rigatou, A and Karampela, I and Dalamaga, M}, title = {Beneath the Surface: The Emerging Role of Ultra-Processed Foods in Obesity-Related Cancer.}, journal = {Current oncology reports}, volume = {}, number = {}, pages = {}, pmid = {40014232}, issn = {1534-6269}, abstract = {PURPOSEOF REVIEW: Ultra-processed foods (UPFs) are becoming more and more important in daily diets around the world; in some cases, they can account for as much as 60% of daily energy intake. Epidemiological evidence suggests that this shift toward high levels of food processing may be partially responsible for the global obesity epidemic and the rise in the prevalence of chronic diseases.<br><br>RECENT FINDINGS: Few prospective studies have examined the relationship between UPF consumption and cancer outcomes. According to currently available information, UPFs may increase the risk of cancer due to their obesogenic properties and exposure to substances that can cause cancer, such as certain food additives and pollution from product processing. The complex relationship between obesity and cancer involves factors such as immune dysregulation, altered adipokine and sex hormone levels, abnormal fatty acid metabolism, extracellular matrix remodeling, and chronic inflammation. Addressing cancer risk associated with UPF consumption could involve a multifaceted approach, including consumer behavior modification programs and robust public health regulations aimed at enhancing food environments. Improved knowledge of the potential dual negative impacts of UPFs on the environment and cancer risk is one of the priority areas we identify for future research and policy implications. Various approaches could be used to prevent cancers associated with UPF consumption, such as consumer behavior change programs and stricter public health regulations needed to improve the food environment. This review examines for the first time the potential role of UPFs in cancer risk associated with obesity, exploring underlying biological mechanisms and identifying key areas for future research and policy action, including the dual environmental and health impact of UPFs.}, }
@article {pmid40014112, year = {2025}, author = {Liu, M and Li, XW and Sun, H and Yan, YQ and Xia, ZY and Refaie, A and Zhang, NY and Wang, S and Tan, C and Sun, LH}, title = {T-2 toxin-induced splenic injury by disrupting the gut microbiota-spleen axis via promoting IL-6/JAK/STAT1 signaling-mediated inflammation and apoptosis and its mitigation by elemental nano-selenium.}, journal = {Archives of toxicology}, volume = {}, number = {}, pages = {}, pmid = {40014112}, issn = {1432-0738}, support = {2023YFD1301005//National Key Research and Development Programs of China/ ; 2023YFD1301003//National Key Research and Development Programs of China/ ; 2662023DKPY002//Fundamental Research Funds for the Central Universities/ ; }, abstract = {T-2 toxin is one of the most toxic A trichothecene mycotoxins prevalent in the environment and food chain, which brings severe health hazards to both animals and humans and it can significantly damage immune function. In this study, we comprehensively explained the impact of T-2 toxin on the spleen through gut microbiota-spleen axis by integrating the transcriptome and microbiome. Our results revealed that dietary T-2 toxin ≥ 1.0 mg/kg exposure significantly inhibited the growth performance and caused spleen injury in broilers chicks, accompanied by oxidative stress and histopathological damage. Cecal microbiome analysis suggested that T-2 toxin exposure caused gut microbial dysbiosis, especially leading to the decrease of some beneficial bacteria genera that enhanced gut barrier and reduced inflammation, including Blautia, Coprococcus, Lachnospira and Anaerostipes belonging to Lachnospiraceae family. Transcriptome analysis suggested that T-2 toxin exposure directly caused splenic inflammation and immune-related signaling, such as cytokine-cytokine receptor interaction, Toll-like receptor signaling pathway, NOD-like receptor signaling pathway and JAK-STAT signaling pathway. Furthermore, by integrating the transcriptome and microbiome analysis, we found that spleen damage induced by T-2 toxin was associated with the abnormal activation of IL-6/JAK/STAT1 signaling pathway-mediated inflammation and apoptosis, which was further verified by western bolt analysis. Notably, dietary selenium supplementation could protect chicks from T-2 toxin-induced adverse effects on growth performance and spleen injury by inhibiting the expression of the IL-6/JAK/STAT1 signaling-related genes. In summary, our findings provided new insights into the immunotoxicity mechanisms of T-2 toxin in the chickens' spleen and highlighted the potential of selenium to alleviate T-2 toxin-induced immunotoxicity.}, }
@article {pmid40013832, year = {2025}, author = {Cai, P and Yang, Q and Lu, J and Dai, X and Xiong, J}, title = {Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0004325}, doi = {10.1128/msystems.00043-25}, pmid = {40013832}, issn = {2379-5077}, abstract = {UNLABELLED: The incidence of colorectal cancer (CRC) has been increasing in recent decades. Current methods for CRC screening have their own drawbacks, thus there is an urgent need to identify the key microbes that drive the development of CRC for wider application in the early detection and prevention of CRC. To address this issue, we performed fecal microbiome analysis by high-throughput sequencing of 16S rRNA gene combined with blood biochemical indicators in patients with CRC stages I, II, III, and IV, healthy people, and patients with polyps. Fecal microbiota of patients with CRC was disturbed, as evidenced by significantly reduced α-diversity in patients with CRC stage IV and markedly different β-diversity. The random forest model identified the top 25 genera from 174 training data, resulting in a diagnostic accuracy of 87.95%. Further, by combining with differential genera analysis, we screened out 11 biomarkers that significantly changed in different groups. Peptostreptococcus, Parvimonas, Shewanella, Oscillibacter, Eggerthella, and Gemella associated with the development of CRC were significantly enriched, while Fenollaria, Staphylococcus, Ezakiella, Finegoldia, and Neisseria associated with the remission of CRC were significantly suppressed in patients with CRC. Importantly, carcinoembryonic antigen (CEA) was significantly correlated with these 11 microbial biomarkers, and carbohydrate antigen 19-9 (CA 19-9) was markedly correlated with Oscillibacter. Notably, co-occurrence network analysis at the genus level exhibited that the microbial co-occurrence network of CRC IV was the most complex and stable. These results suggested that CEA, CA 19-9 and 11 microbial biomarkers may be co-biomarkers for the disease occurrence and development, and non-invasive diagnosis of CRC.<br><br>IMPORTANCE: Identifying the key microbes that drive the development of colorectal cancer (CRC) has been important in this field. We delved into the research on the association between CRC and fecal microbiota in this study, providing a detailed analysis of the characteristics of fecal microbiota during the transition from normal intestine to polyps to cancer. Fecal bacterial biomarkers and blood biochemical indicators may be co-biomarkers in the development of CRC.}, }
@article {pmid40013816, year = {2025}, author = {Mann, AE and Chakraborty, B and O'Connell, LM and Nascimento, MM and Burne, RA and Richards, VP}, title = {Erratum for Mann et al., "Heterogeneous lineage-specific arginine deiminase expression within dental microbiome species".}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0034725}, doi = {10.1128/spectrum.00347-25}, pmid = {40013816}, issn = {2165-0497}, }
@article {pmid40013797, year = {2025}, author = {Bai, Y and Hu, Y and Chen, X and Hu, L and Wu, K and Liang, S and Zheng, J and Gänzle, MG and Chen, C}, title = {Comparative metagenome-associated analysis of gut microbiota and antibiotic resistance genes in acute gastrointestinal injury patients with the risk of in-hospital mortality.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0144424}, doi = {10.1128/msystems.01444-24}, pmid = {40013797}, issn = {2379-5077}, abstract = {UNLABELLED: Acute gastrointestinal injury (AGI) is known for its poor long-term prognosis and the associated increase in mortality among intensive care unit (ICU) patients. As the role of the gut microbiome and resistome in AGI remains unclear, the present study aimed to explore the possible associations between dysbacteriosis and in-hospital mortality in ICU patients with gastrointestinal dysfunction. Fecal samples were collected from a prospective cohort of 210 ICU patients with AGI, and shotgun metagenomic sequencing was used to determine the taxonomic composition of gut microbiota and the differences of antibiotic resistance genes (ARGs) between the Death and Survival groups. Compared to the Survival group, patients in the Death group shifted from strict anaerobes to facultative anaerobes in the fecal microbial community, with more Klebsiella but less Prevotella. The co-occurrence patterns revealed that more ARG subtypes were enriched in microbial taxa in the Death group, especially for Clostridium and Methanobrevibacter. Furthermore, the ARG type had large area under the curve (AUCs) in receiver operating characteristic for predicting the disease severity, and a combined gut microbiota-ARG subtype classifiers showed better performance than either of them. Thus, comparative metagenome-associated analysis can help to obtain valuable information about gut microbiota and gene coding for antibiotic resistance in AGI patients.<br><br>IMPORTANCE: A metagenomic-related strategy was conducted to obtain a highly valuable resource to improve understanding of intestinal microbiota dysbiosis and antibiotic resistance genes (ARGs) profiles. The results indicate that intestinal microbiota, including Klebsiella and Prevotella, changed dramatically in intensive care unit (ICU) patients with acute gastrointestinal injury (AGI). Due to longer ICU stays and receiving more antibiotic treatment, the types and correlations of ARGs in the Death group were significantly higher than those in the Survival group. The findings of this study are expected to expand our knowledge of gut microbiota and resistome profiles reflecting gastrointestinal status, accelerate the identification of disease biomarkers, and provide new insights into the prevention and treatment of AGI-related diseases.}, }
@article {pmid40013793, year = {2025}, author = {Meng, Y and Wang, C and Usyk, M and Kwak, S and Peng, C and Hu, KS and Oberstein, PE and Krogsgaard, M and Li, H and Hayes, RB and Ahn, J}, title = {Association of tumor microbiome with survival in resected early-stage PDAC.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0122924}, doi = {10.1128/msystems.01229-24}, pmid = {40013793}, issn = {2379-5077}, abstract = {The pancreas tumor microbiota may influence tumor microenvironment and influence survival in early-stage pancreatic ductal adenocarcinoma (PDAC); however, current studies are limited and small. We investigated the relationship of tumor microbiota to survival in 201 surgically resected patients with localized PDAC (Stages I-II), from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) cohorts. We characterized the tumor microbiome using RNA-sequencing data. We examined the association of the tumor microbiome with overall survival (OS), via meta-analysis with the Cox PH model. A microbial risk score (MRS) was calculated from the OS-associated microbiota. We further explored whether the OS-associated microbiota is related to host tumor immune infiltration. PDAC tumor microbiome α- and β-diversities were not associated with OS; however, 11 bacterial species, including species of Gammaproteobacteria, confirmed by extensive resampling, were significantly associated with OS (all Q < 0.05). The MRS summarizing these bacteria was related to a threefold change in OS (hazard ratio = 2.96 per standard deviation change in the MRS, 95% confidence interval = 2.26-3.86). This result was consistent across the two cohorts and in stratified analyses by adjuvant therapy (chemotherapy/radiation). Identified microbiota and the MRS also exhibited association with memory B cells and naïve CD4[+] T cells, which may be related to the immune landscape through BCR and TCR signaling pathways. Our study shows that a unique tumor microbiome structure, potentially affecting the tumor immune microenvironment, is associated with poorer survival in resected early-stage PDAC. These findings suggest that microbial mechanisms may be involved in PDAC survival, potentially informing PDAC prognosis and guiding personalized treatment strategies.IMPORTANCEMuch of the available data on the PDAC tumor microbiome and survival are derived from relatively small and heterogeneous studies, including those involving patients with advanced stages of pancreatic cancer. There is a critical knowledge gap in terms of the tumor microbiome and survival in early-stage patients treated by surgical resection; we expect that advancements in survival may initially be best achieved in these patients who are treated with curative intent.}, }
@article {pmid40013791, year = {2025}, author = {Walter, JM and Greses, S and Hagen, LH and Schiml, VC and Pope, PB and González-Fernández, C and Arntzen, M}, title = {Anaerobic digestion of microalgae: microbial response and recovery after organic loading disturbances.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0167424}, doi = {10.1128/msystems.01674-24}, pmid = {40013791}, issn = {2379-5077}, abstract = {UNLABELLED: Industrial anaerobic digestion (AD) represents a relevant energy source beyond today's fossil fuels, wherein organic matter is recycled to methane gas via an intricate and complex microbial food web. Despite its potential, anaerobic reactors often undergo process instability over time, which is frequently caused by substrate composition perturbations, making the system unreliable for stable energy production. To ensure the reliability of AD technologies, it is crucial to identify microbial and system responses to better understand the effect of such perturbations and ultimately detect signatures indicative of process failure. Here, we investigate the effect of the microalgal organic loading rate (OLR) on the fermentation product profile, microbiome dynamics, and disruption/recovery of major microbial metabolisms. Reactors subjected to low- and high-OLR disturbances were operated and monitored for fermentation products and biogas production over time, while microbial responses were investigated via 16S rRNA gene amplicon data, shotgun metagenomics, and metagenome-centric metaproteomics. Both low- and high-ORL fed systems encountered a sudden decline in methane production during OLR disturbances, followed by a recovery of the methanogenic activity within the microbiome. In the high-OLR disturbances, system failure triggered an upregulation of hydrolytic enzymes, an accumulation of fermentation products, and a shift in the methanogenic population from hydrogenotrophic to acetoclastic methanogens, with the latter being essential for recovery of the system after collapse.<br><br>IMPORTANCE: Anaerobic digestion (AD) with microalgae holds great potential for sustainable energy production, but process instability caused by substrate disturbances remains a significant barrier. This study highlights the importance of understanding the microbial dynamics and system responses during organic loading rate perturbations. By identifying key shifts in microbial populations and enzyme activity, particularly the transition from hydrogenotrophic to acetoclastic methanogens during recovery, this research provides critical insights for improving AD system stability and can contribute to optimizing microalgae-based AD processes for more reliable and efficient methane production.}, }
@article {pmid40013780, year = {2025}, author = {Wang, Z and Chen, Y and Li, H and Yue, Y and Yu, H}, title = {Exploring oral microbiome in oral squamous cell carcinoma across environment-associated sample types.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0085224}, doi = {10.1128/spectrum.00852-24}, pmid = {40013780}, issn = {2165-0497}, abstract = {The relationship between the oral microbiome and oral squamous cell carcinoma (OSCC) has been extensively investigated. Nonetheless, most previous studies were single-center, resulting in the absence of systematic evaluations. To address this gap, we performed a comprehensive meta-analysis on 1,255 samples from OSCC-related 16S rRNA gene data sets, representing a diverse range of OSCC phenotypes. It is recognized that the progression of cancer is related to the alterations in the microbiome among different phenotypes. Our findings revealed distinct microbiome characteristics among different sample types, with Biopsy (Bios) and Swab samples exhibiting significant differences between phenotypes. In Bios samples, the microbiomes of the Cancer group and the normal tissue adjacent to the tumor (NAT) group display a higher similarity, while both differ from the microbiome of the Fibroepithelial polyp (FEP) group. Moreover, the identified differential genera and pathways corresponded with these observations. We developed a diagnostic model using the random forest algorithm on Swab samples, achieving an area under the receiver operating characteristic curve (AUC) of 0.918. Importantly, this model exhibited considerable effectiveness (AUC = 0.849) when applied to another sequencing platform. Taken together, our study provides a comprehensive overview of the oral microbiome during various OSCC progression stages, potentially enhancing early detection and treatment.IMPORTANCEThis study answers key questions regarding the universal microbial characteristics and comprehensive oral microbiome dynamics during oral squamous cell carcinoma (OSCC) progression. By integrating multiple data sets, we examine the following critical aspects: (1) Do different sample types harbor distinct microbial communities within the oral cavity? (2) Which sample types offer greater potential for investigating OSCC progression? (3) How are the oral microbiomes of the Cancer group, normal tissue adjacent to the tumor group, and Fibroepithelial polyp group related, and what is their potential association with OSCC development? (4) Can a diagnostic model based on microbial signatures effectively distinguish between Cancer and Health groups using Swab samples?}, }
@article {pmid40013501, year = {2025}, author = {Bhattacharya, A and Shepherd, C and El-Assaad, F and Mather, KA}, title = {Bacteria in the brain: do they have a role in the pathogenesis of Alzheimer's disease?.}, journal = {Current opinion in psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1097/YCO.0000000000000989}, pmid = {40013501}, issn = {1473-6578}, abstract = {PURPOSE OF REVIEW: Worldwide efforts continue to unravel the complex pathological pathways that lead to Alzheimer's disease. The gut-brain-microbiome axis, a communication pathway between the gut, brain and microorganisms, is emerging as a potential mechanism involved in Alzheimer's disease pathogenesis. While the gut microbiome's role in Alzheimer's disease has gained significant attention, the brain microbiome remains relatively unexplored. This review summarizes the latest research on the brain microbiome in Alzheimer's disease.<br><br>RECENT FINDINGS: In the past 4 years, four out of five studies have found bacteria, such as Streptococcus pneumoniae, in postmortem samples of both control and Alzheimer's disease brains, supporting the idea that the brain is not a sterile environment. Two studies report the overabundance of several bacterial phyla, including Proteobacteria and Actinomycetes, in postmortem Alzheimer's disease brains versus controls. One study reported the presence of Borrelia burgdorferi in a subset of Alzheimer's disease cases compared to controls.<br><br>SUMMARY: Limitations and challenges persist in studying the brain microbiome, including the lack of standardized assays and data analysis methods, small sample sizes, and inconsistent use of controls for environmental microbial contamination during sample processing. Well designed studies that employ reproducible and rigorous methods are required to elucidate whether microbes are involved in the pathogenesis of Alzheimer's disease.}, }
@article {pmid40013331, year = {2025}, author = {Standley, JM and Marcelino, J and Yu, F and Ellis, JD}, title = {A Meta-Omics Approach Using eDNA and eRNA for the Assessment of Biotic Communities Associated With Royal Jelly Produced by the Western Honey Bee (Apis mellifera L.).}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14090}, doi = {10.1111/1755-0998.14090}, pmid = {40013331}, issn = {1755-0998}, support = {//University of Florida Entomology and Nematology Gahan Endowment/ ; //Clay County Beekeepers Association/ ; 1019945//USDA/NIFA Multi-State Project/ ; AP22PPQS&amp;T00C189//USDA/APHIS Cooperative Agreement/ ; }, abstract = {Royal jelly (RJ) is a glandular secretion fed to developing honey bee larvae by adult worker bees. It is also a potential source of disease transmission in and between honey bee colonies. We endeavored to characterize the microbiome, virome, and other biota present in RJ via an integrated meta-omics approach. Using a magnetic beads-based extraction protocol, we identified eDNA and eRNA fragments from organisms of interest in RJ using high-throughput metagenomics (DNA-seq), metatranscriptomics (total RNA-seq), and parallel sequencing. This allowed us to enhance the detection of Operational Taxonomic Units (OTUs) undetectable by standard 'omics or amplicon protocols'. Using this integrated approach, we detected OTUs present in RJ from honey bee pests and pathogens, including Melissococcus plutonius, Paenibacillus larvae, Varroa destructor, V. jacobsoni, Aethina tumida, Galleria mellonella, Vairimorpha ceranae, Apis mellifera filamentous virus, Black queen cell virus, Acute bee paralysis virus, Sacbrood virus, Deformed wing virus, Israeli acute bee paralysis virus, Kashmir bee virus, and Slow bee paralysis virus, as well as multiple beneficial gut bacteria from the genera Lactobacillus, Actinobacteria, and Gluconobacter. The presence of DNA and RNA from these organisms does not conclusively indicate the presence of live organisms in the RJ, but it does suggest some exposure of the RJ to these organisms. The results present a comprehensive eDNA and eRNA microbial profile of RJ, demonstrating that our novel method is an effective and sensitive molecular tool for high-resolution metagenomic and metatranscriptomic profiling, and is of value for detection of pathogens of concern for the beekeeping industry.}, }
@article {pmid40013311, year = {2025}, author = {Zhu, M and Li, Y and Wang, W and Liu, L and Liu, W and Yu, J and Xu, Q and Cui, J and Liu, Y and Chen, K and Liu, Y}, title = {Advancing early detection of organ damage and cardiovascular risk prevention: the Suzhou cardiometabolic health study protocol - exploring the role of oral microbiome and metabolic profiling in risk stratification.}, journal = {Frontiers in endocrinology}, volume = {16}, number = {}, pages = {1522756}, pmid = {40013311}, issn = {1664-2392}, mesh = {Humans ; *Cardiovascular Diseases/prevention &amp; control/epidemiology ; Prospective Studies ; Risk Assessment ; Male ; *Early Diagnosis ; *Microbiota ; Female ; China/epidemiology ; Middle Aged ; Adult ; Tongue/microbiology ; Cardiometabolic Risk Factors ; Metabolome ; Risk Factors ; }, abstract = {BACKGROUND: Cardiovascular Disease (CVD) is the leading cause of global mortality, with its incidence rate rising year by year due to the prevalence of metabolic diseases. Existing primary and secondary prevention strategies for cardiovascular disease have limitations in identifying some high-risk groups, and 1.5-level prevention aims to achieve more precise intervention by early identification of subclinical target organ damage. This study introduces oral (tongue coating) microbiota as metabolic markers for the first time, in combination with multiple metabolic factors, to explore their potential in assessing subclinical target organ damage and optimizing cardiovascular risk stratification, in order to provide a new path for the early identification and intervention of CVD.<br><br>METHODS: This study is a prospective cohort study aimed at assessing the association between tongue coating microbiota characteristics and multiple metabolic factors with subclinical target organ damage, and identifying high-risk groups suitable for cardiovascular 1.5-level prevention. The study will be conducted in Suzhou City, Jiangsu Province, China, planning to include 5000-6000 eligible subjects, with inclusion criteria of age &#x2265;18 years, excluding individuals with a history of CVD and other serious diseases. Baseline assessment includes demographic information, lifestyle (including dietary patterns), medical history, physical examination, and collection of tongue coating microbiota samples. Subjects will be followed up every 2 years, with the primary outcome being the first occurrence of coronary heart disease and stroke, and the secondary outcome being subclinical target organ damage.<br><br>DISCUSSION: This study focuses on cardiovascular 1.5-level prevention strategy, combining metabolic factors with tongue coating microbiota characteristics, aiming to optimize the risk assessment system for subclinical target organ damage. This approach can not only fill the gap in traditional risk assessment but also provide new ideas for the early identification and intervention of CVD. In the future, the feasibility and effectiveness of this strategy will be verified through multicenter studies, and it is expected to be promoted to a wider medical system, significantly improving the health management level of high-risk groups for CVD.<br><br>TRIAL REGISTRATION NUMBER: http://itmctr.ccebtcm.org.cn, identifier ITMCTR2024000616.}, }
@article {pmid40013109, year = {2025}, author = {Li, S and Huang, J and Xie, Y and Wang, D and Tan, X and Wang, Y}, title = {Investigation of gut microbiota in pediatric patients with peanut allergy in outpatient settings.}, journal = {Frontiers in pediatrics}, volume = {13}, number = {}, pages = {1509275}, pmid = {40013109}, issn = {2296-2360}, abstract = {OBJECTIVE: Investigate the diversity of the gut microbiota in children with peanut allergies and assess its association with allergic reactions. Identify potential gut microbial biomarkers for the diagnosis and treatment of peanut allergies.<br><br>METHODS: Twenty-nine children with peanut allergy who visited the hospital from December 2020 to December 2022 were selected as the test group (PA), and twenty-seven healthy children who underwent physical examination during the same period and tested negative for peanut IgE were selected as the control group (Ctl). The differences in gut microbiota between the two groups were compared. The study enrolled 29 children with peanut allergy (PA group) and 27 healthy children (Ctl group) from December 2020 to December 2022. The PA group was defined by a positive reaction to peanut-specific IgE tests, while the Ctl group tested negative for peanut IgE and had no history of allergies. Fecal samples were collected and genomic DNA was extracted for 16S rRNA gene sequencing to assess gut microbiota composition. Alpha diversity indices, including the sob, ace, chao, shannon, and simpson indices, were calculated to assess microbial community richness and diversity. Beta diversity was analyzed using Principal Coordinate Analysis (PCoA) and Partial Least Squares Discriminant Analysis (PLS-DA) to compare microbial community structures between the PA and Ctl groups.<br><br>RESULTS: The study identified significant differences in gut microbiota diversity between children with peanut allergy (PA group) and healthy controls (Ctl group). The PA group exhibited reduced alpha diversity, indicated by lower sob, ace, and chao indices (FDR&#x2009;&#x2264;&#x2009;0.05), and a significantly lower Shannon index (FDR&#x2009;&#x2264;&#x2009;0.01). Beta diversity analysis revealed distinct microbial community structures between the two groups. Notably, the PA group showed an increase in Proteobacteria and a decrease in Firmicutes and Bacteroidetes, with significant changes at the genus level, including lower relative abundance of Bacteroides and Faecalibacterium, and higher relative abundance of Bifidobacterium and Lactobacillus (FDR&#x2009;&#x2264;&#x2009;0.05 or FDR&#x2009;&#x2264;&#x2009;0.01). Correlation analysis highlighted a strong negative correlation between IgE levels and specific microbial groups, such as Alistipes and CAG-352 (FDR&#x2009;&#x2264;&#x2009;0.001), and a positive correlation with Veillonella. Blood routine indicators were also found to be correlated with gut microbiota composition.<br><br>CONCLUSION: The findings of this study provide compelling evidence that gut microbiota diversity and composition are significantly altered in children with peanut allergy. The observed shifts in microbial communities, particularly the increase in Proteobacteria and the decrease in beneficial bacteria such as Firmicutes and Bacteroidetes, underscore the potential role of the gut microbiome in the pathogenesis of peanut allergy. These results suggest that modulating the gut microbiota may be a viable therapeutic strategy for managing peanut allergy and highlight the need for further research to explore the clinical implications of these microbial changes.}, }
@article {pmid40013012, year = {2025}, author = {Arishi, RA and Gridneva, Z and Perrella, SL and Cheema, AS and Lai, CT and Payne, MS and Geddes, DT and Stinson, LF}, title = {Breastfeeding patterns and total volume of human milk consumed influence the development of the infant oral microbiome.}, journal = {Journal of oral microbiology}, volume = {17}, number = {1}, pages = {2469892}, pmid = {40013012}, issn = {2000-2297}, abstract = {BACKGROUND: The oral microbiome of breastfed infants is distinct from that of formula-fed infants. However, breastfeeding characteristics, such as time spent breastfeeding (min/24 h), breastfeeding frequency (number of breastfeeds per day), and human milk intake (ml/day) vary significantly between breastfeeding dyads.<br><br>OBJECTIVES: Given that human milk and breastfeeding exposures likely influence early colonisation of the infant oral microbiome, this study aimed to elucidate the impact of breastfeeding characteristics on the development of the infant oral microbiome.<br><br>MATERIALS AND METHODS: Oral swabs (n&#x2009;=&#x2009;55) were collected from infants at three months of age, alongside breastfeeding data collected over a 24-hour period. Bacterial DNA profiles were analysed using full-length 16S rRNA gene sequencing.<br><br>RESULTS: Variations in breastfeeding characteristics contributed to differences in microbial community structure. Total breastfeeding duration (min/24&#x2009;h) was positively associated with Bifidobacterium longum and Lactobacillus gasseri, while breastfeeding frequency was negatively associated with Veillonella sp. Additionally, human milk intake (ml/24&#x2009;h) was negatively associated with Streptococcus parasanguinis.<br><br>CONCLUSION: These findings underscore the significant influence of early life feeding practices on oral microbial communities and emphasise the importance role of breastfeeding in shaping the oral microbiome during early life.}, }
@article {pmid40012789, year = {2025}, author = {Chmielarczyk, A and Golińska, E and Tomusiak-Plebanek, A and Żeber-Lubecka, N and Kulecka, M and Szczepanik, A and Jedlińska, K and Mech, K and Szaciłowski, K and Kuziak, A and Pietrzyk, A and Strus, M}, title = {Microbial dynamics of acute pancreatitis: integrating culture, sequencing, and bile impact on bacterial populations and gaseous metabolites.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1544124}, pmid = {40012789}, issn = {1664-302X}, abstract = {BACKGROUND: Our study examined the composition of the intestinal microflora in a hospitalized patient with AP symptoms treated several months earlier for diverticulitis. The therapeutic intervention necessitated Hartmann's procedure, culminating in colostomy creation.<br><br>AIMS: Employing a thorough microbiological analysis we attempted to demonstrate whether the microflora isolated from the peripancreatic fluid exhibited a stronger correlation with the contents of the stoma or with the rectal swab. Additionally, we sought to determine the association between later onset of AP and diverticulitis.<br><br>METHODS: Following clinical materials from the patient in the initial phase of AP were collected: rectal swab, colostomy bag contents (in the publication referred to as stoma content/stool) and peripancreatic fluid. Microbiological analysis was performed, including classic culture methodology, NGS techniques, and genotyping methodologies. Furthermore, the effect of bile on the shift in the population of selected bacterial species was examined.<br><br>RESULTS: The NGS technique confirmed greater consistency in bacteria percentage (phyla/family) between stoma content and peripancreatic fluid. In both samples, a clear dominance of the Proteobacteria phyla (over 75%) and the Enterobacteriaceae family was demonstrated. Moreover, NGS verified the presence of the Fusobacteriota phylum and Fusobacteriaceae family only in rectal swabs, which may indicate a link between this type of bacteria and the etiology of diverticulitis. We observed that Escherichia coli 33 isolated from stool exhibited active gaseous metabolite production (mainly hydrogen).<br><br>CONCLUSIONS: The abundant production of hydrogen may substantially impact enzymatic processes, inducing specific alterations in disulfide bonds and trypsin inactivation. Our investigation alludes to the conceivable active involvement of bile in effecting qualitative and quantitative modifications in the peripancreatic microbiota composition, establishing a correlation between released bile and bacterial generation of gaseous metabolites.}, }
@article {pmid40012787, year = {2025}, author = {Shallangwa, SM and Ross, AW and Morgan, PJ}, title = {Single, but not mixed dietary fibers suppress body weight gain and adiposity in high fat-fed mice.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1544433}, pmid = {40012787}, issn = {1664-302X}, abstract = {Dietary fiber can suppress excess adipose tissue and weight gain in rodents and humans when fed high fat diets. The gut microbiome is thought to have a key role, although exactly how remains unclear. In a tightly controlled murine study, we explored how different types of dietary fiber and doses affect the gut microbiota and gut epithelial gene expression. We show that 10% pectin and 10% FOS suppress high fat diet (HFD)-induced weight gain, effects not seen at 2% doses. Furthermore, 2 and 10% mixtures of dietary fiber were also without effect. Each fiber treatment stimulated a distinct gut microbiota profile at the family and operational taxonomic unit (OTU) level. Mechanistically it is likely that the single 10% fiber dose shifted selected bacteria above some threshold abundance, required to suppress body weight, which was not achieved by the 10% Mix, composed of 4 fibers each at 2.5%. Plasma levels of the gut hormone PYY were elevated by 10% pectin and FOS, but not 10% mixed fibers, and similarly RNA seq revealed some distinct effects of the 10% single fibers on gut epithelial gene expression. These data show how the ability of dietary fiber to suppress HFD-induced weight gain is dependent upon both fiber type and dose. It also shows that the microbial response to dietary fiber is distinct and that there is not a single microbial response associated with the inhibition of adiposity and weight gain. PYY seems key to the latter response, although the role of other factors such as Reg3γ and CCK needs to be explored.}, }
@article {pmid40012785, year = {2025}, author = {Liu, F and Su, D and Shi, X and Xu, SM and Dong, YK and Li, Z and Cao, B and Ren, DL}, title = {Cross-population tongue image features and tongue coating microbiome changes in the evolution of colorectal cancer.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1442732}, pmid = {40012785}, issn = {1664-302X}, abstract = {INTRODUCTION: Tongue diagnosis, a cornerstone of Traditional Chinese Medicine (TCM), relies significantly on the assessment of tongue coating, which is used to evaluate Zang-fu organ functions, qi and blood dynamics, and the influence of pathogenic factors. This diagnostic method is integral to disease diagnosis and treatment in TCM. Recent research suggests a strong correlation between the characteristics of tongue coating and its microbial composition. These microbial variations may influence the formation and changes in tongue coating and are potentially linked to the progression of specific diseases. However, comprehensive research on the association between tongue coating, its microorganisms, and colorectal cancer (CRC) is limited. Notably, the quantitative aspects of tongue diagnosis and the microbial diversity in tongue coatings across different stages of colorectal cancer (from healthy individuals to colorectal adenoma (CRA) and CRC patients) are yet to be fully elucidated. By studying the cross-population characteristics of tongue image and tongue coating microorganisms during the evolution of colorectal cancer, the differences of tongue image characteristics and tongue coating microorganisms among different populations were further evaluated, providing references for early screening, diagnosis and treatment of colorectal cancer.<br><br>METHODS: The tongue image features of the subjects were collected by DS01-B tongue surface information collection system, mainly including tongue quality and tongue coating, and the tongue image was quantitatively analyzed by color space Lab value. The microbial characteristics of tongue coating were detected by high-throughput sequencing (16SrRNA amplicon sequencing). All subjects came from the patients in the Sixth Affiliated Hospital of Sun Yat-sen University and recruited volunteers (divided into health group, CRA group and CRC group), and obtained the ethical approval of the Sixth Affiliated Hospital of Sun Yat-sen University (ethical batch number: 2021ZSLYEC-328).<br><br>RESULTS: A total of 377 subjects were recruited in this study, including 56 healthy subjects, 65 colorectal adenomas and 256 colorectal cancer patients. The results showed that: in terms of texture of fur, the "thick fur" was a significant statistical difference (p&#x202f;<&#x202f;0.05) in the 3 groups. In addition, there was also a statistical difference in "greasy fur" and "peeled fur" among the 3 groups (p&#x202f;<&#x202f;0.05). Lab quantitative analysis of tongue color and fur color: The results showed that the L value of tongue color in healthy group was significantly different from that in CRA group and CRC group (p&#x202f;<&#x202f;0.01), but there was no significant difference between CRA group and CRC group (p&#x202f;>&#x202f;0.05). Tongue coating microorganisms, there was no significant difference in the richness and diversity of the three groups of subjects (p&#x202f;>&#x202f;0.05). There were 296 species in the three groups, accounting for 44.65%, and the species in colorectal cancer population was the most, reaching 502. From the differences in community composition among the three groups, it was found that there were certain differences in bacterial community composition between healthy people, CRA and CRC, and the differences became more and more obvious with the development of the disease.<br><br>CONCLUSION: This study revealed the specific cross-population tongue image characteristics and the specificity of tongue coating microorganisms in the evolution of CRC, providing new research ideas for early screening, early diagnosis, mechanism exploration, prevention and treatment of colorectal cancer.}, }
@article {pmid40012782, year = {2025}, author = {Gong, D and Gao, Y and Shi, R and Xu, X and Yu, M and Zhang, S and Wang, L and Dong, Q}, title = {The gastric microbiome altered by A4GNT deficiency in mice.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1541800}, pmid = {40012782}, issn = {1664-302X}, abstract = {BACKGROUND: Selective antimicrobial effects have been found for α1,4-linked N-acetylglucosamine residues at the terminus of O-glycans attached to a core protein of gastric gland mucin. A4gnt encodes α1,4-N-acetylglucosaminyl transferase, which is responsible for the biosynthesis of α1,4-linked N-acetylglucosamine. The impact of A4GNT on the establishment and homeostasis of the gastric microbiome remains to be clarified. The aim of this study was to characterize the gastric microbiome in mice deficient for the production of α1,4-linked N-acetylglucosamine.<br><br>METHODS: The gastric microbiome within A4gnt [-/-] mice and wild-type mice was analyzed using high-throughput sequencing of bacterial 16S rRNA.<br><br>RESULTS: In A4gnt [-/-] mice, which spontaneously develop gastric cancer, the community structure of the gastric microbiome was altered. The relative abundance of mutagenic Desulfovibrio and proinflammatory Prevotellamassilia in these mice was significantly increased, especially 4&#x202f;weeks after birth. The co-occurrence network appeared to be much more complex. Functional prediction demonstrated considerable decreases in the relative frequencies of functions associated with polysaccharide metabolism and transportation.<br><br>CONCLUSION: The distinct profile in A4gnt [-/-] mice demonstrated a vital role of A4GNT in the establishment of the gastric microbiome. A dysbiotic gastric microbiome may contribute to the spontaneous development of gastric cancer in mice.}, }
@article {pmid40012772, year = {2025}, author = {Zhang, F and Wu, Z and Zhang, Y and Su, Q and Zhu, K and Chen, X and Hou, S and Gui, L}, title = {Different lysine-to-methionine ratios in a low-protein diet affect the microbiome and metabolome, influencing the jejunal barrier function in Tibetan sheep.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1441143}, pmid = {40012772}, issn = {1664-302X}, abstract = {INTRODUCTION: The objective of this study was to evaluate the effects of the dietary lysine (Lys)/ methionine (Met) ratio in a low-protein diet on short-chain fatty acid (SCFA) profiles, villus morphology, antioxidant capacity, and immune status of the jejunum in Tibetan sheep.<br><br>METHODS: A total of 90 weaned Tibetan sheep, each 2 months old with an initial weight of 15.37 &#xb1; 0.92 kg, were randomly divided into three treatment groups. These groups were supplemented with different Lys/Met ratios of 3 [low protein-high methionine (LP-H)], 2 [low protein-medium methionine (LP-M)], and 1 [low protein-low methionine (LP-L)] in the basal diet (10% crude protein). The feeding trial lasted 100 days, including a 10-day acclimation period and a 90-day experimental period.<br><br>RESULTS: The hematoxylin-eosin (H&amp;E) sections showed that the LP-L group had a significantly increased villus height compared to the LP-M and LP-H groups (p < 0.05). In addition, the LP-L group showed higher levels of Superoxide dismutase (SOD) activity and Total Antioxidant Capacity (T-AOC) concentrations (p < 0.05). A lower concentration of Interleukin-1 beta (IL-1&#x3b2;) was observed in the LP-H group (p < 0.05). The activities of &#x3b1;-amylase, chymotrypsin, and lipase were higher in the LP-L group compared to the LP-H group (p < 0.05). Bacterial sequencing showed that both Chao1 and ACE richness were significantly increased in the LP-L group (p < 0.05), suggesting that the species richness in the jejunum is connected to the ratio of dietary Lys/Met. Furthermore, lowering the dietary Lys/ Met ratio significantly increased the abundance of Romboutsia, the Ruminococcus gauvreauii group, the Lachnospiraceae NK3A20 group, Ruminococcus 2, and the Christensenellaceae R-7 group (p < 0.05) while decreasing the abundance of Methanobrevibacter (p < 0.05). Several differential metabolites, including beta-alanine, pantothenate, pantothenic acid, phosphoenolpyruvate, cysteine, adenosine 5'-diphosphate, isodeoxycholic acid, glutamate conjugated cholic acid, and 3-dehydrocholic acid, were significantly increased in the LP-L group (p < 0.05). The functional analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations indicated that these metabolites were mainly involved in pantothenate and CoA biosynthesis, ferroptosis, and the tricarboxylic acid cycle. Several genes related to barrier function, such as Occludin and Muc- 2, were upregulated in the LP-L group (p < 0.05), while IL-6 and TNF-&#x3b1; were downregulated (p < 0.05).<br><br>DISCUSSION: Collectively, our results suggest that the dietary Met/ Lys ratio could affect the jejunal SCFA concentration by modulating the microbial community and regulating metabolism, thereby contributing to jejunal barrier function. Our findings provide a theoretical basis for the application of Lys/Met diet supplementation in the nutritional management of Tibetan sheep, particularly when reducing the dietary crude protein (CP) level.}, }
@article {pmid40012771, year = {2025}, author = {Dong, Z and Yang, S and Tang, C and Li, D and Kan, Y and Yao, L}, title = {New insights into microbial bile salt hydrolases: from physiological roles to potential applications.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1513541}, pmid = {40012771}, issn = {1664-302X}, abstract = {Gut microbiota has been increasingly linked to metabolic health and diseases over the past few decades. Bile acids (BAs), the major components of bile, are bidirectionally linked to intestinal microbiota, also known as the gut microbiome-BA metabolic axis. Gut microbiota-derived bile salt hydrolase (BSH, EC 3.5.1.24), which catalyzes the "gateway" reaction in a wider pathway of bile acid modification, not only shapes the bile acid landscape, but also modulates the crosstalk between gut microbiota and host health. Therefore, microbial BSHs exhibit the potential to directly or indirectly influence microbial and host physiologies, and have been increasingly considered as promising targets for the modulation of gut microbiota to benefit animal and human health. However, their physiological functions in bacterial and host physiologies are still controversial and not clear. In this review, we mainly discuss the current evidence related to the physiological roles that BSHs played in gut microbiota and human health, and the possible underlying mechanisms. Meanwhile, we also present the potential applications of BSHs and BSH-producing probiotics in various fields. Finally, we describe several important questions that need to be addressed by further investigations. A detailed exploration of the physiological significance of BSHs will contribute to their future diagnostic and therapeutic applications in improving animal and human health.}, }
@article {pmid40012740, year = {2024}, author = {Wiley, JW and Higgins, GA}, title = {Epigenomics and the Brain-gut Axis: Impact of Adverse Childhood Experiences and Therapeutic Challenges.}, journal = {Journal of translational gastroenterology}, volume = {2}, number = {2}, pages = {125-130}, pmid = {40012740}, issn = {2994-8754}, abstract = {The brain-gut axis represents a bidirectional communication network that integrates neural, hormonal, and immunological signaling between the central nervous system and the gastrointestinal tract. Adverse childhood experiences (ACEs) have increasingly been recognized for their profound impact on this axis, with implications for both mental and physical health outcomes. This mini-review explores the emerging field of epigenomics-specifically, how epigenetic modifications incurred by ACEs can influence the brain-gut axis and contribute to the pathophysiology of various disorders. We examine the evidence linking epigenetic mechanisms such as DNA methylation, histone modifications, and non-coding RNAs to the modulation of gene expression involved in stress responses, neurodevelopment, and immune function-all of which intersect at the brain-gut axis. Additionally, we discuss the emerging potential of the gut microbiome as both a target and mediator of epigenetic changes, further influencing brain-gut communication in the context of ACEs. The methodological and therapeutic challenges posed by these insights are significant. The reversibility of epigenetic marks and the long-term consequences of early life stress require innovative and comprehensive approaches to intervention. This underscores the need for comprehensive strategies encompassing psychosocial, pharmacological, neuromodulation, and lifestyle interventions tailored to address ACEs' individualized and persistent effects. Future directions call for a multi-disciplinary approach and longitudinal studies to uncover the full extent of ACEs' impact on epigenetic regulation and the brain-gut axis, with the goal of developing targeted therapies to mitigate the long-lasting effects on health.}, }
@article {pmid40012717, year = {2025}, author = {Li, YI and Pagulayan, K and Rau, H and Hendrickson, R and Schindler, AG}, title = {Gut Microbial Composition Is Associated with Symptom Self-Report in Trauma-Exposed Iraq and Afghanistan Veterans.}, journal = {Neurotrauma reports}, volume = {6}, number = {1}, pages = {1-12}, pmid = {40012717}, issn = {2689-288X}, abstract = {Iraq and Afghanistan War-era Veterans are at elevated risk for physical injuries and psychiatric illnesses, in particular the polytrauma triad of mild traumatic brain injury (mTBI), post-traumatic stress disorder (PTSD), and chronic pain. The gut microbiome has been implicated in modulation of critical processes beyond digestion, including immune system functioning and stress responsivity, and may be an important factor in understanding physical and mental health outcomes following deployment and trauma exposure. However, minimal research to date has sought to characterize gut microbiome composition in this population. Male Veterans of the conflicts in Iraq and Afghanistan who previously completed a Veterans Affairs' comprehensive TBI evaluation were enrolled in the current study. Participants completed self-report measures of PTSD symptom severity, pain intensity and interference, fatigue, cognitive symptoms, substance use, and sleep quality. They also submitted fecal samples, and metagenomic sequencing was used to calculate alpha and beta diversity and taxonomic microbial composition. Associations between microbiome data and clinical variables were then examined. Alpha and beta diversity measures were not significantly correlated with clinical outcomes. Fatigue, post-concussive symptoms, executive function symptoms, and cannabis use were associated with differences in gut microbial composition, specifically Verrucomicrobiota. Together, results suggest that altered gut microbiome composition is associated with psychiatric and cognitive symptoms in Veterans and highlight a potential new therapeutic target of interest. Future research is needed to examine whether probiotic treatment is effective for reducing symptoms common in this clinical population.}, }
@article {pmid40012624, year = {2025}, author = {Dai, J and Wang, W and He, F and Wang, Y and Zou, D}, title = {Alleviation of DSS-induced colitis by Meconopsis polysaccharides correlated with reduced PI3K/AKT signaling and gut microbiome diversity.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1459668}, pmid = {40012624}, issn = {1663-9812}, abstract = {INTRODUCTION: Inflammatory bowel disease (IBD) is a recurrent gastrointestinal disorder that significantly impacts patients' quality of life globally. This study focuses on the polysaccharides (MP) extracted from Meconopsis integrifolia, to investigate its role in alleviating DSS (dextran sulfate sodium)-induced colitis in mice.<br><br>METHODS: The study commenced with a comprehensive chemical characterization of Meconopsis polysaccharides. Subsequently, the colitis-alleviating activity of MP was validated through in vivo experiments.<br><br>RESULTS: The results revealed that MP is primarily composed of ten monosaccharides, exhibits good thermal stability, and has a relatively uniform molecular weight distribution. In vivo experiments demonstrated that MP significantly mitigated DSS-induced weight loss, increased DAI, colon shortening, and tissue damage in mice. Furthermore, MP reduced the levels of inflammatory cytokines such as IL-1&#x3b2;, TNF-&#x3b1;, and IL-6 in serum. Mechanistically, MP exerted its anti-inflammatory effects by inhibiting the activation of the PI3K/AKT signaling pathway. Additionally, MP promoted gut microbiota diversity and regulated SCFA concentrations, contributing to an improved intestinal microenvironment and alleviation of colitis symptoms.<br><br>DISCUSSION: Our findings highlight the superior effectiveness of Meconopsis polysaccharides in alleviating DSS-induced colitis and open new avenues for targeted therapeutic strategies in the treatment of IBD.}, }
@article {pmid40012570, year = {2025}, author = {Sakandar, HA and Zhao, F and Kang, J and Khan, MN and Sun, Z}, title = {Remodeling of Gut Microbiome of Pakistani Expats in China After Ramadan Fasting.}, journal = {Food science &amp; nutrition}, volume = {13}, number = {3}, pages = {e70019}, pmid = {40012570}, issn = {2048-7177}, abstract = {Time-restricted intermittent fasting (TRIF) has gained popularity as an intervention for addressing overweight, obesity, and metabolic syndrome. It may influence the composition of the gut microbiome, potentially affecting various microbiome-mediated functions in humans. However, limited studies have been conducted involving TRIF and microbiome on developing and underdeveloped populations. Here, we investigated the impact of TRIF/Ramadan fasting (16:8) on the changes of gut microbiome and functional profiling of microbial communities during and after the month of Ramadan in Pakistani Expats living in China. We observed substantial change in alpha diversity during TRIF; the changes in gut microbial structure by the end of TRIF were higher vis-a-vis in the beginning. Significant differences were observed among individuals; several bacteria (Clostridium perfringens, Coprococcus comes, and Lactococcus lactis, among others) were changed significantly (p < 0.05). Additionally, amino acid, carbohydrate, and energy metabolism; glycan biosynthesis; and metabolism of cofactors and vitamins were significantly affected by TRIF. Pyridoxamine, glutamate, citrulline, arachidonic acid, and short-chain fatty acids showed substantial differences at different time points based on the predicted metabolic pathways. The preliminary results from this study demonstrate significant potential for elucidating the mechanisms underlying gut microbiome stability and enhancing the effectiveness of microbiome-tailored interventions among the Pakistani populace to ameliorate metabolic disorders.}, }
@article {pmid40012440, year = {2025}, author = {Bø, GH and Härmä, RS and Klingenberg, C and Kuchařová Pettersen, V}, title = {Impact of Gut Microbiome Modulating Interventions on Fecal Metabolome of Infants: A Systematic Review and Quality Assessment.}, journal = {Proteomics}, volume = {}, number = {}, pages = {e202400150}, doi = {10.1002/pmic.202400150}, pmid = {40012440}, issn = {1615-9861}, support = {//Troms&#xf8; Forskningsstiftelse/ ; }, abstract = {The development of the gut microbiome in infancy is a vulnerable process that may be perturbed by antibiotics or supported by probiotics. Although effects of these "biotics" have been well-studied through DNA sequencing, it remains unclear how the resulting compositional changes affect the microbiome metabolic functions. Additionally, limits in method standardization require careful quality assessment of studies reporting fecal metabolome. We conducted a systematic search in Embase and MEDLINE for studies describing fecal metabolites from term and near-term infants, together with anti-, pre-, or probiotic intervention. The search identified 680 articles, of which 60 were assessed for eligibility and 21 were included. We first developed operational checklists for transparent and reproducible reporting and evaluated the quality of metabolomic methodologies. This analysis supported our aim to summarize changes in the fecal metabolome induced by biotic interventions. Despite a varying quality of metabolomic methodology, we identified similarities in the fecal metabolome profiles in response to specific biotic interventions. Among the most frequently observed metabolites, which were consistently reported to be altered after biotic interventions, were bile acids, aromatic amino acids, and short-chain fatty acids. We conclude with a discussion on appropriate experimental design, controls, and metabolomics reporting to guide future research permitting meta-analyses.}, }
@article {pmid40012336, year = {2025}, author = {Thomas, S and Bittinger, K and Livornese, LL}, title = {Utilizing the biosimulator to analyze the environmental microbiome within the intensive care units of a hospital.}, journal = {BioTechniques}, volume = {}, number = {}, pages = {1-10}, doi = {10.1080/07366205.2025.2467550}, pmid = {40012336}, issn = {1940-9818}, abstract = {Hospital-acquired infections (HAIs), also known as nosocomial infections, are illnesses contracted during treatment at a healthcare facility and can result in severe or life-threatening complications. HAIs are caused by microorganisms that exhibit resistance to standard antibiotics. HAIs can lead to severe complications, longer stays, and increased mortality, particularly in vulnerable patients. In our previous study, we demonstrated the ability of an engraved Petri dish, referred to as a "biosimulator," to induce adhesion of non-adherent cells and the microbiome. This paper explores the use of the biosimulator to elucidate the microbiome composition within intensive care units (ICUs) in a hospital setting. The biosimulator, with a nutrient-rich bacterial growth medium, was placed in ICUs for 24 h, then incubated for three days under aerobic and anaerobic conditions. Using 16S rRNA sequencing, we profiled the ICU microbiome from multiple samples. Our findings showed that ICU microbiomes closely mirrored those of patients, with microorganisms in the ICU exhibiting stronger interrelationships than in control conditions. The combined use of the biosimulator and profiling offers an effective approach for analyzing and understanding microbiome changes in healthcare settings, particularly in high-risk areas, such as ICUs.}, }
@article {pmid40012260, year = {2025}, author = {Su, W and Chen, H and Hu, D and Ye, B and Zhang, W and Zhang, G and Si, X and Zhou, X}, title = {The Causal Role of Esophageal Cancer and Gut Microbiota: A Bidirectional Mendelian Randomization Study.}, journal = {Journal of evidence-based integrative medicine}, volume = {30}, number = {}, pages = {2515690X251324793}, doi = {10.1177/2515690X251324793}, pmid = {40012260}, issn = {2515-690X}, mesh = {Humans ; *Mendelian Randomization Analysis ; *Esophageal Neoplasms/genetics/microbiology ; *Gastrointestinal Microbiome ; *Polymorphism, Single Nucleotide ; *Genome-Wide Association Study ; Feces/microbiology ; }, abstract = {AIMS: Gut microbiota are reported to be associated with the incidence and prognosis of Esophageal cancer (EC) but their genetic association is unclear. We carried out a bidirectional MR analysis to assess the causal relationship between EC and gut microbiota from fecal samples.<br><br>METHODS: The microbiome genome-wide association studies (GWAS) data of 18,340 individuals provided by MiBioGen consortium and the EC GWAS data (740 esophageal cancers cases and 372&#x2005;016 controls) provided by UK Biobank were respectively utilized as exposure and/or outcome data. Reliable single nucleotide polymorphisms (SNPs) were obtained after rigorous screening. A bidirectional Mendelian randomization (MR) analysis was conducted using the inverse-variance weighted (IVW) method. The sensitivity analyses including the MR-Egger method, weighted median, weighed mode and leave-one-out method were performed to examine the stability, heterogeneity and pleiotropy of the results.<br><br>RESULTS: Forward MR analysis revealed the increase in abundance of the microbial trait by each standard deviation was associated with a higher risk of EC (Coprobacter (OR&#x2009;=&#x2009;1.001,95%CI&#x2009;=&#x2009;1.000-1.002, P&#x2009;=&#x2009;.0281, FDR&#x2009;=&#x2009;0.0424); Ruminococcus1(OR&#x2009;=&#x2009;1.001,95%CI&#x2009;=&#x2009;1.000-1.002, P&#x2009;=&#x2009;.0318, FDR&#x2009;=&#x2009;0.0424); Senegalimassilia (OR&#x2009;=&#x2009;1.002,95%CI&#x2009;=&#x2009;1.000-1.003, P&#x2009;=&#x2009;.0062, FDR&#x2009;=&#x2009;0.0372); Veillonella (OR&#x2009;=&#x2009;1.001,95%CI&#x2009;=&#x2009;1.000-1.002, P&#x2009;=&#x2009;.0182, FDR&#x2009;=&#x2009;0.0372)) or a lower risk of EC (Eubacterium oxidoreducens (OR&#x2009;=&#x2009;0.999, 95%CI&#x2009;=&#x2009;0.998-1.000, P&#x2009;=&#x2009;.0379, FDR&#x2009;=&#x2009;00&#x2005;433); Lachnospira (OR&#x2009;=&#x2009;0.998,95%CI&#x2009;=&#x2009;0.996-1.000, P&#x2009;=&#x2009;.0186, FDR&#x2009;=&#x2009;0.0372); Romboutsia (OR&#x2009;=&#x2009;0.999,95%CI&#x2009;=&#x2009;0.998-1.000, P&#x2009;=&#x2009;.0482, FDR&#x2009;=&#x2009;0.0482); Turicibacter (OR&#x2009;=&#x2009;0.999,95%CI&#x2009;=&#x2009;0.998-1.000, P&#x2009;=&#x2009;.0133, FDR&#x2009;=&#x2009;0.0372)). Reverse MR analysis showed that genetic liability to EC was also causally linked toincreased susceptibility of changes in the gut microbiome (genera Eggerthella (Beta&#x2009;=&#x2009;37.63,95%CI&#x2009;=&#x2009;4.76-70.50, P&#x2009;=&#x2009;.0248, FDR&#x2009;=&#x2009;0.0331); Coprococcus 2 (Beta&#x2009;=&#x2009;23.90,95%CI&#x2009;=&#x2009;1.65-46.15, P&#x2009;=&#x2009;.0353, FDR&#x2009;=&#x2009;0.0353); Christensenellaceae R.7 (Beta&#x2009;=&#x2009;22.75,95%CI&#x2009;=&#x2009;4.22-41.28, P&#x2009;=&#x2009;.0161, FDR&#x2009;=&#x2009;0.0322); Intestinimonas (Beta&#x2009;=&#x2009;-33.24,95%CI&#x2009;=&#x2009;-54.90-11.58, P&#x2009;=&#x2009;.0026, FDR&#x2009;=&#x2009;0.0104)).<br><br>CONCLUSIONS: Our findings supported a bidirectionally causal relationship between gut microbiota and EC, implying the potential role of gut microbiota in preventing the occurrence and development of EC.}, }
@article {pmid40012216, year = {2025}, author = {Md-Zain, BM and Wan-Mustafa, WAS and Tingga, RCT and Gani, M and Mohd-Ridwan, AR}, title = {High-Throughput DNA Metabarcoding for the Gut Microbiome Assessment of Captive White-Handed Gibbon and Siamang.}, journal = {Journal of medical primatology}, volume = {54}, number = {2}, pages = {e70009}, doi = {10.1111/jmp.70009}, pmid = {40012216}, issn = {1600-0684}, support = {ST-2022-027//The National Conservation Trust Fund for Natural Resources (NCTF),/ ; ST-2021-017//Universiti Kebangsaan Malaysia/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *DNA Barcoding, Taxonomic ; *Animals, Zoo/microbiology ; *Hylobates/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Feces/microbiology ; Malaysia ; High-Throughput Nucleotide Sequencing/veterinary ; Hylobatidae/genetics/microbiology ; Male ; Female ; RNA, Bacterial/analysis/genetics ; }, abstract = {BACKGROUND: The gut microbiota plays a vital role in primates' overall health and well-being, including small apes (Hylobatidae). The symbiotic relationships between bacteria and the gut aid food digestion, maintain host health, and help them adapt to their environment, including captive conditions. Despite being listed as endangered in the International Union for Conservation of Nature (IUCN) red list category, molecular studies on the small ape's gut microbiome are limited compared to other primates. This study aimed to characterize the gut microbiota of captive small apes at Zoo Taiping and Night Safari, Peninsular Malaysia, by evaluating their microbial communities.<br><br>METHODS: Seven fecal samples from Hylobatidae (white-handed gibbon and siamang) were collected, and the bacteria therein were successfully isolated and subjected to high-throughput sequencing of the 16S rRNA gene.<br><br>RESULTS: The acquired amplicon sequence variants (ASVs) were successfully classified into 17 phyla, 82 families, 164 genera, and 43 species of microbes. Each small ape exhibited a unique gut microbiota profile. The phyla Bacteroidota and Firmicutes were dominant in each individual. Environmental conditions and host genetics are among the factors that influence the small ape's gut microbiome composition.<br><br>CONCLUSIONS: These findings provide valuable insights into the gut microbiota composition of small apes at Zoo Taiping and Night Safari, thus contributing to the health management and welfare efforts of small apes in captivity.}, }
@article {pmid40011806, year = {2025}, author = {Stopnisek, N and Hedžet, S and Accetto, T and Rupnik, M}, title = {Insights into diversity, host-range, and temporal stability of Bacteroides and Phocaeicola prophages.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {92}, pmid = {40011806}, issn = {1471-2180}, support = {P3-0387//Javna Agencija za Raziskovalno Dejavnost RS/ ; P3-0387//Javna Agencija za Raziskovalno Dejavnost RS/ ; P4-0097//Javna Agencija za Raziskovalno Dejavnost RS/ ; P3-0387//Javna Agencija za Raziskovalno Dejavnost RS/ ; }, mesh = {*Prophages/genetics/isolation &amp; purification/physiology ; *Host Specificity ; Humans ; *Genome, Bacterial/genetics ; *Bacteroides/virology/genetics ; *Gastrointestinal Microbiome ; Computational Biology/methods ; Phylogeny ; Genetic Variation ; }, abstract = {BACKGROUND: Phages are critical components of the gut microbiome, influencing bacterial composition and function as predators, parasites, and modulators of bacterial phenotypes. Prophages, integrated forms of these phages, are prevalent in many bacterial genomes and play a role in bacterial adaptation and evolution. However, the diversity and stability of prophages within gut commensals, particularly in the genera Bacteroides and Phocaeicola, remain underexplored. This study aims to screen and characterize prophages in these genera, providing insights into their diversity, host range, and temporal dynamics in the human gut.<br><br>RESULTS: Using a combination of three bioinformatic tools-Cenote-Taker 3, Vibrant, and PHASTER-we conducted a comprehensive analysis of prophages in Bacteroides and Phocaeicola. Cenote-Taker 3 identified the most diverse set of prophages, with significant overlaps observed between the tools. After clustering high-quality prophages, we identified 22 unique viral operational taxonomic units (vOTUs). Notably, comparisons between prophages identified in isolated bacterial genomes, metaviromes, and large public gut virome databases revealed a broader host range than initially observed in single isolates. Certain prophages were consistent across time points and individuals, suggesting temporal stability. All identified prophages belonged to the Caudoviricetes class and contained genes related to antibiotic resistance, toxin production, and metabolic processes.<br><br>CONCLUSIONS: The combined use of multiple prophage detection tools allowed for a more comprehensive assessment of prophage diversity in Bacteroides and Phocaeicola. The identified prophages were not only prevalent but also exhibited broad host ranges and temporal stability. The presence of antibiotic resistance and toxin genes suggests that these prophages may significantly influence bacterial community structure and function in the gut, with potential implications for human health. These findings highlight the importance of using diverse detection tools to accurately assess prophage diversity and dynamics.}, }
@article {pmid40011766, year = {2025}, author = {Proctor, DM and Sansom, SE and Deming, C and Conlan, S and Blaustein, RA and Atkins, TK and ,  and Dangana, T and Fukuda, C and Thotapalli, L and Kong, HH and Lin, MY and Hayden, MK and Segre, JA}, title = {Clonal Candida auris and ESKAPE pathogens on the skin of residents of nursing homes.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40011766}, issn = {1476-4687}, abstract = {Antimicrobial resistance is a public health threat associated with increased morbidity, mortality and financial burden in nursing homes and other healthcare settings[1]. Residents of nursing homes are at increased risk of pathogen colonization and infection owing to antimicrobial-resistant bacteria and fungi. Nursing homes act as reservoirs, amplifiers and disseminators of antimicrobial resistance in healthcare networks and across geographical regions[2]. Here we investigate the genomic epidemiology of the emerging, multidrug-resistant human fungal pathogen Candida auris in a ventilator-capable nursing home. Coupling strain-resolved metagenomics with isolate sequencing, we report skin colonization and clonal spread of C. auris on the skin of nursing home residents and throughout a metropolitan region. We also report that most Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Entobacter species (ESKAPE) pathogens and other high-priority pathogens (including Escherichia coli, Providencia stuartii, Proteus mirabilis and Morganella morganii) are shared in a nursing home. Integrating microbiome and clinical microbiology data, we detect carbapenemase genes at multiple skin sites on residents identified as carriers of these genes. We analyse publicly available shotgun metagenomic samples (stool and skin) collected from residents with varying medical conditions living in seven other nursing homes and provide additional evidence of previously unappreciated bacterial strain sharing. Taken together, our data suggest that skin is a reservoir for colonization by C. auris and ESKAPE pathogens and their associated antimicrobial-resistance genes.}, }
@article {pmid40011666, year = {2025}, author = {Yang, YT and Li, XP and Gao, LC and Hu, WX and Zhao, XY and Hu, DG and Liu, J and Qiu, L}, title = {Optimization, application effects and improved microecology of a composite microbial agent containing oyster shells.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {6922}, pmid = {40011666}, issn = {2045-2322}, support = {ZR2023MC035//Natural Science Foundation of Shandong Province/ ; ZR2023MC035//Natural Science Foundation of Shandong Province/ ; 2023RCKY222 and 2023RCKY218//2023RCKY222 and 2023RCKY218/ ; 2023RCKY222 and 2023RCKY218//2023RCKY222 and 2023RCKY218/ ; }, mesh = {Animals ; *Ostreidae/microbiology ; *Animal Shells/chemistry ; *Soil Microbiology ; *Chitosan/chemistry ; Beauveria/growth &amp; development ; Solanum lycopersicum/microbiology/growth &amp; development ; Microbiota ; Ecosystem ; }, abstract = {Oysters are one of the largest marine shellfish species worldwide. However, oyster shells are treated as waste, accumulating on coastal shores and seriously polluting the ecosystem. In this study, a composite microbial agent was developed using calcined oyster shell powder, Beauveria bassiana spore powder, and ecological chitosan. To release the active ingredients, oyster shells were treated by calcination. The optimal application ratio of the agent was determined by detecting tomato growth indicators. Application of the optimized agent to vineyards increased 100-grain weight, carotenoids, and total amino acids by 10.55%, 8.71%, and 29.40%, respectively. Further detection of soil microbial population changes showed that the application of the agent increased the abundance and diversity of soil microbial populations, promoting the metabolism of bacterial amino acids, polysaccharides. These findings suggest that the agent not only enhanced plant growth and fruit quality, but also enriched the diversity and abundance of soil microbial communities.}, }
@article {pmid40011529, year = {2025}, author = {Santangelo, BE and Bada, M and Hunter, LE and Lozupone, C}, title = {Hypothesizing mechanistic links between microbes and disease using knowledge graphs.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {6905}, pmid = {40011529}, issn = {2045-2322}, support = {T15LM009451/NH/NIH HHS/United States ; R01LM013400/NH/NIH HHS/United States ; R01LM013400/NH/NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases/microbiology ; *Parkinson Disease/microbiology ; Host Microbial Interactions/physiology ; }, abstract = {Knowledge graphs have been a useful tool for many biomedical applications because of their effective representation of biological concepts. Plentiful evidence exists linking the gut microbiome to disease in a correlative context, but uncovering the mechanistic explanation for those associations remains a challenge. Here we demonstrate the potential of knowledge graphs to hypothesize plausible mechanistic accounts of host-microbe interactions in disease. We have constructed a knowledge graph of linked microbes, genes and metabolites called MGMLink, and, using a shortest path or template-based search through the graph and a novel path-prioritization methodology based on the structure of the knowledge graph, we show that this knowledge supports inference of mechanistic hypotheses that explain observed relationships between microbes and disease phenotypes. We discuss specific applications of this methodology in inflammatory bowel disease and Parkinson's disease. This approach enables mechanistic hypotheses surrounding the complex interactions between gut microbes and disease to be generated in a scalable and comprehensive manner.}, }
@article {pmid40011507, year = {2025}, author = {Bassols, A and Amigó, N and Pérez-Rodado, M and Saco, Y and Peña, R and Pato, R and Pisoni, L and Devant, M and Marti, S}, title = {Fecal metabolomics to understand intestinal dysfunction in male dairy beef calves at arrival to the rearing farm.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {6887}, pmid = {40011507}, issn = {2045-2322}, support = {PID2019-104021RB-I00/ AEI/10.13039/501100011033//Ministerio de Ciencia e Innovaci&#xf3;n/ ; 2021 SGR 00642//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; }, mesh = {Animals ; Cattle ; *Feces/chemistry ; Male ; *Metabolomics/methods ; Biomarkers/metabolism ; Cattle Diseases/metabolism ; Metabolome ; Colostrum/metabolism/chemistry ; Farms ; Gastrointestinal Microbiome/physiology ; Dairying ; }, abstract = {Fecal biomarkers are becoming an important analytical tool since feces are in direct contact with the inflamed intestine and site for the gut microbiome. The objective of this study was the identification of differential fecal metabolites by means of [1]H-NMR to evaluate the management of male dairy beef calves, and which could become potential biomarkers of gastrointestinal disorders. Holstein calves were subjected to a protocol aimed to simulate real conditions of the dairy beef market. Three groups were studied: Control (CTR: high colostrum, no transport, milk replacer), LCMR (low colostrum, transport, milk replacer) and LCRS (low colostrum, transport, rehydrating solution). Fecal lactoferrin was determined as marker of intestinal inflammation, and metabolomic profiling was performed in feces collected the day after arrival to the farm. 41 polar and 10 non-polar metabolites were identified, of which proline, formate and creatine increased in the LCRS group, whereas butyrate and uracil decreased. Less differences were found in non-polar metabolites. Multivariate analysis indicated that most differences are found between the LCRS group and the others. In conclusion, this study indicates that feed restriction has a more important effect at this age than colostrum uptake and transport. These results should help to identify robust fecal biomarkers to assess calf intestinal health and improve management protocols.}, }
@article {pmid40011462, year = {2025}, author = {Mahajna, A and Geurkink, B and Gacesa, R and Keesman, KJ and Euverink, GW and Jayawardhana, B}, title = {Metatranscriptomes of activated sludge microbiomes from saline wastewater treatment plant.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {348}, pmid = {40011462}, issn = {2052-4463}, mesh = {*Microbiota ; *Sewage/microbiology ; *Wastewater/microbiology ; Netherlands ; Waste Disposal, Fluid ; Transcriptome ; }, abstract = {The activated sludge microbiome (ASM) drives the biological wastewater treatment process in wastewater treatment plants. It has been established in the literature that the ASM is characterized by a high degree of taxonomic and metabolic diversity. However, meta-omics datasets have been derived from domestic wastewater treatment plants with little attention to saline wastewater treatment plants (SWWTP). Existing knowledge of how activated sludge microorganisms impact water quality, interrelate within habitat networks, and respond to environmental perturbations remains limited. Here we present datasets of the metatranscriptomes of SWWTP in The Netherlands, coupled with process data. The dataset represents a two-year and four-month time series of data collected from 2014 to 2017, with samples taken at approximately monthly intervals from the facultative zone in the activated sludge process of an SWWTP. In total, 32 activated sludge samples were analyzed. This dataset can be used to enhance understanding of the unique microbiome composition in SWWTPs, its dynamic responses to environmental variables, and the metabolic functions within the ASM.}, }
@article {pmid40011461, year = {2025}, author = {Souza, JGS and Azevedo, F and Borges, MHR and Costa, RC and Shiba, T and Barak, S and Mayer, Y and Figueiredo, LC and Feres, M and Barão, VAR and Shibli, JA}, title = {Microbiome modulation of implant-related infection by a novel miniaturized pulsed electromagnetic field device.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {36}, pmid = {40011461}, issn = {2055-5008}, mesh = {Humans ; *Microbiota ; *Electromagnetic Fields ; *Bacteria/genetics/classification/radiation effects/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Dental Implants/microbiology ; *Prosthesis-Related Infections/microbiology ; Male ; Female ; Middle Aged ; }, abstract = {Dental implant-related infections, which lack effective therapeutic strategies, are considered the primary cause for treatment failure. Pulsed electromagnetic field (PEMF) technology has been introduced as a safe and effective modality for enhancing biological responses. However, the PEMF effect on modulating microbial diversity has not been explored. Thus, we tested a miniaturized PEMF biomedical device as a healing component for dental implants. PEMF activation did not alter the chemical composition, surface roughness, wettability, and electrochemical performance. PEMF effectively controlled chronic in vitro polymicrobial microbial accumulation. The in vivo study where devices were inserted in the patients' oral cavities and 16S RNA sequencing analysis evidenced a fivefold or more reduction in 23 bacterial species for PEMF group and the absence of some species for this group, including pathogens associated with implant-related infections. PEMF altered bacterial interactions and promoted specific bacterial pathways. PEMF has emerged as an effective strategy for controlling implant-related infections.}, }
@article {pmid40011383, year = {2025}, author = {Clementino, JR and de Oliveira, LIG and Salgaço, MK and de Oliveira, FL and Mesa, V and Tavares, JF and Silva-Pereira, L and Raimundo, BVB and Oliveira, KC and Medeiros, AI and Silva, FA and Sivieri, K and Magnani, M}, title = {β-Glucan Alone or Combined with Lactobacillus acidophilus Positively Influences the Bacterial Diversity and Metabolites in the Colonic Microbiota of Type II Diabetic Patients.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {40011383}, issn = {1867-1314}, abstract = {β-Glucan is a fermentable polysaccharide with prebiotic properties that has been shown to improve metabolic indicators. This study evaluated the effects of spent brewer's yeast β-glucan (BGL) and Lactobacillus acidophilus LA-5 (10[6] CFU/g) (LA5) alone and in combination (LA5-BGL) on the composition of the fecal microbiome of adults with type 2 diabetes mellitus (T2DM) using the Human Gut Microbial Ecosystem Simulator (SHIME®). Short-chain fatty acids (SCFAs), ammonium ions, and cytokines (IL-6 and IL-10) were measured. BGL, LA5, and LA5-BGL increased (p < 0.05) the richness and diversity of microbial communities in the gut microbiome of individuals with T2DM. All treatments increased (p < 0.05) the abundance of Bacteroides, Alistipes, Lactobacillus, Subdoligranulum, and Acidaminococcus, along with increased (p < 0.05) production of SCFAs and anti-inflammatory cytokine (IL-10) compared to the control group. BGL treatments showed a greater increase in microbial diversity, SCFAs levels (butyric, propionic, and acetic acid), and the anti-inflammatory cytokine (IL-10). LA5 showed the highest decrease in ammonium ion levels. Results indicate that BGL may have a prebiotic and immunomodulatory effect on the fecal microbial community and metabolic indicators in adults with type 2 diabetes mellitus (T2DM). Findings underscore the role of BGL as a prebiotic food.}, }
@article {pmid40011297, year = {2025}, author = {González-Serrano, F and Romero-Contreras, YJ and Orta, AH and Basanta, MD and Morales, H and Sandoval García, G and Bello-López, E and Escobedo-Muñoz, AS and Bustamante, VH and Ávila-Akerberg, V and Cevallos, M&#xc1; and Serrano, M and Rebollar, EA}, title = {Amphibian skin bacteria contain a wide repertoire of genes linked to their antifungal capacities.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {3}, pages = {78}, pmid = {40011297}, issn = {1573-0972}, support = {IG200224//Programa de Apoyo a Proyectos de Investigaci&#xf3;n e Innovaci&#xf3;n Tecnol&#xf3;gica (PAPIIT-DGAPA)/ ; IG200224//Programa de Apoyo a Proyectos de Investigaci&#xf3;n e Innovaci&#xf3;n Tecnol&#xf3;gica (PAPIIT-DGAPA)/ ; 373914//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; }, mesh = {Animals ; *Skin/microbiology ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; *Amphibians/microbiology ; Batrachochytrium/genetics ; Multigene Family ; Microbiota/genetics ; Antifungal Agents/pharmacology/metabolism ; Anura/microbiology ; Phylogeny ; Antibiosis ; }, abstract = {Emerging diseases caused by fungi are a serious threat to wildlife biodiversity. The widespread fungal pathogen Batrachochytrium dendrobatidis (Bd) has caused dramatic amphibian population declines and species extinctions worldwide. While many amphibians have been negatively affected by Bd, some populations/species have persisted despite its presence. One factor contributing to amphibian protection against this fungus is the host-associated skin microbiome. In this study, we aimed to identify gene clusters associated with the antifungal activity of amphibian skin bacteria. Specifically, we explored skin bacteria isolated from species that have persisted in the wild despite the presence of Bd: the frogs Agalychnis callidryas, Craugastor fitzingeri, Dendropsophus ebraccatus, and the axolotl Ambystoma altamirani. Bacterial isolates were tested in vitro for their capacity to inhibit the growth of two fungal pathogens: Bd and the phytopathogen Botrytis cinerea (Bc). Genome mining of these bacterial isolates revealed a diverse repertoire of Biosynthetic Gene Clusters (BGCs) and chitin-degrading gene families (ChDGFs) whose composition and abundance differed among bacterial families. We found specific BGCs and ChDGFs that were associated with the capacity of bacteria to inhibit the growth of either Bd or Bc, suggesting that distinct fungi could be inhibited by different molecular mechanisms. By using similarity networks and machine learning, we identified BGCs encoding known antifungal compounds such as viscosin, fengycin, zwittermicin, as well as siderophores and a novel family of beta-lactones. Finally, we propose that the diversity of BGCs found in amphibian skin bacteria comprise a substantial genetic reservoir that could collectively explain the antifungal properties of the amphibian skin microbiome.}, }
@article {pmid40011281, year = {2025}, author = {Haider, K and Abbas, D and Galian, J and Ghafar, MA and Kabir, K and Ijaz, M and Hussain, M and Khan, KA and Ghramh, HA and Raza, A}, title = {The multifaceted roles of gut microbiota in insect physiology, metabolism, and environmental adaptation: implications for pest management strategies.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {3}, pages = {75}, pmid = {40011281}, issn = {1573-0972}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Insecta/microbiology/physiology ; *Bacteria/classification/metabolism ; Symbiosis ; Adaptation, Physiological ; Pest Control/methods ; Insect Control/methods ; }, abstract = {Similar to many other organisms, insects like Drosophila melanogaster, Hypothenemus hampei, and Cockroaches harbor diverse bacterial communities in their gastrointestinal systems. These bacteria, along with other microorganisms like fungi and archaea, are essential to the physiology of their insect hosts, forming intricate symbiotic relationships. These gut-associated microorganisms contribute to various vital functions, including digestion, nutrient absorption, immune regulation, and behavioral modulation. Notably, gut microbiota facilitates the breakdown of complex plant materials, synthesizes essential vitamins and amino acids, and detoxifies harmful substances, including pesticides. Furthermore, these microorganisms are integral to modulating host immune responses and enhancing disease resistance. This review examines the multifaceted roles of gut microbiota in insect physiology, with particular emphasis on their contributions to digestion, detoxification, reproduction, and environmental adaptability. The potential applications of gut microbiota in integrated pest management (IPM) are also explored. Understanding the microbial dynamics within insect pest species opens new avenues for pest control, including developing microbial biocontrol agents, microbial modifications to reduce pesticide resistance, and implementing microbiome-based genetic strategies. In particular, manipulating gut microbiota presents a promising approach to pest management, offering a sustainable and eco-friendly alternative to conventional chemical pesticides.}, }
@article {pmid40011276, year = {2025}, author = {Yasen, M and Li, M and Wang, J}, title = {The diversity pattern of soil bacteria in the rhizosphere of different plants in mountain ecosystems.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {3}, pages = {88}, pmid = {40011276}, issn = {1573-0972}, support = {32160408//National Natural Science Foundation of China/ ; }, mesh = {*Soil Microbiology ; *Rhizosphere ; *Bacteria/classification/genetics/isolation &amp; purification ; China ; *RNA, Ribosomal, 16S/genetics ; *Biodiversity ; *Ecosystem ; *Phylogeny ; Plants/microbiology ; Microbiota ; Soil/chemistry ; Plant Roots/microbiology ; High-Throughput Nucleotide Sequencing ; DNA, Bacterial/genetics ; Phosphorus/metabolism/analysis ; }, abstract = {Research on the composition and diversity of rhizosphere microbial communities of different plant species can help to identify important microbial functional groups or functional potentials, which is of great significance for vegetation restoration and ecological reconstruction. To provide scientific basis for the management of mountain ecosystem, the diversity pattern of rhizosphere bacterial community was investigated using 16 S rRNA high-throughput sequencing method among different host plants (Cirsium japonicum, Artemisia annua, Descurainia sophia, Lepidium apetalum, Phlomis umbrosa, and Carum carvi) in Tomur Peak National Nature Reserve, China. The results showed that the richness and diversity of rhizosphere bacteria were highest in Descurainia sophia, and lowest in Lepidium apetalum. Pseudomonadota, Acidobacteriota, and Actinomycetota were the common dominant phyla, and Sphingomonas was the predominant genus. Furthermore, there were some specific genera in different plants. The relative abundance of non-dominant genera varied among the plant species. Canonical correspondence analysis indicated that available potassium (AK), total phosphorus (TP), total potassium (TK), and soil organic matter (SOM) were the main drivers of bacterial community structure. Based on PICRUSt functional prediction, the bacterial communities in all samples encompass six primary metabolic pathways and 47 secondary metabolic pathways. The major secondary metabolic pathways (with a relative abundance of functional gene sequences > 3%) include 15 categories. Co-occurrence network analysis revealed differences in bacterial composition and interactions among different modules, with rhizosphere microorganisms of different plants exhibiting distinct functional advantages. This study elucidates the distribution patterns of rhizosphere microbial community diversity in mountain ecosystems, which provides theoretical guidance for the ecological protection of mountain soil based on the microbiome.}, }
@article {pmid40011208, year = {2025}, author = {Giddings, HJ and Teodósio, A and Jones, J and McMurray, JL and Hunter, K and Alame, R and Gardiner, I and Abdawn, Z and Butterworth, W and Henderson, IR and Cole, JA and Shannon-Lowe, CD and Rossiter-Pearson, AE}, title = {The Gastric Microbiota Invade the Lamina Propria in Helicobacter pylori-Associated Gastritis and Precancer.}, journal = {Helicobacter}, volume = {30}, number = {1}, pages = {e70016}, doi = {10.1111/hel.70016}, pmid = {40011208}, issn = {1523-5378}, support = {RGS\R2\192312//Royal Society/ ; EDDPMA-Nov21\100008/CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {Humans ; *Gastritis/microbiology/pathology ; *Helicobacter Infections/microbiology/pathology ; *Gastric Mucosa/microbiology/pathology ; *Helicobacter pylori/genetics/isolation &amp; purification/pathogenicity ; Male ; Stomach Neoplasms/microbiology/pathology ; Immunohistochemistry ; Female ; Middle Aged ; Aged ; Gastrointestinal Microbiome ; In Situ Hybridization ; Precancerous Conditions/microbiology/pathology ; Adult ; Metaplasia/microbiology ; }, abstract = {BACKGROUND: Stomach cancer is the fourth leading cause of cancer-related deaths worldwide. Helicobacter pylori is the main risk factor for gastric adenocarcinoma (GAC), yet the precise mechanism underpinning this association remains controversial. Gastric intestinal metaplasia (GIM) represents the precancerous stage and follows H. pylori-associated chronic gastritis (CG). Sequencing studies have revealed fewer H. pylori and more non-H. pylori bacteria in GAC. However, the spatial organization of the gastric microbiota in health and disease is unknown.<br><br>MATERIALS AND METHODS: Here, we have combined RNA in&#xa0;situ hybridization and immunohistochemistry to detect H.&#x2009;pylori, non-H.&#x2009;pylori bacteria, and host cell markers (E-cadherin, Mucins 5AC and 2) on tissue sections from patients with CG (n&#x2009;=&#x2009;15) and GIM (n&#x2009;=&#x2009;17).<br><br>RESULTS: Quantitative analysis of whole slide scans revealed significant correlations of H.&#x2009;pylori and other bacteria in CG and GIM. In contrast to sequencing studies, significantly fewer non-H.&#x2009;pylori bacteria were detected in H.&#x2009;pylori-negative patients. Importantly, whilst H.&#x2009;pylori exclusively colonized the gastric glands, non-H.&#x2009;pylori bacteria invaded the lamina propria in 6/9 CG and 8/10 GIM H.&#x2009;pylori-positive patients. A rapid and cost-effective modified Gram stain was used to confirm these findings and enabled detection of non-H.&#x2009;pylori bacteria in GIM samples.<br><br>CONCLUSIONS: The invasion of the gastric lamina propria by non-H.&#x2009;pylori bacteria during H.&#x2009;pylori-associated CG and GIM represents an overlooked phenomenon in cancer progression. Further work must determine the mechanisms underlying the synergistic roles of H.&#x2009;pylori and other bacteria in carcinogenesis. This observation should redirect attempts to prevent, diagnose, and treat GAC.}, }
@article {pmid40011195, year = {2025}, author = {Li, T and Chen, J and Xu, Y and Ji, W and Yang, S and Wang, X}, title = {Hawthorn Pectin Alleviates DSS-Induced Colitis in Mice by Ameliorating Intestinal Barrier Function and Modulating Gut Microbiota.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.4c07965}, pmid = {40011195}, issn = {1520-5118}, abstract = {Pectin, as a kind of soluble dietary fiber in hawthorns, exhibits a wide range of biological activities. Nevertheless, its role and mechanism in ulcerative colitis (UC) remain unclear. In this study, the effect of hawthorn pectin (HP) against dextran sulfate sodium (DSS)-induced UC in mice and its underlying mechanism were evaluated. HP dramatically alleviated the pathological symptoms related to colitis in mice, displaying an increase in body weight and colon length and inhibition in colon damage. Importantly, HP inhibited the serum levels of inflammation-related factors including tumor necrosis factor-α, IL-1β, and IL-6 as well as decreased the number of F4/80-positive macrophages in the colon. Moreover, the expression levels of ZO-1 and occludin proteins related to intestinal permeability were increased. A significant decrease in a dose-dependent manner at the gut bacterial genus level (such as Alistipes, Colidextribacter, and Blautia) was observed after HP treatment. HP improved the metabolic pathways of gut microbiota and increased the concentrations of short-chain fatty acids in cecal contents of UC mice. Intriguingly, fecal microbiota transplantation intervention with an HP-derived microbiome notably increased the length and relieved histopathological changes of colon in UC mice. Conclusively, our study provided valuable insights into the potential of HP as a prebiotic for maintaining intestinal health and confirmed that HP could ameliorate UC in a gut microbiota-dependent manner.}, }
@article {pmid40011164, year = {2025}, author = {Hussain, M and Adeel, M and White, JC}, title = {Nano-selenium: a novel candidate for plant microbiome engineering.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2025.02.002}, pmid = {40011164}, issn = {1878-4372}, abstract = {The soil microbiome drives plant health and productivity. Recently, Sun and colleagues described a unique plant-microbe signaling cascade that enables selenium nanoparticle (SeNPs) formation by rhizosphere microbiota. These SeNPs boost maize performance by enriching plant-beneficial bacteria in a dose-dependent manner, offering novel paradigm for nano-microbiome engineering to promote sustainable food production.}, }
@article {pmid40011032, year = {2025}, author = {Romano-Zadaka, H and Yissachar, N}, title = {From microbiota to menu: predicting individual responses to dietary components.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-334712}, pmid = {40011032}, issn = {1468-3288}, }
@article {pmid40011030, year = {2025}, author = {Tseng, CH and Wong, S and Yu, J and Lee, YY and Terauchi, J and Lai, HC and Luo, JC and Kao, CY and Yu, SL and Liou, JM and Wu, DC and Hou, MC and Wu, MS and Wu, JJ and Sung, JJY and El-Omar, EM and Wu, CY}, title = {Development of live biotherapeutic products: a position statement of Asia-Pacific Microbiota Consortium.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2024-334501}, pmid = {40011030}, issn = {1468-3288}, abstract = {OBJECTIVE: Live biotherapeutic products (LBPs) are biological products composed of living micro-organisms, developed to prevent, treat, or cure diseases. Examples include cultured strains of Akkermansia muciniphila and Christensenella minuta, as well as treatments using purified Firmicutes spores for recurrent Clostridioides difficile infections. There is a need for guidelines over the increasing interest in developing LBPs. A panel of microbiome experts from Asia-Pacific countries articulates their perspectives on key considerations for LBP development.<br><br>DESIGN: Experts in microbiome research, microbiology, gastroenterology, internal medicine and biotherapeutics industry were invited to form a panel. During the 2023 Inauguration Conference of the Asia-Pacific Microbiota Consortium, an organised, iterative roundtable discussion was conducted to build expert consensus on critical issues surrounding the development of LBP.<br><br>RESULTS: The consensus statements were organised into three main aspects: (a) rationales of LBP development, (b) preclinical studies and (c) preparation for clinical studies. The panel strongly recommended to prioritise human-derived and food-sourced strains for development, with indications based on clinical need and efficacy shown in studies. Preclinical evaluation should involve thorough screening, genotyping and phenotyping, as well as comprehensive in vitro and animal studies to assess functional mechanisms and microbiological safety. Rigorous cell banking practices and genetic monitoring are essential to ensure product consistency and safety throughout the manufacturing process. Clinical trials, including postmarketing surveillance, must be carefully designed and closely monitored, with robust safety and risk management protocols in place.<br><br>CONCLUSIONS: The development of LBP should be approached with a strong emphasis on microbiological evaluation, clinical relevance, scientific mechanisms and safety at every stage. These measures are essential to ensure the safety, effectiveness and long-term success of the product.}, }
@article {pmid40010750, year = {2025}, author = {Handa, A and Slanzon, GS and Ambrosini, YM and Haines, JM}, title = {Effect of Omeprazole on Esophageal Microbiota in Dogs Detected Using a Minimally Invasive Sampling Method.}, journal = {Journal of veterinary internal medicine}, volume = {39}, number = {2}, pages = {e70029}, doi = {10.1111/jvim.70029}, pmid = {40010750}, issn = {1939-1676}, support = {/NH/NIH HHS/United States ; //George and Bernadine Converse Veterinary Medicine Endowment/ ; //Frances Edwards Memorial Research Fund/ ; K01OD030515//Upright Canine Brigade/ ; }, mesh = {Animals ; Dogs ; *Omeprazole/pharmacology/therapeutic use ; *Esophagus/microbiology ; Male ; Female ; Prospective Studies ; Microbiota/drug effects ; RNA, Ribosomal, 16S/genetics ; Longitudinal Studies ; Anti-Ulcer Agents/pharmacology/therapeutic use ; }, abstract = {BACKGROUND: Omeprazole alters the esophageal microbiome (EM) of humans and has associated effects.<br><br>OBJECTIVES: To assess the changes and subsequent recovery of the EM in awake dogs after omeprazole treatment, using the esophageal string test (EST).<br><br>ANIMALS: Ten healthy, client-owned adult dogs.<br><br>METHODS: A prospective longitudinal design was employed, where esophageal samples were initially collected using EST (day 0), involving the oral administration of an EST capsule and subsequent retrieval after 15&#x2009;min for pH-based segment identification. The dogs were then administered 1&#x2009;mg/kg of omeprazole orally, twice daily for 14&#x2009;days. Follow-up EST samplings were conducted on days 15 and 45. Samples were sequenced targeting the V3-V4 region of the 16S rRNA gene and diversity analysis along with differential sequencing (DEseq2) was performed.<br><br>RESULTS: All dogs tolerated the EST without adverse effects. The EST retrieved sufficient biofluid to characterize the EM in this group of dogs. Diversity analysis revealed no significant alterations in alpha (Observed species, Shannon and Simpson indices) and beta diversity (Bray-Curtis) across the time points after omeprazole administration.<br><br>Omeprazole therapy did not alter the EM of healthy dogs in this study. The application of EST in dogs illustrates its use as a minimally invasive tool for investigating the role of EM in esophageal health and disease in dogs.}, }
@article {pmid40010656, year = {2025}, author = {Yang, X and Zhao, Y and Liang, L and Qu, Y and Yu, C and Zhang, J and Lian, W and Zhao, Y}, title = {Protective effect of ginsenoside CK against MPTP-induced Parkinson' s disease mouse model by suppressing oxidative stress and inflammation, and modulating the gut microbiota.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {107409}, doi = {10.1016/j.micpath.2025.107409}, pmid = {40010656}, issn = {1096-1208}, abstract = {Ginsenoside CK (CK) is a metabolite of natural diol ginsenoside in the intestine, which has a unique chemical structure and pharmacological activity. CK has great potential in the treatment of neurologic dysfunction diseases. However, the therapeutic effect and potential mechanism of CK on Parkinson's disease (PD) have not been studied. Accordingly, this study used microbiome analysis to correlate behavioral, physiological and biochemical indices, and combined with WB to elucidate the mechanism of CK's improvement on PD. CK showed significant therapeutic effects on PD mice, which improved behavioral abnormalities such as spatial memory ability and motor coordination in PD mice, increased the activities of T-AOC and GSH-Px, decreased the MDA content, thus alleviating oxidative stress injury, suppressed the levels of pro-inflammatory factors IL-1β, IL-6, and TNF-α, and activated the expression of anti-inflammatory factor IL-2, which then exerted against neuroinflammation, inhibited the apoptosis of dopaminergic neurons in the substantia nigra of PD mice, increased the expression of TH, and prevented the aggregation of α-Syn in the substantia nigra. Microbiomics analysis showed that CK treatment could reshape the gut microbiota of PD mice by increasing the abundance of probiotics (Bacteroides anomalies) and decreasing the number of pathogenic bacteria (Actinomycetes). Correlation analysis showed that gut microbiota had potential correlation with behavioral, physiological and biochemical indexes. Western blot results showed that CK inhibited the expression levels of apoptotic proteins Bax, caspase-3, and Bcl-2, which revealed that CK treatment could improve the dysfunction of MPTP-induced PD mice from the molecular level. Collectively, these findings will provide a basis for further development of CK as an anti-PD drug.}, }
@article {pmid40010549, year = {2025}, author = {Wei, J and Chen, A and Huang, D and Teng, C and Cai, D and Wu, X and Wang, T and Hu, W and Huang, Z and Wang, P and Guan, X and Zheng, X and Chen, X}, title = {Gut microbiome-derived lipopolysaccharides aggravate cognitive impairment via TLR4-mediated inflammatory signaling in neonatal rats following hypoxic-ischemic brain damage.}, journal = {Brain, behavior, and immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.bbi.2025.02.029}, pmid = {40010549}, issn = {1090-2139}, abstract = {Hypoxic-ischemic brain damage (HIBD) is a leading cause of infant mortality and neurological disabilities in children. Recent evidence indicates that gut microbiota significantly contributes to the development of inflammation and cognitive impairments following brain injury. However, the mechanisms by which gut microbiota influence inflammation and cognitive function in the neonates after HIBD are not well understood. This study established a neonatal rat model of HIBD by the classic Rice-Vannucci technique to investigate gut dysbiosis following hypoxic-ischemic (HI) insult and to elucidate the causal relationship between gut dysbiosis and cognitive impairments. Our results demonstrated that HI insult resulted in significant gut microbial dysbiosis, characterized by an expansion of Enterobacteriaceae. This dysbiosis was associated with intestinal barrier damage, lipopolysaccharides (LPS) leakage, and systemic inflammation. Conversely, administration of aminoguanidine (AG) to inhibit Enterobacteriaceae overgrowth restored intestinal barrier integrity and reduced systemic inflammation. Importantly, AG treatment effectively suppressed microglial activation, neuronal damage, and cognitive impairments in the neonatal rats subjected to HI insult. Additionally, RNA sequencing analysis revealed that differentially expressed genes in both colonic and hippocampal tissues were primarily associated with inflammation and neuronal apoptosis after HI insult. Further mechanistic exploration revealed that AG treatment mitigated intestinal LPS leakage, thereby reducing the activation of the TLR4/MyD88/NF-κB signaling pathway and production of the downstream inflammatory cytokines in both the colon and hippocampus. Notably, fecal microbiota transplantation (FMT) from the HIBD rats to the antibiotic cocktail-treated recipient rats resulted in microglial activation, neuronal damage, and cognitive impairments in the recipients. However, these adverse effects were effectively mitigated in the recipient rats that received FMT from the AG-treated donors, as well as in those undergoing hippocampal TLR4 knockdown. In conclusion, our findings indicate that LPS derived from gut Enterobacteriaceae overgrowth plays a critical role in the TLR4-mediated inflammatory signaling, providing a novel microbiota-based therapeutic approach for cognitive impairments following neonatal HIBD.}, }
@article {pmid40010547, year = {2025}, author = {Freeman, LR}, title = {Interactions between sex hormones and the gut microbiome.}, journal = {Brain, behavior, and immunity}, volume = {126}, number = {}, pages = {313-314}, doi = {10.1016/j.bbi.2025.02.025}, pmid = {40010547}, issn = {1090-2139}, }
@article {pmid40010348, year = {2025}, author = {Wei, H and Suo, C and Gu, X and Shen, S and Lin, K and Zhu, C and Yan, K and Bian, Z and Chen, L and Zhang, T and Yan, R and Yang, Z and Yu, Y and Li, Z and Liu, R and He, J and He, Q and Zhong, X and Jia, W and Wong, CM and Dong, Z and Cao, J and Sun, L and Zhang, H and Gao, P}, title = {AKR1D1 suppresses liver cancer progression by promoting bile acid metabolism-mediated NK cell cytotoxicity.}, journal = {Cell metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmet.2025.01.011}, pmid = {40010348}, issn = {1932-7420}, abstract = {Bile acid metabolism and antitumor immunity are both disrupted during liver cancer progression. However, the complex regulatory relationship between them remains largely unclear. Here, we find that loss of aldo-keto reductase 1D1 (AKR1D1) promotes the accumulation of isolithocholic acid (iso-LCA) through gut microbiome dysregulation, thereby impairing the cytotoxic function of natural killer (NK) cells and leading to the accelerated development of hepatocellular carcinoma (HCC). Mechanistically, AKR1D1 deficiency leads to an increased proportion of Bacteroidetes ovatus (B. ovatus), which breaks down chenodeoxycholic acid (CDCA) into iso-LCA. Moreover, accumulated iso-LCA impairs the antitumor activity of hepatic NK cells in a phosphorylated-CREB1 (p-CREB1)-dependent manner. The potassium-sparing diuretic spironolactone treatment significantly enhances the inhibitory effect of anti-PD1 antibody on HCC progression by targeting iso-LCA-mediated tumor immune escape. Taken together, our results uncover a previously unappreciated link between AKR1D1 and HCC and suggest that targeting iso-LCA produced by B. ovatus might be a promising strategy to activate NK cell cytotoxicity to treat HCC.}, }
@article {pmid40010245, year = {2025}, author = {Proaño-Cuenca, F and Millican, MD and Buczkowski, E and Chou, MY and Koch, PL}, title = {Fungal and bacterial community composition and assemblage in managed and unmanaged urban landscapes in Wisconsin.}, journal = {The Science of the total environment}, volume = {969}, number = {}, pages = {178873}, doi = {10.1016/j.scitotenv.2025.178873}, pmid = {40010245}, issn = {1879-1026}, abstract = {Microbial communities play crucial roles in ecosystem functioning, yet their diversity and assembly in urban turfgrass systems remain underexplored. In 2017, microbial communities within 48 samples from managed turfgrass (home lawns, golf course fairways, and putting greens) and an unmanaged grass mixture in Madison, WI, USA were analyzed across leaf, thatch, rhizoplane, and rhizosphere habitats Intensive management, particularly in nitrogen-rich, sand-based putting greens, reduced fungal richness and diversity, whereas bacterial diversity patterns varied. Beta diversity analyses revealed distinct clustering: fungal communities differed most in unmanaged systems, while bacterial communities clustered within managed systems. Functional profiling demonstrated that bacterial communities maintained metabolic stability despite taxonomic shifts, while fungal communities showed dynamic functional responses to management. Furthermore, management practices also impacted microbial community assembly. Bacterial communities were predominantly shaped by neutral, stochastic processes, while fungal communities were more sensitive to management, showing deterministic, niche-based assembly and compositional shifts. These findings underscore the contrasting impacts of management on microbial communities and highlight the importance of sustainable turfgrass practices that balance plant health with microbial ecosystem functions. By linking microbial assembly processes to functional outcomes, this study provides insights for optimizing urban landscapes to enhance soil health and ecosystem resilience.}, }
@article {pmid40010026, year = {2025}, author = {Guan, Y and Chen, Y and Lin, R and Mo, T and Li, S and Cao, Y and Yin, T and Diao, L and Li, Y}, title = {Endometriosis: A new perspective on epigenetics and oxidative stress.}, journal = {Journal of reproductive immunology}, volume = {169}, number = {}, pages = {104462}, doi = {10.1016/j.jri.2025.104462}, pmid = {40010026}, issn = {1872-7603}, abstract = {As a complex chronic gynecological disorder characterized by multifaceted etiology involving genetics, environment, immunity and inflammation, endometriosis (EM) has long been a significant concern for women of reproductive age worldwide. This review aimed to comprehensively examine the interplay between epigenetics and oxidative stress (OS) in the pathogenesis of EM. Through the integration of cutting-edge research, the response of OS signals to epigenetic modifications was explored. The microbiome exerts an influence on this causal regulatory relationship, and these mechanisms collectively contribute to the pathophysiology of EM. Specifically, this article highlighted the roles of epigenetics and OS in EM and underscored the importance of the microbiome as a regulatory link. A discussion was also held on the future directions of biomarkers and precision medicine, including the application prospects of epigenetic and OS markers in the diagnosis and treatment decision-making of EM, and innovations in therapeutic strategies like targeting epigenetic modifications and antioxidant therapies. Moreover, this review emphasized the potential of multi-omics integrated analysis to deepen the understanding of the disease, guide future therapeutic strategies and promote personalized medicine.}, }
@article {pmid40009954, year = {2025}, author = {Lan, Q and Wu, X and Liu, Q and Liang, Q and He, X and Zhu, B}, title = {Integrating temporal dynamics of both microbial taxonomic and functional characteristics as a tool for forensic time since deposition estimation.}, journal = {Forensic science international}, volume = {369}, number = {}, pages = {112406}, doi = {10.1016/j.forsciint.2025.112406}, pmid = {40009954}, issn = {1872-6283}, abstract = {Predicting the time since deposition (TsD) of body fluid stain at a crime scene is highly valuable in forensic investigation, as it can connect a DNA-identified stain donor to a crime or estimate the post-mortem interval in forensic case involving cadaver. Previous study has demonstrated the applicability of microbial taxa for TsD prediction. In this proof-of-concept study, we explored the combined use of taxonomic and functional characteristics in human saliva microbiome for TsD prediction. We investigated the potential correlations between the temporal dynamics in microbial communities and the TsD of saliva stains, utilizing the relative abundance of microbial genera, amplicon sequence variants (AsVs), and the metabolic function pathway profiles. The results revealed that changes in the metabolic function pathway profiles of microbial communities could contribute to TsD estimation of the aged saliva stains. We developed ensemble models with multiple heterogeneous algorithms, also combined microbial species and metabolic function pathway profiles for TsD estimation. The TsD prediction model, developed using the relative abundance of the top 50 microbial genera and metabolic functional pathway profiles with the xgboost algorithm, achieved high accuracy (R[2] = 0.76, mean absolute error = 6.28 days) in a 60-day deposition. Besides, we further interpreted the model and identified potential biomarkers for TsD estimation of saliva stains. The current study provided the first evidence to explore the potential of using multiple data modalities for predicting the TsD of aged saliva stains, offering valuable insight for forensic investigation.}, }
@article {pmid40009543, year = {2025}, author = {Bennett, AJ and Suski, CD and O'Keefe, JM}, title = {Molecular epidemiology of Eimeria spp. parasites and the faecal microbiome of Indiana bats (Myotis sodalis): a non-invasive, multiplex metabarcode survey of an endangered species.}, journal = {Microbial genomics}, volume = {11}, number = {2}, pages = {}, doi = {10.1099/mgen.0.001358}, pmid = {40009543}, issn = {2057-5858}, mesh = {Animals ; *Eimeria/genetics/isolation &amp; purification/classification ; *Feces/microbiology/parasitology ; *Chiroptera/microbiology/parasitology ; *Endangered Species ; *Molecular Epidemiology ; Microbiota/genetics ; Coccidiosis/epidemiology/veterinary/microbiology ; Phylogeny ; Clostridium/genetics/isolation &amp; purification/classification ; }, abstract = {Assessing individual and population health in endangered wildlife poses unique challenges due to the lack of an adequate baseline and ethical constraints on invasive sampling. For endangered bats, minimally invasive samples like guano can often be the ethical and technical limit for studies of pathogens and the microbiome. In this study, we use multiplex metabarcode sequencing to describe the faecal microbiome and parasites of 56 Indiana bats (Myotis sodalis). We show evidence of a high prevalence of Eimeria spp. protozoan parasite and characterize associations between infection and changes to the faecal microbiome. We identify a strong and significant enrichment of Clostridium species in Eimeria-positive bats, including isolates related to Clostridium perfringens.}, }
@article {pmid40009444, year = {2025}, author = {Lauder, E and Kiledal, EA and Maneix, L and Furnholm, T and Santibanez, A and Zhao, D and Sun, Y and Dick, GJ and Reddy, P}, title = {Novel Regulators of GVHD Revealed Through Microbiome and Metabolome Patterns Across Distinct Intestinal Regions.}, journal = {Blood}, volume = {}, number = {}, pages = {}, doi = {10.1182/blood.2024025924}, pmid = {40009444}, issn = {1528-0020}, abstract = {Microbial dysbiosis and metabolite changes in the gastro-intestinal (GI) tract have been linked to pathogenesis and severity of many diseases, including graft-versus-host disease (GVHD), the major complication of allogeneic hematopoietic stem cell transplantation (HCT). However, published studies have only considered the microbiome and metabolome of excreted stool and do not provide insight into the variability of microbial community and metabolite composition throughout the GI tract or the unique temporal dynamics associated with different gut locations. Because such geographical variations are known to influence disease processes, we utilized a multi-omics approach to characterize the microbiome and metabolite profiles of gut contents from different intestinal regions in well-characterized mouse models of GVHD. Our analysis validated analyses from excreted stool, but importantly, uncovered new biological insights from the microbial and metabolite changes between syngeneic and allogeneic hosts that varied by GI location and time after transplantation. Our integrated analysis confirmed the involvement of known metabolic pathways, including SCFA synthesis and bile acid metabolism, and identified additional functional genes, pathways, and metabolites, such as amino acids, fatty acids, and sphingolipids, linked to GI GVHD. Finally, we validated a biological relevance for one such newly identified microbial metabolite, phenyl lactate, that heretofore had not been linked to GI GVHD. Thus, our analysis of the geographic variability in the intestinal microbiome and metabolome offers new insights into GI GVHD pathogenesis and potential for novel therapeutics.}, }
@article {pmid40009378, year = {2025}, author = {Nickel, B and Moynihan, R and Gram, EG and Copp, T and Taba, M and Shih, P and Heiss, R and Gao, M and Zadro, JR}, title = {Social Media Posts About Medical Tests With Potential for Overdiagnosis.}, journal = {JAMA network open}, volume = {8}, number = {2}, pages = {e2461940}, doi = {10.1001/jamanetworkopen.2024.61940}, pmid = {40009378}, issn = {2574-3805}, mesh = {Humans ; *Social Media/statistics &amp; numerical data ; Cross-Sectional Studies ; Overdiagnosis/statistics &amp; numerical data ; Medical Overuse/statistics &amp; numerical data/prevention &amp; control ; Female ; }, abstract = {IMPORTANCE: Social media is an influential source of medical information, but little is known about how posts discuss medical tests that carry potential for overdiagnosis or overuse.<br><br>OBJECTIVE: To investigate how social media posts discuss 5 popular medical tests: full-body magnetic resonance imaging, the multicancer early detection test, and tests for antimullerian hormone, gut microbiome, and testosterone.<br><br>This cross-sectional study assessed posts on Instagram and TikTok between April 30, 2015, and January 23, 2024, that discussed full-body magnetic resonance imaging, the multicancer early detection test, and tests for antimullerian hormone, gut microbiome, and testosterone. Using keywords on newly created accounts, posts were searched and screened until 100 posts for each test on each platform were identified (n&#x2009;=&#x2009;1000). Posts were excluded if they did not discuss 1 of the 5 tests or were not in English or if the account holders had fewer than 1000 followers.<br><br>MAIN OUTCOMES AND MEASURES: The main outcome was information about benefits, harms, and overall tone discussed in the post. All outcomes were summarized descriptively. Logistic regression was used to assess whether the use of evidence or the account holder being a physician or having financial interests influenced how tests were discussed.<br><br>RESULTS: A total of 982 posts from account holders with a combined 194&#x202f;200&#x202f;000 followers were analyzed. Across all tests, benefits were mentioned in 855 posts (87.1%) and harms in 144 (14.7%), with 60 (6.1%) mentioning overdiagnosis or overuse. Overall, 823 posts (83.8%) had a promotional (vs neutral or negative) tone. Evidence was explicitly used in 63 posts (6.4%), personal anecdotes were used in 333 (33.9%), 498 posts (50.7%) encouraged viewers to take action and get the test, and 668 account holders (68.0%) had financial interests. Posts from physicians were more likely to mention harms (odds ratio, 4.49; 95% CI, 2.85-7.06) and less likely to have an overall promotional tone (odds ratio, 0.53; 95% CI, 0.35-0.80).<br><br>CONCLUSIONS AND RELEVANCE: In this cross-sectional study of social media posts about 5 popular medical tests, most posts were misleading or failed to mention important harms, including overdiagnosis or overuse. These data demonstrate a need for stronger regulation of misleading medical information on social media.}, }
@article {pmid40009328, year = {2025}, author = {Mivehchi, H and Eskandari-Yaghbastlo, A and Pour Bahrami, P and Elhami, A and Faghihinia, F and Nejati, ST and Kazemi, KS and Nabi Afjadi, M}, title = {Exploring the role of oral bacteria in oral cancer: a narrative review.}, journal = {Discover oncology}, volume = {16}, number = {1}, pages = {242}, pmid = {40009328}, issn = {2730-6011}, abstract = {A growing body of research indicates that a wide range of cancer types may correlate with human microbiome components. On the other hand, little is known about the potential contribution of the oral microbiota to oral cancer. However, some oral microbiome components can stimulate different tumorigenic processes associated with the development of cancer. In this line, two prevalent oral infections, Porphyromonas gingivalis, and Fusobacterium nucleatum can increase tumor growth. The microbiome can impact the course of the illness through direct interactions with the human body and major modifications to the toxicity and responsiveness to different kinds of cancer therapy. Recent research has demonstrated a relationship between specific phylogenetic groupings and the results of immunotherapy treatment for particular tumor types. Conversely, there has been a recent upsurge in interest in the possibility of using microbes to treat cancer. At the moment, some species, such as Salmonella typhimurium and Clostridium spp., are being explored as possible cancer treatment vectors. Thus, understanding these microbial interactions highlights the importance of maintaining a healthy oral microbiome in preventing oral cancers. From this perspective, this review will discuss the role of the microbiome on oral cancers and their possible application in oral cancer treatment/improvement.}, }
@article {pmid40009223, year = {2025}, author = {Abida, O and Ramiro, R and Bahloul, E and Frikha, R and Charfi, S and Turki, H and Gonçalves, CP and Masmoudi, H}, title = {Distinct anti-microbial peptides expression patterns and microbiome profiles in skin of Tunisian endemic Pemphigus foliaceus patients.}, journal = {Archives of dermatological research}, volume = {317}, number = {1}, pages = {497}, pmid = {40009223}, issn = {1432-069X}, mesh = {Humans ; *Skin/microbiology/pathology ; *Microbiota ; Female ; *Pemphigus/microbiology/diagnosis ; Male ; Middle Aged ; *S100 Calcium Binding Protein A7/metabolism ; *beta-Defensins/metabolism ; Adult ; *Antimicrobial Peptides/metabolism ; *Cathelicidins ; Tunisia ; Aged ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Ribonucleases/metabolism ; Antimicrobial Cationic Peptides/metabolism ; }, abstract = {Pemphigus foliaceus (PF) is a multifactorial skin disease. Substantial evidence for microbiota dysbiosis in skin disorders was gradually revealed. In PF patients' skin lesions, we characterized the profile of microbial communities and the expression of microbial peptides. Using real-time reverse transcriptase PCR and immunohistochemistry, skin lesions were analyzed for gene and protein expression of human β-defensin (hBD) 1, 2, and 3, cathelicidin (LL-37), RNAse-7, and psoriasin. Bacterial 16S rRNA gene sequencing was used for assessing skin microbial communities in 15 samples from PF patients' lesioned skin and 11 PF patients' non-lesioned skin. Gene expression of hBD 2 and 3 and psoriasin were significantly downregulated in skin samples from remittent patients compared to chronic or de novo diagnosed patients. Protein expression of hBD 2, Psoriasin, and LL-37 was increased in skin from de novo patients compared to skin from healthy donors showing markedly different distribution patterns. The skin microbial analysis revealed a substantial difference in microbiome diversity between lesioned and non-lesioned skin of de novo PF patients and, non-lesioned skin of remittent patients. In addition, microbiome diversity within samples of lesioned skin from de novo PF patients showed lower diversity with a lower abundance of specific bacterial genera, namely Dermabacter, Psychrobacter, and Bradyrhizobium. Thus, there is a noticeable over-representation of Staphylococcus and decreased richness in the bacterial communities of PF-active skin lesions. Our data supports the hypothesis that active skin lesions in PF patients exhibit alterations in skin bacterial diversity interlinked with increased expression of AMPs.}, }
@article {pmid40008691, year = {2025}, author = {Duarte, ER and Lima, SM and Freitas, CES and Maia, HAR and Matins-Júnior, VS and Abrão, FO and Alves, JMS and Santos, VL and Geraseev, LC and Cota, J}, title = {Yeasts isolates from bovine rumen can improve the in vitro digestibility of Urochloa decumbens.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {84}, number = {}, pages = {e288025}, doi = {10.1590/1519-6984.288025}, pmid = {40008691}, issn = {1678-4375}, mesh = {Animals ; *Rumen/microbiology/metabolism ; Cattle ; *Digestion/physiology ; *Animal Feed ; Yeasts/metabolism/isolation &amp; purification/classification ; }, abstract = {Commercial yeast has been frequently employed to improve the digestibility of ruminant diets, albeit these microorganisms are not indigenous to the rumen microbiome. In this investigation, our aim was to assess the in vitro digestibility of Urochloa decumbens hay (UDH) with the incorporation of two selected yeast strains isolated of ruminal fluid of Zebu cattle. Rumen fluid was collected at the onset, midpoint, and final of the dry period in a semiarid region Brazil. UDH samples were obtained from the same region. Within simulated ruminal chambers, we included McDougall buffer solution, ruminal fluid, Ankon F-57 bags containing UDH samples. Sabouraud broth (control), V62 yeast (Pichia kudriavzevii), V5 yeast (Rhodotorula mucilaginosa), or a combination thereof (mixture) were evaluated as inoculant to the ruminal fluid. The incorporation of V5, the combination of both isolates, and V5 alone resulted in significantly elevated in vitro dry matter digestibility of UDH for ruminal fluid collected at the initial, intermediate, and final stages of the dry season, respectively. Moreover, the yeast isolates demonstrated resilience to the in vitro acid digestion process, indicating their potential utility in the formulation of probiotics or microbial supplements for ruminants raised in tropical pastures during dry season.}, }
@article {pmid40008244, year = {2025}, author = {Xu, LL and McIlroy, SE and Ni, Y and Guibert, I and Chen, J and Rocha, U and Baker, DM and Panagiotou, G}, title = {Chemical pollution drives taxonomic and functional shifts in marine sediment microbiome, influencing benthic metazoans.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycae141}, pmid = {40008244}, issn = {2730-6151}, abstract = {Microbial communities in marine sediments contribute significantly to the overall health and resiliency of marine ecosystems. However, increased human disturbance undermines biodiversity and, hence, natural functionality provided by marine sediments. Here, through a deep shotgun metagenomics sequencing of the sediment microbiome and COI metabarcoding of benthic metazoans, we demonstrate that >50% of the microorganisms' and metazoan's taxonomic variation can be explained by specific chemical pollution indices. Interestingly, there was a significant correlation between the similarity in microbiome communities' taxonomical and functional attributes and the similarity of benthic metazoans community composition. Furthermore, mediation analysis was conducted to evaluate the microbiome-mediated indirect effect, suggesting that microbial species and functions accounted for 36% and 26%, respectively, of the total effect of pollution on the benthic metazoans. Our study introduces a multi-level perspective for future studies in urbanized coastal areas to explore marine ecosystems, revealing the impact of pollution stress on microbiome communities and their critical biogeochemical functions, which in turn may influence macrofaunal composition.}, }
@article {pmid40008167, year = {2025}, author = {Barbeta, E and López-Aladid, R and Bueno-Freire, L and Llonch, B and Palomeque, A and Motos, A and Mellado-Artigas, R and Zattera, L and Ferrando, C and Soler, A and Fernández-Barat, L and Torres, A}, title = {Biological effects of pulmonary, blood and gut microbiome alterations in patients with acute respiratory distress syndrome.}, journal = {ERJ open research}, volume = {11}, number = {1}, pages = {}, pmid = {40008167}, issn = {2312-0541}, abstract = {There is an overlap between the respiratory, blood and gut microbiomes in patients with acute respiratory distress syndrome. Specific taxa in the lungs and blood are associated with an inflammatory response. https://bit.ly/3TdkHd7.}, }
@article {pmid40008156, year = {2025}, author = {Raposo, PJF and Nguyen, AT and Schmidt, EKA and Espin, AT and Fenrich, KK and Bennett, DJ and Fouad, K}, title = {No Beneficial Effects of the Alfasigma VSL#3 Probiotic Treatment After Cervical Spinal Cord Injury in Rats.}, journal = {Topics in spinal cord injury rehabilitation}, volume = {31}, number = {1}, pages = {1-16}, pmid = {40008156}, issn = {1945-5763}, mesh = {Animals ; *Probiotics/therapeutic use/pharmacology ; *Spinal Cord Injuries/complications ; Rats ; *Gastrointestinal Microbiome/drug effects ; Recovery of Function ; Female ; Rats, Sprague-Dawley ; Disease Models, Animal ; Cervical Cord/injuries ; Dysbiosis ; }, abstract = {BACKGROUND: The bidirectional communication between the gastrointestinal tract and the central nervous system appears to be linked to the intestinal microbiome. Research has shown that spinal cord injury (SCI) can disrupt the gut microbiome, leading to gut dysbiosis. These changes can have several negative impacts, such as exacerbated systemic inflammation and susceptibility to infection. Probiotics administered to mice with SCI have been shown to ameliorate gut dysbiosis, confer neuroprotection, and improve locomotor recovery. However, probiotics have also produced conflicting results, making potential claims regarding the application of probiotics as a therapeutic supplement ambiguous.<br><br>OBJECTIVES: This study aimed to investigate the effects of a commercially available probiotic on recovery in a rat model of cervical SCI.<br><br>METHODS: Rats with cervical contusion SCI received probiotics over 7 days immediately after injury, and their recovery in motor, sensory, and cognitive tasks was compared to that of untreated animals.<br><br>RESULTS: Compared with a control group, the oral administration of probiotics influenced neither motor nor cognitive outcomes. We did observe a significantly different lesion size between the two groups, where the probiotic group had less spared tissue, despite a lack of differences in functional outcomes. In addition, probiotic treatment delayed gut microbiome composition recovery to baseline levels for up to 35 days postinjury (DPI). We found significantly higher proportions of Lactobacillus in the fecal matter of SCI-vehicle rats at 35 DPI, whereas Streptococcus was higher in SCI-probiotics fecal matter at 14 and 35 DPI, and Bacillales was higher in the latter group at 35 DPI.<br><br>CONCLUSION: Taken together, our results do not support the application of the utilized probiotic cocktail as a dietary supplement for the treatment of cervical SCI-induced gut dysbiosis and secondary complications.}, }
@article {pmid40008084, year = {2025}, author = {Zheng, J and Huang, Y and Zhang, L and Liu, T and Zou, Y and He, L and Guo, S}, title = {Role of the Gut-Lung Microbiome Axis in Airway Inflammation in OVA-Challenged Mice and the Effect of Azithromycin.}, journal = {Journal of inflammation research}, volume = {18}, number = {}, pages = {2661-2676}, pmid = {40008084}, issn = {1178-7031}, abstract = {OBJECTIVE: This study aimed to investigate the role of the gut-lung microbiome axis in airway inflammation in asthma and to evaluate the effect of azithromycin on this axis, with a focus on the potential mechanism by which azithromycin reduces allergic airway inflammation.<br><br>METHODS: Haematoxylin and eosin (H&amp;E) and periodic acid-Schiff (PAS) staining were used to assess pathological changes in the lung tissues of asthmatic mice. Leukocyte cell types in bronchoalveolar lavage fluid (BALF) samples were quantified following Wright-Giemsa staining. Total IgE, OVA-specific IgE, IL-4, IL-6, and IL-17A levels in BALF and total IgE in serum were measured by ELISA. The respiratory and gut microbiota were analysed using 16S rRNA gene sequencing and subsequent taxonomic analysis.<br><br>RESULTS: OVA-challenged asthmatic mice with gut microbiota dysbiosis exhibited alterations in the respiratory microbiota, resulting in further aggravation of airway inflammation. Following faecal microbiota transplantation (FMT) to restore gut microbiota, respiratory microbiota dysbiosis was partially improved, and airway inflammation was significantly alleviated. Furthermore, azithromycin reduced airway inflammation in asthmatic mice, particularly non-eosinophilic inflammation, for which low-dose azithromycin combined with budesonide proved more effective. Azithromycin significantly enhanced the diversity and microbial composition of the gut microbiota and also affected the respiratory microbiota. At the phylum level, azithromycin decreased the abundance of Proteobacteria in the gut microbiota. At the genus level, azithromycin reduced the abundance of Pseudomonas in the respiratory microbiota.<br><br>CONCLUSION: The gut-lung microbiome axis plays a crucial role in airway inflammation in asthma. Azithromycin may reduce airway inflammation in asthma through modulation of the gut-lung microbiome axis.}, }
@article {pmid40008040, year = {2025}, author = {Ma, Y and Wang, H and Kang, Y and Wen, T}, title = {Small molecule metabolites drive plant rhizosphere microbial community assembly patterns.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1503537}, pmid = {40008040}, issn = {1664-302X}, abstract = {The assembly of rhizosphere microbial communities is essential for maintaining plant health, yet it is influenced by a wide range of biotic and abiotic factors. The key drivers shaping the composition of these communities, however, remain poorly understood. In this study, we analyzed 108 plant samples and evaluated root traits, plant growth characteristics, soil enzyme activities, rhizosphere metabolites, and soil chemical properties to identify the primary determinants of rhizosphere community assembly. Across 36 soil samples, we obtained 969,634 high-quality sequences, clustering into 6,284 ASVs predominantly classified into Proteobacteria (57.99%), Actinobacteria (30%), and Bacteroidetes (5.13%). Our findings revealed that rhizosphere metabolites accounted for more variance in microbial community composition compared to chemical properties (ANOVA, F = 1.53, p = 0.04), enzyme activities, or root traits (ANOVA, F = 1.04, p = 0.001). Seven small molecule metabolites, including glycerol, sorbitol, phytol, and alpha-ketoglutaric acid, were significantly correlated with βNTI, underscoring their role as critical drivers of microbial community assembly. The genus Rhizobium, significantly associated with βNTI (R = 0.25, p = 0.009), emerged as a keystone taxon shaping community structure. Soil culture experiments further validated that small molecule metabolites can modulate microbial community assembly. The ST treatment, enriched with these metabolites, produced 1,032,205 high-quality sequences and exhibited significant shifts in community composition (Adonis, p = 0.001, R = 0.463), with Rhizobium showing higher abundance compared to the control (CK). Variable selection (βNTI >2) drove phylogenetic turnover in ST, while stochastic processes (|βNTI| < 2) dominated in CK. This study provides quantitative insights into the role of rhizosphere metabolites in shaping microbial community assembly and highlights their potential for targeted modulation of rhizosphere microbiomes.}, }
@article {pmid40007939, year = {2025}, author = {Do, KH and Boo, S and You, R and Kim, S and Kim, S and Seo, KW and Kang, MS and Lee, WK}, title = {Preventive effects of Weissella cibaria CMU on the progression of periodontitis in a rat model.}, journal = {Journal of oral microbiology}, volume = {17}, number = {1}, pages = {2469895}, pmid = {40007939}, issn = {2000-2297}, abstract = {BACKGROUND: Periodontitis is a widespread chronic inflammatory disease impacting 20-50% of the global population.<br><br>METHODS: This study evaluated the effects of Weissella cibaria CMU (CMU) on preventing the progression of periodontitis in a rat model. Periodontitis was induced by injecting lipopolysaccharide into the palatal gingiva around the first and second maxillary molars. CMU was then administered at three concentrations (low: 2&#x2009;&#xd7;&#x2009;10[7] CFU/rat/day; mid: 2&#x2009;&#xd7;&#x2009;10[8] CFU/rat/day; high: 2&#x2009;&#xd7;&#x2009;10[9] CFU/rat/day) for 14&#x2009;days to assess its ability to prevent further periodontal damage.<br><br>RESULTS: The administration of CMU significantly improved gingivitis and plaque indices in a dose-dependent manner. Macroscopic analysis and micro-computed tomography showed a dose-dependent reduction in alveolar bone loss in the CMU groups. Although histopathological analysis indicated a decrease in bone loss, statistical significance was not achieved in the high-dose group. Pro-inflammatory mediators such as TNF-&#x3b1;, IL-6, MMP-1, and MMP-9 were suppressed in a dose-dependent manner in the CMU groups. Additionally, mid- and high-dose CMU increased the relative abundance of Weissella in the oral microbiome.<br><br>CONCLUSIONS: CMU can influence the oral microbiome, reduce inflammatory mediators, and alleviate histological changes in periodontal tissue, highlighting its potential as a probiotic strain for preventing periodontitis.}, }
@article {pmid40007817, year = {2025}, author = {Hoefer, KC and Weber, LT and Jazmati, N and Noack, MJ and Barbe, AG and Graf, I}, title = {Chronic Kidney Disease With Related Oral Health Problems and Alterations in the Tongue Microbiome Illustrated by a 15-Year-Old Girl: A Case Report.}, journal = {Case reports in pediatrics}, volume = {2025}, number = {}, pages = {1018472}, pmid = {40007817}, issn = {2090-6803}, abstract = {Chronic kidney disease (CKD) is characterised by a gradual loss of kidney function over time and is often linked to oral health issues. This case illustrates typical conditions in young CKD patients based on a 15-year-old girl with CKD stage 4 and methylmalonic aciduria, severe gingivitis and hyperplasia of the gingiva, and a need for orthodontic treatment. Oral hygiene interventions, homecare instructions and deep cleaning under antibiotic shielding were necessary to improve the patient's oral health. The immediate worsening of oral health status after extending the interval between regular prophylaxis appointments highlights the need for intensive prevention in young CKD patients to control oral health disorders. This report aims to demonstrate burden-of-care-reducing oral prophylaxis options for patients suffering from severe CKD with oral manifestations. Trial Registration: German Registry of Clinical Trials: DRKS00010580.}, }
@article {pmid40007795, year = {2025}, author = {Li, J and Shi, Y and Hu, L and He, W and Li, Y}, title = {Assessing Gut Microbiome Alterations in Children With Allergic Rhinitis: Associations With Allergen-Specific IgE Levels and Sensitization Patterns.}, journal = {Journal of asthma and allergy}, volume = {18}, number = {}, pages = {269-281}, pmid = {40007795}, issn = {1178-6965}, abstract = {BACKGROUND: The relationship between gut microbiota composition and allergen exposure in children with allergic rhinitis (AR) remains insufficiently explored, particularly concerning variations in gut microbiota at different allergen-specific IgE (sIgE) levels and the distinction between monosensitization and polysensitization to allergens.<br><br>METHODS: We employed metagenomic shotgun sequencing to compare the fecal microbiota of 50&#xa0;healthy controls (HC) to 88 children with AR induced by house dust mites (HDM-AR). We further examined differences in gut microbiota among HDM-AR subgroups with extremely high house dust mite-sIgE (EH-HDM), high HDM-sIgE (H-HDM), as well as between monosensitized (mono-HDM) and polysensitized (poly-HDM) individuals.<br><br>RESULTS: While no significant differences in overall gut microbiome diversity were observed between the HC and HDM-AR groups, a notable increase in the relative abundance of Streptococcus sanguinis within the genus was identified in children with AR. Further analysis revealed a significant enrichment of the Streptococcus genus in the EH-HDM group, particularly highlighting an increased relative abundance of the Streptococcus salivarius. Functional gene analysis via KEGG pathways indicated substantial enrichment in the salivary secretion pathway. Additionally, in comparisons among the HC, mono-HDM, and poly-HDM groups, Streptococcus salivarius emerged as the key differential species, showing a marked increase in the mono-HDM group.<br><br>CONCLUSION: Our study suggests that specific bacterial strains, particularly Streptococcus salivarius, may be potential biomarkers for assessing varying degrees and patterns of HDM sensitization. These findings open the avenues for developing targeted interventions aimed at mitigating the pathophysiology of AR.}, }
@article {pmid40007613, year = {2025}, author = {Zhang, J and Li, L and Zhang, M and Fang, J and Xu, Z and Zheng, Y and Lin, Z and Pan, M}, title = {Distinct vaginal microbiome and metabolome profiles in women with preterm delivery following cervical cerclage.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1444028}, pmid = {40007613}, issn = {2235-2988}, mesh = {Humans ; Female ; *Vagina/microbiology ; Pregnancy ; *Metabolome ; *Premature Birth ; Adult ; *Microbiota ; *Cerclage, Cervical ; Bacteria/classification/metabolism/isolation &amp; purification ; Tandem Mass Spectrometry ; Young Adult ; Metabolomics/methods ; Neutrophils/metabolism ; Chromatography, Liquid ; }, abstract = {Preterm birth (PTB) is a major cause of infant morbidity and mortality. The aim of this study was to investigate the effect of vaginal microbiota and metabolites on the outcome of pregnant women. In this study, a total of 127 pregnant women provided written informed consent prior to enrollment in accordance with the approved institutional guidelines, but only 45 pregnancies met the experimental requirements, and then blood and cervical vaginal fluid (CVF) samples were collected before delivery (at the second week after cervical cerclage). Pregnant women with PTB exhibited high white blood cell and neutrophil contents, high neutrophil-to-lymphocyte ratio (NLR), and high systemic inflammation response index (SIRI) in the blood. Vaginal microbiome revealed that the proportion of beneficial bacteria (including Lactobacillus, [Ruminococcus] gnavus group, and Megamonas) significantly decreased in the PTB group, and the proportion of harmful bacteria (including Desulfovibrionaceae, Helicobacter, and Gardnerella) significantly increased, which is strongly related to the biochemical parameters of blood (white blood cells, neutrophils, NLR, and SIRI). In addition, vaginal metabolomics-based liquid chromatography-Orbitrap-tandem mass spectrometry (LC-Orbitrap-MS/MS) found that the alteration in vaginal metabolites in pregnant women with PTB is involved in starch and sucrose metabolism; arginine and praline metabolism; galactose metabolism; purine metabolism; arginine metabolism; tryptophan metabolism and N-glycan biosynthesis; cysteine and methionine metabolism; taurine and hypotaurine metabolism; amino acid metabolism; propanoate metabolism; valine, leucine, and isoleucine biosynthesis; glycine, serine, and threonine metabolism; and steroid hormone biosynthesis. These results elaborated that distinct vaginal microbiome and metabolome profiles in women with preterm delivery following cervical cerclage provide valuable information for establishing the prediction models for PTB.}, }
@article {pmid40007610, year = {2025}, author = {Cui, Z and Wang, P and Gao, W}, title = {Microbial dysbiosis in periodontitis and peri-implantitis: pathogenesis, immune responses, and therapeutic.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1517154}, pmid = {40007610}, issn = {2235-2988}, mesh = {*Peri-Implantitis/microbiology/immunology ; *Dysbiosis/microbiology ; Humans ; *Periodontitis/microbiology/immunology/therapy ; *Microbiota ; Biofilms/growth &amp; development ; Bacteria/classification/isolation &amp; purification/immunology ; }, abstract = {The oral microbiome comprises over 700 distinct species, forming complex biofilms essential for maintaining oral and systemic health. When the microbial homeostasis in the periodontium is disrupted, pathogens within the biofilm can cause periodontitis and peri-implantitis, inducing host immune responses. Understanding the role of microbial communities and the immune mechanisms in oral health and disease is crucial for developing improved preventive, diagnostic and therapeutic strategies. However, many questions remain about how changes in bacterial populations contribute to the development and progression of these conditions. An electronic and manual literature search was conducted using PubMed, Excerpta Medica, Frontiers Reports and the Wiley Online Library databases for relevant articles. Data from these publications were extracted and the overall findings were summarized in a narrative manner. The variations in microbial communities and immune responses of periodontitis and peri-implantitis are explored. Dysbiosis of the subgingival microbiome-characterized by an increase in pathogenic bacteria such as Porphyromonas gingivalis, Tannerella forsythia, and Aggregatibacter actinomycetemcomitans-plays a pivotal role in the initiation and progression of periodontitis. As for peri-implantitis, alterations include a higher abundance of opportunistic pathogens and reduced microbial diversity around implants. Moreover, oral dysbiosis potentially influencing systemic health through immune-mediated pathways. Regional immunity of periodontium involving neutrophils, T helper cells-17, and immune-related cytokines is crucial for maintaining periodontal homeostasis and responding to microbial imbalances. Additionally, the impact of non-mechanical treatments-such as probiotics and laser therapy-on the oral microbiome is discussed, demonstrating their potential in managing microbial dysbiosis. These findings underscore that bacterial dysbiosis is a central factor in the development of periodontitis and peri-implantitis. Maintaining microbial balance is essential for preventing these diseases, and interventions targeting the microbiome could enhance treatment outcomes. Strategies focusing on controlling pathogenic bacteria, modulating immune responses, and promoting tissue regeneration are key to restoring periodontal stability. Further research is needed to clarify the mechanisms underlying the transition from peri-implant mucositis to peri-implantitis and to optimize prevention and treatment approaches, considering the complex interactions between the microbiome and host immunity.}, }
@article {pmid40007609, year = {2025}, author = {Oh, S and Park, KU}, title = {Human reference microbiome profiles of different body habitats in healthy individuals.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1478136}, pmid = {40007609}, issn = {2235-2988}, mesh = {Humans ; *Saliva/microbiology ; *Feces/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Adult ; *Healthy Volunteers ; Male ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; Middle Aged ; Young Adult ; Reference Values ; Blood/microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; }, abstract = {INTRODUCTION: This study aimed to establish the human reference microbiome profiles in blood, saliva, and stool of healthy individuals, serving as reference values to identify microbiome alterations in human disease.<br><br>METHODS: The study population consisted of a reference group of healthy adults and a second group consisting of adults with periodontal disease (PD). Blood, saliva, and stool samples were subjected to 16S rRNA sequencing. Reference intervals of alpha diversity indices were calculated. To reduce the effects of inherent limitations of microbiome data, the taxonomic profiles of the reference group were estimated as log-scaled fold change (logFC) in the abundance of microorganisms between two habitats within the subjects.<br><br>RESULTS: For stool and saliva microbiomes, differences in the abundances of Firmicutes, Patescibacteria, and Verrucomicrobia distinguished healthy from PD subjects (95% confidence interval (CI) of logFC: [-0.18, 0.31], [-1.19, -0.34], and [-3.68, -2.90], respectively). Differences in the abundances of Cyanobacteria, Fusobacteria, and Tenericutes in stool and blood microbiome of healthy subjects fell within 95% CI of logFC [-0.38, 0.61], [-4.14, -3.01], and [1.66, 2.77], respectively. In saliva and blood, differences in the abundances of Epsilonbacteraeota, Firmicutes, Fusobacteria, and Proteobacteria could be used as reference values (95% CI of logFC: [-3.67, -2.47], [-0.35, 0.49], [-4.59, -3.26], and [-1.20, 0.07], respectively).<br><br>DISCUSSION: As the reference microbiome profiles could discern healthy subjects and individuals with PD, a relatively mild disease state, they can be applied as reference values representing the healthy status of the microbiome and for screening of disease states, preferably in preclinical stages.}, }
@article {pmid40007012, year = {2025}, author = {Bashor, L and Rawlinson, JE and Kozakiewicz, CP and Behzadi, E and Miller, C and Kim, J and Cierzan, M and Nehring, M and Carver, S and Abdo, Z and VandeWoude, S}, title = {Impacts of Antiretroviral Therapy on the Oral Microbiome and Periodontal Health of Feline Immunodeficiency Virus-Positive Cats.}, journal = {Viruses}, volume = {17}, number = {2}, pages = {}, doi = {10.3390/v17020257}, pmid = {40007012}, issn = {1999-4915}, support = {1R21DE029733-01A1/NH/NIH HHS/United States ; }, mesh = {Animals ; Cats ; *Immunodeficiency Virus, Feline/drug effects ; *Microbiota/drug effects ; *Feline Acquired Immunodeficiency Syndrome/virology/drug therapy ; *RNA, Ribosomal, 16S/genetics ; Male ; Mouth/microbiology/virology ; Oral Health ; Female ; Anti-Retroviral Agents/therapeutic use ; Gingivitis/microbiology/drug therapy/virology ; Lentivirus Infections/veterinary/virology ; Bacteria/classification/drug effects/isolation &amp; purification/genetics ; Cat Diseases/microbiology/virology/drug therapy ; }, abstract = {Feline immunodeficiency virus (FIV) is the domestic cat analogue of HIV infection in humans. Both viruses induce oral disease in untreated individuals, with clinical signs that include gingivitis and periodontal lesions. Oral disease manifestations in HIV patients are abated by highly effective combination antiretroviral therapy (cART), though certain oral manifestations persist despite therapy. Microorganisms associated with oral cavity opportunistic infections in patients with HIV cause similar pathologies in cats. To further develop this model, we evaluated characteristics of feline oral health and the oral microbiome during experimental FIV infection over an 8-month period following cART. Using 16S rRNA sequencing, we evaluated gingival bacterial communities at four timepoints in uninfected and FIV-infected cats treated with either cART or placebo. Comprehensive oral examinations were also conducted by a veterinary dental specialist over the experimental period. Gingival inflammation was higher in FIV-infected cats treated with placebo compared to cART-treated cats and the controls at the study endpoint. Oral microbiome alpha diversity increased in all groups, while beta diversity differed among treatment groups, documenting a significant effect of cART therapy on microbiome community composition. This finding has not previously been reported, and indicates cART ameliorates immunodeficiency virus-associated oral disease via the preservation of oral mucosal microbiota. Further, this study illustrates the value of the FIV animal model for investigations of mechanistic associations and therapeutic interventions for HIV's oral manifestations.}, }
@article {pmid40006675, year = {2025}, author = {Wolf, E and Sacchi de Camargo Correia, G and Li, S and Zhao, Y and Manochakian, R and Lou, Y}, title = {Emerging Immunotherapies for Advanced Non-Small-Cell Lung Cancer.}, journal = {Vaccines}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/vaccines13020128}, pmid = {40006675}, issn = {2076-393X}, abstract = {Lung cancer remains the leading cause of cancer-related mortality worldwide. Non-small-cell lung cancer (NSCLC) is the most common type of lung cancer, with nearly half of all patients diagnosed at an advanced stage. Immune checkpoint inhibitors (ICIs) harness the host immune system to combat malignant cells. ICIs, which target programmed death-ligand 1 (PD-L1), programmed cell death 1 (PD-1), and cytotoxic T-cell lymphocyte-4 (CTLA-4), have transformed the treatment landscape for advanced NSCLC. While a subset of patients experiences a long-term durable response, most patients will develop disease progression. New drugs targeting novel pathways are being tested in clinical trials to improve the efficacy of immunotherapy and overcome resistance patterns. This review aims to summarize the currently available ICIs for advanced NSCLC and describe emerging immunotherapies with recently published data from phase I/II clinical trials.}, }
@article {pmid40005851, year = {2025}, author = {Marsella, R}, title = {Skin Barrier in Normal and Allergic Horses: What Do We Know?.}, journal = {Veterinary sciences}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/vetsci12020091}, pmid = {40005851}, issn = {2306-7381}, abstract = {Information on skin barrier in horses is limited. A study on the epidermal ultrastructure of normal and allergic horses documented disorganized amorphous intercellular lipids in the stratum corneum of allergic samples. These findings are similar to atopic canine and human skin. Currently, there is no published study comparing skin barrier function parameters between normal and allergic horses; thus, the functional implications of the ultrastructural changes are unknown. In normal horses, body location, gender, breed, and ambient conditions affect skin barrier parameters, such as Transepidermal Water Loss. Skin microbiome studies on normal horses have highlighted the importance of season and environmental conditions, since horses housed together share similar microbiomes. Skin dysbiosis and predominance of staphylococcus have been described in horses with pastern dermatitis. Transcriptomic studies of the epidermis of normal and allergic horses have found that lesional allergic skin has substantial transcriptomic differences when compared with healthy skin, namely downregulation of genes of tight junctions, keratins, and upregulation of serine proteases and IL-13. Keratinocytes harvested from horses with insect bite hypersensitivity show upregulation of IL-31 gene expression under stimulation. While more research is clearly needed, preliminary results seem to support skin barrier differences between normal and allergic horses.}, }
@article {pmid40005845, year = {2025}, author = {Ali, M and Xu, C and Wang, M and Hina, Q and Ji, Y and Anwar, S and Lu, S and He, Q and Qiu, Y and Li, K}, title = {Gut Barrier Dysfunction and Microbiota Variations in Cryptosporidiosis: A Comprehensive Review.}, journal = {Veterinary sciences}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/vetsci12020085}, pmid = {40005845}, issn = {2306-7381}, support = {32102692//This work was supported by the National Natural Science Foundation of China (32102692)/ ; }, abstract = {Cryptosporidiosis is a zoonotic protozoan parasite-born disease, equally significant in both animals and humans, especially affecting immunocompromised individuals (e.g., AIDS patients) and neonates. The prime concerns of this review article are to demonstrate the disruption of the intestinal barrier and variations in the gut microbiome during cryptosporidiosis, and to explore host gut-parasite interactions that can lead to the development of novel therapeutics. The review concluded that the enteric barrier is particularly maintained by tight junction proteins (e.g., occludin, claudin, and ZO-1, etc.) and mucosal immunity, both of which are severely compromised during Cryptosporidium spp. infections, resulting in increased intestinal barrier permeability, inflammatory responses, diarrhea, and ultimately death in severe cases. Cryptosporidium-induced dysbiosis is characterized by reduced microbial diversity and richness, a shift from commensal to pathogenic bacteria, as evidenced by increased pro-inflammatory taxa like Proteobacteria, and reduced proportions of beneficial SCFAs producing bacteria, e.g., Firmicutes. Recent investigations have highlighted the interrelations between gut microbiota and epithelial barrier integrity, especially during cryptosporidiosis, demonstrating the modulations regarding tight junctions (TJs), immune reactions, and SCFA production, all of which are main players in alleviating this protozoal parasitic infection. This review comprehensively describes the fine details underlying these impairments, including autophagy-mediated TJs' degradation, inflammasome activation, and gut microbiome-driven alterations in metabolic pathways, providing the latest relevant, and well-organized piece of knowledge regarding intestinal barrier alterations and microbial shifts during cryptosporidiosis. This work emphasizes the future need for longitudinal studies and advanced sequencing techniques to understand host gut microbiota-parasite interactions, aiming to formulate innovative strategies to mitigate cryptosporidiosis.}, }
@article {pmid40005832, year = {2025}, author = {Rad, SK and Yeo, KKL and Wu, F and Li, R and Nourmohammadi, S and Tomita, Y and Price, TJ and Ingman, WV and Townsend, AR and Smith, E}, title = {A Systematic Review and Meta-Analysis of 16S rRNA and Cancer Microbiome Atlas Datasets to Characterize Microbiota Signatures in Normal Breast, Mastitis, and Breast Cancer.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020467}, pmid = {40005832}, issn = {2076-2607}, abstract = {The breast tissue microbiome has been increasingly recognized as a potential contributor to breast cancer development and progression. However, inconsistencies in microbial composition across studies have hindered the identification of definitive microbial signatures. We conducted a systematic review and meta-analysis of 11 studies using 16S rRNA sequencing to characterize the bacterial microbiome in 1260 fresh breast tissue samples, including normal, mastitis-affected, benign, cancer-adjacent, and cancerous tissues. Studies published until 31 December 2023 were included if they analyzed human breast tissue using Illumina short-read 16S rRNA sequencing with sufficient metadata, while non-human samples, non-breast tissues, non-English articles, and those lacking metadata or using alternative sequencing methods were excluded. We also incorporated microbiome data from The Cancer Genome Atlas breast cancer (TCGA-BRCA) cohort to enhance our analyses. Our meta-analysis identified Proteobacteria, Firmicutes, Actinobacteriota, and Bacteroidota as the dominant phyla in breast tissue, with Staphylococcus and Corynebacterium frequently detected across studies. While microbial diversity was similar between cancer and cancer-adjacent tissues, they both exhibited a lower diversity compared to normal and mastitis-affected tissues. Variability in bacterial genera was observed across primer sets and studies, emphasizing the need for standardized methodologies in microbiome research. An analysis of TCGA-BRCA data confirmed the dominance of Staphylococcus and Corynebacterium, which was associated with breast cancer proliferation-related gene expression programs. Notably, high Staphylococcus abundance was associated with a 4.1-fold increased mortality risk. These findings underscore the potential clinical relevance of the breast microbiome in tumor progression and emphasize the importance of methodological consistency. Future studies to establish causal relationships, elucidate underlying mechanisms, and assess microbiome-targeted interventions are warranted.}, }
@article {pmid40005827, year = {2025}, author = {Superdock, DK and Johnson, LM and Ren, J and Khan, A and Eno, M and Man, S and Poole, AC}, title = {The Impact of Human Salivary Amylase Gene Copy Number and Starch on Oral Biofilms.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020461}, pmid = {40005827}, issn = {2076-2607}, support = {T32-DK007158/NH/NIH HHS/United States ; NA//Schwartz Research Fund Award for Women and Underrepresented Faculty in the Life Sciences/ ; }, abstract = {The copy number (CN) variant AMY1 encodes the salivary amylase enzyme which promotes starch digestion. Although this gene has been associated with dental caries and periodontal disease susceptibility, the impact of the interaction between AMY1 CN and starch on oral biofilms is unclear. We explored how oral microbiota communities shaped by AMY1 CN respond to starch by employing an in vitro model of biofilm formation. We cultured biofilms using saliva samples from 31 donors with a range of AMY1 CNs (between 2 and 20 copies) and self-reported gum disease states; we used media with and without starch. Many of the most prevalent genera in saliva were also prevalent in the derived biofilms. The presence of starch in the media was associated with lower biofilm alpha diversity. We found a significant interaction between AMY1 CN and the media carbohydrate content that influenced the proportions of Atopobium and Veillonella. Members of these genera have been associated with dental caries and periodontitis. These findings suggest that the effects of carbohydrates on oral microbiome composition depend on AMY1 CN and that human oral bacteria evolved in response to expansion of this host gene locus.}, }
@article {pmid40005816, year = {2025}, author = {Tang, J and Wu, H and Li, Y and Chen, J}, title = {The Response Microbial of the Cucumber Rhizosphere Network Keystone Taxa of the Cucumber Rhizosphere to Continuous Fertilization.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020451}, pmid = {40005816}, issn = {2076-2607}, support = {2022 - 02 - 08 - 00 - 12 - fo1143//Shanghai Agriculture and Rural Affairs Commission; Science and Technology Promoting Agriculture Project of Shanghai Municipal Agricultural and Rural Committee/ ; NMKJXM202209//Key project of Bayannur National Agricultural High tech Industry Demonstration Zone/ ; 2024-02-08-00-12-F00004//Shanghai Agricultural Science and Technology Innovation Project/ ; KJXM2023-12-01//Special Cooperation Project of Inner Mongolia Au-tonomous Region and Shanghai Jiaotong University/ ; }, abstract = {Fertilization is a common agricultural practice used to modify the physicochemical properties of soil, which in turn affects plant growth and the rhizosphere microbial community. However, the mechanisms underlying the variation in the cucumber rhizosphere microecosystem have not been thoroughly investigated. In this study, we conducted three rounds of continuous plant growth experiments in pots to test different fertilizers and reveal the evolutionary features of the rhizosphere microecosystem. Through topological analysis of the microbial co-occurrence networks, we identified putative taxa associated with fertilization disturbances. Structural equation models (SEMs) predict plausible mechanistic links between soil physicochemical properties, plant growth and the rhizosphere microbiome. The results suggest that continuous fertilization with single fertilizers reduces microbial diversity and may disrupt the structure of the microbial network. Furthermore, it was found that the predicted distribution of keystone taxa (Bacteroidetes, Ascomycota, etc.) was significantly sensitive to the application of certain fertilizers. Moreover, it was modeled by the SEMs that the accumulation of NO3[-] and Na[+] in fertilized soil was one of the putative principal causes of rhizosphere microbial network deterioration. This study provides new insights into the dynamic changes in the cucumber rhizosphere microbial community under continuous fertilization and highlights the potential utility of SEMs in analyzing causal relationships in agroecosystem studies before experimental validation.}, }
@article {pmid40005804, year = {2025}, author = {López-Arellanes, ME and López-Pacheco, LD and Elizondo-Luevano, JH and González-Meza, GM}, title = {Algae and Cyanobacteria Fatty Acids and Bioactive Metabolites: Natural Antifungal Alternative Against Fusarium sp.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020439}, pmid = {40005804}, issn = {2076-2607}, support = {I023-IAMSM002-C4-T2-E//Tecnol&#xf3;gico de Monterrey/ ; }, abstract = {Fungal diseases caused by Fusarium spp. significantly threaten food security and sustainable agriculture. One of the traditional strategies for eradicating Fusarium spp. incidents is the use of chemical and synthetic fungicides. The excessive use of these products generates environmental damage and has negative effects on crop yield. It puts plants in stressful conditions, kills the natural soil microbiome, and makes phytopathogenic fungi resistant. Finally, it also causes health problems in farmers. This drives the search for and selection of natural alternatives, such as bio-fungicides. Among natural products, algae and cyanobacteria are promising sources of antifungal bio-compounds. These organisms can synthesize different bioactive molecules, such as fatty acids, phenolic acids, and some volatile organic compounds with antifungal activity, which can damage the fungal cell membrane that surrounds the hyphae and spores, either by solubilization or by making them porous and disrupted. Research in this area is still developing, but significant progress has been made in the identification of the compounds with potential for controlling this important pathogen. Therefore, this review focuses on the knowledge about the mechanisms of action of the fatty acids from macroalgae, microalgae, and cyanobacteria as principal biomolecules with antifungal activity, as well as on the benefits and challenges of applying these natural metabolites against Fusarium spp. to achieve sustainable agriculture.}, }
@article {pmid40005803, year = {2025}, author = {Minerdi, D and Sabbatini, P}, title = {Exploring the Grapevine Microbiome: Insights into the Microbial Ecosystem of Grape Berries.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020438}, pmid = {40005803}, issn = {2076-2607}, abstract = {Plant growth, health, and resilience to stress are intricately linked to their associated microbiomes. Grapevine, functioning as a holobiont, forms essential relationships with fungi and bacteria across both its belowground (roots) and aboveground (leaves and berries) compartments. The root microbiome exhibits a stable, site-specific structure, whereas the microbiomes of ephemeral tissues such as leaves and berries, which regenerate annually, display more stochastic assembly patterns across growing seasons. Among these, grape berries represent a critical component in viticulture due to their direct influence on wine quality and flavor complexity. Berries provide a unique ecological niche, hosting diverse microbial communities composed of yeasts, bacteria, and fungi that interact with the grapevine and its surrounding environment. These microorganisms are not only pivotal to berry development but also contribute significantly to the synthesis of secondary metabolites and fermentation processes, ultimately shaping the sensory and organoleptic properties of wine. This review consolidates current knowledge on the grapevine microbiome, with a particular emphasis on the microbial dynamics of grape berries.}, }
@article {pmid40005796, year = {2025}, author = {Orton, KL and Monaco, CL}, title = {The Vaginal Virome in Women's Health and Disease.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020431}, pmid = {40005796}, issn = {2076-2607}, support = {AI181643//NIH NIAID K08 grant number AI181643/ ; RAMP//HIV Vaccine Trials Network Research and Mentorship Program (RAMP)/ ; }, abstract = {Most research on the vaginal microbiome has focused on bacterial communities (the bacteriome), but viruses, including eukaryotic viruses and bacteriophages, are also important players in vaginal health and disease states. In this review, we will briefly discuss the bacterial microbiome, delve into what is known about the vaginal virome and its impact on women's health, and finish with novel vaginal microbial or microbial-derived therapeutics on the horizon. More studies on the vaginal virome and its impact on women's health are needed to better prevent and treat gynecological, reproductive, and neonatal diseases.}, }
@article {pmid40005760, year = {2025}, author = {Du, H and Li, K and Guo, W and Na, M and Zhang, J and Na, R}, title = {Roughage Sources During Late Gestation and Lactation Alter Metabolism, Immune Function and Rumen Microbiota in Ewes and Their Offsprings.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020394}, pmid = {40005760}, issn = {2076-2607}, support = {RZ2100001561//Natural Science Foundation of Inner Mongolia Autonomous Region of China/ ; NMGIRT2322//Innovative Research Team in Universities of Inner Mongolia Autonomous Region/ ; }, abstract = {Maternal metabolic intensity significantly increases during late gestation and lactation, placing significant stress on cells and tissues. This heightened metabolic demand can lead to inflammatory responses and metabolic disorders, adversely affecting the health of both the mother and her offspring. Diet plays a key role in modulating host health by influencing the gastrointestinal microbiome. This study examined the impact of two roughage sources, corn straw (CS), and alfalfa hay (AH), on ewes and their offspring during late gestation and lactation, with a focus on metabolism, immunity, and the microbiome. Thirty-six multiparous Inner Mongolia cashmere goats, approximately 60 days pregnant, were assigned to CS and AH groups. Samples were collected from the ewes on day 140 of gestation (G140) and day 28 of lactation (L28) for analysis. The results showed that ewes fed AH had reduced body weight loss during lactation (p < 0.05), and increased serum metabolic factors levels (p < 0.05). Additionally, ewes in the AH group exhibited a reduced inflammatory response during both gestation and lactation compared to those in the CS group, as evidenced by a significant decrease in TNF-α and LPS levels and a notable increase in IL-10 (p < 0.05). The rumen microbiomes of ewes in the AH and CS groups exhibited stark differences, with specific microbial markers identified at G140 and L28. Correlation analysis revealed associations between microbiome, volatile fatty acids, cytokines, and metabolic markers. The analysis of the lambs demonstrated that their immune status and microbial composition were significantly influenced by the immune health and microbial community structure of the ewe. Moreover, microbial and immune-related components from the ewes were transmitted to the lambs, further shaping their immune development and rumen microbiota. Overall, different roughage sources during late gestation and lactation had minimal impact on the growth performance of ewes and lambs, given that both diets were iso-nitrogen and iso-energetic. However, ewes fed AH exhibited significant improvements in immune function and overall health for both them and their lambs.}, }
@article {pmid40005740, year = {2025}, author = {Dumitrescu, R and Bolchis, V and Fratila, AD and Jumanca, D and Buzatu, BLR and Sava-Rosianu, R and Alexa, VT and Galuscan, A and Balean, O}, title = {The Global Trends and Advances in Oral Microbiome Research on Oral Squamous Cell Carcinoma: A Systematic Review.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020373}, pmid = {40005740}, issn = {2076-2607}, support = {4814/02.10.2023//Victor Babes University of Medicine and Pharmacy Timsoara/ ; }, abstract = {The oral microbiome is increasingly recognized as a key factor in the development and progression of oral squamous cell carcinoma (OSCC). Dysbiosis has been associated with inflammation and tumorigenesis, highlighting the potential of microbial alterations and salivary biomarkers as tools for early, non-invasive diagnosis. This review examines recent advancements in understanding the oral microbiome's role in OSCC. A comprehensive synthesis of studies from 2016 to 2024 was conducted to identify emerging themes and significant findings in the field. Key topics included the interplay between microbiome-driven mechanisms and cancer development, with a focus on microbial communities and their metabolic byproducts. The findings emphasize the importance of specific microbial alterations in modulating immune responses and tumor microenvironments, as well as the promise of biomarkers such as interleukins and miRNA signatures in improving diagnostic accuracy. Recent research trends indicate growing interest in the therapeutic potential of targeting the oral microbiome in OSCC management. Despite significant advancements, gaps remain in the understanding of the precise mechanisms linking dysbiosis to cancer progression. This review underscores the need for continued research to develop personalized diagnostic and therapeutic strategies based on the oral microbiome, with the potential to transform OSCC management.}, }
@article {pmid40005733, year = {2025}, author = {Romano, FS and Lallo, MA and Romano, RS and Isidoro, LPS and Cardoso, MR and Sodré, LC and Melchert, A and Guimarães-Okamoto, PTC and Pappalardo, MCF and Amaral, AR and Vendramini, THA}, title = {Fecal Microbiota Transplantation as a Treatment for Granulomatous Colitis in a French Bulldog: A Case Report.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020366}, pmid = {40005733}, issn = {2076-2607}, abstract = {Granulomatous colitis, or ulcerative colitis, is an infectious and inflammatory disease that primarily affects the colon and occasionally extends to the ileum, particularly in young Boxer and French Bulldogs. Unlike typical chronic colitis in small animals, the early onset of the disease suggests a genetic predisposition. The condition is characterized by the overgrowth of Escherichia coli, specifically the enteroinvasive variant, which displaces beneficial gut bacteria, contributing to its infectious nature. Secondary dysbiosis and chronic-active inflammation involving histiocytes and other leukocytic infiltrates are prominent features. Clinical manifestations include chronic diarrhea with blood and mucus, frequent tenesmus, and pain, with variable degrees of weight loss depending on disease severity. The final diagnosis is based on clinical history (chronic diarrhea with hematochezia), macroscopic findings from colonoscopy (edema, ulcers, and wall hyperplasia), histopathology (presence of histiocytes), and Escherichia coli growth in culture from a colon fragment. Treatment is guided by colon antibiograms, which often require prolonged antibiotic therapy. Fecal microbiota transplantation (FMT) has emerged as a potential treatment, either as a primary intervention or adjunctive therapy, for conditions such as acute enteritis (e.g., canine parvovirus), dysbiosis, and chronic enteropathies. However, its application to modulate the microbiota and reduce inflammation in granulomatous colitis, potentially leading to longer intervals between relapses, remains an area of ongoing investigation. This is a case report of a French Bulldog diagnosed with ulcerative colitis accompanied by dysbiosis and refractory to standard treatments but sensitive and partially responsive to amikacin. The patient achieved control and sustained improvement in fecal scoring following fecal transplantation. This approach prevented the need for additional antibiotic therapy, ensuring clinical amelioration alongside microbiome restoration.}, }
@article {pmid40005729, year = {2025}, author = {Chao, S and Zhang, Y and Hu, Y and Chen, Y and Li, P and Sun, Y and Song, L and Hu, Y and Wang, H and Wu, J and Lv, B}, title = {Transgenic Maize of ZmMYB3R Shapes Microbiome on Adaxial and Abaxial Surface of Leaves to Promote Disease Resistance.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020362}, pmid = {40005729}, issn = {2076-2607}, support = {2024-02-08-00-12-F00021//Shanghai Agriculture Applied Technology Development Program, China/ ; 32302635//National Natural Science Foundation of China/ ; 22ZR1442500//Natural Science Foundation of Shanghai/ ; SAAS Application Basic Study 2025(08)//2025 SAAS Project on Agricultural Science and Technology Innovation Supporting Area/ ; 016//Shanghai Academy of Agricultural Sciences 2022/ ; 20DZ2255300//Shanghai Engineering Research Center of Specialty Maize/ ; 2023ZD04062//the Science and Technology Innovation 2030 Biological Breeding-Major Projects/ ; 23DZ2290700//Shanghai "Science and Technology Innovation Action Plan" Professional Technical Service Platform Project/ ; }, abstract = {The phyllosphere is one of the largest habitats for microorganisms, and host genetic factors play an important role during the interaction between microorganisms and the phyllosphere. Therefore, the transgene may also lead to changes in the maize phyllosphere. ZmMYB3R was identified as a drought-tolerant gene in Arabisopsis. Here, we employed metagenomic sequencing to analyze the microbiome of the adaxial and abaxial leaf surfaces on ZmMYB3R-overexpressing (OE) and wild-type (WT)·maize, aiming to dissect the possible associations between ZmMYB3R and changes in phyllosphere microbiome functioning. Our results revealed that overexpressing ZmMYB3R altered the alpha and beta diversity of the phyllosphere microbiome. In OE plants, more beneficial microbes accumulated on the phyllosphere, while pathogenic ones diminished, especially on the abaxial surface of ZmMYB3R leaves. Further analysis of disease resistance-related metabolic pathways and abundances of disease resistance genes revealed significant differences between OE and WT. The inoculation experiment between OE and WT proved that ZmMYB3R increased the disease resistance of maize. In conclusion, the results reveal that transgenes affect the phyllosphere microbiome, and ZmMYB3R might alter leaf disease resistance by reshaping the phyllosphere microbiome structure. These findings help us understand how ZmMYB3R regulates leaf disease resistance and may facilitate the development of disease control by harnessing beneficial microbial communities.}, }
@article {pmid40005725, year = {2025}, author = {Han, J and Wang, M and Zhou, S and Wang, Z and Duan, D and Li, M and Li, X and Xin, W and Li, X}, title = {The Joint Contribution of Host Genetics and Probiotics to Pig Growth Performance.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020358}, pmid = {40005725}, issn = {2076-2607}, support = {2021YFD1301202//National Kye Research and Development Program of Chin/ ; 2022020101//Agricultural Breeds Research Project of Henan Province/ ; }, abstract = {Intestinal probiotics significantly regulate the growth performance of their host, with their composition being influenced by various factors. While many studies have explored how gut microbiota composition affects growth traits such as body weight and BMI, the research on probiotics influenced by host genetic factors, and their subsequent impact on host growth performance, remains limited. To address this research gap, we collected fecal and tissue samples, as well as phenotypic data, from 193 Yunong black pigs at 280 days of age. We then sequenced and genotyped all 193 subjects using the 50K SNP BeadChip, yielding a comprehensive dataset for genetic and microbiome analyses. We then employed microbiome-wide association studies (MWAS), a meta-analysis, and microbiome-wide genetic association studies (MGWASs) to examine the relationship between host genetics, gut microbiota, and growth performance. Four key microbial taxa, namely Coprococcus, Blautia, Ruminococcaceae, and RF16, were identified as being significantly associated with body weight and BMI. The MGWAS analysis revealed that both Coprococcus and Ruminococcaceae were significantly associated with host genomic variations. A total of four important single nucleotide polymorphisms (SNPs) were mapped to two chromosomal regions, corresponding to three candidate genes. Among them, the candidate genes INPP4B, SCOC, and PABPC4L were identified as being related to the abundance of key microbes. This study provides new insights into the joint contributions of host genetics and probiotics to host growth traits, offering theoretical guidance and data support for the development of efficient and targeted breeding strategies.}, }
@article {pmid40005693, year = {2025}, author = {Goudy, SL and Bradley, HL and Gacasan, CA and Toma, A and Sekar, KPC and Wuest, WM and Tomov, M and Serpooshan, V and Coskun, A and Jones, RM}, title = {Microbial Changes Occurring During Oronasal Fistula Wound Healing.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020327}, pmid = {40005693}, issn = {2076-2607}, support = {1C06DE030632-02A1/NH/NIH HHS/United States ; }, abstract = {UNLABELLED: The oral microbiome is a complex community that matures with dental development and is recognized as a risk factor for systemic disease. Despite the oral cavity having a substantial microbial burden, healing of superficial oral wounds occurs quickly and with little scarring. By contrast, creation of an oro-nasal fistula (ONF), often occurring after surgery to correct a cleft palate, is a significant wound healing challenge.<br><br>METHODS: In this study, we characterized the changes in the oral microbiome of mice following a freshly inflicted wound in the oral palate that results in an open and unhealed ONF.<br><br>RESULTS: Creation of an ONF in mice significantly lowered oral microbiome alpha diversity, with concurrent blooms of Enterococcus faecalis, Staphylococcus lentus, and Staphylococcus xylosus in the oral cavity. Treatment with oral antibiotics one week before ONF infliction reduced microbiome alpha diversity and prevented E. faecalis, S. lentus, and S. xylosus blooms, but did not impact ONF healing.<br><br>CONCLUSIONS: An ONF in the murine palate leads to a dysbiotic oral microbiome and a bloom of opportunistic pathogens that may prevent ONF healing. Delivery of therapeutics that accelerate ONF healing might restore oral microbiome diversity and inhibit blooms of opportunistic pathogens.}, }
@article {pmid40005690, year = {2025}, author = {Moussa, S and Iasur Kruh, L}, title = {Balancing Nature and Nurture: The Role of Biocontrol Agents in Shaping Plant Microbiomes for Sustainable Agriculture.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020323}, pmid = {40005690}, issn = {2076-2607}, abstract = {Microbial communities in the plant environment are highly dynamic, with bacterial populations rapidly responding to changes. Numerous studies have examined how both inherent plant characteristics and environmental factors shape plant-associated microbiota. These factors determine which bacterial communities thrive and how they interact with plants; certain conditions favor beneficial bacteria, and others support pathogens. In this mini-review, we focus on an additional factor influencing plant microbiomes and their surrounding environments: the use of biocontrol agents. The increasing application of microbial inoculants and their metabolites as biocontrol strategies in agriculture has created a critical knowledge gap about the effects of introducing non-native bacterial species into natural plant ecosystems. The inoculation of plants and their environments with exogenous biocontrol microorganisms has the potential to alter microbial community diversity and composition, presenting both opportunities and challenges for sustainable agricultural practices.}, }
@article {pmid40005685, year = {2025}, author = {Ceasar, J and Pugalenthi Saravanan, D and Harding, BA and Hicks, SD}, title = {Association of Longitudinal Oral Microbiome Activity and Pediatric Concussion Recovery.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020320}, pmid = {40005685}, issn = {2076-2607}, support = {R42NS119119/NH/NIH HHS/United States ; R01NS115942/NH/NIH HHS/United States ; 4100088558//Pennsylvania TSF CURE Fund/ ; }, abstract = {Mild traumatic brain injury (mTBI) results in a constellation of symptoms commonly referred to as a concussion. It is unclear why certain individuals experience persistent symptoms. Given the growing evidence linking the microbiome with cognition and inflammation, we examined whether longitudinal microbiome patterns were associated with concussion symptoms. A cohort study of 118 children (aged 7-21 years) was conducted. Symptoms were assessed at three timepoints post-injury (4, 11, and 30 days) using the Post-Concussion Symptom Inventory. Saliva microbial activity was measured at each timepoint using RNA sequencing. A linear mixed model assessed the relationship between microbial activity and symptom burden while controlling for age, sex, and days post-mTBI. The participants' mean age was 16 (±3) years. The symptom burden decreased across all three timepoints (25 ± 22, 13 ± 17, and 5 ± 12). The longitudinal symptom burden was associated with elevated activity of Lactobacillus (F = 5.47; adj. p = 0.020) and Saccharomyces (F = 6.79; adj. p = 0.020) and reduced activity of Micrococcus (F = 7.94, adj. p = 0.015). These results do not establish a causative relationship, or support the use of microbial measures as a concussion test. Further studies are needed to explore the role of the gut-brain axis in mTBI.}, }
@article {pmid40005682, year = {2025}, author = {Ece, G and Aktaş, A and Caner, A and Sağlık, &#x130; and Kula Atik, T and Ulusan Bağcı, &#xd6; and Bayındır Bilman, F and Demirbakan, H and Güdül Havuz, S and Kaya, E and Koyuncu Özyurt, &#xd6; and Yetkin, G and Zorbozan, O}, title = {The Urogenital System Microbiota: Is It a New Gamechanger in Urogenital Cancers?.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020315}, pmid = {40005682}, issn = {2076-2607}, abstract = {The human microbiome, which encompasses microbial communities and their genetic material, significantly influences health and disease, including cancer. The urogenital microbiota, naturally present in the urinary and genital tracts, interact with factors such as age, lifestyle, and health conditions to affect homeostasis and carcinogenesis. Studies suggest that alterations in this microbiota contribute to the development and progression of genitourinary cancers, emphasizing the concept of oncobiome, which refers to microbial genetic contributions to cancer. Similarly, gut microbiota can influence hormone levels and systemic inflammation, impacting cancers such as cervical and prostate cancer. Advanced studies indicate that microbial communities in genitourinary cancers have distinct profiles that may serve as diagnostic biomarkers or therapeutic targets. Dysbiosis of the urinary microbiota correlates with bladder and kidney cancer. Additionally, gut microbiota influence the effectiveness of cancer treatments. However, further research is necessary to clarify causality, the role of microbial metabolites, and hormonal regulation. The aim of this review is to understand that these dynamics present opportunities for innovative cancer diagnostics and therapies, highlighting the need for integration of microbiology, oncology, and genomics to explore the role of microbiota in genitourinary cancers. For this, a comprehensive search of relevant databases was conducted, applying specific inclusion and exclusion criteria to identify studies examining the association between microbiota and urogenital cancers. Research into the mechanisms by which microbiota influence urogenital cancers may pave the way for new diagnostic and therapeutic approaches, ultimately improving patient outcomes.}, }
@article {pmid40005677, year = {2025}, author = {Neves, ALA and Vieira, RAM and Vargas-Bello-Pérez, E and Chen, Y and McAllister, T and Ominski, KH and Lin, L and Guan, LL}, title = {Impact of Feed Composition on Rumen Microbial Dynamics and Phenotypic Traits in Beef Cattle.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020310}, pmid = {40005677}, issn = {2076-2607}, support = {2013R029R//Alberta Livestock and Meat Agency (Edmonton, Canada)/ ; ALLRP 588541-23//NSERC Discovery Grant, NSERC Alliance program/ ; FDE.18.21C//Beef Cattle Research Council Cluster/ ; }, abstract = {The rumen microbiome is central to feed digestion and host performance, making it an important target for improving ruminant productivity and sustainability. This study investigated how feed composition influences rumen microbial abundance and phenotypic traits in beef cattle. Fifty-nine Angus bulls were assigned to forage- and grain-based diets in a randomized block design, evaluating microbial dynamics, methane emissions, and feed efficiency. Quantitative PCR (qPCR) quantified bacterial, archaeal, fungal, and protozoal populations. Grain-based diets reduced bacterial and fungal counts compared to forage diets (1.1 × 10[11] vs. 2.8 × 10[11] copies of 16S rRNA genes and 1.5 × 10[3] vs. 3.5 × 10[4] copies of 18S rRNA genes/mL, respectively), while protozoan and methanogen populations remained stable. Microbial abundance correlated with feed intake metrics, including dry matter and neutral detergent fiber intakes. Methane emissions were lower in grain-fed bulls (14.8 vs. 18.0 L CH4/kg DMI), though feed efficiency metrics showed no direct association with microbial abundance. Comparative analysis revealed adaptive microbial shifts in response to dietary changes, with functional redundancy maintaining rumen stability and supporting host performance. These findings provide insights into how feed composition shapes rumen microbial dynamics and host phenotypes, highlighting the functional adaptability of the rumen microbiome during dietary transitions.}, }
@article {pmid40005669, year = {2025}, author = {Duan, YX and Zhuang, YH and Wu, YX and Huang, TW and Song, ZR and Du, YZ and Zhu, YX}, title = {Wolbachia Infection Alters the Microbiota of the Invasive Leaf-Miner Liriomyza huidobrensis (Diptera: Agromyzidae).}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020302}, pmid = {40005669}, issn = {2076-2607}, support = {BK20231330//Natural Science Foundation of Jiangsu Province/ ; XCX20240707//the 2024 College Student Innovation and Entrepreneurship Training Program of Yangzhou University/ ; }, abstract = {Microbe-microbe interactions within a host drive shifts in the host's microbiota composition, profoundly influencing host physiology, ecology, and evolution. Among these microbes, the maternally inherited endosymbiont Wolbachia is widespread in the invasive pest Liriomyza huidorbrensis (Diptera: Agromyzidae). However, its influence on the host microbiota remains largely unexplored. In the study presented herein, we investigated the bacterial communities of Wolbachia wLhui-infected (wLhui+) and -uninfected lines (wLhui-) of L. huidorbrensis using 16S rRNA gene high-throughput sequencing. For both leaf-miner lines, Bacteroidota was the dominant phylum (relative abundance: 59.18%), followed by Pseudomonadota (36.63%), Actinomycetota (2.42%), and Bacillota (0.93%). We found no significant differences in alpha-diversity indices between the wLhui+ and wLhui- lines (p > 0.05). However, principal coordinates analysis revealed significant differences in microbiota composition between the wLhui+ and wLhui- lines (PERMANOVA: p < 0.001), explaining 76.70% of the variance in microbiota composition. Correlation network analysis identified robust negative and positive associations between Wolbachia and several genera, suggesting that Wolbachia shapes microbial composition through competitive or cooperative interactions with specific taxa. Overall, our study suggests that Wolbachia plays a key role in shaping the leaf-miner microbiome, potentially affecting host fitness.}, }
@article {pmid40005665, year = {2025}, author = {Hamann, T and Brüggemann, H and Feidenhansl, C and Rruci, E and Gallinger, J and Gallinat, S and Hüpeden, J}, title = {Distinct Intraspecies Variation of Cutibacterium acnes and Staphylococcus epidermidis in Acne Vulgaris and Healthy Skin.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020299}, pmid = {40005665}, issn = {2076-2607}, abstract = {Human skin hosts a diverse array of microorganisms that contribute to its health. Key players in the facial skin microbiome include Cutibacterium acnes and staphylococci, whose colonization patterns may influence dermatological conditions like acne vulgaris. This study examined the facial microbiome composition of 29 individuals, including 14 with moderate to severe acne and 15 with healthy skin, using single locus sequence typing (SLST) amplicon sequencing. The results showed a shift in the relative abundances of C. acnes phylotypes: SLST types A, C, and F were increased in acne, while types H, K, and L were reduced compared to healthy skin. Among staphylococci, the relative abundance of S. epidermidis, S. capitis, and S. saphrophyticus increased in acne, while S. saccharolyticus and S. hominis decreased. The amplicon sequencing approach could also identify a population shift of S. epidermidis: a specific S. epidermidis phylogenetic lineage (type 3) was reduced in acne, while two abundant lineages (types 1 and 2) were elevated. These findings suggest that distinct phylogenetic lineages of both C. acnes and S. epidermidis are linked to healthy versus diseased skin, highlighting a potential role for both microorganisms in disease prevention and aggravation, respectively.}, }
@article {pmid40005649, year = {2025}, author = {Justiz-Vaillant, A and Soodeen, S and Gopaul, D and Arozarena-Fundora, R and Thompson, R and Unakal, C and Akpaka, PE}, title = {Tackling Infectious Diseases in the Caribbean and South America: Epidemiological Insights, Antibiotic Resistance, Associated Infectious Diseases in Immunological Disorders, Global Infection Response, and Experimental Anti-Idiotypic Vaccine Candidates Against Microorganisms of Public Health Importance.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020282}, pmid = {40005649}, issn = {2076-2607}, abstract = {This paper explores various aspects of microbiology and immunology, with a particular focus on the epidemiology and molecular characterisation of infectious diseases in the Caribbean and South America. Key areas of investigation include tuberculosis (TB), experimental vaccines, and bloodborne pathogens. A retrospective study conducted in Jamaica highlights the significance of early HIV screening, timely diagnosis, and inte-grated care. The paper also examines the challenges posed by nosocomial infections, particularly those caused by antibiotic-resistant Gram-negative bacteria and methicillin-resistant Staphylococcus aureus (MRSA), emphasising the critical importance of infection control measures. Additionally, it explores the regional microbiome, the global response to infectious diseases, and immune responses in patients with immunodeficiency disorders such as severe combined immunodeficiency (SCID) and chronic granulomatous disease (CGD), underscoring their heightened susceptibility to a wide range of infections.}, }
@article {pmid40005646, year = {2025}, author = {Choi, Y and Jeong, J and Han, Y and Han, M and Yu, B and Han, K}, title = {Exploring Competitive Relationship Between Haemophilus parainfluenzae and Mitis Streptococci via Co-Culture-Based Molecular Diagnosis and Metabolomic Assay.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020279}, pmid = {40005646}, issn = {2076-2607}, support = {RS-2024-00355393//the Ministry of Education of the Republic of Korea and the National Research Foundation of Korea/ ; }, abstract = {Various bacterial strains with nitrate-reducing capacity (NRC), such as Haemophilus, Actinomyces, and Neisseria, are known to promote NH3 production, control pH in the oral cavity, and inhibit the growth of aciduric bacteria. However, experimental evidence on various estimated bacterial networks within the salivary microbiome is insufficient. This study aims to explore potential bacterial compositional competition observed within saliva samples from dental caries patients through a co-culture assay of mitis Streptococci, which is a primary colonizer in the salivary microbiome, and nitrate-reducing bacteria Haemophilus parainfluenzae. We investigated bacterial growth efficiency change by co-culture time using the qRT-PCR method. In addition, we applied LC/Q-TOF-based metabolites screening to confirm metabolic interactions between oral bacterial species and their association with dental caries from a metabolomics perspective. As a result, we first found that the nitrate reduction ability of H. parainfluenzae is maintained even in a co-culture environment with the mitis Streptococci group through a nitrate reduction test. However, nitrate reduction efficiency was hindered when compared with monoculture-based nitrate reduction test results. Next, we designed species-specific primers, and we confirmed by qRT-PCR that there is an obvious competitive relationship in growth efficiency between H. parainfluenzae and two mitis Streptococci (S. australis and S. sanguinis). Furthermore, although direct effects of nitrate reduction on competition have not been identified, we have potentially confirmed through LC/Q-TOF-based metabolite screening analysis that the interaction of various metabolic compounds synthesized from mitis Streptococci is driving inter-strain competition. In particular, we constructed a basic reference core-metabolites list to understand the metabolic network between each target bacterial species (H. parainfluenzae and mitis Streptococci) within the salivary microbiome, which still lacks accumulated research data. Ultimately, we suggest that our data have potential value to be referenced in further metagenomics and metabolomics-based studies related to oral health care.}, }
@article {pmid40005638, year = {2025}, author = {Samalia, PD and Solanki, J and Kam, J and Angelo, L and Niederer, RL}, title = {From Dysbiosis to Disease: The Microbiome's Influence on Uveitis Pathogenesis.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020271}, pmid = {40005638}, issn = {2076-2607}, abstract = {The microbiome, comprising the diverse microbial communities inhabiting the human body, has emerged as a critical factor in regulating immune function and inflammation. The relationship between the microbiome and uveitis represents a promising frontier in ophthalmological research, with the microbiome increasingly implicated in disease onset and progression. Research has predominantly focused on the gut microbiome, with animal studies providing evidence that dysbiosis is a key factor in autoimmunity. As the understanding of the microbiome increases, so does the potential for developing innovative treatments that leverage the microbiome's impact on immune and inflammatory processes. Future research will be crucial for deciphering the complexities of the interaction between the microbiome and immune system and for creating effective microbiome-based therapies for those with uveitis. Incorporating microbiome research into clinical practice could transform how uveitis is managed, leading to better and more individualized approaches for management. This review discusses the current understanding of the microbiome-uveitis axis, the promise of microbiome-based diagnostics and therapeutics, and the critical need for large-scale, longitudinal studies. Unlocking the potential of microbiome-targeted approaches may revolutionize the management of uveitis and other inflammatory diseases.}, }
@article {pmid40005630, year = {2025}, author = {Song, X and Chen, G and Zheng, L and Shen, J and Xue, C and Chang, Y}, title = {Microbiota Involved in the Degradation of Tremella fuciformis Polysaccharide and Microbial Enzymatic Potential Revealed by Microbiome and Metagenome.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020263}, pmid = {40005630}, issn = {2076-2607}, support = {2023YFD2100605//the National Key R&amp;D Program of China/ ; }, abstract = {Tremella fuciformis, as a traditional edible fungus in Asian countries, is rich in polysaccharides with a variety of bioactivities. Nevertheless, its high molecular weight and complex structure have caused limitations in its application and structural analysis. In this study, we successfully screened a Tremella fuciformis polysaccharide-degrading bacterium from the soil by enriching and screening. The mixed bacterium consisted mainly of Verrucomicrobium (55.4%) and Lysobacter (43.8%), which released extracellular enzymes that enabled the degradation of Tremella fuciformis polysaccharides. The functional annotation using microbiome and metagenome combined with bioinformatics revealed its active carbohydrate metabolism, binding, and catalysis. It exposed the enzymatic potential of the bacterium and provided a basis for the exploration of hydrolytic enzymes for hardly degradable polysaccharides in fungi.}, }
@article {pmid40005625, year = {2025}, author = {Shamoon-Pour, M and Canessa, EH and Macher, J and Fruitwala, A and Draper, E and Policriti, B and Chin, M and Nunez, M and Puccio, P and Fang, Y and Wang, XR and Hathout, Y}, title = {Genomic and Proteomic Analyses of Bacterial Communities of Ixodes scapularis Ticks from Broome County, New York.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020258}, pmid = {40005625}, issn = {2076-2607}, abstract = {The microbial communities of Ixodes scapularis, the primary vector of Lyme disease in North America, exhibit regional variations that may affect pathogen transmission and vector competence. We analyzed bacterial communities in I. scapularis ticks collected from Broome County, New York, using 16S rRNA gene sequencing (18 ticks) as well as mass spectrometry-based proteomics (36 ticks). According to the 16S rRNA analysis, the endosymbiont Rickettsia buchneri was the most abundant species, with significantly higher (p = 0.0011) abundance in females (54.76%) compared to males (31.15%). We detected Borreliella burgdorferi in 44.44% of ticks and Anaplasma phagocytophilum in two nymphs but in high relative abundances (12.73% and 46.46%). Male ticks exhibited higher bacterial diversity, although the community composition showed no significant clustering by sex or life stage. Co-occurrence analysis revealed negative associations between R. buchneri and Pseudomonas (p = 0.0245), but no associations with B. burgdorferi. Proteomic analysis identified 12 R. buchneri-specific proteins, additionally detecting the protozoan pathogen Babesia microti in 18.18% of females. These findings provide the first comprehensive characterization of I. scapularis microbiomes in the Southern Tier region of New York and suggest broader distribution of R. buchneri across tick life stages than previously recognized, with potential implications for pathogen transmission dynamics.}, }
@article {pmid40005624, year = {2025}, author = {Naeem, M and Bourassa, D}, title = {Probiotics in Poultry: Unlocking Productivity Through Microbiome Modulation and Gut Health.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020257}, pmid = {40005624}, issn = {2076-2607}, abstract = {This review explores the role of probiotics in improving productivity and gut health in poultry through microbiome modulation, particularly during early life. Gut health is pivotal to poultry performance, influencing nutrient absorption, immune function, and disease resistance. Early-life interventions target the microbiome to shape long-term health and productivity. Probiotics, live microorganisms providing health benefits, improve gut health through the competitive exclusion of pathogens, immune modulation, antimicrobial compound production, and enhancing gut barrier integrity. Applying probiotics improves growth performance, feed conversion efficiency, body weight gain, and carcass quality by promoting lean muscle growth and reducing fat deposition. For laying hens, probiotics enhance egg production and quality. These benefits are linked to better nutrient utilization, a well-balanced microbiome, and reduced gastrointestinal disorders. However, the efficacy of probiotics depends on strain specificity, dosage, and administration methods. Factors like environmental conditions, storage stability, and interactions with other feed additives also influence their effectiveness. Despite these challenges, advancements in microbiome research and probiotic technologies, such as precision probiotics and synbiotics, provide promising solutions. Future research should focus on optimizing formulations, understanding host-microbiome interactions, and leveraging new technologies for targeted microbiome management.}, }
@article {pmid40005622, year = {2025}, author = {Taneja, V}, title = {Gut Microbes as the Major Drivers of Rheumatoid Arthritis: Our Microbes Are Our Fortune!.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020255}, pmid = {40005622}, issn = {2076-2607}, support = {W81XWH-10-1-0257//Department of Defense/ ; W81XWH-15-1-0213//Department of Defense/ ; Department of Immunology//Mayo Clinic Hospital/ ; }, abstract = {Rheumatoid arthritis (RA) is an autoimmune disease with an unknown etiology. While certain genes provide strong susceptibility factors, the role of environmental factors is becoming increasingly recognized. Among genetic factors, human leukocyte antigen (HLA) genes, encoded within the major histocompatibility complex (MHC), have been linked to predisposition to RA, while among environmental factors, smoking, infections and diet are the major contributors. Genetic and environmental factors impact microbial composition in the host. Based on the dysbiosis observed in the gut and lung microbiome, a mucosal origin of RA has been suggested. However, proving whether genes or microbes provide a stronger risk factor has been difficult. Studies from RA patients and various mouse models, specifically humanized mice expressing HLA class II genes, have been instrumental in defining the role of environmental factors such as smoking and endogenous small intestinal microbes in modulating arthritis severity. The consensus based on most studies support an interaction between host genetic and environmental factors in the onset and severity of disease. However, until now, no microbial markers for disease prognosis or treatment efficacy have been available. Here, the role of gut microbes as markers of disease severity, and the potential for using endogenous commensals for modulating immune responses to suppress inflammation in the context of genetic factors, are discussed.}, }
@article {pmid40005614, year = {2025}, author = {Lee, JL and Yourek, G}, title = {The Microbiome of Catfish (Ictalurus punctatus) Treated with Natural Preservatives During Refrigerated Storage.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020244}, pmid = {40005614}, issn = {2076-2607}, abstract = {Fish is an essential lean protein source worldwide. Unfortunately, fresh fish food products deteriorate rapidly due to microbial spoilage. With consumers' growing concerns about using chemical preservatives, we propose using natural preservatives as safer alternatives to prevent microbial spoilage. In this study, we used Next-Generation Sequencing (NGS) metagenomics to study microbiomes on catfish fillets at early (day one for all samples), middle (day seven for control store-bought and aquaculture-raised samples, day nine for other treatment store-bought samples, and day eleven for other treatment aquaculture-raised samples), and late (day fifteen for all store-bought, day eleven for control aquaculture-raised samples, and day twenty-seven for other treatment aquaculture-raised samples) points. Store-bought and aquaculture-raised catfish were treated individually with natural preservatives (vinegar, lemon, and grapefruit seed [GSE]). We observed bacterial populations and sequenced 16S NGS libraries of catfish microbes. Vinegar treatment showed the greatest suppression of bacterial growth in both groups, and GSE and lemon treatment had similar levels of suppression in the mid and late points (-4 to -5 Log CFU/g vinegar and -0.1 to -4 Log CFU/g other treatments in aquaculture and -1 to -2 Log CFU/g vinegar and -0.2 to -0.5 Log CFU/g other treatments in store-bought). Aquaculture-raised vinegar treatment samples had similar proportional taxonomy abundance values through storage duration. Pseudomonas, Janthinobacterium, and Camobacteriaceae were the dominant bacteria species in the early point for store-bought fish. Still, Pseudomonas was suppressed by vinegar treatment in the middle point, which allowed for less biased relative abundance compared to other treatments. Chryseobacterium, CK-1C4-19, and Cetobacterium were the dominant bacteria species for early point treatments in aquaculture-raised fish. Still, they remained the predominant bacteria for only aquaculture-raised vinegar samples in the middle and late points, which allowed for a similar relative abundance to fresh catfish. Meanwhile, Pseudomonas in most lemon and GSE samples became the dominant species at a later point. This study provides a better understanding of bacterial spoilage of catfish during storage. Additionally, we showed that natural preservative treatments can effectively extend the shelf-life of fishery products.}, }
@article {pmid40005608, year = {2025}, author = {Pasta, A and Formisano, E and Calabrese, F and Marabotto, E and Furnari, M and Bodini, G and Torres, MCP and Pisciotta, L and Giannini, EG and Zentilin, P}, title = {From Dysbiosis to Hepatic Inflammation: A Narrative Review on the Diet-Microbiota-Liver Axis in Steatotic Liver Disease.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020241}, pmid = {40005608}, issn = {2076-2607}, abstract = {The gut microbiota has emerged as a critical player in metabolic and liver health, with its influence extending to the pathogenesis and progression of steatotic liver diseases. This review delves into the gut-liver axis, a dynamic communication network linking the gut microbiome and liver through metabolic, immunological, and inflammatory pathways. Dysbiosis, characterized by altered microbial composition, contributes significantly to the development of hepatic steatosis, inflammation, and fibrosis via mechanisms such as gut barrier dysfunction, microbial metabolite production, and systemic inflammation. Dietary patterns, including the Mediterranean diet, are highlighted for their role in modulating the gut microbiota, improving gut-liver axis integrity, and attenuating liver injury. Additionally, emerging microbiota-based interventions, such as fecal microbiota transplantation and bacteriophage therapy, show promise as therapeutic strategies for steatotic liver disease. However, challenges such as population heterogeneity, methodological variability, and knowledge gaps hinder the translational application of current findings. Addressing these barriers through standardized approaches and integrative research will pave the way for microbiota-targeted therapies to mitigate the global burden of steatotic liver disease.}, }
@article {pmid40005600, year = {2025}, author = {Misu, IJ and Kayess, MO and Siddiqui, MN and Gupta, DR and Islam, MN and Islam, T}, title = {Microbiome Engineering for Sustainable Rice Production: Strategies for Biofertilization, Stress Tolerance, and Climate Resilience.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020233}, pmid = {40005600}, issn = {2076-2607}, abstract = {The plant microbiome, found in the rhizosphere, phyllosphere, and endosphere, is essential for nutrient acquisition, stress tolerance, and the overall health of plants. This review aims to update our knowledge of and critically discuss the diversity and functional roles of the rice microbiome, as well as microbiome engineering strategies to enhance biofertilization and stress resilience. Rice hosts various microorganisms that affect nutrient cycling, growth promotion, and resistance to stresses. Microorganisms carry out these functions through nitrogen fixation, phytohormone and metabolite production, enhanced nutrient solubilization and uptake, and regulation of host gene expression. Recent research on molecular biology has elucidated the complex interactions within rice microbiomes and the signalling mechanisms that establish beneficial microbial communities, which are crucial for sustainable rice production and environmental health. Crucial factors for the successful commercialization of microbial agents in rice production include soil properties, practical environmental field conditions, and plant genotype. Advances in microbiome engineering, from traditional inoculants to synthetic biology, optimize nutrient availability and enhance resilience to abiotic stresses like drought. Climate change intensifies these challenges, but microbiome innovations and microbiome-shaping genes (M genes) offer promising solutions for crop resilience. This review also discusses the environmental and agronomic implications of microbiome engineering, emphasizing the need for further exploration of M genes for breeding disease resistance traits. Ultimately, we provide an update to the current findings on microbiome engineering in rice, highlighting pathways to enhance crop productivity sustainably while minimizing environmental impacts.}, }
@article {pmid40005592, year = {2025}, author = {Ohwofasa, A and Dhami, M and Winefield, C and On, SLW}, title = {Analysis of Bacterial and Fungal Communities and Organic Acid Content in New Zealand Lambic-Style Beers: A Climatic and Global Perspective.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/microorganisms13020224}, pmid = {40005592}, issn = {2076-2607}, abstract = {Beer produced by autochthonous microbial fermentation is a long-established craft beer style in Belgium that has now been implemented commercially in New Zealand. We used a metabarcoding approach to characterize the microbiome of 11 spontaneously fermented beers produced by a single brewery in Oamaru from 2016 to 2022. Key organic acid concentrations were also determined. Both bacterial and fungal populations varied considerably between vintages and between individual brews produced in 2020. Similarly, for organic acids, the concentrations of L-malic acid, succinic acid, and L-lactic acid statistically differed from one vintage to another. Moreover, a correlation between the concentrations of certain organic acids and microbial composition was inferred by ordination analyses. Through reference to publicly available climate data, humidity and maximum temperature seemed to enhance the abundance of Penicillium and Hanseniaspora in beer microbiota. However, comparison with previously published studies of Belgian lambic beers, similar Russian ales, and publicly available temperature data from these regions showed that the microbial populations of these were relatively stable despite greater extremes of weather. Our results suggest that while climatic variables may influence microbial populations during beer making that employs autochthonous fermentation in New Zealand, such variation is not evident where similar beers are produced in facilities with a long-established history of production. These findings have implications for lambic-style beer production in the context of global climate change, notably where microbial populations may lack environmental adaptation.}, }
@article {pmid40005488, year = {2025}, author = {Cao, J and Ma, Q and Shi, J and Wang, X and Ye, D and Liang, J and Zou, J}, title = {Cariogenic Microbiota and Emerging Antibacterial Materials to Combat Dental Caries: A Literature Review.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/pathogens14020111}, pmid = {40005488}, issn = {2076-0817}, support = {82170947//National Natural Science Foundation of China/ ; 82301060//National Natural Science Foundation of China/ ; 2023NSFSC1508//Natural Science Foundation of Sichuan Province/ ; RD-02-202210//Research and Develop Program, West China Hospital of Stomatology Sichuan University/ ; }, mesh = {*Dental Caries/prevention &amp; control/microbiology ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use/adverse effects ; *Microbiota/drug effects ; }, abstract = {Dental caries is the most common oral disease in the world and a chronic infectious disease. The cariogenic microbiome plays an important role in the process of caries. The ecological imbalance of microbiota leads to low pH, which causes caries. Therefore, antibacterial materials have always been a hot topic. Traditional antibacterial materials such as cationic antibacterial agents, metal ion antibacterial agents, and some natural extract antibacterial agents have good antibacterial effects. However, they can cause bacterial resistance and have poor biological safety when used for long-term purposes. Intelligent antibacterial materials, such as pH-responsive materials, nanozymes, photoresponsive materials, piezoelectric materials, and living materials are emerging antibacterial nano-strategies that can respond to the caries microenvironment or other specific stimuli to exert antibacterial effects. Compared with traditional antibacterial materials, these materials are less prone to bacterial resistanceand have good biological safety. This review summarizes the characteristics of cariogenic microbiota and some traditional or emerging antibacterial materials. These emerging antibacterial materials can accurately act on the caries microenvironment, showing intelligent antibacterial effects and providing new ideas for caries management.}, }
@article {pmid40005459, year = {2025}, author = {Rocks, MC and Bhatnagar, P and Verticchio Vercellin, A and Sala, L and Siesky, B and Antman, G and Wood, K and Sacco, R and Harris, A}, title = {Mathematical Modeling and Artificial Intelligence to Explore Connections Between Glaucoma and the Gut Microbiome.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {61}, number = {2}, pages = {}, doi = {10.3390/medicina61020343}, pmid = {40005459}, issn = {1648-9144}, support = {R01EY030851/NH/NIH HHS/United States ; R01EY034718/NH/NIH HHS/United States ; NYEE Foundation grants (grant number N/A)//NYEE Foundation/ ; The Glaucoma Foundation grant (grant number N/A)//The Glaucoma Foundation/ ; Challenge Grant award//Research to Prevent Blindness/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Artificial Intelligence ; *Models, Theoretical ; Glaucoma, Open-Angle/physiopathology/microbiology ; Glaucoma/microbiology/physiopathology ; }, abstract = {Background and Objectives: Glaucoma is a major cause of irreversible blindness, with primary open-angle glaucoma (POAG) being the most prevalent form. While elevated intraocular pressure (IOP) is a well-known risk factor for POAG, emerging evidence suggests that the human gut microbiome may also play a role in the disease. This review synthesizes current findings on the relationship between gut microbiome and glaucoma, with a focus on mathematical modeling and artificial intelligence (AI) approaches to uncover key insights. Materials and Methods: A comprehensive literature search was conducted using PubMed and Google Scholar, covering studies from its inception to 1 August 2024. Selected studies included basic science, observational research, and those incorporating mathematical-related models. Results: Traditional statistical and machine learning approaches, such as random forest regression and Mendelian randomization, have identified associations between specific microbiota and POAG features. These findings highlight the potential of AI to explore complex, nonlinear interactions in the gut-eye axis. However, limitations include variability in study designs and a lack of integrative, mechanistic models. Conclusions: Preliminary evidence supports the existence of a gut-eye axis influencing POAG disease. Combining data-driven and mechanism-driven models with AI could identify therapeutic targets and novel biomarkers. Future research should prioritize longitudinal studies in diverse populations and integrate physiological data to improve model accuracy and clinical relevance. Furthermore, physics-based models could deepen our mechanistic understanding of the gut-eye axis in glaucoma, advancing beyond associative findings to actionable insights.}, }
@article {pmid40005401, year = {2025}, author = {Straume, Z and Krūmiņa, N and Elbere, I and Rozenberga, M and Erts, R and Rudzīte, D and Proskurina, A and Krumina, A}, title = {Impact of Vitamins, Antibiotics, Probiotics, and History of COVID-19 on the Gut Microbiome in Ulcerative Colitis Patients: A Cross-Sectional Study.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {61}, number = {2}, pages = {}, doi = {10.3390/medicina61020284}, pmid = {40005401}, issn = {1648-9144}, support = {1.1.1.1/21/A/029//the European Regional Development Fund (ERDF)/ ; }, mesh = {Humans ; Cross-Sectional Studies ; Female ; *Colitis, Ulcerative/drug therapy/microbiology ; Male ; *Gastrointestinal Microbiome/drug effects ; *COVID-19 ; *Vitamins/therapeutic use ; Adult ; Middle Aged ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Probiotics/therapeutic use ; *SARS-CoV-2 ; Aged ; }, abstract = {Background and Objectives: The human gut microbiome is essential for the health of the host and is affected by antibiotics and coronavirus disease 2019 (COVID-19). The gut microbiome is recognized as a contributing factor in the development of ulcerative colitis. Specific vitamins and probiotics have been demonstrated to positively influence the microbiome by enhancing the prevalence of expected beneficial microorganisms. Materials and Methods: Forty-nine ulcerative colitis (UC) outpatients from Riga East Clinical University Hospital were enrolled in this cross-sectional study from June 2021 to December 2021. All patients were divided into groups based on history of COVID-19 (COVID-19 positive vs. COVID-19 negative) in the last six months. Information about antibiotic, probiotic, and vitamin intake were outlined, and faecal samples were collected. The MetaPhlAn v.2.6.0 tool was used for the taxonomic classification of the gut microbiome metagenome data. Statistical analysis was performed using R 4.2.1. Results: Of the 49 patients enrolled, 31 (63%) were male and 18 (37%) were female. Coronavirus disease 2019 was found in 14 (28.6%) patients in the last 6 months. Verrucomicrobia was statistically significantly lower in the COVID-19 positive group (M = 0.05; SD = 0.11) compared to the COVID-19 negative group (M = 0.5; SD = 1.22), p = 0.03. Antibiotic non-users had more Firmicutes in their microbiome than antibiotic users (p = 0.008). The most used vitamin supplement was vitamin D (N = 18), fifteen (42.9%) of the patients were COVID-19 negative and 3 (21.4%) were COVID-19 positive over the last six months (p > 0.05). Vitamin C users had more Firmicutes in their gut microbiome compared to non-users (Md = 72.8 [IQR: 66.6; 78.7] vs. Md = 60.1 [IQR: 42.4; 67.7]), p = 0.01. Conclusions: Antibiotic non-users had more Firmicutes than antibiotic users in their gut microbiome. Only vitamin C had statistically significant results; in users, more Firmicutes were observed. A mild course of COVID-19 may not influence ulcerative colitis patients' gut microbiome.}, }
@article {pmid40005309, year = {2025}, author = {Jarmakiewicz-Czaja, S and Sokal-Dembowska, A and Filip, R}, title = {Effects of Selected Food Additives on the Gut Microbiome and Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD).}, journal = {Medicina (Kaunas, Lithuania)}, volume = {61}, number = {2}, pages = {}, doi = {10.3390/medicina61020192}, pmid = {40005309}, issn = {1648-9144}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/drug effects ; *Food Additives/adverse effects ; Fatty Liver/etiology/metabolism ; Metabolic Diseases/metabolism ; Obesity/complications/metabolism ; }, abstract = {The purpose of this article is to present selected food additives as disruptors of normal intestinal homeostasis with a potential impact on the development of metabolic dysfunction-associated steatotic liver disease (MASLD). A comprehensive literature search was conducted in three major electronic databases: PubMed, ScienceDirect, and Google Scholar. MASLD is a prevalent liver condition that is closely related to the global rise in obesity. Its pathogenesis is multifactorial, with genetic, environmental, and metabolic factors playing a key role. The "multiple-hit" hypothesis suggests that a Western-style diet, rich in ultra-processed foods, saturated fats, and food additives, combined with low physical activity, contributes to obesity, which promotes lipid accumulation in the liver. Recent studies underscore the role of impaired intestinal homeostasis in the development of MASLD. Food additives, including preservatives, emulsifiers, and sweeteners, affect gut health and liver function. Selected preservatives inhibit pathogenic microorganisms but disrupt the intestinal microbiota, leading to changes in intestinal permeability and liver dysfunction. Some emulsifiers and thickeners can cause inflammation and alter the gut microbiome, contributing to liver steatosis. Furthermore, the use of sweeteners such as sucralose and aspartame has been linked to changes in liver metabolism and intestinal microbial composition, which in turn promotes metabolic disorders.}, }
@article {pmid40005065, year = {2025}, author = {Noureldein, MH and Rumora, AE and Teener, SJ and Rigan, DM and Hayes, JM and Mendelson, FE and Carter, AD and Rubin, WG and Savelieff, MG and Feldman, EL}, title = {Dietary Fatty Acid Composition Alters Gut Microbiome in Mice with Obesity-Induced Peripheral Neuropathy.}, journal = {Nutrients}, volume = {17}, number = {4}, pages = {}, doi = {10.3390/nu17040737}, pmid = {40005065}, issn = {2072-6643}, support = {1R01DK076169-00A1/NH/NIH HHS/United States ; 1R01DK115255-00A1/NH/NIH HHS/United States ; 1K99AG081390-00A1/NH/NIH HHS/United States ; 1R00DK119366-00A1/NH/NIH HHS/United States ; 1P30DK063608-00A20/NH/NIH HHS/United States ; 1R01DK130913-00A1/NH/NIH HHS/United States ; P30DK020572//Michigan Diabetes Research Center/ ; not applicable//Dr. John H. Doran Neuropathy Research Initiative/ ; not applicable//Richard and Jane Manoogian Foundation/ ; not applicable//Nathan and Rose Milstein Research Fund/ ; not applicable//Sinai Medical Staff Foundation/ ; not applicable//Taubman Foundation/ ; not applicable//NeuroNetwork for Emerging Therapies/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Obesity/microbiology ; Mice ; *Peripheral Nervous System Diseases/etiology ; *Mice, Inbred C57BL ; *Fatty Acids/metabolism ; *Diet, High-Fat/adverse effects ; Male ; Fecal Microbiota Transplantation ; Dietary Fats ; Disease Models, Animal ; Fatty Acids, Monounsaturated/metabolism ; }, abstract = {BACKGROUND: Peripheral neuropathy (PN), a complication of diabetes and obesity, progresses through a complex pathophysiology. Lifestyle interventions to manage systemic metabolism are recommended to prevent or slow PN, given the multifactorial risks of diabetes and obesity. A high-fat diet rich in saturated fatty acids (SFAs) induces PN, which a diet rich in monounsaturated fatty acids (MUFAs) rescues, independent of weight loss, suggesting factors beyond systemic metabolism impact nerve health. Interest has grown in gut microbiome mechanisms in PN, which is characterized by a distinct microbiota signature that correlates with sciatic nerve lipidome.<br><br>METHODS: Herein, we postulated that SFA- versus MUFA-rich diet would impact gut microbiome composition and correlate with PN development. To assess causality, we performed fecal microbiota transplantation (FMT) from donor mice fed SFA- versus MUFA-rich diet to lean recipient mice and assessed metabolic and PN phenotypes.<br><br>RESULTS: We found that the SFA-rich diet altered the microbiome community structure, which the MUFA-rich diet partially reversed. PN metrics correlated with several microbial families, some containing genera with feasible mechanisms of action for microbiome-mediated effects on PN. SFA and MUFA FMT did not impact metabolic phenotypes in recipient mice although SFA FMT marginally induced motor PN.<br><br>CONCLUSIONS: The involvement of diet-mediated changes in the microbiome on PN and gut-nerve axis may warrant further study.}, }
@article {pmid40005049, year = {2025}, author = {Aliberti, SM and Capunzo, M}, title = {The Power of Environment: A Comprehensive Review of the Exposome's Role in Healthy Aging, Longevity, and Preventive Medicine-Lessons from Blue Zones and Cilento.}, journal = {Nutrients}, volume = {17}, number = {4}, pages = {}, doi = {10.3390/nu17040722}, pmid = {40005049}, issn = {2072-6643}, mesh = {*Longevity ; Humans ; *Healthy Aging ; *Exposome ; Gastrointestinal Microbiome/physiology ; Life Style ; Environmental Exposure/adverse effects ; Aging/physiology ; Exercise ; Environment ; }, abstract = {Aging and longevity are shaped by the exposome, a dynamic network of environmental, social, and biological factors. Understanding how these exposures interact with biological mechanisms can inform strategies for healthier aging. Background/Objectives: This review explores the exposome as a dynamic system encompassing both protective and risk factors, with a specific focus on how beneficial environmental exposures, microbiome diversity, lifestyle behaviors, and resilience mechanisms contribute to successful aging. By analyzing high-longevity populations, such as the Blue Zones and Cilento, it aims to identify common determinants of successful aging. Methods: A mixed-method study was conducted, combining a systematic review of the English literature (2003-2024) with a comparative analysis of longevity regions. A structured search was performed in PubMed, Scopus, and Google Scholar using keywords such as "longevity", "Blue Zones", "Cilento", "microbiome", "environmental factors", and related terms. Additionally, qualitative and quantitative analysis were applied to assess key protective factors across different aging models. Results: This study identified key factors contributing to successful aging in longevity hotspots, including sustained exposure to biodiverse natural environments, adherence to Mediterranean or plant-based diet rich in polyphenols and probiotics, regular physical activity, strong social networks, and psychological resilience. A novel aspect of this review is the role of the gut microbiome as a mediator between environmental exposures and immune-metabolic health, influencing inflammation modulation and cellular aging. Despite geographic and cultural differences, case studies reveal a shared pattern of protective factors that collectively enhance lifespan and healthspan. Conclusions: The exposome is a critical determinant of aging trajectories, acting through complex interactions between environmental and biological mechanisms. By integrating insights from high-longevity populations, this mixed-method study proposes a comprehensive framework for optimizing microbiome health, enhancing resilience, and promoting protective environmental exposures. These findings provide a translational perspective to guide future interventions in aging research and global health initiatives.}, }
@article {pmid40005018, year = {2025}, author = {Jarrett, H and Medlin, S and Morehen, JC}, title = {The Role of the Gut Microbiome and Probiotics in Sports Performance: A Narrative Review Update.}, journal = {Nutrients}, volume = {17}, number = {4}, pages = {}, doi = {10.3390/nu17040690}, pmid = {40005018}, issn = {2072-6643}, support = {NA//Heights/ ; }, mesh = {*Probiotics/administration &amp; dosage ; Humans ; *Gastrointestinal Microbiome/physiology ; *Athletic Performance/physiology ; Dietary Supplements ; Physical Endurance ; Exercise/physiology ; Sports Nutritional Physiological Phenomena ; }, abstract = {Background/Objectives: Gut microbiome modulation through probiotics is a growing area of research, with several investigations reporting beneficial health outcomes for the host. Physical exercise has been shown to impact gut microbiome diversity. Emerging evidence suggests that probiotic supplementation can affect exercise performance. However, the mechanisms and domain-specific effects of gut microbiome modulation on performance remain to be elucidated. This narrative review aims to investigate the potential mechanisms underpinning the ergogenic benefits of probiotics and further define the current evidence base for specific performance domains. Discussion: The literature suggests that improved recovery after intense training regimes, enhanced nutrient absorption, alleviation of gastrointestinal symptoms, and improved immune function may underpin the beneficial effects of probiotics on sporting performance. A small number of trials also suggest that probiotic supplementation may improve symptoms of performance anxiety. However, further research is warranted on this topic. The evidence is most substantial for improvements in endurance performance, whilst only a few trials have investigated the impact upon power performance, albeit with promising results. Conclusions/Future Perspectives: In summary, probiotic supplementation has been shown to improve sporting performance; future research may wish to further explore the impact on power performance and investigate specific mechanisms of action.}, }
@article {pmid40004999, year = {2025}, author = {Alia, S and Andrenelli, E and Di Paolo, A and Membrino, V and Mazzanti, L and Capecci, M and Vignini, A and Fabri, M and Ceravolo, MG}, title = {Chemosensory Impairments and Their Impact on Nutrition in Parkinson's Disease: A Narrative Literature Review.}, journal = {Nutrients}, volume = {17}, number = {4}, pages = {}, doi = {10.3390/nu17040671}, pmid = {40004999}, issn = {2072-6643}, mesh = {Humans ; *Parkinson Disease/complications ; *Nutritional Status ; *Olfaction Disorders/etiology ; Quality of Life ; Taste Disorders/etiology ; Taste Perception ; Malnutrition/etiology ; }, abstract = {Parkinson's disease (PD) is a neurological disorder characterized by heterogeneous symptomatology, in which the classical motor features of Parkinsonism are associated with clinically significant non-motor symptoms. Olfactory alteration, as a manifestation of PD's premotor or prodromal phase, is well known. These impairments can lead to malnutrition, decreased appetite, and depression, thereby worsening patients' quality of life. However, only a few studies clarify the mechanisms, characteristics, and clinical diagnostic and therapeutic implications of impaired taste perception. Moreover, unlike most motor features of PD, non-motor symptoms often have limited treatment options or responses. The purpose of this review is to collate and describe all relevant studies on taste and smell alterations in patients with PD and how these alterations could affect nutritional status. Our search aimed to identify English-language research articles and reviews published in peer-reviewed journals over the past two decades (2004-2024), while also including older foundational studies when relevant. Several studies show that hyposmia in PD worsens over time, potentially linked to structural changes in the brain's basal ganglia and piriform cortex. Severe hyposmia is also associated with a higher risk of dementia in PD patients and can negatively influence quality of life, affecting social interactions and nutrition. Regarding taste perception, recent studies have suggested that hypogeusia may occur even in the prodromal stage of PD, such as in patients with REM sleep disorder, although the exact mechanisms remain unclear. Additionally, research has explored the role of bitter taste receptors and their possible involvement in inflammation and α-synuclein misfolding, suggesting a link between taste dysfunction and immune system changes in PD. Attention was then focused on the gut microbiota's link to the central nervous system and its contribution to gustatory dysfunctions, as well as how the nasal microbiome influences PD progression by altering the olfactory system. Nowadays, the primary role of a correct diet in the overall treatment of PD patients is becoming increasingly important for practitioners. Diet should be included among the available aids to counteract some aspects of the pathology itself. For all these reasons, it is also crucial to determine whether these chemosensory impairments could serve as disease markers, helping to better understand the underlying mechanisms of the disease.}, }
@article {pmid40004979, year = {2025}, author = {Climent, E and Hevilla, F and Padial, M and Barril-Cuadrado, G and Blanca, M and Jiménez-Salcedo, T and López-Picasso, M and Nogueira-Pérez, &#xc1; and Olveira, G}, title = {Psychobiotic Protection of Nutritional Supplements and Probiotics in Patients Undergoing Hemodialysis: A Randomized Trial.}, journal = {Nutrients}, volume = {17}, number = {4}, pages = {}, doi = {10.3390/nu17040652}, pmid = {40004979}, issn = {2072-6643}, support = {RTC-2017-5959-1//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; PI18/01041//Instituto de Salud Carlos III/ ; }, mesh = {Humans ; *Probiotics/administration &amp; dosage/therapeutic use ; *Dietary Supplements ; *Renal Dialysis ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; *Depression/prevention &amp; control ; *Brain-Derived Neurotrophic Factor/blood/metabolism ; Aged ; *Anxiety ; *Feces/microbiology ; Biomarkers/blood ; Lipopolysaccharides/blood ; Acute-Phase Proteins ; Haptoglobins/metabolism ; Carrier Proteins/blood/metabolism ; Malnutrition/prevention &amp; control ; Membrane Glycoproteins ; Protein Precursors/blood ; }, abstract = {BACKGROUND/OBJECTIVES: The prevalence of depression and anxiety symptoms is remarkably high in malnourished individuals undergoing hemodialysis. The goal of this project was to evaluate the impact of administering an oral nutritional supplement combined with a probiotic blend on the microbiota, intestinal permeability, and depression symptoms in malnourished hemodialysis patients.<br><br>METHODS: With this aim, a randomized trial was conducted with three parallel groups: a control group with individualized diet, a supplement-placebo (SU-PL) group with oral nutritional supplementation (ONS), and a supplement-probiotic (SU-PR) group with ONS in conjunction with a probiotic blend. Blood and fecal samples were collected at basal time, and at 3 and 6 months. Several blood biomarkers, like zonulin, lipopolysaccharide-binding protein (LBP), lipopolysaccharide (LPS), and brain-derived neurotrophic factor (BDNF), were measured, and the fecal microbiome was sequenced with the Illumina platform. The Hospital Anxiety and Depression Scale (HADS) was used for the estimation of depression (HADS-D) and anxiety (HADS-A) symptoms, along with the standardized mental health index SF12-MH from the general health questionnaire SF-12.<br><br>RESULTS: The results showed that patients who consumed the probiotic blend maintained the LPS levels from their baseline readings and decreased their BDNF levels compared to the SU-PL or control groups. Moreover, a significant decrease in HADS-D scores (less depressive symptoms) and an increase in SF12-MH scores (higher quality of life) were found in that group in comparison to the other groups. The intervention produced an impact on the microbiome population, where the SU-PR group had reduced Akkermansia abundance with respect to the other groups, while their Acidaminococcus abundance decreased and their Barnesiella abundance increased with respect to the SU-PL group.<br><br>CONCLUSIONS: Overall, the results indicate that the probiotic with the nutritional supplement could reduce the intestinal permeability biomarkers and improve depressive symptoms and quality of life in malnourished hemodialysis patients.}, }
@article {pmid40004971, year = {2025}, author = {Gweon, TG and Kang, SB and Na, SY and Oh, DJ and Kim, SW and Seo, GS and Cho, JY}, title = {Five-Day Treatment with B. licheniformis Along with Classical Vancomycin Treatment Was Effective in Preserving Gut Microbiota in Patients with Clostridioides difficile Infection.}, journal = {Nutrients}, volume = {17}, number = {4}, pages = {}, doi = {10.3390/nu17040641}, pmid = {40004971}, issn = {2072-6643}, support = {not available//Aju pharmaceutical/ ; }, mesh = {Humans ; *Vancomycin/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; Middle Aged ; *Clostridium Infections/drug therapy/microbiology ; *Anti-Bacterial Agents/administration &amp; dosage ; *Probiotics/administration &amp; dosage/therapeutic use ; Aged ; *Bacillus licheniformis ; Clostridioides difficile/drug effects ; Treatment Outcome ; Adult ; Republic of Korea ; }, abstract = {Background/Objectives:Clostridioides difficile infection (CDI) is an important nosocomial diarrheal disease. The benefits of the probiotic Bacillus licheniformis (B. licheniformis) in the preservation of intestinal microbiota have not been studied in patients with CDI to date. Therefore, we aimed to investigate the efficacy of B. licheniformis in preserving the intestinal microbiota in patients with CDI. Methods: A multicenter, randomized, placebo-controlled trial was carried out at six academic centers in Korea. Individuals diagnosed with mild to moderate CDI were included in this trial. CDI was treated with vancomycin 125 mg four times daily for two weeks. Along with vancomycin, B. licheniformis was administered for five days in this study, while a placebo was given to the placebo group. Microbiome analysis was performed before and five days after administering vancomycin and B. licheniformis or placebo, using 16S rRNA amplicon sequencing. Alpha and beta diversity was compared between the two groups. Results: A total of 35 participants were finally included in this study, with 16 in the study group and 19 in the placebo group. The alpha diversity was similar in both groups before CDI treatment. After five days of the administration of vancomycin and B. licheniformis or placebo, alpha diversity did not decrease in the study group (Chao1 index, p = 0.665; observed features, p = 0.692). In contrast, alpha diversity decreased in the placebo group (Chao1 index, p = 0.011; observed features, p = 0.011). Beta diversity did not differ between the two groups. Conclusions: The addition of B. licheniformis to vancomycin was effective in preserving gut microbiota in patients with CDI.}, }
@article {pmid40004970, year = {2025}, author = {Kaimori, JY and Sakaguchi, Y and Oka, T and Isaka, Y}, title = {Plant-Dominant Low-Protein Diets: A Promising Dietary Strategy for Mitigating Disease Progression in People with Chronic Kidney Disease-A Comprehensive Review.}, journal = {Nutrients}, volume = {17}, number = {4}, pages = {}, doi = {10.3390/nu17040643}, pmid = {40004970}, issn = {2072-6643}, mesh = {Humans ; *Diet, Protein-Restricted/methods ; *Renal Insufficiency, Chronic/diet therapy/therapy ; *Disease Progression ; *Diet, Vegetarian ; Gastrointestinal Microbiome ; }, abstract = {Chronic kidney disease (CKD) is a global health crisis affecting over 10% of the population, with mortality rates increasing significantly. Current management strategies, including expensive medications and renal replacement therapies, highlight the need for cost-effective, conservative approaches. This review examines the evidence for plant-dominant low-protein diets (PLADO) in managing non-dialysis-dependent CKD. Existing guidelines for protein restriction in CKD vary considerably, with inconsistencies and a lack of personalization noted in the KDOQI and KDIGO recommendations. While traditional low-protein diet trials show limited success due to poor adherence and marginal benefits, PLADO offers a potentially more sustainable alternative. PLADO's advantages include improved nutrient density, reduced dietary acid load, anti-inflammatory effects, and beneficial modulation of the gut microbiome, potentially reducing uremic toxins and improving cardiovascular health. However, challenges remain, including adherence issues, potential nutrient deficiencies, and potassium management. Although observational studies show promise, further large-scale randomized controlled trials are necessary to validate PLADO's efficacy and establish optimal dietary composition. A personalized, multidisciplinary approach is essential for successful implementation and monitoring to maximize PLADO's benefits in improving outcomes for individuals with NDD-CKD.}, }
@article {pmid40004966, year = {2025}, author = {Mohammadi, F and Rudkowska, I}, title = {Dietary Lipids, Gut Microbiota, and Their Metabolites: Insights from Recent Studies.}, journal = {Nutrients}, volume = {17}, number = {4}, pages = {}, doi = {10.3390/nu17040639}, pmid = {40004966}, issn = {2072-6643}, mesh = {*Gastrointestinal Microbiome/physiology/drug effects ; Humans ; Animals ; *Dietary Fats ; Bile Acids and Salts/metabolism ; Fatty Acids, Volatile/metabolism ; Fatty Acids ; Fatty Acids, Unsaturated ; }, abstract = {Dietary lipid intake can influence the gut microbiota (GM) and their metabolites, such as short-chain fatty acids (SCFA) and bile acids, which are key mediators of health. The objective is to examine how dietary lipids' quantity and quality influence the GM and metabolite profiles. A literature review of 33 studies in animals and humans was performed on the effects of saturated fatty acids (SFAs), monounsaturated fatty acids (MUFAs), polyunsaturated fatty acids (PUFAs), trans-fatty acids (TFAs), and sterols on GM composition and gut-derived metabolites. The results show that diets rich in MUFAs, n-3 PUFAs, and short-chain FAs have the potential to enhance beneficial bacteria and metabolites. In addition, trans-palmitoleic acid, conjugated linoleic acid, and phytosterols may also have potentially beneficial effects on GM, but more research is needed. Medium-chain FAs and n-6 PUFAs have variable effects on the GM. Conversely, intakes of high-fat diets, long-chain SFAs, industrial TFAs, and cholesterol disrupt GM balance. In conclusion, animal studies clearly demonstrate that dietary fats influence the GM and related metabolites. Yet, human studies are limited. Therefore, well-designed human studies that consider the whole diet and baseline health status are needed to better understand the effects of dietary lipids on GM.}, }
@article {pmid40004925, year = {2025}, author = {Malaweera, A and Huang, L and McMahon, L}, title = {Benefits and Pitfalls of Uraemic Toxin Measurement in Peritoneal Dialysis.}, journal = {Journal of clinical medicine}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/jcm14041395}, pmid = {40004925}, issn = {2077-0383}, abstract = {Chronic kidney disease is a global health burden with a rising incidence and prevalence in developed and developing nations. Once established, it results in a progressive accumulation of a myriad of uraemic toxins. Peritoneal dialysis (PD) uses the body's peritoneal membrane to remove these toxins across a semipermeable membrane to restore and maintain homeostasis. Traditionally, dialysis adequacy has been measured through clearance of urea and creatinine. However, numerous studies have shown marginal links comparing the clearance of urea and creatinine with clinical outcomes reflected in the recent changes to the ISPD guidelines on dialysis adequacy. Instead, attention has focused on protein-bound uraemic toxins (PBTs). Produced by gut bacteria, these molecules are highly protein-bound and poorly removed by either dialysis or absorptive agents. Elevated concentrations of molecules such as p-cresyl sulfate and indoxyl sulfate have been associated with abnormal cellular function and poor patient outcomes. However, widespread use of these measures to determine dialysis adequacy has been limited by the need for specialized techniques required for measurement. Altering the gut microbiome to reduce generation of PBTs through increased dietary fiber might be an alternate approach to better patient outcomes, with some initial positive reports. This report explores advantages and limitations of measuring uraemic toxins in PD, now and in the foreseeable future.}, }
@article {pmid40004729, year = {2025}, author = {Sánchez-Pellicer, P and Álamo-Marzo, JM and Martínez-Villaescusa, M and Núñez-Delegido, E and Such-Ronda, JF and Huertas-López, F and Serrano-López, EM and Martínez-Moreno, D and Navarro-López, V}, title = {Comparative Analysis of Gut Microbiota in Patients with Irritable Bowel Syndrome and Healthy Controls.}, journal = {Journal of clinical medicine}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/jcm14041198}, pmid = {40004729}, issn = {2077-0383}, abstract = {Background/Objectives: Growing evidence highlights the pivotal role of gut dysbiosis in the pathophysiology of irritable bowel syndrome (IBS). Despite this, the identification of an "IBS microbiota signature" remains elusive, primarily due to the influence of genetic, dietary, and environmental factors. To address these confounding variables, it is critical to perform comparative analyses using a control group derived from the same community as the IBS patients. This study aimed to evaluate and contrast the gut microbiota composition of IBS patients with healthy controls. Methods: We compared the gut microbiota from stool samples of 25 IBS patients diagnosed according to the Rome IV criteria, and 110 healthy subjects without acute or chronic diseases and not on continuous medication. The high-throughput sequencing of the V3-V4 regions of the 16S rRNA gene was conducted for microbiota analysis. Results: The IBS gut microbiota was richer but exhibited lower alpha diversity compared to the control group, suggesting simplification and imbalance. A beta diversity analysis revealed overall compositional differences between the two groups. A heat tree analysis highlighted key IBS-associated changes, including a decrease in Firmicutes, mainly due to Clostridia, and an increase in Bacteroidota, driven by an expansion of Bacteroidales families. Differential expression analyses identified important genera within these taxa like Bacteroides, Faecalibacterium, and Blautia, which could serve as microbiota-based biomarkers for IBS. Conclusions: Our results reveal both statistically and clinically significant differences in gut microbiota composition and diversity between IBS patients and healthy controls from the same community. These findings provide a deeper understanding of how alterations in the gut microbiota may contribute to IBS symptoms, offering new insights into the diagnosis and potential treatments.}, }
@article {pmid40004537, year = {2025}, author = {Nai, S and Song, J and Su, W and Liu, X}, title = {Bidirectional Interplay Among Non-Coding RNAs, the Microbiome, and the Host During Development and Diseases.}, journal = {Genes}, volume = {16}, number = {2}, pages = {}, doi = {10.3390/genes16020208}, pmid = {40004537}, issn = {2073-4425}, support = {62450082463091//Shandong University/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *RNA, Untranslated/genetics ; Dysbiosis/microbiology/genetics ; MicroRNAs/genetics ; Animals ; Inflammatory Bowel Diseases/microbiology/genetics ; Obesity/microbiology/genetics ; Cardiovascular Diseases/genetics/microbiology ; Colorectal Neoplasms/microbiology/genetics ; }, abstract = {It is widely known that the dysregulation of non-coding RNAs (ncRNAs) and dysbiosis of the gut microbiome play significant roles in host development and the progression of various diseases. Emerging evidence has highlighted the bidirectional interplay between ncRNAs and the gut microbiome. This article aims to review the current understanding of the molecular mechanisms underlying the crosstalk between ncRNAs, especially microRNA (miRNA), and the gut microbiome in the context of development and diseases, such as colorectal cancer, inflammatory bowel diseases, neurological disorders, obesity, and cardiovascular disease. Ultimately, this review seeks to provide a foundation for exploring the potential roles of ncRNAs and gut microbiome interactions as biomarkers and therapeutic targets for clinical diagnosis and treatment, such as ncRNA mimics, antisense oligonucleotides, and small-molecule compounds, as well as probiotics, prebiotics, and diets.}, }
@article {pmid40004244, year = {2025}, author = {Blankestijn, JM and Baalbaki, N and Beijers, RJHCG and Cornelissen, MEB and Wiersinga, WJ and Abdel-Aziz, MI and Maitland-van der Zee, AH and , }, title = {Exploring Heterogeneity of Fecal Microbiome in Long COVID Patients at 3 to 6 Months After Infection.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, doi = {10.3390/ijms26041781}, pmid = {40004244}, issn = {1422-0067}, support = {LSHM20104; LSHM20068//Health Holland/ ; }, mesh = {Humans ; *COVID-19/microbiology/virology ; *Feces/microbiology/virology ; Male ; Female ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Aged ; *SARS-CoV-2/isolation &amp; purification ; Adult ; Metagenome ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {An estimated 10% of COVID-19 survivors have been reported to suffer from complaints after at least three months. The intestinal microbiome has been shown to impact long COVID through the gut-lung axis and impact the severity. We aimed to investigate the relationship between the gut microbiome and clinical characteristics, exploring microbiome heterogeneity through clustering. Seventy-nine patients with long COVID evaluated at 3 to 6 months after infection were sampled for fecal metagenome analysis. Patients were divided into two distinct hierarchical clusters, based solely on the microbiome composition. Compared to cluster 1 (n = 67), patients in cluster 2 (n = 12) showed a significantly reduced lung function (FEV1, FVC, and DLCO) and during acute COVID-19 showed a longer duration of hospital admissions (48 compared to 7 days) and higher rates of ICU admissions (92% compared to 22%). Additionally, the microbiome composition showed a reduced alpha diversity and lower proportion of butyrate-producing bacteria in cluster 2 together with higher abundances of Ruminococcus gnavus, Escherichia coli, Veillonella spp. and Streptococcus spp. and reduced abundances of Faecalibacterium prausnitzii and Eubacteria spp. Further research could explore the effect of pre- and pro-biotic supplementation and its impact on lung function and societal participation in long COVID.}, }
@article {pmid40004154, year = {2025}, author = {Rissato, JH and de Melo Pereira, N and Romero, CE and Del Cisne Jadán Luzuriaga, G and Kerges Bueno, BV and Fonseca Cafezeiro, CR and de Alencar Neto, AC and Borges, TS and Freitas Carvalhal, S and Ramires, FJA and Nastari, L and Mady, C and Fernandes, F}, title = {Different Gut Microbiome Profiles in Patients with Transthyretin Amyloidosis with and Without Cardiac Involvement.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, doi = {10.3390/ijms26041689}, pmid = {40004154}, issn = {1422-0067}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *Amyloid Neuropathies, Familial/microbiology/pathology/complications ; Aged ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Echocardiography ; Biomarkers ; Case-Control Studies ; Heart Diseases/microbiology ; }, abstract = {Transthyretin amyloidosis (ATTR amyloidosis) is characterized by the buildup of amyloid protein in organs like the gut and the heart. As a result, hypoperfusion, edema, and dysautonomia cause an imbalance in the gut microbiome. We aimed to identify the gut microbiome composition in ATTR amyloidosis patients with and without heart involvement, as well in controls. Sixty participants were divided into three groups: 20 with ATTR amyloidosis and heart involvement (G1), 19 with ATTR amyloidosis but no heart disease (G2), and 21 controls (G3). The microbiome profiles were obtained through 16S rRNA gene sequencing. Additional evaluations included a clinical questionnaire, echocardiogram, six-minute walk tests, troponin, BNP, and genotype analysis. Compared to G3, G1, and G2 groups had different levels of Streptococcus, Lachnospiraceae, and Sellimonas, while the controls showed a higher relative abundance of Methanosphaera. Streptococcus was linked to higher troponin levels. Lachnospiraceae was associated with lower BNP levels and smaller left atrium volumes. Sellimonas was associated with a higher intestinal symptom score, while Methanosphaera with a lower symptom score. ATTR amyloidosis patients have a different intestinal microbiome profile compared to the control group. There were correlations with genotype, gastrointestinal symptoms, heart failure biomarkers, echocardiographic parameters, and the six-minute walk test.}, }
@article {pmid40004095, year = {2025}, author = {Dawe, HR and Di Meglio, P}, title = {The Aryl Hydrocarbon Receptor (AHR): Peacekeeper of the Skin.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, doi = {10.3390/ijms26041618}, pmid = {40004095}, issn = {1422-0067}, support = {MR/W006820/1/MRC_/Medical Research Council/United Kingdom ; 814364/NPF/National Psoriasis Foundation/United States ; ST1/19//Psoriasis Association/ ; ST1/23//Psoriasis Association/ ; }, mesh = {*Receptors, Aryl Hydrocarbon/metabolism ; Humans ; *Skin/metabolism ; Animals ; *Psoriasis/metabolism ; Dermatitis, Atopic/metabolism ; Signal Transduction ; Carbazoles/pharmacology/metabolism ; Resorcinols ; Stilbenes ; Basic Helix-Loop-Helix Transcription Factors ; }, abstract = {In the last decade, the aryl hydrocarbon receptor (AHR) has emerged as a critical peacekeeper for the maintenance of healthy skin. The evolutionary conservation of AHR implied physiological functions for this receptor, beyond the detoxification of man-made compounds, a notion further supported by the existence of physiological AHR ligands, notably derivates of tryptophan by the host and host microbiome. The UV light-derived ligand, 6-formylindolo[3,2-b]carbazole (FICZ), anticipated a role for AHR in skin, a UV light-exposed organ, where physiological AHR activation promotes a healthy skin barrier and constrains inflammation. The clinical development of tapinarof, the first topical AHR modulating drug for inflammatory skin disease, approved by the FDA for mild-to-moderate psoriasis and poised for approval in atopic dermatitis, supports the therapeutic targeting of the AHR pathway to harness its beneficial effect in skin inflammation. Here, we describe how a tightly controlled, physiological activation of the AHR pathway maintains skin homeostasis, and discuss how the pathway is dysregulated in psoriasis and atopic dermatitis, identifying areas offering opportunities for alternative therapeutic approaches, for further investigation.}, }
@article {pmid40004041, year = {2025}, author = {Park, W and Lee, SK and Gwack, J and Lee, SY and Cho, YG and Kang, SB and Park, J}, title = {Dysbiosis of Bile Microbiota in Cholangiocarcinoma Patients: A Comparison with Benign Biliary Diseases.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, doi = {10.3390/ijms26041577}, pmid = {40004041}, issn = {1422-0067}, support = {NRF-2022R1I1A2070940//National Research Foundation/ ; }, mesh = {Humans ; *Cholangiocarcinoma/microbiology ; *Dysbiosis/microbiology ; *Bile/microbiology ; Male ; *Microbiota ; Middle Aged ; Female ; *Bile Duct Neoplasms/microbiology ; *RNA, Ribosomal, 16S/genetics ; Aged ; Bacteria/genetics/classification/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Biliary Tract Diseases/microbiology ; Adult ; }, abstract = {Dysbiosis in the bile microbiota of cholangiocarcinoma (CCA) patients suggests a potential role for microbial alterations in the pathogenesis of CCA. This study aimed to investigate bile microbial communities in patients with CCA and compare them to those in individuals with benign biliary diseases as a control (CTR) group. Microbial profiling was conducted using next-generation sequencing (NGS), targeting the V3-V4 regions of the 16S rRNA gene, followed by bioinformatics analysis using the VSEARCH and EzBioCloud platforms. Alpha and beta diversity analyses were performed to assess microbial richness and structural differences. The linear discriminant analysis effect size (LEfSe) was utilized to identify potential microbial biomarkers. Results: This study identified distinct microbial profiles in the two groups at both the phylum and genus levels. In the CTR group, Pseudomonadota (65%) was the dominant phyla, while Bacillota (49%) was more abundant in the CCA group. At the genus level, Escherichia (29%), Enterobacteriaceae (12%), Enterococcus (8%), Ralstonia (8%), and Clostridium (5%) were more prevalent in the CTR group, whereas Streptococcus (34%), Ralstonia (8%), and Veillonella (5%) were dominant in the CCA group. Although an alpha diversity analysis showed no statistically significant differences in species richness or diversity between groups, a beta diversity analysis revealed significant structural differences associated with disease severity. Our comparative microbiome study using LEfSe analysis suggested a statistically significant inhibition of normal intestinal bacterial flora in patients with CCA who had not received any treatment. These findings suggest that microbial dysbiosis may play a role in the pathogenesis of CCA. Specific microbial taxa were identified as potential biomarkers for distinguishing benign from malignant diseases. These results underscore the potential role of microbial dysbiosis in CCA pathogenesis and highlight the bile microbiota's utility as a diagnostic marker for biliary diseases.}, }
@article {pmid40004029, year = {2025}, author = {Carnazza, M and Werner, R and Tiwari, RK and Geliebter, J and Li, XM and Yang, N}, title = {The Etiology of IgE-Mediated Food Allergy: Potential Therapeutics and Challenges.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, doi = {10.3390/ijms26041563}, pmid = {40004029}, issn = {1422-0067}, mesh = {Humans ; *Immunoglobulin E/immunology ; *Food Hypersensitivity/immunology/therapy ; Animals ; Allergens/immunology ; Probiotics/therapeutic use ; Th2 Cells/immunology/metabolism ; }, abstract = {Immunoglobulin E (IgE)-mediated food allergy has been dramatically increasing in incidence over the last few decades. The combinations of both genetic and environmental factors that affect the microbiome and immune system have demonstrated significant roles in its pathogenesis. The morbidity, and at times mortality, that occurs as the result of this specific, reproducible, but impaired immune response is due to the nature of the shift from a regulatory T (Treg) cellular response to a T helper 2 (Th2) cellular response. This imbalance caused by food allergens results in an interleukin (IL)-4 and IL-13 dominant environment that drives B cell activation and differentiation into IgE-producing plasma cells. The resulting symptoms can range from mild to more severe anaphylaxis, and even death. Current therapeutic strategies involve avoidance and broad symptom management upon accidental exposure; however, no definitive cure exists. This narrative review highlights how the elucidation of the pathogenesis of IgE-mediated food allergy resulted in the development of therapeutics that are more specific to these individual receptors and molecules which have been relatively successful in mitigating this potentially life-threatening allergic response. However, potential adverse effects and re-sensitization following the conclusion of treatment has urged the need for improved therapeutic methods. Therefore, given the understanding of their mechanism of action and the overlap with the mechanism of IgE-mediated food allergies, probiotics and small molecule natural compounds may provide novel therapeutic and preventative strategies. This is compelling, as they have demonstrated success in clinical trials and may provide hope to improve quality of life in allergy patients.}, }
@article {pmid40004026, year = {2025}, author = {Mao, P and Hu, J and Mai, X and Li, N and Liao, Y and Feng, L and Long, Q}, title = {Multi-Omics Analysis of the Gut-Brain Axis Elucidates Therapeutic Mechanisms of Guhong Injection in the Treatment of Ischemic Stroke.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, doi = {10.3390/ijms26041560}, pmid = {40004026}, issn = {1422-0067}, support = {81860610//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Ischemic Stroke/drug therapy/metabolism ; *Brain-Gut Axis ; Male ; Metabolomics/methods ; Drugs, Chinese Herbal/pharmacology/administration &amp; dosage ; Biomarkers ; Fatty Acids, Volatile/metabolism ; Rats, Sprague-Dawley ; Infarction, Middle Cerebral Artery/drug therapy/metabolism ; Disease Models, Animal ; RNA, Ribosomal, 16S/genetics ; Brain/metabolism/drug effects ; Multiomics ; }, abstract = {Guhong injection (GH) is a compound preparation widely utilized in the treatment of cerebrovascular diseases. Accumulating evidence indicates that the gut microbiota is implicated in the development of ischemic stroke (IS). However, although the therapeutic potential of GH in IS may be mediated through the gut microbiota, the intricate relationships among the gut-brain axis, biomarkers, and target proteins remain to be completely explained. A rat model of middle cerebral artery occlusion (MCAO) was utilized to investigate the impact of GH on IS. Our 16S rRNA sequence analysis revealed that GH markedly enhanced the α-diversity of the intestinal microbiome and rectified the imbalance of short-chain fatty acids (SCFAs). Metabolomic analysis indicated that GH reversed 45 biomarkers and 6 disordered metabolic pathways in MCAO rats. Among these, the metabolic pathways of arachidonic acid, α-linolenic acid, fructose, and mannose were closely associated with gut microbiota comprising Lactobacillus modulated by GH. Furthermore, IS-related signaling pathways, including inflammation, autophagy, oxidative stress, and apoptosis, were significantly associated with three gut microbial species influenced by GH. The potential efficacy of GH in the context of IS is mediated through multiple pathways, involving the gut microbiota, SCFAs, biomarkers, and target proteins. This process partly relies on the gut-brain axis.}, }
@article {pmid40003979, year = {2025}, author = {Flynn, CK and Adams, JB and Krajmalnik-Brown, R and Khoruts, A and Sadowsky, MJ and Nirmalkar, K and Takyi, E and Whiteley, P}, title = {Review of Elevated Para-Cresol in Autism and Possible Impact on Symptoms.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, doi = {10.3390/ijms26041513}, pmid = {40003979}, issn = {1422-0067}, support = {N/A//Zoowalk for Autism Research/ ; }, mesh = {*Cresols/metabolism/urine ; Humans ; Animals ; *Gastrointestinal Microbiome ; Autism Spectrum Disorder/metabolism/microbiology ; Autistic Disorder/metabolism ; Mice ; Sulfuric Acid Esters/metabolism/urine ; Child ; }, abstract = {Para-cresol (p-cresol), and its primary human metabolite p-cresol sulfate (pCS), are among the most studied gut-derived metabolites relevant to autism spectrum disorder (ASD). P-cresol is produced by bacterial modification of phenylalanine or tyrosine and is one of many potentially deleterious metabolites produced by the gut microbiota. Seventeen studies have observed p-cresol and/or p-cresol sulfate as being higher in the urine of children with autism spectrum disorder (ASD) vs. controls. P-cresol has harmful effects on the body, including within the gut, brain, kidneys, liver, immune system, and mitochondria. Some of these effects may contribute to autism and comorbid symptoms. In the gut, p-cresol acts as an antibiotic, altering the gut microbiome to favor the bacteria that produce it. In the mitochondria, p-cresol disrupts ATP production and increases oxidative stress, which is also common in autism. In the brain, p-cresol impairs neuronal development. P-cresol inactivates dopamine beta-hydroxylase, which converts dopamine to noradrenaline. P-cresol sulfate impairs kidney function and is linked to chronic kidney disease (CKD), which is more common in ASD adults. P-cresol also interferes with immune function. Three animal studies have demonstrated that p-cresol causes autism-related symptoms in mice, and that mice can be recovered by the administration of fecal microbiota transplant from healthy mice. Similarly, it was found that microbiota transplant therapy treatment in children with ASD significantly reduced p-cresol sulfate levels to normal and led to significant improvements in gastrointestinal (GI) and ASD symptoms. In summary, p-cresol and pCS likely contribute to ASD core symptoms in a substantial subset of children with ASD.}, }
@article {pmid40003931, year = {2025}, author = {Nicotra, D and Mosca, A and Dimaria, G and Massimino, ME and Di Stabile, M and La Bella, E and Ghadamgahi, F and Puglisi, I and Vetukuri, RR and Catara, V}, title = {Mitigating Water Stress in Plants with Beneficial Bacteria: Effects on Growth and Rhizosphere Bacterial Communities.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, doi = {10.3390/ijms26041467}, pmid = {40003931}, issn = {1422-0067}, support = {CUP: E93C23006590006//Consorzio Universitario per le Biotecnologie "Modelli innovativi per applicazioni di scienze omiche avanzate- Area di intervento 2. Applicazioni delle scienze omiche per lo studio del microbioma in relazione all'ambiente e ai cambiamenti climatici' MUR ex/ ; CUP: B64I20000160005//PON "RICERCA E INNOVAZIONE" 2014-2020, Azione II-Obiettivo Specifico 1b - "WA-TER4AGRIFOOD", n. ARS01_00825/ ; CUP E63C22000960006//the European Union Next-Generation EU (Piano Nazionale di Ripresa e Resilienza (PNRR)-missione 4, componente 2, investmento 1.4-D.D. 1032 17/06/2022, CN00000022)/ ; (2019-01316)//FORMAS/ ; CTS 20:464//Carl Tryggers Stiftelse f&#xf6;r Vetenskaplig Forskning/ ; 2019-04270//The Swedish Research Council/ ; 0074727//NOVO Nordisk Foundation/ ; }, mesh = {*Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/growth &amp; development/metabolism ; *Arabidopsis/microbiology/growth &amp; development ; *Solanum lycopersicum/microbiology/growth &amp; development ; Microbiota ; Dehydration ; Droughts ; Plant Roots/microbiology/growth &amp; development ; Stress, Physiological ; Bacillus/physiology/growth &amp; development ; }, abstract = {Climate change has reshaped global weather patterns and intensified extreme events, with drought and soil salinity negatively impacting the yield and quality of crop production. To mitigate the detrimental effects of drought stress, the introduction of beneficial plant growth-promoting rhizobacteria (PGPR) has proven to be a promising approach. In this study, we evaluated a synthetic microbial community (SynCom) comprising bacterial strains belonging to the species Bacillus velezensis, Pseudomonas simiae, P. salmasensis, Glutamicibacter halophytocola, and Leclercia sp., which have been demonstrated to promote tomato growth both individually and collectively. The SynCom and most of its individual bacterial strains were shown to mitigate the detrimental effects of polyethylene glycol (PEG)-induced drought stress in vitro in Arabidopsis thaliana seedlings, either by reducing alterations in xylem elements or promoting the formation of new xylem strands. In a greenhouse trial, soil drenching with the SynCom and two individual strains, B. velezensis PSE31B and P. salmasensis POE54, improved the water stress response in soilless-grown tomato plants under a 40% reduced irrigation regime. Additionally, bacterial treatments positively influenced the diversity of rhizosphere bacterial communities, with distinct changes in bacterial composition, which suggest a treatment-specific interplay between the introduced strains and the native microbiome. These findings highlight the potential of microbial consortia and individual PGPR strains as sustainable tools to improve plant resilience to abiotic stresses.}, }
@article {pmid40003912, year = {2025}, author = {Chatzokou, D and Tsarna, E and Davouti, E and Siristatidis, CS and Christopoulou, S and Spanakis, N and Tsakris, A and Christopoulos, P}, title = {Semen Microbiome, Male Infertility, and Reproductive Health.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, doi = {10.3390/ijms26041446}, pmid = {40003912}, issn = {1422-0067}, mesh = {Male ; Humans ; *Microbiota ; *Semen/microbiology ; *Infertility, Male/microbiology ; *Reproductive Health ; Female ; Reproductive Techniques, Assisted ; Spermatozoa/microbiology ; Fertility ; Pregnancy ; }, abstract = {The semen microbiome, once believed to be sterile, is now recognized as a dynamic ecosystem containing a diverse range of microorganisms with potential implications for male fertility and reproductive health. We aimed to examine the relationship between the semen microbiome, male infertility, and reproductive outcomes, highlighting the transformative role of next generation sequencing techniques and bioinformatics in exploring this intricate interaction, and we present a critical review of the published literature on this issue. Current evidence suggests a complex association between the composition of the semen microbiome and male fertility, with certain bacterial genera, such as Lactobacillus and Prevotella that exert opposing effects on sperm quality and DNA integrity. In addition, the influence of the semen microbiome extends beyond natural fertility, affecting assisted reproductive technologies and pregnancy outcomes. Despite considerable progress, challenges remain in standardizing methodologies and interpreting findings. In conclusion, we identify the lack of a definitive management proposal for couples presenting with this phenomenon, and we underline the need for an algorithm and indicate the questions raised that point toward our goal for a strategy. Continued research is essential to clarify the role of the semen microbiome in male reproductive health and to advance the development of personalized fertility management approaches.}, }
@article {pmid40003878, year = {2025}, author = {Elling, CL and Ryan, AF and Yarza, TKL and Ghaffar, A and Llanes, EGDV and Kofonow, JM and Reyes-Quintos, MRT and Riazuddin, S and Robertson, CE and Tantoco, MLC and Ahmed, ZM and Chan, AL and Frank, DN and Chiong, CM and Santos-Cortez, RLP}, title = {A Novel SLPI Splice Variant Confers Susceptibility to Otitis Media in Humans.}, journal = {International journal of molecular sciences}, volume = {26}, number = {4}, pages = {}, doi = {10.3390/ijms26041411}, pmid = {40003878}, issn = {1422-0067}, support = {5I01BX001205-11//Department of Veterans Affairs, Veterans Health Administration, Office of Research and Development grant/ ; Balik Scientist Program//Philippine Council for Health Research and Development - Department of Science and Technology/ ; 5T32DC012280-10S1/NH/NIH HHS/United States ; 5R01DC000129-41S1/NH/NIH HHS/United States ; 5R01DC015004-06S1/NH/NIH HHS/United States ; 5R01DC019642-04S1/NH/NIH HHS/United States ; }, mesh = {Humans ; *Otitis Media/genetics/microbiology ; *Genetic Predisposition to Disease ; Animals ; Mice ; Female ; Male ; *Alternative Splicing ; Pedigree ; Haemophilus influenzae/genetics ; Ear, Middle/pathology/microbiology ; Child ; Haemophilus Infections/genetics/microbiology ; Child, Preschool ; }, abstract = {Otitis media is the most frequently diagnosed disease and a leading cause of hearing loss in young children. However, genetic contributors to susceptibility and pathogen-host-environment interactions in otitis media remain to be identified. Such knowledge would help identify at-risk individuals and effectively monitor, diagnose, and treat patients with otitis media. Through exome and Sanger sequencing, we identified a rare, deleterious splice variant SLPI c.394+1G>T co-segregating with otitis media in a large pedigree, with a genome-wide significant maximum LOD score of 4.59. Alternative splicing of SLPI was observed in saliva RNA of variant carriers. In bulk mRNA-seq data from an independent cohort of children with otitis media, SLPI was co-expressed with genes involved in infection, immune response, inflammation, and epithelial cell organization. After inoculation of non-typeable Haemophilus influenzae, Slpi was upregulated in polymorphonuclear leukocytes and epithelial cells of mouse middle ears. Furthermore, in the human middle ear, Haemophilus was significantly enriched in non-carriers, whereas Family-XI-Incertae-Sedis and Dialister were significantly enriched in variant carriers. Given the role of SLPI in immune modulation and host defense in mucosal epithelia, our findings support the SLPI variant as modulating susceptibility to otitis media.}, }
@article {pmid40003742, year = {2025}, author = {Castillo, D and Abella, E and Sinpoo, C and Phokasem, P and Chantaphanwattana, T and Yongsawas, R and Cervancia, C and Baroga-Barbecho, J and Attasopa, K and Noirungsee, N and Disayathanoowat, T}, title = {Gut Microbiome Diversity in European Honeybees (Apis mellifera L.) from La Union, Northern Luzon, Philippines.}, journal = {Insects}, volume = {16}, number = {2}, pages = {}, doi = {10.3390/insects16020112}, pmid = {40003742}, issn = {2075-4450}, support = {2022//Mekong - Lancang Special Fund/ ; }, abstract = {Insects often rely on symbiotic bacteria and fungi for various physiological processes, developmental stages, and defenses against parasites and diseases. Despite their significance, the associations between bacterial and fungal symbionts in Apis mellifera are not well studied, particularly in the Philippines. In this study, we collected A. mellifera from two different sites in the Municipality of Bacnotan, La Union, Philippines. A gut microbiome analysis was conducted using next-generation sequencing with the Illumina MiSeq platform. Bacterial and fungal community compositions were assessed using 16S rRNA and ITS gene sequences, respectively. Our findings confirm that adult worker bees of A. mellifera from the two locations possess distinct but comparably proportioned bacterial and fungal microbiomes. Key bacterial symbionts, including Lactobacillus, Bombilactobacillus, Bifidobacterium, Gilliamella, Snodgrassella, and Frischella, were identified. The fungal community was dominated by the yeasts Zygosaccharomyces and Priceomyces. Using the ENZYME nomenclature database and PICRUSt2 software version 2.5.2, a predicted functional enzyme analysis revealed the presence of β-glucosidase, catalase, glucose-6-phosphate dehydrogenase, glutathione transferase, and superoxide dismutase, which are involved in host defense, carbohydrate metabolism, and energy support. Additionally, we identified notable bacterial enzymes, including acetyl-CoA carboxylase and AMPs nucleosidase. Interestingly, the key bee symbionts were observed to have a negative correlation with other microbiota. These results provide a detailed characterization of the gut microbiota associated with A. mellifera in the Philippines and lay a foundation for further metagenomic studies of microbiomes in native or indigenous bee species in the region.}, }
@article {pmid40003717, year = {2025}, author = {Shaker, P and Roshani, Z and Timajchi, E and Sharifi, Z and Nikzadfar Goli, S and Broumand, B and Shafiee, MA}, title = {The Role of Urinary Microbiome Analysis in the Diagnostic Approach and Management of Urinary Incontinence: A Systematic Review.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/life15020309}, pmid = {40003717}, issn = {2075-1729}, abstract = {Urinary incontinence (UI) is a significant global health issue that impacts mainly middle-aged women, severely affecting their quality of life. Emerging research highlights the urinary microbiome's complex role in the etiology and management of UI, with microbial dysbiosis potentially influencing symptom severity and treatment outcomes. This systematic review aimed to evaluate the current evidence on the urinary microbiome's role in diagnosing and managing UI, focusing on variations in microbial composition across UI subtypes. We identified 21 studies, mostly employing 16S rRNA sequencing to characterize urinary microbiota and their associations with various UI subtypes, including urgency urinary incontinence (UUI), overactive bladder (OAB), and stress urinary incontinence (SUI). The findings revealed distinct microbial patterns, such as reduced Lactobacillus levels and increased Gardnerella prevalence, particularly in UUI. Altered microbiome profiles correlated with symptom severity, with reduced Lactobacilli suggesting a protective role in maintaining urinary health. Specific microbial species, including Actinotignum schaalii and Aerococcus urinae, emerged as potential biomarkers for UI diagnosis. Despite promising findings, limitations such as small sample sizes, variability in microbiome profiling methods, and insufficient causal evidence underscore the need for further research.}, }
@article {pmid40003268, year = {2025}, author = {Todor, SB and Ichim, C}, title = {Microbiome Modulation in Pediatric Leukemia: Impact on Graft-Versus-Host Disease and Treatment Outcomes: A Narrative Review.}, journal = {Children (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/children12020166}, pmid = {40003268}, issn = {2227-9067}, abstract = {The gut microbiome significantly influences the outcomes of pediatric leukemia, particularly in patients undergoing hematopoietic stem cell transplantation (HSCT). Dysbiosis, caused by chemotherapy, antibiotics, and immune system changes, contributes to complications such as graft-versus-host disease (GVHD), gastrointestinal issues, and infections. Various microbiome-related interventions, including prebiotics, probiotics, postbiotics, and fecal microbiota transplantation (FMT), have shown potential in mitigating these complications. Specific microbial signatures have been linked to GVHD risk, and interventions like inulin, Lactobacillus, and SCFAs (short-chain fatty acids), particularly butyrate, may help modulate the immune system and improve outcomes. FMT, while showing promising results in restoring microbial balance and alleviating GVHD, still requires careful monitoring due to potential risks in immunocompromised patients. Despite positive findings, more research is needed to optimize microbiome-based therapies and ensure their safety and efficacy in pediatric leukemia care.}, }
@article {pmid40003084, year = {2025}, author = {Gao, J and Cheng, X and Wu, X and Zou, C and He, B and Ma, W}, title = {Integrated Microbiome and Metabolomics Analysis Reveals Altered Aggressive Behaviors in Broiler Chickens Showing Different Tonic Immobility.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/ani15040601}, pmid = {40003084}, issn = {2076-2615}, support = {2017YFE0129900//Molecular regulatory mechanism of stress on broiler chickens based on neuro-endocrine-immune network/ ; }, abstract = {Tonic immobility (TI) serves as an indicator of innate stress response recovery in poultry. Broilers with different TI phenotypes exhibit varying levels of aggressive behavior, which can significantly impact their welfare. However, the influences of TI phenotypes on broiler aggression remain largely unexplored. In this study, broiler chickens were stratified into two distinct phenotypic groups based on the TI duration: short TI (STI) and long TI (LTI). The impacts of TI phenotypes on broiler aggression were investigated by analyzing cecal intestinal morphology, cecal bacteria, plasma metabolites, and corticosterone levels. Compared to LTI broilers, STI broilers showed significantly reduced plasma corticosterone (CORT) levels (p < 0.05) and a decreased frequency of aggressive behaviors, including dominant and subdominant types (p < 0.01). Histological analysis revealed that STI broilers have an increased duodenal villus height and villus-height-to-crypt-depth ratio (p < 0.01), a decreased jejunal crypt depth with an increased villus-height-to-crypt-depth ratio (p < 0.01), and a reduced ileal crypt depth and villus height (p < 0.01) compared to LTI broilers. 16S rDNA sequencing and Linear discriminant analysis effect size (LefSe) identified differential cecal bacterial abundance, notably in the genus cc115 belonging to Firmicutes. Specific microbiota in LTI broilers exhibited significant positive correlations with aggressive behavior and plasma corticosterone, while those in STI broilers showed significant negative correlations. Untargeted plasma metabolomics revealed 21 downregulated and 17 upregulated metabolites between TI phenotypes. Correlation analysis showed that the genus cc115 and 10 plasma metabolites were positively correlated with aggressive behavior, whereas 8 metabolites were negatively correlated. LTI broilers have higher plasma corticosterone content and more intense aggressive behavior than STI broilers. The distinct behavioral and physiological profiles observed in broilers with different TI phenotypes are strongly correlated with their specific gut microbiota and differential plasma metabolite profiles. The identified gut microbial signatures serve as key biomarkers for regulating aggressive behavior in broilers, while the differential plasma metabolites represent potential early indicators for detecting stress and behavioral issues in poultry farming.}, }
@article {pmid40002893, year = {2025}, author = {Oliveira, MME and Campos, LB and Brito, F and de Carvalho, FM and Silva-Junior, GO and da Costa, GL and Pinto, TN and de Sousa, RMP and Miranda, R and Castro, R and Zaltman, C and de Paula, VS}, title = {Oral Microbiota and Inflammatory Bowel Diseases: Detection of Emerging Fungal Pathogens and Herpesvirus.}, journal = {Biomedicines}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/biomedicines13020480}, pmid = {40002893}, issn = {2227-9059}, support = {88887.947447/2024-00//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; JCNE E-26/201.433/2021//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; JCNE E-26/204.581/2024//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 307007/2022-7//National Council for Scientific and Technological Development/ ; }, abstract = {Background/Objectives: Ulcerative colitis (UC) and Crohn's disease (CD) are the usual clinical forms of inflammatory bowel disease (IBD). Changes in the oral microbiota, especially the presence of emerging fungi and herpesviruses, have been shown to worsen the clinical aspects of IBD. The aim of this study was to screen for emerging pathogens in the oral yeast microbiota and the presence of herpesvirus in IBD patients. Methods: Oral swabs of seven UC or CD patients were collected. The samples were plated on Sabouraud Dextrose Agar and subcultured on CHROMagar Candida and CHROMagar Candida Plus. Polyphasic taxonomy was applied and identified using molecular tools, such as MALDI-TOF MS and ITS partial sequencing. Multiplex qPCR was used to identify the herpesvirus. Results: The mean age was 38.67 ± 14.06 years, 57.14% were female, and two had diabetes. The CD patients presented with Rhodotorula mucilaginosa, Candida orthopsilosis and Kodamaea jinghongensis, while the UC patients presented with Cutaneotrichosporon dermatis, Candida glabrata, Candida lusitanea and Candida tropicalis. Two UC individuals had at least one herpesvirus. In the first individual, a co-detection of Herpes Simplex Virus 1 (HSV-1) and C. lusitaniae was observed. The second presented with co-infections of Epstein-Barr virus (EBV), Human Herpesvirus 7 (HHV-7) and C. tropicalis. Conclusions: We identified rarely described yeasts and co-infections in IBD patients, highlighting the need to identify emerging pathogens in the oral microbiota, as they may contribute to opportunistic infections.}, }
@article {pmid40002861, year = {2025}, author = {Devaraja, K and Aggarwal, S}, title = {Dysbiosis of Oral Microbiome: A Key Player in Oral Carcinogenesis? A Critical Review.}, journal = {Biomedicines}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/biomedicines13020448}, pmid = {40002861}, issn = {2227-9059}, abstract = {The oral cavity is known to harbor hundreds of microorganisms, belonging to various genera, constituting a peculiar flora called the oral microbiome. The change in the relative distribution of the constituents of this microbial flora, due to any reason, leads to oral dysbiosis. For centuries, oral dysbiosis has been linked to the etiopathogenesis of several medical illnesses, both locally and systemically-. However, aided by the recent advent of bio-technological capabilities, several reports have re-emerged that link oral dysbiosis to oral carcinogenesis, and numerous studies are currently exploring their association and plausible mechanisms. Some of the proposed mechanisms of oral dysbiosis-induced carcinogenesis (ODIC) include-a bacteria-induced chronic inflammatory state leading to direct cellular damage, inflammatory-cytokine-mediated promotion of cellular proliferation and invasion, release of bacterial products that are carcinogenic, and suppression of local immunity by alteration of the tumor microenvironment. However, the actual interactions between these cellular mechanisms and their role in carcinogenesis are not yet fully understood. This review provides a comprehensive overview of the various hypotheses and mechanisms implicated in the ODIC, along with the corresponding molecular aberrations. Apart from discussing the usual constituents of the oral microbiome profile, the review also summarizes the various dysbiosis profiles implicated in ODIC. The review also sheds light on the potential clinical implications of the research on oral microbiome in the prevention and management of oral cancer.}, }
@article {pmid40002835, year = {2025}, author = {Mafe, AN and Büsselberg, D}, title = {Microbiome Integrity Enhances the Efficacy and Safety of Anticancer Drug.}, journal = {Biomedicines}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/biomedicines13020422}, pmid = {40002835}, issn = {2227-9059}, support = {NPRP 14S0311-210033//QNRF/ ; }, abstract = {The intricate relationship between anticancer drugs and the gut microbiome influences cancer treatment outcomes. This review paper focuses on the role of microbiome integrity in enhancing the efficacy and safety of anticancer drug therapy, emphasizing the pharmacokinetic interactions between anticancer drugs and the gut microbiota. It explores how disruptions to microbiome composition, or dysbiosis, can alter drug metabolism, immune responses, and treatment side effects. By examining the mechanisms of microbiome disruption caused by anticancer drugs, this paper highlights specific case studies of drugs like cyclophosphamide, 5-fluorouracil, and irinotecan, and their impact on microbial diversity and clinical outcomes. The review also discusses microbiome-targeted strategies, including prebiotics, probiotics, postbiotics, and fecal microbiota transplantation (FMT), as promising interventions to enhance cancer treatment. Furthermore, the potential of microbiome profiling in personalizing therapy and integrating these interventions into clinical practice is explored. Finally, this paper proposes future research directions, including developing novel biomarkers and a deeper comprehension of drug-microbiome interactions, to respond to current gaps in knowledge and improve patient outcomes in cancer care.}, }
@article {pmid40002756, year = {2025}, author = {Chulenbayeva, L and Issilbayeva, A and Sailybayeva, A and Bekbossynova, M and Kozhakhmetov, S and Kushugulova, A}, title = {Short-Chain Fatty Acids and Their Metabolic Interactions in Heart Failure.}, journal = {Biomedicines}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/biomedicines13020343}, pmid = {40002756}, issn = {2227-9059}, support = {AP23488818//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; BR21882152//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, abstract = {Short-chain fatty acids (SCFAs), produced through fermentation of dietary fibers by gut bacteria, play a central role in modulating cardiovascular function and heart failure (HF) development. The progression of HF is influenced by intestinal barrier dysfunction and microbial translocation, where SCFAs serve as key mediators in the gut-heart axis. This review examines the complex metabolic interactions between SCFAs and other gut microbiota metabolites in HF, including their relationships with trimethylamine N-oxide (TMAO), aromatic amino acids (AAAs), B vitamins, and bile acids (BAs). We analyze the associations between SCFA production and clinical parameters of HF, such as left ventricular ejection fraction (LVEF), N-terminal pro-B-type natriuretic peptide (NT-proBNP), and glomerular filtration rate (GFR). Gaining insights into metabolic networks offers new potential therapeutic targets and prognostic markers for managing heart failure, although their clinical significance needs further exploration.}, }
@article {pmid40002576, year = {2025}, author = {Pais, RJ and Botelho, J and Machado, V and Alcoforado, G and Mendes, JJ and Alves, R and Bessa, LJ}, title = {Exploring AI-Driven Machine Learning Approaches for Optimal Classification of Peri-Implantitis Based on Oral Microbiome Data: A Feasibility Study.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/diagnostics15040425}, pmid = {40002576}, issn = {2075-4418}, support = {2022.01430.PTDC//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; }, abstract = {Background: Machine learning (ML) techniques have been recently proposed as a solution for aiding in the prevention and diagnosis of microbiome-related diseases. Here, we applied auto-ML approaches on real-case metagenomic datasets from saliva and subgingival peri-implant biofilm microbiomes to explore a wide range of ML algorithms to benchmark best-performing algorithms for predicting peri-implantitis (PI). Methods: A total of 100 metagenomes from the NCBI SRA database (PRJNA1163384) were used in this study to construct biofilm and saliva metagenomes datasets. Two AI-driven auto-ML approaches were used on constructed datasets to generate 100 ML-based models for the prediction of PI. These were compared with statistically significant single-microorganism-based models. Results: Several ML algorithms were pinpointed as suitable bespoke predictive approaches to apply to metagenomic data, outperforming the single-microorganism-based classification. Auto-ML approaches rendered high-performing models with Receiver Operating Characteristic-Area Under the Curve, sensitivities and specificities between 80% and 100%. Among these, classifiers based on ML-driven scoring of combinations of 2-4 microorganisms presented top-ranked performances and can be suitable for clinical application. Moreover, models generated based on the saliva microbiome showed higher predictive performance than those from the biofilm microbiome. Conclusions: This feasibility study bridges complex AI research with practical dental applications by benchmarking ML algorithms and exploring oral microbiomes as foundations for developing intuitive, cost-effective, and clinically relevant diagnostic platforms.}, }
@article {pmid40002565, year = {2025}, author = {Mpakosi, A and Sokou, R and Theodoraki, M and Iacovidou, N and Cholevas, V and Tsantes, AG and Liakou, AI and Drogari-Apiranthitou, M and Kaliouli-Antonopoulou, C}, title = {The Role of Infant and Early Childhood Gut Virome in Immunity and the Triggering of Autoimmunity-A Narrative Review.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {15}, number = {4}, pages = {}, doi = {10.3390/diagnostics15040413}, pmid = {40002565}, issn = {2075-4418}, abstract = {Background: The bacterial gut microbiome has been the subject of many studies that have provided valuable scientific conclusions. However, many different populations of microorganisms that interact with each other to maintain homeostasis coexist inside the gut. The gut virome, especially, appears to play a key role in this interactive microenvironment. Intestinal viral communities, including bacteriophages, appear to influence health and disease, although their role has not yet been fully elucidated. In addition, bacteriophages or viruses that infect bacteria regulate bacterial growth, thus shaping the composition of the gut microbiome and affecting the immune system. Infant Gut Virome: The shaping of the gut microbiome during the first years of life has a significant role in the maturation of the infant's immune system. In contrast, early dysbiosis has been associated with chronic, including metabolic and autoimmune, disorders later in life. Purpose: Although viruses have been shown to be potential triggers of autoimmune diseases, there is a gap in the literature regarding the infant gut virome in autoimmunity development. Despite the lack of evidence, this review attempts to summarize and clarify what is known so far about this timely and important topic in the hope that its findings will contribute to future research.}, }
@article {pmid40002529, year = {2025}, author = {Kalaga, P and Ray, SK}, title = {Mental Health Disorders Due to Gut Microbiome Alteration and NLRP3 Inflammasome Activation After Spinal Cord Injury: Molecular Mechanisms, Promising Treatments, and Aids from Artificial Intelligence.}, journal = {Brain sciences}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/brainsci15020197}, pmid = {40002529}, issn = {2076-3425}, abstract = {Aside from its immediate traumatic effects, spinal cord injury (SCI) presents multiple secondary complications that can be harmful to those who have been affected by SCI. Among these secondary effects, gut dysbiosis (GD) and the activation of the NOD (nucleotide-binding oligomerization domain) like receptor-family pyrin-domain-containing three (NLRP3) inflammasome are of special interest for their roles in impacting mental health. Studies have found that the state of the gut microbiome is thrown into disarray after SCI, providing a chance for GD to occur. Metabolites such as short-chain fatty acids (SCFAs) and a variety of neurotransmitters produced by the gut microbiome are hampered by GD. This disrupts healthy cognitive processes and opens the door for SCI patients to be impacted by mental health disorders. Additionally, some studies have found an increased presence and activation of the NLRP3 inflammasome and its respective parts in SCI patients. Preclinical and clinical studies have shown that NLRP3 inflammasome plays a key role in the maturation of pro-inflammatory cytokines that can initiate and eventually aggravate mental health disorders after SCI. In addition to the mechanisms of GD and the NLRP3 inflammasome in intensifying mental health disorders after SCI, this review article further focuses on three promising treatments: fecal microbiome transplants, phytochemicals, and melatonin. Studies have found these treatments to be effective in combating the pathogenic mechanisms of GD and NLRP3 inflammasome, as well as alleviating the symptoms these complications may have on mental health. Another area of focus of this review article is exploring how artificial intelligence (AI) can be used to support treatments. AI models have already been developed to track changes in the gut microbiome, simulate drug-gut interactions, and design novel anti-NLRP3 inflammasome peptides. While these are promising, further research into the applications of AI for the treatment of mental health disorders in SCI is needed.}, }
@article {pmid40002527, year = {2025}, author = {Eisen, A and Kiernan, MC}, title = {The Neonatal Microbiome: Implications for Amyotrophic Lateral Sclerosis and Other Neurodegenerations.}, journal = {Brain sciences}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/brainsci15020195}, pmid = {40002527}, issn = {2076-3425}, abstract = {Most brain development occurs in the "first 1000 days", a critical period from conception to a child's second birthday. Critical brain processes that occur during this time include synaptogenesis, myelination, neural pruning, and the formation of functioning neuronal circuits. Perturbations during the first 1000 days likely contribute to later-life neurodegenerative disease, including sporadic amyotrophic lateral sclerosis (ALS). Neurodevelopment is determined by many events, including the maturation and colonization of the infant microbiome and its metabolites, specifically neurotransmitters, immune modulators, vitamins, and short-chain fatty acids. Successful microbiome maturation and gut-brain axis function depend on maternal factors (stress and exposure to toxins during pregnancy), mode of delivery, quality of the postnatal environment, diet after weaning from breast milk, and nutritional deficiencies. While the neonatal microbiome is highly plastic, it remains prone to dysbiosis which, once established, may persist into adulthood, thereby inducing the development of chronic inflammation and abnormal excitatory/inhibitory balance, resulting in neural excitation. Both are recognized as key pathophysiological processes in the development of ALS.}, }
@article {pmid40002500, year = {2025}, author = {Arneth, B}, title = {Gut-Brain Axis and Brain Microbiome Interactions from a Medical Perspective.}, journal = {Brain sciences}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/brainsci15020167}, pmid = {40002500}, issn = {2076-3425}, abstract = {Background: The gut microbiome directly impacts brain health and activity, meaning the two are closely associated. This relationship suggests a link between microbial imbalances and diseases such as Alzheimer's, although multiple other contributing factors, such as genetics, also play a part. Additionally, recent studies discovered that cerebrospinal fluid has some microbial deoxyribonucleic acid (DNA), which can be interpreted to mean a microbiome exists in the brain too. The vagus nerve and the central nervous and immune systems are responsible for the connection between the brain and gut microbiome. Aims and Objectives: The main aim of this systematic review is to analyze existing research on the gut-brain axis and the brain microbiome to fill the current knowledge gap. Materials and Methods: A search was conducted on the PubMed database based on a set of predefined MeSH terms. Results: After the search, 2716 articles meeting the MeSH parameters were found in PubMed. This list was then downloaded and analyzed according to the inclusion/exclusion criteria, and 63 relevant papers were selected. Discussion: Bacteria in the gut microbiome produce some substances that are considered neuroactive. These compounds can directly or indirectly affect brain function through the gut-brain axis. However, various knowledge gaps on the mechanisms involved in this connection need to be addressed first.}, }
@article {pmid40002477, year = {2025}, author = {Kalu, A and Ray, SK}, title = {Epigallocatechin-3-Gallate, Quercetin, and Kaempferol for Treatment of Parkinson's Disease Through Prevention of Gut Dysbiosis and Attenuation of Multiple Molecular Mechanisms of Pathogenesis.}, journal = {Brain sciences}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/brainsci15020144}, pmid = {40002477}, issn = {2076-3425}, abstract = {Parkinson's disease (PD) is a neurodegenerative condition in which degeneration mostly occurs in the dopamine (DA)-producing neurons within the substantia nigra in the midbrain. As a result, individuals with this condition suffer from progressively worsening motor impairment because of the resulting DA deficiency, along with an array of other symptoms that, over time, force them into a completely debilitating state. As an age-related disease, PD has only risen in prevalence over the years; thus, an emphasis has recently been placed on discovering a new treatment for this condition that is capable of attenuating its progression. The gut microbiota has become an area of intrigue among PD studies, as research into this topic has shown that imbalances in the gut microbiota (colloquially known as gut dysbiosis) seemingly promote the primary etiologic factors that have been found to be associated with PD and its pathologic progression. With this knowledge, research into PD treatment has begun to expand beyond synthetic pharmaceutical compounds, as a growing emphasis has been placed on studying plant-derived polyphenolic compounds, namely flavonoids, as a new potential therapeutic approach. Due to their capacity to promote a state of homeostasis in the gut microbiota and their long-standing history as powerful medicinal agents, flavonoids have begun to be looked at as promising therapeutic agents capable of attenuating several of the pathologic states seen amidst PD through indirect and direct means. This review article focuses on three flavonoids, specifically epigallocatechin-3-gallate, quercetin, and kaempferol, discussing the mechanisms through which these powerful flavonoids can potentially prevent gut dysbiosis, neuroinflammation, and other molecular mechanisms involved in the pathogenesis and progression of PD, while also exploring their real-world application and how issues of bioavailability and potential drug interactions can be circumvented or exploited.}, }
@article {pmid40002382, year = {2025}, author = {Bian, Z and Li, Z and Chang, H and Luo, J and Jian, S and Zhang, J and Lin, P and Deng, B and Deng, J and Zhang, L}, title = {Resveratrol Ameliorates Chronic Stress in Kennel Dogs and Mice by Regulating Gut Microbiome and Metabolome Related to Tryptophan Metabolism.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/antiox14020195}, pmid = {40002382}, issn = {2076-3921}, support = {2021YFD1300400//National Key R&amp;D Program of China/ ; 31790411//National Natural Science Foundation of China/ ; 32002186//National Natural Science Foundation of China/ ; }, abstract = {Chronic stress poses threats to the physical and psychological well-being of dogs. Resveratrol (Res) is a polyphenol with antidepressant properties and has rarely been studied in dogs. This study aimed to investigate the stress-relieving effects and underlying mechanism of Res in dogs. Dogs were fed a basal diet supplemented with Res for 35 days. The fecal microbiota of the dogs was cultured with Res in vitro. The results show that Res improved the stress-related behaviors and increased the serum levels of 5-hydroxytryptamine (5-HT), brain-derived neurotrophic factor (BDNF), immunoglobulin A, and antioxidant capacity in dogs. Res downregulated the hormones of the hypothalamic-pituitary-adrenal axis. The abundance of butyric-producing bacteria, like Blautia, increased, while the growth of Fusobacterium related to gut inflammation was inhibited in the Res group. A higher content of fecal butyric acid was observed in the Res group. The metabolome indicated that Res increased the fecal and serum levels of tryptophan (Trp) and decreased the consumption of Trp by microorganisms. A chronic unpredictable mild stress mouse model was established, and Res was administered for 35 days. The results show that Res ameliorated the stress-related behavior and increased the levels of Trp and 5-HT in the whole brains of mice. The relative mRNA expression of genes associated with the tight junction protein, aryl hydrocarbon receptor, and Trp transporters in the colon were upregulated. In conclusion, Res could ameliorate canine stress by increasing 5-HT, BDNF, and the antioxidant capacity and improving the immune function and stress response, which was attributed to the role of Res in the restructuring of gut microbiota and the modulation of tryptophan metabolism.}, }
@article {pmid40002227, year = {2025}, author = {Isono, H and Nakajima, S and Watanabe, S and Takeda, AK and Yoshii, H and Shimoda, A and Yagishita, H and Mitsudo, K and Kioi, M}, title = {Involvement of Oral Microbiome in the Development of Oral Malignancy.}, journal = {Cancers}, volume = {17}, number = {4}, pages = {}, doi = {10.3390/cancers17040632}, pmid = {40002227}, issn = {2072-6694}, support = {18K17031//Japan Society for the Promotion of Science/ ; 20H03892//Japan Society for the Promotion of Science/ ; }, abstract = {OBJECTIVE: This study aimed to identify periodontal pathogens involved in the onset and progression of OSCC.<br><br>METHODS: Saliva samples were collected from 112 patients without oral mucosal diseases (OMDs) as controls; 36 patients with oral potentially malignant disorders (OPMDs); and 104 patients with OSCC. Periodontal examinations were performed on all patients. Endpoint PCR was performed for seven species of oral pathogens. The 16S rRNA analysis was performed using 20 DNA samples from each group.<br><br>RESULTS: Periodontitis tended to worsen in the OMDs group compared to the control group. The number of oral bacteria was significantly higher in the OSCC group than in the other groups. The detection rates of P. gingivalis and Aggregatibacter actinomycetemcomitans (A. actinomycetemcomitans) were significantly higher in the OSCC group than those in the control group. From 16S rRNA analysis, the relative abundance of Prevotella buccae and intermedia was significantly higher in OSCC than in the control. Moreover, LPS derived from P. gingivalis contributes to the early development of oral epithelial precancerous lesions and carcinomas in mice.<br><br>CONCLUSIONS: Specific periodontal pathogens are present in the oral cavities of patients with OPMDs and OSCC, and changes in the bacterial flora due to their presence may contribute to the onset and progression of OMDs.}, }
@article {pmid40002058, year = {2025}, author = {Tenea, GN and Cifuentes, V and Reyes, P and Cevallos-Vallejos, M}, title = {Unveiling the Microbial Signatures of Arabica Coffee Cherries: Insights into Ripeness Specific Diversity, Functional Traits, and Implications for Quality and Safety.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/foods14040614}, pmid = {40002058}, issn = {2304-8158}, support = {7874/2023//Universidad T&#xe9;cnica del Norte/ ; }, abstract = {Arabica coffee, one of the most valuable crop commodities, harbors diverse microbial communities with unique genetic and functional traits that influence bean safety and final coffee quality. In Ecuador, coffee production faces challenges due to the spread of pathogenic organisms across cultivars, leading to reduced yields and compromised quality. This study employed a shotgun metagenomic approach to characterize the indigenous microbial diversity present in the cell biomass of fermented coffee cherries from three Coffea arabica varieties: Typica (Group A), Yellow Caturra (Group B), and Red Caturra (Group C), originating from the Intag Valley in northern Ecuador, at two ripe stages: green (immature fruits) and ripe (red/yellow mature fruits). Gene prediction and functional annotation were performed using multiple databases, including EggNOG, COG, KEGG, CAZy, CARD, and BacMet, to explore the potential impact of microbial communities on bean quality and safety. Metagenomic sequencing generated over 416 million high-quality reads, averaging 66 million clean reads per sample and yielding a total of 47 Gbps of data. Analysis revealed distinct differences in species abundance based on the coffee variety and ripening stage. A total of 799,658 protein-coding sequences (CDSs) were predicted, of which 205,937 genes were annotated with EggNOG, 181,723 with COG, 155,220 with KEGG, and 10,473 with CAZy. Additionally, 432 antibiotic resistance genes (ARGs) were identified using CARD, and 8974 biocide and metal resistance genes (BMRGs) were annotated with BacMet. Immature cherries exhibited enriched pathways associated with resistance to antibiotics such as fluoroquinolones, penams, rifamycin, macrolides, carbapenems, and cephalosporins. The abundance of these pathways varied with the ripening stage and variety. Furthermore, green cherries showed a significant increase in BMRGs associated with resistance to substances including hydrochloric acid, copper, nickel, hydrogen peroxide, arsenic, and zinc. Among mature cherries, Typica and Red Caturra shared similar profiles, while Yellow Caturra displayed a divergent microbial and functional profile. These study findings emphasize the interplay between microbial diversity, ripening stages, and coffee varieties, providing a foundation for innovative approaches to enhance coffee quality through microbiome management.}, }
@article {pmid40001890, year = {2025}, author = {Al-Ghamdi, SB}, title = {Probiotics as Renal Guardians: Modulating Gut Microbiota to Combat Diabetes-Induced Kidney Damage.}, journal = {Biology}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/biology14020122}, pmid = {40001890}, issn = {2079-7737}, abstract = {Gut microbiota plays a pivotal role in various health challenges, particularly in mitigating diabetes-induced renal damage. Numerous studies have highlighted that modifying gut microbiota is a promising therapeutic strategy for preserving kidney function and mitigating diabetes-related complications. This study aimed to evaluate the protective effects of Lactobacillus acidophilus ATCC 4356 supplementations on kidney health in a rat model of diabetes-induced renal damage. Four groups were studied: control, probiotic supplementation, diabetic, and diabetic with probiotic supplementation. Diabetes was induced using a single streptozotocin (STZ) injection after a 12 h fast, and probiotic supplementation (1 × 10[9] CFU/kg daily) was administered two weeks prior to diabetes induction and continued throughout the experimental period. Weekly assessments included fasting blood glucose, insulin, glycation markers, and kidney function tests. Glucose metabolism and insulin sensitivity were analyzed through oral glucose tolerance test (OGTT) and insulin sensitivity test (IST). The microbiome was analyzed using 16S rRNA gene sequencing to evaluate changes in diversity and composition. Probiotic supplementation significantly enhanced microbial diversity and composition. Alpha diversity indices such as Shannon and Chao1 demonstrated higher values in the probiotic-treated diabetic group compared to untreated diabetic rats. The Firmicutes/Bacteroidetes ratio, a key indicator of gut health, was also restored in the probiotic-treated diabetic group. Results: Probiotic supplementation significantly improved glycemic control, reduced fasting blood glucose levels, and enhanced insulin sensitivity in diabetic rats. Antioxidant enzyme levels, depleted in untreated diabetic rats, were restored, reflecting reduced oxidative stress. Histological analysis showed better kidney structure, reduced inflammation, and decreased fibrosis. Furthermore, the Comet assay results confirmed a reduction in DNA damage in probiotic-treated diabetic rats. Conclusion: Lactobacillus acidophilus ATCC 4356 supplementation demonstrated significant protective effects against diabetes-induced renal damage by restoring gut microbiota diversity, improving glycemic control, and reducing oxidative stress. These findings highlight the potential of targeting the gut microbiota and its systemic effects on kidney health as a therapeutic approach for managing diabetes-related complications. Further research is needed to optimize probiotic treatments and assess their long-term benefits in diabetes management and kidney health.}, }
@article {pmid40001884, year = {2025}, author = {Luo, W and Ping, X and Zhou, J and Gao, S and Huang, X and Song, S and Xu, J and He, W}, title = {Alternaria alternata JTF001 Metabolites Recruit Beneficial Microorganisms to Reduce the Parasitism of Orobanche aegyptiaca in Tomato.}, journal = {Biology}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/biology14020116}, pmid = {40001884}, issn = {2079-7737}, support = {2022A02005-3//by the Major Science and Technology Projects in Xinjiang Uygur, Autonomous Region/ ; 2023D01B41//the Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; XJARS-07//the Earmarked Fund for XJARS/ ; }, abstract = {Orobanche aegyptiaca is a holoparasitic weed that extracts water, nutrients, and growth regulators from host plants, leading to significant yield and quality losses. Biocontrol microbial metabolites have been shown to enhance plant resistance against parasitic plants, yet the underlying microbial mechanisms remain poorly understood. In this study, we investigated the role of Alternaria alternata JTF001 (J1) microbial metabolites in recruiting beneficial microbes to the tomato rhizosphere and promoting the establishment of a disease-suppressive microbiome. Pot experiments revealed that J1 metabolite application significantly reduced O. aegyptiaca parasitism. High-throughput sequencing of full-length 16S rRNA genes and ITS regions, along with in vitro culture assays, demonstrated an increase in the abundance of plant-beneficial bacteria, particularly Pseudomonas spp. The three candidate beneficial strains (zOTU_388, zOTU_533, and zOTU_2335) showed an increase of 5.7-fold, 5.4-fold, and 4.7-fold, respectively. These results indicate that J1 metabolites induce the recruitment of a disease-suppressive microbiome in tomato seedlings, effectively inhibiting O. aegyptiaca parasitism. Our findings suggest that microbial metabolites represent a promising strategy for managing parasitic plant infestations through microbial community modulation, offering significant implications for sustainable agricultural practices.}, }
@article {pmid40001878, year = {2025}, author = {Kim, H and Lee, SH and Yang, JY}, title = {Mechanobiological Approach for Intestinal Mucosal Immunology.}, journal = {Biology}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/biology14020110}, pmid = {40001878}, issn = {2079-7737}, support = {2021M3A9I4027993, 2021R1C1C1009555, RS-2023-00301938//National Research Foundation of Korea/ ; }, abstract = {The intestinal area is composed of diverse cell types that harmonize gut homeostasis, which is influenced by both endogenous and exogenous factors. Notably, the environment of the intestine is exposed to several types of mechanical forces, including shear stress generated by fluid flow, compression and stretch generated by luminal contents and peristaltic waves of the intestine, and stiffness attributed to the extracellular matrix. These forces play critical roles in the regulation of cell proliferation, differentiation, and migration. Many efforts have been made to simulate the actual intestinal environment in vitro. The three-dimensional organoid culture system has emerged as a powerful tool for studying the mechanism of the intestinal epithelial barrier, mimicking rapidly renewing epithelium from intestinal stem cells (ISCs) in vivo. However, many aspects of how mechanical forces, such as shear stress, stiffness, compression, and stretch forces, influence the intestinal area remain unresolved. Here, we review the recent studies elucidating the impact of mechanical forces on intestinal immunity, interaction with the gut microbiome, and intestinal diseases.}, }
@article {pmid40001576, year = {2025}, author = {Fanijavadi, S and Hansen, TF and Zedan, AH}, title = {NK Cell-Microbiota Interaction Biomarker Strategy: Advancing Prostate Cancer Management.}, journal = {Biomolecules}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/biom15020273}, pmid = {40001576}, issn = {2218-273X}, mesh = {Humans ; Male ; *Killer Cells, Natural/immunology/metabolism ; *Prostatic Neoplasms/immunology/therapy/microbiology ; *Biomarkers, Tumor ; Microbiota/immunology ; Tumor Microenvironment/immunology ; Prognosis ; }, abstract = {The role of natural killer (NK) cells in the management of prostate cancer (PCa) remains incompletely understood. Some have proposed that measuring NK cells in blood samples could serve as a reliable, minimally invasive tool for screening, assessing treatment effects, and predicting survival outcomes in PCa patients. However, the significance of different NK cell phenotypes remains unclear. Given the interplay between NK cells and the microbiome, we hypothesize that a combined signature of NK cell phenotypes derived from blood, along with microbiome profiles from oral, urine, and stool samples, could serve as a surrogate marker for NK cell activity in tumor and its microenvironment. Such an approach provides a practical alternative to invasive tumor biopsies by enabling the indirect assessment of NK cell function in tumors. Additionally, profiling NK cell phenotypes and their interactions with the microbiota has the potential to enhance prognostic accuracy and guide the development of personalized therapeutic strategies. Prospective studies are needed to validate the utility of NK cell and microbiome assays in personalized PCa management, with a focus on minimally invasive procedures and predictive signatures for treatment outcomes.}, }
@article {pmid40001573, year = {2025}, author = {Mafe, AN and Büsselberg, D}, title = {Modulation of the Neuro-Cancer Connection by Metabolites of Gut Microbiota.}, journal = {Biomolecules}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/biom15020270}, pmid = {40001573}, issn = {2218-273X}, support = {NPRP 14S0311-210033//QNRF/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Brain Neoplasms/metabolism/microbiology ; Animals ; Brain-Gut Axis ; Fatty Acids, Volatile/metabolism ; Bile Acids and Salts/metabolism ; Dysbiosis/metabolism/microbiology ; Tryptophan/metabolism ; Fecal Microbiota Transplantation ; Lipopolysaccharides/metabolism ; }, abstract = {The gut-brain-cancer axis represents a novel and intricate connection between the gut microbiota, neurobiology, and cancer progression. Recent advances have accentuated the significant role of gut microbiota metabolites in modulating systemic processes that influence both brain health and tumorigenesis. This paper explores the emerging concept of metabolite-mediated modulation within the gut-brain-cancer connection, focusing on key metabolites such as short-chain fatty acids (SCFAs), tryptophan derivatives, secondary bile acids, and lipopolysaccharides (LPS). While the gut microbiota's impact on immune regulation, neuroinflammation, and tumor development is well established, gaps remain in grasping how specific metabolites contribute to neuro-cancer interactions. We discuss novel metabolites with potential implications for neurobiology and cancer, such as indoles and polyamines, which have yet to be extensively studied. Furthermore, we review preclinical and clinical evidence linking gut dysbiosis, altered metabolite profiles, and brain tumors, showcasing limitations and research gaps, particularly in human longitudinal studies. Case studies investigating microbiota-based interventions, including dietary changes, fecal microbiota transplantation, and probiotics, demonstrate promise but also indicate hurdles in translating these findings to clinical cancer therapies. This paper concludes with a call for standardized multi-omics approaches and bi-directional research frameworks integrating microbiome, neuroscience, and oncology to develop personalized therapeutic strategies for neuro-cancer patients.}, }
@article {pmid40001555, year = {2025}, author = {Jibril, SM and Hu, Y and Yang, K and Wu, J and Li, C and Wang, Y}, title = {Microbiome Analysis of Area in Proximity to White Spot Lesions Reveals More Harmful Plant Pathogens in Maize.}, journal = {Biomolecules}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/biom15020252}, pmid = {40001555}, issn = {2218-273X}, support = {2023YFD1400800//National Key R&amp;D Program of China/ ; 202402AE090026//The Major Science and Technology project in Yunnan/ ; 202401BD070001-013//The Basic Research of Agriculture Joint Special Project in Yunnan/ ; XDYC-QNRC-2023-0421//The Yunnan Provincial Talent Program for Wang Yi/ ; }, mesh = {*Zea mays/microbiology ; *Plant Diseases/microbiology ; *Microbiota ; *Plant Leaves/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Fungi/genetics/pathogenicity/classification ; High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Plant microbiomes play a major role in plant health, growth, and development, enhancing resistance to pathogen invasion. However, despite the extensive research on the phyllosphere microbiome, it remains unclear how the microbiome of leaves in proximity to diseased leaves responds to pathogen invasion. We investigate the response of the maize phyllosphere microbiome to maize white spot by assessing the microbiome dynamics associated with the white spot portion and the area in proximity using 16S and ITS high-throughput sequencing analysis. Our results showed that the bacterial diversities were higher in the diseased portion and area in proximity to the spot than those in healthy plants. At the same time, lower fungal diversity was recorded in the diseased portion compared to portions in proximity to it and healthy leaves. The spot portion had a significant influence on the microbial composition. The diseased portion, the area in proximity to it, and the healthy leaves were dominated by the bacterial genera Sphingomonas, Delftia, Chryseobacterium, Stenotrophomonas, Methylobacterium-methylorubrum, and Bacteroides. Still, the abundance of Sphingomonas decreased in the healthy leaves with a corresponding increase in Stenotrophomonas. Conversely, the fungal genus Setophoma dominated the diseased portion, while the fungal pathogens Cladosporium, Alternaria, and Exserohilum were highly abundant in the samples from the area in proximity to it. In addition, a co-occurrence network analysis revealed a complex fungal network in healthy leaves and those in proximity to leaves infected with white spot compared to the diseased portion. This study suggests that the area in proximity to the maize leaf infected with white spot disease is colonized by more harmful plant pathogenic fungi for disease progression.}, }
@article {pmid40001546, year = {2025}, author = {Interino, N and Vitagliano, R and D'Amico, F and Lodi, R and Porru, E and Turroni, S and Fiori, J}, title = {Microbiota-Gut-Brain Axis: Mass-Spectrometry-Based Metabolomics in the Study of Microbiome Mediators-Stress Relationship.}, journal = {Biomolecules}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/biom15020243}, pmid = {40001546}, issn = {2218-273X}, support = {Ricerca Corrente 2024//Italian Ministry of Health/ ; }, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Metabolomics/methods ; *Mass Spectrometry/methods ; *Brain-Gut Axis/physiology ; Animals ; Brain/metabolism ; Stress, Psychological/metabolism/microbiology ; }, abstract = {The microbiota-gut-brain axis is a complex bidirectional communication system that involves multiple interactions between intestinal functions and the emotional and cognitive centers of the brain. These interactions are mediated by molecules (metabolites) produced in both areas, which are considered mediators. To shed light on this complex mechanism, which is still largely unknown, a reliable characterization of the mediators is essential. Here, we review the most studied metabolites in the microbiota-gut-brain axis, the metabolic pathways in which they are involved, and their functions. This review focuses mainly on the use of mass spectrometry for their determination, reporting on the latest analytical methods, their limitations, and future perspectives. The analytical strategy for the qualitative-quantitative characterization of mediators must be reliable in order to elucidate the molecular mechanisms underlying the influence of the above-mentioned axis on stress resilience or vulnerability.}, }
@article {pmid40001446, year = {2025}, author = {Kövér, Z and Gajdács, M and Polgár, B and Szabó, D and Urbán, E}, title = {The Microbiological Background of Medication-Related Osteonecrosis of the Jaw (MRONJ): Clinical Evidence Based on Traditional Culture and Molecular Biological Detection Methods.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/antibiotics14020203}, pmid = {40001446}, issn = {2079-6382}, support = {No "0272"//HUN-REN-SU, Human Microbiota Study Group/ ; AOK-KA-2019/48//Internal Scientific Grant of Pecs University Medical School/ ; }, abstract = {Background: Medication-related osteonecrosis of the jaw (MRONJ) is a common adverse event following antiresorptive treatment, leading to chronic inflammation and exposed, necrotic bone surfaces in the jawbone. There is an increasing recognition of the role of compositional changes in the colonizing members of the oral microbiota implicated in triggering and/or maintaining MRONJ. The aim of our study was to characterize the culturable and non-culturable microbiota-with particular focus on Actinomyces spp. and Actinomyces-like organisms (ALOs)-from surgically removed bone samples of MRONJ patients and healthy control subjects. Methods: n = 35 patients (median age: 70 years) in various stages of MRONJ, with a history of receiving oral or intravenous antiresorptive treatment were included in the study. The controls (n = 35; median age: 35 years) consisted of otherwise healthy individuals undergoing tooth extraction. Traditional, quantitative, aerobic, and anaerobic culture, and Actinomyces-specific PCR was performed for all bone samples from patients and controls, while microbiome analyses-based on 16S rRNA sequencing-were carried out in 5-5 randomly selected samples. Mann-Whitney U test, Wilcoxon rank sum test (alpha diversity), and PERMANOVA analysis (beta diversity) were performed. Results: In MRONJ samples, 185 anaerobic isolates, corresponding to 65 different species were identified (vs. 72 isolates, corresponding to 27 different species in the control group). The detection of Actinomyces spp. and ALOs was more common in MRONJ bone samples, based on traditional culture (65.7% vs. 17.1%; p < 0.001) and PCR (82.9% vs. 37.1%; p < 0.001), respectively. The isolation of Fusobacterium spp. (22 vs. 7; p = 0.001), Prevotella spp. (22 vs. 6; p = 0.034), and Gram-positive anaerobic cocci (GPAC) (30 vs. 9; p = 0.016) was significantly more common in MRONJ patient samples. The microbiota of the controls' bone samples were characterized by a considerable dominance of Streptococcus spp. and Veillonella spp, while the bacterial abundance rates were substantially more heterogeneous in MRONJ bone samples. Notable differences were not observed among the samples related to the abundance of Actinomyces in the bone microbiota. Conclusions: According to the "infection hypothesis", alterations in the oral microbiome-with Actinomyces and ALOs being the most relevant-may play a key role in the development, aggravation, and progression of MRONJ. The timely detection of Actinomyces in necrotic bone is crucial, as it has important therapeutic implications.}, }
@article {pmid40001355, year = {2025}, author = {Rodríguez-Recio, FR and Garza-Cervantes, JA and Balderas-Cisneros, FJ and Morones-Ramírez, JR}, title = {Genomic Insights into and Lytic Potential of Native Bacteriophages M8-2 and M8-3 Against Clinically Relevant Multidrug-Resistant Pseudomonas aeruginosa.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/antibiotics14020110}, pmid = {40001355}, issn = {2079-6382}, support = {Paicyt 2019-2020, Paicyt 2020-2021, and Paicyt 2022-2023//Universidad Autonoma de Nuevo Le&#xf3;n and CONACyT/ ; 221332//CONACyT/ ; 1502//Fronteras de la Ciencia/ ; 279957//Infraestructura/ ; 316869//Apoyos a la Ciencia de Frontera/ ; CF-2023-I-1327//Grant a Ciencia de Frontera/ ; }, abstract = {Background/Objectives: Antibiotic resistance in pathogenic bacteria poses a critical global health threat, with multidrug-resistant (MDR) strains increasingly undermining conventional treatments. Among these, Pseudomonas aeruginosa is a high-priority pathogen due to its resistance to carbapenems and frequent presence in hospital settings, contributing to severe healthcare-associated infections. This study aimed to isolate and characterize novel bacteriophages from environmental wastewater samples that could specifically target MDR P. aeruginosa. Methods: Two bacteriophages, M8-2 and M8-3, were isolated from wastewater in Monterrey, Mexico. A genomic analysis classified M8-2 and M8-3 within the Caudoviridae family, and next-generation sequencing (NGS) was used to confirm the absence of undesirable antibiotic resistance or virulence genes. Optimization of viral amplification was performed to achieve high titers, with structural proteins characterized by SDS-PAGE. Results: Phages M8-2 and M8-3 exhibited specific lytic activity against MDR strains of P. aeruginosa, offering a targeted approach to combat antibiotic-resistant infections. High genetic similarity (>95%) to known Gram-negative bacterial phages was observed. Optimized viral amplification yielded titers of 4.2 × 10[7] and 1.03 × 10[9] PFUs/mL for M8-2 and M8-3, respectively. The specificity of these phages minimized disruption to the host microbiome, and their significant efficacy in suppressing bacterial growth positions bacteriophages as promising candidates for localized and personalized phage therapy, especially in chronic and hospital-acquired infection settings. Conclusions: These findings highlight the therapeutic potential of M8-2 and M8-3 in addressing antibiotic-resistant P. aeruginosa infections. Their safety profile, high target specificity, and robust lytic activity underscore the feasibility of incorporating phage-based strategies into current antimicrobial protocols. This study contributes to the broader goal of developing sustainable and effective phage therapies for diverse clinical and environmental contexts.}, }
@article {pmid40001319, year = {2025}, author = {Risely, A}, title = {Feather mites selectively feed on specific bacteria and fungi on feathers with potential benefits to hosts.}, journal = {The Journal of animal ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1365-2656.70021}, pmid = {40001319}, issn = {1365-2656}, abstract = {Invited Research Highlight: Matthews, A. E., Trevelline, B. K., Wijeratne, A. J., &amp; Boves, T. J. (2024). Picky eaters: Selective microbial diet of avian ectosymbionts. Journal of Animal Ecology. Trophic interactions such as herbivory and predation are crucial regulators of ecological communities, yet few examples exist for these processes within host-associated microbiomes. In a recent study, Matthews et al. (2024) looked for evidence of selective microbial predation of bacteria and fungi by microscopic mites on the feathers of wild Prothonotary warblers (Protonotaria citrea). The authors quantified the bacterial and fungal diet of commensal feather mites and compared this with the composition of microbial communities living directly on the feather. They found that, despite a large variety of microbes to choose from, mites strongly preferred to eat a small number of bacterial and fungal genera. Some of these selectively enriched taxa are known keratin-degraders, suggesting that mites may protect feathers by selectively consuming harmful microbes. This study presents a rare example of a trophic interaction within the microscopic ecosystem of the feather that may act as an important force shaping microbial communities in ways that benefit the host, providing an overlooked mechanism by which symbioses between birds and mites could evolve.}, }
@article {pmid40001165, year = {2025}, author = {Awasthi, S and Hiremath, VM and Nain, S and Malik, S and Srinivasan, V and Rose, P and Choudhury, A and Grover, R and Sharma, R}, title = {Microbial landscape of Indian homes: the microbial diversity, pathogens and antimicrobial resistome in urban residential spaces.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {25}, pmid = {40001165}, issn = {2524-6372}, support = {CLP0030, CNP0011//Reckitt (India) Ltd, India/ ; JRF//CSIR/ ; }, abstract = {BACKGROUND: Urban dwellings serve as complex and diverse microbial community niches. Interactions and impact of house microbiome on the health of the inhabitants need to be clearly defined. Therefore, it is critical to understand the diversity of the house microbiota, the presence and abundance of potential pathogens, and antimicrobial resistance.<br><br>RESULTS: Shotgun metagenomics was used to analyze the samples collected from 9 locations in 10 houses in New Delhi, India. The microbiota includes more than 1409 bacterial, 5 fungal, and 474 viral species en masse. The most prevalent bacterial species were Moraxella osloensis, Paracoccus marcusii, Microbacterium aurum, Qipengyuania sp YIMB01966, and Paracoccus sphaerophysae, which were detected in at least 80 samples. The location was the primary factor influencing the microbiome diversity in the Indian houses. The overall diversity of different houses did not differ significantly from each other. The surface type influenced the microbial community, but the microbial diversity on the cemented and tiled floors did not vary significantly. A substantial fraction of the bacterial species were potentially pathogenic or opportunistic pathogens, including the ESKAPE pathogens. Escherichia coli was relatively more abundant in bedroom, foyer, and drawing room locations. Analysis of the house microbiome antimicrobial resistome revealed 669 subtypes representing 22 categories of antimicrobial resistance genes, with multidrug resistance genes being the most abundant, followed by aminoglycoside genes.<br><br>CONCLUSIONS: This study provides the first insight into the microbiomes of houses in New Delhi, showing that these houses have diverse microbiomes and that the location within the house significantly influences the microbiota. The presence of potential pathogens and a repertoire of antimicrobial resistance genes reflect possible health risks, as these could lead to infectious disease transmission. This study builds a framework for understanding the microbial diversity of houses in terms of geographical location, environment, building design, cleaning habits, and impact on the health of occupants.}, }
@article {pmid40001134, year = {2025}, author = {Zhang, Z and Kang, L and Gu, Y and Leng, Z and Chen, T and Xu, M}, title = {Alcohol accelerates the development of esophageal squamous cell carcinoma through elevated Gram-negative bacteria in peripheral circulation.}, journal = {Experimental hematology &amp; oncology}, volume = {14}, number = {1}, pages = {19}, pmid = {40001134}, issn = {2162-3619}, support = {82200613, 82473094, 82372921 and 82300642//National Natural Science Foundation of China/ ; 82200613, 82473094, 82372921 and 82300642//National Natural Science Foundation of China/ ; 82200613, 82473094, 82372921 and 82300642//National Natural Science Foundation of China/ ; 82200613, 82473094, 82372921 and 82300642//National Natural Science Foundation of China/ ; 2025PDWSYCQN-03//The Healthcare Talents Youth Program of Shanghai Pudong New Area/ ; 22YF1436400, 21XD1423100, and 21JC1405200//Shanghai Committee of Science and Technology/ ; 22YF1436400, 21XD1423100, and 21JC1405200//Shanghai Committee of Science and Technology/ ; 22YF1436400, 21XD1423100, and 21JC1405200//Shanghai Committee of Science and Technology/ ; }, abstract = {Alcohol consumption is intricately linked to the incidence of esophageal squamous cell carcinoma (ESCC). This study comprehensively investigates the role of alcohol-induced microbial alterations in ESCC progression. A retrospective analysis of 328 patients demonstrated that alcohol consumption markedly increases the risk of ESCC and boosts the expression of the proliferation marker Ki67. Patients with alcohol-related ESCC exhibited substantially higher blood microbiome diversity, characterized by the dominance of Gram-negative bacteria, and elevated serum lipopolysaccharides (LPS) levels. In a mouse model, alcohol consumption not only augmented tumor burden but also compromised gut barrier integrity, facilitating bacterial translocation. Significant elevations in Gram-negative bacteria, such as Bacteroidales in the blood and Escherichia coli in esophageal tissues, were observed. Mechanistically, alcohol and LPS synergistically activated pro-inflammatory pathways, including TNF, TLR, NF-κB, and MAPK, which fueled ESCC cell proliferation. Meanwhile, LPS triggered necroptosis in normal esophageal epithelial cells. These findings reveal that alcohol-induced microbial dysbiosis in peripheral circulation and LPS-mediated inflammatory responses form a novel pathogenic mechanism in ESCC. Targeting Gram-negative bacteria and LPS could provide a promising therapeutic strategy for managing alcohol-related ESCC. Further research is urgently warranted to explore the interaction between microbial changes and the tumor microenvironment.}, }
@article {pmid40001066, year = {2025}, author = {Braun, A and Deng, M and Hasler, JS and Bukavina, L and Handorf, E and Abbosh, PH}, title = {Association between antibiotics and treatment efficacy in metastatic urothelial carcinoma patients.}, journal = {BMC medicine}, volume = {23}, number = {1}, pages = {117}, pmid = {40001066}, issn = {1741-7015}, mesh = {Humans ; Male ; Female ; Aged ; Middle Aged ; *Anti-Bacterial Agents/therapeutic use ; Treatment Outcome ; *Immune Checkpoint Inhibitors/therapeutic use ; Retrospective Studies ; Carcinoma, Transitional Cell/drug therapy/secondary ; Aged, 80 and over ; Neoplasm Metastasis ; Cisplatin/therapeutic use ; Urologic Neoplasms/drug therapy ; Urinary Bladder Neoplasms/drug therapy ; Dysbiosis/chemically induced ; }, abstract = {BACKGROUND: Antibiotic therapy (ABT)-induced dysbiosis may affect the efficacy of immune checkpoint inhibitors (ICI) therapy. We investigated the association between ABT and real-world overall survival (rwOS) and progression-free survival (rwPFS) in patients with metastatic urothelial carcinoma (mUC) receiving ICI or cisplatin-based chemotherapy (CIS).<br><br>METHODS: Three thousand, one hundred seventy-nine patients were included from a nationwide electronic health record-derived de-identified database. Three-month landmark Kaplan-Meier methods and log-rank tests were used to estimate rwOS/PFS between treatment modalities based on ABT groups (stratified by exposure, timing, excretion mode, and administration route). Cox proportional models with time-varying coefficients were used to investigate the associations between ABT, treatment modality, and rwOS/PFS.<br><br>RESULTS: A total of 402 (27.1%) ICI and 655 (38.6%) CIS patients received ABT (p&#x2009;<&#x2009;0.001). ICI receipt (OR 0.65, p&#x2009;<&#x2009;0.001) and advanced age (OR 0.98, p&#x2009;<&#x2009;0.001) were associated with lower ABT use. ICI exclusive findings included a negative correlation with rwOS in patients who received post-treatment initiated (ICI median: pre-13.2 vs post-7.9 vs none-13.3&#xa0;months; p&#x2009;=&#x2009;0.009), oral (median oral-9.6 vs none-13.3&#xa0;months, p&#x2009;=&#x2009;0.03), and renally cleared (median renal-9.9 vs none-13.3&#xa0;months, p&#x2009;=&#x2009;0.04) ABT. ABT's effect was negatively associated with rwOS in ICI patients within first 6&#xa0;months (HR 1.36, 95% CI 1.107-1.74, p&#x2009;=&#x2009;0.01) but not thereafter (p&#x2009;=&#x2009;0.7).<br><br>CONCLUSIONS: This study identified a potential ICI-specific negative correlation between ABT and rwOS in patients with mUC, specifically those exposed to ABT pills and receipt before treatment initiation. These results emphasize the importance of antibiotic stewardship and continued investigation of the role of gut microbiome in mUC treatment efficacy.}, }
@article {pmid40000989, year = {2025}, author = {Zhao, M and Zhang, Y and Liu, S and Wang, F and Zhang, P}, title = {Eradication of Helicobacter pylori reshapes gut microbiota and facilitates the evolution of antimicrobial resistance through gene transfer and genomic mutations in the gut.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {90}, pmid = {40000989}, issn = {1471-2180}, support = {32201393//National Natural Science Foundation of China/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Humans ; *Helicobacter pylori/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; *Helicobacter Infections/microbiology/drug therapy ; *Gene Transfer, Horizontal ; *Feces/microbiology ; Mutation ; Metagenomics ; Klebsiella/genetics/drug effects ; Female ; Male ; Genome, Bacterial/genetics ; Adult ; Escherichia/genetics/drug effects ; Middle Aged ; Genes, Bacterial/genetics ; }, abstract = {Treating Helicobacter pylori (H. pylori) infection requires large quantities of antibiotics, thus dramatically promoting the enrichment and dissemination of antimicrobial resistance (AMR) in feces. However, the influence of H. pylori eradication on the AMR mobility and the gut microbiota evolution has yet to be thoroughly investigated. Here, a study involving 12 H. pylori-positive participants was conducted, and the pre- and post- eradication fecal samples were sequenced. Metagenomic analysis revealed that the eradication treatment drastically altered the gut microbiome, with the Escherichia and Klebsiella genera emerging as the predominant bacteria. Interestingly, the eradication treatment significantly increased the relative abundance and diversity of resistome and mobilome in gut microbiota. Eradication of H. pylori also enriched AMR genes (ARGs) conferring resistance to antibiotics not administered because of the co-location with other ARGs or mobile genetic elements (MGEs). Additionally, the Escherichia and Klebsiella genera were identified as the primary bacterial hosts of these highly transferable ARGs. Furthermore, the genomic variations associated with ARGs in Escherichia coli (E. coli) caused by the eradication treatment were profiled, including the parC, parE, and gyrA genes. These findings revealed that H. pylori eradication promoted the enrichment of ARGs and MGEs in the Escherichia and Klebsiella genera, and further facilitated bacterial evolution through the horizontal transfer of ARGs and genomic variations.}, }
@article {pmid40000617, year = {2025}, author = {Chen, M and Li, Y and Zhai, Z and Wang, H and Lin, Y and Chang, F and Ge, S and Sun, X and Wei, W and Wang, D and Zhang, M and Chen, R and Yu, H and Feng, T and Huang, X and Cheng, D and Liu, J and Di, W and Hao, Y and Yin, P and Tang, P}, title = {Bifidobacterium animalis subsp. lactis A6 ameliorates bone and muscle loss via modulating gut microbiota composition and enhancing butyrate production.}, journal = {Bone research}, volume = {13}, number = {1}, pages = {28}, pmid = {40000617}, issn = {2095-4700}, support = {82202728//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects/physiology ; Animals ; *Butyrates/metabolism ; *Bifidobacterium animalis ; Mice ; *Probiotics/pharmacology/therapeutic use/administration &amp; dosage ; *Mice, Inbred C57BL ; Dysbiosis/microbiology ; Male ; Dextran Sulfate/toxicity ; }, abstract = {Systematic bone and muscle loss is a complex metabolic disease, which is frequently linked to gut dysfunction, yet its etiology and treatment remain elusive. While probiotics show promise in managing diseases through microbiome modulation, their therapeutic impact on gut dysfunction-induced bone and muscle loss remains to be elucidated. Employing dextran sulfate sodium (DSS)-induced gut dysfunction model and wide-spectrum antibiotics (ABX)-treated mice model, our study revealed that gut dysfunction instigates muscle and bone loss, accompanied by microbial imbalances. Importantly, Bifidobacterium animalis subsp. lactis A6 (B. lactis A6) administration significantly ameliorated muscle and bone loss by modulating gut microbiota composition and enhancing butyrate-producing bacteria. This intervention effectively restored depleted butyrate levels in serum, muscle, and bone tissues caused by gut dysfunction. Furthermore, butyrate supplementation mitigated musculoskeletal loss by repairing the damaged intestinal barrier and enriching beneficial butyrate-producing bacteria. Importantly, butyrate inhibited the NF-κB pathway activation, and reduced the secretion of corresponding inflammatory factors in T cells. Our study highlights the critical role of dysbiosis in gut dysfunction-induced musculoskeletal loss and underscores the therapeutic potential of B. lactis A6. These discoveries offer new microbiome directions for translational and clinical research, providing promising strategies for preventing and managing musculoskeletal diseases.}, }
@article {pmid40000332, year = {2025}, author = {Kouidhi, S and Passmore, JS and Setati, ME and Mwapagha, LM and Jimoh, A and Oduaran, OH}, title = {Bridging data gaps: African reference genomes advancing inclusive microbiome research.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.02.001}, pmid = {40000332}, issn = {1878-4380}, abstract = {The need for African-specific microbiome reference genomes is critical as their absence limits research in health, agriculture, and sustainability. Current global guidelines often do not take into account the region's unique needs. This commentary advocates for Africa-focused microbiome initiatives and community-driven genome projects to better reflect the continent's ecological and demographic diversity, leading to more applicable outcomes.}, }
@article {pmid40000267, year = {2024}, author = {Dean, CJ and Ray, T and Peña-Mosca, F and Wehri, TJ and Sharpe, K and Antunes, AM and Doster, E and Fernandes, L and Calles, VF and Bauman, C and Heins, B and Pinedo, P and Machado, V and Caixeta, LS and Noyes, NR}, title = {The teat skin microbiota of organic primiparous dairy cows is dynamic during the transition period.}, journal = {Preventive veterinary medicine}, volume = {}, number = {}, pages = {106402}, doi = {10.1016/j.prevetmed.2024.106402}, pmid = {40000267}, issn = {1873-1716}, abstract = {BACKGROUND: The transition period is a critical developmental period for dairy cows, during which the udder undergoes numerous physiological changes that can impact future cow health and performance. The teat skin is an important anatomical feature of the dairy cow, as it is continuously exposed to the environment, and also represents an important barrier against microbes that could invade the teat canal and mammary gland. Yet little is known about the temporal dynamics of the teat skin microbiota during the transition period. Therefore, the main objective of this study was to describe the temporal composition of the teat skin microbiota during the transition period in primiparous dairy cows using 16S rRNA sequencing.<br><br>RESULTS: Teat skin swabs were collected throughout the transition period from 710 cows starting their first lactation on 5 certified organic dairy farms. Samples were collected bi-weekly beginning 8 weeks prepartum and then weekly for 4-5 weeks after calving. A total of 4827 teat skin swabs were collected and sequenced, and the resulting sequence data were analyzed by farm and time. Microbial richness, diversity and bacterial load changed dynamically as animals moved through late-stage gestation, parturition and lactation. However, the direction, timing and magnitude of these changes were unique to each farm. Principal component analysis revealed that the composition and structure of the teat skin microbiota also underwent a massive shift during the transition period, with significant differences between phases of the transition period, i.e., late-stage gestation, parturition and lactation. This trend was also observed when samples were categorized into community types using Dirichlet Multinomial Mixture models.<br><br>CONCLUSIONS: We observe that the teat skin microbiota comprises a diverse community of bacteria and archaea that experience large shifts in abundance and composition as cows move through the transition period. These shifts begin several weeks prior to calving and continue into the first few weeks postpartum, likely driven by a combination of changing environment, management and host physiology during the same period of time. The specific dynamics of these shifts seem to be fairly unique to each farm, which suggests that farm-level factors are important considerations for future work on the teat skin microbiota of transitioning first-lactation dairy cows.}, }
@article {pmid39999947, year = {2025}, author = {Malook, SU and Arora, AK and Wong, ACN}, title = {The role of microbiomes in shaping insecticide resistance: current insights and emerging paradigms.}, journal = {Current opinion in insect science}, volume = {}, number = {}, pages = {101346}, doi = {10.1016/j.cois.2025.101346}, pmid = {39999947}, issn = {2214-5753}, abstract = {Insecticide resistance is a global challenge in agriculture and public health, with the microbiome increasingly recognized as a key contributor. This review synthesizes current research on the microbiome's roles in insecticide resistance, emphasizing mechanisms like microbe-mediated insecticide detoxification, bioactivation, and modulation of host gene expression and physiology. We also explore how different environmental factors impact microbe-host interactions, and the roles of epigenetics and post-transcriptional regulation in linking microbial effects to resistance. Integrating evidence from various insect species, this review also proposes strategies for resistance management, including genetically engineered microbes to detoxify insecticides and microbial diagnostic tools for monitoring resistance markers.}, }
@article {pmid39999934, year = {2025}, author = {Choi, JH and Lee, ES and Jung, HI and Kim, BI}, title = {Caries prevention effects of nano silver fluoride sustained release orthodontic elastomerics in dental microcosm biofilms.}, journal = {Journal of dentistry}, volume = {}, number = {}, pages = {105649}, doi = {10.1016/j.jdent.2025.105649}, pmid = {39999934}, issn = {1879-176X}, abstract = {OBJECTIVES: To evaluate the clinical applicability of nano silver fluoride sustained release orthodontic elastomerics (NSF-RE) by investigating its effects on inhibiting biofilm formation and enamel demineralization using dental microcosm biofilms.<br><br>METHODS: Two types of 23% NSF coating solutions were prepared depending on the presence or absence of the plasticizer (polyethylene glycol [PEG] 6000: NSF-EP and NSF-E); the elastomerics were dip-coated individually with these. Biofilms were allowed to form on bovine enamel specimens with the elastomerics. Biofilm maturity (red/green ratio) was measured. After 7 days, biofilm thickness, live/dead cell ratio, and cell viability were evaluated. Microbiome taxonomic profiling was conducted on days 3 and 7. Mineral loss beneath the biofilm was quantified from fluorescence loss (&#x394;F) and &#x394;Fmax values obtained. Demineralization at varying distances from the specimen center was evaluated based on the difference in &#x394;F between the control and experimental groups.<br><br>RESULTS: The NSF-EP (elastomerics treated with NSF coating containing PEG) had a 6.7% significantly lower R/G ratio from day 3 and a 36.1% thinner biofilm compared to the negative control with uncoated elastomerics. In the NSF-EP group, cell viability assessments indicated reductions in total and aciduric bacterial counts by 9.4% and 13.0%, respectively. NSF-EP also had the lowest relative abundance of five caries-related bacteria. Additionally, NSF-EP significantly increased &#x394;F and &#x394;Fmax by 34.8% and 38.7%, respectively, indicating reduced mineral loss. Demineralization did not differ according to distance from the elastomerics.<br><br>CONCLUSION: NSF-RE significantly reduces biofilm formation and demineralization, offering a promising caries prevention strategy in orthodontic patients.<br><br>CLINICAL SIGNIFICANCE: By inhibiting both biofilm formation and demineralization, NSF-RE provides a dual-function approach that may effectively prevent dental caries in orthodontic patients.}, }
@article {pmid39999861, year = {2025}, author = {Mejia, G and Jara-Servin, A and Hernández-Álvarez, C and Romero-Chora, L and Peimbert, M and Cruz-Ortega, R and Alcaraz, LD}, title = {Rhizosphere Microbiome Influence on Tomato Growth under Low-Nutrient Settings.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf019}, pmid = {39999861}, issn = {1574-6941}, abstract = {Studies have suggested that reduced nutrient availability enhances microbial diversity around plant roots, positively impacting plant productivity. However, the specific contributions of rhizosphere microbiomes in nutrient-poor environments still need to be better understood. This study investigates tomato (Solanum lycopersicum L.) root microbiome under low-nutrient conditions. Plants were grown in hydroponics with soil-derived microbial community inoculations. We hypothesised that nutrient limitation would increase the selection of beneficial bacterial communities, compensating for nutrient deficiencies. We identified 12 294 OTUs across treatments and controls using 16S rRNA gene sequencing. Increased plant biomass was observed in treatments compared to controls, suggesting a role for the microbiome in mitigating nutrient limitations. The relative abundance of genera such as Luteolibacter and Sphingopyxis relative abundance correlated with plant phenotypic traits (p ≤ 0.05), and their presence was further validated using shotgun metagenomics. We annotated 722 677 protein families and calculated a core set of 48 116 protein families shared across all treatments and assigned them into Bacteria (93.7%) and Eukaryota (6.2%). Within the core bacterial metagenome, we identified protein families associated with pathways involved in positive plant interactions like the nitrogen fixation. Limited nutrient availability enhanced plant productivity under controlled conditions, offering a path to reduce fertiliser use in agriculture.}, }
@article {pmid39999857, year = {2025}, author = {Stannius, RO and Kovács, &#xc1;T}, title = {Plipastatin is a shared good by Bacillus subtilis during combating Fusarium spp.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf020}, pmid = {39999857}, issn = {1574-6941}, abstract = {Bacillus subtilis a Gram-positive soil dwelling bacterium known for its wide range of bioactive secondary metabolites. The lipopeptide plipastatin produced by most B. subtilis isolates have been shown to exhibit potent anti-fungal activity against plant pathogenic fungi. While the effect of these anti-fungal compounds are well studied in the context of biocontrol, much less is known of their role in the environment, which also harbor non-producing strains of these compounds. Fusarium species produce multiple antibacterial compounds resulting in dysbiosis of the plant-associated microbiome and inhibiting plant beneficial bacteria like B. subtilis. While plipastatin is expected to be important for survival of B. subtilis, not all isolates carry the biosynthetic gene cluster for plipastatin suggesting that the protective effect of plipastatin might be shared. In this study, we investigated the protective effect of plipastatin against Fusarium oxysporum in a co-culture using a producer and a non-producer isolate of plipastatin. We tested the survival of single and co-cultured strains under Fusarium challenge in liquid media and solid agar plates to dissect the influence of spatial structure. Our results highlights that plipastatin protects the non-producer strain in a density dependent manner.}, }
@article {pmid39999841, year = {2025}, author = {Liao, Y and Tong, XT and Zhou, T and Xue, WQ and Wang, TM and He, YQ and Zheng, MQ and Jia, YJ and Yang, DW and Wu, YX and Zheng, XH and Zuo, ZX and Chen, MY and Liu, N and Jia, WH}, title = {Unveiling familial aggregation of nasopharyngeal carcinoma: Insights from oral microbiome dysbiosis.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {101979}, doi = {10.1016/j.xcrm.2025.101979}, pmid = {39999841}, issn = {2666-3791}, abstract = {Familial aggregation is common in nasopharyngeal carcinoma (NPC), yet the impact of oral microbiome dysbiosis on this occurrence remains largely unexplored. We recruit 127 families (649 members, 1-5 patients each) and a case-control cohort of 337 individuals, validating findings in an additional cohort of 995 individuals. Significant microbial similarity is observed among family members, with family factors contributing most to microbiome variation, followed by cigarette smoking, age, and gender. Among multi-NPC families, especially those with three or more patients, we identify three NPC-enriched taxa with notable heritability, including Gemella sp. (heritability, h[2] = 53.1%), Lautropia mirabilis (h[2] = 38.8%), and Streptococcus sp. (h[2] = 38.0%). Heritable bacteria present a markedly higher heritability in families with increased clustering of NPC and form closely interacting networks, suggesting their role in NPC familial aggregation. These findings open up possibilities for identifying high-risk individuals, enhancing clinical surveillance, and developing personalized prevention and treatment approaches of NPC through microbiome-based strategies.}, }
@article {pmid39999800, year = {2025}, author = {Zhang, H and Xiang, J and Feng, J and Zhang, M and Xi, Q}, title = {Gut microbiome dysbiosis and inflammatory bowel disease complement each other.}, journal = {Digestive diseases (Basel, Switzerland)}, volume = {}, number = {}, pages = {1-18}, doi = {10.1159/000544771}, pmid = {39999800}, issn = {1421-9875}, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract. The worldwide increase in the incidence of IBD imposes a significant economic burden on patients and communities. Recently, numerous studies have shown that disruption of the balance between the host and microbes, known as dysbiosis, is strongly associated with the development of IBD.<br><br>SUMMARY: Dysbiosis can be influenced by diet, lifestyle rhythms, hygiene conditions, drugs, and the inflammatory state of IBD patients. In the microbiome microenvironment, dysbiosis can be influenced by the microbiome and metabolites. Gut microbiome dysbiosis in IBD patients can play a proinflammatory role by disrupting the intestinal barrier and modulating the immune system, leading to the worsening or recurrence of IBD. In future studies, the mechanisms of dysbiosis in IBD and its influencing factors should be investigated from a more macroscopic perspective to propose new valuable diagnostic and therapeutic approaches.<br><br>KEY MESSAGES: Gut microbiome dysbiosis can lead to the development of inflammatory bowel disease, and inflammatory bowel disease can in turn exacerbate gut microbiome dysbiosis, creating a vicious cycle.}, }
@article {pmid39999639, year = {2025}, author = {Zhang, S and Niu, H and Zhu, J}, title = {Personalized nutrition studies of human gut microbiome-polyphenol interactions utilizing continuous multistaged in vitro fermentation models-a narrative review.}, journal = {Nutrition research (New York, N.Y.)}, volume = {135}, number = {}, pages = {101-127}, doi = {10.1016/j.nutres.2025.01.011}, pmid = {39999639}, issn = {1879-0739}, abstract = {The gut microbiota, a complex community of microorganisms primarily inhabiting the human large intestine, plays a crucial role in human health. Gut dysbiosis, characterized by an imbalance in gut bacterial populations, has been increasingly recognized as a significant factor in the pathogenesis of metabolic diseases such as type 2 diabetes, inflammatory bowel disease, and colorectal cancer. Polyphenols are critical modulators of gut microbial composition and metabolism. However, the extent of polyphenol-induced modulation of the gut microbiome remains largely unexplored. In vitro models offer a convenient and ethical alternative to in vivo studies for investigating nutrient-gut microbiome interactions, facilitating easy sampling and controlled experimental conditions. Among these, continuous multistaged in vitro fermentation models, which simulate different sections of the human gastrointestinal tract (e.g., proximal colon, transverse colon, and distal colon), provide a more accurate representation of the human gut environment compared to single-batch fermentation. Various configurations of these multistaged models have been developed and widely employed in studies examining the effects of polyphenols on the gut microbiome. This review aims to summarize the different configurations of multistaged in vitro fermentation models and recent advancements in their development, highlight key aspects of experimental design, outline commonly used analytical workflows with complementary analyses, and review the restorative effects of polyphenol interventions on dysregulated gut microbiota.}, }
@article {pmid39999537, year = {2025}, author = {Dhanasekaran, D and Venkatesan, M and Sabarathinam, S}, title = {Efficacy of microbiome-targeted interventions in obesity management- A comprehensive systematic review.}, journal = {Diabetes &amp; metabolic syndrome}, volume = {19}, number = {2}, pages = {103208}, doi = {10.1016/j.dsx.2025.103208}, pmid = {39999537}, issn = {1878-0334}, abstract = {BACKGROUND: Obesity is a global health crisis linked to numerous chronic diseases. The gut microbiome plays a crucial role in human metabolism, and emerging evidence suggests that modulating the microbiome may offer novel therapeutic avenues for obesity management.<br><br>OBJECTIVE: This systematic review aimed to assess the efficacy and safety of microbiome-targeted interventions, including probiotics, prebiotics, synbiotics, and fecal microbiota transplantation, in improving body composition, metabolic parameters, and inflammatory markers in overweight and obese adults.<br><br>METHODS: A comprehensive search of PubMed, Scopus, and ScienceDirect was conducted to identify relevant studies published between 2005 and 2023. Included studies were assessed for methodological quality and risk of bias using the Cochrane Collaboration tool.<br><br>RESULTS: Body composition: Most studies demonstrated significant reductions in body weight, Body mass index, and body fat percentage.<br><br>METABOLIC PARAMETERS: Improvements were observed in lipid profiles (reduced cholesterol, triglycerides) and glucose metabolism (improved insulin sensitivity).<br><br>INFLAMMATORY MARKERS: Significant reductions were observed in inflammatory markers such as Interleukins (IL-6, IL-8) and C-reactive protein.<br><br>MICROBIAL COMPOSITION: Interventions generally led to shifts in microbial composition, with increases in beneficial bacteria such as Bifidobacterium and Lactobacillus.<br><br>ADVERSE EVENTS: Adverse events were generally minimal and limited.<br><br>CONCLUSION: This review provides strong evidence that microbiome-targeted interventions can effectively improve body composition, metabolic parameters, and inflammatory markers in individuals with obesity. Further research is needed to optimize intervention strategies, identify specific microbial targets, and translate these findings into effective clinical applications.}, }
@article {pmid39999373, year = {2025}, author = {Wu, Z and Li, L and Chen, S and Gong, Y and Liu, Y and Jin, T and Wang, Y and Tang, J and Dong, Q and Yang, B and Yang, F and Dong, W}, title = {Microbiota contribute to regulation of the gut-testis axis in seasonal spermatogenesis.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf036}, pmid = {39999373}, issn = {1751-7370}, abstract = {Seasonal breeding is an important adaptive strategy for animals. Recent studies have highlighted the potential role of the gut microbiota in reproductive health. However, the relationship between the gut microbiota and reproduction in seasonal breeders remains unclear. In this study, we selected a unique single food source animal, the flying squirrel (Trogopterus xanthipes), as a model organism for studying seasonal breeding. By integrating transcriptomic, metabolomic, and microbiome data, we comprehensively investigated the regulation of the gut-metabolism-testis axis in seasonal breeding. Here, we demonstrated a significant spermatogenic phenotype and highly active spermatogenic transcriptional characteristics in the testes of flying squirrels during the breeding season, which were associated with increased polyamine metabolism, primarily involving spermine and γ-amino butyric acid. Moreover, an enrichment of Ruminococcus was observed in the large intestine during the BS and may contribute to enhanced methionine biosynthesis in the gut. Similar changes in Ruminococcus abundance were also observed in several other seasonal breeders. These findings innovatively revealed that reshaping the gut microbiota regulates spermatogenesis in seasonal breeders through polyamine metabolism, highlighting the great potential of the gut-testis axis in livestock animal breeding and human health management.}, }
@article {pmid39999339, year = {2025}, author = {Hohmann, M and Iliasov, D and Larralde, M and Johannes, W and Janßen, KP and Zeller, G and Mascher, T and Gulder, TAM}, title = {Heterologous Expression of a Cryptic BGC from Bilophila sp. Provides Access to a Novel Family of Antibacterial Thiazoles.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.5c00042}, pmid = {39999339}, issn = {2161-5063}, abstract = {Human health is greatly influenced by the gut microbiota and microbiota imbalance can lead to the development of diseases. It is widely acknowledged that the interaction of bacteria within competitive ecosystems is influenced by their specialized metabolites, which act, e.g., as antibacterials or siderophores. However, our understanding of the occurrence and impact of such natural products in the human gut microbiome remains very limited. As arylthiazole siderophores are an emerging family of growth-promoting molecules in pathogenic bacteria, we analyzed a metagenomic data set from the human microbiome and thereby identified the bil-BGC, which originates from an uncultured Bilophila strain. Through gene synthesis and BGC assembly, heterologous expression and mutasynthetic experiments, we discovered the arylthiazole natural products bilothiazoles A-F. While established activities of related molecules indicate their involvement in metal-binding and -uptake, which could promote the growth of pathogenic strains, we also found antibiotic activity for some bilothiazoles. This is supported by biosensor-experiments, where bilothiazoles C and E show PrecA-suppressing activity, while bilothiazole F induces PblaZ, a biosensor characteristic for β-lactam antibiotics. These findings serve as a starting point for investigating the role of bilothiazoles in the pathogenicity of Bilophila species in the gut.}, }
@article {pmid39999013, year = {2025}, author = {Tashkent, Y and Choo, JM and Richard, A and Wang, Z and Calzadilla-Bertot, L and Vasil, E and Miller, S and Taylor, SL and Ivey, KL and Woodman, R and Adler, B and Ayonrinde, OT and Olynyk, JK and Beilin, LJ and Mori, TA and Wigg, AJ and Muller, KR and Adams, LA and Rogers, GB}, title = {Steatotic Liver Disease in Younger Adults is Associated With Altered Gut Microbiology.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {45}, number = {3}, pages = {e70032}, doi = {10.1111/liv.70032}, pmid = {39999013}, issn = {1478-3231}, support = {//Gastroenterological Society of Australia/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Adult ; Female ; Cross-Sectional Studies ; *Feces/microbiology ; Magnetic Resonance Imaging ; Fatty Liver/microbiology/diagnostic imaging ; }, abstract = {BACKGROUND AND AIMS: Steatotic liver disease (SLD) is a leading cause of chronic liver disease worldwide. As SLD pathogenesis has been linked to gut microbiome alterations, we aimed to identify SLD-associated gut microbiome features early in SLD development by utilising a highly characterised cohort of community-dwelling younger adults.<br><br>METHODS AND RESULTS: At age 27&#x2009;years, 588 participants of the Raine Study Generation 2 underwent cross-sectional assessment. Hepatic steatosis was quantified using a validated magnetic resonance imaging (MRI) volumetric liver fat fraction (VLFF) equation (HepaFat). Of the 588 participants, 488 (83%) were classified as having 'no SLD' (VLFF &#x2264;&#x2009;3.55%), 76 (12.9%) with 'mild-moderate' SLD (VLFF: 3.56%-13.4%) and 24 (4.10%) with 'severe' SLD (VLFF >&#x2009;13.4%). Stool microbiome profiling identified an association between severe SLD and lower microbiota alpha diversity (observed features [p&#x2009;=&#x2009;0.015], Pielou evenness [p&#x2009;=&#x2009;0.001] and Shannon diversity [p&#x2009;=&#x2009;0.002]) compared to no SLD. Faecal microbiota composition differed significantly between no SLD and both mild-moderate (p&#x2009;=&#x2009;0.004) and severe SLD groups (p&#x2009;=&#x2009;0.001). There was no significant difference in microbiota dispersion between SLD groups. Reduced relative abundance of short-chain fatty acid producing bacteria, and higher levels of proinflammatory bacterial taxa, were both significantly associated with severe SLD (q&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: SLD in younger adults is associated with reduced intestinal microbial diversity and a pattern of bacterial taxa depletion that is consistent with other chronic inflammatory conditions. Our characterisation of gut microbiome characteristics in early SLD development provides a potential basis for risk identification and reduction.<br><br>TRIAL REGISTRATION: The Raine Study is registered in the Australian New Zealand Clinical Trials Registry (ACTRN12617001599369).}, }
@article {pmid39998920, year = {2025}, author = {Lundgrin, EL and Hatipoglu, B}, title = {Trending Modalities in Type 2 Diabetes Prevention.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {110}, number = {Supplement_2}, pages = {S187-S192}, doi = {10.1210/clinem/dgaf040}, pmid = {39998920}, issn = {1945-7197}, support = {//This work was supported by the Deborah and Ronald Ratner Fund/ ; //Mary B. Lee Chair/ ; }, mesh = {Humans ; *Diabetes Mellitus, Type 2/prevention &amp; control ; *Prediabetic State/therapy ; Hypoglycemic Agents/therapeutic use ; Fecal Microbiota Transplantation ; Incretins/therapeutic use ; Gastrointestinal Microbiome ; Life Style ; }, abstract = {CONTEXT: Prediabetes now affects a substantial proportion of the population, marking a growing group of individuals at increased risk for the development of type 2 diabetes (T2D). Given the profound effect of T2D on an individual's morbidity and mortality, T2D prevention is of critical importance.<br><br>EVIDENCE ACQUISITION: We searched PubMed and Ovid MEDLINE databases for recent systematic reviews, meta-analyses, and original research articles pertaining to prediabetes and the prevention of T2D.<br><br>EVIDENCE SYNTHESIS: T2D prevention strategies have focused on intensive lifestyle modification as well as numerous medications that ultimately improve insulin resistance. Recently, a better understanding of the gut microbiome's role in diabetes progression has suggested a possible preventive role for fecal transplant. Finally, multiple incretin pharmaceutical agents have been developed that show promise in the prevention and treatment of T2D.<br><br>CONCLUSION: The number of novel ways to prevent T2D is rapidly growing. A thorough understanding of the indications, outcomes, and limitations of these new therapies is critical for all who care for individuals with diabetes.}, }
@article {pmid39998665, year = {2025}, author = {Szóstak, N and Budnik, M and Tomela, K and Handschuh, L and Samelak-Czajka, A and Pietrzak, B and Schmidt, M and Kaczmarek, M and Galus, &#x141; and Mackiewicz, J and Mackiewicz, A and Kozlowski, P and Philips, A}, title = {Exploring correlations between gut mycobiome and lymphocytes in melanoma patients undergoing anti-PD-1 therapy.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {74}, number = {4}, pages = {110}, pmid = {39998665}, issn = {1432-0851}, support = {2017/25/B/NZ5/01949//Narodowe Centrum Nauki/ ; POIR.04.01.02-00-0025/17-00//Narodowe Centrum Bada&#x144; i Rozwoju/ ; }, mesh = {Humans ; *Melanoma/drug therapy/immunology ; *Gastrointestinal Microbiome/immunology/drug effects ; Male ; Female ; Middle Aged ; *Lymphocytes/immunology ; *Immune Checkpoint Inhibitors/therapeutic use ; *Mycobiome ; Aged ; Programmed Cell Death 1 Receptor/antagonists &amp; inhibitors ; Adult ; Skin Neoplasms/immunology/drug therapy/microbiology ; Fungi/immunology ; }, abstract = {Research has shown that the microbiome can influence how the immune system responds to melanoma cells, affecting the course of the disease and the outcome of the therapy. Here, we used the metagenomic approach and flow cytometry analyses of blood cells to discover correlations between gut fungi of metastatic melanoma patients enrolled in anti-PD-1 therapy and lymphocytes in their blood.We analyzed the patterns of associations before the first administration of anti-PD-1 therapy (BT, n = 61) and in the third month of the therapy (T3, n = 37), allowing us to track changes during treatment. To understand the possible impact of gut fungi on the efficacy of anti-PD-1 therapy, we analyzed the associations in clinical beneficiaries (CB, n = 37) and non-beneficiaries (NB, n = 24), as well as responders (R, n = 28) and non-responders (NR, n = 33).Patients with LDH < 338 units/L, overall survival (OS) > 12, CB, as well as R, had lower levels of Shannon diversity (p = 0.02, p = 0.05, p = 0.05, and p = 0.03, respectively). We found that the correlation pattern between intestinal fungi and lymphocytes was specific to the type of response, positive or negative. When comparing CB and NB groups, correlations with opposite directions were detected for C. albicans, suggesting a response-specific immune reaction. For CB, M. restricta exhibited a set of correlations with different types of lymphocytes, with prevalent positive correlations, suggesting a robust immune response in the CB group. This result extends our former research, where M. restricta and C. albicans were associated with an increased risk of melanoma progression and a poorer response to anti-PD-1 treatment.}, }
@article {pmid39998594, year = {2025}, author = {Sabry, I and Zeineldin, M and Kamal, M and Hefnawy, A and El-Attar, H and Abdelraof, Y and Ghanem, M}, title = {Comparative evaluation of lower respiratory tract microbiota in healthy and BRD-affected calves in Egypt.}, journal = {Tropical animal health and production}, volume = {57}, number = {2}, pages = {78}, pmid = {39998594}, issn = {1573-7438}, mesh = {Animals ; Cattle ; Egypt ; *Microbiota ; *Bacteria/isolation &amp; purification/classification/genetics ; Lung/microbiology ; Bovine Respiratory Disease Complex/microbiology ; Male ; Cattle Diseases/microbiology/epidemiology ; }, abstract = {The advent of next-generation sequencing technologies has uncovered the importance of commensal microbial populations in the lower respiratory tract (LRT) for mucosal health and their role in the development of bovine respiratory disease (BRD). In this study, we aimed to characterize and compare the LRT microbiota in healthy and BRD-affected calves in Egypt. After assessing clinical respiratory scores in both groups, post-mortem lung samples from the cranial lobes of six clinically healthy calves and six calves affected by BRD were collected following slaughter. The most prevalent bacterial families in all samples were Moraxellaceae (11.06%), Enterobacteriaceae (8.23%), and Flavobacteriaceae (8.13%). The most common bacterial genera across all samples were Acinetobacter (13.1%), Gracilibacillus (7.9%), and Pseudomonas (5.0%). Notably, the overall microbial community structures differed significantly between healthy and BRD-affected calves. Alpha diversity analysis revealed significant differences in the Shannon (p = 0.0043) and Chao1 (p = 0.0001) indices between the two groups. This study highlights the substantial impact of BRD on the LRT microbiota of calves, highlighting the intricate relationship between host health and the LRT microbial ecosystem. Further investigations involving a larger sample size are necessary to establish the clinical significance of LRT microbiota in maintaining bovine respiratory health.}, }
@article {pmid39998325, year = {2025}, author = {Chen, B and Guan, L and Wu, C and Gong, Y and Wu, L and Zhang, M and Cao, Z and Chen, Y and Yang, C and Wang, B and Li, Y and Li, B and Bi, Y and Ning, G and Wang, J and Wang, W and Liu, R}, title = {Gut Microbiota-Butyrate-PPARγ Axis Modulates Adipose Regulatory T Cell Population.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2411086}, doi = {10.1002/advs.202411086}, pmid = {39998325}, issn = {2198-3844}, support = {92157204//National Natural Science Foundation of China/ ; 92357305//National Natural Science Foundation of China/ ; 91857205//National Natural Science Foundation of China/ ; 81930021//National Natural Science Foundation of China/ ; 82088102//National Natural Science Foundation of China/ ; 82250901//National Natural Science Foundation of China/ ; 82470898//National Natural Science Foundation of China/ ; 81900769//National Natural Science Foundation of China/ ; 2021YFA1301103//National Key Research and Development Program of China/ ; 2022YFC2505201//National Key Research and Development Program of China/ ; 21JC1404400//Science and Technology Commission of Shanghai Municipality/ ; 23XD1422400//Science and Technology Commission of Shanghai Municipality/ ; 20171903Round2//Innovative research team of high-level local universities in Shanghai, Shanghai Municipal Education Commission-Gaofeng Clinical Medicine Grant Support/ ; }, abstract = {Gut microbiota is essential for the function of peripherally-induced regulatory T (pTreg) cells. However, how commensal bacteria affect thymically derived fat-resident Treg cells that harbor a unique expression of peroxisome proliferator-activated receptor (PPAR)-γ and suppress inflammation in visceral adipose tissue (VAT), is not well defined. Here it is revealed that microbiota depletion causes a drastic decline in Treg cell population in VAT, particularly those expressing ST2 (ST2[+] Treg), which are largely restored after gut microbiome reconstruction. Mechanistically, gut microbiota-derived butyrate increases VAT ST2[+] Treg cells through binding PPARγ. Butyrate supplementation and high fiber diet increase VAT ST2[+] Treg population in obese mice, and ameliorated glucose tolerance and visceral inflammation. Furthermore, human omental adipose Treg cells show positive correlation with fecal butyrate and certain butyrate-producing microbes. This study identifies the critical role of gut microbiota-butyrate-PPARγ axis in maintaining VAT Treg population, pinpointing a potential approach to augment VAT Treg population and ameliorate inflammation.}, }
@article {pmid39998297, year = {2025}, author = {Canada, K and Evans, TM and Pelphrey, K}, title = {Microbiome's Effect on White Matter in Autism.}, journal = {Journal of neurophysiology}, volume = {}, number = {}, pages = {}, doi = {10.1152/jn.00607.2024}, pmid = {39998297}, issn = {1522-1598}, support = {MH100028//National Institute of Mental Health and Neurosciences (NIMHANS)/ ; }, abstract = {Autism Spectrum Disorder (ASD) is characterized by deficits in social communication and restricted, repetitive behavioral patterns. While other physiological presentations in individuals with ASD are heterogeneous, neuroimaging studies have consistently revealed a developmental pattern of initial white matter hypermyelination followed by reduced myelination compared to typically developing peers. Multiple studies have demonstrated that core ASD symptoms, including impairments in social skills, language acquisition, learning capabilities, motor performance, and sensory processing, correlate significantly with white matter dysregulation measured through diffusion tensor imaging. Longitudinal studies have shown that decreased gut microbiome diversity, particularly reductions in beneficial bacteria such as Bifidobacterium and Lactobacillus, correlates with symptom severity. Emerging mechanistic evidence suggests bidirectional relationships between microbiome composition and white matter development, both directly through metabolites like short-chain fatty acids (SCFAs) that regulate oligodendrocyte function and subsequent myelination, and indirectly through modulation of neuroinflammatory pathways. By integrating molecular-level gut physiology findings with macro-level brain imaging data, we may identify novel therapeutic approaches targeting the gut-brain axis in ASD management.}, }
@article {pmid39998294, year = {2025}, author = {Wolfe, TM and Jo, J and Pinkham, NV and Garey, KW and Walk, ST}, title = {The impact of ibezapolstat and other Clostridioides difficile infection-relevant antibiotics on the microbiome of humanized mice.}, journal = {Antimicrobial agents and chemotherapy}, volume = {}, number = {}, pages = {e0160424}, doi = {10.1128/aac.01604-24}, pmid = {39998294}, issn = {1098-6596}, abstract = {Ibezapolstat (IBZ) is a competitive inhibitor of the bacterial Pol IIIC enzyme in clinical development for the treatment of Clostridioides difficile infection (CDI). Previous studies demonstrated that IBZ carries a favorable microbiome diversity profile compared to vancomycin (VAN). However, head-to-head comparisons with other CDI antibiotics have not been done. The purpose of this study was to compare microbiome changes associated with IBZ to other clinically used CDI antibiotics. Groups of germ-free (GF) mice received a fecal microbiota transplant from one of two healthy human donors and were subsequently exposed to either IBZ, VAN, fidaxomicin (FDX), metronidazole (MET), or no antibiotic (control). 16S rRNA encoding gene sequencing of temporally collected stool samples was used to compare the gut microbiome perturbations between treatment and no-drug control groups. Among the tested antibiotics, the most significant change in microbiome diversity was observed in MET-treated mice. Each antibiotic had a unique effect, but changes in alpha and beta diversities following FDX- and IBZ-treated groups were less pronounced than those observed in VAN- or MET-treated groups. By the end of therapy, both IBZ and FDZ increased the relative abundance of Bacteroidota (phylum), with IBZ additionally increasing the relative abundance of Actinomycetota (phylum). In microbiome-humanized mice, IBZ and FDX had smaller effects on gut microbiome diversity than VAN and MET. Notable differences were observed between the microbiome of IBZ- and FDX-treated groups, which may allow for differentiation of these two antibiotics in future studies.}, }
@article {pmid39998261, year = {2025}, author = {Woh, PY and Chen, Y and Kumpitsch, C and Mohammadzadeh, R and Schmidt, L and Moissl-Eichinger, C}, title = {Reevaluation of the gastrointestinal methanogenic archaeome in multiple sclerosis and its association with treatment.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0218324}, doi = {10.1128/spectrum.02183-24}, pmid = {39998261}, issn = {2165-0497}, abstract = {The role of the gut archaeal microbiome (archaeome) in health and disease remains poorly understood. Methanogenic archaea have been linked to multiple sclerosis (MS), but prior studies were limited by small cohorts and inconsistent methodologies. To address this, we re-evaluated the association between methanogenic archaea and MS using metagenomic data from the International Multiple Sclerosis Microbiome Study. We analyzed gut microbiome profiles from 115 MS patients and 115 healthy household controls across Buenos Aires (27.8%), Edinburgh (33.9%), New York (10.4%), and San Francisco (27.8%). Metagenomic sequences were taxonomically classified using kraken2/bracken and a curated profiling database to detect archaea, specifically Methanobrevibacter species. Most MS patients were female (80/115), aged 25-72 years (median: 44.5), and 70% were undergoing treatment, including dimethyl fumarate (n = 21), fingolimod (n = 20), glatiramer acetate (n = 14), interferon (n = 18), natalizumab (n = 6), or ocrelizumab/rituximab (n = 1). We found no significant differences in overall archaeome profiles between MS patients and controls. However, treated MS patients exhibited higher abundances of Methanobrevibacter smithii and M. sp900766745 compared to untreated patients. Notably, M. sp900766745 abundance correlated with lower disease severity scores in treated patients. Our results suggest that gut methanogens are not directly associated with MS onset or progression but may reflect microbiome health during treatment. These findings highlight potential roles for M. smithii and M. sp900766745 in modulating treatment outcomes, warranting further investigation into their relevance to gut microbiome function and MS management.IMPORTANCEMultiple sclerosis (MS) is a chronic neuroinflammatory disease affecting the central nervous system, with approximately 2.8 million people diagnosed worldwide, mainly young adults aged 20-30 years. While recent studies have focused on bacterial changes in the MS microbiome, the role of gut archaea has been less explored. Previous research suggested a potential link between methanogenic archaea and MS disease status, but these findings remained inconclusive. Our study addresses this gap by investigating the gut archaeal composition in MS patients and examining how it changes in response to treatment. By focusing on methanogens, we aim to uncover novel insights into their role in MS, potentially revealing new biomarkers or therapeutic targets. This research is crucial for enhancing our understanding of the gut microbiome's impact on MS and improving patient management.}, }
@article {pmid39998243, year = {2025}, author = {Brochu, HN and Zhang, Q and Song, K and Wang, L and Deare, EA and Williams, JD and Icenhour, CR and Iyer, LK}, title = {Characterization of vaginal microbiomes in clinician-collected bacterial vaginosis diagnosed samples.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0258224}, doi = {10.1128/spectrum.02582-24}, pmid = {39998243}, issn = {2165-0497}, abstract = {Bacterial vaginosis (BV) is a type of vaginal inflammation caused by bacterial overgrowth, upsetting the healthy microbiome of the vagina. Existing clinical testing for BV is primarily based upon physical and microscopic examination of vaginal secretions. Modern PCR-based clinical tests target panels of BV-associated microbes, such as the Labcorp NuSwab test that targets Atopobium (Fannyhessea) vaginae, Megasphaera-1, and Bacterial Vaginosis Associated Bacterium (BVAB)-2. Remnant clinician-collected NuSwab vaginal swabs underwent DNA extraction and 16S V3-V4 rRNA gene sequencing to profile microbes in addition to those included in the Labcorp NuSwab test. Community state types (CSTs) were determined using the most abundant taxon detected in each sample. PCR results for NuSwab panel microbial targets were compared against the corresponding microbiome profiles. Metabolic pathway abundances were characterized via metagenomic prediction from amplicon sequence variants (ASVs). 16S V3-V4 rRNA gene sequencing of 75 remnant vaginal swabs yielded 492 unique 16S V3-V4 ASVs, identifying 83 unique genera. NuSwab microbe quantification was strongly concordant with quantification by sequencing (P < 0.01). Samples in CST-I (18 of 18, 100%), CST-II (three of three, 100%), CST-III (15 of 17, 88%), and CST-V (one of one, 100%) were largely categorized as BV-negative via the NuSwab panel, while most CST-IV samples (28 of 36, 78%) were BV-positive or BV-indeterminate. BV-associated microbial and predicted metabolic signatures were shared across multiple CSTs. These findings highlight robust sequencing-based quantification of Labcorp NuSwab BV microbes, accurate discrimination of vaginal microbiome CSTs dominated by distinct Lactobacilli, and expanded the identification of BV-associated bacterial and metabolic biomarkers.IMPORTANCEBacterial vaginosis (BV) poses a significant health burden for women during reproductive years and onward. Current BV diagnostics rely on either panels of select microbes or on physical and microscopic evaluations by technicians. Here, we sequenced the microbiome profiles of samples previously diagnosed by the Labcorp NuSwab test to better understand disruptions to the vaginal microbiome during BV. We show that microbial sequencing can faithfully reproduce targeted PCR diagnostic results and can improve our knowledge of healthy and BV-associated microbial and metabolic biomarkers. This work highlights a robust, agnostic BV classification scheme with potential for future development of sequencing-based BV diagnostic tools.}, }
@article {pmid39998226, year = {2025}, author = {Martino, C and Kellman, BP and Sandoval, DR and Clausen, TM and Cooper, R and Benjdia, A and Soualmia, F and Clark, AE and Garretson, AF and Marotz, CA and Song, SJ and Wandro, S and Zaramela, LS and Salido, RA and Zhu, Q and Armingol, E and Vázquez-Baeza, Y and McDonald, D and Sorrentino, JT and Taylor, B and Belda-Ferre, P and Das, P and Ali, F and Liang, C and Zhang, Y and Schifanella, L and Covizzi, A and Lai, A and Riva, A and Basting, C and Broedlow, CA and Havulinna, AS and Jousilahti, P and Estaki, M and Kosciolek, T and Kuplicki, R and Victor, TA and Paulus, MP and Savage, KE and Benbow, JL and Spielfogel, ES and Anderson, CAM and Martinez, ME and Lacey, JV and Huang, S and Haiminen, N and Parida, L and Kim, H-C and Gilbert, JA and Sweeney, DA and Allard, SM and Swafford, AD and Cheng, S and Inoyue, M and Niiranen, T and Jain, M and Salomaa, V and Zengler, K and Klatt, NR and Hasty, J and Berteau, O and Carlin, AF and Esko, JD and Lewis, NE and Knight, R}, title = {SARS-CoV-2 infectivity can be modulated through bacterial grooming of the glycocalyx.}, journal = {mBio}, volume = {}, number = {}, pages = {e0401524}, doi = {10.1128/mbio.04015-24}, pmid = {39998226}, issn = {2150-7511}, abstract = {The gastrointestinal (GI) tract is a site of replication of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and GI symptoms are often reported by patients. SARS-CoV-2 cell entry depends upon heparan sulfate (HS) proteoglycans, which commensal bacteria that bathe the human mucosa are known to modify. To explore human gut HS-modifying bacterial abundances and how their presence may impact SARS-CoV-2 infection, we developed a task-based analysis of proteoglycan degradation on large-scale shotgun metagenomic data. We observed that gut bacteria with high predicted catabolic capacity for HS differ by age and sex, factors associated with coronavirus disease 2019 (COVID-19) severity, and directly by disease severity during/after infection, but do not vary between subjects with COVID-19 comorbidities or by diet. Gut commensal bacterial HS-modifying enzymes reduce spike protein binding and infection of authentic SARS-CoV-2, suggesting that bacterial grooming of the GI mucosa may impact viral susceptibility.IMPORTANCESevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019, can infect the gastrointestinal (GI) tract, and individuals who exhibit GI symptoms often have more severe disease. The GI tract's glycocalyx, a component of the mucosa covering the large intestine, plays a key role in viral entry by binding SARS-CoV-2's spike protein via heparan sulfate (HS). Here, using metabolic task analysis of multiple large microbiome sequencing data sets of the human gut microbiome, we identify a key commensal human intestinal bacteria capable of grooming glycocalyx HS and modulating SARS-CoV-2 infectivity in vitro. Moreover, we engineered the common probiotic Escherichia coli Nissle 1917 (EcN) to effectively block SARS-CoV-2 binding and infection of human cell cultures. Understanding these microbial interactions could lead to better risk assessments and novel therapies targeting viral entry mechanisms.}, }
@article {pmid39998222, year = {2025}, author = {Williamson, EM and Hammer, TJ and Hogendoorn, K and Eisenhofer, R}, title = {Blanking on blanks: few insect microbiota studies control for contaminants.}, journal = {mBio}, volume = {}, number = {}, pages = {e0265824}, doi = {10.1128/mbio.02658-24}, pmid = {39998222}, issn = {2150-7511}, abstract = {Research on insect-microbe relationships is booming, with DNA sequencing being the most commonly used method to describe insect microbiota. However, sequencing is vulnerable to contamination, especially when the sample has low microbial biomass. Such low-biomass samples are common across insect taxa, developmental stages, and tissue types. Identifying putative contaminants is essential to distinguish between true microbiota and introduced contaminant DNA. It is therefore important that studies control for contamination, but how often this is done is unknown. To investigate the status quo of contamination control, we undertook a systematic literature review to quantify the prevalence of negative control usage and contamination control across the literature on insect microbiota (specifically bacterial communities) over a 10 year period. Two-thirds of the 243 insect microbiota studies evaluated had not included blanks (negative controls), and only 13.6% of the studies sequenced these blanks and controlled for contamination in their samples. Our findings highlight a major lack of contamination control in the field of insect microbiota research. This result suggests that a number of microbes reported in the literature may be contaminants as opposed to insect-associated microbiota and that more rigorous contamination control is needed to improve research reliability, validity, and reproducibility. Based on our findings, we recommend the previously developed guidelines outlined in the RIDE checklist, with the addition of one more guideline. We refer to this as the RIDES checklist, which stands for Report methodology, Include negative controls, Determine the level of contamination, Explore contamination downstream, and State the amount of off-target amplification.IMPORTANCEOur systematic review reveals a major lack of methodological rigor within the field of research on insect-associated microbiota. The small percentage of studies that control for contamination suggests that an unknown but potentially considerable number of bacteria reported in the literature could be contaminants. The implication of this finding is that true microbiota may be masked or misrepresented, especially in insects with low microbial biomass.}, }
@article {pmid39998219, year = {2025}, author = {Marian, M and Antonielli, L and Pertot, I and Perazzolli, M}, title = {Amplicon sequencing and culture-dependent approaches reveal core bacterial endophytes aiding freezing stress tolerance in alpine Rosaceae plants.}, journal = {mBio}, volume = {}, number = {}, pages = {e0141824}, doi = {10.1128/mbio.01418-24}, pmid = {39998219}, issn = {2150-7511}, abstract = {Wild plants growing in alpine regions are associated with endophytic microbial communities that may support plant growth and survival under cold conditions. The structure and function of endophytic bacterial communities were characterized in flowers, leaves, and roots of three alpine Rosaceae plants in Alpine areas using a combined amplicon sequencing and culture-dependent approaches to determine the role of core taxa on plant freezing stress tolerance. Amplicon sequencing analysis revealed that plant tissue, collection site, and host plant are the main factors affecting the richness, diversity, and taxonomic structure of endophytic bacterial communities in alpine Rosaceae plants. Core endophytic bacterial taxa were identified as 31 amplicon sequence variants highly prevalent across all plant tissues. Psychrotolerant bacterial endophytes belonging to the core taxa of Duganella, Erwinia, Pseudomonas, and Rhizobium genera mitigated freezing stress in strawberry plants, demonstrating the beneficial role of endophytic bacterial communities and their potential use for cold stress mitigation in agriculture.IMPORTANCEFreezing stress is one of the major abiotic stresses affecting fruit production in Rosaceae crops. Current strategies to reduce freezing damage include physical and chemical methods, which have several limitations in terms of costs, efficacy, feasibility, and environmental impacts. The use or manipulation of plant-associated microbial communities was proposed as a promising sustainable approach to alleviate cold stress in crops, but no information is available on the possible mitigation of freezing stress in Rosaceae plants. A combination of amplicon sequencing, culture-dependent, and plant bioassay approaches revealed the beneficial role of the endophytic bacterial communities in alpine Rosaceae plants. In particular, we showed that culturable psychrotolerant bacterial endophytes belonging to the core taxa of Duganella, Erwinia, Pseudomonas, and Rhizobium genera can mitigate freezing stress on strawberry seedlings. Overall, this study demonstrates the potential use of psychrotolerant bacterial endophytes for the development of biostimulants for cold stress mitigation in agriculture.}, }
@article {pmid39998205, year = {2025}, author = {James, J and Santos, RE and Watnick, PI}, title = {Carbon source, cell density, and the microbial community control inhibition of V. cholerae surface colonization by environmental nitrate.}, journal = {mBio}, volume = {}, number = {}, pages = {e0406624}, doi = {10.1128/mbio.04066-24}, pmid = {39998205}, issn = {2150-7511}, abstract = {The intestinal diarrheal pathogen Vibrio cholerae colonizes the host terminal ileum, a microaerophilic, glucose-poor, nitrate-rich environment. In this environment, V. cholerae respires nitrate and increases transport and utilization of alternative carbon sources via the cAMP receptor protein (CRP), a transcription factor that is active during glucose scarcity. Here, we show that V. cholerae nitrate respiration in aerated cultures is under control of CRP and, therefore, glucose availability. V. cholerae nitrate respiration results in extracellular accumulation of nitrite because V. cholerae does not possess the machinery for nitrite reduction. This nitrite inhibits V. cholerae biofilm formation via an as-yet unelucidated mechanism that depends on the high cell density master regulator HapR. The genome of Paracoccus aminovorans, an intestinal microbe identified in the microbiome of cholera patients that has been shown to enhance V. cholerae biofilm accumulation in the neonatal mouse gut, encodes enzymes that reduce nitrite to nitrogen gas. We report that, in nitrate-supplemented co-cultures, P. aminovorans metabolizes the nitrite generated by V. cholerae and, thereby, enhances V. cholerae surface accumulation. We propose that V. cholerae biofilm formation in the host intestine is limited by nitrite production but can be rescued by intestinal microbes such as P. aminovorans that have the capacity to metabolize nitrite. Such microbes increase V. cholerae colonization of the host ileum and predispose to symptomatic infection.IMPORTANCEVibrio cholerae colonizes the terminal ileum where both oxygen and nitrate are available as terminal electron acceptors. V. cholerae biofilm formation is inhibited by nitrate due to its conversion to nitrite during V. cholerae respiration. When co-cultured with a microbe that can further reduce nitrite, V. cholerae surface accumulation in the presence of nitrate is rescued. The contribution of biofilm formation to ileal colonization depends on the composition of the microbiota. We propose that the intestinal microbiota predisposes mammalian hosts to cholera by consuming the nitrite generated by V. cholerae in the terminal ileum. Differences in the intestinal abundance of nitrite-reducing microbes may partially explain the differential susceptibility of humans to cholera and the resistance of non-human mammalian models to intestinal colonization with V. cholerae.}, }
@article {pmid39998196, year = {2025}, author = {Islam, N and Hoque, MN and Hossen, S and Gilman, AA and Islam, T}, title = {Microbiome diversity in soils of the agro-ecological zones of Bangladesh.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0123724}, doi = {10.1128/mra.01237-24}, pmid = {39998196}, issn = {2576-098X}, abstract = {Diversity and composition of soil bacteriome across various agro-ecological zones (AEZs) in Bangladesh were unveiled using 16S rRNA gene sequencing. The mapping of bacterial communities in each AEZ has laid a foundation for detailed mapping and engineering of soil microbiome in deltaic Bangladesh soils for mitigating impact of climate change and promoting sustainable agriculture.}, }
@article {pmid39998191, year = {2025}, author = {Klosko, E and Hutchison, E and Almomani, A}, title = {Amplicon microbiome sequencing of compost from conventional and redesigned compost buckets.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0080824}, doi = {10.1128/mra.00808-24}, pmid = {39998191}, issn = {2576-098X}, abstract = {Here, we report using amplicon sequencing to assess microbial growth in both conventional and pyramid-shaped compost buckets. Proteobacteria and Firmicutes were the primary bacterial phyla present, and Ascomycota the primary fungal phylum present. Bucket shape did not significantly affect microbial community composition.}, }
@article {pmid39998180, year = {2025}, author = {Lachnit, T and Ulrich, L and Willmer, FM and Hasenbein, T and Steiner, LX and Wolters, M and Herbst, EM and Deines, P}, title = {Nutrition-induced changes in the microbiota can cause dysbiosis and disease development.}, journal = {mBio}, volume = {}, number = {}, pages = {e0384324}, doi = {10.1128/mbio.03843-24}, pmid = {39998180}, issn = {2150-7511}, abstract = {Eukaryotic organisms are associated with complex microbial communities. Changes within these communities have been implicated in disease development. Nonetheless, it remains unclear whether these changes are a cause or a consequence of disease. Here, we report a causal link between environment-induced shifts in the microbiota and disease development. Using the model organism Hydra, we observed changes in microbial composition when transferring laboratory-grown Hydra to natural lake environments. These shifts were caused not only by new colonizers, through the process of community coalescence (merging of previously separate microbial communities), but also by lake water nutrients. Moreover, selective manipulation of the nutrient environment induced compound-specific shifts in the microbiota followed by disease development. Finally, L-arginine supplementation alone caused a transition in Pseudomonas from symbiotic to pathogenic, leading to an upregulation of immune response genes, tissue degradation, and host death. These findings challenge the notion that the host-associated microbiota is exclusively controlled by the host, highlighting the dynamic interplay between host epithelial environment, microbial colonizer pool, and nutrient conditions of the surrounding water. Furthermore, our results show that overfeeding of the microbiota allows for uncontrolled microbial growth and versatile interactions with the host. Environmental conditions may thus render symbionts a potential hazard to their hosts, blurring the divide between pathogenic and non-pathogenic microbes.IMPORTANCEThis study highlights the critical need to understand the dynamic interplay between host-associated microbiota and environmental factors to obtain a holistic view on organismal health. Our results demonstrate that ecosystem-wide microbial trafficking (community coalescence) and environmental nutrient conditions reshape microbial communities with profound implications for host health. By exploring nutrient-driven changes in microbial composition, our research finds experimental support for the "overfeeding hypothesis," which states that overfeeding alters the functionality of the host microbiota such that an overabundance in nutrients can facilitate disease development, transforming non-pathogenic microbes into pathogens. These findings emphasize the critical role of metabolic interactions driving microbial pathogenicity. Furthermore, our research provides empirical evidence for the "pathogenic potential" concept, challenging traditional distinctions between pathogenic and non-pathogenic microbes and supporting the idea that any microbe can become pathogenic under certain conditions.}, }
@article {pmid39998158, year = {2025}, author = {Chenghan, M and Wanxin, L and Bangcheng, Z and Yao, H and Qinxi, L and Ting, Z and Xiaojie, L and Kun, Z and Yingqian, Z and Zhihui, Z}, title = {Short-chain fatty acids mediate gut microbiota-brain communication and protect the blood-brain barrier integrity.}, journal = {Annals of the New York Academy of Sciences}, volume = {}, number = {}, pages = {}, doi = {10.1111/nyas.15299}, pmid = {39998158}, issn = {1749-6632}, support = {82071349//National Natural Scientific Foundation of China/ ; 2021YFF0702001//National Key Research and Development Program of China/ ; }, abstract = {The human gut, with a complex community of microbes, is essential for maintaining overall health. This gut microbiota engages in two-way communication with the central nervous system, collectively known as the gut microbiota-brain axis. Alterations in gut microbiota have been associated with various neurological disorders, and disruptions to the blood-brain barrier (BBB) may be crucial, though the exact mechanisms remain unknown. In the current study, we investigated the impacts of short-chain fatty acids (SCFAs) on the integrity of the BBB, which was compromised by orally administered antibiotics in rhesus monkeys and C57BL/6n mice. Our results showed that SCFA supplementation notably enhanced BBB integrity in rhesus monkeys with gut dysbiosis. Similar outcomes were observed in mice with gut dysbiosis, accompanied by decreased cortical claudin-5 mRNA levels. In particular, propionate, but not acetate or butyrate, could reverse the antibiotic-induced BBB permeability increase in mice. Additionally, in vitro studies demonstrated that propionate boosted the expression of tight junction proteins in brain endothelial cells. These results suggest that the propionate can maintain BBB integrity through a free fatty acid receptor 2-dependent mechanism. This study offers new insights into the gut-brain axis and underscores potential therapeutic targets for interventions based on gut microbiota.}, }
@article {pmid39997957, year = {2025}, author = {Muhie, S and Gautam, A and Mylroie, J and Sowe, B and Campbell, R and Perkins, EJ and Hammamieh, R and Garcia-Reyero, N}, title = {Effects of Environmental Chemical Pollutants on Microbiome Diversity: Insights from Shotgun Metagenomics.}, journal = {Toxics}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/toxics13020142}, pmid = {39997957}, issn = {2305-6304}, abstract = {Chemical exposure in the environment can adversely affect the biodiversity of living organisms, particularly when persistent chemicals accumulate over time and disrupt the balance of microbial populations. In this study, we examined how chemical contaminants influence microorganisms in sediment and overlaying water samples collected from the Kinnickinnic, Milwaukee, and Menomonee Rivers near Milwaukee, Wisconsin, USA. We characterized these samples using shotgun metagenomic sequencing to assess microbiome diversity and employed chemical analyses to quantify more than 200 compounds spanning 16 broad classes, including pesticides, industrial products, personal care products, and pharmaceuticals. Integrative and differential comparative analyses of the combined datasets revealed that microbial density, approximated by adjusted total sequence reads, declined with increasing total chemical concentrations. Protozoan, metazoan, and fungal populations were negatively correlated with higher chemical concentrations, whereas certain bacterial (particularly Proteobacteria) and archaeal populations showed positive correlations. As expected, sediment samples exhibited higher concentrations and a wider dynamic range of chemicals compared to water samples. Varying levels of chemical contamination appeared to shape the distribution of microbial taxa, with some bacterial, metazoan, and protozoan populations present only at certain sites or in specific sample types (sediment versus water). These findings suggest that microbial diversity may be linked to both the type and concentration of chemicals present. Additionally, this study demonstrates the potential roles of multiple microbial kingdoms in degrading environmental pollutants, emphasizing the metabolic versatility of bacteria and archaea in processing complex contaminants such as polyaromatic hydrocarbons and bisphenols. Through functional and resistance gene profiling, we observed that multi-kingdom microbial consortia-including bacteria, fungi, and protozoa-can contribute to bioremediation strategies and help restore ecological balance in contaminated ecosystems. This approach may also serve as a valuable proxy for assessing the types and levels of chemical pollutants, as well as their effects on biodiversity.}, }
@article {pmid39997764, year = {2025}, author = {Lloyd, AJ and Martinez-Martin, MJP and Warren-Walker, A and Hitchings, MD and Moron-Garcia, OM and Watson, A and Villarreal-Ramos, B and Lyons, L and Wilson, T and Allison, G and Beckmann, M}, title = {Green Tea with Rhubarb Root Reduces Plasma Lipids While Preserving Gut Microbial Stability in a Healthy Human Cohort.}, journal = {Metabolites}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/metabo15020139}, pmid = {39997764}, issn = {2218-1989}, support = {10068218//Innovate UK Better Food for all/ ; NA//Welsh Government Covid Recovery Challenge Fund (part of the Welsh Government's Food and Drink Division funding)/ ; NA//BBSRC OIRC RIPEN Innovation Hub and Biofortification Hub/ ; }, abstract = {Background/Objectives: Cardiovascular diseases remain a leading cause of mortality and morbidity, and dyslipidaemia is one of the major risk factors. The widespread use of herbs and medicinal plants in traditional medicine has garnered increasing recognition as a valuable resource for increasing wellness and reducing the onset of disease. Several epidemiologic and clinical studies have shown that altering blood lipid profiles and maintaining gut homeostasis may protect against cardiovascular diseases. Methods: A randomised, active-controlled parallel human clinical trial (n = 52) with three herbal tea infusions (green (Camellia sinensis) tea with rhubarb root, green tea with senna, and active control green tea) daily for 21 days in a free-living healthy adult cohort was conducted to assess the potential for health benefits in terms of plasma lipids and gut health. Paired plasma samples were analysed using Afinion lipid panels (total cholesterol, LDL (low-density lipoprotein) cholesterol, HDL (high-density lipoprotein) cholesterol, triglycerides, and non-HDL cholesterol) and paired stool samples were analysed using 16S rRNA amplicon sequencing to determine bacterial diversity within the gut microbiome. Results: Among participants providing fasting blood samples before and after the intervention (n = 47), consumption of herbal rhubarb root tea and green tea significantly lowered total cholesterol, LDL-cholesterol, and non-HDL cholesterol (p < 0.05) in plasma after 21 days of daily consumption when compared with concentrations before the intervention. No significant change was observed in the senna tea group. In participants providing stool samples (n = 48), no significant differences in overall microbial composition were observed between pre- and post-intervention, even at the genus level. While no significant changes in overall microbial composition were observed, specific bacterial genera, such as Dorea spp., showed correlations with LDL cholesterol concentrations, suggesting potential microbiota-mediated effects of tea consumption. Diet and BMI was maintained in each of the three groups before and after the trial. Conclusions: It was found that drinking a cup of rhubarb root herbal or green tea infusion for 21 days produced beneficial effects on lipid profiles and maintained gut eubiosis without observable adverse effects in a healthy human cohort. More studies are needed to fully understand the effects of rhubarb root and green tea in fatty acid metabolism and gut microbial composition.}, }
@article {pmid39997763, year = {2025}, author = {Blok, L and Hanssen, N and Nieuwdorp, M and Rampanelli, E}, title = {From Microbes to Metabolites: Advances in Gut Microbiome Research in Type 1 Diabetes.}, journal = {Metabolites}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/metabo15020138}, pmid = {39997763}, issn = {2218-1989}, support = {09150172210050/NWO_/Dutch Research Council/Netherlands ; 09150182010020/NWO_/Dutch Research Council/Netherlands ; }, abstract = {Background: Type 1 diabetes (T1D) is a severe chronic T-cell mediated autoimmune disease that attacks the insulin-producing beta cells of the pancreas. The multifactorial nature of T1D involves both genetic and environmental components, with recent research focusing on the gut microbiome as a crucial environmental factor in T1D pathogenesis. The gut microbiome and its metabolites play an important role in modulating immunity and autoimmunity. In recent years, studies have revealed significant alterations in the taxonomic and functional composition of the gut microbiome associated with the development of islet autoimmunity and T1D. These changes include reduced production of short-chain fatty acids, altered bile acid and tryptophan metabolism, and increased intestinal permeability with consequent perturbations of host (auto)immune responses. Methods/Results: In this review, we summarize and discuss recent observational, mechanistic and etiological studies investigating the gut microbiome in T1D and elucidating the intricate role of gut microbes in T1D pathogenesis. Moreover, we highlight the recent advances in intervention studies targeting the microbiota for the prevention or treatment of human T1D. Conclusions: A deeper understanding of the evolution of the gut microbiome before and after T1D onset and of the microbial signals conditioning host immunity may provide us with essential insights for exploiting the microbiome as a prognostic and therapeutic tool.}, }
@article {pmid39997738, year = {2025}, author = {Zhang, Y and Bu, Y and Chen, Y and Chen, P and Du, B and Hashim, JH and Hashim, Z and Wieslander, G and Norbäck, D and Xia, Y and Fu, X}, title = {A Multicenter Exploration of Sick Building Syndrome Symptoms in Malaysian Schools: Indoor Pollutants, Microbial Taxa, and Metabolites.}, journal = {Metabolites}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/metabo15020111}, pmid = {39997738}, issn = {2218-1989}, abstract = {BACKGROUND: The role of the indoor microbiome in sick building syndrome (SBS) is well-recognized, yet prior studies have been limited to single-center analyses, limiting a broader understanding and applicability of their findings.<br><br>METHODS: We conducted a multicenter indoor microbiome and metabolome investigation for SBS, involving 1139 middle school students across three regions in Malaysia (Johor Bahru, Terengganu, and Penang). Using high-throughput amplicon sequencing and untargeted LC-MS, indoor microbiome and metabolites were characterized from classroom dust samples.<br><br>RESULTS: The study found that the prevalence of SBS symptoms was high across all three centers (51.0% to 54.6%). Environmental characteristics, including indoor NO2 and CO2 concentrations and total weight of indoor dust, were positively associated with SBS (p < 0.01, linear regression). Curtobacterium in Terengganu was negatively associated with SBS, and Clostridium perfringens in Johor Bahru was positively associated with SBS (p < 0.01, FDR < 0.05). Whereas all identified fungal taxa, including an uncharacterized uc_f_Auriculariaceae_sp., Duportella kuehneroides, and Wallemia mellicola, were positively associated with SBS (p < 0.01, FDR < 0.05) in Johor Bahru and Terengganu. Mediation analysis revealed that the adverse health effects of NO2 on SBS were partially mediated by the increased abundance of uc_f_Auriculariaceae_sp. (p < 0.05, total effect mediated 51.40%). Additionally, potential protective metabolites (S-adenosylmethionine, N-acetylserotonin, sphinganine, 4-hydroxy-2-quinolone, and (2E,4Z,8E)-Colneleic acid) were mainly derived from environmental microorganisms, conferring protective effects against nasal symptoms and tiredness. In contrast, synthetic chemicals were associated with higher SBS symptoms, inducing eye and nasal symptoms.<br><br>CONCLUSIONS: This study emphasizes both the significance of fostering a balanced indoor microbiome/metabolite and the necessity to reduce exposure to deleterious substances, providing new insights for future targeted intervention strategies.}, }
@article {pmid39997574, year = {2025}, author = {Franović, B and Čandrlić, M and Blašković, M and Renko, I and Komar Milas, K and Markova-Car, EP and Mohar Vitezić, B and Gabrić, D and Gobin, I and Vranić, SM and Perić Kačarević, &#x17d; and Peloza, OC}, title = {The Microbial Diversity and Biofilm Characteristics of d-PTFE Membranes Used for Socket Preservation: A Randomized Controlled Clinical Trial.}, journal = {Journal of functional biomaterials}, volume = {16}, number = {2}, pages = {}, doi = {10.3390/jfb16020040}, pmid = {39997574}, issn = {2079-4983}, support = {IP-2020-02-7875//Croatian science fond/ ; UNIRI-iskusni-biomed-23-167//University of Rijeka/ ; }, abstract = {BACKGROUND: Understanding microbial colonization on different membranes is critical for guided bone regeneration procedures such as socket preservation, as biofilm formation may affect healing and clinical outcomes. This randomized controlled clinical trial (RCT) investigates, for the first time, the microbiome of two different high-density polytetrafluoroethylene (d-PTFE) membranes that are used in socket preservation on a highly molecular level and in vivo.<br><br>METHODS: This RCT enrolled 39 participants, with a total of 48 extraction sites, requiring subsequent implant placement. Sites were assigned to two groups, each receiving socket grafting with a composite bone graft (50% autogenous bone, 50% bovine xenograft) and covered by either a permamem[&#xae;] (group P) or a Cytoplast&#x2122; (group C). The membranes were removed after four weeks and analyzed using scanning electron microscopy (SEM) for bacterial adherence, qPCR for bacterial species quantification, and next-generation sequencing (NGS) for microbial diversity and composition assessment.<br><br>RESULTS: The four-week healing period was uneventful in both groups. The SEM analysis revealed multispecies biofilms on both membranes, with membranes from group C showing a denser extracellular matrix compared with membranes from group P. The qPCR analysis indicated a higher overall bacterial load on group C membranes. The NGS demonstrated significantly higher alpha diversity on group C membranes, while beta diversity indicated comparable microbiota compositions between the groups.<br><br>CONCLUSION: This study highlights the distinct microbial profiles of two d-PTFE membranes during the four-week socket preservation period. Therefore, the membrane type and design do, indeed, influence the biofilm composition and microbial diversity. These findings may have implications for healing outcomes and the risk of infection in the dental implant bed and should therefore be further explored.}, }
@article {pmid39997529, year = {2025}, author = {Hashi, R and Thamer, R and Hassan, A and Canna, K and Ahmed, M and Hassan, MT and Badi, S and Ahmed, MH}, title = {A Contemporary Multifaceted Insight into the Association Between Diabetes Mellitus and Diverticular Disease: An Update About Geriatric Syndrome.}, journal = {Geriatrics (Basel, Switzerland)}, volume = {10}, number = {1}, pages = {}, doi = {10.3390/geriatrics10010030}, pmid = {39997529}, issn = {2308-3417}, abstract = {Introduction: Diverticular disease, once considered a rare geriatric gastrointestinal condition, has now become a prevalent disorder associated with increased morbidity and healthcare costs. The spectrum of complications from diverticular disease ranges from incidental findings to more serious issues such as bleeding and diverticulitis. Symptomatic diverticular disease represents a significant economic burden in the western world. Diabetes mellitus is a major global health issue. As global aging accelerates, geriatric syndromes such as diabetes mellitus (DM) and diverticular disease (DD) are becoming increasingly prevalent. Understanding their interplay is critical, particularly within the geriatric population. Both conditions are linked to lifestyle, dietary habits, and changes in gut physiology. Additionally, age-related alterations in the gut microbiome and immune system make this association more complex, contributing to morbidity and healthcare burdens in older adults. The primary aim of this review is to provide an update on the association between diabetes mellitus and diverticular disease. Methods: This narrative review explores the association between diabetes mellitus and diverticular disease. Relevant articles were identified by searching major databases. Results: Risk factors for diverticular disease include insulin resistance, diabetes mellitus, smoking, non-alcoholic fatty liver disease, lack of physical activity, a low-fibre diet, and a high-carbohydrate diet. These risk factors are also associated with the development of diabetes mellitus. Major population studies indicate that diabetes can either increase the risk of diverticular disease or have a neutral impact. A complication of diabetes mellitus includes impaired intestinal peristalsis and enteric nervous system dysfunction, which can ultimately lead to the formation of intestinal diverticula. High-calorie foods low in fibre are a staple in the diets of many type 2 diabetes mellitus patients, contributing to gut dysbiosis. A detrimental consequence of dysbiosis is a breach in the protective intestinal barrier, which promotes the development of diverticulosis. Conclusions: Diabetes mellitus may be associated with diverticular disease, and the risk factors that contribute to diabetes mellitus can also be linked to diverticular disease. Further studies are needed to explore the complex relationship between diabetes mellitus and diverticular disease.}, }
@article {pmid39997096, year = {2025}, author = {Beltrán-Velasco, AI and Clemente-Suárez, VJ}, title = {Harnessing Gut Microbiota for Biomimetic Innovations in Health and Biotechnology.}, journal = {Biomimetics (Basel, Switzerland)}, volume = {10}, number = {2}, pages = {}, doi = {10.3390/biomimetics10020073}, pmid = {39997096}, issn = {2313-7673}, abstract = {The gut microbiota is a complex and dynamic ecosystem that plays a fundamental role in human health by regulating immunity, metabolism, and the gut-brain axis. Beyond its critical physiological functions, it has emerged as a rich source of inspiration for biomimetic innovations in healthcare and biotechnology. This review explores the transformative potential of microbiota-based biomimetics, focusing on key biological mechanisms such as resilience, self-regulation, and quorum sensing. These mechanisms have inspired the development of innovative applications, including personalized probiotics, synbiotics, artificial microbiomes, bioinspired biosensors, and bioremediation systems. Such technologies aim to emulate and optimize the intricate functions of microbial ecosystems, addressing challenges in healthcare and environmental sustainability. The integration of advanced technologies, such as artificial intelligence, bioengineering, and multi-omics approaches, has further accelerated the potential of microbiota biomimetics. These tools enable the development of precision therapies tailored to individual microbiota profiles, enhance the efficacy of diagnostic systems, and facilitate the design of environmentally sustainable solutions, such as waste-to-energy systems and bioremediation platforms. Emerging areas of innovation, including gut-on-chip models and synthetic biology, offer unprecedented opportunities for studying and applying microbiota principles in controlled environments. Despite these advancements, challenges remain. The replication of microbial complexity in artificial environments, ethical concerns regarding genetically engineered microorganisms, and equitable access to advanced therapies are critical hurdles that must be addressed. This review underscores the importance of interdisciplinary collaboration and public awareness in overcoming these barriers and ensuring the responsible development of microbiota-based solutions. By leveraging the principles of microbial ecosystems, microbiota biomimetics represents a promising frontier in healthcare and sustainability. This approach has the potential to revolutionize therapeutic strategies, redefine diagnostic tools, and address global challenges, paving the way for a more personalized, efficient, and sustainable future in medicine and biotechnology.}, }
@article {pmid39997066, year = {2025}, author = {Baimakhanova, B and Sadanov, A and Trenozhnikova, L and Balgimbaeva, A and Baimakhanova, G and Orasymbet, S and Tleubekova, D and Amangeldi, A and Turlybaeva, Z and Nurgaliyeva, Z and Seisebayeva, R and Kozhekenova, Z and Sairankyzy, S and Shynykul, Z and Yerkenova, S and Turgumbayeva, A}, title = {Understanding the Burden and Management of Urinary Tract Infections in Women.}, journal = {Diseases (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/diseases13020059}, pmid = {39997066}, issn = {2079-9721}, support = {BR21882248//This research was funded by the Development and organization of original domestic medicines production according to GMP standards/ ; }, abstract = {Urinary tract infections (UTIs) represent a prevalent health concern among the female population, with anatomical and physiological determinants such as a shorter urethra and its proximity to the rectum augmenting vulnerability. The presence of Escherichia coli and various other pathogens plays a significant role in the etiology of these infections, which can be aggravated by sexual intercourse and disturbances to the vaginal microbiome. The physiological alterations associated with pregnancy further elevate the likelihood of UTIs, with untreated cases potentially leading to severe complications such as pyelonephritis, preterm labor, and stillbirth. Furthermore, postmenopausal women encounter an augmented risk of UTIs attributable to estrogen deficiency and vaginal atrophy, as well as conditions including pelvic organ prolapse (POP) and urinary incontinence (UI), which hinder optimal bladder functionality. The aforementioned factors, in conjunction with the rising prevalence of cesarean deliveries and catheterization, complicate the management of UTIs. While precise diagnosis is paramount, it remains a formidable challenge, notwithstanding advancements in molecular diagnostic techniques. Management strategies encompass antibiotic-sparing therapies; however, the increasing incidence of multidrug resistance represents an alarming trend. Diverse guidelines from various medical specialties endeavor to standardize treatment approaches, yet significant inconsistencies continue to exist. This study systematically appraises the extant guidelines, evaluating the quality of evidence while identifying areas of agreement and discord to supply practitioners with effective strategies for UTI management.}, }
@article {pmid39996827, year = {2025}, author = {Lu, D and Ma, X and Tao, K and Lei, H}, title = {Advancements in the Pathogenesis, Diagnosis, and Therapeutic Implications of Intestinal Bacteria.}, journal = {Current issues in molecular biology}, volume = {47}, number = {2}, pages = {}, doi = {10.3390/cimb47020106}, pmid = {39996827}, issn = {1467-3045}, support = {2024AFB070//Hubei Natural Science Foundation/ ; 2023XHYN043//Science Foundation of Union Hospital/ ; 82403220//National Natural Science Foundation of China/ ; }, abstract = {Intestinal bacteria form one of the most complex microbial communities in the human body, playing a crucial role in maintaining host health and contributing to the development of various diseases. Here, we provide a comprehensive overview of the composition and function of intestinal bacteria, the factors affecting their homeostasis, and their association and mechanisms with a range of diseases (e.g., inflammatory bowel diseases, colorectal cancer, metabolic diseases). Additionally, their advanced potential in disease diagnosis and treatment is highlighted. Therapies, such as chemotherapy, radiotherapy, and immunotherapy, are significantly impacted by intestinal bacteria, with research indicating that bacteria can enhance chemoimmunotherapy efficiency by affecting T cell recruitment and immune cell infiltration. Fecal microbiota transplantation has emerged as a promising option for treating recurrent Clostridium difficile infections and certain metabolic and neurological disorders. Gut bacteria-related serum metabolites serve as non-invasive indicators for diagnosing CRC, while fecal immunochemical tests offer promising applications in CRC screening. Future research is needed to better understand the causal relationships between intestinal bacteria and diseases, develop more precise diagnostic tools, and evaluate the effectiveness and safety of microbiome-targeted therapies in clinical treatment. This study provides deeper insights into the role of intestinal bacteria in human health and disease, providing a scientific basis for innovative therapeutic strategies that have the potential to transform the landscape of healthcare.}, }
@article {pmid39996800, year = {2025}, author = {Nakadate, K and Saitoh, H and Sakaguchi, M and Miruno, F and Muramatsu, N and Ito, N and Tadokoro, K and Kawakami, K}, title = {Advances in Understanding Lipopolysaccharide-Mediated Hepatitis: Mechanisms and Pathological Features.}, journal = {Current issues in molecular biology}, volume = {47}, number = {2}, pages = {}, doi = {10.3390/cimb47020079}, pmid = {39996800}, issn = {1467-3045}, support = {23K08620//JSPS KAKENHI/ ; }, abstract = {Lipopolysaccharide (LPS), a key component of Gram-negative bacterial membranes, plays a central role in the pathogenesis of inflammatory liver diseases. In this review, we aimed to explore the role of LPS in hepatic injury. Upon hepatic infiltration, LPS activates Kupffer cells via toll-like receptor 4 (TLR4) signaling, inducing proinflammatory cytokines such as tumor necrosis factor-α and interleukin-1β. These mediators amplify hepatocyte apoptosis, endothelial damage, and platelet aggregation, thereby contributing to sinusoidal thrombosis and tissue ischemia. Pathological features, such as hepatocyte shrinkage, sinusoidal expansion, and fibrin deposition, are hallmark indicators of LPS-induced hepatic inflammation. Therapeutically, aspirin shows promise for attenuating cytokine release, protecting endothelial integrity, and reducing thrombogenesis. Emerging strategies include targeting TLR4 pathways, modulating the gut-liver axis, and utilizing biomolecular approaches such as RNA interference for LPS suppression. The integration of public health interventions, such as dietary optimization and microbiome regulation, offers additional preventive measures. In this review, the dual roles of LPS in inflammation and thrombosis have been emphasized. Advancing our understanding of LPS-driven mechanisms and enhancing treatment strategies are pivotal for managing hepatic inflammation and its systemic implications. Future research should focus on refining biomarkers, optimizing therapeutic efficacy, and addressing safety concerns for clinical applications.}, }
@article {pmid39996420, year = {2025}, author = {Zhang, Y and Wu, H and Huilian, C and Fu, L}, title = {Detoxification Mechanism and the Impact of Transamidation-Modified Gliadin on Celiac-Based Gluten Sensitivity: The Potential of Unlocking Gluten Tolerance in Functional Food.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {2}, pages = {1682-1693}, doi = {10.1021/acs.jafc.4c10318}, pmid = {39996420}, issn = {1520-5118}, mesh = {*Gliadin/chemistry/immunology ; *Celiac Disease/immunology ; Animals ; *Mice, Inbred BALB C ; Humans ; *Glutens/chemistry/immunology ; Mice ; Caco-2 Cells ; *Triticum/chemistry/immunology ; Functional Food ; Female ; Gastrointestinal Microbiome/drug effects ; Dendritic Cells/immunology/drug effects ; Male ; }, abstract = {Transamidation of gliadin under reducing conditions has shown promise in mitigating celiac disease-related gluten toxicity. However, comprehensive evaluation in both in vitro and in vivo models is crucial. This study investigated the effects of transamidated gliadin (GM) on celiac toxicity using Caco-2 cell monolayers, bone marrow-derived dendritic cells (BMDCs), and a BALB/c mouse model. In cellular level, GM mitigated intestinal damage compared to unmodified gliadin and stimulated a less pronounced pro-inflammatory response, suggesting a reduced activation of the T-cell-mediated immune system. In vivo, the GM group displayed lower levels of pro-inflammatory factors and less pronounced Th1/Th2 imbalance compared to the unmodified gliadin group. Notably, the GM also improved the balance of the intestinal microbiome. In brief, GM exhibited significantly reduced celiac toxicity in both cellular and animal models that mimics the intestinal environment of celiac disease. These findings suggest that transamidation treatment holds potential as a safer alternative strategy to lower the toxicity of wheat gliadin/wheat flour, potentially paving the way for developing modified gluten-based foods with desirable texture or ingredients as a nutritional enhancer or structure improver, benefiting individuals with specific needs.}, }
@article {pmid39996222, year = {2025}, author = {Miranda Thais, R and Sarofim, M and Gilmore, A}, title = {Complicated Sigmoid Diverticulitis Mimicking Pelvic Pain in a Patient With Giant Uterine Fibroids: A Case Report.}, journal = {Cureus}, volume = {17}, number = {1}, pages = {e77979}, pmid = {39996222}, issn = {2168-8184}, abstract = {This report describes the case of a woman in her late forties with a history of large uterine fibroids who presented to the Emergency Department with colicky suprapubic pain and urinary symptoms. Initial computed tomography (CT) showed uncomplicated acute diverticulitis but despite antibiotic treatment, her condition worsened, and a follow-up CT revealed sigmoid perforation, requiring high anterior resection and subtotal hysterectomy. The case highlights how large fibroids exert external pressure on the colon, impairing motility and increasing the risk of diverticula formation. Alterations in the gut microbiome may contribute to colonic mucosal inflammation, commonly seen in diverticular disease. Patients with uterine fibroids have altered microbiome composition, which could further increase the risk of diverticular disease. These findings provide a pathway for future research into the influence of uterine fibroids on the pathophysiology of diverticular disease.}, }
@article {pmid39996103, year = {2025}, author = {Anirvan, P and Khan, ZH and Bhuyan, P and Dixit, S and Dash, R and Mishra, P and Venugopal, G and Balachander, GM and Bharali, P and Gogoi, M and Panigrahi, MK and Ranjit, M and Ramadass, B and Singh, SP}, title = {Gut Microbiota and Genetic Polymorphisms Appear to Drive Disease Expression of Nonalcoholic Fatty Liver Disease in Lean Individuals.}, journal = {Journal of clinical and experimental hepatology}, volume = {15}, number = {3}, pages = {102503}, pmid = {39996103}, issn = {0973-6883}, abstract = {BACKGROUND/OBJECTIVES: There are very few comparative studies worldwide between 'lean' and 'nonlean/obese nonalcoholic fatty liver disease (NAFLD)' patients analyzing the differences in gut microbiome, genotype, and serum bile acids. Our aim was to compare the genotype, gut microbiome, bile acid profile, and metabolic patterns of lean NAFLD and obese NAFLD patients with special reference to hepatic fibrosis.<br><br>METHODS: Both lean and obese NAFLD patients diagnosed by ultrasonography along with matched controls were included. Genotyping, fecal microbiome analysis and estimation of serum total bile acid levels were done for patients as well as controls.<br><br>RESULTS: Biochemical and metabolic patterns of lean and obese NAFLD patients were comparable. Lean NAFLD patients had lower fasting plasma glucose (FPG) and homoeostasis model assessment-insulin resistance (HOMA-IR), although the proportions of patients having elevated HOMA-IR and metabolic syndrome (MS) were comparable. Noninvasive scores of liver fibrosis were also comparable. A greater proportion of lean NAFLD patients had the PNPLA3 rs738409 (G/G) genotype. However, there was no association of genetic polymorphisms with steatosis or fibrosis. Nonlean and lean NAFLD patients had comparable serum total bile acid levels. On microbiome analysis, lean NAFLD patients were found to have distinct expression of bacterial species while beta diversity was found to be significantly different across all groups.<br><br>CONCLUSION: Lean NAFLD patients were found to have the PNPLA3 rs738409 (G/G) genotype. Lean NAFLD patients were also found to have unique gut microbial&#xa0;signatures, while beta diversity significantly differed across all groups. Differential expression of gut microbiota and genetic polymorphisms could underlie the pathogenesis of lean NAFLD.}, }
@article {pmid39996076, year = {2025}, author = {An, L and Lu, X and Zhang, P and Sun, J and Cong, B and Sa, R and He, D}, title = {Effects of continuous cropping on bacterial community diversity and soil metabolites in soybean roots.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1534809}, pmid = {39996076}, issn = {1664-302X}, abstract = {The alternating planting of corn and soybeans is regarded as an effective strategy in addressing the challenges faced in soybean cultivation. However, the precise mechanisms that control the bacterial microbiome in soybean roots in the soil, particularly in continuous cropping and rotational corn-soybean farming rotations, are remain unclear. This study employed both field and pot positioning experiments, using high-throughput and generic metabolomics sequencing techniques to explore the dynamics between soybean plants, root microflora, and soil metabolites, especially in the context of continuous cropping and fluctuating corn-soybean crop rotation. The process that included rotating corn soybeans significantly enhanced their grain yield, dry weight, soil nitrogen concentration, urease activity, as well as the accumulation of nitrogen, phosphorus, and potassium in various plant organs, compared to the traditional practice of continuous soybean cultivation. There is a significant reduction in the transit of bacterial operational taxonomic units (OTUs) from the rhizosphere to the endosphere through rhizoplane. The number of bacterial OTUs that are consumed and enriched on rhizoplane is greater than those that are enriched and absorbed in the endosphere. Continuous cropping practices significantly boost Burkholderiales, whereas chloroplast microorganisms significantly improve crop rotation techniques. Soil environmental factors, such as urease and accessible phosphorus, are crucial in establishing the relative prevalence of Rhodanobacter and other bacterial groups. Soil metabolites, such as benzyl alcohol, show a positive correlation with Cyanobacteria, while acidic compounds, such as D-arabinitol, are positively linked with Burkholderiales. This study indicates that the rotation of corn and soybean crops facilitates the growth of soybeans, increases nutrient accumulation in both plants and soil, enhances the presence of beneficial bacteria, and improves soybean yields.}, }
@article {pmid39996012, year = {2025}, author = {Liu, Y and Dai, J and Zhou, G and Chen, R and Bai, C and Shi, F}, title = {Innovative Therapeutic Strategies for Asthma: The Role of Gut Microbiome in Airway Immunity.}, journal = {Journal of asthma and allergy}, volume = {18}, number = {}, pages = {257-267}, pmid = {39996012}, issn = {1178-6965}, abstract = {There is a growing acknowledgment of the gut microbiome's impact on widespread immune responses, which holds considerable importance for comprehending and addressing asthma. Recent research has clarified the complex interactions between gut microbiota and airway immune systems, demonstrating that microbial diversity and composition can affect both the initiation and advancement of asthma. Gut microbial species and metabolites primarily short-chain fatty acids (SCFAs) may either worsen or reduce airway inflammation by regulating the balance of helper T cell 1 (Th1) / helper T cell 2 (Th2) and other immune mediators. This interaction presents innovative therapeutic possibilities, including modulation of gut microbiome during early life through breastfeeding and control of antibiotic use, particularly with prebiotics, which could selectively stimulate the growth of beneficial bacteria, promote immune maturation, reducing susceptibility to asthma and allergic airway inflammation. Besides, investigating the gut-lung axis reveals new opportunities for personalized medicine in asthma treatment, emphasizing the necessity for integrated strategies that take individual microbiome profiles into account. This paper examines the latest developments in comprehending the mechanisms by which gut microbiota affect airway inflammation and hypersensitivity, especially focusing on treatment strategies.}, }
@article {pmid39995854, year = {2025}, author = {Massara, M and Ballabio, M and Dolfi, B and Morad, G and Wischnewski, V and Lamprou, E and Lourenco, J and Claudinot, S and Gallart-Ayala, H and Méndez, RS and Kauzlaric, A and Fournier, N and Damania, AV and Wong, MC and Ivanisevic, J and Ajami, NJ and Wargo, JA and Joyce, JA}, title = {The bacterial microbiome modulates the initiation of brain metastasis by impacting the gut-to-brain axis.}, journal = {iScience}, volume = {28}, number = {2}, pages = {111874}, pmid = {39995854}, issn = {2589-0042}, abstract = {Brain metastases (BrMs) are the most common brain tumors in patients and are associated with poor prognosis. Investigating the systemic and environmental factors regulating BrM biology represents an important strategy to develop effective treatments. Toward this goal, we explored the contribution of the gut microbiome to BrM development by using in vivo breast-BrM models under germ-free conditions or antibiotic treatment. This revealed a detrimental role of gut microbiota in fostering BrM initiation. We thus evaluated the impact of antibiotics and BrM outgrowth on the gut-brain axis. We found the bacterial genus Alistipes was differentially present under antibiotic treatment and BrM progression. In parallel, we quantified circulating metabolites, revealing kynurenic acid as a differentially abundant molecule that impaired the interaction between cancer cells and the brain vasculature in ex vivo functional assays. Together, these results illuminate the potential role of gut microbiota in modulating breast-BrM via the gut-to-brain axis.}, }
@article {pmid39995673, year = {2025}, author = {Li, M and Wang, J and Liu, Q and Liu, Y and Mi, W and Li, W and Li, J}, title = {Beyond the dichotomy: understanding the overlap between atopic dermatitis and psoriasis.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1541776}, pmid = {39995673}, issn = {1664-3224}, mesh = {*Psoriasis/immunology ; *Dermatitis, Atopic/immunology ; Humans ; Microbiota/immunology ; Skin/pathology/immunology ; Animals ; }, abstract = {Atopic dermatitis and psoriasis have traditionally been considered distinct inflammatory skin diseases with unique pathogenic mechanisms. However, accumulating evidence suggests significant overlap in their immunological pathways, metabolic features, and microbiome characteristics, challenging this conventional dichotomy. This review comprehensively examines the complex relationship between psoriasis and atopic dermatitis, with particular emphasis on their shared and distinct pathogenic mechanisms. We analyze the immunological networks, metabolic pathways, and microbial factors contributing to their development and progression. The review expands upon the disease spectrum hypothesis and discusses the nomenclature for conditions exhibiting features of both diseases. We critically evaluate the clinical and histopathological characteristics of concomitant psoriasis and atopic dermatitis, highlighting recent advances in molecular diagnostics for accurate disease differentiation. Importantly, we propose standardized diagnostic criteria for psoriasis dermatitis and examine current therapeutic strategies for managing overlapping conditions. Recent developments in targeted therapies and their implications for treatment selection are thoroughly discussed. By synthesizing current evidence and identifying knowledge gaps, this review provides insights into the complex interplay between psoriasis and atopic dermatitis, aiming to guide clinical decision-making and future research directions in this evolving field.}, }
@article {pmid39995620, year = {2025}, author = {Benítez-Porres, J and Murri, M}, title = {Editorial: Diet and training strategies to optimize health parameters.}, journal = {Frontiers in public health}, volume = {13}, number = {}, pages = {1556859}, pmid = {39995620}, issn = {2296-2565}, }
@article {pmid39995512, year = {2025}, author = {Su, X and Lin, Q and Liu, B and Zhou, C and Lu, L and Lin, Z and Si, J and Ding, Y and Duan, S}, title = {The promising role of nanopore sequencing in cancer diagnostics and treatment.}, journal = {Cell insight}, volume = {4}, number = {2}, pages = {100229}, pmid = {39995512}, issn = {2772-8927}, abstract = {Cancer arises from genetic alterations that impact both the genome and transcriptome. The utilization of nanopore sequencing offers a powerful means of detecting these alterations due to its unique capacity for long single-molecule sequencing. In the context of DNA analysis, nanopore sequencing excels in identifying structural variations (SVs), copy number variations (CNVs), gene fusions within SVs, and mutations in specific genes, including those involving DNA modifications and DNA adducts. In the field of RNA research, nanopore sequencing proves invaluable in discerning differentially expressed transcripts, uncovering novel elements linked to transcriptional regulation, and identifying alternative splicing events and RNA modifications at the single-molecule level. Furthermore, nanopore sequencing extends its reach to detecting microorganisms, encompassing bacteria and viruses, that are intricately associated with tumorigenesis and the development of cancer. Consequently, the application prospects of nanopore sequencing in tumor diagnosis and personalized treatment are expansive, encompassing tasks such as tumor identification and classification, the tailoring of treatment strategies, and the screening of prospective patients. In essence, this technology stands poised to unearth novel mechanisms underlying tumorigenesis while providing dependable support for the diagnosis and treatment of cancer.}, }
@article {pmid39995421, year = {2025}, author = {Freyria, NJ and de Oliveira, TC and Meng, A and Pelletier, E and Lovejoy, C}, title = {Shotgun metagenomics reveals the flexibility and diversity of Arctic marine microbiomes.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf007}, pmid = {39995421}, issn = {2730-6151}, abstract = {Polar oceanographic regions are exposed to rapid changes in temperature, salinity, and light fields that determine microbial species distributions, but resilience to an increasingly unstable climate is unknown. To unravel microbial genomic potential of the Northern Baffin Bay's polynya, we constructed eight metagenomes from the same latitude but targeting two sides of Pikialasorsuaq (The North Water) that differ by current systems, stratification, and temperature regimes. Samples from the surface and subsurface chlorophyll maximum (SCM) of both sides were collected 13 months apart. Details of metabolic pathways were determined for 18 bacteria and 10 microbial eukaryote metagenome-assembled genomes (MAGs). The microbial eukaryotic MAGs were associated with the dominant green algae in the Mamiellales and diatoms in the Mediophyceae, which tended to respectively dominate the eastern and western sides of Pikialasorsuaq. We show that microbial community taxonomic and functional signatures were ca. 80% similar at the latitude sampled with only 20% of genes associated with local conditions. From the metagenomes we found genes involved in osmotic regulation, antifreeze proteins, and photosystem protection, with hydrocarbon biodegradation and methane oxidation potential detected. The shared genomic compliment was consistent with adaptation to the Arctic's extreme fluctuating conditions, with implications for their evolutionary history and the long-term survival of a pan-arctic microbiome. In particular, previously unrecognized genetic capabilities for methane bio-attenuation and hydrocarbon metabolism in eukaryotic phytoplankton suggest adaptation to dark conditions that will remain, despite climate warming, in the high latitude offshore waters of a future Arctic.}, }
@article {pmid39995201, year = {2025}, author = {Gonzalez, T and Zhivov, EV and Nagalla, RR and Verpile, R and Abreu Nunes, V and Tomic-Canic, M and Resnik, B and Lev-Tov, H and Pastar, I}, title = {Comprehensive Approach for Microbial Isolation from Hidradenitis Suppurativa Tunnels.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {216}, pages = {}, doi = {10.3791/67630}, pmid = {39995201}, issn = {1940-087X}, mesh = {*Hidradenitis Suppurativa/microbiology ; Humans ; Microbiota ; }, abstract = {Hidradenitis Suppurativa (HS) is a debilitating condition marked by painful nodules and abscesses, progressing to sinus tracts (tunnels) within the skin's dermal layers, causing significant discomfort, foul-smelling discharge, disfigurement, contractures, and scarring, which severely diminish the quality of life. HS is associated with alterations in the skin microbiome, impacting immune regulation and the skin's defense against harmful bacteria. Despite its prevalence, the contribution of the HS microbiome to disease pathology and the limited response to treatment remains largely unknown. To date, multiple 16S rRNA sequencing studies on HS tissue have only achieved genus-level granularity, identifying an increase in Gram-negative anaerobes and a decrease in skin commensals. A deeper understanding of microbial dysbiosis in individuals with HS is essential for optimizing treatment strategies. This requires a two-pronged approach to assessing the HS microbiome, including the isolation of bacterial species, which are often underutilized in translational studies focused on skin disorders. Isolating individual microorganisms from HS tissue is crucial for elucidating the role of bacteria in HS pathogenesis. Here, we highlight reproducible methods to successfully isolate anaerobic pathogens from HS tunnel tissue, providing the initial and most critical step in understanding bacterial role in HS. This method paves the way for targeted research into microbial contributions to HS and for developing more effective, personalized treatment strategies that address the complex microbial burden of this chronic condition.}, }
@article {pmid39994842, year = {2025}, author = {Cryan, JF}, title = {Gut microbiota: our fellow travellers in health &amp; disease.}, journal = {The FEBS journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/febs.70045}, pmid = {39994842}, issn = {1742-4658}, abstract = {The last two decades have seen a major increase in our understanding of the role of the microbiome in health and disease. We now realise that these fellow travellers are really important regulators of various systems in the body across the lifespan. In this Special Issue, we bring together a collection of articles from leading authors who summarise the current state of the art of host-microbe interactions. While we celebrate the breakthroughs in microbiome science, we also acknowledge the challenges-variability in microbiota composition, the complexities of host-microbe interactions and the need for standardised methodologies. As research progresses, harnessing the power of the microbiome may pave the way for novel diagnostic and therapeutic strategies, reaffirming the notion that we are never alone-our microbial fellow travellers accompany us through life, for better or worse.}, }
@article {pmid39994836, year = {2025}, author = {Wan, J and Zhou, J and Wang, Z and Liu, D and Zhang, H and Xie, S and Wu, K}, title = {Recent advances in epidemiology, pathogenesis, diagnosis, and treatment of inflammatory bowel disease: Insights from the past two years.}, journal = {Chinese medical journal}, volume = {}, number = {}, pages = {}, pmid = {39994836}, issn = {2542-5641}, abstract = {Inflammatory bowel disease (IBD), including ulcerative colitis and Crohn's disease, is a chronic inflammation of the gastrointestinal tract with unknown etiology. The cause of IBD is widely considered multifactorial, with prevailing hypotheses suggesting that the microbiome and various environmental factors contribute to inappropriate activation of the mucosal immune system in genetically susceptible individuals. Although the incidence of IBD has stabilized in Western countries, it is rapidly increasing in newly industrialized countries, particularly China, making IBD a global disease. Significant changes in multiple biomarkers before IBD diagnosis during the preclinical phase provide opportunities for earlier diagnosis and intervention. Advances in technology have driven the development of telemonitoring tools, such as home-testing kits for fecal calprotectin, serum cytokines, and therapeutic drug concentrations, as well as wearable devices for testing sweat cytokines and heart rate variability. These tools enable real-time disease activity assessment and timely treatment strategy adjustments. A wide range of novel drugs for IBD, including interleukin-23 inhibitors (mirikizumab, risankizumab, and guselkumab) and small-molecule drugs (etrasimod and upadacitinib), have been introduced in the past few years. Despite these advancements, approximately one-third of patients remain primary non-responders to the initial treatment, and half eventually lose response over time. Precision medicine integrating multi-omics data, advanced combination therapy, and complementary approaches, including stem cell transplantation, psychological therapies, neuromodulation, and gut microbiome modulation therapy, may offer solutions to break through the therapeutic ceiling.}, }
@article {pmid39994714, year = {2025}, author = {Khatiwada, S and Ngunjiri, J and Boley, PA and Yadav, KK and Ghorbani, A and Abundo, M and Lee, CM and Poelstra, JW and Lee, CW and Gharaibeh, S and Rajashekara, G and Kenney, SP}, title = {Age-based host response to Turkey arthritis reovirus in commercial Turkeys in the presence of maternally derived antibodies.}, journal = {BMC veterinary research}, volume = {21}, number = {1}, pages = {96}, pmid = {39994714}, issn = {1746-6148}, support = {2021-67015-34465//USDA NIFA AFRI/ ; 2021-67015-34465//USDA NIFA AFRI/ ; }, mesh = {Animals ; *Turkeys ; *Reoviridae Infections/veterinary/immunology ; *Poultry Diseases/virology/microbiology/immunology ; Age Factors ; Virus Shedding ; Gastrointestinal Microbiome ; Immunity, Maternally-Acquired ; Female ; Reoviridae/immunology ; Antibodies, Viral/blood ; Cloaca/virology/microbiology ; Viral Tropism ; Orthoreovirus, Avian/immunology ; Tendons/microbiology/virology ; }, abstract = {BACKGROUND: Turkey arthritis reovirus (TARV) causes arthritic lameness in market-age turkeys. Since 2011, highly pathogenic TARV strains have caused significant economic losses in the turkey industry due to increased culling, reduced market weights, and decreased carcass quality, necessitating more effective control measures. Autogenous vaccine prevention strategies have been inefficacious partly due to a limited understanding of age-related susceptibility of turkeys to TARV. This study investigated age-related host and gut microbiota responses to TARV infection in commercial turkeys derived from vaccinated breeder hens. Poults with known maternally derived antibody titers were orally challenged with TARV O'Neil strain at 1-, 3-, and 7- weeks of age (WOA) and monitored for cloacal virus shedding, gastrocnemius tendon viral tropism, tendon inflammation, weight gain, and changes in gut microbiota.<br><br>RESULTS: A transient TARV-induced weight gain suppression was evident in poults infected at 1- and 3- WOA during the first 3 weeks post-infection. Age-dependent variations in cloacal viral shedding, virus isolation from tendons, and tendon inflammation severity were also observed. There was significant dissimilarity in ileal and cecal bacterial communities between mock and infected groups, but the effect of age of infection was unclear.<br><br>CONCLUSIONS: Age dependent host response was observed to TARV based on cloacal virus shedding, weight gain suppression and viral tendon tropism. Our study also indicates that maternally derived antibodies appeared insufficient to prevent virus translocation to the tendons and subsequent pathological changes. This study lays the groundwork for future investigations of better vaccines/vaccination strategies and alternative preventive measures.<br><br>IMPORTANCE: Turkey arthritis reovirus (TARV) causes lameness due to arthritis and tenosynovitis, commonly in market-age turkeys, resulting in significant economic losses. As a control strategy, the turkey industry used autogenous vaccines, prepared from field TARV isolates in breeder hens, to protect the poults in the early stage of life through maternally derived antibodies (MDAs). This study establishes the level of protection provided by MDAs in young poults with age-based responses to TARV O'Neil reovirus strain. Additionally, this study reveals the dynamics of gut dysbiosis in infected poults at different timepoints, paving the way to ground-breaking investigations into gut microbiome modulation interventions that could potentially improve vaccine efficacy and reduce virus transmission and disease severity.}, }
@article {pmid39994558, year = {2025}, author = {Hu, X and Claerbout, J and Vandecasteele, B and Craeye, S and Geelen, D}, title = {The bacterial and fungal strawberry root-associated microbiome in reused peat-based substrate.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {245}, pmid = {39994558}, issn = {1471-2229}, mesh = {*Fragaria/microbiology ; *Plant Roots/microbiology ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; *Fungi/genetics/physiology/isolation &amp; purification ; *Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; }, abstract = {BACKGROUND: Reuse of plant growing substrate can contribute to lowering the carbon footprint of horticulture production systems. Here, we assessed the impact of substrate reusing on the root-associated microbiome of strawberries. The cultivars Elsanta and Malling Centenary were grown in a substrate-based hydroponic system using either fresh peat-based substrate or substrate reused up to three times, with comparisons made between not steamed and steam-treated substrate. The root-associated microbiome was analyzed using 16S rRNA gene and ITS1 DNA sequencing to determine bacterial and fungal communities.<br><br>RESULTS: Substrate reusing without steaming increased the bacterial and fungal community diversity whereas steaming reduced the bacterial diversity and increased fungal diversity in the root-associated microbiome. The root-associated bacterial communities recruited by the two cultivars were diverse, even more so than the diversity recorded for the different times of reused substrate.<br><br>CONCLUSION: These observations demonstrate the ability of strawberry to establish a genotype-specific root-associated microbiome when plants are cultured on reused substrate. The bacterial microbiome showed a higher consistency over the times substrate was reused, while the fungal community composition showed stronger adaptation to the substrate reusing. Pathogenic fungi accumulated over the reusing times, underscoring the necessity of substrate sanitation through steaming to minimize the risk of pathogen infections.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid39994494, year = {2025}, author = {Tingga, RCT and Mohd-Ridwan, AR and Denel, A and Md-Zain, BM}, title = {Profiling the Gut Microbiome of Hylobatidae and Cercopithecinae: Insights Into the Health of Primates in Captivity.}, journal = {Journal of medical primatology}, volume = {54}, number = {2}, pages = {e70008}, doi = {10.1111/jmp.70008}, pmid = {39994494}, issn = {1600-0684}, support = {ST2022027//The National Conservation Trust Fund for Natural Resources/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *RNA, Ribosomal, 16S/genetics ; Macaca fascicularis/microbiology ; Animals, Zoo/microbiology ; Macaca nemestrina/microbiology ; Bacteria/classification/isolation &amp; purification/genetics ; High-Throughput Nucleotide Sequencing ; RNA, Bacterial/analysis/genetics ; Male ; Endangered Species ; Female ; }, abstract = {BACKGROUND: A healthy gut microbiome is essential for digestion in primates, for developing the gut immune system, and for defense against pathogen invasion. Next-generation sequencing allows for determining the microbiome composition and enables the continuous monitoring of primate health.<br><br>METHODS: To comprehensively analyze the gut microbiome diversity of three endangered primate species at Matang Wildlife Centre-Hylobates abbotti, Macaca fascicularis, and Macaca nemestrina, using high-throughput sequencing of the 16S rRNA gene.<br><br>RESULTS: A total of 18 phyla, 84 families, 188 genera, and 46 species were successfully classified. H. abbotti exhibited the highest microbial diversity with a distinct microbiome profile from the Macaca species. The presence of Treponema (nonpallidum), Bifidobacterium, and Faecalibacterium prausnitzii is critical for gut health, promoting digestion and maintaining the microbial balance.<br><br>CONCLUSION: This study highlights the importance of monitoring microbial diversity in captive primates to better understand their health and facilitate the early detection of potential pathogens. This also offers insights into microbiome-based strategies for improving overall animal welfare.}, }
@article {pmid39994329, year = {2025}, author = {Abdelqader, EM and Mahmoud, WS and Gebreel, HM and Kamel, MM and Abu-Elghait, M}, title = {Correlation between gut microbiota dysbiosis, metabolic syndrome and breast cancer.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {6652}, pmid = {39994329}, issn = {2045-2322}, mesh = {Humans ; Female ; *Metabolic Syndrome/microbiology ; *Gastrointestinal Microbiome ; *Breast Neoplasms/microbiology/epidemiology ; *Dysbiosis/microbiology ; Middle Aged ; Adult ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Bifidobacterium/isolation &amp; purification/genetics ; Lactobacillus/isolation &amp; purification/genetics ; Risk Factors ; }, abstract = {Breast cancer is a widespread cancer with a high death rate globally. The incidence of breast cancer is expected to increase, particularly in low and middle-income countries due to environmental factors and lifestyle changes. Several risk factors, such as age, family history, hormonal and reproductive factors, have been identified to influence breast cancer development. Metabolic syndrome, is a metabolic disorder that has also been linked to breast cancer risk. The gut microbiome has been suggested as one of the environmental factors leading to breast cancer. The human microbiome is mainly colonized in the intestine by various bacterial species, including Lactobacillus, Bifidobacterium, and Streptococcus and protect the host against pathogenic microorganisms and regulate the immune system. This study included 50 female breast cancer patients and 50 healthy controls with matched ages. Stool fresh samples were taken from test and control groups and stored at - 20 °C until further investigations. DNA of the bacteria in stool samples was extracted using reverse transcription-quantitative polymerase chain reaction to check for the bacterial 16s rRNA gene. The exclusion criteria included other malignancies, recent intestinal surgery, infectious diarrhea, prolonged use of antibiotics, substance addiction, and pregnancy or lactation. Our findings exhibited that breast cancer patients had a higher incidence of metabolic syndrome (60%) compared to cancer-free controls (40%). Furthermore, breast cancer patients had significantly lower Bifidobacterium and Lactobacillus counts than the controls. No significant difference was found in Streptococcus counts between groups. These findings support the relationship between breast cancer and metabolic syndrome and suggest the potential involvement of Lactobacillus and Bifidobacterium in breast cancer pathophysiology. Our study supports the relation between breast cancer and disorder of metabolic syndrome and suggests the potential involvement of Lactobacillus and Bifidobacterium in breast cancer pathophysiology. Further research is necessary to investigate the complex interactions between genes, the environment, and the gut microbiome in breast cancer development. Understanding these interactions could lead to the progress of novel strategies for breast cancer prevention and treatment.}, }
@article {pmid39994074, year = {2025}, author = {Grobbelaar, A and Osthoff, G and Deacon, F and Cason, ED}, title = {The Faecal Microbiome Analysed from Healthy, Free-Roaming Giraffes (Giraffa camelopardalis).}, journal = {Current microbiology}, volume = {82}, number = {4}, pages = {151}, pmid = {39994074}, issn = {1432-0991}, support = {RA201126576714//National Research Foundation/ ; }, mesh = {Animals ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Giraffes/microbiology ; South Africa ; Male ; Female ; Gastrointestinal Microbiome ; Microbiota ; }, abstract = {Similar to other herbivores, healthy giraffes (Giraffa camelopardalis) rely on a variety of symbiotic microorganisms in their digestive systems to break down cellulose and hemicellulose. In this study, we investigate the impact that external stimuli might have on the faecal prokaryote composition of healthy, free-roaming giraffes. Faecal samples were collected from six male and seven female giraffe individuals, over a 2-year period, during the wet and dry seasons, from six locations within the Free State Province, South Africa. Giraffe populations were exposed to one of two feeding practices which included provision of supplemental feed or only naturally available vegetation. Seventeen (17) different prokaryotic phyla, consisting of 8370 amplicon sequence variants (ASVs), were identified from the 13 healthy, adult, free-roaming giraffes included in the study. Overall, the bacterial phyla with the largest relative abundance included Fusobacteria (22%), followed by Lentisphaera (17%) and Cyanobacteria (16%), which included 21 dominant prokaryotic ASVs. The relative abundance of Ruminococcaceae UCG 014 and Treponema 2 were found to be significantly (P < 0.05) higher and Escherichia / Shigella, Romboutsia and Ruminococcus 1 significantly lower for giraffes receiving supplemental feed compared to natural available vegetation. This is the first study to investigate the composition of the faecal prokaryotic communities of healthy, free-roaming giraffes. The analysis of faecal prokaryotes contributes to the development of non-invasive methods for assessing the nutritional status and identifying health issues in giraffe populations. Ultimately, such advances are beneficial towards the larger-scale conservation, determining nutritional needs and management of other sensitive wildlife species, as well.}, }
@article {pmid39993645, year = {2025}, author = {Muhammad, A and Khan, MHU and Kong, X and Zheng, S and Bai, N and Li, L and Zhang, N and Muhammad, S and Li, Z and Zhang, X and Miao, C and Zhang, Z}, title = {Rhizospheric crosstalk: A mechanistic overview of how plant secondary metabolites alleviate abiotic stresses.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {354}, number = {}, pages = {112431}, doi = {10.1016/j.plantsci.2025.112431}, pmid = {39993645}, issn = {1873-2259}, abstract = {Plants often encounter incompatible growing conditions, such as drought, extreme temperatures, salinity, and heavy metals, which negatively impact their growth and development, resulting in reduced yield and, in severe cases, plant death. These stresses trigger the synthesis of plant secondary metabolites (PSMs), which help plants develop strategies to deter enemies, combat pathogens, outcompete competitors, and overcome environmental restraints. PSMs are released into the rhizosphere and play crucial roles in plant defense and communication. The multifunctionality of PSMs offers new insights into the plant intricate adaptive responses, which can refine our understanding of plant tolerance mechanisms in challenging environments. Thus, elucidating the chemical composition and functions of plant-derived specialized metabolites in the rhizosphere is the key to understanding interactions in this belowground environment. In this review, we aim to elucidate how PSMs exudation shapes the activities and abundance of the rhizosphere microbiome. We also highlight key environmental factors that regulate the structure and diversity of microbial communities. Finally, we discuss various preventive roles of PSMs, exploring how plants recruit microbes preemptively to mitigate diverse abiotic stresses. Additionally, we emphasize the significant contribution of phenolic compounds to the antioxidant defense response in plants, regulated through the shikimate pathway and is considered as a distinctive plant stress resilience component as compared to other PSMs under abiotic stress. Collectively, this study reveals the significance of understanding the multifaceted crosstalk between PSMs and the microbiome, which will facilitate the potential for developing methods to manipulate PSMs-microbiome interaction with predictive outcomes for sustainable crop production.}, }
@article {pmid39993618, year = {2025}, author = {Li, X and Tang, Q and Hou, M and Pang, Y and Li, D and Chen, Y and Fang, R and Deng, Y and Zhang, J and Zhao, C and Li, J and Chen, Y and Zhao, Y and Guo, J and Qian, K}, title = {Early life imidacloprid and copper exposure affects the gut microbiome, metabolism, and learning ability of honey bees (Apis mellifera).}, journal = {Environmental research}, volume = {}, number = {}, pages = {121134}, doi = {10.1016/j.envres.2025.121134}, pmid = {39993618}, issn = {1096-0953}, abstract = {The pesticide imidacloprid and the heavy metal copper provide some degree of protection to plants, while at the same time causing varying degrees of damage to bees. However, few studies have investigated the negative effects of imidacloprid and copper exposure on newly emerged bees (young bees), especially when both are present in a mix. In this study, young bees were exposed to sterile sucrose solutions containing imidacloprid (10 μg/L, 100 μg/L), copper (10 mg/L, 50 mg/L), or a mix of both (10 μg/L + 10 mg/L) for 5 days to assess their gut system and behavior, with survival and dietary consumption recorded over 21 days. We found that imidacloprid and copper reduced honeybee survival, dietary intake, and learning ability, decreased gut microbiota diversity, and caused metabolic disruptions. Notably, the mix of imidacloprid and copper had a synergistic negative effect. Correlation analyses revealed that the honeybee gut microbiota influences bee immunity and behavior by regulating metabolic pathways related to ascorbate, tryptophan, and carbohydrates. Our results demonstrate that imidacloprid and copper, either alone or in a mix, alter young bee health through a complex mechanism of toxicity. These findings highlight imidacloprid and copper's negative effects on young honeybees, offering insights for future pesticide and heavy metal impact research.}, }
@article {pmid39993425, year = {2025}, author = {Tingting, L and Zhang, P and Yang, L and Li, R and Wang, R}, title = {The effects of topical antimicrobial-corticosteroid combination therapy in comparison to topical steroids alone on the skin microbiome of patients with atopic dermatitis.}, journal = {The Journal of dermatological treatment}, volume = {36}, number = {1}, pages = {2470379}, doi = {10.1080/09546634.2025.2470379}, pmid = {39993425}, issn = {1471-1753}, mesh = {Humans ; *Dermatitis, Atopic/drug therapy/microbiology/pathology ; Male ; Female ; Adult ; *Microbiota/drug effects ; *Drug Therapy, Combination ; *Skin/microbiology/drug effects/pathology ; Young Adult ; *Administration, Cutaneous ; Treatment Outcome ; Adolescent ; Middle Aged ; Administration, Topical ; Severity of Illness Index ; Adrenal Cortex Hormones/administration &amp; dosage/pharmacology ; }, abstract = {OBJECTIVE: This study aims to analyze the different therapeutic responses between topical antimicrobial-corticosteroid combination and topical corticosteroids alone on improving the skin microbiome and skin barrier of patients with atopic dermatitis (AD).<br><br>METHODS: Forty patients with mild-to-moderate AD were randomly assigned to receive two kinds of treatment. Skin swabs were collected from the lesional sites and nearby nonlesional sites at baseline, after topical medication treatment and 2&#x2009;weeks post-treatment, and were analyzed by DNA sequencing of the fungal internal transcribed spacer (ITS)1-5 rDNA gene and the V3V4 region of the bacterial 16S rRNA gene.<br><br>RESULTS: According to our research analysis, both topical steroids alone and combination treatment of steroids and antimicrobials effectively improved the severity of AD and repaired skin barrier. AD lesions were characterized by a decreased sebum level, lower abundance of Cutibacterium and a higher abundance of Staphylococcus. A combined topical treatment with an antimicrobial and steroid showed better responses in increasing skin sebum level and restoring the skin bacterial microbiome, whereas topical steroid alone did not improve skin dysbiosis.<br><br>CONCLUSION: A combined therapy with antimicrobial and steroid helps to recover the skin microbiome. Further studies are necessary to explore the therapeutic effects of treatments aiming at balancing the microbiome.}, }
@article {pmid39993268, year = {2025}, author = {Mak, P and Yin, X and Clairmont, L and Bean-Hodgins, L and Kiarie, E and Tang, J and Lepp, D and Diarra, M}, title = {Cecal Microbiome in Broiler Chicken Related to Antimicrobial Feeding and Bird's Sex.}, journal = {Canadian journal of microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1139/cjm-2024-0190}, pmid = {39993268}, issn = {1480-3275}, abstract = {This study investigated the cecal microbiome of broilers raised under specific antimicrobial feeding programs (AFPs). A total of 2,304-day-old Ross-708 male (M, n=1,152) and female (F, n=1,152) chicks were distributed into 48 floor pens which were allocated to one of three AFPs: Conventional (CON), raised without medically important antibiotics (RWMIA), and raised without antibiotics (RWA). At 28 (D28) and 41 (D41) days of age, cecal contents were collected for culture dependent and independent analyses. At both 28 and 41 days, Enterococcus was more abundant in RWA-raised broilers than other groups with the most abundance of this bacterium being found in female birds (P < 0.05). At D41, the most abundant Eimeria tenella counts was observed in RWA-raised broiler ceca (P < 0.05). Sex effects were observed on the abundances of four of the 248 identified antimicrobial resistance genes (ARGs) while abundances of 10 were modulated by AFPs (P <0.05). Ceca of females birds showed more tssB than males, and ceca of RWMIA-raised birds contained the highest abundance of chuY genes regardless of sex. This study showed that in a specific feeding program, cecal resistome can be affected by chicken's sex contributing to understand the AMR related to the AMU.}, }
@article {pmid39993127, year = {2025}, author = {Atabieke, F and Aierken, A and Aierken, M and Rehaman, M and Zhang, QQ and Li, J and Xia, Y and Aizezi, Y and Dilixiati, D and Gao, HL and Zhang, ZQ}, title = {Investigating casual association among gut microbiome and esophageal cancer: A Mendelian randomization study.}, journal = {Medicine}, volume = {104}, number = {8}, pages = {e41563}, doi = {10.1097/MD.0000000000041563}, pmid = {39993127}, issn = {1536-5964}, support = {2022TSYCTD0018//The Technology Innovation Team (Tianshan Innovation Team) Project/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Mendelian Randomization Analysis ; *Esophageal Neoplasms/microbiology/genetics/epidemiology ; *Polymorphism, Single Nucleotide ; *Genome-Wide Association Study ; }, abstract = {The gut microbiota has been strongly linked to gastrointestinal cancer, but the relationship between gut microbiota and esophageal cancer (EC) is still not fully understood. We conducted a 2-sample Mendelian randomization (MR) study to unveil the potential impact of intestinal microorganisms on EC in East Asian populations. In order to delve deeper into the potential causal relationship between gut microbiota and EC, we conducted a 2-sample MR analysis, utilizing 211 single nucleotide polymorphisms associated with gut microbiota, sourced from the largest genome-wide association study on gut microbiota, for our analysis. To estimate the causal relationship, we employed the inverse variance weighting method. In addition, to assess the potential influence of pleiotropy, we used MR-Egger regression in our analysis. Among the 10 specific bacterial taxa identified using the inverse variance weighting as being associated with the risk of EC, we observed a positive association between family Bacteroidaceae (P = .04), genus Bacteroides (P = .04), genus Bilophila (P = .02), genus Candidatus Soleaferrea (P = .02) and the EC, while family Victivallaceae (P = .03), genus Eubacterium coprostanoligenes (P = .01), genus Catenibacterium (P = .01), genus Coprococcus2 (P = .01), unknowngenus.id.959 (P = .02) and unknowngenus.id.1868 (P = .01) may be associated with a reduced risk of EC. Our MR analysis indicate a probable association between gut microbiota and the development and advancement of EC. These findings offer novel perspectives on the possible application of targeted gut bacteria for the prevention and management of EC.}, }
@article {pmid39993092, year = {2025}, author = {Lei, W and Liu, Z and Lai, HP and Fu, R}, title = {Gut microbiota and risk of iron deficiency anemia: A two-sample Mendelian randomization study.}, journal = {Medicine}, volume = {104}, number = {8}, pages = {e41617}, doi = {10.1097/MD.0000000000041617}, pmid = {39993092}, issn = {1536-5964}, mesh = {Humans ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics ; *Anemia, Iron-Deficiency/microbiology/genetics/epidemiology ; *Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; Risk Factors ; Female ; Male ; Middle Aged ; }, abstract = {Previous studies have suggested a link between gut microbiota and iron-deficiency anemia (IDA). However, interpreting these findings is difficult due to various factors that influence microbiome composition and the limitations of observational studies, such as confounding variables and reverse causation. This study aims to explore the causal relationship between gut microbiota and IDA using Mendelian randomization (MR) to overcome these limitations. We conducted a 2-sample MR analysis using data from genome-wide association studies from the MiBioGen Consortium and the UK Biobank. The gut microbiome data included 211 genus-level microbes linked to single-nucleotide polymorphisms from 18,340 participants in the MiBioGen Consortium. The outcome data for IDA were obtained from 484,598 participants in the UK Biobank, with 2941 cases and 481,657 controls. We assessed causal relationships using various MR techniques, primarily inverse variance weighting, and performed sensitivity analyses to confirm the robustness of our results. Nine genus-level gut microbes were significantly associated with IDA (P < .05). Protective factors included Clostridia, Actinomycetaceae, Pasteurellaceae, Oscillospira, Prevotella, and Roseburia, while risk factors included Ruminococcus gnavus group, Hungatella, and Parasutterella. Sensitivity analyses showed the reliability of these findings without significant variability. This study provides evidence for a causal relationship between specific gut bacteria and IDA risk, identifying potential targets for therapies aimed at improving outcomes for those with IDA. Further research is needed to clarify the bacteria involved.}, }
@article {pmid39992946, year = {2025}, author = {Liu, P and Chen, G and Zhao, S and Kong, L and Liao, X and Cheng, M}, title = {The alteration of uterine microbiota participated in the activation of the decidual inflammatory response in early spontaneous abortion.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0317595}, doi = {10.1371/journal.pone.0317595}, pmid = {39992946}, issn = {1932-6203}, mesh = {Female ; Humans ; Adult ; *Abortion, Spontaneous/microbiology/immunology ; *Microbiota ; Pregnancy ; *Decidua/immunology/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Uterus/microbiology/pathology/immunology ; Inflammation/microbiology ; Neutrophils/immunology/metabolism ; Interleukin-1beta/metabolism/genetics ; }, abstract = {BACKGROUND: Early spontaneous abortion (ESA) is one of the most common clinically recognized pregnancy complications. While multiple factors such as embryo abnormalities and maternal conditions may contribute to ESA, early identification and screening of maternal risk factors are increasingly important to explore the potential etiologies and improve prevention and treatment strategies for ESA. This study investigates the changes in uterine microbiota and the decidual immune response in ESA patients without embryo abnormalities.<br><br>METHODS: ESA patients without embryo abnormality and artificial abortion (AA) controls were enrolled for clinical characteristics analysis. The decidual endometrium was subsequently collected for histological evaluation and inflammatory indicator detection. Moreover, 16S rRNA gene sequencing of uterine secretions was performed to investigate the differences in uterine microorganisms between the ESA and AA groups.<br><br>RESULTS: Clinical analysis showed higher inflammatory response with elevated neutrophil counts in ESA patients. The increase in leukocytes, including neutrophils, was positively correlated with ESA. ESA patients presented significantly increased IL-1&#x3b2; expression in decidual stromal cells. 16S rRNA gene sequencing revealed greater diversity in the uterine microbiota of the ESA group, which presented decreased Lactobacillus abundance and increased abundance of other bacteria at the genus and species levels.<br><br>CONCLUSIONS: Changes in the uterine microbiome are likely related to inflammatory response and lead to early pregnancy loss.}, }
@article {pmid39992705, year = {2025}, author = {Roesel, R and Strati, F and Basso, C and Epistolio, S and Spina, P and Djordjevic, J and Sorrenti, E and Villa, M and Cianfarani, A and Mongelli, F and Galafassi, J and Popeskou, SG and Facciotti, F and Caprera, C and Melle, F and Majno-Hurst, PE and Franzetti-Pellanda, A and De Dosso, S and Bonfiglio, F and Frattini, M and Christoforidis, D and Iezzi, G}, title = {Combined tumor-associated microbiome and immune gene expression profiling predict response to neoadjuvant chemo-radiotherapy in locally advanced rectal cancer.}, journal = {Oncoimmunology}, volume = {14}, number = {1}, pages = {2465015}, doi = {10.1080/2162402X.2025.2465015}, pmid = {39992705}, issn = {2162-402X}, mesh = {Humans ; *Rectal Neoplasms/therapy/immunology/genetics ; *Neoadjuvant Therapy/methods ; Male ; Female ; Middle Aged ; *Gene Expression Profiling ; Aged ; Adult ; Gastrointestinal Microbiome ; Microbiota ; Treatment Outcome ; }, abstract = {Locally advanced rectal cancer (LARC) is treated with neoadjuvant chemo-radiotherapy (nCRT) followed by surgery. A minority of patients show complete response (CR) to nCRT and may avoid surgery and its functional consequences. Instead, most patients show non-complete response (non-CR) and may benefit from additional treatments to increase CR rates. Reliable predictive markers are lacking. Aim of this study was to identify novel signatures predicting nCRT responsiveness. We performed a combined analysis of tumor-associated microbiome and immune gene expression profiling of diagnostic biopsies from 70 patients undergoing nCRT followed by rectal resection, including 16 with CR and 54 with non-CR. Findings were validated by an independent cohort of 49 patients, including 7 with CR and 42 with non-CR. Intratumoral microbiota significantly differed between CR and non-CR groups at genus and species level. Colonization by bacterial species of Ruminococcus genera was consistently associated with CR, whereas abundance of Fusobacterium, Porhpyromonas, and Oscillibacter species predicted non-CR. Immune gene profiling revealed a panel of 59 differentially expressed genes and significant upregulation of IFN-gamma and -alpha response in patients with CR. Integrated microbiome and immune gene profiling analysis unraveled clustering of microbial taxa with each other and with immune cell-related genes and allowed the identification of a combined signature correctly identifying non-CRS in both cohorts. Thus, combined intratumoral microbiome-immune profiling improves the prediction of response to nCRT. Correct identification of unresponsive patients and of bacteria promoting responsiveness might lead to innovative therapeutic approaches based on gut microbiota pre-conditioning to increase nCRT effectiveness in LARC.}, }
@article {pmid39992604, year = {2025}, author = {Zuo, S and Zhang, Q and Yang, S and Wang, H}, title = {Polycaprolactam microplastics reduce allelopathic potential of Iris pseudacorus via toxic effects on stimulatory bacteria.}, journal = {Ecotoxicology (London, England)}, volume = {}, number = {}, pages = {}, pmid = {39992604}, issn = {1573-3017}, abstract = {Many studies have investigated the toxic effects of microplastics (MPs) ingested by aquatic animals, but the effects of MPs that adhere to the roots of macrophytes require further exploration. Thus, the present study investigated the dose-dependent toxic effects of adding 10-500 mg/kg of polycaprolactam microplastics (PCM) on allelopathic cyanobacterial inhibition by a wetland macrophyte due to the influence on rhizosphere bacteria in a pot trial. First, comparisons of sterilized and unsterilized Iris pseudacorus rhizosphere soil showed that the unsterilized soil could enhance the root activity and allelopathic inhibition of Microcystis aeruginosa cyanobacteria. Furthermore, adding 50-100 mg/kg PCM to the unsterilized soil significantly altered the abundances of many types of bacteria, and decreased the root activity and bacterial biodiversity in the rhizosphere. Importantly, PCM changed the secondary metabolites profile in the roots, as well as decreasing production of the allelochemical palmitic acid and the allelopathic potential of I. pseudacorus. Moreover, a dominant strain of functional bacterium AAP51 was identified as an allelopathic promoter, isolated, and successfully inoculated into the sterilized soil. The decomposition of PCM produced the toxic monomer caprolactam in the rhizosphere soil at an average rate of 0.067 mg/kg·d under treatment with 50 mg/kg PCM. Toxicological testing showed that 5 mg/kg caprolactam inhibited the activities of the dominant bacteria and expression of the allelopathic gene FAD2 to weaken the allelopathic effect of I. pseudacorus. Thus, the findings obtained in this study indicate that PCM inhibited the allelopathic potential of the macrophyte due to the release of toxic caprolactam damaging bacteria in the rhizosphere. Consequently, it is necessary to remove MP pollutants from aquatic ecosystems in order to maintain the strong allelopathic potential of macrophytes and efficiently control cyanobacterial blooms.}, }
@article {pmid39992189, year = {2025}, author = {Spatola, G and Giusti, A and Gasperetti, L and Nuvoloni, R and Dalmasso, A and Chiesa, F and Armani, A}, title = {16S rRNA metabarcoding applied to the microbiome of insect products (novel food): a comparative analysis of three reference databases.}, journal = {Italian journal of food safety}, volume = {14}, number = {1}, pages = {}, doi = {10.4081/ijfs.2025.13171}, pmid = {39992189}, issn = {2239-7132}, abstract = {The 16S rRNA metabarcoding, based on Next-Generation Sequencing (NGS), is used to assess microbial biodiversity in various matrices, including food. The process involves a "dry-lab" phase where NGS data are processed through bioinformatic pipelines, which finally rely on taxonomic unit assignment against reference databases to assign them at order, genus, and species levels. Today, several public genomic reference databases are available for the taxonomic assignment of the 16S rRNA sequences. In this study, 42 insect-based food products were chosen as food models to find out how reference database choice could affect the microbiome results in food matrices. At the same time, this study aims to evaluate the most suitable reference database to assess the microbial composition of these still poorly investigated products. The V3-V4 region was sequenced by Illumina technology, and the R package "DADA2" was used for the bioinformatic analysis. After a bibliographic search, three public databases (SILVA, RDP, NCBI RefSeq) were compared based on amplicon sequence variant (ASV) assignment percentages at different taxonomic levels and diversity indices. SILVA assigned a significantly higher percentage of ASVs to the family and genus levels compared to RefSeq and RDP. However, no significant differences were noted in microbial composition between the databases according to α and β diversity results. A total of 121 genera were identified, with 56.2% detected by all three databases, though some taxa were identified only by one or two. The study highlights the importance of using updated reference databases for accurate microbiome characterization, contributing to the optimization of metabarcoding data analysis in food microbiota studies, including novel foods.}, }
@article {pmid39992155, year = {2025}, author = {Márquez Rosales, S and Bouchard, PI and Olmstead, EM and Parthasarathy, R}, title = {UV-irradiated rotifers for the maintenance of gnotobiotic zebrafish larvae.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0069824}, doi = {10.1128/msphere.00698-24}, pmid = {39992155}, issn = {2379-5042}, abstract = {Host-associated microbial communities profoundly impact the health of humans and other animals. Zebrafish have proven to be a useful model for uncovering mechanisms of host-microbe interactions, but the difficulty of maintaining germ-free or gnotobiotic zebrafish beyond 1 week post-fertilization has limited their utility. To address this, we have developed a simple protocol using UV irradiation of rotifers, a common and nutrient-rich prey species for larval zebrafish, to reduce the bacterial load associated with the rotifers by several orders of magnitude while maintaining their motility and viability. We find that though feeding with UV-treated rotifers does not preserve the sterility of germ-free fish, it enables the maintenance of pre-existing bacterial communities. Normal feeding, in striking contrast, leads to the near-total depletion of these prior populations. We measure the abundance of single- and three-species consortia of zebrafish-commensal bacteria inoculated into initially germ-free larvae in a series of experiments extending to 8 days of feeding, or 13 days post-fertilization. We find, in fish-fed UV-treated rotifers, the persistence of bacterial populations on timescales of days, together with strong species-specific variation. In addition, re-inoculation of differently labeled strains of the same zebrafish-commensal species alongside feeding leads to colonization by the new bacteria without displacement of earlier microbes. Our method will facilitate the use of gnotobiotic zebrafish for investigations of phenomena that emerge later in animal development and for studies that probe microbiome composition fluctuations and stability over extended timescales.IMPORTANCEAll animals, including humans, are host to vast microbial communities that contribute to health and disease through mechanisms that remain largely mysterious. These microbiomes are challenging to study, spurring the use of various model organisms, including zebrafish. Zebrafish, however, are difficult to raise beyond 1 week post-fertilization under gnotobiotic conditions, in other words, germ free or with known microbial constituents, a consequence of normally feeding on live prey that brings their own, generally unknown, microbes. Therefore, we developed a simple protocol in which UV irradiation of rotifers, a widely used small-animal food for larval zebrafish, facilitates the maintenance of gnotobiotic larvae. We show that pre-existing bacterial communities in larvae are minimally affected by feeding on UV-treated rotifers, in strong contrast to feeding on untreated rotifers. We demonstrate that this feeding method allows investigations of zebrafish-associated bacterial community stability over several days, allowing investigation of previously intractable questions about microbiome stability.}, }
@article {pmid39991711, year = {2025}, author = {Lin, T}, title = {Editorial: New techniques in microbiome research - volume II: Host-microbiome interactions using 'meta-omics' techniques.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1541881}, pmid = {39991711}, issn = {2235-2988}, }
@article {pmid39991683, year = {2025}, author = {Darnindro, N and Abdullah, M and Sukartini, N and Rumende, CM and Pitarini, A and Nursyirwan, SA and Fauzi, A and Makmun, D and Nelwan, EJ and Shatri, H and Rinaldi, I and Tanadi, C}, title = {Differences in diversity and composition of mucosa-associated colonic microbiota in colorectal cancer and non-colorectal cancer in Indonesia.}, journal = {World journal of gastroenterology}, volume = {31}, number = {7}, pages = {100051}, pmid = {39991683}, issn = {2219-2840}, mesh = {Humans ; Indonesia/epidemiology ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Case-Control Studies ; *Colonoscopy ; *Colon/microbiology ; *Intestinal Mucosa/microbiology ; *RNA, Ribosomal, 16S/genetics ; Aged ; Adult ; Metagenomics/methods ; Bacteria/isolation &amp; purification/genetics/classification ; }, abstract = {BACKGROUND: Colorectal cancer is the third most common malignancy and the fourth leading cause of cancer-related deaths worldwide. Several studies have shown an association between gut microbiota and colorectal cancer. Gut microbiota is unique and can be influenced by geographic factors and habits. This study aimed to determine the diversity and composition of colonic mucosal microbiota in patients with and without colorectal cancer.<br><br>AIM: To determine the diversity and composition of colonic mucosal microbiota in patients with and without colorectal cancer in Indonesia.<br><br>METHODS: This case-control study included 59 subjects (35 colorectal cancer patients and 24 non-colorectal cancer patients indicated for colonoscopy at Dr. Cipto Mangunkusumo Gastrointestinal Endoscopy Center and Fatmawati Hospital. Microbiota examination was performed using 16S rRNA sequencing. Bioinformatics analysis was performed using the wf-metagenomics pipeline from EPI2Me-Labs (Oxford Nanopore Technologies platform).<br><br>RESULTS: Patients with colorectal cancer had a higher median index value on the Shannon index (3.28 vs 2.82, P > 0.05) and a lower value on the Simpson index (0.050 vs 0.060, P > 0.05). Significant differences in beta diversity were observed at the genus (P = 0.002) and species levels (P = 0.001). Firmicutes, Proteobacteria, Bacteroidetes, and Fusobacteria were the dominant phyla. The genera Bacteroides, Campylobacter, Peptostreptococcus, and Parvimonas were found more frequently in colorectal cancer, while Faecalibacterium, Haemophilus, and Phocaeicola were more frequently found in non-colorectal cancer. The relative abundance of Fusobacterium nucleatum, Bacteroides fragilis, Enterococcus faecalis, Campylobacter hominis, and Enterococcus faecalis species was significantly elevated in patients with colorectal cancer. Meanwhile, Faecalibacterium prausnitzii, Faecalibacterium duncaniae, and Prevotella copri were more commonly found in non-colorectal cancer.<br><br>CONCLUSION: Patients with colorectal cancer exhibit distinct differences in the composition and diversity of their colonic mucosal microbiota compared to those with non-colorectal cancer. This study was reviewed and approved by the Ethics Committee of Faculty of Medicine, Universitas Indonesia (No. KET-1517/UN2.F1/ETIK/PPM.00.02/2023).}, }
@article {pmid39991550, year = {2025}, author = {Jensen, N and Weiland-Bräuer, N and Chibani, CM and Schmitz, RA}, title = {Microbiota-derived β carotene is required for strobilation of Aurelia aurita by impacting host retinoic acid signaling.}, journal = {iScience}, volume = {28}, number = {2}, pages = {111729}, pmid = {39991550}, issn = {2589-0042}, abstract = {The strobilation process, an asexual reproduction mechanism in Aurelia aurita, transitions from the sessile polyp to the pelagic medusa stage. This study explored the essential role of the microbiome in strobilation, particularly through bacterial beta carotene's impact on the host's retinoic acid signaling pathway. Experiments demonstrated that native polyps undergo normal strobilation while sterile polyps exhibit morphological defects. Supplementing sterile polyps with provitamin A beta carotene or the vitamin A metabolite 9-cis retinoic acid (RA) remedied these defects, underscoring their crucial role in strobilation. Transcriptional analysis revealed that beta carotene and 9-cis RA restored expression of strobilation genes in sterile polyps to native levels. Inhibition of key enzymes in the RA pathway disrupted strobilation, further confirming its importance. The expression of bacterial β-carotenoid synthesis genes in the native microbiome, contrasted with tremendously reduced expression in antibiotic-treated polyps, emphasizes the microbiome's pivotal role in beta carotene provision, facilitating A. aurita's strobilation through RA signaling.}, }
@article {pmid39991271, year = {2025}, author = {Morales, SE and Tobias-Hünefeldt, SP and Armstrong, E and Pearman, WS and Bogdanov, K}, title = {Marine phytoplankton impose strong selective pressures on in vitro microbiome assembly, but drift is the dominant process.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf001}, pmid = {39991271}, issn = {2730-6151}, abstract = {Phytoplankton are known ecosystem engineers that modulate ocean community assembly processes, but the universality and extent of their microbiome control remains unclear. We used in vitro incubations and 16S ribosomal RNA gene amplicon sequencing to test the influence of Southern and South Pacific oceans dominant phytoplankton on assembly processes and community successions in response to phytoplankton blooms. Phytoplankton grown with reduced-diversity cultures or supplemented with exogenously added microbiomes showed reduced diversity, suggesting environmental filtering. Community profiles were distinct under all culture conditions, further confirming strong selection for specific microbiomes based on phytoplankton. Analysis of core, abundant, and rare organisms in each culture condition showed a conserved response in which core organisms were enriched under conditions of exogenously added phytoplankton. Progression through phytoplankton growth phases selected first for rare and abundant organisms, with increased selection for core members during the exponential phase and relaxing of selection during the death phase, as seen throughout incubations for microbiome-only controls. Surprisingly, selection process quantification identified drift as the dominant process across all conditions and growth phases, with homogenous selection and dispersal limitation accounting for the remainder. Altogether, using Southern Ocean-derived model organisms we confirmed the role phytoplankton play in community assembly but also demonstrated that stochastic processes still predominately drive community selection.}, }
@article {pmid39991258, year = {2025}, author = {Figueiredo, AM and Shaw, D and Tunali, V and Gentekaki, E and Tsaousis, AD and Carmena, D}, title = {Update on Blastocystis: highlights from the Fourth International Blastocystis Conference.}, journal = {Open research Europe}, volume = {5}, number = {}, pages = {11}, pmid = {39991258}, issn = {2732-5121}, abstract = {While the stramenopile Blastocystis, first discovered in 1911, is considered the most prevalent enteric protist in humans, its biology remains largely unexplored. Clinical studies have only recently begun investigating the role of Blastocystis in the gut and its relationship with the gut microbiome, and whether it plays a pathogenic role in human and animal health. Aiming to gather leading researchers in the field to encourage and stimulate cross-disciplinary dialogue while fostering long-term international collaborations, the Fourth International Blastocystis Conference was hosted from the 17 [th] to the 19 [th] of September 2024 in Heraklion (Crete, Greece). The event was mainly supported by the COST Action CA21105, " Blastocystis under One Health", and the Microbiology Society. The multi- and interdisciplinary conference programme covered all aspects related to Blastocystis evolutionary biology and advances in omics, intestinal ecology (gut microbiome), clinical significance and association with disease, diagnosis and molecular characterisation, as well as epidemiology and One Health. The high-quality presentations discussed at the conference provided researchers with a synthesis of recent advancements, while key research questions, knowledge gaps, and future steps in Blastocystis research were identified. Herein, we aim to provide a thorough overview of the presentations at the congress. The COST Action CA21105, 'Blastocystis under One Health,' will build on the insights and collaborations fostered during the conference, promoting integrative research approaches, advancing our understanding of Blastocystis, and driving future efforts to translate these findings into improved public health strategies.}, }
@article {pmid39991100, year = {2025}, author = {Bajinka, O and Ouedraogo, SY and Li, N and Zhan, X}, title = {Multiomics as instrument to promote 3P medical approaches for the overall management of respiratory syncytial viral infections.}, journal = {The EPMA journal}, volume = {16}, number = {1}, pages = {217-238}, pmid = {39991100}, issn = {1878-5077}, abstract = {Respiratory syncytial viral (RSV) infection is a leading persisting pulmonary disease-causing agent. It causes loss of lives especially among infants, old ages, and adults immunocompromised individuals. This viral pathogen infects children more especially those under the age of 2 and may lead to death. It causes 3 million hospitalizations and up to 60,000 deaths annually for under the age of 5. The most vulnerable are immunocompromised individuals and asthmatic children with suboptimal antiviral defenses. It is associated with bronchiolitis, pneumonia, and bronchopneumonia. Despite all the current interventions and clinical trials, the only available therapeutic strategies for this viral infection are palliative care. Therefore, it is imperative to understand the pathogenicity of RSV and the corresponding host immune response to depict a sort of a targeted intervention. With the increasingly cutting-edge methods in harnessing the pathogenicity of this viral infection, high throughput systems including omics technological advances are at the spotlight. For instance, the associated genes with RSV complications for the host, the set of microbiome identified as operational taxonomic unit, the upregulated or downregulated metabolites, the protein subtypes, and the small molecules can help explain the viral microenvironment. Moreover, these big data will lead to RSV patients' stratification through individualized patient profiles that will bring in targeted prevention and treatment algorithms tailored to individualized patients' profiles. Through this, the virus and host interactions based on the pathogenicity of infection will provide a strong ground for depicting the prevention, prediction, and personalized medicine (3PM) for RSV. The 3PM approach brought cutting edge functional medicine to the healthcare givers, thus conferring targeted prevention and precision medicine while observing personalized treatment as well as preventive regularities. The viral replication mechanisms against the host defense mechanisms are crucial for the development of safe and effective therapy. Integrative personal omics profiles, whose analysis is based on the combined proteomics, transcriptomics, genomics, proteoformics, metabolomics, and autoantibody profiles, are very robust for predicting the risk of RSV infection. The targeted prevention will emerge from the patient stratification when the diagnosis is accurately predicted. In addition, the personalized medical services will give an effective prognostic assessment for RSV complications.}, }
@article {pmid39990509, year = {2025}, author = {Mak, JWY and Lo, ATW and Ng, SC}, title = {Early life factors, diet and microbiome, and risk of inflammatory bowel disease.}, journal = {Journal of the Canadian Association of Gastroenterology}, volume = {8}, number = {Suppl 2}, pages = {S44-S50}, pmid = {39990509}, issn = {2515-2092}, abstract = {Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), result from a loss of immune tolerance to gut microbiota, leading to inflammation. Their incidence is increasing, especially in newly industrialized countries. The etiology is multifactorial, involving genetic, immune, microbiota, and environmental factors. Maternal microbiome changes during pregnancy can elevate IBD risk in offspring, influenced by diet, smoking, and antibiotic exposure. Early life microbiota manipulation shows promise for preventing IBD. Epidemiological and pre-clinical studies highlight diet's significant role in IBD development. High-inflammatory dietary patterns correlate with increased CD risk, while Mediterranean-like diets promote beneficial gut microbiome changes and reduce inflammation. Certain food additives, such as emulsifiers and artificial sweeteners, may exacerbate IBD by altering gut microbiota. A systematic review indicates that higher ultra-processed food consumption significantly increases CD risk. Lifestyle modifications, including healthy dietary adherence, could substantially reduce IBD risk, with studies showing that favorable choices can halve the risk in genetically predisposed individuals. Additionally, maternal diet impacts offspring IBD risk, as seen in mouse models where high-fat diets led to increased inflammation. Evidence suggests that maternal probiotics and specific dietary patterns may mitigate these risks. Overall, these findings emphasize the potential for dietary interventions to modulate gut microbiota and immune responses, offering promising avenues for IBD prevention and management. Further large-scale studies are needed to explore the impact of dietary strategies on IBD risk and gut health.}, }
@article {pmid39990507, year = {2025}, author = {Galipeau, HJ and Verdu, EF}, title = {Is the microbiome important in celiac disease?.}, journal = {Journal of the Canadian Association of Gastroenterology}, volume = {8}, number = {Suppl 2}, pages = {S51-S55}, pmid = {39990507}, issn = {2515-2092}, abstract = {Celiac disease (CeD) is an autoimmune condition driven by gluten in genetically predisposed individuals. CeD is characterized by small intestinal villous atrophy but presents with a spectrum of gastrointestinal and systemic manifestations. Its only treatment is a strict, life-long adherence to a gluten-free diet, which is difficult to manage and does not always lead to symptomatic or mucosal recovery. About 40% of the population express the CeD-associated risk genes, but only 1%-2% of the worldwide population has CeD. This, along with the rising prevalence of CeD suggests other cofactors in disease pathogenesis. The gut microbiome has been implicated in CeD based on epidemiology studies and clinical associations. Mechanistic studies using relevant in vitro and in vivo preclinical models have begun to elucidate mechanisms through which microbes can influence CeD. Ultimately, a better understanding of these cofactors and their mechanisms will provide rationale intervention strategies and novel therapeutic targets to prevent or treat CeD.}, }
@article {pmid39990475, year = {2025}, author = {Yang, JL and Zhu, H and Sadh, P and Aumiller, K and Guvener, ZT and Ludington, WB}, title = {Commensal acidification of specific gut regions produces a protective priority effect against enteropathogenic bacterial infection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.12.637843}, pmid = {39990475}, issn = {2692-8205}, abstract = {The commensal microbiome has been shown to protect against newly introduced enteric pathogens in multiple host species, a phenomenon known as a priority effect. Multiple mechanisms can contribute to this protective priority effect, including antimicrobial compounds, nutrient competition, and pH changes. In Drosophila melanogaster , Lactiplantibacillus plantarum has been shown to protect against enteric pathogens. However, the strains of L. plantarum studied were derived from laboratory flies or non-fly environments and have been found to be unstable colonizers of the fly gut that mainly reside on the food. To study the priority effect using a naturally occurring microbial relationship, we isolated a wild-fly derived strain of L. plantarum that stably colonizes the fly gut in conjunction with a common enteric pathogen, Serratia marcescens . Flies stably associated with the L. plantarum strain were more resilient to oral Serratia marcescens infection as seen by longer lifespan and lower S. marcescens load in the gut. Through in vitro experiments, we found that L. plantarum inhibits S. marcescens growth due to acidification. We used gut imaging with pH-indicator dyes to show that L. plantarum reduces the gut pH to levels that restrict S. marcescens growth in vivo . In flies colonized with L. plantarum prior to S. marcescens infection, L. plantarum and S. marcescens are spatially segregated in the gut and S. marcescens is less abundant where L. plantarum heavily colonizes, indicating that acidification of specific gut regions is a mechanism of a protective priority effect.}, }
@article {pmid39990411, year = {2025}, author = {Caldeira, MO and McDonald, KS and Martinez, ESM and Moraes, JGN and Sellmer Ramos, I and Poock, SE and Ortega, MS and Lucy, MC}, title = {Short- and long-term effects of uterine disease on oocyte developmental capacity in postpartum dairy cows.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.07.636469}, pmid = {39990411}, issn = {2692-8205}, abstract = {UNLABELLED: The hypothesis was that early postpartum uterine disease would reduce the developmental capacity of oocytes thus contributing to the reduced fertility of dairy cows with uterine disease. Dairy cows were diagnosed healthy or with metritis at 7 to 10 d postpartum. The reproductive tract was collected at approximately 1 mo (Exp. 1) or approximately 80 or 165 d (Exp. 2) postpartum for the collection of cumulus-oocyte complexes (COC). The COC were matured, co- incubated with sperm for fertilization, and cultured to the blastocyst stage (8 d) in vitro. For Exp.1, the disease diagnosis (healthy or metritis) did not affect the number of collected COC or the subsequent embryo development to the blastocyst stage. The presence of purulent material in the uterine lumen (endometritis) at time of oocyte collection, however, was associated with a reduced cleavage rate evaluated 3 d following fertilization. For Exp. 2, there was no effect of disease diagnosis (healthy or metritis) on the number of COC or their subsequent development. Reduced cleavage rates were observed in COC retrieved from cows slaughtered at 80 d postpartum, but not at 165 d postpartum, and this reduction was associated with a vaginal microbiome indicative of uterine disease at 4 to 5 wk postpartum. Regression analyses that included plasma haptoglobin or energy metabolite concentrations or uterine bacterial genera abundance did not explain a large percentage of the variation in oocyte development in vitro. We conclude that there is an effect of uterine disease at one month postpartum on the oocyte and its capacity for development (Exp. 1) and this effect may be present at 80 d postpartum (Exp. 2). In later postpartum cows (165 d postpartum; Exp. 2) there was no effect of uterine disease on in vitro oocyte development.<br><br>HIGHLIGHTS: Oocytes collected at 1 month postpartum from dairy cows with endometritis (purulent uterine lumen) had a lower cleavage rate following in vitro fertilization when compared with oocytes collected from healthy cows (Exp. 1).Oocytes collected at approximately 80 d postpartum from dairy cows with evidence of uterine disease at 4 to 5 wk postpartum had a lower cleavage rate following in vitro fertilization but this disease-associated difference was not observed when oocytes were collected from cows later postpartum (approximately 165 d postpartum; Exp. 2).Regardless of the study (Exp. 1 or 2), uterine disease primarily affected the percentage of oocytes that cleaved after fertilization.Statistical associations between circulating metabolites or relative abundance of uterine bacteria were either not significant or explained only a small percentage of the variation in the in vitro embryo development in either experiment.}, }
@article {pmid39990405, year = {2025}, author = {Thinnes, CC and Waschkowitz, R and Courtney, E and Culligan, E and Fahy, K and Ferrazza, RAM and Ferris, C and Lagali, A and Lane, R and Maye, C and Murphy, O and Noone, D and Ryan, S and Bet, M and Corr, MC and Cummins, H and Hackett, D and Healy, E and Kulczycka, N and Lang, N and Madden, L and McHugh, L and Pyne, I and Varley, C and Harkin, N and Meade, R and O'Donnell, G and Nap, B and Martinelli, F and Heinken, A and Thiele, I}, title = {The MicroMap is a network visualisation resource for microbiome metabolism.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.13.637616}, pmid = {39990405}, issn = {2692-8205}, abstract = {The human microbiome plays a crucial role in metabolism and thereby influences health and disease. Constraint-based reconstruction and analysis (COBRA) has proven an attractive framework to generate mechanism-derived hypotheses along the nutrition-host-microbiome-disease axis within the computational systems biology community. Unlike for human, no large-scale visualisation resource for microbiome metabolism has been available to date. To address this gap, we created the MicroMap, a manually curated microbiome metabolic network visualisation, which captures the metabolic content of over a quarter million microbial genome-scale metabolic reconstructions. The MicroMap contains 5,064 unique reactions and 3,499 unique metabolites, including for 98 drugs. The MicroMap allows users to intuitively explore microbiome metabolism, inspect microbial metabolic capabilities, and visualise computational modelling results. Further, the MicroMap shall serve as an educational tool to make microbiome metabolism accessible to broader audiences beyond computational modellers. For example, we utilised the MicroMap to generate a comprehensive collection of 257,429 visualisations, corresponding to the entire scope of our current microbiome reconstruction resources, to enable users to visually compare and contrast the metabolic capabilities for different microbes. The MicroMap seamlessly integrates with the Virtual Metabolic Human (VMH, www.vmh.life) and the COBRA Toolbox (opencobra.github.io), and is freely accessible at the MicroMap dataverse (https://dataverse.harvard.edu/dataverse/micromap), in addition to all the generated reconstruction visualisations.}, }
@article {pmid39990360, year = {2025}, author = {Xu, W and Jalomo-Khayrova, E and Gumerov, VM and Ross, PA and Köbel, TS and Schindler, D and Bange, G and Zhulin, IB and Sourjik, V}, title = {Specificities of Chemosensory Receptors in the Human Gut Microbiota.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.11.637667}, pmid = {39990360}, issn = {2692-8205}, abstract = {The human gut is rich in metabolites and harbors a complex microbial community, yet the sensory repertoire of its commensal bacteria remains largely uncharacterized. Here we systematically mapped ligand specificities of extracytoplasmic sensory domains from twenty members of the human gut microbiota, with a primary focus on the abundant and physiologically important class of Clostridia. We identified diverse metabolites as specific stimuli for three major functional classes of transmembrane receptors. We further characterized novel subsets of sensors belonging to the Cache superfamily, specific for lactate, dicarboxylic acids, and for uracil and short-chain fatty acids (SCFAs), respectively, and investigated the evolution of their ligand specificity. Structural and biochemical analysis of the newly described dCache_1UR domain revealed an independent binding of uracil and SCFA at distinct modules. Altogether, we could identify or predict specificities for over a half of the Cache-type chemotactic sensors in the selected gut commensals, with the carboxylic acids representing the largest class of ligands. Among those, the most commonly found specificities were for lactate and formate, indicating particular importance of these metabolites in the human gut microbiome and consistent with their observed beneficial impact on the growth of selected bacterial species.}, }
@article {pmid39990153, year = {2025}, author = {Wu, Z and Xie, ZP and Cui, XX and Sun, XB and Zhao, FY and Wang, N and Li, Y and Wang, H and Zhang, L and Shen, J and Chen, F and Sun, H and He, J}, title = {HIV and the gut microbiome: future research hotspots and trends.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1466419}, pmid = {39990153}, issn = {1664-302X}, abstract = {BACKGROUND: The use of highly active antiretroviral therapy has transformed AIDS into a chronic infectious disease, but issues of chronic inflammation and immune system activation persist. Modulating the gut microbiome of patients may improve this situation, yet the specific association mechanisms between HIV and the gut microbiome remain unclear. This study aims to explore the research hotspots and trends of the HIV and the gut microbiome, providing direction for future research.<br><br>METHODS: We conducted a search of the Web of Science Core Collection database up to April 30, 2024 to retrieve articles related to the relationship between the HIV and the gut microbiome. The scientific achievements and research frontiers in this field were analyzed using CiteSpace, VOSviewer, and Bibliometrix statistical software.<br><br>RESULTS: As of April 30, 2024, a total of 379 articles met the inclusion criteria. The number of publications in this field peaked in 2023, and the number of articles published after 2020 declined. The country with the highest number of publications was the United States (184 articles), and the institution with the most publications was the University of Colorado (USA) (21 articles). The author with the most publications was Routy Jean-Pierre (Canada) (14 articles). High-frequency keywords, aside from the key terms, included "HIV," "inflammation," "immune activation," "gut microbiota," and "translocation." Keyword burst results indicated that short-chain fatty acids, T cells and obesity might become the focus of future research.<br><br>CONCLUSION: The research hotspots in this field should prioritize examining the role of the primary gut microbiome metabolite, short-chain fatty acids, in reducing immune system activation and inflammation. Another emerging area of interest could be the investigation into the annual increase in obesity rates within this field. Furthermore, understanding the metabolic mechanisms of short-chain fatty acids in T cells is essential. Additionally, multi-omics analysis holds potential.}, }
@article {pmid39990124, year = {2025}, author = {Carpenter, RE and Almas, S and Tamrakar, VK and Sharma, R}, title = {Dataset for comparative analysis of precision metagenomics and traditional methods in urinary tract infection diagnostics.}, journal = {Data in brief}, volume = {59}, number = {}, pages = {111339}, pmid = {39990124}, issn = {2352-3409}, abstract = {This study presents a comprehensive dataset comparing three diagnostic methodologies-microbial culture, polymerase chain reaction (PCR), and precision metagenomics (precision metagenomics)-for the detection and classification of uropathogens in urine samples from patients with suspected urinary tract infections (UTIs). While microbial culture remains the gold standard for UTI diagnosis, it has limitations in sensitivity, particularly for fastidious or non-culturable microorganisms. PCR offers higher sensitivity but is restricted to pre-targeted organisms, limiting its diagnostic range. Precision Metagenomics, a target-agnostic sequencing method, provides a more inclusive approach by enabling the identification of a broad spectrum of pathogens, including bacteria, viruses, fungi, and parasites, without prior knowledge of the organisms. The dataset includes 47 urine samples, each analyzed by microbial culture, PCR, and precision metagenomics, followed by bioinformatic classification using the Explify® platform. precision metagenomics identified significantly more uropathogens (62 distinct organisms) compared to PCR (19 organisms) and microbial culture (13 organisms), with 98 % of samples testing positive for polymicrobial infections via precision metagenomics. The precision metagenomics method demonstrated superior diagnostic yield by detecting pathogens that were missed by both microbial culture and PCR, particularly in culture-negative and PCR-negative cases. This dataset holds substantial reuse potential for further research into the microbiome of urinary tract infections, pathogen discovery, antimicrobial resistance studies, and the development of more accurate diagnostic models for UTI management. By offering insights into both polymicrobial infections and rare pathogens, this dataset supports the advancement of diagnostic strategies for complex and chronic UTIs.}, }
@article {pmid39989751, year = {2025}, author = {Arantes, JA and Di Pietro, R and Ratté, M and Arroyo, LG and Leclère, M and Costa, MC}, title = {Changes in bacterial viability after preparation and storage of fecal microbiota transplantation solution using equine feces.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18860}, pmid = {39989751}, issn = {2167-8359}, mesh = {Animals ; Horses/microbiology ; *Feces/microbiology ; *Fecal Microbiota Transplantation/methods ; *Microbial Viability/drug effects ; Cryoprotective Agents/pharmacology ; Freezing ; Glycerol/pharmacology ; Cryopreservation/methods ; Bacteria/drug effects ; }, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) has been used as a treatment option for horses (Equus caballus) with gastrointestinal diseases. Several preparation and conservation protocols to improve bacterial survival have been studied in other species.<br><br>METHODS: This study aimed to evaluate the impact of oxygen exposure and different protectant solutions on bacterial viability before and after freezing using horse feces. Fecal samples from 10 healthy horses were aliquoted and diluted in cryoprotectant solutions containing antioxidants (n = 40) or 10% glycerol (n = 40). Half of the aliquots from each dilution condition were prepared inside an anaerobic chamber, while the other half were prepared under ambient air conditions. Each sample was also analyzed fresh and after freezing at -20 &#xb0;C for 90 days. Bacterial viability was assessed using flow cytometry. A mixed linear model and the Friedman and Wilcoxon tests were used depending on data distribution.<br><br>RESULTS: Freeze-thawing decreased bacterial viability by 47% (mean &#xb1; SD: 51 &#xb1; 27% before, 27 &#xb1; 8% after; p < 0.001). Glycerol was superior to the cryoprotectant after freezing (32 &#xb1; 8% glycerol, 24 &#xb1; 8% cryoprotectant; p < 0.001). Oxygen exposure did not affect viability (p = 0.13). There was no statistical difference between protectant solutions in fresh samples (p = 0.16).<br><br>CONCLUSIONS: Fresh FMT solutions may be better for treating horses with dysbiosis, but if freezing cannot be avoided, glycerol should be used to dilute feces.}, }
@article {pmid39989601, year = {2025}, author = {Tjandrawinata, RR and Amalia, N and Tandi, YYP and Athallah, AF and Afif Wibowo, C and Aditya, MR and Muhammad, AR and Azizah, MR and Humardani, FM and Nojaid, A and Christabel, JA and Agnuristyaningrum, A and Nurkolis, F}, title = {The forgotten link: how the oral microbiome shapes childhood growth and development.}, journal = {Frontiers in oral health}, volume = {6}, number = {}, pages = {1547099}, pmid = {39989601}, issn = {2673-4842}, abstract = {Childhood stunting, defined as impaired linear growth and development, remains a significant global health challenge with long-term consequences on cognitive and physical well-being. Emerging evidence highlights the pivotal role of the oral microbiome-a dynamic microbial ecosystem-in influencing nutritional status, immune response, and overall systemic health. This review explores the intricate interplay between the oral microbiome and stunting, emphasizing mechanisms such as microbial dysbiosis, its impact on nutrient absorption, and immune modulation. Disruptions in the oral microbiome can lead to nutrient malabsorption and systemic inflammation, further exacerbating growth impairments in children. Furthermore, the potential for microbiome-targeted diagnostics and interventions, including probiotics and prebiotics, offers novel strategies to address stunting. A deeper understanding of these interactions may inform innovative diagnostic tools and therapeutic interventions aimed at mitigating stunting through oral microbiome modulation. Integrating oral microbiome research into stunting prevention efforts could provide valuable insights for public health strategies to improve child growth and development, particularly in resource-limited settings. Future research should focus on elucidating the molecular pathways linking the oral microbiome to stunting and developing personalized interventions that optimize microbiome health in early life.}, }
@article {pmid39989432, year = {2025}, author = {Adams, L and Rasid, O and Hulme, H and Quon, T and Burchmore, R and Milling, S and Goodwin, RJA and Wall, DM}, title = {Spatial mapping of dextran sodium sulphate-induced intestinal inflammation and its systemic effects.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {39}, number = {4}, pages = {e70415}, doi = {10.1096/fj.202402780R}, pmid = {39989432}, issn = {1530-6860}, support = {BB/V001876/1//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Industrial CASE studentship//UKRI | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {Animals ; *Dextran Sulfate/toxicity ; Mice ; *Inflammation/metabolism/pathology ; *Mice, Inbred C57BL ; *Inflammatory Bowel Diseases/chemically induced/pathology/metabolism ; Disease Models, Animal ; Male ; Female ; Intestinal Mucosa/metabolism/pathology ; Intestines/pathology ; }, abstract = {Inflammatory bowel disease (IBD) is a multifactorial disease, and patients frequently experience extraintestinal manifestations affecting multiple sites. Causes of systemic inflammation remain poorly understood, but molecules originating from the intestine likely play a role, with microbial and host small molecules polarizing host immune cells towards a pro- or anti-inflammatory phenotype. Using the dextran sodium sulfate (DSS) mouse model, which mimics the disrupted barrier function, microbial dysbiosis, and immune cell dysregulation of IBD, we investigated metabolomic and phenotypic changes at intestinal and systemic sites. Using spatial biology approaches, we mapped the distribution and relative abundance of molecules and cell types across a range of tissues, revealing significant changes in DSS-treated mice. Molecules identified as contributing to the statistical separation of treated from control mice were spatially localized within organs to determine their effects on cellular phenotypes through imaging mass cytometry. This spatial approach identified both intestinal and systemic molecular drivers of inflammation, including several not previously implicated in inflammation linked to IBD or the systemic effects of intestinal inflammation. Metabolic and inflammatory pathway interplay underpins systemic disease, and determining drivers at the molecular level may aid the development of new targeted therapies.}, }
@article {pmid39989409, year = {2025}, author = {Liu, T and Zhang, M and Xie, Q and Gu, J and Zeng, S and Huang, D}, title = {Unveiling the Antiobesity Mechanism of Sweet Potato Extract by Microbiome, Transcriptome, and Metabolome Analyses in Mice.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.4c13173}, pmid = {39989409}, issn = {1520-5118}, abstract = {This study aimed to elucidate the antiobesity mechanisms of sweet potato extract (SPE) through biochemical, gut microbiome, liver transcriptome, and metabolome analyses. Administration of SPE to high-fat-diet-fed mice significantly reduced body weight gain, serum low-density lipoprotein cholesterol, hepatic lipid accumulation, and adipocyte hypertrophy, which were closely linked to gut microbiome composition. SPE notably increased the abundance of Eubacterium_coprostanoligenes_group_unclassified and decreased that of Kineothrix, both of which were strongly associated with short-chain fatty acid (SCFA) production. LC-QTOF-MS analysis identified resin glycoside compounds from SPE with reduced levels in mouse feces, suggesting their utilization in vivo. SPE also promoted dietary fat excretion. Liver transcriptomic and metabolomic profiling revealed that SPE may exert antiobesity effects by modulating the bile-sphingolipid metabolism, which was closely correlated with the reshaped gut microbiomes and SCFAs. These findings provide new insights into the antiobesity effects and mechanisms of SPE.}, }
@article {pmid39988792, year = {2025}, author = {Puglisi, CH and Kim, M and Aldhafeeri, M and Lewandowski, M and Vuong, HE}, title = {Interactions of the maternal microbiome with diet, stress, and infection influence fetal development.}, journal = {The FEBS journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/febs.70031}, pmid = {39988792}, issn = {1742-4658}, support = {CON000000101629//Pew Charitable Trusts/ ; //Alfred P. Sloan Foundation/ ; //Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; }, abstract = {Humans and other animals contain multitudes of microorganisms including bacteria, fungi, and viruses, which make up a diverse microbiome. Across body sites including skin, gastrointestinal tract, and oral cavity there are distinct microbial niches that are made up of trillions of microorganisms that have co-evolved to inhabit and interact with the host. The microbiome also interacts with the changing environment. This tripartite interaction between the host, microbiome, and environment suggests microbial communities play a key role in the biological processes of the host, such as development and behaviors. Over the past two decades, emerging research continues to reveal how host and microbe interactions impact nervous system signaling and behaviors, and influence neurodevelopmental, neurological, and neurodegenerative disorders. In this review, we will describe the unique features of the maternal microbiome that exist during the perinatal period and discuss evidence for the function of the maternal microbiome in offspring development. Finally, we will discuss how the maternal environment interacts with the microbiome and nervous system development and then postulate how the maternal microbiome can modify early offspring development to have lasting influence on brain health.}, }
@article {pmid39988585, year = {2025}, author = {Parhizkar, E and Vosough, P and Baneshi, M and Keshavarzi, A and Lohrasbi, P and Taghizadeh, S and Savardashtaki, A}, title = {Probiotics and gut microbiota modulation: implications for skin health and disease management.}, journal = {Archives of microbiology}, volume = {207}, number = {3}, pages = {68}, pmid = {39988585}, issn = {1432-072X}, mesh = {*Probiotics/therapeutic use/administration &amp; dosage ; Humans ; *Gastrointestinal Microbiome ; *Skin Diseases/microbiology/therapy ; *Skin/microbiology ; *Dysbiosis/microbiology/therapy ; Dermatitis, Atopic/microbiology/therapy ; }, abstract = {The gut microbiota, consisting of a varied population of microorganisms in the digestive tract, is essential for sustaining overall human health, encompassing skin health. This review explored the intricate relationship between gut microbiota and various skin disorders, investigating the pathways through which gut dysbiosis may have impacted the development and progression of these conditions. We focused on the impact of gut microbiota on atopic dermatitis, psoriasis, acne vulgaris, acne rosacea, and melanoma. The review highlighted the potential of probiotics as a therapeutic strategy for modulating gut microbiota composition and, consequently, improving skin health. We discussed the evidence supporting the use of probiotics in managing these skin disorders and explored the mechanisms by which probiotics delivered their positive effects. Finally, we discussed the potential role of gut microbiota in other skin diseases, emphasizing the need for further research to unravel the complex interplay between the gut and the skin. Significant gaps remain in understanding the gut-skin axis, how microbial interactions contribute to skin disorders, and how to effectively manipulate the microbiome for therapeutic purposes. This review provided extensive research on the gut-skin axis, highlighting the promising prospects of modulating gut microbiota as a therapeutic strategy for various dermatological conditions.}, }
@article {pmid39988056, year = {2025}, author = {Gupta, T and Murtaza, M}, title = {Advancing Targeted Therapies in Pancreatic Cancer: Leveraging Molecular Aberrations for Therapeutic Success.}, journal = {Progress in biophysics and molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pbiomolbio.2025.02.003}, pmid = {39988056}, issn = {1873-1732}, abstract = {Pancreatic cancer is one of the most deadly with poor prognosis and overall survival rate due to the dense stroma in the tumors which often is challenging for the delivery of drug to penetrate deep inside the tumor bed and usually results in the progression of cancer. The conventional treatment such as chemotherapy, radiotherapy or surgery shows a minimal benefit in the survival due to the drug resistance, poor penetration, less radiosensitivity or recurrence of tumor. There is an urgent demand to develop molecular- level targeted therapies to achieve therapeutic efficacy in the pancreatic ductal adenocarcinoma (PDAC) patients. The precision oncology focuses on the unique attributes of the patient such as epigenome, proteome, genome, microbiome, lifestyle and diet habits which contributes to promote oncogenesis. The targeted therapy helps to target the mutated proteins responsible for controlling growth, division and metastasis of tumor in the cancer cells. It is very important to consider all the attributes of the patient to provide the suitable personalized treatment to avoid any severe side effects. In this review, we have laid emphasis on the precision medicine; the utmost priority is to improve the survival of cancer patients by targeting molecular mutations through transmembrane proteins, inhibitors, signaling pathways, immunotherapy, gene therapy or the use of nanocarriers for the delivery at the tumor site. It will become beneficial therapeutic window to be considered for the advanced stage pancreatic cancer patients to prolong their survival rate.}, }
@article {pmid39987825, year = {2025}, author = {Huang, X and Yang, J and Yang, X and Wang, T and Meng, J and Guo, X and Wang, Y and Xiong, W and Zeng, J and Wu, Z and Li, K and Jeppesen, E}, title = {Leaf metabolomic traits decipher the invasiveness of Alternanthera philoxeroides in urban wetlands.}, journal = {The Science of the total environment}, volume = {968}, number = {}, pages = {178888}, doi = {10.1016/j.scitotenv.2025.178888}, pmid = {39987825}, issn = {1879-1026}, abstract = {Urbanisation has been considered to promote exotic plant invasion. Ecophysiology predicts phenotypic variation and potential evolution following urbanisation and can be used to evaluate plant invasiveness. However, few studies have included the role of ecophysiological traits for such invasiveness in urban ecosystems. Traditional plant functional traits have been used but have their limitations. Novel approaches such as metabolomics may potentially be useful. The present study explored the invasiveness of the cosmopolitan noxious invasive plant Alternanthera philoxeroides in urban and periurban areas of a megacity city in China using both traditional leaf functional traits and novel leaf metabolome as indicators. We found that traditional leaf functional traits, including specific leaf area, nitrogen concentration, carbon:nitrogen ratio and construction costs, did not differ between urban and periurban A. philoxeroides populations. However, metabolomic profiling showed that the urban populations had an up-regulated expression of zeatin and purine, two cytokinins correlated with plant growth and a down-regulated expression of isoflavonoids, a defensive metabolite for herbivory. Leaf metabolome may, therefore, be sensitive in deciphering the facilitative effects of urbanisation on plant invasion. We also found that the urban populations of A. philoxeroides accumulated more beneficial microbes, which might enhance their invasiveness. Urbanisation likely promotes exotic plants invasion through generation of metabolites, which stimulates growth via modification of the soil microbiome. Our results indicate that leaf metabolome may be used for interpreting plant invasiveness and predicting plant invasion.}, }
@article {pmid39987671, year = {2025}, author = {Farzi, A and Tatzl, E and Kashofer, K and Trajanoski, S and Herbert, MK and Holzer, P}, title = {Antibiotic-induced decrease of bacterial load in guinea pig intestine reduces α2-adrenoceptor expression and activity in peristaltic motor inhibition.}, journal = {British journal of pharmacology}, volume = {}, number = {}, pages = {}, doi = {10.1111/bph.70001}, pmid = {39987671}, issn = {1476-5381}, support = {//Medizinische Universit&#xe4;t Graz/ ; 613979//European Commission/ ; }, abstract = {BACKGROUND AND PURPOSE: The use of analgosedatives in critically ill patients carries the risk of impairing gastrointestinal (GI) propulsion and could thereby lead to sepsis. The gut microbiota can influence GI motility, but whether GI microbial dysbiosis modifies GI peristalsis impairment by analgosedative drugs has not yet been analysed. This question was addressed in the guinea pig small intestine following a decrease of bacterial load by antibiotic pretreatment.<br><br>EXPERIMENTAL APPROACH: Guinea pigs were enorally (within the mouth) pretreated with meropenem, neomycin and vancomycin, and antibiotic-induced decrease of bacterial load was confirmed by 16S rDNA sequencing. Peristalsis in the isolated guinea pig small intestine was evaluated by determining the pressure threshold at which a peristaltic wave is triggered. The expression of factors that may be relevant to communication between GI microbiota and the motor system was examined at the mRNA (quantitative (q)PCR]) and/or protein (enzyme-linked immunosorbent assay [ELISA]) level.<br><br>KEY RESULTS: Antibiotic treatment disturbed the small intestinal microbiome as shown by decrease of bacterial load and reduced alpha diversity. Microbial dysbiosis did not affect peristalsis at baseline but blunted the ability of &#x3b1;2 agonists to inhibit peristalsis, while the anti-peristaltic effects of sufentanil, midazolam, neostigmine and propofol were inconsistently affected. These functional alterations were complemented by a decreased expression of &#x3b1;2-adrenoceptors, toll-like receptors (TRL) 3, 4 &amp; 7, IFN-&#x3b3; and iNOS.<br><br>CONCLUSION AND IMPLICATIONS: Antibiotic-induced decrease of bacterial load in the small intestine selectively blunts the ability of &#x3b1;2 agonists to impair peristalsis. This effect is explained by decreased &#x3b1;2-adrenoceptor expression, which may arise from TLR down-regulation in the dysbiotic gut.}, }
@article {pmid39987504, year = {2025}, author = {Sweeney, CJ and Bottoms, M and Kaushik, R and Aderjan, E and Sherborne, N}, title = {Functional versus compositional tests in the risk assessment of the impacts of pesticides on the soil microbiome.}, journal = {Environmental toxicology and chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/etojnl/vgaf012}, pmid = {39987504}, issn = {1552-8618}, support = {//Syngenta/ ; }, abstract = {The Organisation of Economic Co-operation and Development (OECD) 216 nitrogen transformation test is used to understand the impacts of plant protection products (PPPs) on the soil microbiome. However, there is significant interest in developing the European PPP risk assessment to include new technologies such as amplicon sequencing to assess impacts on soil microbial community composition and diversity. We have little understanding of how to generate endpoints from amplicon sequencing data sets, their robustness, and whether they provide an appropriate level of protection to the soil microbiome. Our study addresses this key knowledge gap. We conducted a dose-response OECD 216 study with two chemicals, nitrapyrin and streptomycin, and calculated traditional functional endpoints, in accordance with the OECD 216 guideline, and used amplicon sequencing techniques to generate a range of endpoints based on soil bacterial diversity, richness, dissimilarity from the control, species sensitivity distributions, and threshold indicator analysis. We show it is possible to generate a range of endpoints from amplicon sequencing data sets; however, these endpoints varied significantly based on the calculation method, with up to a 101-fold difference between the least and most sensitive endpoints. Additionally, the relative sensitivity of these endpoints compared to the currently used functional OECD 216 metrics was compound dependent, with many endpoint calculation methods unable to detect the impacts of nitrapyrin on the soil microbiome at concentrations deemed ecotoxicologically relevant by OECD 216. Our study shows amplicon sequencing methods to study soil microbial ecotoxicology did not perform consistently and reliably when considering both nitrapyrin and streptomycin treatments and in many cases did not consistently provide an enhanced degree of protection over the functional OECD 216 assessments already integrated into the PPP risk assessment.}, }
@article {pmid39987122, year = {2025}, author = {Chen, X and Sun, F and Wang, X and Feng, X and Aref, AR and Tian, Y and Ashrafizadeh, M and Wu, D}, title = {Inflammation, microbiota, and pancreatic cancer.}, journal = {Cancer cell international}, volume = {25}, number = {1}, pages = {62}, pmid = {39987122}, issn = {1475-2867}, abstract = {Pancreatic cancer (PC) is a malignancy of gastrointestinal tract threatening the life of people around the world. In spite of the advances in the treatment of PC, the overall survival of this disease in advanced stage is less than 12%. Moreover, PC cells have aggressive behaviour in proliferation and metastasis as well as capable of developing therapy resistance. Therefore, highlighting the underlying molecular mechanisms in PC pathogenesis can provide new insights for its treatment. In the present review, inflammation and related pathways as well as role of gut microbiome in the regulation of PC pathogenesis are highlighted. The various kinds of interleukins and chemokines are able to regulate angiogenesis, metastasis, proliferation, inflammation and therapy resistance in PC cells. Furthermore, a number of molecular pathways including NF-κB, TLRs and TGF-β demonstrate dysregulation in PC aggravating inflammation and tumorigenesis. Therapeutic regulation of these pathways can reverse inflammation and progression of PC. Both chronic and acute pancreatitis have been shown to be risk factors in the development of PC, further highlighting the role of inflammation. Finally, the composition of gut microbiota can be a risk factor for PC development through affecting pathways such as NF-κB to mediate inflammation.}, }
@article {pmid39987010, year = {2025}, author = {Kullin, BR and Gitome, S and Happel, AU and Pidwell, T and Lefevre, M and Madikida, A and Wekesa, P and Mahlangu, K and Ochieng, J and Awili, L and Agolla, W and Otieno, R and Mutharimi, A and Ganief, Y and Daniels, R and Chicken, A and Welp, K and Livingstone, H and Swanepoel, C and Claassen-Weitz, S and Kanyoka, P and Ravel, J and Humphrys, M and Bilski, L and Mulder, N and Bekker, LG and Gill, K and Jaspan, H and Bukusi, EA and Passmore, JS}, title = {Vaginal Microbiome Research Consortium for Africa: study protocol of a multicentre prospective clinical study to evaluate temporal vaginal microbial composition associated with maintenance of reproductive health in women in South Africa and Kenya.}, journal = {BMJ open}, volume = {15}, number = {2}, pages = {e090938}, doi = {10.1136/bmjopen-2024-090938}, pmid = {39987010}, issn = {2044-6055}, mesh = {Humans ; Female ; Kenya ; *Vagina/microbiology ; South Africa ; Prospective Studies ; *Microbiota ; *Reproductive Health ; Adult ; RNA, Ribosomal, 16S/genetics ; Young Adult ; Multicenter Studies as Topic ; Adolescent ; Research Design ; }, abstract = {INTRODUCTION: The Vaginal Microbiome Research Consortium for Africa (VMRC4Africa) study is a multicentre observational cohort study. We aim to enrol parallel cohorts of 100 women from two sites in two African countries (N=200) (Desmond Tutu HIV Centre [DTHC], South Africa; Kenya Medical Research Institute [KEMRI], Kenya) to evaluate detailed temporal fluctuations in vaginal microbiota in young, generally healthy women from Southern and Eastern Africa.<br><br>METHODS AND ANALYSIS: Cohorts in Kenya and South Africa will be followed up twice a week for 10&#x2009;weeks to create detailed profiles of vaginal microbial community state types (CSTs; by 16S rRNA gene sequencing) and fungal communities (by internal transcribed spacer (ITS) sequencing) and to identify women with stable Lactobacillus crispatus-dominated microbiota, with no evidence of genital inflammation, as assessed by the measurement of inflammatory cytokines.<br><br>DISCUSSION: Through the establishment of this African vaginal sample biorepository, the intention will be to cultivate Lactobacillus isolates to create a biobank from which to ultimately select geographically diverse Lactobacillus strains with health-promoting characteristics that can be co-formulated into live biotherapeutic products (LBPs) to treat bacterial vaginosis (BV) for women in sub-Saharan Africa.<br><br>ETHICS AND DISSEMINATION: The VMRC4Africa study has been granted ethical approval by the Human Research Ethics Committees in South Africa (UCT HREC: 611/2022) and Kenya (KEMRI Scientific and Ethics Review Unit: SERU No. 4569). Deidentified microbial community compositional data will be made available on public databases. Results of the study will be published in peer-reviewed journals.}, }
@article {pmid39986982, year = {2025}, author = {Li, Z and Huang, X and Wang, Q and Gopinath, D}, title = {Causal Association Between Microbiome and Oral-Oropharyngeal Cancer: A Mendelian Randomization Study.}, journal = {International dental journal}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.identj.2025.01.017}, pmid = {39986982}, issn = {1875-595X}, abstract = {INTRODUCTION AND AIMS: This study aimed to examine the causal link between oral microbiome and the risk of oral and oropharyngeal squamous cell carcinoma (OOPSCC) using Mendelian randomization (MR).<br><br>METHODS: Utilizing single nucleotide polymorphisms as instrumental variables, we applied the MR inverse-variance weighted approach to assess the impact of salivary and tongue microbiome on OOPSCC. The data were obtained from the CNGBdb database and the UK Biobank, and analytical procedures were performed using the R package 'TwoSampleMR'. To ensure the robustness of our findings, we conducted sensitivity studies, which included the MR-Egger intercept test, to establish strong correlations and eliminate the phenomenon of horizontal pleiotropy.<br><br>RESULT: Our large-scale MR study revealed a genetically predisposed causal relationship between 13 microbial taxa, each from saliva and tongue, with OOPSCC. Notably, microbial taxa from six genera, including Prevotella, Neisseria, Veillonella, Granulicatella, Treponema, and Streptococcus, in both salivary and tongue microbiomes, showed this relationship. Conversely, several taxa, including Hemophilus, Solobacterium, Campylobacter, and Porphyromonas, predominantly demonstrated an inverse relationship, suggesting a protective effect. The robustness of our findings was further confirmed through sensitivity analyses, providing additional confidence in our results.<br><br>CONCLUSION: Our MR study indicates that the oral microbiota has a significant causal impact on the risk of oral and oropharyngeal cancers. The microbial biomarkers we identified, which are linked to OOPSCC, have the potential to uncover the underlying mechanisms and pave the way for new therapeutic approaches for targeted treatment of these malignancies.}, }
@article {pmid39986781, year = {2025}, author = {Tampanna, N and Wanitsuwan, W and Chewatanakornkul, S and Wangkulangkul, P and Theapparat, Y and Detarun, P and Wichienchot, S}, title = {The role of kratom (Mitragyna speciosa Korth.) extract in medical foods for obese patients: Effects on gut microbiota in a colon model.}, journal = {Food research international (Ottawa, Ont.)}, volume = {204}, number = {}, pages = {115935}, doi = {10.1016/j.foodres.2025.115935}, pmid = {39986781}, issn = {1873-7145}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Obesity/microbiology/metabolism ; *Plant Extracts/pharmacology ; *Mitragyna/chemistry ; *Colon/microbiology/metabolism ; *Fermentation ; Feces/microbiology ; Male ; Adult ; Female ; Fatty Acids, Volatile/metabolism ; RNA, Ribosomal, 16S/genetics ; Polyphenols/pharmacology ; Bacteria/classification/genetics/drug effects/metabolism ; Functional Food ; Dietary Supplements ; }, abstract = {Kratom (Mitragyna speciosa Korth.), rich in mitragynine and polyphenols, suppresses and affects the metabolism of macronutrients, making it a functional ingredient in medical food for obese patients. This research focuses on the formulation of a kratom-supplemented medical food (MKT) and its effects on the gut microbiota of obese patients using in vitro fecal fermentation, as well as the production of their metabolites in a simulated human colon system. The 16S rRNA gene sequencing and studies on α- and β-diversity revealed favorable outcomes for MKT, demonstrating the promotion of beneficial bacteria and the suppression of pathogens in obese patients. However, the commercial medical food (MC) resulted in the production of more short-chain fatty acids. In conclusion, the developed kratom-supplemented formula shows potential for use in the diets of obese patients. However, further investigation through animal and human trials is needed to confirm its safety and effectiveness.}, }
@article {pmid39986595, year = {2025}, author = {Nama, AA and Sandeepa, GM and Buddolla, V and Mastan, A}, title = {Advances in understanding therapeutic mechanisms of probiotics in cancer management, with special emphasis on breast cancer: a comprehensive review.}, journal = {European journal of pharmacology}, volume = {}, number = {}, pages = {177410}, doi = {10.1016/j.ejphar.2025.177410}, pmid = {39986595}, issn = {1879-0712}, abstract = {The increasing global prevalence of cancer, particularly breast cancer, necessitates the development of innovative therapeutic strategies. Probiotics, proficient in promoting gut health, have emerged as promising candidates for cancer treatment due to their immunomodulatory and potential anticancer properties. This review focuses on the therapeutic mechanisms of probiotics in breast cancer, examining their anticancer efficacy through metabolic, immune, and molecular mechanisms. Probiotics enhance cancer therapies, minimize side effects, and offer new adjuvant approaches in oncology. Recent advancements discussed in the review include the utilization of probiotics as oncolytic gene expression systems and drug delivery vectors, as well as personalized probiotic interventions aimed at optimizing cancer therapy. Clinical studies are critically evaluated, highlighting both the outcomes and limitations of probiotic use in cancer patients, particularly those suffering from breast cancer. Additionally, the review explores factors influencing anticancer effects of probiotics, focusing on their role in modulating the tumor microenvironment. Challenges in translating preclinical findings to clinical practice are discussed, along with future research directions, focusing on the relationship between probiotics, the microbiome, and cancer treatment. Ultimately, this review advocates for further investigation into the therapeutic potential of probiotics in breast cancer, aiming to harness their benefits in oncology.}, }
@article {pmid39986571, year = {2025}, author = {Santamaria, J and Gilaberte, Y and Prudkin, L and Piquero-Casals, J}, title = {POLLUTION, A RELEVANT EXPOSOME FACTOR IN SKIN AGING AND THE ROLE OF MULTI-BENEFIT PHOTOPROTECTION.}, journal = {Actas dermo-sifiliograficas}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ad.2024.11.025}, pmid = {39986571}, issn = {1578-2190}, abstract = {Skin aging is a complex, continuous, multifactorial process resulting from cumulative morphological and functional changes in the skin over time.This happens because of 2 processes: intrinsic and extrinsic skin aging. Intrinsic skin aging occurs naturally over time and reflects each person's genetic makeup, or heredity. Extrinsic skin aging, on the other hand, is due to exposomal factors, such as solar radiation, air pollution, tobacco or nutrition, being the first 2 the most important of all. Exposure to air pollutants, primarily gases such as ground-level ozone and particulate matter, can accelerate the process via 4 key mechanisms: reactive oxygen species generation, inflammation, skin microbiome disruption, and aryl hydrocarbon receptor activation. Regarding solar radiation, all wavelengths reaching the Earth's surface have an impact on the skin, having a synergistic effect with air pollution ("photo-pollution"). Here, we discuss this phenomenon and mitigation strategies, including sunscreens, cosmetics with film-forming plus antioxidant ingredients, and oral supplementation.}, }
@article {pmid39986536, year = {2025}, author = {Sangfuang, N and McCoubrey, LE and Awad, A and Marzorati, M and Ghyselinck, J and Verstrepen, L and Munck, J and Medts, J and Gaisford, S and Basit, AW}, title = {Effects of senotherapeutics on gut microbiome dysbiosis and intestinal inflammation in Crohn's Disease: A Pilot Study.}, journal = {Translational research : the journal of laboratory and clinical medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.trsl.2025.02.004}, pmid = {39986536}, issn = {1878-1810}, abstract = {Inflammatory Bowel Disease (IBD) is characterized by chronic inflammation in the gastrointestinal tract, and is usually accompanied by dysbiosis in the gut microbiome, a factor that contributes to disease progression. Excessive production of reactive oxygen species (ROS) because of gut microbiome dysbiosis-one of the hallmark features of IBD-promotes chronic inflammation and facilitates the transformation of normal cells into senescent cells. Cellular senescence is associated with the development of various chronic and age-related diseases. We hypothesise that senolytic agents, specifically dasatinib (D) and quercetin (Q), could have a beneficial effect on both the gut microbiome and intestinal cells in IBD. The modulatory effects of a combination of D+Q was assessed in the M-SHIME model with faecal microbiota sourced from Crohn's disease patients. D+Q significantly modulated butyrate and lactate levels in the samples from specific patients. In addition, metabolomic analysis showed that D+Q positively impacted the abundance of anti-inflammatory bacteria while also significantly reducing the several species of pathogenic bacteria. Findings from a Caco-2 cell/THP1 co-culture model of IBD demonstrated that D+Q exerted strong immunomodulatory effects on the gut epithelium, evidenced by reduced NF-kB activity, and lower levels of the pro-inflammatory markers TNF-α, CXCL-10, and MCP-1. Furthermore, D+Q induced the secretion of anti-inflammatory cytokines, including IL-6 and IL-10. However, it should be noted that D+Q also led to the secretion of the pro-inflammatory cytokines IL-8. These findings suggest that D+Q could offer a novel therapeutic approach for advanced IBD management by modulating both the gut microbiome and inflammatory pathways. The results support the potential repurposing of senotherapeutic agents as a strategy for addressing the chronic inflammation central to IBD pathogenesis.}, }
@article {pmid39986496, year = {2025}, author = {Herman, RA and Zhang, ZP and Khurshid, M and Ayepa, E and Yan, CH and Anankware, JP and Wang, J}, title = {Microbial community formation during dietary exposure to Fe3O4-urease nanoconjugates in silkworm (Bombyx mori): Principal fungi groups facilitate functional flux.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {141367}, doi = {10.1016/j.ijbiomac.2025.141367}, pmid = {39986496}, issn = {1879-0003}, abstract = {The gut microbiota of the silkworm (Bombyx mori) is essential for metabolic processes, including digestion and immunity. Nonetheless, the role of specific gut fungi in optimizing nutrient recycling influenced by infiltrated biomaterials remains inadequately elucidated. This study investigates the potential mechanisms through which gut fungi affect the dynamics of nutrient absorption in silkworms. For this purpose, 5th instar silkworms were exposed to Fe3O4-urease nanoconjugates for 168 h following the utilization of high-throughput microbiome sequencing to identify shifts in principal fungal groups. The conditional fungi groups Mucoromycota and Basidiomycota significantly increased from 10.28 % to 47.16 % and 0.53 % to 2.63 % respectively (p < 0.05), while Ascomycota decreased from 86.57 % to 52.29 %, having no negative impact on the growth and sustainability of the host insect. Functional analysis using FunGuild showed enriched trophic nodes including pathotrophs, saprotrophs and symbiotrophs while functions of DEGs demonstrated an increased metabolic capacity associated with iron and heme binding, and lipase activity. This reveals significant restructuring of the gut fungi microbiota with specific fungal taxa exhibiting enhanced abundance and diversity correlated with the presence of Fe3O4-urease nanoconjugates, serving as a potential for engineered nanomaterials to promote the sustainability and development of sericulture.}, }
@article {pmid39986419, year = {2025}, author = {Zhao, J and Duan, G and Chang, J and Wang, H and Zhu, D and Li, J and Zhu, Y}, title = {Co-exposure to cyazofamid and polymyxin E: variations in microbial community and antibiotic resistance in the soil-animal-plant system.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121160}, doi = {10.1016/j.envres.2025.121160}, pmid = {39986419}, issn = {1096-0953}, abstract = {Human activity is accelerating the emergence of fungal pathogens, prompting substantial efforts to discover novel fungicides. Meanwhile, the runoff and spray drift from agricultural fields adversely affect aquatic and terrestrial nontarget organisms. However, few studies have examined the effects of co-contamination by agrochemical fungicides and pharmaceutical antibiotics on microorganisms and antibiotic resistance genes (ARGs) in the soil-animal-plant system. To further explore the mechanisms, an investigation was conducted into the individual and combined effects of a widely used fungicide (cyazofamid, CZF) and a last-resort antibiotic (colistin, polymyxin E, PME) in the soil-earthworm-tomato system. This study revealed that CZF and PME co-contamination exerted synergistic toxicity, significantly reducing earthworm survival and inhibiting tomato growth. This study found that the structure of microbial communities was more severely disturbed by the fungicide CZF than by the antibiotic PME, with the most severe impact being that of CZF+PME co-contamination. Fungicides and antibiotics had significantly distinct effects on bacterial functional pathways: CZF and CZF+PME treatments enhanced compound degradation, whereas PME treatments promoted biological nitrogen cycling. Moreover, co-contamination significantly increased the abundance of insertional and plasmid-associated genes and number of total ARGs in bulk and rhizosphere soil. In addition, the relationships between bacterial communities and the antibiotic resistome were investigated. The analysis revealed that Gram-positive bacteria (Sporosarcina, Bacillus, and Rhodococcus) capable of resistance and degradation, as well as the genes MexB (multidrug) and aadA2 (aminoglycoside) were enriched. Taken together, interactions between co-pollutants can significantly increase toxicity levels and the risk of ARG proliferation. The findings provide new insights into the potential impacts of co-contamination in complex real-life environments, such as soil-animal-plant systems.}, }
@article {pmid39986398, year = {2025}, author = {Khan, ZA and Song, SS and Xu, H and Ahmad, M and Wang, A and Abdullah, A and Jiang, L and Ding, X}, title = {Elimination of Intracellular Microbes using Drug Combination Therapy and Unveiling Survival mechanism of Host Cells upon Microbial Invasion.}, journal = {International journal of antimicrobial agents}, volume = {}, number = {}, pages = {107471}, doi = {10.1016/j.ijantimicag.2025.107471}, pmid = {39986398}, issn = {1872-7913}, abstract = {Intracellular microbes are actively present in various tumor types in low biomass and play a major role in metastasis. Eliminating intracellular microbes on a cellular level with precision remains a challenge. To address this issue, we designed a screening pipeline to characterize intracellular microbes and their interaction with host cells. We used host and microbial in-vitro lab based constant and reproducible model, host as (mammalian cancer HeLa) and microbial strain as (Escherichia coli 25922). To study the pharmacological impact on intracellular bacterial load, we used antibiotics (ampicillin, roxithromycin, ciprofloxacin) and chemotherapy drugs (doxorubicin and cisplatin) as external stimuli for both host and microbes. We found that increasing pharmacological stress does not increase microbial load inside the host cells. Eliminations of intracellular bacteria was done by using Permutation Orthogonal Arrays (POA), where we acquired optimal drug combination in particular sequence of drugs, which reduced 90-95% of intracellular microbial load. Proteomic analysis reveals that upon the invasion of Escherichia coli 25922, HeLa cells enriched ATP production pathways to activate intermediate filaments, which should be investigated closely via in-vivo models.}, }
@article {pmid39986317, year = {2025}, author = {Litchman, E}, title = {Climate change effects on the human gut microbiome: complex mechanisms and global inequities.}, journal = {The Lancet. Planetary health}, volume = {9}, number = {2}, pages = {e134-e144}, doi = {10.1016/S2542-5196(24)00332-2}, pmid = {39986317}, issn = {2542-5196}, mesh = {*Climate Change ; Humans ; *Gastrointestinal Microbiome/physiology ; Diet ; }, abstract = {Ongoing global climate change is affecting all aspects of life on Earth, including human health. The gut microbiota is an important determinant of health in humans and other organisms, but how climate change affects gut microbiota remains largely unexplored. In this Review, I discuss how the changing climate might affect gut microbiota by altering the quantity and quality of food, as well as environmental microbiomes, such as enteric pathogen pressure and host physiology. Climate change-induced variability in food supply, shifts in elemental and macromolecular composition of plant and animal food, the proliferation of enteric pathogens, and the direct effects of high temperatures on gut physiology might alter gut microbiota in undesirable ways, increasing the health burden of climate change. The importance of different pathways might depend on many geographical, economic, and ecological factors. Microbiomes of populations in low-income countries might be disproportionally affected through greater climate change effects and poor mitigation on diet, pathogen burden, and host physiology.}, }
@article {pmid39986292, year = {2025}, author = {Theodosiou, AA and Bogaert, D and Cleary, DW and Dale, AP and Gbesemete, DF and Guy, JM and Laver, JR and Raud, L and Jones, CE and Read, RC}, title = {Controlled human infection model of Neisseria lactamica in late pregnancy investigating mother-to-infant transmission in the UK: a single-arm pilot trial.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {100986}, doi = {10.1016/j.lanmic.2024.100986}, pmid = {39986292}, issn = {2666-5247}, abstract = {BACKGROUND: The infant respiratory microbiome is derived largely from the mother and is associated with downstream health and disease. Manipulating maternal respiratory flora peripartum to influence the infant microbiome has not previously been investigated. Neisseria lactamica is a harmless pharyngeal commensal that correlates inversely with Neisseria meningitidis carriage and disease. Intranasal N lactamica inoculation is a safe and well characterised controlled human infection model (CHIM) in non-pregnant healthy adults. We hypothesised that N lactamica inoculation in pregnancy induces mother-to-infant N lactamica transmission postnatally.<br><br>METHODS: In this single-arm trial, 21&#xa0;healthy pregnant female participants aged 18&#xa0;years or older were inoculated at 36-38&#xa0;weeks' gestation with 10[5] colony-forming units of N&#xa0;lactamica Y92-1009&#xa0;at University Hospital Southampton Clinical Research Facility, Southampton, UK. N&#xa0;lactamica selective culture, genome sequencing, and serological testing were performed on maternal and infant oral, nasopharyngeal, breastmilk, and serum samples over 15&#xa0;weeks postpartum. Seven female participants naturally colonised with N&#xa0;lactamica at baseline were followed up, but not inoculated. Oral samples were obtained from 12&#xa0;cohabiting siblings younger than 5&#xa0;years. The primary endpoint was infant N&#xa0;lactamica colonisation. This study was registered with ClinicalTrials.gov, NCT04784845, and is now complete.<br><br>FINDINGS: Between Oct 25, 2021, and March 7, 2022, 31&#xa0;adult female participants (median age 33&#xb7;5&#xa0;years [range&#xa0;23&#xb7;1-39&#xb7;9]; 26 [84%] were White, British) were screened and enrolled, of whom seven were already colonised with N&#xa0;lactamica. After exclusion of three participants, 21&#xa0;participants were inoculated, of whom 15 (71%) became N&#xa0;lactamica-colonised, and no sustained N&#xa0;lactamica Y92-1009&#xa0;transmission to their infants was observed. Conversely, non-Y92-1009 N&#xa0;lactamica strain sharing was observed in four (57%) of seven uninoculated mother-sibling pairs, and Moraxella catarrhalis strain sharing in nine (38%) of 24 mother-infant pairs completing the study. Anti-N&#xa0;lactamica serum IgG titres increased in seven (88%) of eight N&#xa0;lactamica Y92-1009-colonised female participants, but none of their infants (where paired sera were available). There were no serious adverse reactions to the inoculum.<br><br>INTERPRETATION: As the world's first perinatal CHIM, this trial demonstrates that this model in pregnancy is feasible, and that N&#xa0;lactamica Y92-1009&#xa0;can safely and efficiently colonise pregnant individuals. Lack&#xa0;of sustained mother-to-infant N&#xa0;lactamica transmission, despite evidence supporting mother-to-infant M&#xa0;catarrhalis and sibling-to-mother N&#xa0;lactamica transmission, challenges conventional perceptions of infants as passive recipients of maternal microbes, suggesting that respiratory commensal transmission is selective and microbe-specific.<br><br>FUNDING: Medical Research Council and National Institute for Health Research Southampton Biomedical Research Centre.}, }
@article {pmid39986164, year = {2025}, author = {Wang, S and Li, H and Jiao, Y and Li, L and Zhou, Q and Sun, H and Shao, Z and Wang, C and Jing, J and Gao, Z}, title = {Insight into the effect of electric fields on bioremediation of petroleum-contaminated soil: A micro-ecological response.}, journal = {Journal of environmental management}, volume = {377}, number = {}, pages = {124624}, doi = {10.1016/j.jenvman.2025.124624}, pmid = {39986164}, issn = {1095-8630}, abstract = {The voltage gradient plays a crucial role in the process of electro-bioremediation for petroleum-contaminated soil. However, the micro-ecological response mechanisms of relevance have been scarcely documented. This study compared petroleum degradation characteristics, soil physicochemical properties, and bacterial microbiome indicators under 0.5 V cm[-1], 1 V cm[-1], and 2 V cm[-1] conditions to elucidate the interaction mechanism among soil micro-ecological factors. The findings indicated that the treatment at 1 V cm[-1] resulted in the most effective synergistic enhancement of electrokinetics and bioremediation, yielding a peak petroleum degradation ratio of 43.54 ± 1.64% over 105 days. The improvement in biodegradation resulted from the direct stimulation of bio-metabolism by higher ratios of "window condition" (RWC, 0.5331) and the indirect sustenance of microbial physiological activity by favorable soil conditions. The 1 V cm[-1] voltage gradient either maintained or fostered the soil microbiome's response to the remediation system. The structural equation models (SEMs) demonstrated that variations in microbiome properties across different voltage gradients resulted from the influences of effective current intensity, soil pH, redox potential (Eh), dissolved organic carbon (DOC), and electrical conductivity (EC). Optimizing voltage gradients is a practical approach for developing effective micro-ecosystems to efficiently remediate petroleum-contaminated soil and implement electro-bioremediation in various engineering applications.}, }
@article {pmid39986157, year = {2025}, author = {Xu, L and Lin, Q and Wang, S and Chen, S and Yang, R and Liu, C and Hu, Q and Zhao, Z and Cao, Z}, title = {Efficacy of black soldier fly larvae in converting kitchen waste and the dynamic alterations of their gut microbiome.}, journal = {Journal of environmental management}, volume = {377}, number = {}, pages = {124613}, doi = {10.1016/j.jenvman.2025.124613}, pmid = {39986157}, issn = {1095-8630}, abstract = {The escalating demand for food, driven by population growth and improved living standards, has prompted the development of efficient and eco-friendly kitchen waste (KW) treatment technologies. This study focused on the feasibility of utilizing KW through the application of black soldier fly larvae (BSFL), with a specific interest in the dynamic changes in the intestinal bacterial community during the treatment process. After a 10-day KW processing period, BSFL gained an average of 0.84 g/hundred worms/day, achieving a conversion efficiency of 18.52% for KW. This demonstrated their capacity to efficiently utilize KW nutrients for good growth performance. Additionally, the bioconversion of KW by BSFL could markedly decrease the presence of potentially pathogenic bacteria in the feed matrix within one day (P < 0.001), including Escherichia coli, Shigella spp., Salmonella spp., and Staphylococcus aureus. Notably, the diversity of the intestinal bacterial community in BSFL increased with age and sustained KW consumption (P < 0.05), accompanied by enhanced stability. In particular, the average relative abundance of potential probiotic genera associated with nutrient absorption and antimicrobial compounds synthesis, including Fusobacterium, Phascolarctobacterium, Enterococcus, and Actinomyces, increased. Conversely, the prevalence of pathogenic genera like Morganella and Escherichia-Shigella, decreased. Co-occurrence network analysis identified Lactobacillus, Brevibacterium, Erythrobacter, and Enterobacteriaceae as keystone species. Despite their low abundance in the BSFL intestine, these species were potentially crucial for KW bioconversion. Our findings underscore the potential of BSFL for sustainable KW conversion, providing strong support for effective waste management strategies.}, }
@article {pmid39985639, year = {2025}, author = {Zhang, N and Tran, S and Moskatel, LS}, title = {The Gut Microbiome and Migraine: Updates in Understanding.}, journal = {Current neurology and neuroscience reports}, volume = {25}, number = {1}, pages = {20}, pmid = {39985639}, issn = {1534-6293}, mesh = {Humans ; *Migraine Disorders/microbiology ; *Gastrointestinal Microbiome/physiology ; Animals ; *Brain-Gut Axis/physiology ; Dysbiosis/microbiology ; Probiotics/therapeutic use ; }, abstract = {PURPOSE OF REVIEW: We provide an overview of the field of microbiome research, the current understanding of the microbiome-gut-brain axis, and the most recent updates on the interplay between migraine and the gut microbiome.<br><br>RECENT FINDINGS: Pre-clinical studies suggest that gut microbiota is required for normal pain sensation. There is also evidence in rodent models that there is potential application of food, herbal medicines, probiotics, and short chain fatty acids (SCFAs) as novel therapies for migraine. Evidence from human cohorts suggests that there is altered gut microbiota in people with migraine, and that the microbiome dysbiosis is from both compositional and functional aspects. Recent metagenome-wide association studies (MWAS) that employ Mendelian Randomization support the causal association between gut microbiota and migraine. The connection between migraine and the gut microbiome remains underexplored, but recent preclinical and clinical studies support the association between gut microbiota and the development of migraine.}, }
@article {pmid39985596, year = {2025}, author = {Chen, S and Chen, M and Han, Y and Chen, Z and Mu, X and He, C and Zhao, J and Zhang, L and Huang, Z}, title = {Analysis of microbial environment changes in wound healing of pressure ulcers in rats promoted by moist exposed burn ointment.}, journal = {Archives of dermatological research}, volume = {317}, number = {1}, pages = {451}, pmid = {39985596}, issn = {1432-069X}, support = {2022KJJH034//QingYuan Municipal Science and Technology Program, China/ ; 2020B1515120088//Natural Region Joint Fund, China/ ; }, mesh = {Animals ; *Pressure Ulcer/drug therapy/microbiology ; *Wound Healing/drug effects ; Rats ; Male ; *Disease Models, Animal ; *Rats, Sprague-Dawley ; *Microbiota/drug effects ; Burns/microbiology/drug therapy ; Skin/microbiology/pathology/drug effects ; RNA, Ribosomal, 16S/genetics ; Ointments/administration &amp; dosage ; Humans ; Sitosterols ; }, abstract = {This study explored the effects of Moist Exposed Burn Ointment (MEBO) on the healing process of pressure-induced wounds. Using a stage IV pressure ulcer model established in 42 rats, divided equally into a control gel group and an MEBO group, we investigated the efficacy of MEBO through topical application. The control group received Carbomer gel, while the MEBO group was treated with MEBO until complete wound healing. Results showed that MEBO significantly accelerated wound healing compared to the control group. Histological analysis, including hematoxylin and eosin (HE) staining and Masson's trichrome staining, revealed enhanced epithelialization and collagen deposition in the MEBO group. Furthermore, 16S rRNA sequencing indicated that MEBO reduced microbial diversity at the wound site and reshaped the microbial composition. Notably, The increased abundance of Acinetobacter and Staphylococcus, coupled with a reduction in Pseudomonas, may reflect a shift in the wound microbiome that could be conducive to healing. However, the exact role of these microbial shifts in promoting wound healing requires further investigation, as microbial dynamics in wound environments are complex and context-dependent. These findings suggest that MEBO facilitates wound healing by optimizing the wound microbiome, thereby offering a promising therapeutic approach for managing pressure ulcers.}, }
@article {pmid39985278, year = {2025}, author = {Hayes, C and Mitchell, A and Huerlimann, R and Jolly, J and Li, C and Booth, DJ and Ravasi, T and Nagelkerken, I}, title = {Stomach Microbiome Simplification of a Coral Reef Fish at Its Novel Cold-Range Edge Under Climate Change.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17704}, doi = {10.1111/mec.17704}, pmid = {39985278}, issn = {1365-294X}, support = {DP170101722//Australian Research Council/ ; OIST Kick-start fund//Okinawa Institute of Science and Technology Graduate University/ ; }, abstract = {Climate-driven range extensions of animals into higher latitudes are often facilitated by phenotypic plasticity. Modifications to habitat preference, behaviour and diet can increase the persistence of range-extending species in novel high-latitude ecosystems. These strategies may be influenced by changes in their gut and stomach microbial communities that are critical to host fitness and potentially adaptive plasticity. Yet, it remains unknown if the gut and stomach microbiome of range-extending species is plastic in their novel ranges to help facilitate these modifications. Here, we categorised stomach microbiome communities of a prevalent range-extending coral reef fish along a 2000-km latitudinal gradient in a global warming hotspot, extending from their tropical core range to their temperate cold range edge. At their cold range edge, the coral reef fish's stomach microbiome showed a 59% decrease in bacterial diversity and a 164% increase in the relative abundance of opportunistic bacteria (Vibrio) compared to their core range. Microbiome diversity was unaffected by fish body size, water temperature, physiology (cellular defence and damage) and habitat type (turf, barren, oyster, kelp and coral) across their range. The observed shifts in microbiome composition suggest dysbiosis and low plasticity of tropical range-extending fishes to novel environmental conditions (e.g., temperate prey and lower seawater temperature) at their novel range edges, which may increase their susceptibility to disease in temperate ecosystems. We conclude that fishes extending their ranges to higher latitudes under ocean warming can experience a simplification (i.e., reduced diversity) of their stomach microbiome, which could restrict their current rate of range extensions or establishment in temperate ecosystems.}, }
@article {pmid39985228, year = {2025}, author = {Song, MJ and Freund, F and Tribble, CM and Toffelmier, E and Miller, C and Bradley Shaffer, H and Li, FW and Rothfels, CJ}, title = {The nitrogen-fixing fern Azolla has a complex microbiome characterized by varying degrees of cophylogenetic signal.}, journal = {American journal of botany}, volume = {}, number = {}, pages = {e70010}, doi = {10.1002/ajb2.70010}, pmid = {39985228}, issn = {1537-2197}, support = {//California Conservation Genomics Project, with funding provided to the University of California by the State of California, State Budget Act of 2019 [UC Award ID RSI-19-690224]./ ; }, abstract = {PREMISE: Azolla is a genus of floating ferns that has closely evolved with a vertically transmitted obligate cyanobacterium endosymbiont-Anabaena azollae-that fixes nitrogen. There are also other lesser-known Azolla symbionts whose role and mode of transmission are unknown.<br><br>METHODS: We sequenced 112 Azolla specimens collected across the state of California and characterized their metagenomes to identify the common bacterial endosymbionts and assess their patterns of interaction.<br><br>RESULTS: Four genera were found across all samples, establishing that multiple Azolla endosymbionts were consistently present. We found varying degrees of cophylogenetic signal across these taxa as well as varying degrees of isolation by distance and of pseudogenation, which demonstrates that multiple processes underlie how this endosymbiotic community is constituted. We also characterized the entire Azolla leaf pocket microbiome.<br><br>CONCLUSIONS: These results show that the Azolla symbiotic community is complex and features members at potentially different stages of symbiosis evolution, further supporting the utility of the Azolla microcosm as a system for studying the evolution of symbioses.}, }
@article {pmid39985099, year = {2025}, author = {Peng, C and Li, X and Li, Y and Xu, X and Ouyang, Y and Li, N and Lu, N and Zhu, Y and He, C}, title = {Sex-specific effects of gastrointestinal microbiome disruptions on Helicobacter pylori-induced gastric carcinogenesis in INS-GAS mice.}, journal = {Biology of sex differences}, volume = {16}, number = {1}, pages = {15}, pmid = {39985099}, issn = {2042-6410}, support = {82260133//National Natural Science Foundation of China/ ; SKLF-KF-202406//open project program of State Key Laboratory of Food Science and Resources from Nanchang University/ ; }, mesh = {Animals ; Female ; Male ; *Helicobacter pylori ; *Helicobacter Infections/microbiology/pathology/complications ; *Gastrointestinal Microbiome ; *Stomach Neoplasms/microbiology/pathology ; *Sex Characteristics ; *Mice, Transgenic ; Carcinogenesis ; Insulin/metabolism/blood ; Gastrins/metabolism ; Mice ; Gastric Mucosa/microbiology/pathology/metabolism ; }, abstract = {BACKGROUND: Accumulating evidence indicates that the dysbiosis of gastrointestinal microbiota is associated with the development of gastric carcinogenesis. However, the sex-specific traits of gastrointestinal microbiota and their correlation with the sexually dimorphic response to gastric cancer remain poorly understood.<br><br>METHODS: Male and female transgenic FVB/N insulin-gastrin (INS-GAS) mice as a model of gastric cancer were randomly administered Brucella Broth or Helicobacter pylori (H. pylori). Stomachs were evaluated by histopathology. The gastric inflammation was examined by immunohistochemical and immunofluorescence staining. Gastric mucosal and fecal samples were collected for microbiota analysis using 16S rRNA gene sequencing.<br><br>RESULTS: Following H. pylori infection, male mice showed heightened inflammatory infiltration and notably greater intestinal metaplasia compared to female mice. The structure of gastrointestinal microbiota was different between male and female mice, with relative higher diversity in females than males. Notably, we found gender disparities in the alterations of gastric and intestinal microbiota in mice post H. pylori infection. While the enrichment of Bifidobacterium and Lachnospiraceae was observed in female mice, Escherichia_Shigella and Akkermansia were more abundant in males. Furthermore, the microbial profile was distinct in estrogen-deficient ovariectomized (OVX) mice, including the overgrowth of Akkermansia and the loss of Butyricicoccus. Infected OVX females developed significantly more severe gastric lesions, which was normalized through co-housing with intact females.<br><br>CONCLUSIONS: We have identified a novel microbiome-based mechanism that provides insight into the sexual dimorphism in the development of H. pylori-associated gastric cancer.}, }
@article {pmid39985070, year = {2025}, author = {Sulaimi, F and Ong, TSK and Tang, ASP and Quek, J and Pillay, RM and Low, DT and Lee, CKL and Siah, KTH and Ng, QX}, title = {Risk factors for developing irritable bowel syndrome: systematic umbrella review of reviews.}, journal = {BMC medicine}, volume = {23}, number = {1}, pages = {103}, pmid = {39985070}, issn = {1741-7015}, mesh = {*Irritable Bowel Syndrome/epidemiology/etiology ; Humans ; Risk Factors ; }, abstract = {BACKGROUND: Irritable bowel syndrome (IBS) is a debilitating disorder affecting 4-9% of the global population. It is a multifaceted disorder with complex and varied causes. This review aims to consolidate the evidence regarding IBS risk factors by examining existing systematic reviews and meta-analyses, covering potential genetic, immunological, psychological, and dietary causes.<br><br>METHODS: Systematic literature searches were conducted in MEDLINE, Embase and Cochrane library databases. Study selection and data extraction were conducted independently by four authors, with discrepancies resolved by consensus with a senior author. Systematic reviews examining risk factors of IBS development were eligible for review. Results were narratively synthesized. Quality of reviews were analysed using AMSTAR 2, and evidence were appraised using GRADE methodology.<br><br>RESULTS: A total of 69 systematic reviews were included in this study. Most reviews were of "critically low" quality, while the remaining were "low" quality. Common shortcomings included the absence of a list of excluded studies with justifications for their exclusion and inadequate consideration of the risk of bias in individual studies. Eight major categories of risk factors for IBS identified were as follows: dietary, genetic, environmental, psychological, gut microbiome, socio-economic, physiological, and pathological, albeit overlaps exist. The most frequently reported risk factors for IBS development were female gender and anxiety disorders, with overall GRADE evaluation of "low"; depression and gastroenteritis, with overall GRADE evaluation of "moderate".<br><br>CONCLUSIONS: Clinical practice should prioritize recognition of these risk factors. Future reviews should improve their reporting of results based on the PRISMA guidelines, to enhance the quality of research in this field.<br><br>PROTOCOL REGISTRATION: PROSPERO CRD42023493739.}, }
@article {pmid39984806, year = {2025}, author = {Langat, R and Chakrawarti, A and Klatt, NR}, title = {Cannabis Use in HIV: Impact on Inflammation, Immunity and the Microbiome.}, journal = {Current HIV/AIDS reports}, volume = {22}, number = {1}, pages = {19}, pmid = {39984806}, issn = {1548-3576}, mesh = {Humans ; *HIV Infections/immunology/drug therapy/microbiology ; *Gastrointestinal Microbiome/drug effects/immunology ; *Inflammation/immunology/drug therapy ; Dysbiosis/immunology/microbiology ; Cannabis ; }, abstract = {PURPOSE OF REVIEW: This review explores how cannabis impacts the gut microbiome, immune system, and ART outcomes in people with HIV (PWH). Given the increasing prevalence of cannabis use among PWH, we investigated its potential to reduce chronic inflammation and enhance gut health, both of which can influence HIV pathogenesis.<br><br>RECENT FINDINGS: Cannabis has immunomodulatory and anti-inflammatory effects, including reducing systemic inflammatory biomarkers (such as MCP-1 and IP-10) and improving gut barrier integrity through increased short-chain fatty acid (SCFA) production. Studies have shown that cannabis use is associated with increased gut mucosal immunity, decreased immune activation, and a unique microbiome composition. Preliminary evidence indicates that cannabis may influence HIV reservoirs, although the results remain inconclusive. Cannabis shows promise in managing inflammation, gut dysbiosis, and immune dysfunction in PWH. However, its effects on HIV reservoirs, adherence to antiretroviral therapy, and long-term outcomes need further investigation through rigorous clinical trials using standardized formulations.}, }
@article {pmid39984724, year = {2025}, author = {Willis, AD and Clausen, DS}, title = {Planning and describing a microbiome data analysis.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {39984724}, issn = {2058-5276}, support = {R35 GM133420/GM/NIGMS NIH HHS/United States ; }, }
@article {pmid39984410, year = {2025}, author = {Maubach, G and Kanthasamy, AK and Gogia, S and Naumann, M}, title = {The enigma of maladaptation in gastric pathophysiology.}, journal = {Trends in cancer}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.trecan.2025.01.014}, pmid = {39984410}, issn = {2405-8025}, abstract = {Despite a decline in global incidence, gastric cancer (GC) remains a major health concern. The development of GC is a sequential, multistage maladaptive process involving numerous different factors. Understanding the complexity of GC development is crucial for early detection, effective treatment, and, ultimately, prevention. In this respect, identifying the impact of risk factors contributing to the emergence or progression of GC, such as Helicobacter pylori infection, host and bacterial genetics, alcohol consumption, smoking, and preserved foods, will aid in combatting this disease. In this review, we focus on recent developments in understanding the role of the microbiome, dysfunctional molecular pathways, and immune evasion in gastric pathophysiology. We also highlight challenges and advances in treatment of GC.}, }
@article {pmid39984283, year = {2025}, author = {Adouane, E and Hubas, C and Leblanc, C and Lami, R and Prado, S}, title = {Multi-omics analysis of the correlation between surface microbiome and metabolome in Saccharina latissima (Laminariales, Phaeophyceae).}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiae160}, pmid = {39984283}, issn = {1574-6941}, abstract = {The microbiome of Saccharina latissima, an important brown macroalgal species in Europe, significantly influences its health, fitness, and pathogens resistance. Yet, comprehensive studies on the diversity and function of microbial communities (bacteria, eukaryotes, and fungi) associated with this species are lacking. Using metabarcoding, we investigated the epimicrobiota of S. latissima and correlated microbial diversity with metabolomic patterns (LC-MS/MS). Specific epibacterial and eukaryotic communities inhabit the S. latissima surface, alongside a core microbiota, while fungal communities show lower and more heterogeneous diversity. Metabolomic analysis revealed a large diversity of mass features, including putatively annotated fatty acids, amino derivatives, amino acids, and naphthofurans. Multiple-factor analysis linked microbial diversity with surface metabolome variations, driven mainly by fungi and bacteria. Two taxa groups were identified: one associated with bacterial consortia and the other with fungal consortia, each correlated with specific metabolites. This study demonstrated a core bacterial and eukaryotic microbiota associated with a core metabolome and highlighted interindividual variations. Annotating the surface metabolome using Natural Products databases suggested numerous metabolites potentially involved in inter-species chemical interactions. Our findings establish a link between microbial community structure and function, identifying two microbial consortia potentially involved in the chemical defense of S. latissima.}, }
@article {pmid39983982, year = {2025}, author = {Mukhatayev, Z and Kovenskiy, A and Ren, Z and Rangel, SM and Katkenov, N and Khuanbai, Y and Shivde, R and Daniel, M and Dellacecca, ER and Cedercreutz, K and Ostapchuk, Y and Nurgozhina, A and Chulenbayeva, L and Nurgaziyev, M and Jarmukhanov, Z and Nurlankyzy, M and Kozhdan, K and Seidulla, S and Mukhanbetzhanova, Z and Sergazy, S and Kozhakhmetov, S and Ali, Y and Daftary, KM and Green, SJ and Kundu, RV and Kushugulova, A and Le Poole, IC}, title = {Escherichia abundance and metabolism align with vitiligo disease activity.}, journal = {The Journal of investigative dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jid.2025.01.032}, pmid = {39983982}, issn = {1523-1747}, abstract = {Vitiligo is a cutaneous autoimmune disorder characterized by progressive depigmentation due to melanocyte destruction by cytotoxic T cells. Genetic factors predispose patients to the disease, supported by environmental factors often initiating new disease episodes. We questioned whether disease outcomes are partially defined by pathogenic microbes driving nutrient deficiencies and inflammation. Our study presents results from research on the diet and gut microbiome composition of vitiligo patients and healthy controls from Kazakhstan and the USA. Dietary nutrient intake was assessed using NIH-generated Diet History Questionnaires. Vitiligo patients with active disease exhibited limited intake of specific fatty acids, amino acids, and zinc. Disease activity was further characterized by an abundance of Odoribacter and Escherichia genera in the gut. Metabolic pathway analysis supported a role for the Escherichia genus in disease activity by limiting energy metabolism and amino acid biosynthetic pathways. Disease activity also aligned with elevated circulating pro-inflammatory cytokines. These findings suggest that nutritional limitations are not compensated by metabolites from the gut microbiome in active disease, potentially leaving room for inflammation and exacerbating vitiligo. The intricate relationship between diet, gut microbiome composition, and disease progression in vitiligo highlights potential avenues for targeted interventions to reduce autoimmune activity and improve patient outcomes.}, }
@article {pmid39983969, year = {2025}, author = {Xiang, ST and Qiu, J and Mao, Z and Pan, X and Ma, Y and Huang, R}, title = {Alterations of early-life gut microbiome in hospitalized infants with chemical pollutants exposure.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121187}, doi = {10.1016/j.envres.2025.121187}, pmid = {39983969}, issn = {1096-0953}, abstract = {Exposure to chemical pollutants and their effects on the gut microbiome during early life are scarce, especially the effects of mixed exposures. Plasma pollutants levels were measured using gas chromatography -triple quadrupole mass spectrometer (GC-MS/MS) among 304 infants in the neonatal ward at Hunan Children's hospital, China, and gut microbiota was derived from 16S rRNA sequencing. We assessed exposure and alpha diversity using generalized linear models, and variation in beta diversity (Bray-Curtis), taxa abundance (MaAsLin2), and employed Bayesian kernel machine regression (BKMR) to investigate the association of pollutants mixture with alpha diversity and taxa. PBDE-99 was positively associated with the Chao1 index (β=4.29, 95%CI:1.54,7.03). Exposure to the pesticides trifluralin, γ-BHC, and methidathion significantly affected beta diversity (all PFDR < 0.05). PBDE-100, β-BHC, phosalone, methiamitron, fenpropathrin, δ-BHC, and o,p'-DDT were associated with changes in taxa abundance, including negative associations [e.g., Staphylococcus, Bacteroides, Bifidobacterium, and Corynebacterium] and positive associations [e.g., Acinetobacter and Pseudomonas]. An interaction between o,p'-DDT and δ-BHC on Pseudomonas was also found in BKMR models. Our findings suggest that chemical pollutants are associated with gut microbiome changes in hospitalized infants, providing new insights into the mechanisms of chemical pollutants toxicity. Further validation is necessary to confirm these associations and explore their long-term health effects.}, }
@article {pmid39983937, year = {2025}, author = {Han, L and Liu, W and Yuan, F and Liu, Q and Cheng, H and Jin, X and Sun, Y}, title = {Integration of microbiomics and metabolomics reveals energy metabolism imbalance in crucian carp (Carassius auratus) under saline-alkaline exposure.}, journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP}, volume = {}, number = {}, pages = {110145}, doi = {10.1016/j.cbpc.2025.110145}, pmid = {39983937}, issn = {1532-0456}, abstract = {The ecological conditions of freshwater aquaculture are deteriorating by degrees in recent years. Consequently, the comprehensive utilization of saline-alkaline water has garnered increasing societal attention. Here, crucian carp (Carassius auratus) were exposed to 20, 40 mmol/L NaHCO3 for 30 days (T, F group). Metabolomic analyses were conducted using UPLC-QTOF/MS, complemented by biochemical and microbiology profiling to elucidate the damage of the saline environment to the intestinal microbial structure, which in turn interfered with the energy metabolism. It was observed that carbonate alkalinity (CA) exposure not only caused intestine oxidative stress but also changed the levels of several digestive enzymes, including α-amylase (AMS), chymotrypsin (CHY), lipase (LPS). Metabolomic analysis identified 22 different metabolites (DEMs) in T group and 77 DEMs in F group. MetaboAnalyst analysis indicated that these metabolites are primarily involved in energy-related pathways, including the citric acid cycle, galactose metabolism, and glycine, serine, and threonine metabolism. Intestinal microbial diversity and community composition were altered under carbonate alkalinity exposure, with increase in Proteobacteria abundance and decline in Firmicutes, abundance alongside enrichment of Sphingomonas. Herein, saline-alkaline stress disrupted the physiological homeostasis of the crucian carp intestine, leading to microbial dysbiosis and energy metabolic imbalance. This study provides a theoretical foundation for understanding the stress response of the crucian carp intestine and the role of the intestinal microbiome in host resilience under adverse environmental conditions.}, }
@article {pmid39983896, year = {2025}, author = {Yi, Q and Xiong, L}, title = {From sensory organs to internal pathways: A comprehensive review of amino acid sensing in Drosophila.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {}, number = {}, pages = {111828}, doi = {10.1016/j.cbpa.2025.111828}, pmid = {39983896}, issn = {1531-4332}, abstract = {Organisms require various nutrients to provide energy, support growth, and maintain metabolic balance. Amino acid is among the most basic nutrients, serving as fundamental building blocks for protein synthesis while playing vital roles in growth, development, and reproduction. Understanding the mechanisms by which organisms perceive amino acids is key to unraveling how they select appropriate food sources and adapt to environmental challenges. The fruit fly, Drosophila melanogaster, serves as a powerful model for understanding fundamental genetic and physiological processes. This review focuses on recent advances in amino acid sensing mechanisms in Drosophila melanogaster and their relevance to feeding behavior, nutrient homeostasis, and adaptive responses, and integrates insights into peripheral sensory systems, such as the legs and proboscis, as well as internal regulatory mechanisms within the gut, fat body, and brain. It highlights key molecular players, including ionotropic receptors, gut-derived hormones, neuropeptides, and the microbiome-gut-brain axis. Additionally, the manuscript identifies knowledge gaps and proposes directions for future research, providing a comprehensive overview of this dynamic field.}, }
@article {pmid39983850, year = {2025}, author = {Haarmann-Stemmann, T and Reichert, D and Coumoul, X and Lawrence, BP and Perdew, GH and Sherr, DH and Weighardt, H and Rolfes, KM and Esser, C}, title = {The Janus-facedness of the aryl hydrocarbon receptor pathway Report of the 6th International AHR Meeting: Research, Prevention, Therapy.}, journal = {Biochemical pharmacology}, volume = {}, number = {}, pages = {116808}, doi = {10.1016/j.bcp.2025.116808}, pmid = {39983850}, issn = {1873-2968}, abstract = {The ability to sense and process environmental cues is a fundamental aspect of an organism's biology. The evolutionary ancient transcription factor AHR (aryl hydrocarbon receptor) has evolved in animals to sense low molecular weight compounds derived from environmental exposure, dietary plants, the gut/skin microbiome, or generated endogenously from tryptophan upon ultraviolet light (UV) exposure or enzymatic catabolism. The binding of such molecules results in a cascade of events leading to the transcription of target genes. The AHR gene locus was first identified in mice in 1982. Since then, the beneficial and detrimental effects of AHR agonist-driven activation or lack thereof have been studied, particularly in relation to environmental chemical toxicity, carcinogenicity, or tissue homeostasis, e.g. barrier tissues. AHR ligands are also being considered as a potential new therapeutic class of molecules for the treatment of cancer, debilitating and chronic inflammatory diseases or metabolic disorders. A series of international meetings initiated twenty years ago have provided a comprehensive overview of AHR research. At the meeting in Düsseldorf in 2024, the identification of tailor-made ligands using modern, artificial intelligence (AI)-based approaches was a key topic of discussion, as were current attempts to resolve the dual nature of AHR activation - beneficial and harmful. While our understanding is still in its infancy, research was also presented that highlights previously unrecognized roles of the AHR in many diseases.}, }
@article {pmid39983848, year = {2025}, author = {Ford, D}, title = {Interactions between the intestinal microbiota and drug metabolism - Clinical implications and future opportunities.}, journal = {Biochemical pharmacology}, volume = {}, number = {}, pages = {116809}, doi = {10.1016/j.bcp.2025.116809}, pmid = {39983848}, issn = {1873-2968}, abstract = {The importance of the intestinal microbita in a multitude of physiological processes is well-evidenced. These include metabolism of nutrients and xenobiotics, biosynthesis of vitamin K and vitamin B12, immunomodulation, maintenance of the gut mucosal barrier integrity and protection against some pathogens. Interindividual differences in the intestinal microbiota composition have impacts on health. The bioavailability and activity of some pharmaceuticals are heavily influenced by interindividual variability in metabolism, which has a genetic basis. This variability, primarily occurring in the liver but also in the intestine, has been studied extensively. Despite the advancement of this field - pharmacogenetics - its integration into clinical practice remains limited for reasons discussed herein. This highlights the even greater challenge of applying emerging knowledge on variability in the gut microbiota to drug therapy. However, ignoring these opportunities would be a mistake. While clinical applications of microbiota-guided drug therapy are currently absent and the ideas in this article are largely theoretical, research is uncovering that in cases where a substantial portion of a drug or its metabolites reaches the colon, or where drugs are formulated for colonic delivery, the gut microbiota can significantly affect drug metabolism and activity. Greater focus should be placed on research into how interindividual variability in the intestinal microbiome can modify pharmaceutical bioavailability and activity. This article is deliberately speculative and exploratory but proposes that, though there are still no clinical examples of microbiome-guided drug therapy, these interactions could afford opportunities for improvements in personalised medicine and also for drug design.}, }
@article {pmid39983845, year = {2025}, author = {Sah, A and Singewald, N}, title = {The (neuro)inflammatory system in anxiety disorders and PTSD: Potential treatment targets.}, journal = {Pharmacology &amp; therapeutics}, volume = {}, number = {}, pages = {108825}, doi = {10.1016/j.pharmthera.2025.108825}, pmid = {39983845}, issn = {1879-016X}, abstract = {Targeting the immune system has recently garnered attention in the treatment of stress- associated psychiatric disorders resistant to existing pharmacotherapeutics. While such approaches have been studied in considerable detail in depression, the role of (neuro)inflammation in anxiety-related disorders, or in anxiety as an important transdiagnostic symptom, is much less clear. In this review we first critically review preclinical and clinical evidence of central and peripheral immune dysregulation in anxiety disorders and post-traumatic stress disorder (PTSD) and briefly discuss proposed mechanisms of how inflammation can affect anxiety-related symptoms. We then give an overview of existing and potential future targets in inflammation-associated signal transduction pathways and discuss effects of different immune-modulatory drugs in anxiety-related disorders. Finally, we discuss key gaps in current clinical trials such as the lack of prospective studies involving anxiety patient stratification strategies based on inflammatory biomarkers. Overall, although evidence is rather limited so far, there is data to indicate that increased (neuro)inflammation is present in subgroups of anxiety disorder patients. Although exact identification of such immune subtypes of anxiety disorders and PTSD is still challenging, these patients will likely particularly benefit from therapeutic targeting of aspects of the inflammatory system. Different anti-inflammatory treatment approaches (microglia-directed treatments, pro-inflammatory cytokine inhibitors, COX-inhibitors, phytochemicals and a number of novel anti-inflammatory agents) have indeed shown some efficacy even in non-stratified anxiety patient groups and appear promising as novel alternative or complimentary therapeutic options in specific ("inflammatory") subtypes of anxiety disorder and PTSD patients.}, }
@article {pmid39983749, year = {2025}, author = {Davido, B and Merrick, B and Kuijper, E and Benech, N and Biehl, LM and Corcione, S and , }, title = {How can the gut microbiome be targeted to fight multidrug-resistant organisms?.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101063}, doi = {10.1016/j.lanmic.2024.101063}, pmid = {39983749}, issn = {2666-5247}, abstract = {The rise of antimicrobial resistance presents a challenge to public health, undermines the efficacy of antibiotics, and compromises the management of infectious diseases. Gut colonisation by multidrug-resistant organisms, such as multidrug-resistant Enterobacterales and vancomycin-resistant enterococci, is associated with increased morbidity and mortality rates, as well as health-care costs. Of late, the role of the gut microbiome in combating colonisation by multidrug-resistant organisms, which could precede invasive infection, has garnered interest. Innovative interventions, including faecal microbiota transplantation, probiotics, phage therapy, and bacterial consortia, represent potential preventive or therapeutic options to counteract colonisation by multidrug-resistant organisms. In this Personal View, we have synthesised the current findings on these interventions and elucidated their potential as solutions to the crisis of antimicrobial resistance.}, }
@article {pmid39983440, year = {2025}, author = {Hong, MS and Lee, JS and Lee, MC and Lee, JS}, title = {Ecotoxicological effects of per- and polyfluoroalkyl substances in aquatic organisms: A review.}, journal = {Marine pollution bulletin}, volume = {214}, number = {}, pages = {117678}, doi = {10.1016/j.marpolbul.2025.117678}, pmid = {39983440}, issn = {1879-3363}, abstract = {Per- and polyfluoroalkyl substances (PFAS) are found throughout the environment due to their chemical stability. Their widespread use in industrial and consumer products has resulted in their frequent detection in aquatic environments, making them contaminants of significant concern. Recent studies focus on the adverse effects of PFAS on aquatic organisms in an effort to elucidate their toxic mechanisms and physiological changes. Here, we comprehensively review the major effects of PFAS on aquatic organisms, including general toxicity, metabolic disruption, and microbiome alterations, and explore how these changes affect biological function and ecosystem balance. In addition to toxic responses in aquatic organisms reported previously, PFAS disrupt metabolic pathways, causing abnormalities in carbohydrate metabolism, lipid homeostasis, and hormonal regulation. They also cause gut microbiome imbalances and reduce the prevalence of beneficial bacteria while promoting pathogen proliferation, which contributes to physiological dysfunction and damages liver and other organ tissues. Experimental evidence emphasizes the multifaceted threats PFAS pose to aquatic health and ecosystem stability and provide a crucial foundation for understanding their long-term impacts from both physiological and ecological perspectives.}, }
@article {pmid39983354, year = {2025}, author = {Esener, N}, title = {Exploring trends in reproductive system microbiome research in farm animals: A bibliometric approach.}, journal = {Research in veterinary science}, volume = {186}, number = {}, pages = {105583}, doi = {10.1016/j.rvsc.2025.105583}, pmid = {39983354}, issn = {1532-2661}, abstract = {This study presents a comprehensive bibliometric analysis of literature on the microbiome of reproductive systems in farm animals, utilizing data from the Web of Science (WoS) and Scopus databases. The primary aim was to evaluate the scientific content and bibliometric characteristics of articles published on the reproductive tract microbiome in farm animals. The advanced tool Bibliometrix was employed to explore bibliometric networks, providing insights into the scope of microbiome research within this field. Findings indicate that research in reproductive microbiomes is still emerging, with significant contributions from developed countries, particularly the United States, China, Brazil, and Spain. The field remains heavily focused on bovine studies, while substantial knowledge gaps persist regarding other livestock, including ovines, caprines, and camelids. One of the most notable advancements in this area has been the adoption of next-generation sequencing (NGS), which has shifted microbiome research away from labour-intensive, culture-based methods to culture-independent, high-throughput approaches. Although NGS has significantly facilitated the study of bacterial communities within reproductive systems, limited research has been conducted on fungal and viral microbiomes. This bacterial emphasis is partly due to the accessibility and cost of NGS technologies, which remain prohibitively high for many institutions in developing regions, thus limiting participation. Clustering analysis identified three main themes: genetic influences on pregnancy, microbial-reproductive health interactions, and male fertility with a focus on sperm quality. Additionally, emerging research topics were identified, including microbial species associated with reproductive diseases in livestock.}, }
@article {pmid39983320, year = {2025}, author = {Yu, D and Wang, T and Zhang, L and Gao, N and Huang, Y and Zhang, J and Yan, J}, title = {Identification of body fluid sources based on microbiome antibiotic resistance genes using high-throughput qPCR.}, journal = {Forensic science international. Genetics}, volume = {77}, number = {}, pages = {103241}, doi = {10.1016/j.fsigen.2025.103241}, pmid = {39983320}, issn = {1878-0326}, abstract = {Identifying the origin of body fluids is a critical step in forensic investigation. Recently, the development of high-throughput sequencing technology has led to the use of microbiomes for body fluid identification in forensic studies. However, high-throughput sequencing data are difficult to analyze, the sequencing protocol is complicated. An increasing number of studies have focused on antibiotic resistance genes (ARGs) in the human microbiome. The abundance and diversity of ARGs in different parts of the human body can be detected using quantitative polymerase chain reaction (qPCR). To date, no studies have inferred the sources of body fluids based on ARGs. Therefore, we attempted to use ARGs as a tool to infer the origin of body fluids. We assessed the abundance and diversity of 64 ARGs in blood, semen, saliva, vaginal secretions (VS), nasal secretions (NS), and fecal samples using high-throughput qPCR. The results showed that ARGs were more diverse in fecal samples, which was significantly higher than those of other sample types (P < 0.05). Principal coordinate analysis (PCoA) showed that the samples clustered mainly according to their type. We constructed a random forest classification model based on 64 ARGs with a prediction accuracy of 92.68 %. Next, we evaluated the importance of the features in the random forest model (mean decrease accuracy, MDA). Subsequently, we constructed prediction models for the top 40 and 20 ARGs after sorting genes with the highest MDA, and their prediction accuracies were both 92.68 %. The accuracy of the top 10 ARGs was 87.80 %. Notably, when only the top 10 characterized ARGs were used to construct models for saliva, semen, and VS samples, the prediction accuracy reached was 95.24 %. This shows that blood, semen, saliva, NS, VS, and fecal samples can be accurately identified using ARGs. Our results suggest that ARGs are promising markers for forensic body fluid identification.}, }
@article {pmid39983259, year = {2025}, author = {Lyte, JM and Jia, X and Caputi, V and Zhang, D and Daniels, KM and Phillips, GJ and Lyte, M}, title = {Heat stress in chickens induces temporal changes in the cecal microbiome concomitant with host enteric serotonin responses.}, journal = {Poultry science}, volume = {104}, number = {3}, pages = {104886}, doi = {10.1016/j.psj.2025.104886}, pmid = {39983259}, issn = {1525-3171}, abstract = {Heat stress is a potent modulator of the avian neuroendocrine system with concomitant impact on the gut microbiome. As an interkingdom signaling molecule, serotonin is largely derived from the gut and found in large concentrations in the avian gut lumen. Despite the role of serotonin in animal stress physiology and related host-microbe interactions, whether heat stress alters avian enteric concentrations of serotonin is unknown. As such, the present study sought to determine whether acute or chronic exposure to moderate heat stress alters both enteric serotonin concentrations and the microbiome in the chicken gut. Chickens were, or were not, subjected to an acute (1 day), repeated acute (2 days) or chronic (6 days) moderate ambient cyclic heat stress (12h per day, 31°C). Enteric concentrations of serotonin were significantly decreased in the acute heat stress group (P < 0.05), and rebounded to become elevated in the chronic heat stress group (P < 0.05). Shotgun metagenomic sequencing revealed heat stress caused both functional and taxonomic changes in the cecal microbiome. Abundances of bacterial taxa that are known to interact with the host via the serotonergic system, including Lactobacillus spp., and Bifidobacterium spp., were significantly (P < 0.05) altered by heat stress. As these findings demonstrate that heat stress can alter serotonin concentrations in the chicken intestinal tract, with distinct outcomes depending on duration of the stressor, serotonergic signaling may serve as potential leverageable point of intervention in host-microbe interactions including foodborne pathogen colonization in the chicken gut. In addition, this study provides novel insight into the impact of acute and chronic heat stress on the avian microbiome, and its relationship to stress-driven changes in the enteric serotonergic system.}, }
@article {pmid39982954, year = {2025}, author = {Aminu, K and Aladelusi, TO and Adisa, AO and Ezeagu, CN and Salami, AA and Nwafor, JN and Uwambaye, P and Amzat, J and Murererehe, J and Omoleke, SA and Abdulaziz, M and Jayasinghe, RD and Kanmodi, KK}, title = {Epidemiology, literacy, risk factors, and clinical status of oral cancer in East Africa: A scoping review.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0317217}, doi = {10.1371/journal.pone.0317217}, pmid = {39982954}, issn = {1932-6203}, mesh = {Humans ; *Mouth Neoplasms/epidemiology ; Africa, Eastern/epidemiology ; Risk Factors ; Health Literacy ; }, abstract = {BACKGROUND: Oral cancer (OC) is a topical public health issue in East Africa due to increasing incidence of the disease. Public health efforts to address the oral cancer burden depends largely on the available empirical evidence. Hence, this scoping review aims to map the existing empirical evidence on oral cancer in East African countries.<br><br>METHODS: The Preferred Reporting Items for Systematic Review and Meta-analysis Extension for Scoping Reviews (PRISMA-ScR) was used as a guideline for reporting this scoping review. Additionally, we ensured quality assessment of the methodology and reporting process of this study using the AMSTAR 2 checklist. We conducted a systematic search of nine research databases on 17th November 2023, and reviewed studies published in English from year 2000 to 17th November 2023. The team developed data extraction form and data extraction was done by two reviewers. Thematic analyses were conducted manually and presented in texts, tables and flow chart.<br><br>RESULTS: Only 30 full manuscripts were included in this review. Twenty-nine out of 30 studies were either hospital- or clinic-based while two were community-based. Only four studies showed gaps and obvious disparities in awareness and knowledge levels across East Africa, however, higher levels of awareness were reported among dentists and dental patients relative to the general population. Most neoplasms were presented and diagnosed late. The review finding also highlighted the significant impact of Toombak use on the oral microbiome composition, potentially contributing to oral cancer risks. Further, this review elucidated the prognostic relevance of PD-L1 expression at the invasive tumor front and microbial composition, with Candida correlating with adverse prognosis and Malassezia showing associations with improved survival rates. Also, Toombak usage, tumor staging, and mucosal field alterations emerged as predictors of local recurrence, while lymph node involvement and extranodal extension were associated with regional recurrence among Sudanese cohorts. Finally, a few studies undertook an evaluation of instrument validity for OC detection, revealing promising outcomes concerning diagnostic accuracy and instrument reliability.<br><br>CONCLUSIONS: There is a dire need for targeted interventions and early detection strategies tailored to the unique epidemiological and clinical profiles of oral and maxillofacial tumors in East Africa. Public health interventions aimed at curbing the prevalence of Toombak use and promoting healthier lifestyle choices to reduce the oral diseases incidence in Sudan and other regions where these behaviors are prevalent remain germane.}, }
@article {pmid39982577, year = {2025}, author = {Bhute, S and Sanders, JG and Song, SJ and Lavoie, S and Swafford, A and Guccione, C and Patel, L and Gonzalez, A and Rooks, MG and Knight, R and Bartko, A}, title = {ChIP provides 10-fold microbial DNA enrichment from tissue while minimizing bias.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {258}, pmid = {39982577}, issn = {1573-4978}, support = {NIH/NIGMS T32GM007198//University of California San Diego Medical Scientist Training Program/ ; }, mesh = {Animals ; Swine ; Humans ; *Chromatin Immunoprecipitation/methods ; *RNA, Ribosomal, 16S/genetics ; *DNA, Bacterial/genetics ; Microbiota/genetics ; Gastrointestinal Microbiome/genetics ; Bias ; }, abstract = {BACKGROUND: Host DNA depletion is a critical tool for accessing the microbiomes of samples that have a small amount of microbial DNA contained in a high host background. Of critical practical importance is the ability to identify microbial DNA sequences in frozen tissue specimens. Here, we compare four existing commercial methods and two newly introduced methods involving chromatin immunoprecipitation (ChIP) on frozen human and pig intestinal biopsies.<br><br>RESULTS: We find that all methods that rely on differential lysis of host and microbial cells introduce substantial biases as assessed by 16&#xa0;S rRNA gene amplicon profiling. However, ChIP enables 10-fold enrichment of microbial DNA while introducing less bias, sufficient to make assessment possible against background, in both pigs and humans.<br><br>CONCLUSIONS: We recommend ChIP in situations where host depletion is important but where minimizing taxonomic bias is essential, and the MolYsis or Zymo kit for situations where host depletion level is more important than taxonomic bias.<br><br>CONCLUSIONS: We recommend ChIP in situations where host depletion is important but where minimizing taxonomic bias is essential, and the MolYsis or Zymo kit for situations where host depletion level is more important than taxonomic bias.}, }
@article {pmid39982433, year = {2025}, author = {Xie, QY and Granato, A and Wong, A and Yau, C and Noseworthy, R and Chen, T and Gianetto-Hill, C and Allen-Vercoe, E and Guidos, CJ and Hamilton, JK and Danska, JS}, title = {Metabolic dysfunction associated with alterations in gut microbiota in adolescents with obesity.}, journal = {Diabetes}, volume = {}, number = {}, pages = {}, doi = {10.2337/db24-0866}, pmid = {39982433}, issn = {1939-327X}, abstract = {Obesity in childhood is associated with adulthood obesity, type 2 diabetes (T2D), and future metabolic complications. The gut microbiome is a modifier of host metabolic function with altered bacterial composition associated with disease risk. Few studies have investigated the relationships between metabolic disease, inflammation and the gut microbiota in youth where these connections likely originate. Here we characterized the gut microbiome of a cohort of 56 non-diabetic adolescents with obesity using fecal DNA sequencing with absolute bacterial quantitation together with immune and metabolic profiling. We observed multi-log order variation in absolute bacterial biomass dependent on host environment and associated with bacterial taxonomic composition based on a nested case-control comparison. Participants with higher biomass displayed a healthier phenotype with higher gut microbiome diversity, lower abundance of taxa associated with inflammation and pathogenicity such as Escherichia Coli, and lower levels of neutrophil activities. Further association analysis revealed sex-dependent variation, with higher levels of insulin resistance, fasting triglycerides, and markers of neutrophil activities in male adolescents with lower bacterial biomass. Together these results suggest that intestinal bacterial biomass and composition are associated with metabolic and inflammatory dysregulation evident before T2D diagnosis and identify sex differences in microbiome-associated metabolic dysfunction in adolescents with obesity.}, }
@article {pmid39982394, year = {2025}, author = {Gong, E and Fulop, DJ and Serebrenik, J and Labiner, AJ and Cohen, DJ and Sigel, KM and Lucas, AL}, title = {Antibiotic treatment and survival in patients with resected, early-stage pancreatic ductal adenocarcinoma receiving chemotherapy.}, journal = {JNCI cancer spectrum}, volume = {}, number = {}, pages = {}, doi = {10.1093/jncics/pkaf024}, pmid = {39982394}, issn = {2515-5091}, abstract = {BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is a clinically challenging malignancy, largely due to chemoresistance. Bacteria within the PDAC microbiome may mediate chemoresistance, suggesting that alteration of the microbiome with antibiotics could improve chemotherapy response.<br><br>METHODS: We utilized the SEER-Medicare database to select patients with resected, early-stage PDAC diagnosed between 2007 and 2017. The primary outcome of this study was overall survival (OS). Receipt of antibiotic treatment within one month after adjuvant chemotherapy initiation was determined from Medicare claims data. Propensity scores (PSs) were used to match patients who received antibiotics with patients who did not receive antibiotics. The Kaplan-Meier method was used to calculate 5-year OS rates, and cox regression analysis was used to assess association between receiving antibiotics and OS. All hypotheses were 2-sided.<br><br>RESULTS: Of the 712 patients with resected, early-stage PDAC, 629 (88.3%) were treated with adjuvant gemcitabine and 177 (24.9%) received antibiotics in the one month following chemotherapy initiation. The mean (SD) age at diagnosis was 73.7 (5.1) years and patients were mostly women, White, and from metropolitan areas in the northeastern or western US. A total of 143&#x2009;PS-matched pairs were evaluated. Among patients treated with gemcitabine, antibiotic treatment was associated with a 37% improvement in OS and a 30% improvement in cancer-specific survival.<br><br>CONCLUSIONS: Antibiotic treatment in the one month following adjuvant gemcitabine initiation was associated with improved survival. These findings provide additional support for the hypothesis that antibiotic treatment may alter the pancreatic microbiome in a manner that reduces chemoresistance, potentially improving PDAC outcomes.}, }
@article {pmid39982320, year = {2025}, author = {Kiouri, DP and Batsis, GC and Chasapis, CT}, title = {Structure-Based Deep Learning Framework for Modeling Human-Gut Bacterial Protein Interactions.}, journal = {Proteomes}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/proteomes13010010}, pmid = {39982320}, issn = {2227-7382}, abstract = {Background: The interaction network between the human host proteins and the proteins of the gut bacteria is essential for the establishment of human health, and its dysregulation directly contributes to disease development. Despite its great importance, experimental data on protein-protein interactions (PPIs) between these species are sparse due to experimental limitations. Methods: This study presents a deep learning-based framework for predicting PPIs between human and gut bacterial proteins using structural data. The framework leverages graph-based protein representations and variational autoencoders (VAEs) to extract structural embeddings from protein graphs, which are then fused through a Bi-directional Cross-Attention module to predict interactions. The model addresses common challenges in PPI datasets, such as class imbalance, using focal loss to emphasize harder-to-classify samples. Results: The results demonstrated that this framework exhibits robust performance, with high precision and recall across validation and test datasets, underscoring its generalizability. By incorporating proteoforms in the analysis, the model accounts for the structural complexity within proteomes, making predictions biologically relevant. Conclusions: These findings offer a scalable tool for investigating the interactions between the host and the gut microbiota, potentially yielding new treatment targets and diagnostics for disorders linked to the microbiome.}, }
@article {pmid39982073, year = {2025}, author = {McPherson, JK and Hurdle, JG and Baker, ML and Hussain, T and Kumar, A and Garey, KW}, title = {The microbiome-restorative potential of ibezapolstat for the treatment of Clostridioides difficile infection is predicted through variant PolC-type DNA polymerase III in Lachnospiraceae and Oscillospiraceae.}, journal = {Antimicrobial agents and chemotherapy}, volume = {}, number = {}, pages = {e0167924}, doi = {10.1128/aac.01679-24}, pmid = {39982073}, issn = {1098-6596}, abstract = {Ibezapolstat (IBZ), a first-in-class antibiotic targeting the PolC-type DNA polymerase III alpha-subunit (PolC) in low G + C bacteria, is in clinical development for the treatment of Clostridioides difficile infection (CDI). In the phase 2 trials, IBZ had potent activity against C. difficile while sparing or causing regrowth of Lachnospiraceae, Oscillospiraceae, and Erysipelotrichales, common commensal low G + C bacteria. The purpose of this study was to utilize in silico approaches to better interpret the narrower than expected IBZ spectrum of activity. IBZ susceptibility to human commensal microbiota was predicted using genomic analysis and PolC phylogenetic tree construction in relation to C. difficile and commensal low G + C bacteria. Protein structure prediction was performed using AlphaFold2 and binding pocket homology modeling was performed using Schrodinger Maestro and UCSF ChimeraX. An amino acid phylogenetic tree identified certain residues that were phylogenetically variant in Lachnospiraceae, Oscillospiraceae, and Erysipelotrichales and conserved in C. difficile. Chemical modeling showed that these residues ablated key PolC•IBZ predicted interactions including two lysine "gates" (CdiPolCLys1148 and CdiPolCLys1327) that "latch" onto the compound; an "anchoring" interaction (CdiPolCThr1331) to the central moiety; and a stabilized set of C. difficile sensitizer residues (CdiPolCThr1291 and CdiPolCLys1292) that resulted in the prolonged inhibition of a catalytic residue (CdiPolCAsp1090). The observed IBZ sparing of Lachnospiraceae, Oscillospiraceae, and Erysipelotrichaceae/Coprobacillaceae was predicted using in silico techniques. Further studies that confirm a PolC structural basis for the IBZ narrower than expected activity are needed to confirm these in silico phylogenetic and chemical modeling data.}, }
@article {pmid39982054, year = {2025}, author = {Chou, M-Y and Patil, AT and Huo, D and Lei, Q and Kao-Kniffin, J and Koch, P}, title = {Fungicide use intensity influences the soil microbiome and links to fungal disease suppressiveness in amenity turfgrass.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0177124}, doi = {10.1128/aem.01771-24}, pmid = {39982054}, issn = {1098-5336}, abstract = {UNLABELLED: Disease-suppressive soils have been documented in many economically important crops, but not in turfgrass, one of the most intensively managed plant systems in the United States. Dollar spot, caused by the fungus Clarireedia jacksonii, is the most economically important disease of managed turfgrass and has historically been controlled through the intensive use of fungicides. However, previous anecdotal observations of lower dollar spot severity on golf courses with less intensive fungicide histories suggest that intensive fungicide usage may suppress microbial antagonism of pathogen activity. This study explored the suppressive activity of transplanted microbiomes against dollar spot from seven locations in the Midwestern U.S. and seven locations in the Northeastern U.S. with varying fungicide use histories. Creeping bentgrass was established in pots containing homogenized sterile potting mix and field soil and inoculated with C. jacksonii upon maturity. Bacterial and fungal communities of root-associated soil and phyllosphere were profiled with short-amplicon sequencing to investigate the microbial community associated with disease suppression. The results showed that plants grown in the transplanted soil microbiome collected from sites with lower fungicide intensities exhibited reduced disease severity. Plant growth-promoting and pathogen-antagonistic microbes may be responsible for disease suppression, but further validation is required. Additional least squares regression analysis of the fungicides used at each location suggested that contact fungicides such as chlorothalonil and fluazinam had a greater influence on the microbiome disease suppressiveness than penetrant fungicides. Potential organisms antagonistic to Clarireedia were identified in the subsequent amplicon sequencing analysis, but further characterization and validation are required.<br><br>IMPORTANCE: Given the current reliance on fungicides for plant disease control, this research provides new insights into the potential non-target effects of repeated fungicide usage on disease-suppressive soils. It also indicates that intensive fungicide usage can decrease the activity of beneficial soil microbes and lead to a more disease conducive microbial environment in turfgrass. The results from this study can be used to identify more sustainable disease management strategies for a variety of economically important and intensively managed pathosystems. Understanding the factors that facilitate disease-suppressive soils will contribute to more sustainable plant protection practices.}, }
@article {pmid39981843, year = {2025}, author = {Zeng, Q and Hu, HW and Ge, AH and Xiong, C and Zhai, CC and Duan, GL and Han, LL and Huang, SY and Zhang, LM}, title = {Plant-microbiome interactions and their impacts on plant adaptation to climate change.}, journal = {Journal of integrative plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jipb.13863}, pmid = {39981843}, issn = {1744-7909}, support = {42277289//National Natural Science Foundation of China/ ; 42207142//National Natural Science Foundation of China/ ; 2023YFD1700801//National Key Research and Development Program of China/ ; }, abstract = {Plants have co-evolved with a wide range of microbial communities over hundreds of millions of years, this has drastically influenced their adaptation to biotic and abiotic stress. The rapid development of multi-omics approaches has greatly improved our understanding of the diversity, composition, and functions of plant microbiomes, but how global climate change affects the assembly of plant microbiomes and their roles in regulating host plant adaptation to changing environmental conditions is not fully known. In this review, we summarize recent advancements in the community assembly of plant microbiomes, and their responses to climate change factors such as elevated CO2 levels, warming, and drought. We further delineate the research trends and hotspots in plant-microbiome interactions in the context of climate change, and summarize the key mechanisms by which plant microbiomes influence plant adaptation to the changing climate. We propose that future research is urgently needed to unravel the impact of key plant genes and signal molecules modulated by climate change on microbial communities, to elucidate the evolutionary response of plant-microbe interactions at the community level, and to engineer synthetic microbial communities to mitigate the effects of climate change on plant fitness.}, }
@article {pmid39981802, year = {2025}, author = {Bartlett, A and Blakeley-Ruiz, JA and Richie, T and Theriot, CM and Kleiner, M}, title = {Large Quantities of Bacterial DNA and Protein in Common Dietary Protein Source Used in Microbiome Studies.}, journal = {Proteomics}, volume = {}, number = {}, pages = {e202400149}, doi = {10.1002/pmic.202400149}, pmid = {39981802}, issn = {1615-9861}, support = {593607//Foundation for Food and Agriculture Research/ ; R35GM138362//National Institute of General Medical Sciences of the National Institutes of Health/ ; }, abstract = {Diet has been shown to greatly impact the intestinal microbiota. To understand the role of individual dietary components, defined diets with purified components are frequently used in diet-microbiota studies. Defined diets frequently use purified casein as the protein source. Previous work indicated that casein contains microbial DNA potentially impacting results of microbiome studies. Other diet-based microbially derived molecules that may impact microbiome measurements, such as proteins detected by metaproteomics, have not been determined for casein. Additionally, other protein sources used in microbiome studies have not been characterized for their microbial content. We used metagenomics and metaproteomics to identify and quantify microbial DNA and protein in a casein-based defined diet to better understand potential impacts on metagenomic and metaproteomic microbiome studies. We further tested six additional defined diets with purified protein sources with an integrated metagenomic-metaproteomic approach and found that contaminating microbial protein is unique to casein within the tested set as microbial protein was not identified in diets with other protein sources. We also illustrate the contribution of diet-derived microbial protein in diet-microbiota studies by metaproteomic analysis of stool samples from germ-free mice (GF) and mice with a conventional microbiota (CV) following consumption of diets with casein and non-casein protein. This study highlights a potentially confounding factor in diet-microbiota studies that must be considered through evaluation of the diet itself within a given study.}, }
@article {pmid39981727, year = {2025}, author = {Fahad, M and Tariq, L and Li, W and Wu, L}, title = {MicroRNA gatekeepers: Orchestrating rhizospheric dynamics.}, journal = {Journal of integrative plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jipb.13860}, pmid = {39981727}, issn = {1744-7909}, support = {LZ25C130007//the Natural Science Foundation of Zhejiang Province/ ; 2022KJCX48//the Sanya Science and Technology Innovation Program/ ; 2021C02064-6//Zhejiang Major Scientific and Technological Project of Agricultural (Upland crop) Breeding/ ; 32370341 and 32441002//National Natural Science Foundation of China/ ; }, abstract = {The rhizosphere plays a crucial role in plant growth and resilience to biotic and abiotic stresses, highlighting the complex communication between plants and their dynamic rhizosphere environment. Plants produce a wide range of signaling molecules that facilitate communication with various rhizosphere factors, yet our understanding of these mechanisms remains elusive. In addition to protein-coding genes, increasing evidence underscores the critical role of microRNAs (miRNAs), a class of non-coding single-stranded RNA molecules, in regulating plant growth, development, and responses to rhizosphere stresses under diverse biotic and abiotic factors. In this review, we explore the crosstalk between miRNAs and their target mRNAs, which influence the development of key plant structures shaped by the belowground environment. Moving forward, more focused studies are needed to clarify the functions and expression patterns of miRNAs, to uncover the common regulatory mechanisms that mediate plant tolerance to rhizosphere dynamics. Beyond that, we propose that using artificial miRNAs and manipulating the expression of miRNAs and their targets through overexpression or knockout/knockdown approaches could effectively investigate their roles in plant responses to rhizosphere stresses, offering significant potential for advancing crop engineering.}, }
@article {pmid39981313, year = {2025}, author = {Arghavani, S and Chorfi, Y and Segura, M and Lesaux, AA and Costa, MC}, title = {Impact of Saccharomyces cerevisiae on the intestinal microbiota of dogs with antibiotic-induced dysbiosis.}, journal = {Frontiers in veterinary science}, volume = {12}, number = {}, pages = {1462287}, pmid = {39981313}, issn = {2297-1769}, abstract = {INTRODUCTION: The gut microbiota plays an important role in the health of dogs, but treatment with antibiotics causes marked dysbiosis. The objectives of this study were to evaluate the impact of yeast probiotic Saccharomyces cerevisiae supplementation on the fecal microbiota of dogs and its potential to prevent dysbiosis induced by antibiotics.<br><br>METHODS: Twenty healthy adult dogs were divided into a control and a yeast probiotic group receiving 1g/kg of S. cerevisiae (Actisaf[&#xae;], Phileo by Lesaffre, Marcq-en-Bar&#x153;ul, France) daily from D0 to D31. Both groups were given oral metronidazole from D11 to D17. Fecal swabs were collected on D0, 3, 11, 17, 20, 24, and 31 for microbiota analysis and blood on D0 and D24 for measurements of cytokines and cortisol.<br><br>RESULTS AND DISCUSSION: At D0, two distinct microbiota profiles comprised of dogs from both groups, control and probiotic, were identified. One profile had higher abundances of species related to stress and inflammation, and the other comprised species associated with good intestinal health. After three days of supplementation with yeast probiotic S. cerevisiae, all five dogs from the probiotic group having a stress-related microbiota (membership) shifted to a healthy microbiota. Metronidazole markedly changed the microbiota of both groups (p <0.001). Still, treated dogs had significantly different microbiota on D17 (end of antibiotics treatment). The dysbiosis was resolved in both groups by D24. TNF-&#x3b1; remarkably decreased from D0 to D24 (p = 0.002) in the probiotic group, which also had lower levels than controls on D24 (p = 0.040). There were no significant differences in the other measured cytokines. It was concluded that the use of yeast probiotic S. cerevisiae positively shifted the microbiota composition of healthy adult dogs carrying an abnormal microbial profile and that it has the potential to attenuate the dysbiosis caused by oral metronidazole.}, }
@article {pmid39981239, year = {2025}, author = {Timmermans, S and Wallaeys, C and De Beul, S and Garcia-Gonzales, N and Libert, C}, title = {Detection of chimeric alpha-defensin transcripts and peptides in mouse Paneth cells.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1543059}, pmid = {39981239}, issn = {1664-3224}, mesh = {Animals ; *Paneth Cells/metabolism/immunology ; *alpha-Defensins/genetics/metabolism ; Mice ; RNA, Messenger/genetics/metabolism ; Proteomics/methods ; }, abstract = {INTRODUCTION: In mammals, Paneth cells, located in the crypts of the small intestine, produceantimicrobial peptides that serve to keep the intestinal microbiome under control. a-Defensins are the primary antimicrobial peptides produced by these cells.<br><br>METHODS: We used 148 publicly available bulk RNA-seq samples on purified PCs, proteomics on enriched purified PC proteins and Defa peptide activity assays to detect all Defa transcrips, including potential chimeric transcrips.<br><br>RESULTS: We identified 28 expressed Defa genes in mice, with up to 85% of Paneth cell RNA reads mapping to these genes. Chimeric mRNAs, involving sequences from two different Defa genes, were detected in most experiments. Despite their low abundance (less than 0.3%), mass spectrometry confirmed the presence of chimeric peptides. Synthetic versions of these peptides demonstrated antibacterial activity against multiple bacterial species.<br><br>CONCLUSION: We show the existence of chimeric Defa transcripts and peptides in mice that are biologically active. We propose a possible stochatic mechanism or that the activation of the UPR patway may play a role in their production.}, }
@article {pmid39981114, year = {2025}, author = {Zhu, L and Liang, Y and Yang, L and Yang, Q and Yin, J and Wang, T and Xu, X and Zhang, Q}, title = {Helicobacter mastomyrinus infection induces autoimmune hepatitis in mice.}, journal = {Journal of translational autoimmunity}, volume = {10}, number = {}, pages = {100275}, pmid = {39981114}, issn = {2589-9090}, abstract = {BACKGROUND: Autoimmune hepatitis (AIH) is a chronic progressive liver disease caused by the immune system mistakenly attacking its own hepatocytes. The role of the gut microbiome in the pathogenesis and progression of AIH is of considerable significance. However, the dearth of suitable animal models has significantly constrained advancements in the pathogenesis and the development of therapeutic strategies for AIH. Helicobacter mastomyrinus (H. mastomyrinus, Hm) is a potentially zoonotic pathogenic microorganism capable of causing diseases of the enterohepatic system in rodent laboratory animals. Nevertheless, research on its role and mechanisms in causing liver disease is severely limited.<br><br>METHODS: In this study, male BALB/c mice were infected with Hm isolate Hm-17, and were sacrificed at 4 w, 8 w, 14 w and 22 w after infection, respectively. The serum was collected for detecting a number of AIH indicators, including the aminotransferases level, IgG content and autoantibody level. Additionally, the liver tissue was examined for pathological analysis, fibrosis, bacterial content, and the distribution of immune cells.<br><br>RESULTS: It was observed that the infection initially caused focal necrotizing hepatitis and subsequently progressed to interface hepatitis with lymphocyte/plasma cell infiltration, as well as hypergammaglobulinemia and autoantibody reactions, predominantly to Anti-nuclear and anti-smooth muscle antibodies. Furthermore, as the infection persisted, the mice exhibited a progressive increase in liver fibrosis and mild steatosis. Despite the maintenance of a low level of Hm colonization in the liver, there was a notable infiltrate of macrophages, T and B lymphocytes. In particular, the inflammatory foci in the Hm-infected liver were highly enriched for IL17[+] cells.<br><br>CONCLUSION: The present study provides an animal model of immunological liver injury induced by Hm infection that exhibits main characteristics similar to those observed in AIH-1 patients. This model may serve as a novel animal model for the study of the pathogenesis and potential therapeutic strategies for human AIH.}, }
@article {pmid39981106, year = {2024}, author = {Musyoki, VM and Mureithi, M and Heikinheimo, A and Maleche-Obimbo, E and Kithinji, D and Musau, S and Njaanake, K and Anzala, O}, title = {Effect of hyperglycemia on lung microbiota and treatment outcome in pulmonary tuberculosis: A scoping review.}, journal = {F1000Research}, volume = {13}, number = {}, pages = {1543}, pmid = {39981106}, issn = {2046-1402}, mesh = {Humans ; *Tuberculosis, Pulmonary/microbiology/immunology/drug therapy ; *Hyperglycemia/microbiology/immunology ; *Lung/microbiology/immunology ; *Microbiota ; Treatment Outcome ; Cytokines/blood ; }, abstract = {The comorbidity due to pulmonary tuberculosis (TB) and diabetes mellitus (DM) is a global health problem, but its mechanism remains unclear. It is suspected that hyperglycemic alteration of the immune response to TB and the composition of the lung microbiota play an important role. This scoping review aimed to contribute to the understanding of the mechanisms by mapping evidence on the effect of hyperglycemia on physical health indicators, immune cell counts, cytokine levels, and the composition of lung microbiota in patients with the DM-TB comorbidity. A systematic search for research articles about the relationship between hyperglycemia and physical health, immune cells, and cytokine levels in humans was conducted in MEDLINE, Scopus, and CINAHL Plus. Then, articles on the interactions between the immune cells, cytokines, and lung microbiota were identified through Google Scholar and Google search engines. Characteristics of the studies focusing on effects of hyperglycemia, the findings of the articles relevant to the research objectives, and strengths and weaknesses of the selected articles were charted in a data extraction tool. Twenty-one articles on the effects of hyperglycemia on immune mediators and health outcomes of patients with DM-TB were included. The evidence showed hyperglycemia to be associated with unfavorable treatment outcomes; altered counts and functioning of dendritic cells, monocytes, and CD4+ T cells; and changes in cytokine levels (mainly INF-γ, IL-17, IL-1β, IL-2, IL-6, IL-10, and TNF-α) in patients with DM-TB. The composition of the lung microbiota changed in correlation with changes in physical health outcomes, counts of immune cells, and cytokine levels. Thus, hyperglycemia, immune responses, and dysbiosis of the lung microbiota are integral in the pathogenesis of DM-TB and TB treatment outcomes. A prospective cohort study, especially in individuals with newly diagnosed DM versus known DM and concomitant latent TB versus active TB, is recommended to define causal relationships.}, }
@article {pmid39981100, year = {2025}, author = {Xiao, Z and Liu, S and Li, Z and Cui, J and Wang, H and Wang, Z and Ren, Q and Xia, L and Wang, Z and Li, Y}, title = {Corrigendum: The maternal microbiome programs the m[6]A epitranscriptome of the mouse fetal brain and intestine.}, journal = {Frontiers in cell and developmental biology}, volume = {13}, number = {}, pages = {1553431}, doi = {10.3389/fcell.2025.1553431}, pmid = {39981100}, issn = {2296-634X}, abstract = {[This corrects the article DOI: 10.3389/fcell.2022.882994.].}, }
@article {pmid39980568, year = {2025}, author = {Davis, T and Decker, KT and Hosseini, D and Jameson, G and Borazanci, E}, title = {Skin microbiome differences in pancreatic adenocarcinoma, other cancers, and healthy controls: a pilot study.}, journal = {Frontiers in oncology}, volume = {15}, number = {}, pages = {1495500}, pmid = {39980568}, issn = {2234-943X}, abstract = {INTRODUCTION: Many studies have reported the importance of the human microbiome in relationship to the overall health of its host. While recent studies have explored the microbiome's role in various types of cancer compared to healthy patients, this pilot study is the first to investigate differences in the skin microbiome composition among pancreatic adenocarcinoma patients, individuals with other cancers, and cancer-free controls.<br><br>METHODS: The study characterizes the skin microbiome's potential associations with cancer status by analyzing skin swabs from the forehead and cheek of 58 participants using Next Generation Sequencing (NGS), differential abundance analysis, and machine learning techniques.<br><br>RESULTS: The study results indicated that the cancer group displayed a significantly higher mean alpha diversity compared to the control group. Additionally, a machine learning classification model achieved a mean F1 Score of 0.943 in predicting cancer status, indicating measurable differentiation in the skin microbiome between the study groups. This differentiation is supported by differential abundance methods, including ANCOM-BC and MaAsLin2.<br><br>DISCUSSION: This pilot study suggests that skin microbiome profiling could serve as a non-invasive biomarker for cancer detection and monitoring, which warrants a larger, longitudinal study to validate these results.}, }
@article {pmid39980340, year = {2025}, author = {Byrd, DA and Gomez, M and Hogue, S and Wan, Y and Ortega-Villa, A and Warner, A and Dagnall, C and Jones, K and Hicks, B and Albert, P and Murphy, G and Sinha, R and Vogtmann, E}, title = {Effects of high-fiber, high-fruit and high-vegetable, low-fat dietary intervention on the rectal tissue microbiome.}, journal = {Journal of the National Cancer Institute}, volume = {}, number = {}, pages = {}, doi = {10.1093/jnci/djaf034}, pmid = {39980340}, issn = {1460-2105}, abstract = {BACKGROUND: Emerging evidence suggests that bacteria residing in colorectal tissue are plausibly associated with colorectal cancer (CRC). Prior studies investigated the effects of dietary interventions on the fecal microbiome, but few assessed colorectal tissue microbiome endpoints. We investigated the effects of a high-fiber, high-fruit and -vegetable, low-fat dietary intervention on the rectal tissue microbiome in the Polyp Prevention Trial (PPT).<br><br>METHODS: PPT is a 4-year randomized clinical trial with intervention goals of consuming: 1) &#x2265; 18&#x2009;g of fiber per 1,000&#x2009;kcal/day; 2) &#x2265;3.5 servings of fruits and vegetables per 1,000&#x2009;kcal/day; and 3) <20% of kcal/day from fat. Using 16S rRNA gene sequencing, we characterized bacteria in rectal biopsies collected at baseline and the end of years 1 and 4 (N&#x2009;=&#x2009;233 in intervention arm and N&#x2009;=&#x2009;222 in control arm). We estimated effects of the intervention on alpha/beta diversity and relative abundance of a priori-selected bacteria using repeated-measures linear mixed-effects models.<br><br>RESULTS: The intervention did not statistically significantly modify rectal tissue alpha diversity. Compared to the control arm, relative abundance of a priori-selected Porphyromonas (absolute intervention effects [standard errors] at T1 vs T0=-0.24 [0.07] and T4 vs T0=-0.12 [0.07]; P&#x2009;=&#x2009;.004) and Prevotella (absolute intervention effects at T1 vs T0=-0.40 [0.14] and at T4 vs T0=-0.32 [0.15]; P&#x2009;=&#x2009;.01) were more strongly decreased in the intervention arm.<br><br>CONCLUSION: The PPT intervention did not influence rectal tissue microbiome diversity nor the relative abundance of most bacteria, except for two oral-originating bacteria that were previously associated with CRC presence.<br><br>NCT00339625.}, }
@article {pmid39980334, year = {2025}, author = {Martinez-Medina, JN and Ghazisaeedi, F and Kramer, C and Ziegler, JF and McParland, V and Mönch, PW and Siegmund, B and Jarquín-Díaz, VH and Fulde, M and Forslund-Startceva, SK}, title = {Mucosal washes are useful for sampling intestinal mucus-associated microbiota despite low biomass.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2464296}, doi = {10.1080/19490976.2025.2464296}, pmid = {39980334}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; Humans ; *Intestinal Mucosa/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/isolation &amp; purification/genetics ; *DNA, Bacterial/genetics ; Mice, Inbred C57BL ; Male ; Biomass ; Female ; Ileum/microbiology ; Feces/microbiology ; Biopsy ; Mucus/microbiology ; Specimen Handling/methods ; }, abstract = {Understanding the dynamic relationship between mucus-associated microbiota and host health is critical. However, studies predominantly using stool samples may not accurately represent these bacterial communities. Here, we investigated the mucus-associated microbiota in the gastrointestinal tract of mice and the terminal ileum of humans using different sample types: mucosal washes, brushes, scrapings, and intestinal contents in mice and biopsies, brushes and mucosal washes in humans. We used DNA quantification and 16S rRNA amplicon sequencing to evaluate the comparability of the information yielded from the different sample types under a controlled benchmark. In mice, mucosal washes and brushes had comparative bacterial DNA and host DNA contamination than scraping samples. Similarly, in humans, washes outperformed biopsies in bacterial DNA content. Read counts and microbiota alpha diversity remained remarkably similar in mice and between brushes and washes in humans. The composition of the microbiota varied based on the subsegment and sample type in mice and sample type in humans. We conclude that washes and brushes reduce host contamination without inducing substantial compositional bias when sampling mucosal microbiota. Our findings suggest that mucosal washes and brushes are a viable alternative to biopsies in humans and scrapings in mice, thereby improving the transferability of results across hosts. Our study highlights the importance of focusing on mucus-associated microbiota to better capture host-microbiome interactions at their closer interface.}, }
@article {pmid39980264, year = {2025}, author = {Huang, X and Liu, J and Luo, H and Zou, W}, title = {Research progress on the diversity, physiological and functional characteristics of lactic acid bacteria in the Nongxiangxing baijiu microbiome.}, journal = {Journal of food science}, volume = {90}, number = {2}, pages = {e70082}, doi = {10.1111/1750-3841.70082}, pmid = {39980264}, issn = {1750-3841}, support = {2023NSFSC0184//Sichuan Science and Technology Program/ ; NJ2023-07//Liquor Making Biological Technology and Application of key laboratory of Sichuan Province/ ; }, mesh = {*Fermentation ; *Lactobacillales/physiology/metabolism ; *Microbiota/physiology ; Lactic Acid/metabolism ; Food Microbiology ; Taste ; Flavoring Agents/metabolism ; }, abstract = {Nongxiangxing baijiu (NXXB) is one of the main types of Chinese Baijiu. Its unique flavor is formed during fermentation by the combined action of various microorganisms, with lactic acid bacteria (LAB) making a great contribution. Lactate fermentation produces the precursors of key flavor compounds, such as lactic acid, acetic acid, and other flavor compounds, which combine to produce the unique sensory characteristics of NXXB. This review focuses on the diversity of LAB species and their physiological and metabolic characteristics. These characteristics include key species involved at different fermentation stages, metabolite biosynthesis, acid-tolerance mechanisms, interactions with yeasts, and factors influencing LAB community composition. It also discusses current challenges and future research directions for LAB in relation to NXXB production, aiming to advance understanding and potential future applications of these bacteria.}, }
@article {pmid39980076, year = {2025}, author = {Huang, P and Xiao, Y and He, Y}, title = {The causal relationships between gut microbiota and venous thromboembolism: a Mendelian randomization study.}, journal = {Hereditas}, volume = {162}, number = {1}, pages = {25}, pmid = {39980076}, issn = {1601-5223}, support = {2023A04J2143//Guangzhou Basic and Applied Basic Research Foundation/ ; 82203678//the National Natural Science Foundation of China/ ; }, mesh = {*Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics ; Humans ; *Venous Thromboembolism/genetics/microbiology/epidemiology ; *Polymorphism, Single Nucleotide ; *Genome-Wide Association Study ; }, abstract = {BACKGROUND: Venous thromboembolism (VTE) is still one of the most severe health issues, increasing mortality and lengthening hospital stays. Different abundances of gut microbiota have been clinically linked to VTE and coagulopathy. However, whether gut microbiota affected VTE formation remained uncertain.<br><br>METHODS: The causative links between VTE and 211 gut microbiota at phylum, class, order, family and genus level were separately investigated using two-sample Mendelian Randomization (MR) analysis. Firstly, single nucleotide polymorphisms (SNPs) locus-wide significantly (P&#x2009;<&#x2009;1.0&#x2009;&#xd7;&#x2009;10[-&#x2009;5]) related with gut microbiome abundance were extracted from large genome-wide analysis (GWAS) meta-analysis summary data. Instrumental variables (IVs) without pleiotropy were selected using the PhenoScanner and MR PRESSO test. Then, the MR analysis was implemented using the inverse variance weighted (IVW) method. Moreover, weighted median method, MR Egger method, simple median method and MR PRESSO were conducted to validate the causal associations. The reliability of the results was also assessed utilizing various sensitivity analyses, reverse MR analysis and multivariate Mendelian Randomization analysis (MVMR).<br><br>RESULTS: We found the phylum Firmicutes was robustly protective against VTE with MR analysis. Moreover, five taxa of Actinobacteria phylum (Bifidobacteriales order, Actinomycetales order, Bifidobacteriaceae family, Actinomycetaceae family, Slackia genus) and two taxa of Firmicutes phylum (Bacillales order, Lachnospiraceae UCG-010 genus) were suggestively protective for VTE. While three taxa of Firmicutes phylum (Bacilli class, Lactobacillales order and Lactococcus genus) might suggestively increase the risk of VTE. Sensitivity analyses indicated no significant horizontal pleiotropy, heterogeneity, or reverse causal associations. Furthermore, MVMR analysis unveiled independently positive causal association of Firmicutes phylum and Lachnospiraceae UCG-010 genus with risk of VTE.<br><br>CONCLUSION: Two taxa of gut microbes (Firmicutes phylum and Lachnospiraceae UCG-010 genus) were independently protective against VTE, which suggests a potential avenue for developing new cost-effective strategies with minor side effects for VTE prevention and treatment.}, }
@article {pmid39979818, year = {2025}, author = {Li, W and Yang, J}, title = {Investigating the Anna Karenina principle of the breast microbiome.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {81}, pmid = {39979818}, issn = {1471-2180}, support = {202203021222244//Basic Research Program of Shanxi Province/ ; TYSGJ202201//Critical Talent Workstation Project/ ; 202105AC160030//Top Experts training Project for the Academy and Technology in Yunnan province/ ; XDYC-MY-2022-0005//Famous doctor project of Xingdian talent plan in Yunnan province/ ; 202201AY070001-232//The Scientific Research Fund of Yunnan province of China, Kunming Medical University Joint Research Project/ ; 2024EKKFKT-03//Neonatal Key Specialty of Yunnan province/ ; L-2024015//Yunnan health training project of high level talents/ ; }, mesh = {Humans ; *Microbiota ; Female ; *Mastitis/microbiology/veterinary ; *Milk, Human/microbiology/chemistry ; *Bacteria/classification/isolation &amp; purification/genetics ; *Breast/microbiology ; Breast Neoplasms/microbiology ; RNA, Ribosomal, 16S/genetics ; Adult ; }, abstract = {The relationship between the microbiome and disease has long been a central focus of research in human microbiome. Inspired by Leo Tolstoy's dictum, the Anna Karenina Principle (AKP) offers a framework for understanding the complex dynamics of microbial communities in response to perturbations, suggesting that dysbiotic individuals exhibit greater variability/heterogeneity in their microbiome compared to healthy counterparts. While some studies have proved the alignment of microbiome responses to disease with the AKP effect, it remains uncertain whether the human breast microbiome responds similarly to breast disease. This study used beta-diversity and similarity in Hill numbers, along with shared species analysis (SSA), to explore this issue. We observed that during mastitis, changes in both the taxa richness and composition in the breast milk microbiome align with the AKP effect, while alterations in abundant taxa exhibit an anti-AKP effect. The response of breast tissue microbiome to breast cancer differs from that of milk microbiome to mastitis. Breast cancer induce anti-AKP effects in taxa richness, and non-AKP effects in common taxa and taxa composition. Overall, our findings identified different responses to breast diseases across taxa abundance in the breast microbiome. Mastitis primarily involves increasing the heterogeneity of rare taxa in the breast milk microbiome, while breast cancer associates with decreased dispersion of rare taxa in the tissue microbiome.}, }
@article {pmid39979617, year = {2025}, author = {Ohlsson, C and Lawenius, L and Jiang, Y and Horkeby, K and Wu, J and Nilsson, KH and Koskela, A and Tuukkanen, J and Movérare-Skrtic, S and Henning, P and Sjögren, K}, title = {The beneficial effects of a probiotic mix on bone and lean mass are dependent on the diet in female mice.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {6182}, doi = {10.1038/s41598-025-91056-2}, pmid = {39979617}, issn = {2045-2322}, mesh = {Animals ; Female ; *Probiotics/pharmacology/administration &amp; dosage ; Mice ; *Bone Density/drug effects ; Diet, High-Fat/adverse effects ; Bone and Bones/drug effects ; Mice, Inbred C57BL ; Ovariectomy ; Gastrointestinal Microbiome/drug effects ; Diet ; }, abstract = {Bone mass and lean mass decrease with age and these changes are associated with increased fracture risk and sarcopenia. Previous studies demonstrated that a probiotic mixture of Lacticaseibacillus paracasei DSM13434, Lactiplantibacillus plantarum DSM 15312 and DSM 15313 (L. Mix) prevents bone loss in ovariectomized (ovx) female mice. The purpose of the present study is to test if the beneficial effect of L. Mix is modified by the diet. Female mice were fed either a high-fat (HFD, 60% kcal from fat) or a low-fat (LFD, 10% kcal from fat) diet and subjected to either sham or ovx surgery and treated with L. Mix for 12 weeks. L. Mix treatment increased total body bone mineral density (p ≤ 0.01), by increasing cortical bone area, and total body lean mass (p = 0.035) in mice on LFD but not in mice on HFD. Metagenome sequencing of cecal content showed that L. Mix treatment increased the relative abundance of Lacticaseibacillus paracasei and, Lactiplantibacillus plantarum, demonstrating successful treatment. In addition, the probiotic treatment affected the overall gut microbiota composition and functionality. These findings demonstrate that the L. Mix in combination with a healthy diet is beneficial for musculoskeletal health in female mice.}, }
@article {pmid39979613, year = {2025}, author = {Mi, Y and Chen, L and Liao, N and Wan, M}, title = {Mendelian randomization analysis revealed a gut microbiota-eye axis in acute anterior uveitis.}, journal = {Eye (London, England)}, volume = {}, number = {}, pages = {}, pmid = {39979613}, issn = {1476-5454}, support = {Y20210997//Wenzhou Municipal Science and Technology Bureau (Wenzhou Municipal Sci - Tech Bureau)/ ; }, abstract = {BACKGROUND: Observational studies suggest that gut microbiome (GM) may contribute to acute anterior uveitis (AAU) development, but causality remains unclear. This study was conducted to test whether specific GM taxa were causally associated with AAU.<br><br>METHODS: The GM data were obtained from the DMP, which included 7738 individuals' faecal samples and an analysis of host genotype-taxa abundance associations. The AAU data were derived from the FinnGen Consortium (8624 cases and 473,095 controls). We primarily employed the inverse-variance weighted method, complemented by supplementary sensitivity analyses.<br><br>RESULTS: Higher abundance of Lachnospiraceae noname (OR&#x2009;=&#x2009;0.86, 95% CI 0.81-0.91, P&#x2009;=&#x2009;5.7 &#xd7; 10[-8]), Alistipes finegoldii (OR&#x2009;=&#x2009;0.87, 95% CI 0.78-0.96, P&#x2009;=&#x2009;0.008), Erysipelotrichaceae (OR&#x2009;=&#x2009;0.90, 95% CI 0.81-0.99, P&#x2009;=&#x2009;0.037), Erysipelotrichia (OR&#x2009;=&#x2009;0.90, 95% CI 0.81-0.99, P&#x2009;=&#x2009;0.037), Erysipelotrichales (OR&#x2009;=&#x2009;0.90, 95% CI 0.81-0.99, P&#x2009;=&#x2009;0.037), and Bacteroides ovatus (OR&#x2009;=&#x2009;0.93, 95% CI 0.87-1.00, P&#x2009;=&#x2009;0.039) predicted a lower AAU risk. Conversely, higher abundance of Bifidobacterium catenulatum (OR&#x2009;=&#x2009;1.06, 95% CI: 1.02-1.10, P&#x2009;=&#x2009;0.005), Bacteroides coprocola (OR&#x2009;=&#x2009;1.11, 95% CI: 1.02-1.21, P&#x2009;=&#x2009;0.014), Parabacteroides unclassified (OR&#x2009;=&#x2009;1.12, 95% CI 1.03-1.22, P&#x2009;=&#x2009;0.010), and Prevotella (OR&#x2009;=&#x2009;1.15, 95% CI: 1.01-1.29, P&#x2009;=&#x2009;0.029) predicted a higher AAU risk. The results also showed a reverse causation from AAU to Bifidobacterium catenulatum (OR&#x2009;=&#x2009;1.39, 95% CI: 1.03-1.86, P&#x2009;=&#x2009;0.005).<br><br>CONCLUSION: This study suggests that specific GM is causally associated with AAU risk, warranting more mechanistic validation and clinical trials.}, }
@article {pmid39979448, year = {2025}, author = {Wu, Z and Gong, C and Wang, B}, title = {The relationship between dietary index for gut microbiota and diabetes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {6234}, pmid = {39979448}, issn = {2045-2322}, support = {ZR2022LZY011//Shandong Provincial Natural Science Foundation Innovation and Development Joint Fund/ ; GZY-KJS-SD-2023-046//Science and Technology Department of the State Administration of Traditional Chinese Medicine/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Diet ; Adult ; *Nutrition Surveys ; *Diabetes Mellitus/epidemiology/microbiology ; Risk Factors ; Aged ; Logistic Models ; }, abstract = {This study aims to explore the relationship between the Dietary Index for Gut Microbiota (DI-GM) and diabetes. In recent years, there has been increasing attention to the role of the gut microbiome in regulating host metabolism. However, the relationship between DI-GM and the risk of diabetes has not been sufficiently studied. This study utilized relevant data from the National Health and Nutrition Examination Survey (NHANES) 2007-2018. Multiple logistic regression analysis was conducted to explore the relationship between DI-GM and the risk of diabetes. The dose-response relationship between DI-GM and the risk of diabetes was observed using restricted cubic splines (RCS). Threshold effect analysis was performed based on RCS results. Subgroup analyses were used to conduct a sensitivity analysis of the relationship between DI-GM and the risk of diabetes. The results from multiple logistic regression analysis indicated a significant negative correlation between DI-GM and the risk of diabetes (OR, 0.954, 95%CI, 0.918-0.991). RCS results also showed a significant nonlinear negative relationship between DI-GM and the risk of diabetes (P < 0.001, P for nonlinear = 0.010). The threshold effect analysis revealed that when DI-GM was below 6.191, there was a significant negative correlation between DI-GM and the risk of diabetes (OR, 0.921, 95% CI, 0.876-0.969). However, when DI-GM exceeded 6.191, the relationship between DI-GM and the risk of diabetes was no longer significant. Subgroup analysis revealed that the negative correlation between DI-GM and the risk of diabetes remained significant in Whites, participants with a poverty-income ratio > 3.5, body mass index > 24, current drinkers, never or current smokers, and those without chronic kidney disease (P < 0.05). This study demonstrates a nonlinear negative correlation between DI-GM and the risk of diabetes. Maintaining DI-GM above 6.191 may help prevent diabetes.}, }
@article {pmid39979394, year = {2025}, author = {Grenda, A and Iwan, E and Kuźnar-Kamińska, B and Bomba, A and Bielińska, K and Krawczyk, P and Chmielewska, I and Frąk, M and Szczyrek, M and Rolska-Kopińska, A and Jankowski, T and Kieszko, R and Milanowski, J}, title = {Gut microbial predictors of first-line immunotherapy efficacy in advanced NSCLC patients.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {6139}, pmid = {39979394}, issn = {2045-2322}, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/therapy/microbiology/drug therapy/pathology ; *Gastrointestinal Microbiome ; Male ; Female ; *Lung Neoplasms/therapy/drug therapy/microbiology/pathology ; Middle Aged ; Aged ; *Immunotherapy/methods ; RNA, Ribosomal, 16S/genetics ; Adult ; Treatment Outcome ; Feces/microbiology ; Progression-Free Survival ; Immune Checkpoint Inhibitors/therapeutic use ; Aged, 80 and over ; Bacteria/genetics/classification ; }, abstract = {The composition of the gut microbiome of patients with advanced non-small cell lung cancer is currently considered a factor influencing the effectiveness of treatment with immune checkpoint inhibitors. We aimed to evaluate the baseline gut microbiome composition in patients before receiving first-line immunotherapy alone or combined with chemoimmunotherapy. We performed 16S rRNA sequencing based on hypervariable regions. Stool samples were collected from 52 patients with advanced NSCLC treated with immunotherapy or chemoimmunotherapy before treatment. We found that the Ruminococcaceae family, species Alistipes sp. genus Eubacterium ventriosum group and genus Marvinbryantia may be intestinal, microbiological predictors of response to treatment. Genus Akkermansia and species from the [Clostridum] leptum group predicted the length of PFS (progression-free survival). Longer OS (overall survival) is associated with bacteria from the Ruminococcaceae family genera [Eubacterium] ventriosum group, Marvinbryantia, Colidextribacter and species [Clostridum] leptum. Bacteria that have an adverse effect (shortening of PFS or OS) on the response to treatment using immune checkpoint inhibitors are Rothia genus, Streptococus salivarius, Streptococus, Family XIII AD3011 group and Family XIII AD3011 group, s. uncultured bacterium. The composition of intestinal flora can be a predictive factor for immunotherapy in NSCLC patients. Specific bacteria can be positively or negatively associated with response to treatment, progression-free survival, and overall survival. They can be potentially used as predictive markers in NSCLC patients treated with immunotherapy.}, }
@article {pmid39979340, year = {2025}, author = {Di Costanzo, F and Di Marsico, M and Orefice, I and Kristoffersen, JB and Kasapidis, P and Chaumier, T and Ambrosino, L and Miralto, M and Aiese Cigliano, R and Verret, F and Tirichine, L and Trindade, M and Van Zyl, L and Di Dato, V and Romano, G}, title = {High-quality genome assembly and annotation of Thalassiosira rotula (synonym of Thalassiosira gravida).}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {310}, pmid = {39979340}, issn = {2052-4463}, mesh = {*Diatoms/genetics ; Genome ; Molecular Sequence Annotation ; DNA Methylation ; Transcriptome ; DNA Transposable Elements ; Metagenome ; }, abstract = {Diatoms are unicellular eukaryotic microorganisms thriving in most aquatic environments thanks to the expression of biosynthetic pathways for secondary metabolites involved in defence and adaptation to environmental changes. The sequencing of the transcriptome of the cosmopolitan diatom Thalassiosira rotula Meunier 1910 (synonym of Thalassiosira gravida Cleve 1896) and of the metagenome of its associated microbiome revealed the presence of biosynthetic pathways synthesising molecules and compounds useful for the algae survival and with potential biotechnological applications. Here we present the genome of a Neapolitan T. rotula strain, which is 672 Mbp in size due to a high proportion of repetitive elements (63.59%) and segmental duplications (14%), while the number of predicted genes resulted to be comparable to that of smaller diatom genomes. DNA methylation was predominantly located in transposable elements.}, }
@article {pmid39979293, year = {2025}, author = {Hoeferlin, GF and Grabinski, SE and Druschel, LN and Duncan, JL and Burkhart, G and Weagraff, GR and Lee, AH and Hong, C and Bambroo, M and Olivares, H and Bajwa, T and Coleman, J and Li, L and Memberg, W and Sweet, J and Hamedani, HA and Acharya, AP and Hernandez-Reynoso, AG and Donskey, C and Jaskiw, G and Ricky Chan, E and Shoffstall, AJ and Bolu Ajiboye, A and von Recum, HA and Zhang, L and Capadona, JR}, title = {Bacteria invade the brain following intracortical microelectrode implantation, inducing gut-brain axis disruption and contributing to reduced microelectrode performance.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1829}, pmid = {39979293}, issn = {2041-1723}, mesh = {Animals ; *Microelectrodes ; Mice ; *Electrodes, Implanted/adverse effects ; *Brain-Computer Interfaces ; *Brain ; *Blood-Brain Barrier ; *Mice, Inbred C57BL ; Gastrointestinal Microbiome ; Male ; Brain-Gut Axis/physiology ; Bacteria ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Brain-machine interface performance can be affected by neuroinflammatory responses due to blood-brain barrier (BBB) damage following intracortical microelectrode implantation. Recent findings suggest that certain gut bacterial constituents might enter the brain through damaged BBB. Therefore, we hypothesized that damage to the BBB caused by microelectrode implantation could facilitate microbiome entry into the brain. In our study, we found bacterial sequences, including gut-related ones, in the brains of mice with implanted microelectrodes. These sequences changed over time. Mice treated with antibiotics showed a reduced presence of these bacteria and had a different inflammatory response, which temporarily improved microelectrode recording performance. However, long-term antibiotic use worsened performance and disrupted neurodegenerative pathways. Many bacterial sequences found were not present in the gut or in unimplanted brains. Together, the current study established a paradigm-shifting mechanism that may contribute to chronic intracortical microelectrode recording performance and affect overall brain health following intracortical microelectrode implantation.}, }
@article {pmid39979287, year = {2025}, author = {Tsenkova, M and Brauer, M and Pozdeev, VI and Kasakin, M and Busi, SB and Schmoetten, M and Cheung, D and Meyers, M and Rodriguez, F and Gaigneaux, A and Koncina, E and Gilson, C and Schlicker, L and Herebian, D and Schmitz, M and de Nies, L and Mayatepek, E and Haan, S and de Beaufort, C and Cramer, T and Meiser, J and Linster, CL and Wilmes, P and Letellier, E}, title = {Ketogenic diet suppresses colorectal cancer through the gut microbiome long chain fatty acid stearate.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1792}, pmid = {39979287}, issn = {2041-1723}, mesh = {*Gastrointestinal Microbiome ; Animals ; *Diet, Ketogenic ; *Colorectal Neoplasms/microbiology/diet therapy/pathology/metabolism ; Mice ; Humans ; Stearic Acids/metabolism ; Male ; Cell Line, Tumor ; Mice, Inbred C57BL ; Female ; Disease Models, Animal ; Apoptosis ; Stearates ; }, abstract = {Colorectal cancer (CRC) patients have been shown to possess an altered gut microbiome. Diet is a well-established modulator of the microbiome, and thus, dietary interventions might have a beneficial effect on CRC. An attenuating effect of the ketogenic diet (KD) on CRC cell growth has been previously observed, however the role of the gut microbiome in driving this effect remains unknown. Here, we describe a reduced colonic tumor burden upon KD consumption in a CRC mouse model with a humanized microbiome. Importantly, we demonstrate a causal relationship through microbiome transplantation into germ-free mice, whereby alterations in the gut microbiota were maintained in the absence of continued selective pressure from the KD. Specifically, we identify a shift toward bacterial species that produce stearic acid in ketogenic conditions, whereas consumers were depleted, resulting in elevated levels of free stearate in the gut lumen. This microbial product demonstrates tumor-suppressing properties by inducing apoptosis in cancer cells and decreasing colonic Th17 immune cell populations. Taken together, the beneficial effects of the KD are mediated through alterations in the gut microbiome, including, among others, increased stearic acid production, which in turn significantly reduces intestinal tumor growth.}, }
@article {pmid39896483, year = {2025}, author = {Gray, SM and Wood, MC and Mulkeen, SC and Ahmed, S and Thaker, SD and Chen, B and Sander, WR and Bibeva, V and Zhang, X and Yang, J and Herzog, JW and Zhang, S and Dogan, B and Simpson, KW and Balfour Sartor, R and Montrose, DC}, title = {Dietary protein source mediates colitis pathogenesis through bacterial modulation of bile acids.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39896483}, issn = {2692-8205}, abstract = {Evidence-based dietary recommendations for individuals with inflammatory bowel diseases (IBD) are limited. Red meat consumption is associated with increased IBD incidence and relapse in patients, suggesting that switching to a plant-based diet may limit gut inflammation. However, the mechanisms underlying the differential effects of these diets remain poorly understood. Feeding diets containing plant- or animal-derived proteins to murine colitis models revealed that mice given a beef protein (BP) diet exhibited the most severe colitis, while mice fed pea protein (PP) developed mild inflammation. The colitis-promoting effects of BP were microbially-mediated as determined by bacterial elimination or depletion and microbiota transplant studies. In the absence of colitis, BP-feeding reduced abundance of Lactobacillus johnsonii and Turicibacter sanguinis and expanded Akkermansia muciniphila, which localized to the mucus in association with decreased mucus thickness and quality. BP-fed mice had elevated primary and conjugated fecal bile acids (BAs), and taurocholic acid administration to PP-fed mice worsened colitis. Dietary psyllium protected against BP-mediated inflammation, restored BA-modulating commensals and normalized BA ratios. Collectively, these data suggest that the protein component of red meat may be responsible, in part, for the colitis-promoting effects of this food source and provide insight into dietary factors that may influence IBD severity.}, }
@article {pmid39981552, year = {2025}, author = {Adams, MS and Enichen, E and Demmig-Adams, B}, title = {Reframing Diabetes Prevention: From Body Shaming to Metabolic Reprogramming.}, journal = {American journal of lifestyle medicine}, volume = {19}, number = {2}, pages = {168-191}, pmid = {39981552}, issn = {1559-8284}, abstract = {This review integrates new developments in psychology with updated physiological insight on the complex relationships among chronic psychological stress (arising from weight stigmatization and body shaming), food composition, physical activity and metabolic health for the example of diabetes. We address how visual measures of health, such as body mass index (BMI) and waist-to-hip ratio, do not adequately capture metabolic health and can instead contribute to weight stigmatization, chronic stress, and system-wide impairment of metabolic health. We also emphasize the importance of food composition over calorie counting. We summarize how chronic stress interacts with nutritional deficiencies and physical inactivity to disrupt the stress response, immune response, gut microbiome, and function of fat depots. We specifically address how interactions among lifestyle factors and the gut microbiome regulate whether fat stored around the waist has a negative or positive effect on metabolic health. We aim to provide a resource and updated framework for diabetes prevention and health promotion by (i) highlighting metabolic imbalances triggered by lifestyle changes during the transition to industrialized society and (ii) detailing the potential to support metabolic health through access to modest, but comprehensive lifestyle adjustments.}, }
@article {pmid39979198, year = {2025}, author = {Fukasawa, N and Tsunoda, J and Sunaga, S and Kiyohara, H and Nakamoto, N and Teratani, T and Mikami, Y and Kanai, T}, title = {The gut-organ axis: Clinical aspects and immune mechanisms.}, journal = {Allergology international : official journal of the Japanese Society of Allergology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.alit.2025.01.004}, pmid = {39979198}, issn = {1440-1592}, abstract = {The gut-brain axis exemplifies the bidirectional connection between the intestines and the brain, as evidenced by the impact of severe stress on gastrointestinal symptoms including abdominal pain and diarrhea, and conversely, the influence of abdominal discomfort on mood. Clinical observations support the notion of the gut-brain connection, including an increased prevalence of inflammatory bowel disease (IBD) in patients with depression and anxiety, as well as the association of changes in the gut microbiota with neurological disorders such as multiple sclerosis, Parkinson's disease, stroke and Alzheimer's disease. The gut and brain communicate via complex mechanisms involving inflammatory cytokines, immune cells, autonomic nerves, and gut microbiota, which contribute to the pathogenesis in certain gut and brain diseases. Two primary pathways mediate the bidirectional information exchange between the intestinal tract and the brain: signal transduction through bloodstream factors, such as bacterial metabolites and inflammatory cytokines, and neural pathways, such as neurotransmitters and inflammatory cytokines within the autonomic nervous system through the interaction between the nerve cells and beyond. In recent years, the basic mechanisms of the pathophysiology of the gut-brain axis have been gradually elucidated. Beyond the gut-brain interaction, emerging evidence suggests the influence of the gut extends to other organs, such as the liver and lungs, through intricate inter-organ communication pathways. An increasing number of reports on this clinical and basic cross-organ interactions underscore the potential for better understanding and novel therapeutic strategies targeting inter-organs networks. Further clarification of interactions between multiorgans premises transformative insights into cross-organ therapeutic strategies.}, }
@article {pmid39978693, year = {2025}, author = {Jiang, Y and Shi, L and Qu, Y and Ou, M and Du, Z and Zhou, Z and Zhou, H and Zhu, H}, title = {Multi-omics analysis reveals mechanisms of FMT in Enhancing antidepressant effects of SSRIs.}, journal = {Brain, behavior, and immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.bbi.2025.02.011}, pmid = {39978693}, issn = {1090-2139}, abstract = {OBJECTIVE: This study explores the behavioral and molecular biological impacts of Fecal Microbiota Transplantation (FMT) on depressive mice unresponsive to treatment with Selective Serotonin Reuptake Inhibitors (SSRIs).<br><br>METHODS: Healthy male C57BL/6 mice were used to establish a depression model through chronic restraint stress, treated with fluoxetine, and categorized into Response and Non-response groups. An FMT treatment was added to the Non-response group. Behavioral tests were conducted to assess symptoms of depression. The gut microbiome, plasma metabolites, and hippocampal tissue gene expression and function changes were analyzed using 16S rRNA gene sequencing, LC-MS, and RNA sequencing.<br><br>RESULTS: FMT significantly improved the depressive symptoms in SSRIs-resistant mice. There was a partial restoration in the diversity and structure of the gut microbiota in the FMT group. Compared to the Non-response group, significant changes were noted in the metabolomic profiles of the FMT group, identifying various differential metabolites. Functional annotations indicated that these metabolites are involved in multiple metabolic pathways. In the Non-response group, certain gene expression levels were significantly restored. GO and KEGG enrichment analyses revealed that these differential genes mainly involve cytokine activity, receptor signaling regulation, and NOD-like receptor signaling pathways. Joint analysis suggested that FMT may exert its effects through an increase in the abundance of g__Paraprevotella, leading to decreased baicalin content and increased Tal2 expression.<br><br>CONCLUSION: FMT has potential in improving depressive symptoms unresponsive to SSRIs treatment. Its mechanism may be related to the modulation of the gut microbiota and its metabolites, subsequently affecting gene expression.}, }
@article {pmid39978622, year = {2025}, author = {Rizzo, C and Caruso, G and Maimone, G and Patrolecco, L and Termine, M and Bertolino, M and Giannarelli, S and Rappazzo, AC and Elster, J and Lena, A and Papale, M and Pescatore, T and Rauseo, J and Soldano, R and Spataro, F and Aspholm, PE and Azzaro, M and Lo Giudice, A}, title = {Microbiome and pollutants in the freshwater sponges Ephydatia muelleri (Lieberkühn, 1856) and Spongilla lacustris (Linnaeus, 1758) from the sub-Arctic Pasvik River (Northern Fennoscandia).}, journal = {Environmental research}, volume = {}, number = {}, pages = {121126}, doi = {10.1016/j.envres.2025.121126}, pmid = {39978622}, issn = {1096-0953}, abstract = {Despite the ecosystem functions offered by sponges in freshwater habitats, fragmentary studies have targeted their microbiome and the bioaccumulation of legacy and emerging organic micropollutants, making it difficult to test hypotheses about sponge-microbe specificity and response to environmental factors and stressors. The sponge species Ephydatia muelleri and Spongilla lacustris, coexisting in two sites of the Pasvik River (northern Fennoscandia), were analyzed for persistent organic pollutant (POPs) and chemicals of emerging concern (CECs), along with quali-quantitative microbiological features. River water and sediment were similarly treated to establish if the obtained data were site- or sponge-specific. CECs mainly occurred in abiotic matrices, with trimethoprim and ciprofloxacin prevailing in water and sediment, respectively. Only ciprofloxacin and diclofenac were detected in sponges, with higher concentrations generally determined in S. lacustris than E. muelleri. Overall, POP concentrations were in the order polycyclic aromatic hydrocarbons>chlorobenzenes>polychlorobiphenyls>polychloronaphthalenes, with higher values in sponges with respect to abiotic matrices. Generally, POPs occurred at higher concentrations in S. lacustris than E. muelleri. Enzyme activity measurements displayed diverse trends across samples and sites, with E. muelleri displaying higher glycolytic activity than S. lacustris. Prokaryotic abundance in sponges generally exceeded that found in abiotic matrices. Proteobacteria, Planctomycetota, Actinobacteriota, Verrucomicrobiota, and Cyanobacteria predominated in sponge samples, with slight differences between sponge species and sampling sites, whereas Desulfobacterota and Acidobacterota were retrieved mostly in sediment samples. The sponge-associated bacterial communities appeared to be differently affected by pollutant concentration at the site level. Overall, this study highlights the ecological role of freshwater sponges, shedding light on their microbial associations, pollutant bioaccumulation, and potential as bioindicators of aquatic ecosystem health. The findings emphasize the importance of considering both microbial diversity and contaminant accumulation for a holistic understanding of the roles played by freshwater sponges in human-impacted environments.}, }
@article {pmid39978595, year = {2025}, author = {Holle, J and Reitmeir, R and Behrens, F and Singh, D and Schindler, D and Potapenko, O and McParland, V and Anandakumar, H and Kanzelmeyer, N and Sommerer, C and Hartleif, S and Andrassy, J and Heemann, U and Neuenhahn, M and Forslund-Startceva, SK and Gerhard, M and Oh, J and Wilck, N and Löber, U and Bartolomaeus, H}, title = {Gut microbiome alterations precede graft rejection in kidney transplantation patients.}, journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajt.2025.02.010}, pmid = {39978595}, issn = {1600-6143}, abstract = {Kidney transplantation (KT) is the best treatment for end-stage kidney disease, with graft survival critically affected by the recipient's immune response. The role of the gut microbiome in modulating this immune response remains underexplored. Our study investigates how microbiome alterations might associate with allograft rejection by analyzing the gut microbiome using 16S rRNA gene amplicon sequencing of a multicenter prospective study involving 562 samples from 245 individuals of which 217 received KT. Overall, gut microbiome composition showed gradual recovery post-KT, mirroring CKD-to-health transition as indicated by an increase of Shannon diversity. Prior to graft rejection, we observed a decrease in microbial diversity and SCFA-producing taxa. Functional analysis highlighted a decreased potential for SCFA production in patients preceding the rejection event, validated by quantitative PCR for the production potential of propionate and butyrate. Post-rejection analysis revealed normalization of these microbiome features. Comparison to published microbiome signatures from CKD patients demonstrated a partial overlap of the microbiome alterations preceding graft rejection with the alterations typically found in CKD. Our findings suggest that alterations in gut microbiome composition and function may precede and influence KT rejection, suggesting potential implications as biomarkers or for early therapeutic microbiome-targeting interventions.}, }
@article {pmid39978531, year = {2025}, author = {Perrotta, BG and Kidd, KA and Marcarelli, AM and Paterson, G and Walters, DM}, title = {Effects of chronic metal exposure and metamorphosis on the microbiomes of larval and adult insects, and riparian spiders through the aquatic-riparian food web.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {125867}, doi = {10.1016/j.envpol.2025.125867}, pmid = {39978531}, issn = {1873-6424}, abstract = {The macroinvertebrate microbiome controls various aspects of the host's physiology, from regulation of environmental contaminants to reproductive output. Aquatic insects provide critical nutritional subsidies linking aquatic and riparian food webs while simultaneously serving as a contaminant pathway for riparian insectivores in polluted ecosystems. Previous studies have characterized the transport and transfer of contaminants from aquatic to riparian ecosystems through insect metamorphosis, but both contaminant exposure and metamorphosis are energetically intensive processes that may cause host microbiomes to undergo radical transformation in structure and function, potentially affecting the host's physiology. We collected arthropods from three sites within Torch Lake, a historical copper mine in the Keweenaw Peninsula, Michigan, USA, and three sites within a nearby reference lake. Our objectives were to: 1) characterize the variation in microbiome communities and predicted metagenomic functions with legacy copper mining activity across space, among host types and family-level host taxonomy, 2) characterize how insect metamorphosis alters the microbiome community, including the degree of endosymbiotic infection, and predicted metagenomic function. We field-collected organisms, extracted their DNA, and sequenced the 16S region of the rRNA gene to characterize microbiome communities, then predicted metagenomic function. Site, lake, and host taxonomy affected the host microbiome community composition. Copper exposure increased the abundance of xenobiotic and lipid metabolism pathways in the Araneidae spider microbiome. Metamorphosis reduced the alpha diversity, altered the community composition, and predicted metagenomic function. We observed a bioconcentration of endosymbiotic bacteria in adult insects, especially holometabolous insects. Through metamorphosis, we observed a transition in function from xenobiotic degradation pathways to carbohydrate metabolism. Overall, contaminant exposure alters the microbiome composition in aquatic insects and riparian spiders and alters the function of the microbiome across the aquatic-riparian interface. Furthermore, metamorphosis is a critical element in shaping the aquatic insect microbiome across its life history.}, }
@article {pmid39978530, year = {2025}, author = {Zhao, K and Yang, F and Wu, M and Pan, X and Xiang, S and Tang, Y and Song, F and Peng, Y and Wu, S and Cao, Y and Liu, C and Qiu, J}, title = {Association of thallium exposure in early life with gut microbiota in neonates.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {125876}, doi = {10.1016/j.envpol.2025.125876}, pmid = {39978530}, issn = {1873-6424}, abstract = {Previous research has found a correlation between heavy metals and gut microbiota in humans. However, there are few population-based studies examining the impact of early life thallium (Tl) exposure on neonatal microbiome. 342 newborns were recruited from Hunan Children's Hospital and subsequently divided into three groups (low, medium, and high) based on the 25th and 75th percentiles of serum Tl concentration. Additionally, the relationship between Tl and gut microbiota was analyzed in subgroups (preterm or full-term neonates). The association between Tl and gut microbiota in neonates was analyzed by Redundancy analysis, Spearman correlation analysis and MaAsLin2. The detection rate of Tl in neonates was 100%, with the median concentration of 0.021 μg/L. In all neonates, we found significant differences in the Chao1 and ACE indices of α-diversity in gut microbiota, and the relative abundances of Bacteroidota and Bacteroidetes were significantly different among groups (p < 0.05). Following the covariate adjustment, Tl was negatively correlated with Gemmatimonadota (Coef = 0.265, p < 0.05) in preterm neonates. In full-term neonates, Tl exhibited a positive correlation with the relative abundance of Robinsoniella (Coef = 0.563, p = 0.009) and a negative correlation with that of Pseudomonas (Coef = - 0.592, p = 0.012). Tryptophan and renin-angiotensin system pathways might exert important roles in Tl exposure. This study indicated that Tl exposure was associated with changes in α-diversity and the composition of gut microbiota in neonates, with Gemmatimonadota being predominantly affected in preterm neonates and Robinsoniella and Pseudomonas in full-term neonates.}, }
@article {pmid39978410, year = {2025}, author = {Hawley, JA and Forster, SC and Giles, EM}, title = {Exercise, Gut Microbiome, and Gastrointestinal Diseases: Therapeutic Impact and Molecular Mechanisms.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2025.01.224}, pmid = {39978410}, issn = {1528-0012}, abstract = {The benefits of regular physical activity (PA) on disease prevention and treatment outcomes have been recognized for centuries. However, only recently has interorgan communication triggered by the release of "myokines" from contracting skeletal muscles emerged as a putative mechanism by which exercise confers protection against numerous disease states. Cross-talk between active skeletal muscles and the gut microbiota reveal how regular PA boosts host immunity, facilitates a more diverse gut microbiome and functional metabolome, and plays a positive role in energy homeostasis and metabolic regulation. In contrast, and despite the large interindividual variation in the human gut microbiome, reduced microbial diversity has been implicated in several diseases of the gastrointestinal (GI) tract, systemic immune diseases, and cancers. Although prolonged, intense, weight-bearing exercise conducted in extreme conditions can increase intestinal permeability, compromising gut-barrier function and resulting in both upper and lower GI symptoms, these are transient and benign. Accordingly, the gut microbiome has become an attractive target for modulating many of the positive effects of regular PA on GI health and disease, although the precise dose of exercise required to induce favourable changes in the microbiome and enhance host immunity is currently unknown. Future efforts should concentrate on gaining a deeper understanding of the factors involved in exercise-gut interactions through the generation of functional 'omics readouts (ie, metatranscriptomics, metaproteomics, and metabolomics) that have the potential to identify functional traits of the microbiome that are linked to host health and disease states, and validating these interactions in experimental and preclinical systems. A greater understanding of how PA interacts with the GI tract and the microbiome may enable targeted therapeutic strategies to be developed for individuals and populations at risk for a variety of GI diseases.}, }
@article {pmid39978335, year = {2025}, author = {Wang, Z and Tian, L and Jiang, Y and Ning, L and Zhu, X and Chen, X and Xuan, B and Zhou, Y and Ding, J and Ma, Y and Zhao, Y and Huang, X and Hu, M and Fang, JY and Shen, N and Cao, Z and Chen, H and Wang, X and Hong, J}, title = {Synergistic role of gut-microbial L-ornithine in enhancing ustekinumab efficacy for Crohn's disease.}, journal = {Cell metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmet.2025.01.007}, pmid = {39978335}, issn = {1932-7420}, abstract = {The role of the intestinal microbiome in Crohn's disease (CD) treatment remains poorly understood. This study investigates microbe-host interactions in CD patients undergoing ustekinumab (UST) therapy. Fecal metagenome, metabolome, and host transcriptome data from 85 CD patients were analyzed using multi-omics integration and mediation analysis. Our findings reveal significant microbiome-metabolite-host interactions. Specifically, Faecalibacterium prausnitzii was linked to altered L-ornithine biosynthesis, resulting in higher L-ornithine levels in patients before UST therapy. In vivo and in vitro studies demonstrated that microbiome-derived L-ornithine enhances UST treatment sensitivity in CD by disrupting the host IL-23 receptor signaling and inhibiting Th17 cell stabilization through the IL-12RB1/TYK2/STAT3 axis. L-ornithine significantly enhances the therapeutic efficacy of UST in CD patients, as demonstrated in a prospective clinical trial. These findings suggest that targeting specific microbe-host metabolic pathways may improve the efficacy of inflammatory bowel disease (IBD) treatments.}, }
@article {pmid39978276, year = {2025}, author = {Luo, X and Cheng, P and Fang, Y and Wang, F and Mao, T and Shan, Y and Lu, Y and Wei, Z}, title = {Yinzhihuang formula modulates the microbe‒gut‒liver axis and bile acid excretion to attenuate cholestatic liver injury.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {139}, number = {}, pages = {156495}, doi = {10.1016/j.phymed.2025.156495}, pmid = {39978276}, issn = {1618-095X}, abstract = {BACKGROUND: Cholestatic liver injury is a hepatobiliary disorder primarily characterized by cholestasis, which significantly contributes to liver damage. The Yinzhihuang (YZH) oral preparation is an effective clinical treatment for cholestatic liver injury; however, the specific mechanism of action has not been clarified.<br><br>PURPOSE: This study investigated YZH's pharmacological mechanisms associated with the microbe&#x2012;gut&#x2012;liver axis in cholestatic mice, offering new perspectives for the treatment of cholestasis.<br><br>METHODS: YZH's protective effects were evaluated by evaluating serum liver injury indices and liver staining in an alpha-nephthyl isothiocyanate (ANIT)-induced intrahepatic cholestasis mouse model. Colon hematoxylin&#x2012;eosin (H&amp;E) and alcian blue staining and FITC&#x2012;dextran leakage assays were performed to assess intestinal barrier integrity. Fluorescence in situ hybridization was employed to analyze bacterial translocation. Additionally, 16S rRNA sequencing, fecal microbiota transplantation, and bile acid metabolomics analysis were conducted to examine the relationships among the microbiome, bile acid metabolism, and YZH formula.<br><br>RESULTS: We found that YZH administration alleviated symptoms of ANIT-induced hepatic pathological injury and fibrosis. In addition, YZH reduced the transfer of gut bacteria to liver tissue by maintaining an intact intestinal barrier. Notably, YZH influenced the intestinal microbiota composition, upregulated the abundance of bile acid metabolism-associated probiotic bacteria, including Clostridiales, Lachnospiraceae and Bifidobacterium pseudolongum; and downregulated the abundance of Escherichia-Shigella and Serratia, thereby promoting bile acid excretion.<br><br>CONCLUSION: YZH protects against cholestatic liver damage by promoting bile excretion and maintaining intestinal mucosal barrier integrity. Furthermore, YZH alleviates cholestasis in a gut microbiota-dependent manner, and upregulation of probiotics may be crucial for YZH's influence on bile acid metabolism.}, }
@article {pmid39978196, year = {2025}, author = {Yang, H and Zheng, G and Qin, G and Zhang, Q and Zhang, Z and Chen, B and Lei, C and Liu, M and Cui, R and Sun, L and Xia, S and Peijnenburg, WJGM and Lu, T and Tang, T and Qian, H}, title = {The combination of microplastics and glyphosate affects the microbiome of soil inhabitant Enchytraeus crypticus.}, journal = {Journal of hazardous materials}, volume = {489}, number = {}, pages = {137676}, doi = {10.1016/j.jhazmat.2025.137676}, pmid = {39978196}, issn = {1873-3336}, abstract = {Microplastics and pesticides are emerging contaminants that threaten soil ecosystems, yet their combined effects on soil health and soil fauna remain poorly understood. In this study, we constructed a microcosm to assess the individual and combined effects of microplastics and glyphosate on soil physicochemical properties, microbial communities, and the gut microbiome of soil invertebrates (Enchytraeus crypticus). Biodegradable polylactic acid (PLA) and conventional polyethylene terephthalate (PET) were introduced at environmentally relevant concentrations. Our results revealed that PLA had a stronger disruptive effect on soil microbial communities than PET, altering microbial diversity and functional composition. Glyphosate, in contrast, primarily influenced the gut microbiome of E. crypticus, reducing microbial diversity and inducing oxidative stress. Combined exposure to microplastics and glyphosate significantly intensified oxidative stress but did not amplify microbial dysbiosis beyond the effects of microplastics alone. Compare to PET, PLA combined with glyphosate had the most pronounced effects on both soil and gut microbiomes, suggesting that biodegradable microplastics may pose greater ecological risks than conventional microplastics when used alongside pesticides. These findings underscore the need for a reassessment of biodegradable plastic use in agriculture and highlight the complex interactions between microplastics and pesticides in shaping soil ecosystem health.}, }
@article {pmid39978144, year = {2025}, author = {Sudakov, K and Rana, A and Faigenboim-Doron, A and Gordin, A and Carmeli, S and Shimshoni, JA and Cytryn, E and Minz, D}, title = {Diverse effects of Bacillus sp. NYG5-emitted volatile organic compounds on plant growth, rhizosphere microbiome, and soil chemistry.}, journal = {Microbiological research}, volume = {295}, number = {}, pages = {128089}, doi = {10.1016/j.micres.2025.128089}, pmid = {39978144}, issn = {1618-0623}, abstract = {Bacterial strains in the rhizosphere secrete volatile organic compounds (VOCs) that play critical roles in inter- and intra-kingdom signaling, influencing both microbe-microbe and microbe-plant interactions. In this study we evaluated the plant growth-promoting effects of VOCs emitted by Bacillus sp. NYG5 on Arabidopsis thaliana, Nicotiana tabacum, and Cucumis sativus, focusing on VOC-induced alterations in plant metabolic pathways, rhizosphere microbial communities, and soil chemical properties. NYG5 VOCs enhanced plant biomass across all tested species and induced significant shifts in rhizosphere microbial community composition, specifically increasing relative abundance of Gammaproteobacteria and reducing Deltaproteobacteria (Linear discriminant analysis Effect Size, p < 0.05). Soil analysis revealed a considerable reduction in humic substance concentrations following VOCs exposure, as detected by fluorescent spectral analysis. Using SPME-GC-MS, several novel VOCs were identified, some of which directly promoted plant growth. Transcriptomic analysis of N. tabacum exposed to NYG5 VOCs demonstrated activation of pathways related to phenylpropanoid biosynthesis, sugar metabolism, and hormone signal transduction. Within the phenylpropanoid biosynthesis pathway, a significant upregulation (p adj = 1.16e-14) of caffeic acid 3-O-methyltransferase was observed, a key enzyme leading to lignin and suberin monomer biosynthesis. These results highlight the complex mechanisms through which bacterial VOCs influence plant growth, including metabolic modulation, rhizosphere microbiome restructuring, and soil chemical changes. Collectively, this study highlights the pivotal role of bacterial VOCs in shaping plant-microbe-soil interactions.}, }
@article {pmid39978123, year = {2025}, author = {Jin, G and Wang, X and Cui, R and Yuan, S and Wang, M and Chen, Z}, title = {Comprehensive assessment of antibiotic impacts and risk thresholds on aquatic microbiomes and resistomes.}, journal = {Water research}, volume = {276}, number = {}, pages = {123262}, doi = {10.1016/j.watres.2025.123262}, pmid = {39978123}, issn = {1879-2448}, abstract = {Understanding the impacts of environmentally relevant low-level antibiotics on aquatic microbiomes and resistomes is crucial for risk assessment of anthropogenic antibiotic contamination. Here, we investigated the effects of seven subinhibitory concentrations of trimethoprim and lincomycin (10 ng/L to 10 mg/L), individually and in combination, on surface water microcosms over 1 and 7 days, using unspiked samples as controls. Metagenomic sequencing revealed a decrease in bacterial community α-diversity and an increase in resistome α-diversity with rising antibiotic concentrations upon 7 days of exposure. Notably, the β-diversity of both bacterial communities and resistomes exhibited a biphasic response, decreasing and then increasing with breakpoint concentrations of 2.73 µg/L and 0.68 µg/L, respectively. We also observed concentration-dependent increases in certain metagenome-assembled antibiotic-resistant bacteria (MAARB) and antibiotic resistance genes (ARGs), with minimum selective concentrations (MSCs) of 2.28 µg/L for trimethoprim targeting OXA-21 and 32.4 µg/L for lincomycin targeting erm(F). Among various metrics for identifying risk thresholds that induce significant changes in microbial taxa, resistomes, individual ARGs, and MAARB, the breakpoint concentration derived from resistome β-diversity was the most conservative. We propose integrating this metric into environmental risk assessment frameworks for antibiotics. Our study provides a systematic evaluation of antibiotic impacts on aquatic microbiomes and resistomes, offering key insights for refining risk assessments of antibiotic contamination in aquatic environments.}, }
@article {pmid39978008, year = {2025}, author = {Hong, J and Kim, HS and Adams, S and Scaria, J and Patterson, R and Woyengo, TA}, title = {Growth performance and gut health of nursery pigs fed diet containing sodium butyrate or enzymatically hydrolyzed yeast product.}, journal = {Animal : an international journal of animal bioscience}, volume = {19}, number = {3}, pages = {101448}, doi = {10.1016/j.animal.2025.101448}, pmid = {39978008}, issn = {1751-732X}, abstract = {Weaned pigs are highly susceptible to gut infections, underscoring the need to develop feeding strategies to manage gut health. A study was conducted to determine the effects of lipid-coated sodium butyrate (NaB) and enzymatically hydrolyzed yeast cell wall product (EYP) on growth performance and indicators of intestinal structure and function in nursery pigs. A total of 96 weaned pigs (initial BW = 6.60 ± 0.88 kg) housed in 24 pens (four pigs/pen) were fed three diets in a randomized complete block design. The diets were corn-soybean meal-based without (CON) or with 0.05% NaB or 0.1% EYP. Growth performance and fecal score were determined by the feeding phase. During days 10-13, one pig from each pen was euthanized for measuring organ weights, blood immune response, histology and permeability of small intestine, electrophysiological parameters of jejunum mounted in Ussing chambers, and gut microbiome. Dietary NaB, but not EYP, increased (P < 0.05) overall gain-to-feed ratio by 16%. In comparison to CON, dietary EYP increased (P < 0.05) the cecum weight by 36%, and dietary NaB or EYP tended to increase (P < 0.10) the villous height to crypt depth ratio in duodenum by 12%. Dietary NaB or EYP had no influence on the serum concentrations of immunoglobulins A, G, M, and tumor-necrosis factor-α. Dietary NaB decreased (P < 0.05) the jejunal flux of fluorescein isothiocyanate-dextran flux by 32%, whereas dietary EYP tended to reduce (P = 0.10) it by 21% compared to CON. Also, dietary Nab and EYP decreased (P < 0.05) jejunal short circuit current by 52 and 50%, respectively, compared to CON. Dietary EYP increased (P < 0.05) the relative abundance of Sporobacter and Desulfovibrio genera in the cecum. Dietary EYP increased (P < 0.05) the relative abundance of Verrucomicrobia phylum and Odoribacter, Enterococcus, and YRC22 genera in feces. In conclusion, dietary NaB improved feed efficiency and reduced jejunal permeability to fluorescein isothiocyanate-dextran 4 kDa, implying that it improved intestinal integrity in nursery pigs. Thus, NaB product fed in the current study can be included in diets for weaned pigs to improve their performance through improved gut integrity. Dietary EYP increased cecum weight, implying that dietary EYP improved cecal fermentation capacity. It also modified cecal and fecal microbial composition. Thus, the EYP product fed in the current study can be added in diets for weaned pigs to improve the fermentation of feed in the hindgut.}, }
@article {pmid39977582, year = {2025}, author = {Yang, L and Zhang, J and Chen, Z and Chen, Y and Wang, C and Yu, H and Zuo, F and Huang, W}, title = {Probiotic-Enzyme Synergy Regulates Fermentation of Distiller's Grains by Modifying Microbiome Structures and Symbiotic Relationships.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.4c11539}, pmid = {39977582}, issn = {1520-5118}, abstract = {The high fiber content and low rumen digestibility prevent the efficient use of distiller's grains (DGS) in ruminant feeds. This study investigated the effects of probiotics (Lactiplantibacillus plantarum and Bacillus subtilis) and enzymes (β-glucanase, xylanase, β-mannanase, and cellulase) on DGS nutrient content, ruminal degradability, and microbial communities under anaerobic storage for 30 days. Groups included control (C), probiotics (B), enzymes (E), and their mixture (EB). As compared to groups C, B, and E, neutral detergent fiber (NDF), acid detergent fiber (ADF), hemicellulose, and cellulose contents were significantly decreased and the ruminal degradability of NDF and ADF at 48 h was significantly increased in group EB (p < 0.05). Enzyme activities significantly affected bacterial abundance, and the contents of these enzymes were negatively correlated with the content of fibrous components. The abundances of Bacillus and Rummeliibacillus were negatively correlated with fiber content but positively correlated with the activities of these enzymes. The symbiotic relationship between Bacillus and Anaerocolumna in the EB group sustained the synergistic effects of probiotics and enzymes. Co-fermentation of probiotics and enzyme additives enhanced the nutritional value of DGS, which was associated not only with probiotic-enzyme synergy but also variations in dominant microbes and microbiome commensal relationships.}, }
@article {pmid39977580, year = {2025}, author = {Zhang, F and Zhu, M and Chen, Y and Wang, G and Yang, H and Lu, X and Li, Y and Chang, HM and Wu, Y and Ma, Y and Yuan, S and Zhu, W and Dong, X and Zhao, Y and Yu, Y and Wang, J and Mu, L}, title = {Harnessing omics data for drug discovery and development in ovarian aging.}, journal = {Human reproduction update}, volume = {}, number = {}, pages = {}, doi = {10.1093/humupd/dmaf002}, pmid = {39977580}, issn = {1460-2369}, support = {2024YFC2706600//National Key Research and Development Project of China/ ; Z230013//Beijing Natural Science Foundation/ ; BYSY2022043//Key Clinical Projects of Peking University Third Hospital/ ; 82225019//National Natural Science Foundation of China/ ; DMR-113-080//China Medical University Hospital Research Foundation/ ; }, abstract = {BACKGROUND: Ovarian aging occurs earlier than the aging of many other organs and has a lasting impact on women's overall health and well-being. However, effective interventions to slow ovarian aging remain limited, primarily due to an incomplete understanding of the underlying molecular mechanisms and drug targets. Recent advances in omics data resources, combined with innovative computational tools, are offering deeper insight into the molecular complexities of ovarian aging, paving the way for new opportunities in drug discovery and development.<br><br>OBJECTIVE AND RATIONALE: This review aims to synthesize the expanding multi-omics data, spanning genome, transcriptome, proteome, metabolome, and microbiome, related to ovarian aging, from both tissue-level and single-cell perspectives. We will specially explore how the analysis of these emerging omics datasets can be leveraged to identify novel drug targets and guide therapeutic strategies for slowing and reversing ovarian aging.<br><br>SEARCH METHODS: We conducted a comprehensive literature search in the PubMed database using a range of relevant keywords: ovarian aging, age at natural menopause, premature ovarian insufficiency (POI), diminished ovarian reserve (DOR), genomics, transcriptomics, epigenomics, DNA methylation, RNA modification, histone modification, proteomics, metabolomics, lipidomics, microbiome, single-cell, genome-wide association studies (GWAS), whole-exome sequencing, phenome-wide association studies (PheWAS), Mendelian randomization (MR), epigenetic target, drug target, machine learning, artificial intelligence (AI), deep learning, and multi-omics. The search was restricted to English-language articles published up to September 2024.<br><br>OUTCOMES: Multi-omics studies have uncovered key mechanisms driving ovarian aging, including DNA damage and repair deficiencies, inflammatory and immune responses, mitochondrial dysfunction, and cell death. By integrating multi-omics data, researchers can identify critical regulatory factors and mechanisms across various biological levels, leading to the discovery of potential drug targets. Notable examples include genetic targets such as BRCA2 and TERT, epigenetic targets like Tet and FTO, metabolic targets such as sirtuins and CD38+, protein targets like BIN2 and PDGF-BB, and transcription factors such as FOXP1.<br><br>WIDER IMPLICATIONS: The advent of cutting-edge omics technologies, especially single-cell technologies and spatial transcriptomics, has provided valuable insights for guiding treatment decisions and has become a powerful tool in drug discovery aimed at mitigating or reversing ovarian aging. As technology advances, the integration of single-cell multi-omics data with AI models holds the potential to more accurately predict candidate drug targets. This convergence offers promising new avenues for personalized medicine and precision therapies, paving the way for tailored interventions in ovarian aging.<br><br>REGISTRATION NUMBER: Not applicable.}, }
@article {pmid39977215, year = {2025}, author = {Zhang, Y and Sun, X and Zhang, Y and Zou, Y and Zhang, Y and Wang, J and Gao, L and Ding, W and Diao, F and Liu, J and Kwak-Kim, JYH and Ma, X}, title = {Immune Dysregulation and Endometrial Receptivity Impairment in Women with Repeated Implantation Failure and Dyslipidemia.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1210/clinem/dgaf100}, pmid = {39977215}, issn = {1945-7197}, abstract = {CONTEXT: Dyslipidemia adversely affects reproduction outcomes; however, its relation with repeated implantation failure (RIF) remains unclear.<br><br>OBJECTIVE: This study aims to analyze the impact of dyslipidemia on assisted reproductive technology (ART) outcomes, endometrial transcriptome, and microbiome of RIF women.<br><br>DESIGN: A retrospective real-world analysis and a prospective study.<br><br>SETTING: University Clinic.<br><br>PATIENTS: 6,499 infertile women, including 5,618 non-RIF, and 881 RIF.<br><br>INTERVENTIONS: Dyslipidemia.<br><br>MAIN OUTCOME MEASURES: Implantation rate (IR), clinical pregnancy rate (CPR), and live birth rate (LBR) were compared in RIF women with or without dyslipidemia. Results of endometrial studies, including RNA-seq-based endometrial receptivity test (ERT), 16S rRNA-based microbiome study, next-generation-sequencing (NGS)-based gene comparison, and bulk RNA-seq deconvolution analysis were analyzed.<br><br>RESULTS: The prevalence of dyslipidemia in RIF women was significantly higher. In dyslipidemia women, IR, CPR, and LBR were significantly lower, and the prevalence of non-receptive ERT and the presence of endometrial pathogenic bacteria were higher than those of controls. After the personalized treatment, CPR 73.3% and LBR 60.0% were achieved in dyslipidemia women. NGS revealed that 176 differentially expressed genes in the endometrium of RIF women with dyslipidemia compared to those without, suggesting highly enriched in cholesterol and steroid biosynthesis and monocyte differentiation processes. An increased endometrial CD56dim NK cells and macrophage (M)1/M2 ratio with dysregulated immune factors, were found by bulk RNA-seq deconvolution analysis.<br><br>CONCLUSION: RIF women with dyslipidemia have significantly poorer ART outcomes. In women with dyslipidemia, immune homeostasis was breached in the luteal phase endometrium, implicating a possible immune mechanism for dyslipidemia-related implantation failure.}, }
@article {pmid39976948, year = {2025}, author = {Schmiester, M and Jenq, RR}, title = {Appreciating the oral microbiome's impact on GVHD.}, journal = {Blood}, volume = {145}, number = {8}, pages = {791-793}, doi = {10.1182/blood.2024027670}, pmid = {39976948}, issn = {1528-0020}, }
@article {pmid39976842, year = {2025}, author = {Klimaszyk, K and Wirstlein, P and Bednarek-Rajewska, K and Jankowski, M and Svarre Nielsen, H and Wender Ożegowska, E and Kędzia, M}, title = {Endometrial factors and pregnancy loss frequency in recurrent pregnancy loss patients: comparing RT-PCR microbiology, microbial cultures, and immunohistochemistry of endometrium biopsy.}, journal = {Journal of applied genetics}, volume = {}, number = {}, pages = {}, pmid = {39976842}, issn = {2190-3883}, support = {SDUM-DGB 06/05/22//Uniwersytet Medyczny im. Karola Marcinkowskiego w Poznaniu/ ; }, abstract = {The objective of this study is to investigate the presence of bacteria in endometrial samples from patients with recurrent pregnancy loss (RPL) and explore potential correlations between bacterial presence, chronic endometritis, and previous pregnancy loss history. Endometrial samples from 90 RPL patients were analysed using RT-PCR to detect 10 specific bacterial species. A subgroup of 65 patients underwent additional microbial culture and immunohistochemistry for plasma cell identification. Correlations between bacterial presence, chronic endometritis, and the number of previous pregnancy losses were evaluated. We detected at least one out of 10 chosen bacteria DNA by RT-PCR in 24.4% (22/90) of endometrial samples. Patients with PCR-identified bacteria had a significantly higher number of previous pregnancy losses (median 3 vs 2, p = 0.01). No correlation was observed between bacterial presence and chronic endometritis diagnosis. A significant correlation was found between bacterial detection by PCR and microbial culture (p = 0.03), though culture methods detected fewer positive cases. In RPL patients, detecting DNA from at least one of 10 selected bacterial species by RT-PCR correlates with a higher number of previous pregnancy losses. However, this bacterial presence does not correlate with chronic endometritis diagnosis based on the CD138 immunohistochemistry-identified plasma cell count. These findings suggest a potential role of endometrial bacteria in RPL that may be independent of the classical inflammatory response associated with chronic endometritis.}, }
@article {pmid39976822, year = {2025}, author = {Greene, LK and Andriatiavina, T and Foss, ED and Andriantsalohimisantatra, A and Rivoharison, TV and Rakotoarison, F and Randriamboavonjy, T and Yoder, AD and Ratsoavina, F and Blanco, MB}, title = {The gut microbiome of Madagascar's lemurs from forest fragments in the central highlands.}, journal = {Primates; journal of primatology}, volume = {}, number = {}, pages = {}, pmid = {39976822}, issn = {1610-7365}, support = {1906416//National Science Foundation PRFB/ ; }, abstract = {The gut microbiome is now understood to play essential roles in host nutrition and health and has become a dominant research focus in primatology. Over the past decade, research has clarified the evolutionary traits that govern gut microbiome structure across species and the ecological traits that further influence consortia within them. Nevertheless, we stand to gain resolution by sampling hosts in understudied habitats. We focus on the lemurs of Madagascar's central highlands. Madagascar's highlands have a deep history as heterogeneous grassland-forest mosaics, but due to significant anthropogenic modification, have long been overlooked as lemur habitat. We collected fecal samples from Verreaux's sifakas (Propithecus verreauxi), common brown lemurs (Eulemur fulvus), and Goodman's mouse lemurs (Microcebus lehilahytsara) inhabiting two protected areas in the highlands and used amplicon sequencing to determine gut microbiome diversity and membership. As expected, the lemurs harbored distinct gut consortia tuned to their feeding strategies. Mouse lemurs harbored abundant Bifidobacterium and Alloprevotella that are implicated in gum metabolism, sifakas harbored abundant Lachnospiraceae that are implicated in leaf-fiber metabolism, and brown lemurs harbored diverse consortia with abundant WCBH1-41 that could be associated with frugivory in harsh seasons and habitats. Within brown lemurs, a suite of bacteria varied between seed-packed and leaf-packed feces, a proxy for dietary intakes, collected from the same group over days. Our results underscore the evolutionary and ecological factors that govern primate gut microbiomes. More broadly, we showcase the forests of Madagascar's central highlands as rich habitat for future research of lemur ecology and evolution.}, }
@article {pmid39976733, year = {2025}, author = {de Oliveira Sousa, T and Araújo da Silva, N and de Melo Oliveira, V and da Silva Ramos, AV and Barbosa Filho, JPM and Batista, JMDS and Brandão Costa, RMP and Porto, ALF and Bezerra Pinheiro de Lima, S and de Paula Ferreira Teixeira, M and Nascimento, TP}, title = {Use of proteases for animal feed supplementation: scientific and technological updates.}, journal = {Preparative biochemistry &amp; biotechnology}, volume = {}, number = {}, pages = {1-13}, doi = {10.1080/10826068.2025.2465957}, pmid = {39976733}, issn = {1532-2297}, abstract = {The global market is rapidly evolving, with biotechnological advances supporting production centers through innovative techniques. A key focus is on bioprocesses for extracting, purifying, and applying proteases, particularly in animal feed within the agricultural sector. Although the cost reduction may vary depending on the animal species, supplementation with proteases allows for the formulation of more cost-effective diets, improving nutrient digestibility and absorption, optimizing energy efficiency, preserving intestinal integrity, enhancing carcass quality, modulating the intestinal microbiome, and reducing nitrogen excretion. This study aimed to update on protease use in monogastric animal feed, drawing from digital databases (Science Direct, Google Scholar, and Scielo) and industrial property databases (INPI). Despite the significant potential of proteases in monogastric animal nutrition, there is a lack of studies, especially on patented technologies. While their benefits are recognized, substantial investments are needed to develop new technologies and identify alternative protease sources. These advancements could enhance animal performance and strengthen Brazil's productive sector, highlighting the need for further research and innovation. The literature review showed promising results, but research is mainly focused on microbial proteases for poultry, pigs, and fish. There is significant potential to explore diverse protease production sources and their application across various species.}, }
@article {pmid39976704, year = {2025}, author = {Mizutani, Y and Orita, R and Kimura, K and Funabara, D}, title = {Hypoxia-induced changes in the gill and hepatopancreatic bacterial communities of the ark shell Anadara kagoshimensis.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {27}, number = {2}, pages = {53}, pmid = {39976704}, issn = {1436-2236}, support = {Y-2023-1-008//Institute for Fermentation, Osaka/ ; }, mesh = {Animals ; *Gills/microbiology ; *Hepatopancreas/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/drug effects ; *Anti-Bacterial Agents/pharmacology ; Arcidae/microbiology ; Chloramphenicol/pharmacology ; RNA, Ribosomal, 16S/genetics ; Hypoxia/microbiology ; Microbiota/drug effects ; }, abstract = {Coastal hypoxia is an increasing environmental concern affecting marine ecosystems globally, particularly impacting benthic organisms such as bivalves. Although previous studies focused on the physiological responses of bivalves to hypoxic stress, the role of resident bacteria in the host response to hypoxia remains poorly understood. This study investigated changes in the resident bacterial communities in the gills and hepatopancreatic tissues of the ark shell (Anadara kagoshimensis) under hypoxic conditions. Specimens were assigned to three treatment groups: untreated control, hypoxia, and hypoxia with chloramphenicol supplementation (5.0 mg/L). After 3 days, specimens exposed to hypoxia exhibited black precipitation in the culture water, whereas antibiotic treatment reduced these effects. Amplicon sequencing revealed distinct bacterial communities between the tissues, with Arcobacteraceae and Alkalispirochaetaceae dominating in the gills and Metamycoplasmataceae being predominant in the hepatopancreas. The hepatopancreas displayed greater bacterial community changes than the gills under hypoxic conditions, including an increase in the abundance of Metamycoplasmataceae. The predicted metabolic functions suggested that these bacteria contribute to iron sulfide precipitation through sulfate reduction and iron respiration. The antibiotic-treated group displayed bacterial communities more similar to those of the control group, confirming the effectiveness of chloramphenicol in suppressing bacterial changes under hypoxia. This study provided new insights into tissue-specific bacterial responses to hypoxia in A. kagoshimensis and highlighted the potential role of Metamycoplasmataceae in the bivalve's response to hypoxic stress.}, }
@article {pmid39976448, year = {2025}, author = {Nieciecki, VF and Blum, FC and Johnson, RC and Testerman, TL and McAvoy, TJ and King, MC and Gushchin, V and Whitmire, JM and Frey, KG and Glang, L and Peña-Gomez, D and Bishop-Lilly, KA and Sardi, A and Merrell, DS and Metcalf, JL}, title = {Cross-laboratory replication of pseudomyxoma peritonei tumor microbiome reveals reproducible microbial signatures.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0065224}, doi = {10.1128/msphere.00652-24}, pmid = {39976448}, issn = {2379-5042}, abstract = {Recent work has demonstrated that cancer-specific microbial communities often colonize tumor tissues. However, untangling low-biomass signals from environmental contamination makes this research technically challenging. We utilize pseudomyxoma peritonei (PMP), a cancer characterized by the spread of mucus-secreting cells throughout the peritoneal cavity, to develop a robust workflow for identifying reproducible tumor microbiomes. Typically originating from the rupture of an appendiceal tumor into the peritoneal cavity, metastasized tumors have been previously shown to harbor a core set of microbes. However, that work did not control for the potential contamination of these low microbial biomass samples. We expand upon these prior findings by characterizing the microbiome of 70 additional PMP tumors and six normal peritoneal control tissues along with appropriate laboratory controls. Additionally, DNA from a subset of 25 tissues was extracted and sequenced at an independent laboratory. We found evidence of reproducible microbial signatures between the replicates of six different PMP tumors that include a set of core taxa that may be introduced from surgical contamination, as well as patient-specific taxa that are also commonly implicated in colorectal cancer. In addition, preoperative chemotherapy treatment was found to reduce tumor microbiome diversity. Our findings demonstrate how independent sample replication can be a powerful approach to investigate low-biomass microbial communities associated with tumor tissues that will improve low microbial biomass research.IMPORTANCERecent work has demonstrated that microbial communities colonize over 30 different types of tumor tissues. The origin of these communities and their possible involvement in carcinogenesis or cancer treatment outcomes remains an unclear, yet important area of research. A current major challenge in characterizing low-biomass, tumor-associated microbiomes is the introduction of environmental contamination during collection, handling, DNA extraction, PCR, and sequencing. Here, we provide a framework for replicating low-biomass tumor microbiome samples to help identify tumors with robust microbial signals and low background contamination. Using this replication approach, we show that pseudomyxoma peritonei (PMP) tumors host reproducible microbial communities, including organisms that have previously been associated with colorectal cancer. Incorporating sample replication into future tumor microbiome studies is a promising approach that will help identify robust signals and increase reproducibility in the field.}, }
@article {pmid39976436, year = {2025}, author = {Bokulich, NA}, title = {Integrating sequence composition information into microbial diversity analyses with k-mer frequency counting.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0155024}, doi = {10.1128/msystems.01550-24}, pmid = {39976436}, issn = {2379-5077}, abstract = {UNLABELLED: k-mer frequency information in biological sequences is used for a wide range of applications, including taxonomy classification, sequence similarity estimation, and supervised learning. However, in spite of its widespread utility, k-mer counting has been largely neglected for diversity estimation. This work examines the application of k-mer counting for alpha and beta diversity as well as supervised classification from microbiome marker-gene sequencing data sets (16S rRNA gene and full-length fungal internal transcribed spacer [ITS] sequences). Results demonstrate a close correspondence with phylogenetically aware diversity metrics, and advantages for using k-mer-based metrics for measuring microbial biodiversity in microbiome sequencing surveys. k-mer counting appears to be a suitable and efficient strategy for feature processing prior to diversity estimation as well as supervised learning in microbiome surveys. This allows the incorporation of subsequence-level information into diversity estimation without the computational cost of pairwise sequence alignment. k-mer counting is proposed as a complementary approach for feature processing prior to diversity estimation and supervised learning analyses, enabling large-scale reference-free profiling of microbiomes in biogeography, ecology, and biomedical data. A method for k-mer counting from marker-gene sequence data is implemented in the QIIME 2 plugin q2-kmerizer (https://github.com/bokulich-lab/q2-kmerizer).<br><br>IMPORTANCE: k-mers are all of the subsequences of length k that comprise a sequence. Comparing the frequency of k-mers in DNA sequences yields valuable information about the composition of these sequences and their similarity. This work demonstrates that k-mer frequencies from marker-gene sequence surveys can be used to inform diversity estimates and machine learning predictions that incorporate sequence composition information. Alpha and beta diversity estimates based on k-mer frequencies closely correspond to phylogenetically aware diversity metrics, suggesting that k-mer-based diversity estimates are useful proxy measurements especially when reliable phylogenies are not available, as is often the case for some DNA sequence targets such as for internal transcribed spacer sequences.}, }
@article {pmid39976139, year = {2025}, author = {Von-Graffenried, T and Karemera, M and Pampori, E and Thorens Borgeat, M and Nydegger, A and Rock, NM}, title = {[Pediatric autoimmune digestive diseases].}, journal = {Revue medicale suisse}, volume = {21}, number = {906}, pages = {314-319}, doi = {10.53738/REVMED.2025.21.906.314}, pmid = {39976139}, issn = {1660-9379}, mesh = {Humans ; Child ; *Autoimmune Diseases/therapy/diagnosis/immunology ; *Celiac Disease/diagnosis/therapy/immunology/epidemiology ; Quality of Life ; Digestive System Diseases/therapy/diagnosis/immunology ; Inflammatory Bowel Diseases/therapy/diagnosis/immunology ; Hepatitis, Autoimmune/therapy/diagnosis/immunology ; Genetic Predisposition to Disease ; }, abstract = {In pediatric gastroenterology and hepatology, autoimmune diseases, such as inflammatory bowel diseases, celiac disease, and autoimmune hepatitis, are challenging for practitioners due to their increasing incidence, high morbidity, and substantial impact on children's quality of life. These conditions share similar pathophysiological mechanisms, including genetic predisposition, the role of the microbiome, and the influence of environmental and immunological factors. This review aims to explore their pathophysiology, diagnostic strategies, treatments, and future perspectives. It highlights the importance of early and multidisciplinary management to improve outcomes for affected children.}, }
@article {pmid39976005, year = {2025}, author = {Li, S and Niu, XX and Liu, JL and Su, M and Li, QQ and Wang, CY and Wang, JJ and Chen, HY and Ji, D}, title = {Leveraging the gut microbiome to understand the risk factor of cognitive impairment in patients with liver cirrhosis.}, journal = {European journal of gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1097/MEG.0000000000002934}, pmid = {39976005}, issn = {1473-5687}, abstract = {OBJECTIVES: The role of the gut-liver axis in liver cirrhosis is becoming increasingly recognized. We investigated the fecal microbiome in patients with liver cirrhosis and its potential function as a predictive biomarker of hepatic encephalopathy.<br><br>METHODS: Patients were divided into either a high plasma ammonia (HPA) group or a low plasma ammonia (LPA) group according to the upper limit of normal of plasma ammonia concentration. 16S rRNA sequencing of fecal samples was performed to study how the microbiota affects the clinical symptoms of liver cirrhosis. The Stroop test was used to assess the ability of the brain to inhibit habitual behaviors.<br><br>RESULTS: Totally, 21 subjects were enrolled. Among the 18 patients with liver cirrhosis, 14 were male, the age range was 42-56&#x2005;years, and the plasma ammonia level range was 20-125.9&#x2005;&#x3bc;mol/l. The Stroop test showed more severe cognitive impairment in HPA than in LPA individuals. At the same time, there were significant differences in fecal microbiome characteristics between the two groups, characterized by a further increase in the abundance of the Proteobacteria phylum in the gut (especially aerobic Enterobacteriaceae). Function predictions of Phylogenetic Investigation of Communities by Reconstruction of Unobserved States in the microbiome further explained the increase in the Enterobacteriaceae-dominated polyamine synthesis pathway in the gut microbiome of HPA groups.<br><br>CONCLUSION: Cirrhotic patients with hyperammonemia have a specific fecal bacterial composition (characterized via expansion of Enterobacteriaceae). The ability to bio-synthesize polyamines that Enterobacteriaceae possesses is likely to be a key factor in the elevation of plasma ammonia.}, }
@article {pmid39975991, year = {2024}, author = {Wu, Y and Zhang, K and Zheng, Y and Jin, H}, title = {A review of potential mechanisms and treatments of gastric intestinal metaplasia.}, journal = {European journal of gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, pmid = {39975991}, issn = {1473-5687}, abstract = {Gastric intestinal metaplasia (GIM) is a pathological process where gastric mucosal epithelial cells are replaced by intestinal-type cells, serving as a precursor lesion for gastric cancer. This transformation involves various genetic and environmental factors, affecting key genes and signaling pathways. Recent research has revealed complex mechanisms, including changes in gene expression, abnormal signaling pathway activation, and altered cell behavior. This review summarizes the latest research on GIM, discussing its pathogenesis, current treatment strategies, and potential efficacy of emerging approaches like gene editing, microbiome interventions, and integrative medicine. By exploring these strategies, we aim to provide more effective treatments for GIM and reduce gastric cancer incidence. The review also highlights the importance of interdisciplinary studies in understanding GIM mechanisms and improving treatment strategies.}, }
@article {pmid39975892, year = {2025}, author = {AlHilli, MM and Sangwan, N and Myers, A and Tewari, S and Lindner, DJ and Cresci, GAM and Reizes, O}, title = {The effects of dietary fat on gut microbial composition and function in ovarian cancer.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-5904007/v1}, pmid = {39975892}, issn = {2693-5015}, abstract = {Objectives : The gut microbiome (GM) is pivotal in regulating inflammation, immune responses, and cancer progression. This study investigates the effects of a ketogenic diet (KD) and a high-fat/low-carbohydrate (HF/LC) diet on GM alterations and tumor growth in a syngeneic mouse model of high-grade serous ovarian cancer (EOC). Methods : Thirty female C57BL/6J mice injected with KPCA cells were randomized into KD, HF/LC, and low-fat/high-carbohydrate (LF/HC) diet groups. Tumor growth was monitored with live, in vivo imaging. Stool samples were collected at the time of euthanasia and analyzed by 16SrRNA sequencing and shotgun metagenomic sequencing was performed to identify differential microbial taxonomic composition and metabolic function. Results : Our findings revealed that KD and HF/LC diets significantly accelerated EOC tumor growth compared to the LF/HC diet in a xenograft model. GM diversity was markedly reduced in KD and HF/LC-fed mice, correlating with increased tumor growth, whereas LF/HC-fed mice showed higher GM diversity. Metagenomic analyses identified distinct alterations in microbial taxa including Bacteroides , Lachnospiracae bacterium , Bacterium_D16_50, and Enterococcus faecalis predominantly abundant in HF/LC-fed mice, Dubsiella_newyorkensis predominantly abundant in LF/HC-fed, and KD fed mice showing a higher abundance of Akkermansia and Bacteroides . Functional pathways across diet groups indicated polyamine biosynthesis and fatty acid oxidation pathways were enriched in HF/LC-fed mice. Conclusions These results highlight the intricate relationship between diet, the gut microbiome, and tumor metabolism. The potential role of dietary interventions in cancer prevention and treatment warrants further investigation.}, }
@article {pmid39975576, year = {2025}, author = {Wang, R and Sun, S and Zhang, Q and Wu, G and Ren, F and Chen, J}, title = {Maternal Milk Orchestrates the Development of Infant Gut Microbiota: Implications for Health and Future Research Directions.}, journal = {Research (Washington, D.C.)}, volume = {8}, number = {}, pages = {0558}, pmid = {39975576}, issn = {2639-5274}, abstract = {Human breast milk serves as a vital source of nutrition for infants, and it also plays a critical role in shaping the infant gut microbiota and establishing intestinal homeostasis. This process substantially impacts immune function, neurodevelopment, and overall health. The noninvasive nature of breast milk collection makes it an ethical and accessible area for research, positioning it as a key focus for future studies. These future directions include the identification of novel bacteria combination, the establishment of comprehensive databases on infant microbiota, and the use of computational models to predict interactions between breast milk components and the gut microbiome. Additionally, the creation of diverse biological models and the establishment of infant stool banks will further enhance understanding of host-microbiome interactions and support disease prevention strategies.}, }
@article {pmid39975550, year = {2025}, author = {Kucharski, R and Sobocki, BK and Stachowska, E and Bulman, N and Kalinowski, L and Kaźmierczak-Siedlecka, K}, title = {Dental problems and oral microbiome alterations in ulcerative colitis.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1502605}, pmid = {39975550}, issn = {1664-3224}, mesh = {Humans ; *Colitis, Ulcerative/microbiology/immunology ; *Microbiota/immunology ; *Mouth/microbiology ; Dysbiosis/microbiology/immunology ; Periodontitis/microbiology/immunology ; Gastrointestinal Microbiome/immunology ; }, abstract = {Ulcerative colitis is a chronic disease that has not well-established etiology. The role of microbial dysregulation in its pathogenesis has been recently highlighted. Overall, microbiome alterations concern the reduction of bacterial abundance and diversity, resulting in gut microbiome imbalance negatively affecting immunological aspects. There is a link between ulcerative colitis and the oral microbiome. The changes of oral microbiome are found at many levels, from gently dysbiotic composition to the presence of the main periodontal microbes. The analysis of oral microbiome can be a part of personalized medicine due to the fact that it is a potential biomarker. Patients with ulcerative colitis may manifest dental symptoms/problems, such as periodontitis (strongly related to the red-complex pathogens-Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, and bacteria belonging to the other complexes, such as Fusobacterium nucleatum and Aggregatibacter actinomycetecomitans), dental caries, oral ulcerations, leukoplakia, halitosis, and others. Notably, the DMFT (Decayed, Missing, Filled Teeth) index is higher in these patients compared to healthy subjects. According to some data, oral lichen planus (which is a disease with an immunological background) can also be observed in ulcerative colitis patients. It seems that deep understanding of ulcerative colitis in association with oral microbiome, immunology, and dental manifestations may be crucial to provide complex treatment from a dental point of view.}, }
@article {pmid39975414, year = {2025}, author = {Ghose, SL and Eisen, JA}, title = {Skin microbiomes of frogs vary among individuals and body regions, revealing differences that reflect known patterns of chytrid infection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.05.636728}, pmid = {39975414}, issn = {2692-8205}, abstract = {The amphibian skin microbiome is an important line of defense against pathogens including the deadly chytrid fungus, Batrachochytrium dendrobatidis (Bd). Intra-species variation in disease susceptibility and intra-individual variation in infection distribution across the skin, therefore, may relate to differences in skin microbiomes. However, characterization of microbiome variation within and among amphibian individuals is needed. We utilized 16S rRNA gene amplicon sequencing to compare microbiomes of ten body regions from nine captive R. sierrae individuals and their tank environments. While frogs harbored distinct microbial communities compared to their tank environments, tank identity was associated with more variation in frog microbiomes than individual frog identity. Within individuals, we detected differences between microbiomes of body regions where Bd infection would be expected compared to regions that infrequently experience infection. Notably, the bacterial families Burkholderiaceae (phylum Proteobacteria) and Rubritaleaceae (phylum Verrucomicrobia) were dominant on frog skin, and the relative abundances of undescribed members of these families were important to describing differences among and within individuals. Two undescribed Burkholderiaceae taxa were found to be putatively Bd -inhibitory, and both showed higher relative abundance on body regions where Bd infection is often localized. These findings highlight the importance of considering intrapopulation and intraindividual heterogeneities, which could provide insights relevant to predicting localized interactions with pathogens.}, }
@article {pmid39975358, year = {2025}, author = {Dohadwala, S and Shah, P and Farrell, M and Politch, J and Marathe, J and Costello, CE and Anderson, DJ}, title = {Sialidases derived from Gardnerella vaginalis remodel the sperm glycocalyx and impair sperm function.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.01.636076}, pmid = {39975358}, issn = {2692-8205}, abstract = {UNLABELLED: Bacterial vaginosis (BV), a dysbiosis of the vaginal microbiome, affects approximately 29 percent of women worldwide (up to 50% in some regions) and is associated with several adverse health outcomes including preterm birth and increased incidence of sexually transmitted infection (STI). BV-associated bacteria, such as Gardnerella vaginalis and Prevotella timonensis, damage the vaginal mucosa through the activity of sialidase enzymes that remodel the epithelial glycocalyx and degrade mucin glycoproteins. This damage creates an inflammatory environment which likely contributes to adverse health outcomes. However, whether BV-associated glycolytic enzymes also damage sperm during their transit through the reproductive tract has not yet been determined. Here, we show that sialidase-mediated glycocalyx remodeling of human sperm increases sperm susceptibility to damage within the female reproductive tract. In particular, we report that desialylated human sperm demonstrate increased susceptibility to complement lysis and agglutination, as well as decreased sperm transit through cervical mucus. Our results demonstrate a mechanism by which BV-associated sialidases may affect sperm survival and function and potentially contribute to adverse reproductive outcomes such as preterm birth and infertility.<br><br>SIGNIFICANCE STATEMENT: Sperm surface glycans are crucial for reproductive and immune processes in the female reproductive tract. We found that sialidases derived from BV-associated bacteria remodel the sperm glycocalyx resulting in aberrant agglutination, mucus trapping, and complement-mediated cytolysis of sperm. These results implicate glycolytic damage to sperm as a potential mechanism for BV-associated adverse reproductive outcomes. Classification: Biological Sciences, Immunology and Inflammation.}, }
@article {pmid39975193, year = {2025}, author = {Liu, M and Liu, C and Cevallos, N and Orbach, BN and Hernandez, CJ and Fu, X and Lee, J and Booth, SL and Shea, MK}, title = {Dietary Menaquinone-9 Supplementation Does Not Influence Bone Tissue Quality or Bone Mineral Density in Mice.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.29.635567}, pmid = {39975193}, issn = {2692-8205}, abstract = {UNLABELLED: Vitamin K has been implicated in skeletal health because vitamin K-dependent proteins are present in bone. While there are multiple forms of vitamin K, most research has focused on phylloquinone, which is found mainly in plant-based foods, and its metabolite menaquinone-4 (MK4). However, there are additional forms of vitamin K that are bacterially produced that appear to influence bone health but have not yet been studied extensively. Herein, we evaluated the effects of menaquinone-9 (MK9), a bacterially produced form of vitamin K on bone tissue quality and density in young mice. Four-week-old male (n=32) and female (n=32) C57BL/6 mice were supplemented with 0.06 mg/kg diet or 2.1 mg/kg diet of MK9 for 12 weeks. During week 11, a sub-group of mice (n=7/sex/group) received daily deuterium-labeled MK9 to trace its metabolic fate in bone. Liver MK4 and MK9 were significantly higher in mice fed 2.1 mg MK9/kg compared to those receiving 0.06 mg MK9/kg, regardless of sex (all p ≤ 0.017). MK4 was the only vitamin K form detected in bone, with 63-67% of skeletal MK4 in mice fed 2.1 mg MK9/kg derived from deuterium-labeled MK9. Femoral tissue strength, maximum bending moment, section modulus, and bone mineral density did not differ significantly across diet groups in either sex (all p≥0.083). Cross-sectional area (p=0.003) and moment of inertia (p=0.001) were lower in female mice receiving 2.1 mg MK9/kg compared to those receiving 0.06 mg MK9/kg, but no differences were found in male mice. Higher bone MK4 concentrations did not correlate with higher bone tissue quality or density. Despite dietary MK9 being a dietary precursor to MK4 in bone, dietary MK9 supplementation did not affect bone tissue quality or bone mineral density.<br><br>LAY SUMMARY: Most research about vitamin K and bone health has focused on phylloquinone, the plant-based vitamin K form, and its metabolite menaquinone-4. Because interest in bacterially produced forms of vitamin K, which are abundant in the intestinal microbiome, is growing, we evaluated the effect of menaquinone-9 (a bacterially-produced form of vitamin K) on skeletal health. We supplemented mice with low and high doses of menaquinone-9 and also used stable-isotope labeled menaquinone-9 to trace its conversion to menaquinone-4 in bone. We found menaquinone-9 served as a precursor to menaquinone-4 in bone, but menaquinone-9 supplementation did not improve bone health.}, }
@article {pmid39975153, year = {2025}, author = {Treat, BR and Hobeika, J and Duggar, M and Fields, T and Guy, C and Black, M and Kohler, CM and Margolis, EB}, title = {In vivo Imaging and Tracking of VRE-microbiota Interactions via Anaerobic Fluorescent Reporters in Extremely Drug-resistant Bacteria.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.08.637206}, pmid = {39975153}, issn = {2692-8205}, abstract = {Vancomycin-resistant Enterococcus faecium (VREfm) has emerged as a major nosocomial pathogen, but studying its host and microbiome interactions remains challenging due to limited genetic tools. Current obstacles include extensive intrinsic and acquired resistance that precludes use of conventional selection markers, poor plasmid maintenance, and oxygen-dependent reporters unsuitable for gut environments. Here we present an integrated toolkit that enables robust genetic manipulation and in vivo tracking of VREfm. We developed a universal puromycin selection system effective across diverse clinical isolates and an enhanced pheS** counterselection marker for stable genomic integration. We identified two neutral genomic loci that support reporter genes insertion without fitness cost. Using this system, we demonstrate long-term tracking of VREfm colonization, strain competition and host-microbiome interactions in mouse models via chromosomally-integrated anaerobic fluorescent proteins (eUnaG2 and smURFP). This toolkit advances the study of VREfm pathogenesis by enabling stable genetic manipulation of even the most resistant clinical isolates and direct visualization of host-microbe interactions in ecologically and immunologically relevant in vivo environments.}, }
@article {pmid39975146, year = {2025}, author = {Munoz Briones, J and Ball, BK and Jena, S and Lescun, TB and Chan, DD and Brubaker, DK}, title = {Rumenomics: Evaluation of rumen metabolites from healthy sheep identifies differentially produced metabolites across sex, age, and weight.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.05.636747}, pmid = {39975146}, issn = {2692-8205}, abstract = {BACKGROUND: The rumen harbors a diverse and dynamic microbiome vital in digesting vegetation into metabolic byproducts for energy and general biological function. Although previous studies have reported connections between the rumen and the overall health of the sheep, the exact biological process by which this occurs is not well understood. Therefore, our study aimed to quantify sheep rumen metabolites to determine if enriched biological pathways are differentiable across phenotypic features of sex, age, and weight.<br><br>RESULTS: We collected and quantified metabolites of rumen samples from sixteen sheep using liquid chromatography-tandem mass spectrometry. We performed a series of univariate and multivariate statistical analyses to interpret the rumen metabolomics data. To identify metabolic pathways associated with the phenotypic features of sex, weight, and age, we used MetaboAnalyst, which identified amino acid metabolism as a distinguishing factor. Among the pathways, phenylalanine metabolism emerged as a key pathway differentiating sheep based on sex and age. Additionally, phenylalanine, tyrosine, and tryptophan biosynthesis were exclusively associated with age. In univariate linear models, we also discovered that these amino acid and protein pathways were associated with weight by age-corrected effect. Finally, we identified arginine and proline biosynthesis as a pathway linked to metabolites with weight.<br><br>CONCLUSION: Our study identified differential pathways based on the sex, age, and weight features of sheep. Metabolites produced by the rumen may act as an indicator for sheep health and other ruminants. These findings encourage further investigation of the differentially produced metabolites to assess overall sheep health.}, }
@article {pmid39975143, year = {2025}, author = {Sudi, S and Suresh, SD and Kolli, T and Porras, AM}, title = {Trymethylamine-N-oxide, a gut-derived metabolite, induces myofibroblastic activation of valvular interstitial cells through endoplasmic reticulum stress.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.06.636980}, pmid = {39975143}, issn = {2692-8205}, abstract = {Calcific aortic valve disease currently lacks effective treatments beyond surgical valve replacement, due to an incomplete understanding of its pathogenesis. Emerging evidence suggests that the gut microbiome influences cardiovascular health through the production of metabolites derived from dietary components. Among them, trimethylamine-N-oxide (TMAO) has been identified as a potential causal factor for several cardiovascular conditions. However, its role in the development of aortic valve disease remains poorly understood. This study sought to investigate the impact of TMAO on valvular interstitial cells (VICs), the most abundant cell type in the aortic valve. Here, we demonstrate that TMAO activates VICs towards a myofibroblastic profibrotic phenotype. Using an in vitro protocol to generate quiescent VICs, we found that TMAO induces the upregulation of myofibroblastic markers in a sex-independent manner. These quiescent VICs were more sensitive to TMAO than conventionally cultured VICs. Treatment with TMAO also elevated extracellular matrix production and oxidative stress, phenotypic hallmarks of an activated profibrotic state. Finally, inhibition of the endoplasmic reticulum stress kinase prior to TMAO treatment blocked all effects of this metabolite. These findings suggest that TMAO contributes to the early stages of valve disease by promoting VIC activation through endoplasmic reticulum stress mechanisms. Understanding the role of TMAO and other gut-derived metabolites in the pathogenesis of valve disease could inform the development of novel preventive or therapeutic strategies to modify or delay disease progression. Furthermore, these insights underscore the importance of host-microbiome interactions and highlight the potential for targeted dietary interventions to mitigate cardiovascular disease risk.}, }
@article {pmid39975140, year = {2025}, author = {Oppenheimer, M and Tao, J and Moidunny, S and Roy, S}, title = {Anxiety-like behavior during protracted morphine withdrawal is driven by gut microbial dysbiosis and attenuated with probiotic treatment.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.29.633224}, pmid = {39975140}, issn = {2692-8205}, abstract = {The development of anxiety during protracted opioid withdrawal heightens the risk of relapse into the cycle of addiction. Understanding the mechanisms driving anxiety during opioid withdrawal could facilitate the development of therapeutics to prevent negative affect and promote continued abstinence. Our lab has previously established the gut microbiome as a driver of various side effects of opioid use, including analgesic tolerance and somatic withdrawal symptoms. We therefore hypothesized that the gut microbiome contributes to the development of anxiety-like behavior during protracted opioid withdrawal. In this study, we first established a mouse model of protracted morphine withdrawal, characterized by anxiety-like behavior and gut microbial dysbiosis. Next, we used fecal microbiota transplantation (FMT) to show that gut dysbiosis alone is sufficient to induce anxiety-like behavior. We further demonstrate that probiotic therapy during morphine withdrawal attenuates the onset of anxiety-like behavior, highlighting its therapeutic potential. Lastly, we examined transcriptional changes in the amygdala of morphine-withdrawn mice treated with probiotics to explore mechanisms by which the gut-brain axis mediates anxiety-like behavior. Our results support the use of probiotics as a promising therapeutic strategy to prevent gut dysbiosis and associated anxiety during opioid withdrawal, with potential implications for improving treatment outcomes in opioid recovery programs.}, }
@article {pmid39975138, year = {2025}, author = {Cohen, Z and Choi, J and Peregrina, K and Khan, S and Wolfson, S and Sherman, C and Augenlicht, L and Kelly, L}, title = {Diet links gut chemistry with cancer risk in C57Bl/6 mice and human colorectal cancer patients.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.27.635083}, pmid = {39975138}, issn = {2692-8205}, abstract = {BACKGROUND &amp; AIMS: Western-style diets, characterized by higher fat and protein, and low micronutrient levels, promote the development of colorectal cancer (CRC). Here, we investigate the role of a Western diet on microbiome composition, sulfide production, and intestinal epithelial damage in pre-CRC mice, and validate taxonomic changes in a meta-analysis of human CRC patients.<br><br>METHODS: NWD1 is a purified Western-style diet that produces sporadic intestinal and colon tumors in wild-type C57BL/6 mice in the absence of genetic or carcinogen exposure. To determine how this diet influences cancer risk by shaping microbial composition and sulfide chemistry, mice were fed NWD1 or a purified control diet for 24 weeks. Microbiome composition, sulfide production, and intestinal stem cell mRNA expression were assessed. Observed microbiome changes were validated in a human CRC meta-analysis.<br><br>RESULTS: Fecal sulfide levels were tripled in NWD1-fed mice (P< 0.00001), concurrent with increased abundance of the sulfidogenic Erysipelotrichaceae family. NWD1-fed mice had increased expression of mitochondrial sulfide oxidation genes in Lgr5 [hi] intestinal stem cells, demonstrating an adaptive response to elevated sulfide. In a meta-analysis of human CRC studies, we observed that Erysipelotrichaceae were associated with CRC, validating both canonical CRC microbes such as Solobacterium moorei and highlighting the potential contribution of previously unrecognized, disease-associated microbes.<br><br>CONCLUSIONS: Our analyses connect the risk factors of Western diet, sulfide, and epithelial damage in a pre-cancer mouse model to microbiome changes observed in human CRC patients and suggest that microbial signatures of CRC and gut ecosystem alteration may manifest long before disease development.}, }
@article {pmid39975029, year = {2025}, author = {Zhang, XS and Wang, Y and Sun, H and Zerbe, C and Falcone, E and Bhattacharya, S and Zhang, M and Gao, Z and Diaz-Rubio, ME and Bharj, D and Patel, D and Pan, S and Ro, G and Grenard, J and Armstrong, A and Yin, YS and Dominguez-Bello, MG and Holland, S and Su, X and Blaser, MJ}, title = {Gut microbiota phospholipids regulate intestinal gene expression and can counteract the effects of antibiotic treatment.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.28.633906}, pmid = {39975029}, issn = {2692-8205}, abstract = {The gut microbiome influences immune and metabolic homeostasis. Our research using non-obese diabetic (NOD) mice revealed that early-life antibiotic exposure remodels the gut microbiome affecting metabolism and accelerating type 1 diabetes (T1D) incidence, with cecal material transplant (CMT) mitigating the damage. Now examining murine intestinal lipidomic profiles, we identified 747 compounds. Comparing the lipidomic profiles of cecal contents of conventional and germ-free mice and their diets, we identified 87 microbially-produced lipids reduced by antibiotic exposure but CMT-restored. Parallel analysis of human fecal lipid profiles after azithromycin-exposure showed significant alterations with substantial overlap with mice. In vitro co-culture with mouse macrophages or small intestinal epithelial cells and human colonic epithelial cells identified phospholipids that repress inflammation through the NF κ B pathway. Oral administration of these phospholipids to antibiotic-treated NOD mice reduced expression of ileal genes involved in early stages of T1D pathogenesis. These findings indicate potential therapeutic anti-inflammatory roles of microbially-produced lipids.}, }
@article {pmid39975011, year = {2025}, author = {Ziemski, M and Gehret, L and Simard, A and Dau, SC and Risch, V and Grabocka, D and Matzoros, C and Wood, C and Cabrera, PM and Hernández-Velázquez, R and Herman, C and Evans, K and Robeson, MS and Bolyen, E and Caporaso, JG and Bokulich, NA}, title = {MOSHPIT: accessible, reproducible metagenome data science on the QIIME 2 framework.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.27.635007}, pmid = {39975011}, issn = {2692-8205}, abstract = {Metagenome sequencing has revolutionized functional microbiome analysis across diverse ecosystems, but is fraught with technical hurdles. We introduce MOSHPIT (https://moshpit.readthedocs.io), software built on the QIIME 2 framework (Q2F) that integrates best-in-class CAMI2-validated metagenome tools with robust provenance tracking and multiple user interfaces, enabling streamlined, reproducible metagenome analysis for all expertise levels. By building on Q2F, MOSHPIT enhances scalability, interoperability, and reproducibility in complex workflows, democratizing and accelerating discovery at the frontiers of metagenomics.}, }
@article {pmid39974997, year = {2025}, author = {Qu, EB and Baker, JS and Markey, L and Khadka, V and Mancuso, C and Tripp, D and Lieberman, TD}, title = {Intraspecies associations from strain-rich metagenome samples.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.07.636498}, pmid = {39974997}, issn = {2692-8205}, abstract = {Genetically distinct strains of a species can vary widely in phenotype, reducing the utility of species-resolved microbiome measurements for detecting associations with health or disease. While metagenomics theoretically provides information on all strains in a sample, current strain-resolved analysis methods face a tradeoff: de novo genotyping approaches can detect novel strains but struggle when applied to strain-rich or low-coverage samples, while reference database methods work robustly across sample types but are insensitive to novel diversity. We present PHLAME, a method that bridges this divide by combining the advantages of reference-based approaches with novelty awareness. PHLAME explicitly defines clades at multiple phylogenetic levels and introduces a probabilistic, mutation-based, framework to accurately quantify novelty from the nearest reference. By applying PHLAME to publicly available human skin and vaginal metagenomes, we uncover previously undetected clade associations with coexisting species, geography, and host age. The ability to characterize intraspecies associations and dynamics in previously inaccessible environments will propel new mechanistic insights from accumulating metagenomic data.}, }
@article {pmid39974986, year = {2025}, author = {Wasney, M and Briscoe, L and Wolff, R and Ghezzi, H and Tropini, C and Garud, N}, title = {Uniform bacterial genetic diversity along the guts of mice inoculated with human stool.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.28.635365}, pmid = {39974986}, issn = {2692-8205}, abstract = {Environmental gradients exist throughout the digestive tract, driving spatial variation in the membership and abundance of bacterial species along the gut. However, less is known about the distribution of genetic diversity within bacterial species along the gut. Understanding this distribution is important because bacterial genetic variants confer traits important for the functioning of the microbiome and are also known to impart phenotypes to the hosts, including local inflammation along the gut and the ability to digest food. Thus, to be able to understand how the microbiome functions at a mechanistic level, it is essential to understand how genetic diversity is organized along the gut and the ecological and evolutionary processes that give rise to this organization. In this study, we analyzed bacterial genetic diversity of approximately 30 common gut commensals in five regions along the gut lumen in germ-free mice colonized with the same healthy human stool sample. While species membership and abundances varied considerably along the gut, genetic diversity within species was substantially more uniform. Driving this uniformity were similar strain frequencies along the gut, implying that multiple, genetically divergent strains of the same species can coexist within a host without spatially segregating. Additionally, the approximately 60 unique evolutionary adaptations arising within mice tended to sweep throughout the gut, showing little specificity for particular gut regions. Together, our findings show that genetic diversity may be more uniform along the gut than species diversity, which implies that species presence-absence may play a larger role than genetic variation in responding to varied environments along the gut.}, }
@article {pmid39974953, year = {2025}, author = {Cansado-Utrilla, C and Saldaña, MA and Golovko, G and Khanipov, K and Wild, AL and Brettell, LE and Weaver, SC and Heinz, E and Hughes, GL}, title = {Mosquito host background influences microbiome-ZIKV interactions in field and laboratory-reared Aedes aegypti.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.02.636091}, pmid = {39974953}, issn = {2692-8205}, abstract = {UNLABELLED: The mosquito microbiota represents an intricate assemblage of microorganisms, comprising bacteria, fungi, viruses, and protozoa. Factors modulating microbiome abundance and composition include host genetic background, environmental parameters, and pathogen exposure. Conversely, the microbiome profoundly influences pathogen infection of the mosquito host and thus harbours considerable potential to impact the transmission of vector-borne diseases. As such, there is a growing interest in using the microbiome in novel vector-control strategies, including exploiting the natural ability of some microbes to interfere with infection of the vectors by pathogens. However, before novel microbiome-based vector control approaches can move towards translation, a more complete understanding of the interactions between mosquitoes, their microbiome, and the pathogens they transmit, is required to better appreciate how variation in the microbiome of field mosquitoes affects these interactions. To examine the impact of the host background and the associated diversity of microbiomes within distinct hosts, but without artificially manipulating the microbiome, we exposed several laboratory-reared and field-collected Aedes aegypti mosquito lines to Zika virus (ZIKV) and correlated their microbial load and composition to pathogen exposure and viral infection success. We observed significant differences in ZIKV exposure outcomes between the different mosquito lines and their associated microbiomes, and found that ZIKV alteration of the microbiomes was distinct in different lines. We also identified microbial taxa correlating with either ZIKV infection or a lack of infection. In summary, our study provides novel insights into the variability of pathogen interactions within the mosquito holobiont. A more complete understanding of which factors influence the tripartite interactions between Aedes mosquitoes, their microbiome, and arboviral pathogens, will be critical for the development of microbial-based interventions aimed at reducing vector-borne disease burden.<br><br>AUTHOR SUMMARY: The mosquito microbiome composition differs within an individual across its development, as well as between individual mosquitoes at the same developmental stage, and between spatially or genomically different mosquito populations. The microbiome is highly relevant for the ability of mosquitoes to transmit pathogens. Furthermore, certain microbes have been shown to influence pathogen infection of the mosquito, while conversely, infection with a pathogen can alter the mosquito microbiome. However, we have a poor understanding how universally conserved these pathogen-related effects observed in a specific host-microbiome combination are in different mosquito populations with their respective microbiomes. To address this, we infected different mosquito lines, either reared in the laboratory or caught in the field and examined the microbiomes after exposure to Zika virus (ZIKV) compared to unchallenged microbiomes. We also examined how the virus infection progressed in different mosquito lines and correlations with further microbiome changes. The observed microbiome responses differed between host lines, potentially due to either different microbiomes associated with the respective hosts. Alternatively, the host may respond differently to the viral infection, which subsequently alters the microbiome in a distinct manner, or a combination of host and microbiome effects may occur. As microbes are being evaluated for novel approaches to control mosquito-borne disease, our findings are highly relevant to contribute to a more complete understanding of host-microbe interactions which will be critical to develop these approaches. Variation of the microbiome of different mosquito lines need to be considered in experimental designs and when interpreting results from specific studies. It is especially relevant for deployment of interventions in the field where microbial variability is known to be higher and where variation is observed between mosquito populations.}, }
@article {pmid39974910, year = {2025}, author = {Castro-Cordova, P and Lopez-Garcia, OK and Orozco, J and Montes-Bravo, N and Gil, F and Pizarro-Guajardo, M and Paredes-Sabja, D}, title = {Clostridioides difficile major toxins remodel the intestinal epithelia, affecting spore adherence/internalization into intestinal tissue and their association with gut vitronectin.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.29.635439}, pmid = {39974910}, issn = {2692-8205}, abstract = {The most common cause of healthcare-associated diarrhea and colitis in the U.S., is Clostridioides difficile , a spore-forming pathogen. Two toxins, TcdA and TcdB, are major virulence factors essential for disease manifestations, while C. difficile spores are essential for disease transmission and recurrence. Both toxins cause major damage to the epithelial barrier, trigger massive inflammation, and reshape the microbiome and metabolic composition, facilitating C. difficile colonization. C. difficile spores, essential for transmission and recurrence of the disease, persist adhered and internalized in the intestinal epithelia. Studies have suggested that toxin-neutralization in combination with antibiotic during CDI treatment in humans significantly reduces disease recurrence, suggesting a link between toxin-mediated damage and spore persistence. Here, we show that TcdA/TcdB-intoxication of intestinal epithelial Caco-2 cells leads to remodeling of accessible levels of fibronectin (Fn) and vitronectin (Vn) and their cognate alpha-integrin subunits. While TcdB-intoxication of intestinal tissue had no impact in accessible levels of Fn and Vn, but significantly increased levels of intracellular Vn. We observed that Fn and Vn released to the supernatant readily bind to C. difficile spores in vitro , while TcdB-intoxication of intestinal tissue led to increased association of C. difficile spores with gut Vn. Toxin-intoxication of the intestinal tissue also contributes to increased adherence and internalization of C. difficile spores. However, TcdB-intoxicated ligated loops infected of mice treated with Bezlotoxumanb (monoclonal anti- TcdB antibodies) did not prevent TcdB-mediated increased spore adherence and internalization into intestinal tissue. This study highlights the importance of studying the impact of C. difficile toxins of host tissues has in C. difficile interaction with host surfaces that may contribute to increased persistence and disease recurrence.}, }
@article {pmid39974825, year = {2024}, author = {Wu, RR and Nie, DR and He, FH and Li, ZH and Xu, F}, title = {Combined metabolomics and 16S rDNA sequence analyses of the gut microbiome reveal the action mechanism of Fructus Akebiae against hepatic fibrosis.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1492383}, pmid = {39974825}, issn = {2296-858X}, abstract = {OBJECTIVES: To explore the mechanism underlying the effect of Fructus Akebiae (FAE) against hepatic fibrosis in mice through combined network pharmacology, liver metabolomics, and 16S rDNA analyses of the gut microbiota.<br><br>METHODS: In this study, we randomly divided mice into the control, model, FAE high-dose, FAE medium-dose, and FAE low-dose groups to analyze the pathological changes in the hepatic fibrosis and levels of the &#x3b1;-SMA, collagen 1, Nuclear Factor Kappa B (NF-&#x3ba; B), Toll Like Receptor 4 (TLR4). The gut microbiota was analyzed through 16S rDNA sequencing analysis of liver metabolites using liquid chromatography-mass spectrometry. Furthermore, network pharmacology was used to determine the specific molecular regulation mechanism of FAE in hepatic fibrosis treatment.<br><br>RESULTS: FAE treatment markedly improved the pathological changes in the hepatic fibrosis. Analysis revealed that FAE administration reversed the carbon tetrachloride (CCl4)-induced dysbiosis by increasing the abundance of Akkermansia and reducing that of Cyanobacteria. Additionally, metabolomic analysis showed that FAE treatment reversed the CCl4-induced metabolic disorders by regulating amino and nucleotide sugar metabolism. Furthermore, correlation analysis showed that Akkermansia and Verrucomicobiota were closely related to D-tolasaccharide and maltotetraose saccharide. Moreover, network pharmacology indicated that FAE might regulate the signaling pathway through the JUN/CASP3/NOS3/PTGS2/HSP90AA1 during treatment.<br><br>CONCLUSION: FAE may be a promising treatment for hepatic fibrosis, and its protective effects are associated with improvements in the microbiome and metabolic disorders.}, }
@article {pmid39974372, year = {2024}, author = {Wu, H and Li, Y and Jiang, Y and Li, X and Wang, S and Zhao, C and Yang, X and Chang, B and Yang, J and Qiao, J}, title = {Machine learning prediction of obesity-associated gut microbiota: identifying Bifidobacterium pseudocatenulatum as a potential therapeutic target.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1488656}, pmid = {39974372}, issn = {1664-302X}, abstract = {BACKGROUND: The rising prevalence of obesity and related metabolic disorders highlights the urgent need for innovative research approaches. Utilizing machine learning (ML) algorithms to predict obesity-associated gut microbiota and validating their efficacy with specific bacterial strains could significantly enhance obesity management strategies.<br><br>METHODS: We leveraged gut microbiome data from 1,563 healthy individuals and 2,043 overweight patients sourced from the GMrepo database. We assessed the anti-obesity effects of Bifidobacterium pseudocatenulatum through experimentation with Caenorhabditis elegans and C3H10T1/2 cells.<br><br>RESULTS: Our analysis revealed a significant correlation between gut bacterial composition and body weight. The top 40 bacterial species were utilized to develop ML models, with XGBoost demonstrating the highest predictive accuracy. SHAP analysis indicated a negative association between the relative abundance of six bacterial species, including B. pseudocatenulatum, and body mass index (BMI). Furthermore, B. pseudocatenulatum was shown to reduce lipid accumulation in C. elegans and inhibit lipid differentiation in C3H10T1/2 cells.<br><br>CONCLUSION: Bifidobacterium pseudocatenulatum holds potential as a therapeutic agent for managing diet-induced obesity, underscoring its relevance in microbiome-based obesity research and intervention.}, }
@article {pmid39974142, year = {2025}, author = {Dravillas, C and Williams, N and Husain, M and Hoyd, R and Hussein, A and Meara, A and Lynn, M and Bibi, A and Conrad, B and Lepola, N and Gray, S and Bodnar, M and Arya, N and Roberts, S and Hoang, P and Apparicio, J and Merrill, D and Wu, R and Verschraegen, C and Burd, CE and Kendra, K and Spakowicz, D}, title = {The Association of the Microbiome with Melanoma Tumor Response to Immune Checkpoint Inhibitor Treatment and Immune-Related Adverse Events (NCT05102773).}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.30.25321413}, pmid = {39974142}, abstract = {Improved understanding of the factors that underlie immune checkpoint inhibitor (ICI) response and toxicity are needed as only half of patients with metastatic melanoma respond, and 10-40% experience immune-related adverse events (irAEs). Modifying the gut microbiome could positively affect response to ICIs and reduce toxicities. Here, we sought to determine if the pre-treatment gut microbiome predicts ICI response or toxicity in the setting of metastatic melanoma. Melanoma patients (n=88) over 18 years of age, planning to receive ICI therapy enrolled in a prospective observational cohort study at The Ohio State University Comprehensive Cancer Center Skin Cancer Clinic. Patients taking corticosteroids for indications other than adrenal physiologic replacement were excluded. Stools were collected at baseline, within 10 days of an irAE as determined by CTCAE v 5.0 criteria, and at 12 weeks. ICI response and progression-free survival (PFS) were evaluated q12 weeks using Response Evaluation Criteria in Solid Tumors (RECIST v1.1). Metagenomic whole-genome shotgun sequencing of the microbiome was classified using MetaPhlAn4/HUMAnN3 and differential abundance analyzed with ANCOM-BC2. Of the 88 patients enrolled, 41 had metastatic disease and complete data. There were 25 participants classified as responders, defined as having complete response or partial response according to RECIST criteria, or stable disease with 6-month PFS. Grade ≥ 1 irAEs were observed in 15/41 participants. The abundance of Intestinimonas butyriciproducens (q-value = 0.002) and Longicatena caecimuris (q-value = 0.003) were enriched in responders, Tenericutes (q-value= 0.001) and Lachnospira sp. NSJ 43 (q-value =0.002) in non-responders. Blautia luti , as well as several other Lachnospiraceae , were associated with response and no irAE (response q-value = 0.02, no irAE q-value = 0.02). The association of response to ICIs with several taxa in the family Lachnospiraceae , a prevalent microbial family in the gut, is consistent with prior research, which has found that this family may influence treatment outcomes through various mechanisms, such as immune regulation, metabolism, and pathogen exclusion. While no statistical relationship was observed between response and irAEs in this cohort, the microbes associated with both could serve as biomarkers. Future studies to assign causal roles for (specific microbes) in response and toxicity could identify mechanisms to improve patient outcomes.}, }
@article {pmid39974080, year = {2025}, author = {McCann, JR and Yang, C and Bihlmeyer, N and Tang, R and Truong, T and An, J and Jawahar, J and Ilkayeva, O and Muehlbauer, M and Hu, ZZ and Dressman, H and Poppe, L and Granek, J and David, LA and Shi, P and Balikcioglu, PG and Shah, S and Armstrong, SC and Newgard, CB and Seed, PC and Rawls, JF}, title = {Branched chain amino acid metabolism and microbiome in adolescents with obesity during weight loss therapy.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.03.25321363}, pmid = {39974080}, abstract = {BACKGROUND: Towards improving outcomes for adolescents with obesity, we aimed to define metabolic and microbiome phenotypes at baseline and post-weight loss intervention.<br><br>METHODS: The Pediatric Obesity Microbiome and Metabolism Study enrolled 220 adolescents aged 10-18 with severe obesity (OB) and 67 healthy weight controls (HWC). Blood, stool, and clinical measures were collected at baseline and after a 6-month intervention for the OB group. Serum metabolomic and fecal microbiome data were analyzed for associations with BMI, insulin resistance, and inflammation. Fecal microbiome transplants were performed on germ-free mice using samples from both groups to assess weight gain and metabolomic changes.<br><br>RESULTS: Adolescents with OB exhibited elevated serum branched-chain amino acids (BCAA) but reduced ketoacid metabolites (BCKA) compared to HWC. This pattern was sex- and age-dependent, unlike adults with OB, who showed elevated levels of both. The fecal microbiomes of adolescents with OB and HWC had similar diversity but differed in membership and functional potential. FMT from OB and HWC donors had similar effects on mouse body weight, with specific taxa linked to weight gain in FMT recipients. Longitudinal analysis identified metabolic and microbial features correlated with changes in health measures during the intervention.<br><br>CONCLUSION: Adolescents with OB have unique metabolomic adaptations and microbiome signatures compared to their HWC counterparts and adults with OB.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT03139877 (Observational Study) and NCT02959034 (Repository).<br><br>FUNDING SOURCES: American Heart Association Grants: 17SFRN33670990, 20PRE35180195National Institute of Diabetes and Digestive and Kidney Diseases Grant: R24-DK110492.}, }
@article {pmid39974037, year = {2025}, author = {Ancira, J and Gabrilska, R and Tipton, C and Miller, C and Stickley, Z and Omeir, K and Wakeman, C and Little, T and Wolcott, J and Philips, CD}, title = {A Structural Equation Model Predicts Chronic Wound Healing Time Using Patient Characteristics and Wound Microbiome Composition.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.23.25320984}, pmid = {39974037}, abstract = {Wound etiology, host characteristics, and the wound microbiome contribute to chronic wound development. Yet, there is little accounting for the relative importance of these factors to predict wound healing. Here, a structural equation model was developed to provide such an explanatory and predictive framework. Chronic wounds from 565 patients treated at a clinic practicing biofilm-based wound care were included. Patient information included DNA sequencing-based wound microbiome clinical reports corresponding to initial clinical visit. Wound microbiome data was integrated into the SEM as a latent variable using a pre-modeling parcel optimization routine presented herein for the first time (available as R library parcelR). A microbiome latent construct associated with improved healing was validated, and the final SEM included this latent construct plus three species associated with diminished healing (Anaerococcus vaginalis, Finegoldia magna, Pseudomonas aeruginosa), as well as smoking, wound volume, slough, exudate, edema, percent granulation, and wound etiology This model explained 46% of variation in healing time with the microbiome contributing the largest proportion of variance explained. Model validity was confirmed with an independent cohort (n = 79) through which ∼60% of variation in healing time was predicted. This model can serve as foundation for development of a predictive tool that may have clinical utility.}, }
@article {pmid39974023, year = {2025}, author = {Igudesman, D and Yu, G and Dutta, T and Carnero, EA and Krajmalnik-Brown, R and Smith, SR and Corbin, KD}, title = {Global metabolite profiling in feces, serum, and urine yields insights into energy balance phenotypes induced by diet-driven microbiome remodeling.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.02.05.25321733}, pmid = {39974023}, abstract = {BACKGROUND: Preclinical literature and behavioral human data suggest that diet profoundly impacts the human gut microbiome and energy absorption-a key determinant of energy balance. To determine whether these associations are causal, domiciled controlled feeding studies with precise measurements of dietary intake and energy balance are needed. Metabolomics-a functional readout of microbiome modulation-can help identify putative mechanisms mediating these effects. We previously demonstrated that a high-fiber, minimally processed Microbiome Enhancer Diet (MBD) fed at energy balance decreased energy absorption and increased microbial biomass relative to a calorie-matched fiber-poor, highly processed Western Diet (WD).<br><br>OBJECTIVE: To identify metabolic signatures distinguishing MBD from WD feeding and potential metabolomic mechanisms mediating the MBD-induced negative energy balance.<br><br>METHODS: We deployed global metabolomics in feces, serum, and urine using samples collected at the end of a randomized crossover controlled feeding trial delivering 22 days of an MBD and a WD to 17 persons without obesity. Samples were collected while participants were domiciled on a metabolic ward and analyzed using Ultrahigh Performance Liquid Chromatography-Tandem Mass Spectroscopy. Linear mixed effects models tested metabolite changes by diet. Weighted gene network correlation analysis identified metabolite modules correlated with energy balance phenotypes.<br><br>RESULTS: Numerous metabolites consistently altered in the feces, fasting serum, and/or urine may serve as putative dietary biomarkers of MBD feeding. Fecal diet-microbiota co-metabolites decreased by an MBD correlated with reduced energy absorption and increased microbial biomass. An MBD shifted the urinary metabolome from sugar degradation to ketogenesis-evidence of negative energy balance.<br><br>CONCLUSIONS: Precisely controlled diets disparate in microbiota-accessible substrates led to distinct metabolomic signatures in feces, fasting serum, and/or urine. These diet-microbiota co-metabolites may be biomarkers of a "fed" (MBD) or "starved" (WD) gut microbiota associated with energy balance. These findings lay the foundation for unveiling causal pathways linking diet-microbiota co-metabolism to energy absorption.}, }
@article {pmid39973939, year = {2025}, author = {Wang, L and Xi, M and Cao, W and Qin, H and Qin, D and Chen, S and Zhou, S and Hou, Y and Chen, Y and Xiao, X and Zheng, Q and Li, D and Li, Y}, title = {Electroacupuncture alleviates functional constipation by upregulating host-derived miR-205-5p to modulate gut microbiota and tryptophan metabolism.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1517018}, pmid = {39973939}, issn = {1664-302X}, abstract = {Electroacupuncture (EA) has shown promise as a treatment for Functional constipation (FC), with growing evidence suggesting it may enhance gut motility. MicroRNAs (miRNAs) serve as key regulatory molecules mediating host-microbiota interactions. However, the specific fecal miRNAs regulating microbiota composition and metabolism in EA-treated constipated mice, along with their key targets, remain unidentified. We examined fecal microbiome composition, metabolism, and colonic miRNA expression in loperamide-induced constipated mice and EA-treated mice to identify differentially expressed miRNAs and assess their relationships with microbial abundance, metabolism, and gut motility. An antibiotic cocktail and adeno-associated virus were employed to interfere with the gut microbiota and target miRNA in vivo, thereby validating the proposed mechanism. Our results indicate that miR-205-5p, significantly upregulated in fecal and colonic tissues of EA-treated constipated mice, promotes intestinal motility in a microbiome-dependent manner. Specifically, EA promoted the growth of Lactobacillus reuteri, enriched in the feces of constipation-recovered mice, through host-derived miR-205-5p regulation. Furthermore, Lactobacillus reuteri and its tryptophan metabolites (indole-3-acetamide, indole-3-acetic acid, and indole-3-carboxaldehyde) alleviated loperamide-induced constipation. These findings underscore the pivotal role of host-derived miR-205-5p in modulating microbial composition and tryptophan metabolites to enhance intestinal motility through EA.}, }
@article {pmid39973938, year = {2025}, author = {Drago, L and De La Motte, LR and Deflorio, L and Sansico, DF and Salvatici, M and Micaglio, E and Biazzo, M and Giarritiello, F}, title = {Systematic review of bidirectional interaction between gut microbiome, miRNAs, and human pathologies.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1540943}, pmid = {39973938}, issn = {1664-302X}, abstract = {MicroRNAs (miRNAs) and the gut microbiome are key regulators of human health, with emerging evidence highlighting their complex, bidirectional interactions in chronic diseases. miRNAs, influence gene expression and can modulate the composition and function of the gut microbiome, impacting metabolic and immune processes. Conversely, the microbiome can affect host miRNA expression, influencing inflammatory pathways and disease susceptibility. This systematic review examines recent studies (2020-2024) focusing exclusively on human subjects, selected through rigorous inclusion and exclusion criteria. Studies were included if they investigated the interaction between miRNAs and the gut microbiome in the context of gastrointestinal diseases, obesity, autoimmune diseases, cognitive and neurodegenerative disorders, and autism. In vitro, in vivo and in silico analyses were excluded to ensure a strong translational focus on human pathophysiology. Notably, miRNAs, stable and abundant in patients, are emerging as promising biomarkers of microbiome-driven inflammation. This systematic review provides an overview of miRNAs, their regulatory effects on bacterial strains, and their associations with specific diseases. It also explores therapeutic advances and the potential of miRNA-based therapies to restore microbial balance and reduce inflammation.}, }
@article {pmid39973489, year = {2025}, author = {van der Maden, MM and Verbeek, MM and Beckers, M}, title = {Lactobacillaceae and Parkinson's disease: An apparent paradox.}, journal = {Journal of Parkinson's disease}, volume = {}, number = {}, pages = {1877718X241312401}, doi = {10.1177/1877718X241312401}, pmid = {39973489}, issn = {1877-718X}, abstract = {Parkinson's disease (PD) is a neurodegenerative disorder predominantly known for its motor symptoms such as bradykinesia, rigidity and tremor, but the disorder is also increasingly recognized for its association with impaired gastrointestinal function. The composition of the gut microbiome is known to be different in PD compared with healthy individuals. One of the bacterial families with increased abundance in people with PD is Lactobacillaceae. Interestingly, opposite effects have been ascribed to Lactobacillaceae in PD. A number of studies have linked Lactobacillaceae spp. in the gut to worse motor function, and to premature degradation of levodopa. However, other studies have linked administration of Lactobacillaceae-containing probiotics to improved motor function and reduced gastrointestinal problems. In this narrative review, we investigate this apparent paradox. The key to its understanding appears to lie in the specific species of Lactobacillaceae. The species L. plantarum in particular seemed to show a correlation with improved motor symptoms, as well as a reduction in intestinal inflammation, whereas L. brevis, L. curvatus and L. fermentum have properties that might be detrimental to people with PD.}, }
@article {pmid39973244, year = {2025}, author = {Shen, H and Huang, Y and Lin, X and Dai, Z and Zhao, H and Su, WQ and Dahlgren, RA and Xu, J}, title = {Recoupling of Soil Carbon, Nitrogen, and Phosphorus Cycles along a 30 Year Fire Chronosequence in Boreal Forests of China.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c08790}, pmid = {39973244}, issn = {1520-5851}, abstract = {The biogeochemical coupling of soil carbon, nitrogen, and phosphorus (C-N-P) cycles is crucial for maintaining the ecological balance of boreal forests. Yet, the current understanding of wildfire disturbance is only based on changes in elemental contents, thereby lacking any within-ecosystem corroboration of biogeochemical coupling. Here, we conducted a field survey of microbial functional associations for 53 genes related to soil C-N-P cycling from 17 locations spanning a 30 year succession period after high-severity forest fires in the Greater Khingan Mountains (Inner Mongolia-China). We found that bacteria proliferated and dominated the competition with fungi by encoding genes for recalcitrant C decomposition, N fixation, and inorganic N cycling during the postfire early succession. Wildfire prominently decoupled the microbial functional associations of soil C-N-P cycling, particularly in organic-inorganic N turnover. However, over the 30 year succession period, these functional associations recoupled in both soil organic and mineral horizons. Notably, the decoupling of microbial functional associations recovered from a wildfire disturbance faster than the soil C-N-P imbalance. This strong resilience of the microbiome will aid in the recovery of the soil elemental balance and ecosystem stability from the increased intensity of wildfires projected for the boreal forests of China.}, }
@article {pmid39973079, year = {2025}, author = {Prakoeswa, CRS and Huda, BKN and Indrawati, D and Umborowati, MA and Anggraeni, S and Damayanti,  and Murtiastutik, D and Kerob, D}, title = {Effectiveness and Tolerability of an Emollient "Plus" Compared to Urea 10% in Patients With Mild-to-Moderate Atopic Dermatitis.}, journal = {Journal of cosmetic dermatology}, volume = {24}, number = {2}, pages = {e70051}, doi = {10.1111/jocd.70051}, pmid = {39973079}, issn = {1473-2165}, support = {//La Roche-Posay Laboratoire Dermatologique/ ; }, mesh = {Humans ; *Dermatitis, Atopic/drug therapy ; *Emollients/administration &amp; dosage/adverse effects ; *Urea/administration &amp; dosage/adverse effects ; Female ; Adult ; Male ; *Severity of Illness Index ; Young Adult ; Treatment Outcome ; Water Loss, Insensible/drug effects ; Middle Aged ; Skin Cream/administration &amp; dosage/adverse effects ; Quality of Life ; Administration, Cutaneous ; Pruritus/drug therapy/etiology ; Adolescent ; }, abstract = {BACKGROUND: Atopic dermatitis (AD) poses a challenge due to its chronic inflammatory nature. Recent research highlights microbiome dysbiosis as a key contributor. Emollients "plus" are modern moisturizers containing bacterial lysate, improving skin barrier function and reducing Staphylococcus aureus colonization, thus mitigating AD symptoms. Emollient "plus" containing Vitreoscilla filiformis biomass (Aqua Posae filiformis) is efficient in AD, as single adjunct for milder forms or adjunctive to systemic treatments in more severe forms. Standard recommended moisturizers for AD in Indonesia contain urea 10%.<br><br>AIMS: This trial compared an emollient "plus" (Group A) with urea 10% moisturizer (Group B) in the treatment of mild-to-moderate AD.<br><br>PATIENTS/METHODS: Sixty subjects with mild-to-moderate AD were randomized into Groups A and B (30 subjects/group). Test products were applied twice daily for 12&#x2009;weeks. Clinical and instrumental endpoints assessed at Weeks 0, 4, 8, and 12 included Severity Scoring of AD (SCORAD), Pruritus Visual Analog Scale (PVAS), Eczema Area and Severity Index (EASI), Dermatology Life Quality Index (DLQI), Transepidermal Water Loss (TEWL), skin hydration, skin pH, as well as tolerance evaluation.<br><br>RESULTS: Significant differences in favor of the emollient "plus" versus urea 10% were observed on TEWL and skin pH values at Weeks 4, 8, and 12, on SCORAD and skin hydration values at Weeks 8 and 12. EASI, DLQI, and PVAS values differed significantly at Week 12 in favor of Group A. Both products were well tolerated.<br><br>CONCLUSIONS: This emollient "plus" has superior efficacy in improving AD symptoms and skin barrier function compared to urea 10% moisturizer.}, }
@article {pmid39972378, year = {2025}, author = {Gu, W and Huang, Z and Fan, Y and Li, T and Yu, X and Chen, Z and Hu, Y and Li, A and Zhang, F and Fu, Y}, title = {Peripheral blood microbiome signature and Mycobacterium tuberculosis-derived rsRNA as diagnostic biomarkers for tuberculosis in human.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {204}, pmid = {39972378}, issn = {1479-5876}, support = {2017ZX10201301-003-005//National Major Science and Technology Projects of China/ ; LH2024H014//Heilongjiang provincial natural science foundation/ ; }, mesh = {Humans ; *Tuberculosis/blood/diagnosis/microbiology ; *Mycobacterium tuberculosis/genetics ; *Biomarkers/blood ; Male ; Female ; *Microbiota/genetics ; Case-Control Studies ; Adult ; Middle Aged ; RNA, Bacterial/blood/genetics ; ROC Curve ; Exosomes ; }, abstract = {BACKGROUND: Tuberculosis (TB) is a major global health issue. Early diagnosis of TB is still a challenge. Studies are seeking non-sputum biomarker-based TB test. Emerging evidence indicates potential significance of blood microbiome signatures for diseases. However, blood microbiome RNA profiles are unknown in TB. We aimed to characterize the blood microbiome of TB patients and identify Mycobacterium tuberculosis (Mtb) genome-derived small RNA molecules to serve as diagnostic biomarkers for TB.<br><br>METHODS: RNA sequencing data of the blood from TB patients and healthy controls were retrieved from the NCBI-SRA database for analyzing the blood microbiome and identifying rRNA-derived small RNA (rsRNA) of Mtb. Small RNA-seq was performed on plasma exosomes from TB patients and healthy controls. The levels of the candidate Mtb rsRNAs were determined by real-time quantitative reverse transcription PCR (RT-qPCR) on plasma from a separate cohort of 73&#xa0;TB patients and 62 healthy controls.<br><br>RESULTS: The blood microbiome of TB patients consisted of RNA signals from bacteria, fungi, archaea, and viruses, with bacteria accounting for more than 97% of the total. Reduced blood microbial diversity and abundance of 6 Mycobacterium-associated bacterial genera, including Mycobacterium, Priestia, Nocardioides, Agrobacterium, Bradyrhizobium, and Escherichia, were significantly altered in the blood of TB patients. A diagnostic model for TB based on the 6 genera achieved an area under the curve (AUC) of 0.8945. rsRNAs mapped to the Mtb genome were identified from blood and plasma exosomes of TB patients. RT-qPCR results showed that 2 Mtb-derived rsRNAs, 16&#xa0;S-L1 and 16&#xa0;S-L2, could be used as diagnostic biomarkers to differentiate TB patients from healthy controls, with a high co-diagnostic efficacy (AUC&#x2009;=&#x2009;0.7197).<br><br>CONCLUSIONS: A panel of blood microbiome signatures and Mtb-derived rsRNAs can serve as blood biomarkers for TB diagnosis.}, }
@article {pmid39972005, year = {2025}, author = {An, J and Kwon, H and Oh, SY and Kim, YJ}, title = {Association between breast cancer risk factors and blood microbiome in patients with breast cancer.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {6115}, pmid = {39972005}, issn = {2045-2322}, support = {RS-2021-NR058775//National Research Foundation of Korea (NRF) grants funded by the Korean government (MSIT)/ ; RS-2023-00262969//The Ministry of Health and Welfare/ ; 202201770001//Korean Association for Women Surgeons/ ; }, mesh = {Humans ; *Breast Neoplasms/microbiology/blood ; Female ; Risk Factors ; Middle Aged ; *Microbiota ; *Body Mass Index ; Hyperlipidemias/microbiology/blood/complications ; Adult ; Fatty Liver/microbiology/blood ; Hyperglycemia/blood/microbiology ; Faecalibacterium/isolation &amp; purification ; Prognosis ; Aged ; }, abstract = {This study investigated the relationship between risk factors for breast cancer (BC) and the microbiome by comparing the microbiomes of BC patients with fatty liver disease to those with a normal liver. Bacterial extracellular vesicles were collected from each blood sample, and next-generation sequencing was performed. The analysis identified specific microbiome profiles shared among groups with hyperglycaemia, hyperlipidaemia, and high body mass index (BMI), which were then compared with functional biomarkers. In particular, the genus Faecalibacterium was a specific bacterium found in the groups with high concentrations of low-density lipoprotein cholesterol, high BMI, and fatty liver disease. Therefore, when the prognosis of patients with BC was analysed based on Faecalibacterium presence, it was confirmed that patients' prognoses tended to deteriorate. In this study, BC risk factors, such as hyperglycaemia, hyperlipidaemia, fatty liver, and high BMI, were interconnected through the microbiome. This provides insights into how the risk factors for BC are linked and their impact on the microbiome and human health.}, }
@article {pmid39971934, year = {2025}, author = {Jang, EY and Moon, JH and Lee, JH}, title = {Complete genome and transcriptome datasets of Streptococcus salivarius strains from healthy Korean subjects.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {296}, pmid = {39971934}, issn = {2052-4463}, support = {NRF-2021R1A2C2008180//National Research Foundation of Korea (NRF)/ ; }, mesh = {Humans ; *Transcriptome ; Republic of Korea ; *Genome, Bacterial ; *Streptococcus salivarius/genetics ; Fusobacterium nucleatum/genetics ; }, abstract = {The oral microbiome plays a crucial role in maintaining health, with Streptococcus salivarius recognized for its beneficial probiotic functions, including inhibiting pathogenic bacteria and supporting immune regulation, particularly in healthy individuals. While research on S. salivarius has primarily focused on strains originating from non-Asian populations, particularly New Zealand, with some studies also reporting European strains, research on strains originating from Korea has been notably lacking. This dataset provides the complete genome sequences and transcriptomic profiles of 12 S. salivarius strains isolated from healthy Korean individuals. PacBio SMRTbell technology was employed for genome sequencing. Our dataset includes transcriptomic data that reveal functional gene expression patterns under standard growth conditions. The strains analyzed here are particularly valuable as each exhibits a unique interaction with Fusobacterium nucleatum, a pathogen associated with periodontal disease and colorectal cancer, collectively demonstrating diverse patterns of interaction. By offering comprehensive data on strain variation, this resource can serve as a valuable tool for research aimed at understanding and utilizing beneficial oral bacteria.}, }
@article {pmid39971928, year = {2025}, author = {Peesh, P and Blasco-Conesa, MP and El Hamamy, A and Khan, R and Guzman, GU and Honarpisheh, P and Mohan, EC and Goodman, GW and Nguyen, JN and Banerjee, A and West, BE and Ko, KA and Korf, JM and Tan, C and Fan, H and Colpo, GD and Ahnstedt, H and Couture, L and Roh, S and Kofler, JK and Moruno-Manchon, JF and Maniskas, ME and Aronowski, J and Ritzel, RM and Lee, J and Li, J and Bryan, RM and Chauhan, A and Venna, VR and McCullough, LD and Ganesh, BP}, title = {Benefits of equilibrium between microbiota- and host-derived ligands of the aryl hydrocarbon receptor after stroke in aged male mice.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1767}, pmid = {39971928}, issn = {2041-1723}, support = {1R01AG070934-01//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; AG058463//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; P30 AG066468/AG/NIA NIH HHS/United States ; 1F31NS118984-01//U.S. Department of Health &amp; Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS)/ ; R35 NS132265/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; *Receptors, Aryl Hydrocarbon/metabolism ; Male ; *Gastrointestinal Microbiome ; Mice ; Ligands ; Humans ; *Microglia/metabolism/immunology ; *Stroke/immunology/metabolism/microbiology ; *Kynurenine/metabolism ; *Dysbiosis/immunology/microbiology ; Mice, Inbred C57BL ; Indoles ; Disease Models, Animal ; Infarction, Middle Cerebral Artery/metabolism/immunology ; Aging/immunology ; Germ-Free Life ; Neuroinflammatory Diseases/immunology/metabolism ; }, abstract = {Recent studies have highlighted the crucial role of microglia (MG) and their interactions with the gut microbiome in post-stroke neuroinflammation. The activation of immunoregulatory pathways, including the aryl hydrocarbon receptor (AHR) pathway, is influenced by a dynamic balance of ligands derived from both the host and microbiota. This study aimed to investigate the association between stroke-induced dysbiosis and the resultant imbalance in AHR ligand sources (loss of microbiota-derived [indole-based] and increase of host-derived [kynurenine-based]) after stroke. Microbiota-derived AHR ligands decreased in human plasma and remained low for days following an ischemic stroke highlighting the translational significance. Transient-middle-cerebral-artery-occlusion was performed in aged wild-type and germ-free male mice. MG-AHR expression and activity increased in both in vivo and ex vivo stroke models. Germ-free mice showed altered neuroinflammation and antigen presentation while aged mice showed reduced infarct volume and neurological deficits following treatment with microbiota-derived AHR ligands after stroke. Restoring a balanced pool of host- and microbiota-derived AHR ligands may be beneficial after stroke and may represent a therapeutic target.}, }
@article {pmid39971742, year = {2025}, author = {Akagbosu, CO and McCauley, KE and Namasivayam, S and Romero-Soto, HN and O'Brien, W and Bacorn, M and Bohrnsen, E and Schwarz, B and Mistry, S and Burns, AS and Perez-Chaparro, PJ and Chen, Q and LaPoint, P and Patel, A and Krausfeldt, LE and Subramanian, P and Sellers, BA and Cheung, F and Apps, R and Douagi, I and Levy, S and Nadler, EP and Hourigan, SK}, title = {Gut microbiome shifts in adolescents after sleeve gastrectomy with increased oral-associated taxa and pro-inflammatory potential.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2467833}, doi = {10.1080/19490976.2025.2467833}, pmid = {39971742}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome ; Adolescent ; Humans ; *Gastrectomy/adverse effects ; Animals ; Female ; Male ; *Feces/microbiology ; Mice ; Inflammation/microbiology ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; Th17 Cells/immunology ; T-Lymphocytes, Regulatory/immunology ; Bariatric Surgery ; Metabolome ; Obesity, Morbid/surgery/microbiology ; Child ; Leukocyte L1 Antigen Complex/analysis/metabolism ; }, abstract = {Bariatric surgery is highly effective in achieving weight loss in children and adolescents with severe obesity, however the underlying mechanisms are incompletely understood, and gut microbiome changes are unknown. Here, we show that adolescents exhibit significant gut microbiome and metabolome shifts several months after laparoscopic vertical sleeve gastrectomy (VSG), with increased alpha diversity and notably with enrichment of oral-associated taxa. To assess causality of the microbiome/metabolome changes in phenotype, pre-VSG and post-VSG stool was transplanted into germ-free mice. Post-VSG stool was not associated with any beneficial outcomes such as adiposity reduction compared pre-VSG stool. However, post-VSG stool exhibited a potentially inflammatory phenotype with increased intestinal Th17 and decreased regulatory T cells. Concomitantly, we found elevated fecal calprotectin and an enrichment of proinflammatory pathways in a subset of adolescents post-VSG. We show that in some adolescents, microbiome changes post-VSG may have inflammatory potential, which may be of importance considering the increased incidence of inflammatory bowel disease post-VSG.}, }
@article {pmid39971348, year = {2025}, author = {Coxon, J and Linder, E and Sweet, C and Magness, S and Green, L}, title = {Replicating Host-Microbiome Interactions: Harnessing Organ-on-a-Chip and Organoid Technologies to Model Vaginal and Lung Physiology.}, journal = {Annual review of biomedical engineering}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-bioeng-110122-122343}, pmid = {39971348}, issn = {1545-4274}, abstract = {Organ-on-a-chip (OOC) and organoid technologies are at the forefront of developing sophisticated in vitro systems that replicate complex host-microbiome interactions, including those associated with vaginal health and lung infection. We explore how these technologies provide insights into host-microbiome and host-pathogen interactions and the associated immune responses. Integrating omics data and high-resolution imaging in analyzing these models enhances our understanding of host-microbiome interactions' temporal and spatial aspects, paving the way for new diagnostic and treatment strategies. This review underscores the potential of OOC and organoid technologies in elucidating the complexities of vaginal health and lung disease, which have received less attention than other organ systems in recent organoid and OCC studies. Yet, each system presents notable characteristics, rendering them ideal candidates for these designs. Additionally, this review describes the key factors associated with each organ system and how to choose the technology setup to replicate human physiology.}, }
@article {pmid39971202, year = {2025}, author = {Li, T and Wu, X and Li, X and Chen, M}, title = {Cancer-associated fungi: An emerging powerful player in cancer immunotherapy.}, journal = {Biochimica et biophysica acta. Reviews on cancer}, volume = {}, number = {}, pages = {189287}, doi = {10.1016/j.bbcan.2025.189287}, pmid = {39971202}, issn = {1879-2561}, abstract = {The role of the human microbiome in cancer has been extensively studied, focusing mainly on bacteria-host interactions and their impact on tumor development and treatment response. However, fungi, an immune-active component of the human microbiome, have received less attention regarding their roles in cancer. Recent studies have identified the widespread and specific colonization and distribution of fungi in multiple sites in patients across various cancer types. Importantly, host-fungal immune interactions significantly influence immune regulation within the tumor microenvironment. The rapid advancement of immune-checkpoint blockade (ICB)-based cancer immunotherapy creates an urgent need for effective biomarkers and synergistic therapeutic targets. Cancer-associated fungi and their associated antifungal immunity demonstrate significant potential and efficacy in enhancing cancer immunotherapy. This review summarizes and discusses the growing evidence of the functions and mechanisms of commensal and pathogenic cancer-associated fungi in cancer immunotherapy. Additionally, we emphasize the potential of fungi as predictive biomarkers and therapeutic targets in cancer immunotherapy.}, }
@article {pmid39970995, year = {2025}, author = {Nohesara, S and Abdolmaleky, HM and Pettinato, G and Pirani, A and Thiagalingam, S and Zhou, JR}, title = {IUPHAR Review: Eating Disorders, Gut Microbiota Dysbiosis and Epigenetic Aberrations.}, journal = {Pharmacological research}, volume = {}, number = {}, pages = {107653}, doi = {10.1016/j.phrs.2025.107653}, pmid = {39970995}, issn = {1096-1186}, abstract = {Eating disorders (EDs) are a heterogeneous class of increasing mental disorders that are characterized by disturbances in eating behaviors, body weight regulation, and associated psychological dysfunctions. These disorders create physiological imbalances that alter the diversity and composition of the gut microbiota. While evidence suggests that EDs can arise from epigenetic aberrations, alterations in gut microbial communities may also contribute to the development and/or persistence of EDs through epigenetic mechanisms. Understanding the interplay among gut microbial communities, epigenetic processes, and the risk of EDs provides opportunities for designing preventive and/or therapeutic interventions through gut microbiome modulation. This review highlights how microbiome-based therapeutics and specific dietary interventions can contribute to improving various subtypes of EDs by modulating gut microbial communities and mitigating epigenetic aberrations. First, we briefly review the literature on links between epigenetic aberrations and the pathophysiology of EDs. Second, we examine the potential role of the gut microbiome in the pathogenesis of EDs through epigenetic mechanisms. Next, we explore the associations between EDs and other psychiatric disorders, and examine the potential roles of the microbiome in their pathogenesis. Finally, we present evidence supporting the potential of microbiome-based therapeutics and specific dietary interventions to improve EDs through epigenetic modifications.}, }
@article {pmid39970695, year = {2025}, author = {Ferrocino, I and Pagiati, L and Soulis, KX and Kazou, M and Anastasiou, R and Kalivas, D and Tsakalidou, E}, title = {The microbial terroir of Agiorgitiko cv. in the Nemea PDO zone.}, journal = {International journal of food microbiology}, volume = {433}, number = {}, pages = {111111}, doi = {10.1016/j.ijfoodmicro.2025.111111}, pmid = {39970695}, issn = {1879-3460}, abstract = {Agiorgitiko is a major Greek red winegrape variety of high economic importance cultivated almost exclusively in the Nemea PDO zone in Peloponnese, Greece. Here, we describe the microbiota and mycobiota of grape and soil samples collected over three consecutive harvest periods (September 2019, 2020 and 2021). The results revealed a common microbiome composition across the Nemea PDO zone vineyards, despite significant variations in the community structure regarding dominant bacterial and fungal taxa per sampling year, which were associated with weather factors. Grape samples of 2019 were enriched in several plant growth promoting bacteria, including Bradyrhizobium, Streptomyces, Massilia and Sphingomonas, selected by the particular weather conditions. On the other hand, the predominance of Botrytis in the same samples was observed, indicating again the impact of weather conditions on the microbial structure. Understanding these dynamics could improve management practices aimed at vine cultivation and wine quality.}, }
@article {pmid39970561, year = {2025}, author = {Gullì, M and Cangioli, L and Frusciante, S and Graziano, S and Caldara, M and Fiore, A and Klonowski, AM and Maestri, E and Brunori, A and Mengoni, A and Pihlanto, A and Diretto, G and Marmiroli, N and Bevivino, A}, title = {The relevance of biochar and co-applied SynComs on maize quality and sustainability: Evidence from field experiments.}, journal = {The Science of the total environment}, volume = {968}, number = {}, pages = {178872}, doi = {10.1016/j.scitotenv.2025.178872}, pmid = {39970561}, issn = {1879-1026}, abstract = {Adoption of sustainable maize cropping practices is urgently needed. Synthetic microbial communities (SynComs) made of plant growth-promoting microorganisms (PGPMs), coupled with biochar from residual biomass, offer an environmentally compatible alternative to inorganic fertilizers and may improve soil fertility. This article extends in a two-year field trial with preliminary results obtained in previous pot experiments, monitoring plant physiology, soil biology and chemistry, and kernel metabolomics. Here, we report the synergistic effect of the co-application of biochar, SynComs, and arbuscular mycorrhizal fungi on the soil microbiome, maize growth, and kernel metabolomic profile. SynComs application did not affect the diversity and richness of soil microbial communities; therefore, it posed a low risk of long-term effects on soil microbial ecology. With SynComs and biochar co-application to the soil, the physiology of maize plants was characterized by higher chlorophyll content, ear weight, and kernel weight. The combination of SynComs and biochar also affected the kernel metabolome, resulting in enriched health-beneficial and anti-stress metabolites. Since the preliminary evidence on the environmental and economic impact of these new associations was more favorable than that of conventional fertilizers, it seems reasonable that their large-scale implementation can eventually favor the transition to more sustainable agriculture.}, }
@article {pmid39970359, year = {2024}, author = {Stawarz-Janeczek, M and Curlej-Wądrzyk, A and Pytko-Polończyk, J}, title = {The role of magnesium in the prevention and treatment of dental caries - the latest research.}, journal = {Folia medica Cracoviensia}, volume = {64}, number = {3}, pages = {111-118}, doi = {10.24425/fmc.2024.152171}, pmid = {39970359}, issn = {0015-5616}, mesh = {Humans ; *Dental Caries/prevention &amp; control ; *Magnesium/therapeutic use/pharmacology ; Biofilms/drug effects ; Anti-Bacterial Agents/therapeutic use/pharmacology ; }, abstract = {Magnesium is one of the bioelements necessary for proper human functioning. It is classified as a macronutrient. Together with calcium and phosphorus, it is the main building component of teeth. It has antibacterial properties, as consequence of which it can impede the formation of biofilm and thus reduce inflammation caused by bacterial toxins. Along with calcium, phosphorus and vitamins, magnesium helps maintain the health of the human body. The scientific literature contains an increasing number of studies describing new methods for preventing caries resulting from interference with the oral microbiome. Modification of the microbiome and the use of prebiotics may prove to be groundbreaking. Magnesium may have the potential to function as a prebiotic because it promotes the colonization of commensal streptococci in the oral cavity. By changing the oral microbiome, it could play an important role in dental caries prevention. Nanotechnology is a new concept of material production that has emerged both in dentistry and other fields. In view of the resistance of certain bacteria to antibiotics and other bactericidal agents, alternative dental materials with increased antibacterial properties are being sought by adding antibacterial nanoparticles (NP) to their composition. One of the most commonly used metal oxides is magnesium oxide. Its antibacterial action involves disrupting the bacterial cell membrane. It seems that nanoparticles may be promising fillers for dental composites. However, due to the limited character of the clinical trials to date, there is a need for further experiments.}, }
@article {pmid39970355, year = {2024}, author = {Doroszewska, K and Zapała, B and Stefura, T and Milewicz, T}, title = {Intestinal microbiome in gestational diabetes - review.}, journal = {Folia medica Cracoviensia}, volume = {64}, number = {3}, pages = {73-80}, doi = {10.24425/fmc.2024.152167}, pmid = {39970355}, issn = {0015-5616}, mesh = {Humans ; *Diabetes, Gestational/microbiology ; Pregnancy ; Female ; *Gastrointestinal Microbiome/physiology ; }, abstract = {Gestational diabetes is one of the most common metabolic complications of pregnancy. Numerous studies have shown the gut microbiota changes significantly during pregnancy and intestinal microbiota also influences the development of diabetes during pregnancy. The aim of this study was to review the studies about gut microbiome in gestational diabetes.}, }
@article {pmid39970112, year = {2024}, author = {Rybina, OY and Pasyukova, EG}, title = {[Multi-Omic Rejuvenation: A New Strategy for Lifespan Extension].}, journal = {Molekuliarnaia biologiia}, volume = {58}, number = {5}, pages = {684-693}, pmid = {39970112}, issn = {0026-8984}, mesh = {*Longevity/genetics ; Humans ; *Rejuvenation/physiology ; *Transcriptome ; *Aging/genetics/metabolism ; Animals ; Epigenesis, Genetic ; Proteome/metabolism/genetics ; DNA Methylation ; Metabolome ; Microbiota ; Gene Expression Regulation ; Multiomics ; }, abstract = {Various age-related disorders accumulate during aging, causing a decline in tissue and organ function, raising the risk of disease development, and leading to death. Age-related phenotypes are tightly related to an increase in coordinated, progressive changes in the transcriptome, proteome, metabolome, microbiome, and epigenome. Age-dependent modifications of the transcriptome, caused by changes in epigenetic, transcriptional, and post-transcriptional regulation of gene expression, lead to the accumulation of age-related changes in the proteome and metabolome. In turn, dynamic changes in the microbiota during aging also affect gene expression and thus lead to age-related changes in the proteome and metabolome. Recent studies have shown that multi-omic rejuvenation technologies decrease age-related disorders and extend longevity. For example, the short-term induction of the expression of transcription factors that ensure the reprogramming of somatic cells into pluripotent stem cells is accompanied by the restoration of the DNA methylation pattern and transcriptome expression profile characteristic of younger tissues, resulting in an increased lifespan. In this review, we discuss existing multi-omic rejuvenation technologies and the prospects for extending and improving life.}, }
@article {pmid39970096, year = {2024}, author = {Begmatov, SA and Beletsky, AV and Rakitin, AL and Lukina, AP and Sokolyanskaya, LO and Rakitin, AV and Glukhova, LB and Mardanov, AV and Karnachuk, OV and Ravin, NV}, title = {[Antibiotic Resistance Genes in Cattle Gut Microbiota: Influence of Housing Conditions].}, journal = {Molekuliarnaia biologiia}, volume = {58}, number = {6}, pages = {996-1006}, pmid = {39970096}, issn = {0026-8984}, mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome/drug effects/genetics ; *Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; Housing, Animal ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics/drug effects ; beta-Lactams/pharmacology ; beta-Lactamases/genetics ; }, abstract = {Resistance to antimicrobial drugs is an urgent problem not only in public health, but also in animal husbandry. The widespread use of antimicrobials in feed additives is one of the main reasons for the rapid spread of antibiotic resistance in the microbiota of the gastrointestinal tract of farm animals. To characterize antibiotic resistance genes (resistome), we performed metagenomic analysis of the feces of 24 cattle from different regions of Russia, including cows of different breeds and yaks. Animals differed in the type of housing: year-round on pastures or in barns of conventional farms, with consumption of feed additives. Although genes of resistance to aminoglycosides, β-lactams, glycopeptides, MLS antibiotics (macrolides, lincosamides, and streptogramins), phenicols, and tetracyclines were detected in samples from both groups of animals, the content of the resistome in the fecal microbiome of stall-bred cattle was about ten times higher than in animals kept on pastures. The resistome of stall cattle was dominated by β-lactamases and tetracycline resistance genes, the content of which in the microbiome was 24 and 60 times higher, respectively, than in animals kept on pastures. Apparently, the spread of resistance to β-lactams and tetracyclines in stall cattle reflects the active use of these antibiotics in livestock production. Metagenomic analysis of livestock feces can be used to quantify antibiotic resistance genes for the purpose of monitoring antimicrobial drugs used in animal husbandry.}, }
@article {pmid39969428, year = {2025}, author = {Bloom, PP and Bassis, CM and Crossette, E and Silber, JL and Norman, JM and Young, VB and Lok, ASF}, title = {Safety and efficacy of a defined bacterial consortium, VE303, to treat HE.}, journal = {Hepatology communications}, volume = {9}, number = {3}, pages = {}, doi = {10.1097/HC9.0000000000000650}, pmid = {39969428}, issn = {2471-254X}, mesh = {Humans ; Male ; Middle Aged ; Female ; *Gastrointestinal Microbiome/drug effects ; *Hepatic Encephalopathy/drug therapy ; Aged ; Treatment Outcome ; Vancomycin/therapeutic use/adverse effects ; Anti-Bacterial Agents/therapeutic use/adverse effects/administration &amp; dosage ; Feces/microbiology/chemistry ; Lactulose/therapeutic use ; Rifaximin/therapeutic use ; Adult ; }, abstract = {BACKGROUND: Novel therapies are needed to treat HE, and microbiome modulation is a promising target. VE303 is a defined consortium of 8 purified, clonal bacterial strains, known to produce metabolites that may be beneficial in HE. We evaluated the safety and efficacy of VE303 to treat HE.<br><br>METHODS: We performed a single-center, randomized, placebo-controlled trial of VE303 in adult patients with a history of overt HE (NCT04899115). Eligible patients were taking lactulose and rifaximin, had no recent systemic antibiotics, and had MELD &#x2264;20. All patients received 5 days of oral vancomycin followed by randomization to 14 days of VE303 or placebo (2:1). The primary endpoints were incidence of serious adverse events and change in psychometric HE score (PHES) from baseline to 4 weeks after treatment. Stool samples underwent metagenomic sequencing and metabolite quantification.<br><br>RESULTS: Eighteen patients completed the trial, 56% men, with a mean age of 59 years and a mean MELD of 11. Patients who received VE303 had a mean change in PHES of +1.5 versus -1.0 in those who received a placebo (p=0.20). Two of the 12 patients who received VE303 had at least 1 serious adverse event (all overt HE hospitalizations), compared with 0/6 patients who received a placebo. In the patients who received VE303, 2 of 8 strains engrafted in >50% of patients. Both VE303 strain engraftment and increased stool butyrate production had a trend toward improved PHES.<br><br>CONCLUSIONS: VE303 was well tolerated in patients with cirrhosis and a history of overt HE, leading to the engraftment of certain VE303 strains and a higher percentage of patients with improved PHES.}, }
@article {pmid39969325, year = {2024}, author = {Li, W and Li, A}, title = {Exploring the causal relationship between gut microbiota and atopic dermatitis: A Mendelian randomization study.}, journal = {Medicine}, volume = {103}, number = {52}, pages = {e40193}, doi = {10.1097/MD.0000000000040193}, pmid = {39969325}, issn = {1536-5964}, mesh = {*Dermatitis, Atopic/microbiology/genetics ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics ; Humans ; *Genome-Wide Association Study ; }, abstract = {Accumulating evidence indicates a correlation between gut microbiota (GM) and atopic dermatitis (AD). Nevertheless, the causal relationship between specific pathogenic bacterial taxa and AD remains uncertain. This investigation utilized a two-sample Mendelian randomization (MR) analysis to assess the causal association between GM and AD, identifying the most influential GM taxa. An MR study was conducted utilizing summary statistics derived from genome-wide association studies encompassing 207 GM taxa and their association with AD risk. The genome-wide association studies summary statistics for 207 GM taxa (from phylum to species level) were generated by the Dutch Microbiome Project. The genetic variants (P < 1 × 10-5) correlated with GM (n = 7738) were identified from this investigation. Additionally, 4 supplementary MR approaches, simple mode, MR-Egger, weighted mode, and weighted median, supported the inverse-variance weighted approach. Furthermore, sensitivity analyses were executed using leave-one-out analysis, Cochran Q test, MR-Egger intercept test, MR pleiotropy residual sum and outlier global test, and MR Steiger test. The MR analysis identified 17 distinct bacterial taxa involving 2 orders, 4 families, 5 genera, and 6 species. The inverse-variance weighted method demonstrated that 6 bacterial taxa were positively associated with AD. These taxa included the order Pasteurellales, family Burkholderiales noname, family Pasteurellaceae, genus Burkholderiales noname, species Burkholderiales bacterium_1_1_47, and species Desulfovibrio piger. Eleven bacterial taxa were negatively associated with AD, comprising the order Actinomycetales, family Micrococcaceae, family Oscillospiraceae, genus Rothia, genus Collinsella, genus Oscillibacter, genus Pseudoflavonifractor, species Oscillibacter_unclassified, species Roseburia hominis, species R mucilaginosa, and species Parabacteroides merdae. Moreover, the MR-Egger intercept test and MR pleiotropy residual sum and outlier global test validated that the MR analysis remained unaffected by horizontal pleiotropy (P > .05). Furthermore, the leave-one-out analysis contributed to validating the robustness of the outcomes. Finally, an MR Steiger directionality test confirmed the assessment of potential causal direction (P < .001). This investigation identified specific intestinal flora causally associated with AD risk, offering novel insights for future investigations and innovative avenues for AD diagnosis, therapeutic intervention, and prognostic assessment.}, }
@article {pmid39969294, year = {2024}, author = {Liu, J and Luo, W and Hu, Z and Zhu, X and Zhu, L}, title = {Causal relationship between gut microbiota and androgenetic alopecia: A Mendelian randomization study.}, journal = {Medicine}, volume = {103}, number = {52}, pages = {e41106}, doi = {10.1097/MD.0000000000041106}, pmid = {39969294}, issn = {1536-5964}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Mendelian Randomization Analysis ; *Alopecia/genetics/microbiology ; *Genome-Wide Association Study ; Male ; }, abstract = {Recent studies have found a strong correlation between gut microbiota and the risk of skin diseases and proposed a "gut-skin axis." Androgenetic alopecia (AGA) is the most common type of alopecia, and androgen plays an important role in its pathogenesis. It has been found that the gut microbiome is closely related to androgens; however, whether this relationship is causal or merely coincidental remains uncertain. To address this issue, Mendelian randomization (MR) analysis was performed to explore the association between gut microbiota and AGA. Genome-wide association studies (GWAS) have compiled summary statistics of the gut microbiota, including 211 taxa (131 genera, 35 families, 20 orders, 16 classes, and 9 phyla), with data from MiBioGen's comprehensive study. We collected genetic associations with AGA from the IEU OpenGWAS project. We performed MR Analyses to assess the causal relationship between the genetically predicted gut microbiota and AGA. In order to verify the reliability of the findings, we systematically performed sensitivity analyses and heterogeneity tests and performed a heterogeneity test. MR Analysis provides important evidence for the causal relationship between genetically predicted gut microbiota and AGA. Lachnospiraceae UCG008 (OR = 0.939, 95%CI 0.175-0.775, P < .01), Oxalobacte (OR = 0.932, 95%CI 0.896-0.969, P < .01) would reduce the risk of AGA. Eubacterium rectale group (OR = 1.102, 95%CI 1.025-1.186, P < .01), Roseburia (OR = 1.183, 95%CI 1.048-1.336, P < .01) would increase the risk of AGA. Further sensitivity and heterogeneity analyses confirmed the robustness of these results. The results of this study indicate that there is a potential genetic susceptibility between gut microbiota and AGA, and screen out protective and risk factors. These results provide a theoretical basis for the prevention and treatment of AGA by regulating gut microbiota.}, }
@article {pmid39969201, year = {2025}, author = {Zuo, J and Wang, P and Xue, K and Tan, Y and Zhang, T and Li, Y and He, F and Wu, W and Yan, Z and Cong, L and Li, G}, title = {Lipid alterations in acute myocardial infarction are associated with gut microbiota.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0237024}, doi = {10.1128/spectrum.02370-24}, pmid = {39969201}, issn = {2165-0497}, abstract = {Although lipid metabolism and gut microbiota dysregulation are known to participate in cardiovascular disease, few studies have examined these alterations and associations in acute myocardial infarction (AMI) patients. This study reveals altered and associated lipid metabolism and gut microbiome based on proteomic and lipidomic analyses of fecal and plasma samples from 30 patients with AMI and 33 healthy volunteers. Twenty-three differential plasma lipids, nine altered fecal lipids, and nine differential fecal bacterial species were identified in AMI patients relative to healthy volunteers, with nine plasma lipids, three fecal lipids, and two fecal bacteria as potential biomarkers. Correlation analysis revealed that the abundances of Stenotrophomonas and Bilophila were positively correlated with sphingosine and ceramide levels, respectively. Alistipes indistinctus and Porphyromonas were correlated with blood lipid indicators (total cholesterol, triglycerides, and low-density lipoprotein-C), and A. indistinctus, Bilophila, and Stenotrophomonas were associated with myocardial injury indicators (cTnI, CK, CK-MB, LDH, and BNP). This study identified potential lipid and gut microbe biomarkers and their associations in AMI patients.IMPORTANCEAcute myocardial infarction (AMI) remains a leading cause of morbidity and mortality worldwide. While lipid metabolism and gut microbiota are known to play important roles in cardiovascular diseases, their interactions in the context of AMI are not fully understood. In this study, we explore the lipidomic and microbiome alterations in AMI patients, identifying key biomarkers associated with myocardial injury. By correlating specific lipid changes with bacterial species in fecal samples, we highlight the potential of lipid-microbe interactions in the pathogenesis of AMI. These findings provide novel insights into the complex mechanisms underlying AMI and suggest potential targets for early diagnosis and therapeutic interventions aimed at modulating lipid and microbial profiles to improve patient outcomes.}, }
@article {pmid39969199, year = {2025}, author = {Vilanova-Cuevas, B and DeRito, CM and Ritchie, IT and Kellogg, CA and Evans, JS and Zimmerman, A and Williams, SM and Brandt, M and Sevier, M and Gittens, S and Budd, KA and Warham, M and Sharp, WC and Delgado, GA and Hylkema, A and Kitson-Walters, K and Quod, J-P and Breitbart, M and Hewson, I}, title = {Investigating the influence of Diadematidae scuticociliatosis on host microbiome composition.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0141824}, doi = {10.1128/msystems.01418-24}, pmid = {39969199}, issn = {2379-5077}, abstract = {Mass mortality of Diadematidae urchins, caused by the Diadema antillarum scuticociliatosis Philaster clade (DScPc), affected the Caribbean in spring 2022 and subsequently spread to the eastern Mediterranean, Red Sea, and western Indian Ocean. A key question around Diadematidae scuticociliatosis (DSc), the disease caused by the scuticociliate, is whether the urchin microbiome varies between scuticociliatosis-affected and grossly normal urchins. Tissue samples from both grossly normal and abnormal Diadema antillarum were collected in the field during the initial assessment of the DSc causative agent and from an experimental challenge of DScPc culture on aquacultured D. antillarum. Specimens were analyzed using 16S rRNA gene amplicon sequencing. Additional abnormal urchin samples were collected from the most recent outbreak site in the western Indian Ocean (Réunion Island). At reference (i.e., unaffected by DSc) sites, Kistimonas spp., Propionigenium spp., and Endozoicomonas spp. were highly represented in amplicon libraries. DSc-affected urchin amplicon libraries had lower taxonomic richness and a greater representation of taxa related to Fangia hongkongensis and Psychrobium spp. Amplicon libraries of urchins experimentally challenged with the DSc pathogen had some shifts in microbial composition, but F. hongkongensis was not a part of the core bacteria in DSc-challenged specimens. DSc-affected Echinothrix diadema from Réunion Island showed a similar high representation of F. hongkongensis as that seen on Caribbean D. antillarum. Our results suggest that DSc alters Diadematidae microbiomes and that F. hongkongensis may be a candidate bacterial biomarker for DSc in environmental samples. The mechanism driving microbiome variation in host-pathogen interactions remains to be explored.IMPORTANCEThe mass mortality of Diadematidae urchins due to Diadema antillarum scuticociliatosis (DSc) has had significant ecological impacts, spreading from the Caribbean to the eastern Mediterranean, Red Sea, and western Indian Ocean. This study investigates whether the microbiome of urchins varies between those affected by DSc and those that are not. Using 16S rRNA gene amplicon sequencing, researchers found that DSc-affected urchins had lower taxonomic richness and a greater representation of Fangia hongkongensis and Psychrobium spp. The findings indicate that F. hongkongensis could serve as a bacterial biomarker for DSc in environmental samples, providing a potential tool for early detection and management of the disease. Understanding these microbiome changes is crucial for developing strategies to mitigate the spread and impact of DSc on marine ecosystems.}, }
@article {pmid39969175, year = {2025}, author = {Spring, J and Gurbuxani, S and Golovkina, T}, title = {Microbiota does not influence tumor development in two models of heritable cancer.}, journal = {mBio}, volume = {}, number = {}, pages = {e0386624}, doi = {10.1128/mbio.03866-24}, pmid = {39969175}, issn = {2150-7511}, abstract = {UNLABELLED: Microbial impact on tumorigenesis of heritable cancers proximal to the gut is well-documented. Whether the microbiota influences cancers arising from inborn mutations at sites distal to the gut is undetermined. Using two models of heritable cancer, Trp53-deficient mice and Wnt1-transgenic mice, and a gnotobiotic approach, we found the microbiota to be inconsequential for tumor development. This work furthers our understanding of the degree of the microbial impact on tumor development.<br><br>IMPORTANCE: The influence of the microbiome on the development of cancer is well-documented with many if not all published studies reporting either a positive or a negative impact. None of the published studies, however, presented data on the influence of the microbiome on the development of heritable cancer. We find that the microbiota has no influence on cancer development in two models of spontaneous cancers driven by germline Trp53 deficiency and constitutive Wnt1 signaling.}, }
@article {pmid39968863, year = {2025}, author = {Živković, T and Carrell, AA and Granath, G and Shaw, AJ and Pelletier, DA and Schadt, CW and Klingeman, DM and Nilsson, MB and Helbig, M and Warshan, D and Klarenberg, IJ and Gilbert, D and Kostka, JE and Weston, DJ}, title = {Host Species-Microbiome Interactions Contribute to Sphagnum Moss Growth Acclimation to Warming.}, journal = {Global change biology}, volume = {31}, number = {2}, pages = {e70066}, doi = {10.1111/gcb.70066}, pmid = {39968863}, issn = {1365-2486}, support = {ERKP909//U.S.Department of Energy's Office of Science, Biological, and Environmental Research (DOE BER) Early Career Research Program/ ; 2018-04872//Swedish research council (VR)/ ; DE-SC0007144//DOE Environmental System Science Program/ ; DE-SC0012088//DOE Environmental System Science Program/ ; DE-SC0023297//DOE Genomic Science Program/ ; }, mesh = {*Sphagnopsida/microbiology/growth &amp; development ; *Microbiota ; *Acclimatization ; *Climate Change ; Temperature ; }, abstract = {Sphagnum moss is the dominant plant genus in northern peatlands responsible for long-term carbon accumulation. Sphagnum hosts diverse microbial communities (microbiomes), and its phytobiome (plant host + constituent microbiome + environment) plays a key role in nutrient acquisition along with carbon cycling. Climate change can modify the Sphagnum-associated microbiome, resulting in enhanced host growth and thermal acclimation as previously shown in warming experiments. However, the extent of microbiome benefits to the host and the influence of host-microbe specificity on Sphagnum thermal acclimation remain unclear. Here, we extracted Sphagnum microbiomes from five donor species of four peatland warming experiments across a latitudinal gradient and applied those microbiomes to three germ-free Sphagnum species grown across a range of temperatures in the laboratory. Using this experimental system, we test if Sphagnum's growth response to warming depends on the donor and/or recipient host species, and we determine how the microbiome's growth conditions in the field affect Sphagnum host growth across a range of temperatures in the laboratory. After 4 weeks, we found that the highest growth rate of recipient Sphagnum was observed in treatments of matched host-microbiome pairs, with rates approximately 50% and 250% higher in comparison to maximum growth rates of non-matched host-microbiome pairs and germ-free Sphagnum, respectively. We also found that the maximum growth rate of host-microbiome pairs was reached when treatment temperatures were close to the microbiome's native temperatures. Our study shows that Sphagnum's growth acclimation to temperature is partially controlled by its constituent microbiome. Strong Sphagnum host-microbiome species specificity indicates the existence of underlying, unknown physiological mechanisms that may drive Sphagnum's ability to acclimatize to elevated temperatures. Together with rapid acclimation of the microbiome to warming, these specific microbiome-plant associations have the potential to enhance peatland resilience in the face of climate change.}, }
@article {pmid39968682, year = {2025}, author = {Yu, RL and Weber, HC}, title = {Irritable bowel syndrome, the gut microbiome, and diet.}, journal = {Current opinion in endocrinology, diabetes, and obesity}, volume = {}, number = {}, pages = {}, doi = {10.1097/MED.0000000000000905}, pmid = {39968682}, issn = {1752-2978}, abstract = {PURPOSE OF REVIEW: To provide an update of recent studies exploring the role of the gut microbiota and diet in the pathogenesis and treatment of irritable bowel syndrome (IBS).<br><br>RECENT FINDINGS: The human gut microbiome has been recognized as an important, active source of signaling molecules that explain in part the disorder of the gut brain interaction (DGBI) in IBS. Subsequent changes in the metabolome such as the production of short-chain fatty acids (SCFA) and serotonin are associated with IBS symptoms. Dietary components are recognized as important triggers of IBS symptoms and a diet low in fermentable oligo-, di-, monosaccharides, and polyols (FODMAPs) has been shown effective and safe, even when used long-term. Fecal microbiota transplantation (FMT) in IBS has not shown sustained and effective IBS symptom reduction in controlled clinical trials.<br><br>SUMMARY: This update elucidates recent developments in IBS as it relates to clinical trial results targeting dietary and gut microbiota interventions. The gut microbiome is metabolically active and affects the bi-directional signaling of the gut-brain axis.}, }
@article {pmid39968641, year = {2025}, author = {Rodriguez, VR and Essex, M and Poddubnyy, D}, title = {The gut microbiota in spondyloarthritis: an update.}, journal = {Current opinion in rheumatology}, volume = {}, number = {}, pages = {}, doi = {10.1097/BOR.0000000000001079}, pmid = {39968641}, issn = {1531-6963}, abstract = {PURPOSE OF REVIEW: This review provides an updated overview of the gut microbiota's involvement in spondyloarthritis (SpA) from a clinical perspective. It explores mechanisms by which the gut microbiota may influence SpA pathogenesis and considers the therapeutic implications of targeting the microbiome in SpA treatment.<br><br>RECENT FINDINGS: The pathogenesis of SpA is multifactorial, involving genetic predisposition, external factors and dysregulation of the immune system. Recent studies have identified alterations in the gut microbiome of patients with SpA, including changes in microbial diversity and specific taxa linked to disease activity. HLA-B27 status seems to influence gut microbiota composition, potentially impacting disease progression. In HLA-B27 transgenic rats, the association between gut microbiota and SpA development has been confirmed, supporting findings from human studies. A compromised gut barrier, influenced by proteins like zonulin, may allow microbial antigens to translocate, triggering immune responses associated with SpA.<br><br>SUMMARY: These findings highlight the potential for microbiota-modulating therapies, such as probiotics, prebiotics, diet and exercise, in managing SpA. However, methodological variability in human studies exposes the need for more rigorous research to better understand these associations. This may offer the opportunity to refine treatment strategies, offering a personalized approach to managing the disease.}, }
@article {pmid39968496, year = {2025}, author = {Zhang, X and Chan, DCL and Zhu, J and Sin, DZY and Peng, Y and Wong, MKL and Zhu, W and Tsui, Y and Haqq, AM and Ting, JY and Kozyrskyj, A and Chan, FKL and Ng, SC and Tun, HM}, title = {Early-life antibiotic exposure aggravates hepatic steatosis through enhanced endotoxemia and lipotoxic effects driven by gut Parabacteroides.}, journal = {MedComm}, volume = {6}, number = {3}, pages = {e70104}, pmid = {39968496}, issn = {2688-2663}, abstract = {Compelling evidence supports a link between early-life gut microbiota and the metabolic outcomes in later life. Using an early-life antibiotic exposure model in BALB/c mice, we investigated the life-course impact of prenatal and/or postnatal antibiotic exposures on the gut microbiome of offspring and the development of metabolic dysfunction-associated steatotic liver disease (MASLD). Compared to prenatal antibiotic exposure alone, postnatal antibiotic exposure more profoundly affected gut microbiota development and succession, which led to aggravated endotoxemia and metabolic dysfunctions. This was primarily resulted from the overblooming of gut Parabacteroides and hepatic accumulation of cytotoxic lysophosphatidyl cholines (LPCs), which acted in conjunction with LPS derived from Parabacteroides distasonis (LPS_PA) to induce cholesterol metabolic dysregulations, endoplasmic reticulum (ER) stress and apoptosis. Integrated serum metabolomics, hepatic lipidomics and transcriptomics revealed enhanced glycerophospholipid hydrolysis and LPC production in association with the upregulation of PLA2G10, the gene controlling the expression of the group X secretory Phospholipase A2s (sPLA2-X). Taken together, our results show microbial modulations on the systemic MASLD pathogenesis and hepatocellular lipotoxicity pathways following early-life antibiotic exposure, hence help inform refined clinical practices to avoid any prolonged maternal antibiotic administration in early life and potential gut microbiota-targeted intervention strategies.}, }
@article {pmid39968350, year = {2025}, author = {Lee, CZ and Worsley, SF and Davies, CS and Silan, E and Burke, T and Komdeur, J and Hildebrand, F and Dugdale, HL and Richardson, DS}, title = {Metagenomic analyses of gut microbiome composition and function with age in a wild bird; little change, except increased transposase gene abundance.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf008}, pmid = {39968350}, issn = {2730-6151}, abstract = {Studies on wild animals, mostly undertaken using 16S metabarcoding, have yielded ambiguous evidence regarding changes in the gut microbiome (GM) with age and senescence. Furthermore, variation in GM function has rarely been studied in such wild populations, despite GM metabolic characteristics potentially being associated with host senescent declines. Here, we used 7 years of repeated sampling of individuals and shotgun metagenomic sequencing to investigate taxonomic and functional changes in the GM of Seychelles warblers (Acrocephalus sechellensis) with age. Our results suggest that taxonomic GM species richness declines with age and in the terminal year, with this terminal decline occurring consistently across all ages. Taxonomic and functional GM composition also shifted with host age. However, the changes we identified occurred linearly with age (or even mainly during early years prior to the onset of senescence in this species) with little evidence of accelerated change in later life or during their terminal year. Therefore, the results suggest that changes in the GM with age are not linked to senescence. Interestingly, we found a significant increase in the abundance of a group of transposase genes with age, which may accumulate passively or due to increased transposition induced as a result of stressors that arise with age. These findings reveal taxonomic and functional GM changes with age, but not senescence, in a wild vertebrate and provide a blueprint for future wild functional GM studies linked to age and senescence.}, }
@article {pmid39968349, year = {2025}, author = {Bhandari, R and Robbins, CJ and Arora, AK and Chaston, JM and Kang, DS}, title = {Motility genes are associated with the occurrence of Drosophila melanogaster-associated gut microbes.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf013}, pmid = {39968349}, issn = {2730-6151}, abstract = {Recent work highlighted the role of motility genes in dispersing fly-associated microbes and their spread between hosts. We investigated whether bacterial genes encoding motility are associated with the occurrence of bacteria above passive dispersal levels in the gut of wild Drosophila melanogaster. We revisited 16S amplicon and shotgun metagenome data of wild flies and correlated four genera of bacteria (Commensalibacter, Gluconobacter, Lactobacillus, and Tatumella) with motility genes. We plotted the microbes against neutral models of ecological drift and passive dispersal. Microbes with positive correlations to motility were exclusively found at or above neutral model predictions, suggesting motility genes are crucial for fly microbiota spread and colonization. This information is crucial for understanding how specific gene functions contribute to microbial community dispersal and colonization within the fly host. Moreover, this study's findings serve as a proof of concept for using the neutral model to predict microbial functions essential for survival and dissemination in diverse hosts.}, }
@article {pmid39968048, year = {2024}, author = {Nene, M and Kunene, NW and Pierneef, R and Hadebe, K}, title = {Profiling the diversity of the village chicken faecal microbiota using 16S rRNA gene and metagenomic sequencing data to reveal patterns of gut microbiome signatures.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1487595}, pmid = {39968048}, issn = {1664-302X}, abstract = {INTRODUCTION: The production environment of extensively raised village chickens necessitates their adaptability to low-resource systems. The gut microbiome plays a critical role in supporting this adaptability by influencing health and productivity. This study aimed to investigate the diversity and functional capacities of the faecal microbiome in village chickens from Limpopo and KwaZulu-Natal provinces of South Africa.<br><br>METHODS: Using a combination of 16S rRNA gene sequencing and shotgun metagenomic sequencing technologies, we analysed 98 16S rRNA and 72 metagenomic datasets. Taxonomic profiles and functional gene annotations were derived, focusing on microbial diversity, antibiotic resistance genes (ARGs), and potential zoonotic pathogens.<br><br>RESULTS: Taxonomic analysis showed that the predominant phyla in both provinces were Firmicutes, Bacteroidota, Proteobacteria, and Actinobacteria. At the genus level, Escherichia and Shigella were prevalent, with Escherichia coli and Shigella dysenteriae identified as major contributors to the gut microbiome. ARGs were identified, with MarA, PmrF, and AcrE detected in KwaZulu-Natal, and cpxA, mdtG, and TolA in Limpopo. These genes primarily mediate antibiotic efflux and alteration.<br><br>DISCUSSION: The detection of zoonotic bacteria such as Escherichia coli and Streptococcus spp. highlights potential health risks to humans through the food chain, emphasizing the importance of improved household hygiene practices. This study underscores the role of the gut microbiome in village chicken health and adaptability, linking microbial diversity to production efficiency in low-resource settings. Targeted interventions and further research are crucial for mitigating zoonotic risks and enhancing sustainability in village chicken farming.}, }
@article {pmid39968046, year = {2024}, author = {Battie-Laclau, P and Taudière, A and Bernard, M and Bodénan, L and Duchemin, M and de Roman, Y and Yol, A and Barry-Etienne, D}, title = {Terroir and farming practices drive arbuscular mycorrhizal fungal communities in French vineyards.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1463326}, pmid = {39968046}, issn = {1664-302X}, abstract = {BACKGROUND: Nature-based management of vineyards is at the heart of a sustainable development for the next decades. Although much is known about grapevine benefits from Arbuscular Mycorrhizal Fungi (AMF), little is known about the influence of vineyard terroir and farming practices on AMF communities.<br><br>METHODS: We examined the relative effect of wine terroir and agricultural practices (organic, conversion, and conventional) on AMF abundance and diversity across 75 vineyards distributed over 14 wine terroirs in 6 winegrowing regions in France. We estimate AMF abundance by measuring spore density and root mycorrhization rates, and characterize AMF communities composition using metabarcoding by sampling both root and spore compartments for each vineyard.<br><br>RESULTS: Organic farming slightly increases AMF abundance (spore density and mycorrhization rate). Vineyards under conversion and using organic practices display a higher AMF diversity than conventional ones. Terroirs vary widely in terms of AMF abundance and diversity, with the median of OTUs count per sample ranging from 9 (C&#xf4;te des Blancs) to 35 (Gigondas). The composition of AMF communities is structured mainly by terroir and in a lesser extent by practice. The effect of terroir on AMF communities is partially explained by distance decay and soil properties, but the majority of variation is still explained only by the terroir identity. Organic practices improve both abundance and diversity of AMF in vineyards, possibly leading to more productivity and resilience of grapevines.<br><br>CONCLUSION: This large-scale study highlights the importance of terroir in our understanding of vineyard microbiome and paves the way to incorporation of AMF in microbial terroir studies and applications.}, }
@article {pmid39967801, year = {2024}, author = {Ito, M and Kataoka, M and Sato, Y and Nachi, H and Nomoto, K and Okada, N}, title = {Diverse vaginal microbiota in healthy Japanese women: a combined relative and quantitative analyses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1487990}, pmid = {39967801}, issn = {2235-2988}, mesh = {Humans ; Female ; *Vagina/microbiology ; Adult ; *Microbiota/genetics ; Cross-Sectional Studies ; *Lactobacillus/isolation &amp; purification/genetics ; *RNA, Ribosomal, 16S/genetics ; Japan ; Hydrogen-Ion Concentration ; Young Adult ; Healthy Volunteers ; Middle Aged ; DNA, Bacterial/genetics ; Body Mass Index ; Lactobacillus crispatus/isolation &amp; purification/genetics ; Lactobacillus gasseri ; Bacteria/classification/genetics/isolation &amp; purification ; East Asian People ; }, abstract = {INTRODUCTION: This cross-sectional study aimed to characterize the viable vaginal microbiota and identify host factors influencing this microbiota by employing a combination of relative and quantitative analyses.<br><br>METHODS: Twenty-four vaginal fluid samples were collected from healthy adult Japanese women for analysis. Vaginal fluid pH was measured using a portable pH meter. DNA was extracted from the vaginal fluid, and the 16S ribosomal RNA gene sequences in the V3-V4 regions were analyzed to identify bacterial species. Additionally, the vaginal fluid was cultured on four types of selective agar plates. The predominant species in the growing colonies were identified using colony polymerase chain reaction, and the colonies were counted.<br><br>RESULTS: The vaginal microbiota was classified into four categories based on the characterization of the dominant bacterial population: Lactobacillus crispatus, Lactobacillus iners, Lactobacillus gasseri, and a diversity group. The predominant bacterial species were consistent across methods; however, the levels of the viable population varied significantly. Body mass index had a significant influence on the total number of viable bacteria and vaginal pH, while age only affected vaginal pH.<br><br>CONCLUSIONS: Our findings indicate that the vaginal microbiome of healthy Japanese women is not only highly diverse but also affected by host factors such as BMI and age.}, }
@article {pmid39967732, year = {2025}, author = {Dou, Y and Niu, Y and Shen, H and Wang, L and Lv, Y and Liu, S and Xie, X and Feng, A and Liu, X}, title = {Identification of disease-specific gut microbial markers in vitiligo.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1499035}, pmid = {39967732}, issn = {1664-302X}, abstract = {There is a potential correlation between vitiligo and gut microbiota, although research in this area is currently limited. The research employed high-throughput sequencing of 16S rRNA to examine the gut microbiome in the stool samples of 49 individuals with vitiligo and 49 without the condition. The study encompassed four comparison groups: (1) DI (disease) group vs. HC (healthy control) group; (2) DI_m group (disease group of minors) vs. HC_m group (healthy control group of minors); (3) DI_a group (adult disease group) vs. HC_a group (adult healthy control group); (4) DI_m group vs. DI_a group. Research findings have indicated the presence of spatial heterogeneity in the gut microbiota composition between individuals with vitiligo and healthy controls. A significant reduction in gut microbiota diversity has been observed in vitiligo patients across both minors and adult groups. However, variations have been noted in the composition of disease-related differential microbial markers among different age groups. Specifically, Bacteroides and Parabacteroides have been identified as specific markers of the intestinal microbiota of vitiligo patients in both minor and adult groups. Correlative analyses have revealed a positive correlation of these two genera with the Vitiligo Area Scoring Index (VASI) and disease duration. It is noteworthy that there are no significant differences in diversity between the DI_m group and the DI_a group, with similarities in microbiota composition and functional characteristics. Nevertheless, correlative analyses suggest a declining trend in Bacteroides and Parabacteroides with increasing age. Individuals with vitiligo exhibit distinct features in their gut microbiome when contrasted with those in the healthy control group. Additionally, the microbial marker genera that show variances between patients and healthy controls vary among different age groups. Disease-specific microbial marker genera (Bacteroides and Parabacteroides) are associated with VASI, duration of the condition, and age. These findings are essential for improving early diagnosis and developing potential treatment strategies for individuals with vitiligo.}, }
@article {pmid39967574, year = {2025}, author = {Colón-González, M and Aguirre-Dugua, X and Guerrero-Osornio, MG and Avelar-Rivas, JA and DeLuna, A and Mancera, E and Morales, L}, title = {Thriving in Adversity: Yeasts in the Agave Fermentation Environment.}, journal = {Yeast (Chichester, England)}, volume = {}, number = {}, pages = {}, doi = {10.1002/yea.3989}, pmid = {39967574}, issn = {1097-0061}, support = {//This work was supported by CONAHCYT [grant numbers CB-2016-01 284992, FORDECYT-PRONACES/103000/2020, CF-2023-G-695], by PAPIIT-DGAPA-UNAM [grant numbers IN209021, IN212524], and by a SEP-CINVESTAV award [number 23]. Maritrini Col&#xf3;n-Gonz&#xe1;lez currently receives a postdoctoral fellowship from CONAHCYT under the program Estancias Postdoctorales por M&#xe9;xico 2022. Mariana G. Guerrero-Osornio is a PhD student from Posgrado en Ciencias Biol&#xf3;gicas, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico (UNAM) and receives fellowship 2023-000002-01NACF-03323 from CONAHCYT./ ; }, abstract = {Agave spirits have gained global recognition and hold a central position within the cultural heritage of Mexico. Traditional distilleries, characterized by open fermentations driven by local microbial communities, persist despite the rise of industrial-scale counterparts. In this review, we explore the environmental conditions and production practices that make the must of cooked agave stems a unique habitat for colonizing microorganisms. Additionally, we review selected studies that have characterized yeast species within these communities, with a focus on their metabolic traits and genomic features. Over 50 fungal species, predominantly Saccharomycetales and few Basidiomycetes, along with a similar number of lactic and acetic acid bacteria, have been identified. Despite variations in the chemical composition of the agave substrates and diversity of cultural practices associated with each traditional fermentation process, yeast species such as Saccharomyces cerevisiae, Kluyveromyces marxianus, Torulaspora delbrueckii, and several Pichia species have been consistently isolated across all agave spirit-producing regions. Importantly, cooked agave must is rich in fermentable sugars, yet it also contains inhibitory compounds that influence the proliferation dynamics of the microbial community. We discuss some of the genetic traits that may enable yeasts to flourish in this challenging environment and how human practices may shape microbial diversity by promoting the selection of microbes that are well-adapted to agave fermentation environments. The increasing demand for agave spirits, combined with concerns about the preservation of natural resources and cultural practices associated with their production, underscores the need to deepen our understanding of all key players, including the yeast communities involved.}, }
@article {pmid39967569, year = {2025}, author = {Zhao, L and Xie, H and Kang, L and Liao, G}, title = {Association Between Recurrent Aphthous Ulcers and Oral Biodiversity: A Systematic Review and Meta-Analysis.}, journal = {Journal of evidence-based medicine}, volume = {18}, number = {1}, pages = {e70001}, doi = {10.1111/jebm.70001}, pmid = {39967569}, issn = {1756-5391}, support = {32071462//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Stomatitis, Aphthous/microbiology ; Microbiota ; Mouth/microbiology ; Dysbiosis/microbiology ; Biodiversity ; Saliva/microbiology ; }, abstract = {OBJECTIVE: This study aimed to investigate the relationship between recurrent aphthous ulcers (RAU) and dysbiosis of the oral microbiota.<br><br>METHODS: A systematic search was conducted across several databases, including the Cochrane Library, PubMed, Web of Science Core Collection, Embase, Scopus, CBM, CNKI, WanFang, and VIP, to identify relevant studies from the inception of the library until September 20, 2024. All included studies were evaluated for quality using the Newcastle-Ottawa scale. These studies assessed the diversity and abundance of oral microorganisms in patients with RAU in comparison to healthy individuals. Results were synthesized via random-effects meta-analysis (I[2] statistic for heterogeneity). Mean differences (MD) and 95% confidence intervals (CI) were applied to evaluate the pooled effects of outcomes. The systematic review was registered in PROSPERO (CRD42024615516).<br><br>RESULTS: A total of 10 studies involving 343 patients and 348 controls were included in this study, 7 of these were utilized for meta-analysis to conduct a quantitative assessment. The meta-analysis showed that in terms of alpha diversity, saliva samples collected from patients with RAU exhibited a significantly lower Chao 1 index of alpha diversity (MD = -41.22, 95% CI -64.34 to -18.09, p < 0.01), and that patients with ulcerated sites in the oral mucosa demonstrated a higher Chao 1 index when compared to healthy sites within the oral mucosa (MD = 27.48, 95% CI 2.98 to 51.97, p = 0.03).<br><br>CONCLUSIONS: Significant differences in the Chao 1 index between patients and healthy controls, along with variations in beta diversity and the relative abundance of taxa, indicate that microbial dysbiosis may play a crucial role in the development of RAU.}, }
@article {pmid39967259, year = {2025}, author = {Azara, CRP and Didier Peixe, CL and Cardoso, CEF and Azara, MEP and Elias, M and Freitas-Silva, O and Teodoro, AJ}, title = {Physicochemical, microbiology, and sensory characteristics of kombucha prepared with Tommy mango peel flour.}, journal = {Food science and technology international = Ciencia y tecnologia de los alimentos internacional}, volume = {}, number = {}, pages = {10820132251319930}, doi = {10.1177/10820132251319930}, pmid = {39967259}, issn = {1532-1738}, abstract = {Fermented foods are a good option due to the beneficial compounds generated in the fermentation process and the low pH that allows conservation without additives. The objective of the study was to produce and include Tommy mango peel flour in the production of kombucha and evaluate its effects on the physicochemical and sensory properties, antioxidant capacity, and microbiological profile. The kombucha was developed with green tea and the addition of Tommy mango peel flour (10% and 20%). The kombuchas were evaluated in the first fermentation (aerobic) and at the end of the second fermentation (anaerobic), the granulometry and colorimetry of the flour and the antioxidant profile were evaluated. Microbiome analysis was performed by 16S DNA extraction. For sensory analysis, an affective test was performed for global evaluation, flavor, texture, and oral perception. The results showed that the total phenolic content was 4.86 mg EAG/mL in F1, 8.79 mg EAG/mL in F2 with 10% mango peel flour, and 8.83 ± 0.54 mg EAG/mL in F2 with 20% mango peel flour, evidencing a significant increase in the second fermentation with the addition of the flour. In addition, the antioxidant activity was also higher in the second fermentation. The values obtained were F1 = 15.27 µmol TE/mL; F2 with 10% FCMT = 18.80 µmol TE/mL; and F2 with 20% FCMT = 26.76 µmol TE/mL. These findings indicate that the antioxidant capacity increases significantly during the second fermentation, directly correlating with the amount of mango peel flour added. The most abundant bacterial genera were Liquorilactobacillus nagelii (72%), Acetobacter (13%), and Komagataeibacter (12%) and for fungi (90%) Brettanomyces/Dekkera bruxellensis. The beverage obtained different levels of acceptance among consumers and non-consumers only in terms of flavor, proving to be a good alternative for the food industry for applying a mango byproduct to drinks.}, }
@article {pmid39967180, year = {2025}, author = {Uthaiah, NM and Venkataramareddy, SR and Mudhol, S and Sheikh, AY}, title = {EPA-rich Nannochloropsis oceanica biomass regulates gut microbiota, alleviates inflammation and ameliorates liver fibrosis in rats.}, journal = {Food research international (Ottawa, Ont.)}, volume = {202}, number = {}, pages = {115733}, doi = {10.1016/j.foodres.2025.115733}, pmid = {39967180}, issn = {1873-7145}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Eicosapentaenoic Acid/pharmacology ; *Liver Cirrhosis/metabolism/drug therapy/prevention &amp; control/pathology ; Male ; *Microalgae ; Inflammation ; Liver/drug effects/pathology/metabolism ; Biomass ; Stramenopiles ; Carbon Tetrachloride ; Rats, Wistar ; }, abstract = {Omega-3 fatty acids are believed to show anti-fibrotic effects by lowering inflammation and regulating the gut microflora. Marine microalgae are an alternative, sustainable source of omega-3 fatty acids to the conventionally used fish oil. Microalgae N. oceanica is a promising source of EPA, one of the essential omega-3 PUFAs. Current study investigates the inhibitory effects of EPA rich N. oceanica biomass against CCl4 induced liver fibrosis in rats. Here, we studied the anti-fibrotic effects in N. oceanica biomass fed groups: T1 - Low dose (4.16 mg/kg EPA), T2 - Medium dose (8.33 mg/kg EPA) and T3 - High dose (16.66 mg/kg EPA), when compared to fish oil fed group (FO - 16.66 mg/kg EPA) as a positive control. The elevated levels of serum liver biomarker enzymes and cholesterol induced by CCl4 showed a significant reduction in T3. Histopathological analysis showed the protective effects of biomass feeding on inflammation and hepatocyte degeneration. In addition, the abundance of the SCFA producing bacteria like Blautia argi, Romboutsia ilealis, Romboutsia timonensis, Stomatobaculum longum and Limosilactobacillus reuteri markedly increased in the PUFA fed groups. The cholesterol metabolising bacteria Eubacterium coprostanoligenes showed a noteworthy increase upon PUFA administration. Overall results indicate that the ameliorative effects observed upon administration of N. oceanica biomass were comparable to FO in a dose dependent manner. Therefore, we can conclude that N. oceanica biomass supplementation is associated with the alleviation of liver fibrosis in rats.}, }
@article {pmid39967179, year = {2025}, author = {Jaeger, A and Nyhan, L and Sahin, AW and Zannini, E and Meehan, D and Li, J and O'Toole, PW and Arendt, EK}, title = {In vitro digestibility of bioprocessed brewer's spent yeast: Demonstrating protein quality and gut microbiome modulation potential.}, journal = {Food research international (Ottawa, Ont.)}, volume = {202}, number = {}, pages = {115732}, doi = {10.1016/j.foodres.2025.115732}, pmid = {39967179}, issn = {1873-7145}, mesh = {*Gastrointestinal Microbiome ; *Digestion ; *Fermentation ; *Amino Acids/metabolism ; Nutritive Value ; Saccharomyces cerevisiae/metabolism ; Dietary Proteins/metabolism ; Humans ; }, abstract = {With an ever-increasing global population and dwindling natural resources, a shift towards more sustainable food systems is required. Important aspects to aid in this transition are the reduction of food waste, and a movement towards non-animal protein sources. Brewers spent yeast (BSY) is an abundant by-product of the brewing industry, which is generally regarded as waste, despite its high nutritional value. Previous work has shown that fermentation of BSY with Lactobacillus amylovorus FST 2.11 resulted in changes in composition, functionality, and improved palatability of the processed raw material (PBSY). In this study, in vitro protein digestibility, amino acid bioaccessability, and protein quality of PBSY was explored using the static INFOGEST in vitro model. In vitro protein digestibility of PBSY (73.0 %) was almost two-fold higher than that of CBSY (40.0 %), while PBSY also displayed significantly higher in vitro bioaccessability values for all essential amino acids, except for tryptophan. Investigation of protein quality using the digestible indispensable amino acid score (DIAAS) values and the FAO recommended amino acid scoring pattern for individuals >3 years old showed that the protein quality for CBSY was low (DIAAS of 17.0 %), while PBSY was considered to be of "good" protein quality (DIAAS of 98.2 %). Investigation of the modulation potential of PBSY on the gut microbiome using an in vitro colon model system showed an increase in gut microbiome α-diversity indices and an abundance of beneficial Mediterranean diet-responsive taxa after 24 h. Overall, this study highlights the potential of BSY as raw material for the production of a high-quality food ingredient with potential prebiotic effects, aiding in the reduction food waste and supporting global food systems.}, }
@article {pmid39967141, year = {2025}, author = {Zhou, F and Shang, BH and Liu, CW and Fang, WW and Wen, S and Zeng, HZ and Huang, JA and Liu, ZH}, title = {Comparative study of the anti-obesity effects of white tea and dark tea: Insights from microbiome and metabolomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {202}, number = {}, pages = {115666}, doi = {10.1016/j.foodres.2025.115666}, pmid = {39967141}, issn = {1873-7145}, mesh = {Animals ; *Tea/chemistry ; *Obesity/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Metabolomics ; Male ; Rats ; *Plant Extracts/pharmacology ; *Diet, High-Fat/adverse effects ; *Anti-Obesity Agents/pharmacology ; *Rats, Sprague-Dawley ; Polyphenols/pharmacology ; Amino Acids/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The anti-obesity effects of tea and its functional components have been extensively studied. However, the protective effects of different types of tea against obesity induced by a high-fat diet (HFD) and the underlying mechanisms remain unclear. This study systematically compared the effects of white tea and dark tea on obese rats and explored their mechanisms. The results indicated that dark tea extracts (DT) higher concentrations of theabrownins and gallic acid, while white tea extracts (WT) contained abundant levels of polyphenols and amino acids. Moreover, both WT and DT effectively improved obesity-related symptoms, including weight loss, reduced fat accumulation, improved dyslipidemia, and alleviated liver and colon damage. Specifically, WT primarily functioned by inhibiting white fat accumulation and enhancing UCP1 expression in brown fat, leading to more significant weight loss. Conversely, DT increased both the quantity and uniform distribution of colonic goblet cells and elevated the expression levels of tight junction proteins in obese rats, thereby providing better protection for the intestinal barrier. Furthermore, 16S rRNA sequencing revealed that WT and DT regulated gut microbiota imbalances, restored microbiota diversity, inhibited the growth of potentially harmful bacteria, and promoted the proliferation of beneficial bacteria. Metabolomics analyses demonstrated that WT and DT increased the concentration of short-chain fatty acids in the feces of obese rats, regulated the biosynthesis of phenylalanine, tyrosine, and tryptophan, as well as the biosynthesis pathways of valine, leucine, and isoleucine, while decreasing the levels of these amino acids in feces. In conclusion, this study provides new evidence supporting the idea that tea can mitigate HFD-induced obesity through the regulation of gut microbiota and alteration of fecal metabolite profiles.}, }
@article {pmid39967137, year = {2025}, author = {Espí-Malillos, A and López-Almela, I and Ruiz-García, P and López-Mendoza, MC and Carrón, N and González-Torres, P and Quereda, JJ}, title = {Raw milk at refrigeration temperature displays an independent microbiota dynamic regardless Listeria monocytogenes contamination.}, journal = {Food research international (Ottawa, Ont.)}, volume = {202}, number = {}, pages = {115637}, doi = {10.1016/j.foodres.2024.115637}, pmid = {39967137}, issn = {1873-7145}, mesh = {*Listeria monocytogenes/growth &amp; development/genetics/isolation &amp; purification ; *Milk/microbiology ; Animals ; *Refrigeration ; *Microbiota ; *Food Microbiology ; RNA, Ribosomal, 16S/genetics ; Food Contamination/analysis ; Cold Temperature ; }, abstract = {Dairy products made of raw milk are associated with hypervirulent L. monocytogenes clonal complexes (CCs) CC1, CC4, and CC6, and cause half of the reported listeriosis outbreaks in Europe. However, it is currently unknown whether the overrepresentation of L. monocytogenes hypervirulent clones in dairy products made of raw milk is conditioned by an alteration in the native raw milk microbiota growth and/or composition. In this study, the lag phase, maximal growth rate, and the final maximal concentration of mesophilic aerobic bacteria from native raw milk bacteria were measured at refrigerated temperature (4 °C) in the presence and absence of L. monocytogenes contamination. The raw milk microbiota composition and dynamics were evaluated in the presence and absence of L. monocytogenes hypervirulent (CC1, CC4, CC6), and hypovirulent (CC9 and CC121) clones at 4 °C by using 16S rRNA high-throughput sequencing. Our results showed that the growth and composition of the microbial communities naturally present in raw milk are independent of the contamination with hyper- or hypovirulent L. monocytogenes CCs at refrigeration temperature. Pseudomonas was the most abundant genus in raw milk on days 11 and 21, while Carnobacterium was the second most abundant genus regardless of the contaminant L. monocytogenes CCs. Altogether these results suggest that the overrepresentation of hypervirulent L. monocytogenes CC1, CC4, and CC6 in dairy products is not the consequence of a differential alteration in the native composition of the raw milk microbiota.}, }
@article {pmid39967085, year = {2025}, author = {Marangelo, C and Marsiglia, R and Nissen, L and Scanu, M and Toto, F and Siroli, L and Gottardi, D and Braschi, G and Chierico, FD and Bordoni, A and Gianotti, A and Lanciotti, R and Patrignani, F and Putignani, L and Vernocchi, P}, title = {Functional foods acting on gut microbiota-related wellness: The multi-unit in vitro colon model to assess gut ecological and functional modulation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {202}, number = {}, pages = {115577}, doi = {10.1016/j.foodres.2024.115577}, pmid = {39967085}, issn = {1873-7145}, mesh = {*Gastrointestinal Microbiome/physiology ; *Probiotics ; *Cheese/microbiology ; *Functional Food ; *Streptococcus thermophilus/metabolism ; *Lacticaseibacillus rhamnosus ; Colon/microbiology/metabolism ; Humans ; Fermentation ; Digestion ; Models, Biological ; Lactobacillus ; }, abstract = {The aim of this study was to investigate the effect of a functional probiotic cheese (FPC) on gut microbiota (GM), after simulated digestion performed by a multi-unit in vitro colon model (MICODE). Squacquerone-like cheese was produced using the starter Streptococcus thermophilus (control, CTRL), and supplemented with the probiotic Lacticaseibacillus rhamnosus, which was either subjected to high pressure homogenization (LrH) or not (Lr). Samples were stratified by cheese type, storage time, and colonic fermentation phase. Samples were then digested with MICODE and digests were characterized for ecological and functional profiles. The lactobacilli detected in Lr and LrH cheeses (9.0 log CFU/g) were represented by the probiotic strain L. rhamnosus and remained unchanged after storage at 4 °C. Lactobacilli levels in CTRLs increased from 1.5 log CFU/g to 2.0 log CFU/g after six days at 4 °C, while total coliforms remained below 1.5 log CFU/g in all samples. Real-time qPCR indicated a positive GM response after FPC simulated digestion, highlighting an abundance of bifidobacteria, lactobacilli and Clostridium group IV in LrH samples. Metataxonomy revealed higher levels of Firmicutes and Proteobacteria (p ≤ 0.05) after simulated digestion, as well as Megasphaera, Escherichia, Prevotella and Dorea. Moreover, an increase of short and medium chain fatty acids were detected by metabolomics. Overexpression of inferred KEGG metabolic pathways showed mainly fatty acids, novobiocin and amino acid metabolism. Understanding how functional foods can modify the GM may lead to the development of targeted microbiome-based therapies and the exploitation of these foods for the benefit of human health.}, }
@article {pmid39966979, year = {2025}, author = {Ali, AY and Zahran, SA and Eissa, M and Kashef, MT and Ali, AE}, title = {Gut microbiota dysbiosis and associated immune response in systemic lupus erythematosus: impact of disease and treatment.}, journal = {Gut pathogens}, volume = {17}, number = {1}, pages = {10}, pmid = {39966979}, issn = {1757-4749}, abstract = {BACKGROUND: Gut microbial dysbiosis and leaky gut play a role in systemic lupus erythematosus (SLE). Geographical location and dietary habits affect the microbiome composition in diverse populations. This study explored the gut microbiome dysbiosis, leaky gut, and systemic immune response to gut bacterial consortium in patients with SLE exhibiting mild/moderate and severe disease activity.<br><br>METHODS: Fecal and blood samples were collected from patients with SLE and healthy volunteers. Genomic DNA was extracted from the stool samples and subjected to 16S rRNA amplicon sequencing and microbiome profiling. Additionally, enzyme-linked immunosorbent assays were employed to determine the serum lipopolysaccharide level, as an assessment of gut permeability, and the systemic immune response against gut bacteria.<br><br>RESULTS: Patients with SLE showed significantly lower gut bacterial richness and diversity, indicated by observed OTUs (56.6 vs. 74.44; p&#x2009;=&#x2009;0.0289), Shannon (3.05 vs. 3.45; p&#x2009;=&#x2009;0.017) and Simpson indices (0.91 vs. 0.94; p&#x2009;=&#x2009;0.033). A lower Firmicutes-to-Bacteroidetes ratio (1.07 vs. 1.69; p&#x2009;=&#x2009;0.01) was observed, with reduced genera such as Ruminococcus 2 (0.003 vs. 0.026; p&#x2009;=&#x2009;0.0009) and Agathobacter (0.003 vs. 0.012; p&#x2009;<&#x2009;0.0001) and elevated Escherichia-Shigella (0.04 vs. 0.006; p&#x2009;<&#x2009;0.0001) and Bacteroides (0.206 vs. 0.094; p&#x2009;=&#x2009;0.033). Disease severity was associated with a higher relative abundance of Prevotella (0.001 vs. 0.0001; p&#x2009;=&#x2009;0.04). Medication effects included lower Romboutsia (0.0009 vs. 0.011; p&#x2009;=&#x2009;0.005) with azathioprine and higher Prevotella (0.003 vs. 0.0002; p&#x2009;=&#x2009;0.038) with cyclophosphamide. Furthermore, categorization by prednisolone dosage revealed significantly higher relative abundances of Slackia (0.0007 vs. 0.00002; p&#x2009;=&#x2009;0.0088), Romboutsia (0.009 vs. 0.002; p&#x2009;=&#x2009;0.0366), and Comamonas (0.002 vs. 0.00007; p&#x2009;=&#x2009;0.0249) in patients receiving high-dose prednisolone (>&#x2009;10&#xa0;mg/day). No differences in serum lipopolysaccharide levels were found, but SLE patients exhibited elevated serum gut bacterial antibody levels, suggesting a systemic immune response.<br><br>CONCLUSION: This study confirms the gut microbiome dysbiosis in patients with SLE, influenced by disease severity and specific medication usage.}, }
@article {pmid39966965, year = {2025}, author = {Centeno-Delphia, RE and Long, EA and Ellis, AC and Hofmann, S and Mosier, K and Ulloa, N and Cheng, JJ and Richards, A and Boerman, JP and Koziol, J and Verma, MS and Johnson, TA}, title = {Nasal pathobiont abundance does not differ between dairy cattle with or without clinical symptoms of bovine respiratory disease.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {16}, pmid = {39966965}, issn = {2524-4671}, support = {2020-68014-31302//USDA Agriculture and Food Research Initiative/ ; 2020-68014-31302//USDA Agriculture and Food Research Initiative/ ; 2020-68014-31302//USDA Agriculture and Food Research Initiative/ ; 2020-68014-31302//USDA Agriculture and Food Research Initiative/ ; 2020-68014-31302//USDA Agriculture and Food Research Initiative/ ; 2020-68014-31302//USDA Agriculture and Food Research Initiative/ ; 2020-68014-31302//USDA Agriculture and Food Research Initiative/ ; 2020-68014-31302//USDA Agriculture and Food Research Initiative/ ; }, abstract = {BACKGROUND: Bovine respiratory disease (BRD) remains a significant health and economic problem to the dairy cattle industry. Multiple risk factors contribute to BRD susceptibility including the bacterial pathobionts Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis. Studies have characterized and quantified the abundance of these bacteria in the nasal cavity of cattle to infer and help disease diagnosis; nonetheless, there is still discrepancy in the results observed of when these microbes are commensal or pathogenic. Additionally, some of these studies are limited to a specific farm. The goal of this study is to compare the nasal microbiome community (diversity and composition) and the abundance of the four bacterial pathogens (by qPCR) in the nasal cavity to identify differences between dairy calves that are apparently healthy and those identified to have BRD. Nasal swabs were collected from approximately 50 apparently healthy and 50 BRD-affected calves sampled from five different dairy farms in the US (CA, IN, NY (two farms), and TX).<br><br>RESULTS: Calves diagnosed with BRD in NY, and TX had lower nasal microbiome diversity compared to the apparently healthy calves. Differences in the nasal microbiome composition were observed between the different farms predicted by Bray-Curtis and weighted UniFrac dissimilarities. Commensal and pathobiont genera Acinetobacter, Moraxella, Psychrobacter, Histophilus, Mannheimia, Mycoplasma, and Pasteurella were prevalent in the bovine nasal microbiome regardless of farm or disease status. The BRD-pathobiont H. somni was the most prevalent pathobiont among all the samples and M. bovis the least prevalent. Only in CA was the abundance of a pathobiont different according to disease status, where M. haemolytica was significantly more abundant in the BRD-affected animals than apparently healthy animals.<br><br>CONCLUSIONS: This study offers insight into the nasal microbiome community composition in both animals diagnosed with BRD and healthy animals, and shows that the farm effect plays a more significant role in determining the microbiome community than disease status in young dairy calves.}, }
@article {pmid39966840, year = {2025}, author = {Wang, N and Wu, S and Huang, L and Hu, Y and He, X and He, J and Hu, B and Xu, Y and Rong, Y and Yuan, C and Zeng, X and Wang, F}, title = {Intratumoral microbiome: implications for immune modulation and innovative therapeutic strategies in cancer.}, journal = {Journal of biomedical science}, volume = {32}, number = {1}, pages = {23}, pmid = {39966840}, issn = {1423-0127}, support = {No.12175167//National Natural Science Foundation of China/ ; No. 2022CFA005//Science Fund for Creative Research Groups of the Natural Science Foundation of Hubei Province/ ; No. ZNLH202209//Basic and Clinical Medical Research Joint Fund of Zhongnan Hospital, Wuhan University/ ; }, mesh = {Humans ; *Neoplasms/immunology/therapy/microbiology ; *Microbiota/immunology ; Immunotherapy/methods ; Tumor Microenvironment/immunology ; }, abstract = {Recent advancements have revealed the presence of a microbiome within tumor tissues, underscoring the crucial role of the tumor microbiome in the tumor ecosystem. This review delves into the characteristics of the intratumoral microbiome, underscoring its dual role in modulating immune responses and its potential to both suppress and promote tumor growth. We examine state-of-the-art techniques for detecting and analyzing intratumoral bacteria, with a particular focus on their interactions with the immune system and the resulting implications for cancer prognosis and treatment. By elucidating the intricate crosstalk between the intratumoral microbiome and the host immune system, we aim to uncover novel therapeutic strategies that enhance the efficacy of cancer treatments. Additionally, this review addresses the existing challenges and future prospects within this burgeoning field, advocating for the integration of microbiome research into comprehensive cancer therapy frameworks.}, }
@article {pmid39966610, year = {2025}, author = {Li, Q and Xiao, Y and Han, L and Luo, W and Dai, W and Fang, H and Wang, R and Xu, Y and Cai, S and Goel, A and Bai, F and Cai, G}, title = {Microbiome dysbiosis, neutrophil recruitment and mesenchymal transition of mesothelial cells promotes peritoneal metastasis of colorectal cancer.}, journal = {Nature cancer}, volume = {}, number = {}, pages = {}, pmid = {39966610}, issn = {2662-1347}, support = {T2125002//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82241230//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82341007//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82103154//National Natural Science Foundation of China (National Science Foundation of China)/ ; 8217112384//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Peritoneal metastasis (PM) is common in colorectal cancer (CRC), yet its underlying mechanisms are poorly understood. Here, we explored the transcriptional profile of CRC, PM and adjacent tissues revealing key players that facilitate PM. Single-cell analysis of 48 matched samples from 12 patients revealed that remodeling of malignant cells and the tumor microenvironment promotes CRC progression and metastasis. Multiplexed imaging confirmed depletion in PM by enrichment in CRC tissues of neutrophils associated with mucosal immunity disruption, intestinal microbiota dysbiosis and mesenchymal transition of both cancerous and mesothelial cells. Functional analyses in cell lines, organoids and in vivo models demonstrated that dysbiosis promoted inflammation and protumor neutrophil recruitment, while coupled mesenchymal transition of malignant and mesothelial cells disrupted the stromal structure and increased cancer cell invasiveness. Our findings suggest that targeting mesothelial cells and tumor microenvironment remodeling may offer therapeutic strategies for CRC-PM.}, }
@article {pmid39966566, year = {2025}, author = {Chen, S and Lee, YB and Song, MY and Lim, C and Cho, H and Shim, HJ and Kim, JS and Park, BH and Kim, JK and Bae, EJ}, title = {Cannabidiol reshapes the gut microbiome to promote endurance exercise in mice.}, journal = {Experimental &amp; molecular medicine}, volume = {}, number = {}, pages = {}, pmid = {39966566}, issn = {2092-6413}, support = {20012892//Ministry of Trade, Industry and Energy (Ministry of Trade, Industry and Energy, Korea)/ ; 20012892//Ministry of Trade, Industry and Energy (Ministry of Trade, Industry and Energy, Korea)/ ; }, abstract = {Cannabidiol (CBD), a nonpsychoactive compound from Cannabis, has various bioactive functions in humans and animals. Evidence suggests that CBD promotes muscle injury recovery in athletes, but whether and how CBD improves endurance performance remains unclear. Here we investigated the effects of CBD treatment on exercise performance in mice and assessed whether this effect involves the gut microbiome. CBD administration significantly increased treadmill running performance in mice, accompanied by an increase in oxidative myofiber composition. CBD also increased mitochondrial biogenesis and the expression of associated genes such as PGC-1α, phosphorylated CREB and AMPK in muscle tissue. Interestingly, CBD altered the composition of the gut microbiome, and antibiotic treatment reduced the muscle endurance-enhancing effects of CBD and mitochondrial biogenesis. We isolated Bifidobacterium animalis, a microbe increased by CBD administration, and named it KBP-1. Treatment with B. animalis KBP-1 in mice resulted in improved running performance. Whole-genome analysis revealed that B. animalis KBP-1 presented high expression of genes involved in branched-chain amino acid biosynthesis, expression of branched-chain amino acid release pumps and metabolism of lactic acid. In summary, our study identified CBD and B. animalis KBP-1 as potential endurance exercise-promoting agents.}, }
@article {pmid39966546, year = {2025}, author = {Pietrasanta, C and Ronchi, A and Carlosama, C and Lizier, M and Silvestri, A and Fornasa, G and Melacarne, A and D'Ambrosi, F and Lutterotti, M and Carbone, E and Cetin, I and Fumagalli, M and Ferrazzi, E and Penna, G and Mosca, F and Pugni, L and Rescigno, M}, title = {Effect of prenatal antibiotics on breast milk and neonatal IgA and microbiome: a case-control translational study protocol.}, journal = {Pediatric research}, volume = {}, number = {}, pages = {}, pmid = {39966546}, issn = {1530-0447}, abstract = {BACKGROUND: Up to 25-35% of women receive antibiotics (ABX) during pregnancy, but little is known about the consequences on a key mucosal interface such as the mammary gland, and on the development of the neonatal gut's microbiota and IgA. We hypothesize that prenatal ABX negatively affect the immune functionality of mammary gland, the composition of breast milk microbiota, the development of neonatal fecal microbiota and the abundance of neonatal fecal IgA.<br><br>METHODS: Case-control translational cohort study on women and neonates in the presence or absence (N&#x2009;=&#x2009;41&#x2009;+&#x2009;41 pairs) of exposure to prenatal ABX for at least 7 consecutive days after 32 weeks of gestation.<br><br>RESULTS: We will evaluate IgA concentration in breast milk and in neonatal feces up to one year after delivery. We will also evaluate clinical parameters, neurodevelopment and the composition of the IgA-coated and uncoated fractions of breast milk and fecal microbiota by means of magnetic-activated cell sorting (MACS) coupled with shotgun metagenomics. Finally, we will measure the concentration of the chemokine CCL28 on maternal serum and breast milk, as a marker of activity of the entero-mammary pathway.<br><br>CONCLUSIONS: Our results might support a data-driven evaluation of breast milk immune function in women exposed to prenatal ABX.<br><br>IMPACT: Breast milk IgA and microbiota are critical to determine the positive effects of breastfeeding in infants. This research protocol will investigate breast milk IgA, microbiota, and the IgA[+] / IgA[-] fractions of neonatal fecal microbiota upon exposure to prenatal antibiotics. Fecal IgA and microbiota in infants exposed or not exposed to prenatal antibiotics will be analyzed up to 1 year after birth. This research will clarify the impact of prenatal antibiotics on the immune function of breast milk. This, in turn, might support the selective evaluation of breast milk IgA/microbiota in mothers exposed to prenatal antibiotics, or in donor human milk.}, }
@article {pmid39966438, year = {2025}, author = {Priest, T and Oldenburg, E and Popa, O and Dede, B and Metfies, K and von Appen, WJ and Torres-Valdés, S and Bienhold, C and Fuchs, BM and Amann, R and Boetius, A and Wietz, M}, title = {Author Correction: Seasonal recurrence and modular assembly of an Arctic pelagic marine microbiome.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1733}, doi = {10.1038/s41467-025-57128-7}, pmid = {39966438}, issn = {2041-1723}, }
@article {pmid39966419, year = {2025}, author = {Heidrich, V and Fackelmann, G and Malesevic, M and Armanini, F and Dey, H and Mengoni, C and Stanisavljevic, N and Vukotic, G and Segata, N}, title = {Newly identified species from the dog dental plaque microbiome highlight little overlap with humans.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {30}, pmid = {39966419}, issn = {2055-5008}, mesh = {Animals ; Dogs ; *Dental Plaque/microbiology ; *Microbiota ; Humans ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; Metagenomics/methods ; Phylogeny ; Pets/microbiology ; }, abstract = {Understudied pet-associated microbiomes represent a rich source for the discovery of microbial taxa important for pet and human health. From a cohort of 23 dogs, we sampled and metagenomically sequenced 64 dental plaque microbiomes, generating 1945 metagenome-assembled genomes spanning 347 microbial species, including 277 undercharacterized species without cultivated representatives. Integration with human microbiome data revealed the dog plaque microbiome is more diverse than - and shows little overlap (5.9% species in common) with - the human plaque microbiome, even though some shared periodontal pathobionts arise as a potential concern.}, }
@article {pmid39966379, year = {2025}, author = {Schubert, C and Nguyen, BD and Sichert, A and Näpflin, N and Sintsova, A and Feer, L and Näf, J and Daniel, BBJ and Steiger, Y and von Mering, C and Sauer, U and Hardt, WD}, title = {Monosaccharides drive Salmonella gut colonization in a context-dependent or -independent manner.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1735}, pmid = {39966379}, issn = {2041-1723}, support = {10.001.588//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 51NF40_180575//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 310030_19256//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 51NF40_180575//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; SCHU 3606/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Animals ; Mice ; *Salmonella typhimurium/genetics/pathogenicity ; *Monosaccharides/metabolism ; Gastrointestinal Microbiome/physiology ; Fructose/metabolism ; Glucose/metabolism ; Cecum/microbiology ; Salmonella Infections/microbiology ; Mice, Inbred C57BL ; Female ; Galactose/metabolism ; Mutation ; Disease Models, Animal ; Mannose/metabolism ; }, abstract = {The carbohydrates that fuel gut colonization by S. Typhimurium are not fully known. To investigate this, we designed a quality-controlled mutant pool to probe the metabolic capabilities of this enteric pathogen. Using neutral genetic barcodes, we tested 35 metabolic mutants across five different mouse models with varying microbiome complexities, allowing us to differentiate between context-dependent and context-independent nutrient sources. Results showed that S. Typhimurium uses D-mannose, D-fructose and likely D-glucose as context-independent carbohydrates across all five mouse models. The utilization of D-galactose, N-acetylglucosamine and hexuronates, on the other hand, was context-dependent. Furthermore, we showed that D-fructose is important in strain-to-strain competition between Salmonella serovars. Complementary experiments confirmed that D-glucose, D-fructose, and D-galactose are excellent niches for S. Typhimurium to exploit during colonization. Quantitative measurements revealed sufficient amounts of carbohydrates, such as D-glucose or D-galactose, in the murine cecum to drive S. Typhimurium colonization. Understanding these key substrates and their context-dependent or -independent use by enteric pathogens will inform the future design of probiotics and therapeutics to prevent diarrheal infections such as non-typhoidal salmonellosis.}, }
@article {pmid39966341, year = {2025}, author = {Qin, L and Sun, T and Li, X and Zhao, S and Liu, Z and Zhang, C and Jin, C and Xu, Y and Gao, X and Cao, Y and Wang, J and Han, T and Yan, L and Song, J and Zhang, F and Liu, F and Zhang, Y and Huang, Y and Song, Y and Liu, Y and Zhang, J and Zhang, X and Yao, Z and Chen, H and Zhang, Z and Zhao, S and Feng, Y and Zhang, YN and Yu, Q and Cao, F and Zhao, L and Xie, L and Geng, L and Feng, Q and Zhao, H and Chen, ZJ}, title = {Population-level analyses identify host and environmental variables influencing the vaginal microbiome.}, journal = {Signal transduction and targeted therapy}, volume = {10}, number = {1}, pages = {64}, pmid = {39966341}, issn = {2059-3635}, mesh = {Female ; Humans ; *Vagina/microbiology ; *Microbiota/genetics ; Adult ; Middle Aged ; *RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; Vaginosis, Bacterial/microbiology/genetics ; Lactobacillus/genetics ; China ; }, abstract = {The vaginal microbiome is critical for the reproductive health of women, yet the differential impacts exerted by the host and by ambient environmental variables on the vaginal microbiome remain largely unknown. Here, we conducted a comprehensive cross-sectional study of the relationships between the vaginal microbiome and 81 matched host and environmental variables across 6755 Chinese women. By 16S rRNA sequencing, we identified four core vaginal microbiota with a prevalence of over 90% and a total median abundance of 98.8%. Twenty-four variables, including physiology, lifestyle behaviors, gynecologic history, social and environmental information, were found associated with the microbiome composition, of which bacterial vaginosis (BV) showed the largest effect size. Age was among the strongest explanatory variables and the vaginal microbiome dynamically succeeded with increasing age, especially with a composition turning point at the age of 45. Our mediation analyses indicated that the effects of age on the microbiome could be mediated by variables such as parity number and lifestyles. We further classified the vaginal microbiomes of the population into 13 "Vagitypes". Women with Lactobacillus iners- and Lactobacillus jensenii-dominated Vagitypes had significantly higher live birth rate than those with Vagitype dominated by Fannyhessea vaginae (53.40%, 59.09% vs 21.43%; OR [95% CI]: 3.62 [1.12-14.87], 5.39 [1.27-27.36]; P = 0.031, P = 0.021). This study provides a comprehensive overview of the associations between identified variables and the vaginal microbiome, representing an important step toward understanding of environment-microbe-host interactions.}, }
@article {pmid39966327, year = {2025}, author = {Barichello, T and Kluwe-Schiavon, B and Borba, LA and Pedro, LC and Niero, FS and Dos Santos, LN and Leonardo, LM and Ignácio, ZM and Morales, R and Ceretta, LB and Reus, GZ}, title = {Alterations in Gut Microbiome Composition and Increased Inflammatory Markers in Post-COVID-19 Individuals.}, journal = {Molecular neurobiology}, volume = {}, number = {}, pages = {}, pmid = {39966327}, issn = {1559-1182}, abstract = {Dysfunctions in the immune system and alterations in the microbiome composition following SARS-CoV-2 infection contribute to persistent neurological issues observed in long COVID-19 survivors. We hypothesize that alterations in the gut microbiome composition and peripheral inflammatory profile following COVID-19 may play pivotal roles in behavior changes among individuals experiencing long-term illness. This cross-sectional study included a sample of post-COVID-19 and non-COVID-19 subjects. We assessed the presence of psychiatric conditions utilizing standardized diagnostic criteria, Hamilton Rating Scale for Anxiety (HAM-A), Hamilton Rating Scale for Depression (HAM-D), Biological Rhythms in Neuropsychiatry Assessment Interview (BRIAN), and Functional Assessment Short Test (FAST). Plasma samples were analyzed to examine lipid and inflammatory profiles. Fecal samples were evaluated by 16S rRNA sequencing to identify the gut microbiome composition. Noteworthy findings include a significant increase in the myeloid progenitor inhibitory factor 1 (MPIF-1), interleukin (IL)-17, and triglyceride among post-COVID-19 individuals. While α-diversity in the gut microbiome composition showed no significant differences, β-diversity demonstrated a notable distinction between the healthy control and post-COVID-19 groups. Post-COVID-19 individuals exhibited a decreased abundance of phylum, class, and order of Verrucomicrobia, family, and genus of Akkermansia, a short-chain fatty acid producer and microbial group significantly associated with intestinal barrier homeostasis and the amelioration of metabolic diseases. No difference was found between the behavioral and clinical data. In post-COVID-19 individuals, there were elevated IL-17 and MPIF-1 levels, compared to non-COVID-19 individuals. Additionally, there were notable alterations in gut microbiome composition, as evidenced by changes in β-diversity and a decrease of Verrucomicrobia, family, and Akkermansia genus abundance.}, }
@article {pmid39965787, year = {2025}, author = {Hasan, Z and Begum, N and Ahmed, S and Yasmin, M}, title = {Association of opportunistic bacterial pathogens with female infertility: A case-control study.}, journal = {The journal of obstetrics and gynaecology research}, volume = {51}, number = {2}, pages = {e16243}, doi = {10.1111/jog.16243}, pmid = {39965787}, issn = {1447-0756}, support = {17-2022//University Grants Commission of Bangladesh/ ; }, mesh = {Humans ; Female ; Case-Control Studies ; Adult ; *Infertility, Female/microbiology ; *Vagina/microbiology ; Opportunistic Infections/microbiology/complications ; Bacterial Infections/microbiology ; }, abstract = {AIM: Infertility affects a significant proportion of women worldwide, and the colonization of certain vaginal pathogens has been suggested as a possible contributing factor. To explore the relationship between bacterial pathogens and female infertility, a case-control study was conducted involving 55 infertile women as cases and 5 fertile women as controls.<br><br>METHOD: Conventional culture-based techniques and biochemical assays followed by 16S rDNA sequence analysis were employed for the identification of vaginal isolates from the two groups. The strength of association between the isolated bacterium and infecundity was derived by odds ratio calculation.<br><br>RESULTS: The investigation revealed the presence of bacteria including Enterococcus faecalis, Escherichia coli, Bacillus spp., Acinetobacter baumannii, Pseudomonas spp., Micrococcus luteus, Staphylococcus aureus, Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus capitis, Staphylococcus epidermidis, and Staphylococcus saprophyticus in the vaginal swabs of infertile women. Of these, the odds ratios for Staphylococcus aureus, Klebsiella pneumoniae, E. faecalis, and E. coli were 5.43 (95% CI&#x2009;=&#x2009;0.28, 103.49), 4.59 (95% CI&#x2009;=&#x2009;0.24, 87.93), 2.25 (95% CI&#x2009;=&#x2009;0.11, 44.16), and 1.70 (95% CI&#x2009;=&#x2009;0.09, 34.01), respectively, displaying an association with infertility. Moreover, vaginal colonization of these four bacterial species was also dominant in cases that were diagnosed with pelvic inflammatory disease and idiopathic infertility by laparoscopic examination.<br><br>CONCLUSION: Overall, the findings of this study indicate a probable association between specific pathogenic microorganisms and women's barrenness, emphasizing the significant role of these disease-causing agents in hindering conception. This highlights the significance of a complete understanding of the vaginal microbiome and emphasizes further research in this area.}, }
@article {pmid39965269, year = {2025}, author = {Dhillon, J and Pandey, S and Newman, JW and Fiehn, O and Ortiz, RM}, title = {Almond consumption for 8 weeks differentially modulates metabolomic responses to an acute glucose challenge compared to crackers in young adults.}, journal = {Nutrition research (New York, N.Y.)}, volume = {135}, number = {}, pages = {67-81}, doi = {10.1016/j.nutres.2025.01.003}, pmid = {39965269}, issn = {1879-0739}, abstract = {This study investigated the dynamic responses to an acute glucose challenge after 8 weeks of almond or cracker consumption (clinicaltrials.gov ID: NCT03084003). Young adults (n = 73, age: 18-19 years, BMI: 18-41 kg/m[2]) participated in an 8-week randomized, controlled, parallel-arm intervention and were assigned to consume either almonds (2 oz/d, n = 38) or an isocaloric control snack of graham crackers (325 kcal/d, n = 35) daily. Twenty participants from each group underwent a 2-hour oral glucose tolerance test (oGTT) at the end of the intervention. Metabolite abundances in the oGTT serum samples were quantified using untargeted metabolomics, and targeted analyses for free PUFAs, total fatty acids, oxylipins, and endocannabinoids. We hypothesized that 8-week almond consumption would differentially modulate the metabolomic response to a glucose challenge compared to crackers. Multivariate, univariate, and chemical enrichment analyses were conducted to identify significant metabolic shifts. Findings exhibit a biphasic lipid response with higher levels of unsaturated triglycerides earlier in the oGTT followed by lower levels later in the almond vs cracker group (p-value <.05, chemical enrichment analyses). Almond (vs cracker) consumption was also associated with higher AUC120 min of aminomalonate, and oxylipins (P-value <.05), but lower AUC120 min of l-cystine, N-acetylmannosamine, and isoheptadecanoic acid (P-value <.05). Additionally, the Matsuda Index in the almond group correlated with AUC120 min of CE 22:6 (r = -0.46; P-value <.05) and 12,13 DiHOME (r = 0.45; P-value <.05). Almond consumption for 8 weeks leads to dynamic, differential shifts in response to an acute glucose challenge, marked by alterations in lipid and amino acid mediators involved in metabolic and physiological pathways.}, }
@article {pmid39964413, year = {2025}, author = {Mojgani, N and Ashique, S and Moradi, M and Bagheri, M and Garg, A and Kaushik, M and Hussain, MS and Yasmin, S and Ansari, MY}, title = {Gut Microbiota and Postbiotic Metabolites: Biotic Intervention for Enhancing Vaccine Responses and Personalized Medicine for Disease Prevention.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {39964413}, issn = {1867-1314}, support = {RGP .2 /244/45//Deanship of Scientific Research, King Khalid University/ ; RGP .2 /244/45//Deanship of Scientific Research, King Khalid University/ ; }, abstract = {The creation of vaccines has revolutionized several aspects of the game in the fight against transmissible diseases, protecting countless individuals around the globe. Several vaccines against potentially fatal diseases such as diphtheria, pertussis, polio, measles, tetanus, influenza, and smallpox have significantly reduced disease risks and successfully immunized individuals against these serious health threats. The immune response generated by vaccination plays a crucial role in mitigating disease risks by stimulating the production of specific antibodies targeting the relevant pathogens. However, the efficacy of vaccines can vary among communities and people due to several factors, including heredity, age, sex, and preexisting health conditions. The multitude of microbes that call the human digestive tract the microbiota have a pivotal role in regulating immunological reactions to immunization, according to mounting data from both experimental models and research trials. Nutritional supplementation with beneficial microbes, such as probiotic bacteria, has been shown to have immune-related benefits, including enhancements of immune system responses, and has the potential to modify the variety that makes up the microbiota. The effectiveness of vaccines can be enhanced by using probiotics, which work by fostering a balanced gut microbiome. New research reveals that the immune response can be influenced by both live and dormant probiotic bacteria, as well as postbiotics, which are byproducts of the metabolism of probiotics. These substances have immunomodulatory functions and are essential in regulating how the immune system reacts to vaccines. This review aims to summarize the available research, explore the possible immune system functions that could explain these effects, and ultimately speculate about how postbiotics, aimed at the biotic microbiota, could improve the efficacy of vaccines. The review further addresses postbiotics' challenges, regulatory aspects, and future directives for biotherapeutic products that could enhance vaccine efficacy and be tailored for personalized treatments.}, }
@article {pmid39964161, year = {2025}, author = {Babalola, OO and Adedayo, AA and Akinola, SA}, title = {Microbiome insights from a South African cultural and natural landmark cave using metagenomics next-generation sequencing.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0118324}, doi = {10.1128/mra.01183-24}, pmid = {39964161}, issn = {2576-098X}, abstract = {The microbiome study of Sterkfontein Cave (a natural and cultural cave) revealed fascinating insights into its metagenome study and functional annotation. The largely unexplored cave soil microbiota showcases intricate survival adaptations with promising potential for various human applications. Here, we report the microbial diversity and functions associated with Sterkfontein Cave soil.}, }
@article {pmid39964099, year = {2025}, author = {Beamer, MA and Furuta, S}, title = {Redefining Cell Culture Using a 3D Flipwell Co-culture System: A Mimetic for Gut Architecture and Dynamics In Vitro.}, journal = {Current protocols}, volume = {5}, number = {2}, pages = {e70107}, doi = {10.1002/cpz1.70107}, pmid = {39964099}, issn = {2691-1299}, mesh = {*Coculture Techniques/methods ; Humans ; Intestinal Mucosa/microbiology/cytology/drug effects/metabolism ; Cell Culture Techniques, Three Dimensional/methods ; Animals ; }, abstract = {Gut mucosae are composed of stratified layers of microbes, a selectively permeable mucus, an epithelial lining, and connective tissue homing immune cells. Studying cellular and chemical interactions between the gut mucosal components has been limited without a good model system. We have engineered a three-dimensional (3D) multi-cellular co-culture system we coined "3D Flipwell system" using cell culture inserts stacked against each other. This system allows an assessment of the impact of a gut mucosal environmental change on interactions between gut bacteria, epithelia, and immune cells. As such, this system can be utilized in examining the effects of exogenous stimuli, such as dietary nutrients, bacterial infection, and drugs, on the gut mucosa that could predetermine how these stimuli might influence the rest of body. Here, we describe the methods of construction and application of the new 3D Flipwell system we utilized previously in assessing the crosstalk between the gut mucosa and macrophage polarization. We demonstrate the physiological responses of different components of the co-cultures to Sepiapterin (SEP), the precursor of the nitric oxide synthase cofactor tetrahydrobiopterin (BH4). We reported previously that SEP induces a pro-immunogenic shift of macrophages having acquired an immune suppressive phenotype. We also showed that SEP induces a defense mechanism of commensal gut bacteria. The protocol describing the assembly and use of the 3D Flipwell co-culture system herein would grant its utility in evaluating the concurrent effects of pharmacologic and microbiologic stimuli on gut mucosal components. © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: 3D Flipwell construction, assembly, and collagen coating Basic Protocol 2: Flipwell cell seeding and cell culture Basic Protocol 3: Addition of bacterial culture to the Flipwell system Basic Protocol 4: Flipwell disassembly for scanning electron microscopy (SEM) studies Basic Protocol 5: Immunofluorescence antibody staining for confocal microscopy.}, }
@article {pmid39963971, year = {2025}, author = {Martin-Castaño, B and Diez-Echave, P and García-García, J and Hidalgo-García, L and Ruiz-Malagon, AJ and Molina-Tijeras, JA and Rodríguez-Sojo, MJ and Redruello-Romero, A and Martínez-Zaldívar, M and Mota, E and Cobo, F and Díaz-Villamarin, X and Alvarez-Estevez, M and García, F and Morales-García, C and Merlos, S and Garcia-Flores, P and Colmenero-Ruiz, M and Hernández-Quero, J and Nuñez, M and Rodriguez-Cabezas, ME and Carazo, A and Martin, J and Moron, R and Rodríguez Nogales, A and Galvez, J}, title = {The relationship between gut and nasopharyngeal microbiome composition can predict the severity of COVID-19.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, doi = {10.7554/eLife.95292}, pmid = {39963971}, issn = {2050-084X}, support = {CV20-99908//Junta de Andaluc&#xed;a/ ; }, mesh = {*COVID-19/microbiology/virology/diagnosis ; Humans ; Male ; *Nasopharynx/microbiology/virology ; *Gastrointestinal Microbiome ; Female ; Middle Aged ; Prospective Studies ; *Feces/microbiology/virology ; *SARS-CoV-2/isolation &amp; purification ; Severity of Illness Index ; Aged ; Adult ; Microbiota ; Prognosis ; Dysbiosis/microbiology ; Prevotella/isolation &amp; purification ; }, abstract = {Coronavirus disease 2019 (COVID-19) is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that displays great variability in clinical phenotype. Many factors have been described to be correlated with its severity, and microbiota could play a key role in the infection, progression, and outcome of the disease. SARS-CoV-2 infection has been associated with nasopharyngeal and gut dysbiosis and higher abundance of opportunistic pathogens. To identify new prognostic markers for the disease, a multicentre prospective observational cohort study was carried out in COVID-19 patients divided into three cohorts based on symptomatology: mild (n = 24), moderate (n = 51), and severe/critical (n = 31). Faecal and nasopharyngeal samples were taken, and the microbiota was analysed. Linear discriminant analysis identified Mycoplasma salivarium, Prevotella dentalis, and Haemophilus parainfluenzae as biomarkers of severe COVID-19 in nasopharyngeal microbiota, while Prevotella bivia and Prevotella timonensis were defined in faecal microbiota. Additionally, a connection between faecal and nasopharyngeal microbiota was identified, with a significant ratio between P. timonensis (faeces) and P. dentalis and M. salivarium (nasopharyngeal) abundances found in critically ill patients. This ratio could serve as a novel prognostic tool for identifying severe COVID-19 cases.}, }
@article {pmid39963956, year = {2025}, author = {Ast, HK and Hammer, M and Zhang, S and Bruton, A and Hatsu, IE and Leung, B and McClure, R and Srikanth, P and Farris, Y and Norby-Adams, L and Robinette, LM and Arnold, LE and Swann, JR and Zhu, J and Karstens, L and Johnstone, JM}, title = {Gut microbiome changes with micronutrient supplementation in children with attention-deficit/hyperactivity disorder: the MADDY study.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2463570}, doi = {10.1080/19490976.2025.2463570}, pmid = {39963956}, issn = {1949-0984}, mesh = {Humans ; *Attention Deficit Disorder with Hyperactivity/drug therapy/diet therapy ; *Gastrointestinal Microbiome/drug effects ; *Micronutrients/administration &amp; dosage ; Child ; *Dietary Supplements ; Male ; Female ; *Feces/microbiology ; Double-Blind Method ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification/drug effects ; Adolescent ; }, abstract = {Micronutrients have demonstrated promise in managing inattention and emotional dysregulation in children with attention-deficit/hyperactivity disorder (ADHD). One plausible pathway by which micronutrients improve symptoms is the gut microbiome. This study examines changes in fecal microbial composition and diversity after micronutrient supplementation in children with ADHD (N = 44) and highlights potential mechanisms responsible for the behavioral improvement, as determined by blinded clinician-rated global improvement response to micronutrients. Participants represent a sub-group of the Micronutrients for ADHD in Youth (MADDY) study, a double blind randomized controlled trial in which participants received micronutrients or placebo for 8 weeks, followed by an 8-week open extension. Stool samples collected at baseline, week 8, and week 16 were analyzed using 16S rRNA amplicon sequencing targeting the V4 hypervariable region. Pairwise compositional analyses investigated changes in fecal microbial composition between micronutrients versus placebo and responders versus non-responders. A significant change in microbial evenness, as measured by alpha diversity, and beta-diversity, as measured by Bray-Curtis, was observed following micronutrients supplementation. The phylum Actinobacteriota decreased in the micronutrients group compared to placebo. Two butyrate-producing bacterial families: Rikenellaceae and Oscillospiraceae, exhibited a significant increase in change following micronutrients between responders versus non-responders. These findings suggest that micronutrients modulated the composition of the fecal microbiota and identified specific bacterial changes associated with micronutrient responders.}, }
@article {pmid39963931, year = {2025}, author = {}, title = {Correction: Correction to Changes in the Firmicutes to Bacteriodetes ratio in the gut microbiome in individuals with anorexia nervosa following inpatient treatment: A systematic review and a case series.}, journal = {Brain and behavior}, volume = {15}, number = {2}, pages = {e70204}, doi = {10.1002/brb3.70204}, pmid = {39963931}, issn = {2162-3279}, }
@article {pmid39963784, year = {2025}, author = {Li, J and Jia, J and Teng, Y and Wang, X and Xia, X and Song, S and Zhu, B and Xia, X}, title = {Sea cucumber polysaccharides overcome immunotherapy resistance in tumor-bearing mice via modulation of the gut microbiome.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4fo05449k}, pmid = {39963784}, issn = {2042-650X}, abstract = {Cancer immunotherapy has been successful in patients with different types of cancers, but its efficacy in treating certain types of colorectal cancer (CRC) is limited. The aim of this study was to explore whether sea cucumber polysaccharides (SCP) could impact resistance to anti-programmed cell death-1 (anti-PD1) immunotherapy of CRC and the role of microbiota in mediating their effects. Mice inoculated with immunotherapy resistant CT-26 CRC cells were pretreated with SCP, followed by treatment with/without the anti-PD1 antibody. SCP alone exhibited no inhibitory effect on tumor growth, but they drastically enhanced the efficacy of anti-PD1 treatment, which alone showed minimal effect on tumor development. Compared to anti-PD1 only treatment, a combination of SCP and anti-PD1 increased CD8[+] T cells, especially IFN-γ[+] cytotoxic CD8[+] T cells, and decreased regulatory CD4[+] T cells. SCP modulated gut microbiota and increased the relative abundance of bacteria including Bifidobacterium and Faecalibaculum. A fecal microbiota transplantation experiment showed that the sensitizing effect of SCP was at least partly mediated by microbiota. Furthermore, oral supplementation of Bifidobacterium pseudolongum or Faecalibaculum rodentium recapitulated the beneficial effect of SCP in potentiating anti-PD1 efficacy. Altogether, these findings demonstrated that SCP could be potentially developed as a dietary adjuvant to increase the efficacy of immunotherapy in CRC.}, }
@article {pmid39963528, year = {2025}, author = {Liu, H and Zhang, Y and Zhang, L and Liu, Y and Chen, Y and Shi, Y}, title = {Nano-selenium strengthens potato resistance to potato scab induced by Streptomyces spp., increases yield, and elevates tuber quality by influencing rhizosphere microbiomes.}, journal = {Frontiers in plant science}, volume = {16}, number = {}, pages = {1523174}, pmid = {39963528}, issn = {1664-462X}, abstract = {INTRODUCTION: The application of selenium could directly or indirectly modulate the activity of antioxidant enzymes in crops, thereby mitigating the detrimental effects of abiotic and biotic stresses on crop health. However, there are few studies on the effects of nano-selenium fertilizer on potato scab caused by Streptomyces spp., potato yield and tuber quality.<br><br>METHODS: We aimed to elucidate the impact of nano-selenium fertilizer on potato disease resistance, yield, tuber quality, antioxidant enzyme activity and rhizosphere soil bacterial communities, and to determine the optimal frequency and growth stages of nano-selenium fertilizer spraying.<br><br>RESULTS AND DISCUSSION: The application of nano-selenium fertilizer twice during the seedling stage significantly reduced the disease index of potato scab, enhanced potato yield, tuber quality (dry matter, Vitamin C, crude protein, and selenium content), and antioxidant enzyme activity (glutathione peroxidase, peroxidase, polyphenol oxidase, superoxide dismutase, and phenylalanine ammonia lyase). The diversity of the rhizosphere bacterial community of potatoes subjected to selenium fertilizer spraying at the seedling stage increased significantly, and concurrently, the symbiotic network of rhizosphere bacterial microbiome grew more complex. Beneficial microorganisms such as bacteria of the genus Bacillus were enriched in the rhizosphere soil. The current study provided theoretical support for the exploration of a potato selenium-enriched technology system and supplies scientific guidance for the utilization of nano-selenium.}, }
@article {pmid39963501, year = {2024}, author = {Nelson, AR and Rhoades, CC and Fegel, TS and Roth, HK and Caiafa, MV and Glassman, SI and Borch, T and Wilkins, MJ}, title = {Wildfire impact on soil microbiome life history traits and roles in ecosystem carbon cycling.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae108}, pmid = {39963501}, issn = {2730-6151}, abstract = {Wildfires, which are increasing in frequency and severity with climate change, reduce soil microbial biomass and alter microbial community composition and function. The soil microbiome plays a vital role in carbon (C) and nitrogen (N) cycling, but its complexity makes it challenging to predict post-wildfire soil microbial dynamics and resulting impacts on ecosystem biogeochemistry. The application of biogeochemically relevant conceptual trait-based frameworks to the soil microbiome can distill this complexity, enabling enhanced predictability of soil microbiome recovery following wildfire and subsequent impacts to biogeochemical cycles. Conceptual frameworks that have direct links to soil C and N cycling have been developed for the soil microbiome; the Y-A-S framework overviews soil microbiome life history strategies that have tradeoffs with one another and others have proposed frameworks specific to wildfire. Here, we aimed to delineate post-wildfire changes of bacterial traits in western US coniferous forests to inform how severe wildfire influences soil microbiome recovery and resultant biogeochemical cycling. We utilized a comprehensive metagenome-assembled genome catalog from post-wildfire soils representing 1 to 11 years following low- and high-severity burning to identify traits that enable the persistence of microbial taxa in burned soils and influence ecosystem C and N cycling. We found that high-severity wildfire initially selects for fast growers and, up to a decade post-fire, taxa that invest in genes for acquiring diverse resources from the external environment, which in combination could increase soil C losses. This work begins to disentangle how climate change-induced shifts in wildfire behavior might alter microbially mediated soil biogeochemical cycling.}, }
@article {pmid39963423, year = {2024}, author = {Kelliher, JM and Xu, Y and Flynn, MC and Babinski, M and Canon, S and Cavanna, E and Clum, A and Corilo, YE and Fujimoto, G and Giberson, C and Johnson, LYD and Li, KJ and Li, PE and Li, V and Lo, CC and Lynch, W and Piehowski, P and Prime, K and Purvine, S and Rodriguez, F and Roux, S and Shakya, M and Smith, M and Sarrafan, S and Cholia, S and McCue, LA and Mungall, C and Hu, B and Eloe-Fadrosh, EA and Chain, PSG}, title = {Standardized and accessible multi-omics bioinformatics workflows through the NMDC EDGE resource.}, journal = {Computational and structural biotechnology journal}, volume = {23}, number = {}, pages = {3575-3583}, pmid = {39963423}, issn = {2001-0370}, abstract = {Accessible and easy-to-use standardized bioinformatics workflows are necessary to advance microbiome research from observational studies to large-scale, data-driven approaches. Standardized multi-omics data enables comparative studies, data reuse, and applications of machine learning to model biological processes. To advance broad accessibility of standardized multi-omics bioinformatics workflows, the National Microbiome Data Collaborative (NMDC) has developed the Empowering the Development of Genomics Expertise (NMDC EDGE) resource, a user-friendly, open-source web application (https://nmdc-edge.org). Here, we describe the design and main functionality of the NMDC EDGE resource for processing metagenome, metatranscriptome, natural organic matter, and metaproteome data. The architecture relies on three main layers (web application, orchestration, and execution) to ensure flexibility and expansion to future workflows. The orchestration and execution layers leverage best practices in software containers and accommodate high-performance computing and cloud computing services. Further, we have adopted a robust user research process to collect feedback for continuous improvement of the resource. NMDC EDGE provides an accessible interface for researchers to process multi-omics microbiome data using production-quality workflows to facilitate improved data standardization and interoperability.}, }
@article {pmid39963412, year = {2025}, author = {Jiang, H and Zeng, W and Zhu, F and Zhang, X and Cao, D and Peng, A and Wang, H}, title = {Exploring the associations of gut microbiota with inflammatory and the early hematoma expansion in intracerebral hemorrhage: from change to potential therapeutic objectives.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1462562}, pmid = {39963412}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Cerebral Hemorrhage/microbiology ; Male ; Female ; Middle Aged ; *RNA, Ribosomal, 16S/genetics ; Aged ; *Dysbiosis/microbiology ; *Hematoma/microbiology ; *Inflammation ; Bacteria/classification/genetics/isolation &amp; purification ; Probiotics/administration &amp; dosage ; }, abstract = {BACKGROUND: Although a great deal of research has explored the possibility of a systemic inflammatory response and dysbiosis of the gut microbiota after an intracerebral hemorrhage (ICH), the relationships between gut microbiota and blood inflammatory indicators as well as their role in the hematoma expansion following an early-stage mild-to-moderate ICH (emICH) remain unknown. This study analyzes these changes and associations in order to predict and prevent hematoma expansion after emICH.<br><br>METHODS: The study included 100 participants, with 70 individuals diagnosed with emICH (30 with hematoma expansion and 40 without hematoma expansion, referred to as the HE and NE groups) and 30 healthy controls matched in terms of age and gender (HC). We used 16S rRNA gene sequencing to explore the gut microbial structure and its underlying associations with blood inflammatory parameters in the HE group.<br><br>RESULTS: Our findings showed a significant decrease in the diversity and even distribution of microorganisms in the HE group when compared to the HC and NE groups. The composition of the gut microbiota experienced notable alterations in the emICH group, especially in HE. These changes included a rise in the number of gram-negative pro-inflammatory bacteria and a decline in the level of probiotics. Furthermore, we observed strong positive connections between bacteria enriched in the HE group and levels of systemic inflammation. Several microbial biomarkers (e.g. Escherichia_Shigella, Enterobacter, and Porphyromonas) were revealed in disparateiating HE from HC and NE. Analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) exposed disturbances in essential physiological pathways, especially those related to inflammation (such as the Toll-like receptor signaling pathway), in the HE group.<br><br>CONCLUSIONS: Our exploration indicated that individuals with emICH, especially those with HE, demonstrate notably different host-microbe interactions when compared to healthy individuals. We deduced that emICH could rapidly trigger the dysbiosis of intestinal flora, and the disturbed microbiota could, in turn, exacerbate inflammatory response and increase the risk of hematoma expansion. Our comprehensive research revealed the potential of intestinal flora as a potent diagnostic tool, emphasizing its significance as a preventive target for HE.}, }
@article {pmid39963409, year = {2025}, author = {Kolo, AO and Brayton, KA and Collins, NE and Bastos, ADS and Matthee, S and Gall, CA and Wentzel, J and Neves, L and Oosthuizen, MC}, title = {Bacterial blood microbiome of Mastomys rodents: implications for disease spill-over at the animal-human interface within the Bushbuckridge-East community, South Africa.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1520086}, pmid = {39963409}, issn = {2235-2988}, mesh = {Animals ; South Africa ; *Microbiota/genetics ; *Murinae/microbiology ; Humans ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Zoonoses/microbiology ; Disease Reservoirs/microbiology ; DNA, Bacterial/genetics ; Phylogeny ; Blood/microbiology ; Bartonella/isolation &amp; purification/genetics/classification ; Rodent Diseases/microbiology/epidemiology ; }, abstract = {The Bushbuckridge-East community in Mpumalanga Province, South Africa is bordered by nature reserves, including the Manyeleti Game Reserve. Murid rodents are prevalent in both Manyeleti and communal rangelands adjoining the community households. Although rodents are reservoir hosts for a broad range of viral, bacterial and parasitic pathogens, the rodent microbial diversity and transmission of zoonotic agents to humans in the community is understudied. In this study we investigated bacterial diversity in wild and commensal rodents sampled from different habitats. The 16S rRNA gene was amplified from DNA extracted from the blood of 24 wild Mastomys and one Steatomys sp. and subjected to PacBio circular consensus sequencing. As Bartonella species were dominant in the blood microbiome, gltA gene characterization was performed to delineate species. Rodents sampled from peri-urban and communal rangelands had higher proportions of Bartonella spp. [Hlalakahle (77.7%), Gottenburg (47.8%), Tlhavekisa (83.8%)] compared to those from the protected habitat (43.8%). Ehrlichia spp., Anaplasma spp., and Coxiella burnetii were detected at <1% of the sequence reads. Conventional PCR and sequencing validated the detection of Bartonella spp. with the first confirmation of Bartonella mastomydis infection in Mastomys in South Africa. Additionally, 317 mites, 90 fleas, 10 ticks and eight lice were collected from the rodents, providing evidence of possible vectors of the organisms detected. The detection of zoonotic agents in rodents in Bushbuckridge-East community, together with prior serological confirmation of Bartonella and Coxiella in non-malarial acute febrile patients from this community, highlights the possible risks that commensal rodents pose to human health.}, }
@article {pmid39963348, year = {2025}, author = {Maltoni, G and Candela, E and Tornese, G}, title = {Editorial: Challenges in pediatric endocrinology regarding alterations in glucose metabolism, growth disorders, disorders of sex development, and puberty in adolescents.}, journal = {Frontiers in pediatrics}, volume = {13}, number = {}, pages = {1561951}, pmid = {39963348}, issn = {2296-2360}, }
@article {pmid39963326, year = {2025}, author = {Wang, J and Lu, L and Ren, L and Zhu, R and Jiang, Y and Qiao, Y and Li, Y}, title = {Dysbiosis and Metabolic Dysregulation of Salivary Microbiota in Schizophrenia.}, journal = {Journal of multidisciplinary healthcare}, volume = {18}, number = {}, pages = {813-825}, pmid = {39963326}, issn = {1178-2390}, abstract = {BACKGROUND: Schizophrenia (SZ) is a chronic, severe mental disorder that presents significant challenges to diagnosis and effective treatment. Emerging evidence suggests that gut microbiota may play a role in the disease's pathogenesis. However, fewer studies have directly investigated the potential links between oral microbiota and SZ.<br><br>PURPOSE: This study aimed to explore the relationship between salivary microbiota dysbiosis and SZ, examining microbial and metabolic alterations that may contribute to SZ pathophysiology.<br><br>METHODS: Salivary samples from 30&#xa0;hospitalized patients diagnosed with SZ and 10&#xa0;healthy controls were collected. The microbial and metabolic profiles were analyzed using 16S rRNA gene sequencing and metabolomic profiling. Clinical parameters, including oral health status, were also evaluated to minimize variability in sampling.<br><br>RESULTS: Patients with SZ exhibited significantly poorer oral health compared to healthy controls, with more missing teeth and worse periodontal status. Microbiota sequencing revealed notable alterations in the overall structure and composition of the salivary microbiome in SZ patients, characterized by increased abundance of specific genera such as Neisseria and Porphyromonas. Metabolomic analysis indicated significant differences between the SZ and control groups, with upregulation of key metabolic pathways, including "&#x3b2;-alanine metabolism" and "vitamin digestion and absorption". Correlations between microbial dysbiosis and elevated levels of certain metabolites, such as L-methionine sulfoxide (L-MetO) and tyramine, were observed, suggesting links to oxidative stress.<br><br>CONCLUSION: The study highlights the presence of significant dysbiosis and metabolic dysfunction in the salivary microbiota of SZ patients, suggesting that alterations in the oral microbiome may contribute to SZ pathogenesis. These results provide new insights into potential diagnostic biomarkers and therapeutic targets for SZ. Further studies with larger sample sizes are required to validate these findings.}, }
@article {pmid39962981, year = {2025}, author = {Valderrama, B and Daly, I and Gunnigle, E and O'Riordan, KJ and Chichlowski, M and Banerjee, S and Skowronski, AA and Pandey, N and Cryan, JF and Clarke, G and Nagpal, J}, title = {From in silico screening to in vivo validation in zebrafish - a framework for reeling in the right psychobiotics.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4fo03932g}, pmid = {39962981}, issn = {2042-650X}, abstract = {The potential of gut bacteria to interact with the nervous system is now well known. Therefore, the characterization of bacterial strains that can modulate signalling pathways of the nervous system is a topic of growing interest, as it represents a potential alternative therapeutic target to treat central nervous system disorders. However, a streamlined screening framework is required to guide the rational identification and selection of such bacteria, known as psychobiotics. In this work, we introduce a framework that integrates in silico, in vitro and in vivo approaches to identify psychobiotic candidates capable of both metabolising prebiotics of interest and producing neuroactive molecules. To prove the effectiveness of the approach, we characterized a bacterial strain, Lactiplantibacillus plantarum APC2688, for its capacity to modulate the GABAergic system and alter the stress-related behaviour of zebrafish larvae. In brief, in silico analyses of the genomic content of APC2688 identified it as capable of degrading different prebiotics and producing neuroactive compounds known to modulate the stress response in animal models. Then, in vitro results confirmed the ability of this strain to produce GABA, tryptophan and acetate, while growing with the candidate prebiotics of interest, fructooligosaccharides (FOS), galactooligosaccharides (GOS) and inositol. In vivo experiments demonstrated that the administration of bacterial supernatants induced changes in the expression of gad1 and gabra1 in zebrafish larvae, two essential genes in the GABAergic signalling pathway, and altered the anxiety-like behaviour of the larvae. These results highlight the efficiency of our framework in integrating orthogonal approaches to discover and characterise bacteria capable of modulating the microbiome-gut-brain axis.}, }
@article {pmid39962881, year = {2025}, author = {Liang, Y and Mao, J and Qiu, T and Li, B and Zhang, C and Zhang, K and Sun, Z and Zhang, G}, title = {Predicting nasal diseases based on microbiota relationship network.}, journal = {Science progress}, volume = {108}, number = {1}, pages = {368504251320832}, doi = {10.1177/00368504251320832}, pmid = {39962881}, issn = {2047-7163}, mesh = {Humans ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Female ; Bacteria/genetics/isolation &amp; purification/classification ; Male ; Sinusitis/microbiology/diagnosis ; Nose Diseases/microbiology/diagnosis ; Machine Learning ; Middle Aged ; Adult ; Rhinitis/microbiology/diagnosis ; }, abstract = {OBJECTIVES: Increasing evidence indicates that the local microbiome can be used to predict host disease states. However, constructing models that obtain better results with fewer features is still challenging.<br><br>METHODS: In this study, we established a nasal microbiome database consisting of 132 chronic rhinosinusitis patients, 27 nasal inverted papilloma patients, and 45 control patients. 16S rRNA gene sequencing was used to identify the species and abundance of bacteria in each sample, and a nasal microbiome database was generated after low-abundance bacteria were eliminated. The correlation data network of different groups of bacteria was constructed by calculating the correlation coefficient among bacterial genera, and the correlation parameters of the network were calculated based on graph theory. Through the development and application of a machine learning framework to optimize the screening process, combined with microbiome relationship network parameters based on graph theory, basic bacteria with high contributions to classification prediction were selected for the prediction of nasal diseases.<br><br>RESULTS: We found that patients with nasal disease have a specific nasal microbiome signature and identified Moraxella, Prevotella, and Rothia as keystone genera that are markers of nasal disease; these markers can be interpreted as key control routes through graph theory analysis of the microbiota. With this strategy, we were able to characterize microbial community changes in nasal disease patients, which could reveal the potential role of the nasal microbiome in nasal disease.<br><br>CONCLUSION: This study can provide a reference for the formulation of disease prevention and control policies. Our framework can be applied to other diseases to identify keystone genera that influence disease states and can be used to predict disease states.}, }
@article {pmid39962804, year = {2025}, author = {Zhao, A and Li, J and Peterson, M and Black, M and Gaulke, CA and Jeffery, EH and Miller, MJ}, title = {Cooked Broccoli Alters Cecal Microbiota and Impacts Microbial Metabolism of Glucoraphanin in Lean and Obese Mice.}, journal = {Molecular nutrition &amp; food research}, volume = {}, number = {}, pages = {e202400813}, doi = {10.1002/mnfr.202400813}, pmid = {39962804}, issn = {1613-4133}, support = {2019-38420-28973//USDA-NIFA/ ; 2023-67017-39758//USDA-NIFA/ ; //Division of Nutritional Sciences at the University of Illinois/ ; 202108040001//China Scholarship Council/ ; RB22044//University of Illinois Campus Research Board/ ; #ILLU-698-339//USDA Cooperative State Research, Education and Extension Service Hatch/ ; }, abstract = {SCOPE: Brassica vegetables contain unique compounds known as glucosinolates (GSLs), which, when hydrolyzed by plant or microbial myrosinase, form bioactive isothiocyanates (ITCs) that offer health benefits to the host. The present study evaluated the impact of cooked broccoli (broccoli myrosinase inactivated) consumption on cecal microbial metabolism of glucoraphanin (GRP) in lean and obese mice and characterized the changes in cecal microbiota following broccoli-containing diets.<br><br>METHODS AND RESULTS: Twenty lean and 20 diet-induced obese (DIO) mice were randomized to consume control or cooked broccoli supplemented diets for 7 days. Cooked broccoli consumption increased ex vivo microbial GRP hydrolysis by cecal contents collected from lean and obese mice, led to increased production of sulforaphane (SF), sulforaphane-cysteine (SF-CYS), total ITC, and colonic NAD(P)H: Quinone Oxidoreductase (NQO1) activity. Further investigation revealed increased abundance of health-promoting gut microbiota, including Lachnospiraceae NK4A136 group and Dubosiella newyorkensis, following broccoli-containing diets. The Peptococcaseae family, the Blautia genus, and an amplicon sequence variation (ASV) from the Oscillospiraceae family exhibited negative correlation with total ITC production.<br><br>CONCLUSION: These finding suggest that cooked broccoli consumption enhances microbial GRP hydrolysis to produce more bioactive ITCs and inform future strategies toward altering microbial GSL metabolism to promote gut health in both lean and obese individuals.}, }
@article {pmid39962619, year = {2025}, author = {Foucault, P and Halary, S and Duval, C and Goto, M and Marie, B and Hamlaoui, S and Jardillier, L and Lamy, D and Lance, E and Raimbault, E and Allouti, F and Troussellier, M and Bernard, C and Leloup, J and Duperron, S}, title = {A summer in the greater Paris: trophic status of peri-urban lakes shapes prokaryotic community structure and functional potential.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {24}, pmid = {39962619}, issn = {2524-6372}, support = {COM2LIFE (ANR-20-CE32-0006)//Agence Nationale de la Recherche/ ; COM2LIFE (ANR-20-CE32-0006)//Agence Nationale de la Recherche/ ; }, abstract = {With more than 12 million inhabitants, the Greater Paris offers a "natural laboratory" to explore the effects of eutrophication on freshwater lake's microbiomes within a relative restricted area (~ 70 km radius). Here, a 4-months survey was carried out during summertime to monitor planktonic microbial communities of nine lakes located around Paris (Île-de-France, France) of comparable morphologies, yet distinct trophic statuses from mesotrophic to hypereutrophic. By thus minimizing the confounding factors, we investigated how trophic status could influence prokaryotic community structures (16S rRNA gene sequencing) and functions (shotgun metagenomics). These freshwater lakes harbored highly distinct and diverse prokaryotic communities, and their trophic status appears as the main driver explaining both differences in community structure and functional potential. Although their gene pool was quite stable and shared among lakes, taxonomical and functional changes were correlated. According to trophic status, differences in phosphorus metabolism-related genes were highlighted among the relevant functions involved in the biogeochemical cycles. Overall, hypereutrophic lakes microbiomes displayed the highest contrast and heterogeneity over time, suggesting a specific microbial regime shift compared to eutrophic and mesotrophic lakes.}, }
@article {pmid39962509, year = {2025}, author = {Sun, J and Lu, L and Lian, Y and Xu, S and Zhu, Y and Wu, Y and Lin, Q and Hou, J and Li, Y and Yu, Z}, title = {Sodium butyrate attenuates microglia-mediated neuroinflammation by modulating the TLR4/MyD88/NF-κB pathway and microbiome-gut-brain axis in cardiac arrest mice.}, journal = {Molecular brain}, volume = {18}, number = {1}, pages = {13}, pmid = {39962509}, issn = {1756-6606}, support = {No. 81772039//National Natural Science Foundation of China/ ; No. 2022020801010474//Knowledge Innovation Program Project of Wuhan Municipal Science and Technology Bureau/ ; CZ2024020001//Project of Healthcare Talent "Chutian Talent Program" in Hubei Province/ ; }, mesh = {Animals ; *Myeloid Differentiation Factor 88/metabolism ; *Toll-Like Receptor 4/metabolism ; *Microglia/drug effects/metabolism/pathology ; *NF-kappa B/metabolism ; *Butyric Acid/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Signal Transduction/drug effects ; Male ; *Mice, Inbred C57BL ; Mice ; *Neuroinflammatory Diseases ; *Heart Arrest/complications ; *Brain-Gut Axis/drug effects/physiology ; Cell Line ; Inflammation/pathology ; }, abstract = {Cardiac arrest (CA) is one of the most common illnesses worldwide. Post-CA brain injury (PCABI) is a major cause of death and poor recovery in CA patients and the current CA treatments are not very effective. The microbiome-gut-brain axis has been found to significantly affect brain ischemia injury. Furthermore, in ischemic stroke patients, short-chain fatty acids (SCFA), especially sodium butyrate (SB), have been observed to promote neuroprotective effects by modulating inflammatory response and microglial polarization in the cortex. However, the precise mechanism of SB on CA-induced injury remains elusive. Therefore, this research study established an oxygen-glucose deprivation and reoxygenation (OGD/R) model using BV-2 microglial and HT22 cells to simulate cerebral ischemia/reperfusion injury in vitro and a potassium chloride-induced CA mouse model to mimic CA in vivo. The data revealed that SB markedly improved neurological scores and reduced neuronal death and apoptosis. Moreover, it reduced M1 microglia and neuroinflammation in CA mice. In addition, SB increased intestinal integrity and alleviated systemic inflammation. The 16S rDNA sequencing analysis indicated that SB intervention mitigated CA-induced gut microbiota dysbiosis and SCFA depletion. It was also observed that CA mice's brain and OGD/R-exposed BV2 cells had substantially increased levels of MyD88, phosphorylated NF-κB p65, and TLR4 proteins, which were reduced after SB treatment. In summary, this study revealed that SB can protect against cerebral ischemia-reperfusion injury by controlling microglia polarization and microbiome-gut-brain axis to inhibit brain inflammation via the TLR4/MyD88/NF-κB pathway.}, }
@article {pmid39962355, year = {2025}, author = {}, title = {Erratum to "Neopolyploidy has variable effects on the diversity and composition of the wild strawberry microbiome".}, journal = {American journal of botany}, volume = {}, number = {}, pages = {e70009}, doi = {10.1002/ajb2.70009}, pmid = {39962355}, issn = {1537-2197}, }
@article {pmid39962023, year = {2025}, author = {Chen, J and Zhu, L and Wang, F and Zhu, Y and Chen, J and Liang, C and Liu, B and Pang, A and Yang, X}, title = {Plasma Metabolites as Mediators Between Gut Microbiota and Parkinson's Disease: Insights from Mendelian Randomization.}, journal = {Molecular neurobiology}, volume = {}, number = {}, pages = {}, pmid = {39962023}, issn = {1559-1182}, support = {202301AS070045,202101AY070001-115//Applied Basic Research Foundation of Yunnan Province/ ; 81960242//National Natural Science Foundation of China/ ; 202102AA310069//Yunnan Province Clinical Research Center for Geriatric Disease/ ; 202305AS350019//The Innovative Team of Yunnan Province/ ; }, abstract = {Recent evidence supports the causal role of both plasma metabolites and gut microbiota (GM) in Parkinson's disease (PD). However, it remains unclear whether GM are responsible for causing PD through plasma metabolites. Here, we used Mendelian randomization (MR) to investigate the intrinsic causal relationships among GM, plasma metabolites, and PD. Summary statistics were derived from a GWAS of 1400 metabolites (N = 8299), GM (N = 18,340), and PD (Ncase = 33,674 and Ncontrol = 449,056). We used two-step/mediation MR (TSMR) to study the mediating effect of plasma metabolites on the association between GM and the risk of developing PD. We detected 54 genetic traits that were causally associated with PD development. According to the TSMR analysis, ceramide had a mediating effect on the relationship between the genus Clostridium sensu stricto 1 and the risk of developing PD (15.35% mediation; 95% CI = 1.29-32.75%). 7-Alpha-hydroxy-3-oxo-4-cholestenoate had a mediating effect on the relationship between the genus Eubacterium xylanophilum group and the risk of developing PD (11.04% mediation; 95% CI = 0.11-27.07%). In the present study, we used MR analysis to investigate the connections among GM, plasma metabolites, and PD. This comprehensive investigation offers insights into the pathogenic mechanisms of PD and the roles of the intestinal microbiota and metabolites in this disease.}, }
@article {pmid39961999, year = {2025}, author = {Popov, IV and Popov, IV and Chebotareva, IP and Tikhmeneva, IA and Peshkova, DA and Krikunova, AA and Tkacheva, EV and Algburi, AR and Abdulhameed, AM and Jargalsaikhan, A and Ganbold, O and Chikindas, ML and Venema, K and Ermakov, AM}, title = {Differences in gut microbiota composition, diversity, and predicted functional activity between wild and captive zoo Carollia perspicillata in a One Health perspective.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {39961999}, issn = {1678-4405}, support = {075-10-2021-093//Ministry of Science and Higher Education of the Russian Federation/ ; 23-14-00316//Russian Science Foundation/ ; }, abstract = {Bats play an important role in global microbial ecology, as they are the host of various microbes. Carollia perspicillata is one of the most popular bat species in zoos. The influence of the captive environment on the gut microbiota of this species is underinvestigated. In this study, we compared gut microbiota composition, diversity, and the potential functional activity of wild and captive C. perspicillata from Panama and Russia (Moscow Zoo), respectively, based on high-throughput 16S rRNA sequencing data. The abundance of 13 bacterial phyla and 35 bacterial genera significantly differed. Environment- and farm animal health-related bacteria (Mannheimia, unclassified Pasteurellaceae, Staphylococcus, and Mycoplasma) dominated wild bats, while bacteria important for public health (Bacteroides, Clostridium sensu stricto 1, and Acinetobacter) were higher in zoo bats. We also observed significantly greater alpha diversity in zoo bats, while there were no significant differences in beta diversity. These findings were accompanied by significant differences in the abundance of 32 functional pathways of gut bacteria, which are probably associated with the different diets of wild and zoo bats. This study shows that the rearing environment significantly affects the gut microbiota of C. perspicillata and highlights that the outcomes of microbiome research of captive bats need to be interpreted with care. Such differences in gut bacterial communities should be the basis for the development of new handling and veterinary care protocols, and also be the justification for further studies of the impact of microbiota of wild and zoo bats on One Health.}, }
@article {pmid39961991, year = {2025}, author = {Booth, ME and Wood, HM and Travis, MA and ,  and Quirke, P and Grabsch, HI}, title = {The relationship between the gastric cancer microbiome and clinicopathological factors: a metagenomic investigation from the 100,000 genomes project and The Cancer Genome Atlas.}, journal = {Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association}, volume = {}, number = {}, pages = {}, pmid = {39961991}, issn = {1436-3305}, abstract = {BACKGROUND: Findings from previous gastric cancer microbiome studies have been conflicting, potentially due to patient and/or tumor heterogeneity. The intratumoral gastric cancer microbiome and its relationship with clinicopathological variables have not yet been characterized in detail. We hypothesized that variation in gastric cancer microbial abundance, alpha diversity, and composition is related to clinicopathological characteristics.<br><br>METHODS: Metagenomic analysis of 529 GC samples was performed, including whole exome sequencing data from The Cancer Genome Atlas (TCGA) and whole genome sequencing data from the 100,000 Genomes Project. Microbial abundance, alpha diversity, and composition were compared across patient age, sex, tumor location, geographic origin, pathological depth of invasion, pathological lymph node status, histological phenotype, microsatellite instability status, and TCGA molecular subtype.<br><br>RESULTS: Gastric cancer microbiomes resembled previous results, with Prevotella, Selenomonas, Stomatobaculum, Streptococcus, Lactobacillus, and Lachnospiraceae commonly seen across both cohorts. Within the TCGA cohort, microbial abundance and alpha diversity were greater in gastric cancers with microsatellite instability, lower pathological depth&#xa0;of invasion, intestinal-type histology, and those originating from Asia. Microsatellite instability status was associated with microbiome composition in both cohorts. Sex and pathological depth&#xa0;of invasion&#xa0;were associated with microbiome composition in the TCGA cohort.<br><br>CONCLUSION: The intratumoral gastric cancer microbiome appears to differ according to clinicopathological factors. Certain clinicopathological factors associated with favourable outcomes in gastric cancer were observed to be associated with greater microbial abundance and diversity. This highlights the need for further work to understand the underlying biological mechanisms behind the observed microbiome differences and their potential clinical and therapeutic impact.}, }
@article {pmid39961944, year = {2025}, author = {Andraskar, J and Khan, D and Yadav, S and Kapley, A}, title = {Metagenomic Analysis of Microbial Community Associated with Food Waste Composting.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {39961944}, issn = {1559-0291}, support = {DBT/JRF/BET-18/1/2018/AL/23//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, abstract = {Food waste is an increasing cause of concern in India. Its management through composting plays a vital role in managing the biodegradable fraction of municipal solid waste. However, the existing composting process has many challenges, such as the lack of optimum microenvironment and microbiome knowledge, which limits efficient outcomes. Therefore, the present study aims to bridge the gap by applying metagenomics to study microbial community dynamicity during different stages of composting. The bacterial community analysis showed that genus Marionobacter (9.4%) and Halomonas (7.4%) were prevalent during the mesophilic stage, whereas the Bacillus (12.2%) and Cellulomonas (0.1%) were prevalent during the thermophilic and maturation stage of composting. The functional profiling of metagenome indicated the abundance of genes involved in degradation of polymeric compounds such as carbohydrates, lipids, and proteins. The relative abundance of arginine and proline metabolisms increased during the thermophilic stage. Whereas the relative abundance of genes involved in fatty acid, tryptophan, galactose, and propanoate metabolisms declined. Similarly, the CAZyme tool predicted that the genes encoding for glycoside hydrolase (GH) families were higher during the mesophilic and thermophilic stages of composting. These enzymes play an important role in degradation of complex polysaccharides such as cellulose and hemicellulose. The data obtained from the present study could be utilized for the optimization and improving the composting process.}, }
@article {pmid39961936, year = {2025}, author = {Alqarni, SS and Khan, NU}, title = {Integrating alternative therapies in overcoming chemotherapy resistance in tumors.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {239}, pmid = {39961936}, issn = {1573-4978}, mesh = {Humans ; *Drug Resistance, Neoplasm/genetics ; *Neoplasms/drug therapy/therapy/genetics ; *Complementary Therapies/methods ; Tumor Microenvironment/drug effects ; Antineoplastic Agents/therapeutic use/pharmacology ; Immunotherapy/methods ; }, abstract = {Chemotherapy-resistant tumors present a significant challenge in oncology, often leading to treatment failures owing to mechanisms such as genetic mutations, drug efflux, altered metabolism, and adaptations within the tumor microenvironment. These factors limit the effectiveness of treatment and contribute to tumor resistance. This review highlights the role of alternative therapies aimed at overcoming resistance mechanisms. Several alternative strategies with high efficacy rate against tumor resistance are being explored, including targeted therapies (58-64%), immunotherapy (80%), hormone therapy (22-61%), and emerging approaches such as herbal therapies (90%), probiotics (34-90%), metabolic therapies (> 50%), epigenetic therapies (51-89%), microbiome-based therapies (50%), gene therapy (67-80%), photodynamic therapy/hypothermia (86-99%), and nanotechnology (50-67%). Integrating these alternative strategies with conventional treatments has the potent-al to augment the therapeutic efficacy and patient outcomes. Despite this progress, limitations in cancer therapeutics include the lack of predictive biomarkers, resistance mechanisms, and tumor heterogeneity, all of which contribute to treatment failure and relapse. To address these limitations, advancements in molecular diagnostics, as well as early detection through liquid biopsies, and the use of biomarkers to monitor resistance and guide treatment are crucial. Additionally, expanding clinical trials is essential to validate new therapies and improve patient outcomes.}, }
@article {pmid39961644, year = {2025}, author = {Huwart, SJP and Morales-Puerto, N and Everard, A}, title = {Gut microbiota-related neuroinflammation at the crossroad of food reward alterations: implications for eating disorders.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2024-333397}, pmid = {39961644}, issn = {1468-3288}, abstract = {The link between gut microbiome and eating behaviours, especially palatable food intake, is a growing focus of scientific investigation. The complex ecosystem of microorganisms in the gut influences host metabolism, immune function and neurobehavioural signalling. This review explores the role of neuroinflammation in dysregulations of food-induced reward signalling and the potential causal role of the gut microbiota on these proinflammatory processes. Particular attention is given to eating disorders (ED, specifically anorexia nervosa, binge eating disorder and bulimia nervosa) and potential links with the gut microbiota, food reward alterations and neuroinflammation. Finally, we propose gut microbiota modulation as a promising therapeutic strategy in food reward alterations and ED.}, }
@article {pmid39961523, year = {2025}, author = {Shanmugam, NRS and Yin, Y}, title = {CAZyme3D: a database of 3D structures for carbohydrate-active enzymes.}, journal = {Journal of molecular biology}, volume = {}, number = {}, pages = {169001}, doi = {10.1016/j.jmb.2025.169001}, pmid = {39961523}, issn = {1089-8638}, abstract = {CAZymes (Carbohydrate Active EnZymes) degrade, synthesize, and modify all complex carbohydrates on Earth. CAZymes are extremely important to research in human health, nutrition, gut microbiome, bioenergy, plant disease, and global carbon recycling. Current CAZyme annotation tools are all based on sequence similarity. A more powerful approach is to detect protein structural similarity between query proteins and known CAZymes indicative of distant homology. Here, we developed CAZyme3D (https://pro.unl.edu/CAZyme3D/) to fill the research gap that no dedicated 3D structure databases are currently available for CAZymes. CAZyme3D contains a total of 870,740 AlphaFold predicted 3D structures (named Whole dataset). A subset of CAZymes 3D structures from 188,574 nonredundant sequences (named ID50 dataset) were subject to structural similarity-based clustering analyses. Such clustering allowed us to organize all CAZyme structures using a hierarchical classification, which includes existing levels defined by the CAZy database (class, clan, family, subfamily) and newly defined levels (subclasses, structural cluster [SC] groups, and SCs). The inter-family structural clustering successfully grouped CAZy families and clans with the same structural folds in the same subclasses. The intra-family structural clustering classified structurally similar CAZymes into SCs, which were further classified into SC groups. SCs and SC groups differed from sequence similarity-based CAZy subfamilies. With CAZyme structures as the search database, we created job submission pages, where users can submit query protein sequences or PDB structures for a structural similarity search. CAZyme3D will be a useful new tool to assist the discovery of novel CAZymes by providing a comprehensive database of CAZyme 3D structures.}, }
@article {pmid39960648, year = {2025}, author = {Gui, S and Liu, Y and Pu, J and Wang, D and Zhong, X and Chen, W and Chen, X and Chen, Y and Chen, X and Tao, W and Xie, P}, title = {Systematical Comparison Reveals Distinct Brain Transcriptomic Characteristics in Depression Models Induced by Gut Microbiota Dysbiosis and Chronic Stress.}, journal = {Molecular neurobiology}, volume = {}, number = {}, pages = {}, pmid = {39960648}, issn = {1559-1182}, support = {2022MD723735//The China Postdoctoral Science Foundation/ ; CSTB2022NSCQ-BHX0011//The Chongqing Natural Science Foundation/ ; cstc2022ycjh-bgzxm0033//The Natural Science Foundation of Chongqing/ ; 82101596//The Natural Science Foundation Project of China/ ; 2021QNRC001//The Young Elite Scientists Sponsorship Program by CAST/ ; 2023CCXM003//The Joint project of Chongqing Municipal Science and Technology Bureau and Chongqing Health Commission/ ; }, abstract = {Major depressive disorder (MDD) is a devastating psychiatric illness with various etiologies. Both chronic stress and gut microbiome dysbiosis are implicated in the pathogenesis of MDD. However, limited research has been conducted to delineate the distinct effects of these two pathogenic factors on the brain transcriptome. We generated and compared transcriptomic features of the anterior cingulate cortex (ACC) from depressive-like mice induced by gut microbiome dysbiosis and canonical chronic stress paradigms, focusing on gene expression patterns and network characteristics. Data derived from MDD patients served as a reference standard to filter the molecular alterations associated with the disorder. Chronic stress induced a plethora of altered genes and biological functions associated with depression, prominently involving mitochondrial dysfunction. However, gut microbiota dysbiosis specifically regulated narrower range of genes and biological mechanisms, targeting aberrations in vesicular transport systems and perturbations of autophagy pathways. Network analysis revealed that hierarchical gene co-expression was specifically affected by gut microbiota dysbiosis rather than chronic stress. Further functional clustering analysis, along with the central distribution of inflammation-related differentially expressed genes, suggested an intricate interplay between disrupted autophagy processes, microglia-mediated inflammation, and synaptic dysfunctions in the network influenced by gut microbiota dysbiosis. Our findings reveal the distinctive transcriptomic alterations of brain shaped by gut microbiota and chronic stress in the development of MDD, contributing to a deeper understanding the heterogeneity of depression. Additionally, we provide a valuable data resource and bioinformatic analysis template for future studies.}, }
@article {pmid39963611, year = {2011}, author = {Yeoman, CJ and Chia, N and Yildirim, S and Miller, MEB and Kent, A and Stumpf, R and Leigh, SR and Nelson, KE and White, BA and Wilson, BA}, title = {Towards an Evolutionary Model of Animal-Associated Microbiomes.}, journal = {Entropy (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {570-594}, pmid = {39963611}, issn = {1099-4300}, abstract = {Second-generation sequencing technologies have granted us greater access to the diversity and genetics of microbial communities that naturally reside endo- and ecto-symbiotically with animal hosts. Substantial research has emerged describing the diversity and broader trends that exist within and between host species and their associated microbial ecosystems, yet the application of these data to our evolutionary understanding of microbiomes appears fragmented. For the most part biological perspectives are based on limited observations of oversimplified communities, while mathematical and/or computational modeling of these concepts often lack biological precedence. In recognition of this disconnect, both fields have attempted to incorporate ecological theories, although their applicability is currently a subject of debate because most ecological theories were developed based on observations of macro-organisms and their ecosystems. For the purposes of this review, we attempt to transcend the biological, ecological and computational realms, drawing on extensive literature, to forge a useful framework that can, at a minimum be built upon, but ideally will shape the hypotheses of each field as they move forward. In evaluating the top-down selection pressures that are exerted on a microbiome we find cause to warrant reconsideration of the much-maligned theory of multi-level selection and reason that complexity must be underscored by modularity.}, }
@article {pmid39960190, year = {2025}, author = {Gao, Y and Zhou, Y and Ji, X and Graham, AJ and Dundas, CM and Miniel Mahfoud, IE and Tibbett, BM and Tan, B and Partipilo, G and Dodabalapur, A and Rivnay, J and Keitz, BK}, title = {Translating Extracellular Electron Transfer Activities with Organic Electrochemical Transistors.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {215}, pages = {}, doi = {10.3791/67928}, pmid = {39960190}, issn = {1940-087X}, mesh = {*Shewanella/metabolism ; Electron Transport ; *Transistors, Electronic ; Polystyrenes/chemistry ; Geobacter/metabolism ; Electrochemical Techniques/methods/instrumentation ; Bridged Bicyclo Compounds, Heterocyclic/chemistry ; Thiophenes ; }, abstract = {Extracellular electron transfer (EET) is a process through which certain microorganisms can transfer electrons across their cell membranes to external electron acceptors, linking cellular metabolism to their environment. While Geobacter and Shewanella have been the primary models for EET research, emerging studies reveal that EET-active species are also associated with fermentation and the human gut microbiome. Leveraging the ability of EET to bridge biological and electronic systems, we present a protocol for using organic electrochemical transistors (OECTs) to translate microbial EET activity into easily detectable electrical signals. This system enables the use of cellular responses to external stimuli for biosensing and biocomputing applications. Specifically, we demonstrated the de-doping of the p-type poly(3,4-ethylenedioxythiophene): poly(styrenesulfonate) (PEDOT: PSS) channel in the OECT is driven by cellular EET from Shewanella oneidensis. By transcriptionally controlling EET flux by genetic circuits, we establish the biosensing capability of this hybrid OECT system to detect chemical stimuli, such as inducer molecules. Furthermore, we introduce plasmid-based Boolean logic gates within the cells, allowing them to process environmental signals and drive current changes in the OECTs, further demonstrating the biocomputing potential of these devices. This method provides a novel interface between biological systems and electronics, enabling future high-throughput screening, biosensing, and biocomputing applications.}, }
@article {pmid39960092, year = {2025}, author = {Narayanasamydamodaran, S and Kumar, N and Zuo, J}, title = {Profiling and metabolic analysis of microorganisms in bioretention cells vegetated with vetiver and cattail species treating nitrogen and phosphorous.}, journal = {International journal of phytoremediation}, volume = {}, number = {}, pages = {1-13}, doi = {10.1080/15226514.2025.2452942}, pmid = {39960092}, issn = {1549-7879}, abstract = {Bioretention cells (BRCs) are increasingly used to treat nutrients in stormwater runoff, with plants known to enhance nitrogen (TN) and phosphorus (TP) uptake. This study investigated the role of rhizosphere microbial communities in TN, TP, and COD removal across three BRCs: an unvegetated control (CP), one vegetated with vetiver (P1), and another with cattail (P2). Detailed microbiome profiling revealed key taxa across phylum, family, and genus levels contributing to nutrient cycling, with P2 showing the highest species richness and diversity based on OTU counts and diversity indices. Proteobacteria, Acidobacteria, and Verrucomicrobiota were the most prominent phyla, aligning with their known roles in nutrient uptake. Key functional taxa included denitrifiers (e.g., Ramlibacter, TRA3-20), Ammonia Oxidizing Bacteria (AOBs) (e.g., MND1, Ellin 6067), and Phosphate Accumulating Organisms (PAOs) (e.g., Comamonadaceae, Vicinamibacteria), supporting TN (>79%) and TP (>84%) removal rates. Distinct microbial compositions between vegetated BRCs confirmed the role of root exudates in microbial selection and enhanced nutrient removal. These findings emphasize the importance of plant-specific rhizosphere effects and microbial selection in optimizing BRC design for stormwater treatment applications.}, }
@article {pmid39959986, year = {2025}, author = {Ancira, J and Gabrilska, R and Tipton, C and Miller, C and Stickley, Z and Omeir, K and Wakeman, C and Little, T and Wolcott, J and Philips, CD}, title = {A structural equation model predicts chronic wound healing time using patient characteristics and wound microbiome composition.}, journal = {Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society}, volume = {33}, number = {1}, pages = {e70004}, doi = {10.1111/wrr.70004}, pmid = {39959986}, issn = {1524-475X}, support = {R15GM141973/NH/NIH HHS/United States ; }, mesh = {Humans ; *Wound Healing/physiology ; *Microbiota ; Male ; Female ; Chronic Disease ; Middle Aged ; Wounds and Injuries/microbiology ; Aged ; Time Factors ; Biofilms/growth &amp; development ; Adult ; }, abstract = {Wound aetiology, host characteristics and the wound microbiome contribute to chronic wound development. Yet, there is little accounting for the relative importance of these factors to predict wound healing. Here, a structural equation model was developed to provide such an explanatory and predictive framework. Chronic wounds from 565 patients treated at a clinic practicing biofilm-based wound care were included. Patient information included DNA sequencing-based wound microbiome clinical reports corresponding to the initial clinical visit. Wound microbiome data was integrated into the SEM as a latent variable using a pre-modelling parcel optimization routine presented herein for the first time (available as R library parcelR). A microbiome latent construct associated with improved healing was validated, and the final SEM included this latent construct plus three species associated with diminished healing (Anaerococcus vaginalis, Finegoldia magna and Pseudomonas aeruginosa), as well as smoking, wound volume, slough, exudate, edema, percent granulation and wound etiology. This model explained 46% of variations in healing time, with the microbiome contributing the largest proportion of variance explained. Model validity was confirmed with an independent cohort (n = 79) through which ~60% of the variation in healing time was predicted. This model can serve as a foundation for the development of a predictive tool that may have clinical utility.}, }
@article {pmid39959974, year = {2025}, author = {Orchanian, SB and Hsiao, EY}, title = {The microbiome as a modulator of neurological health across the maternal-offspring interface.}, journal = {The Journal of clinical investigation}, volume = {135}, number = {4}, pages = {}, doi = {10.1172/JCI184314}, pmid = {39959974}, issn = {1558-8238}, mesh = {Humans ; Female ; Animals ; *Gastrointestinal Microbiome ; Pregnancy ; Brain-Gut Axis/physiology ; Neurodevelopmental Disorders/microbiology ; Brain/microbiology ; }, abstract = {The maternal microbiome is emerging as an important factor that influences the neurological health of mothers and their children. Recent studies highlight how microbial communities in the maternal gut can shape early-life development in ways that inform long-term health trajectories. Research on the neurodevelopmental effects of maternal microbiomes is expanding our understanding of the microbiome-gut-brain axis to include signaling across the maternal-offspring unit during the perinatal period. In this Review, we synthesize existing literature on how the maternal microbiome modulates brain function and behavior in both mothers and their developing offspring. We present evidence from human and animal studies showing that the maternal microbiome interacts with environmental factors to impact risk for neurodevelopmental abnormalities. We further discuss molecular and cellular mechanisms that facilitate maternal-offspring crosstalk for neuromodulation. Finally, we consider how advancing understanding of these complex interactions could lead to microbiome-based interventions for promoting maternal and offspring health.}, }
@article {pmid39959969, year = {2025}, author = {Kim, YJ and Bunyavanich, S}, title = {Microbial influencers: the airway microbiome's role in asthma.}, journal = {The Journal of clinical investigation}, volume = {135}, number = {4}, pages = {}, doi = {10.1172/JCI184316}, pmid = {39959969}, issn = {1558-8238}, mesh = {*Asthma/microbiology/immunology ; Humans ; *Microbiota/immunology ; Animals ; Respiratory System/microbiology/immunology ; }, abstract = {Asthma is a common chronic respiratory disease affecting people of all ages globally. The airway hosts diverse microbial communities increasingly recognized as influential in the development and disease course of asthma. Here, we review recent findings on the airway microbiome in asthma. As relationships between the airway microbiome and respiratory health take root early in life, we first provide an overview of the early-life airway microbiome and asthma development, where multiple cohort studies have identified bacterial genera in the infant airway associated with risk of future wheeze and asthma. We then address current understandings of interactions between environmental factors, the airway microbiome, and asthma, including the effects of rural/urban environments, pet ownership, smoking, viral illness, and antibiotics. Next, we delve into what has been observed about the airway microbiome and asthma phenotypes and endotypes, as airway microbiota have been associated with asthma control, severity, obesity-related asthma, and treatment effects as well as with type 2 high, type 2 low, and more newly described multi-omic asthma endotypes. We then discuss emerging approaches to shape the microbiome for asthma therapy and conclude the Review with perspectives on future research directions.}, }
@article {pmid39959949, year = {2025}, author = {Tessier, MEM and Shneider, BL and Petrosino, JF and Preidis, GA}, title = {Bile acid and microbiome interactions in the developing child.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1002/jpn3.70014}, pmid = {39959949}, issn = {1536-4801}, support = {5K23DK119567//NIH NIDDK/ ; }, abstract = {Interactions between the gut microbiome and bile acids are complex and are linked to outcomes in pediatric liver disease by mechanisms that are incompletely understood. In adults, primary bile acids are synthesized in the liver and secreted into the intestine, where complex communities of gut microbes deconjugate, oxidize, epimerize, and 7α-dehydroxylate bile acids into a diverse array of unconjugated, secondary, allo-, iso-, and oxo-bile acids. In contrast, the infant gut microbiota contains a simple, Bifidobacterium-dominant community that transitions to a more diverse, adult-like community as additional microbes colonize the gut. This microbial succession gradually confers deconjugation, oxidation, epimerization, and 7α-dehydroxylation activities that mature the bile acid pool from a profile dominated by primary bile acids early in life to a more diverse, adult-like bile acid profile in later childhood. Altered bile acid profiles in pediatric cholestatic disorders have the potential to change the developmental trajectory of the microbiome. Conversely, alterations in the gut microbiome may re-shape the bile acid pool and hepatic bile acid metabolism. Understanding the mechanisms underlying these interactions will increase our understanding of liver pathophysiology and will motivate new therapeutic strategies for pediatric hepatic disorders. This review aims to highlight differences between the pediatric and adult intestinal microbiome and bile acid pool, and to discuss interactions between gut microbes and bile acids that are critical in early life and that may impact outcomes in infants and children with cholestatic liver disease, including biliary atresia.}, }
@article {pmid39959709, year = {2025}, author = {Hadimani, A and Raman, T and Esack, E and Loganathan, M and Jaganathan, D and Kantharaju, V and Selvarajan, R}, title = {Deciphering the microbiome dynamics in an effective banana Fusarium wilt biocontrol interaction system.}, journal = {3 Biotech}, volume = {15}, number = {3}, pages = {59}, pmid = {39959709}, issn = {2190-572X}, abstract = {UNLABELLED: This study explored the effects of bacterial and fungal biocontrol agents (consortia) on the microbiome of Fusarium wilt (Foc TR4)-infected Cavandish banana soils in terms of alteration of prevalence and abundance. The results showed a significant shift in microbial diversity, dominance, abundance, evenness, richness and composition core and indicator microbiome in response to soil applied consortia and untreated controls. A total of 2857 bacterial OTUs from 331 families across 40 phyla dominated with Bacillaceae (40.2%), Acidobacteriaceae (14.2%), Haloarculaceae (12.6%), and Paenibacillaceae (9.4%). There were 4,868 fungal OTUs from 520 families across 18 phyla dominant with Mortierellaceae (20.9%), Cortinariaceae (7.6%), Aspergillaceae (6.2%), Pandeidae (5.6%), and Pyronemataceae (5.0%). Alpha diversity analysis indicated that bacterial diversity varied across treatments where T2 has the highest OTUs, while fungal diversity remained relatively stable across the treatments. Beta diversity and PCoA analysis revealed the differences in community compositions across treatments in both bacterial and fungal microbiome. Bacterial communities in T3 and T5 were highly similar, whereas T4 had a notable difference in fungal communities. This study identified a total of 192 bacterial core OTUs dominated with Firmicutes, Proteobacteria, and Acidobacteriia. In the case of fungi, 59 core OTUs from Ascomycota, Basidiomycota, and Mucoromycota are the most abundant ones within the treatments. Venn diagram revealed unique, common and shared OTUs suggesting antagonistic interactions of the soil applied consortia. DESeq2 analysis revealed a significant shift of core microbiome, where positive fold changes in Betaproteobacteria for bacterial, and Fusarium sp. for fungi were noticeable. Heatmap analysis revealed the treatment-dependent differences in community composition where T2 has higher bacterial abundance and T4 has higher fungal abundance suggesting that the biocontrol treatments affect the soil microbiome differently depending on the combinations and the origins of the consortia. The indicator species analysis identified 37 bacterial and 34 fungal OTUs that were specific and indicative of particular treatments that suggest microbial consortia might be selectively enhancing the growth of functionally beneficial microbial populations of the soil that promote soil health and disease suppressiveness. This study recommends that the use of biocontrol agents in the form of consortia would not only expand the diversity of the soil microbiome but also improve the effectiveness and the sustainability of Fusarium wilt management.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04223-7.}, }
@article {pmid39959658, year = {2024}, author = {Nilsson, A and D'Alvise, P and Milbrath, MO and Forsgren, E}, title = {Lactic acid bacteria in Swedish honey bees during outbreaks of American foulbrood.}, journal = {Ecology and evolution}, volume = {14}, number = {2}, pages = {e10964}, pmid = {39959658}, issn = {2045-7758}, abstract = {The honey bee microbiota is involved in several important functions, and alterations in the composition could have a severe effect on honey bee health. Among the bacteria identified in the honey bee microbiome are a group of non-pathogenic honey bee-specific lactic acid bacteria (hbs-LAB) that have been shown to inhibit the growth of bacterial pathogens such as Paenibacillus larvae, the causative agent of American foulbrood (AFB). While P. larvae only causes disease in larvae and not in adult honey bees, there are reports of the pathogen causing changes in the microbiota composition of the adults. The aim of this study was to investigate how AFB in the colony affect the hbs-LAB composition in adult honey bees. Adult bees were collected from colonies with and without AFB during three outbreaks of AFB in Sweden. The hbs-LAB was analyzed using qPCR to detect and quantify the number of ten hbs-LAB (five Lactobacilli, two Apilactobacilli, one Bombilactobacilli, and two Bifidobacterium). The hbs-LAB composition was compared between AFB outbreaks and depending on the AFB status of the honeybee colony at the time of sampling. The data analyses revealed differences in the abundance of individual hbs-LAB between outbreaks and an overall difference in bacterial community composition depending on AFB status. Also, a higher hbs-LAB diversity was observed in samples that were P. larvae culture positive.}, }
@article {pmid39959619, year = {2025}, author = {Hao, J and Xu, H and Chang, B and Ren, J and Wang, H and Ji, L}, title = {Acupuncture mediates the "gut-testis axis" to improve asthenozoospermia.}, journal = {Frontiers in endocrinology}, volume = {16}, number = {}, pages = {1514010}, pmid = {39959619}, issn = {1664-2392}, mesh = {Male ; Animals ; *Asthenozoospermia/therapy/metabolism ; Mice ; *Testis/metabolism ; *Acupuncture Therapy ; *Sperm Motility ; Gastrointestinal Microbiome/physiology ; Spermatozoa/metabolism ; Disease Models, Animal ; Blood-Testis Barrier/metabolism ; }, abstract = {BACKGROUND: Asthenozoospermia is a common cause of male infertility. Studies have shown that sperm quality and motility are affected by the gut-testis axis that can regulate testicular metabolism and function through the gut microbiota and its metabolites. Acupuncture is an important modality of complementary and alternative medicine. It can improve sperm motility, but it remains unclear whether acupuncture can enhance sperm vitality by influencing the gut-testis axis.<br><br>METHODS: In this study, sperm quality, testicular pathology, and serum hormone levels were assessed using a cyclophosphamide-induced mouse model. Real-time PCR, a western blot analysis, and immunofluorescence techniques were used to assess the effects of acupuncture on the gut barrier and blood-testis barrier functions. In addition, gut microbiome and metabolomics were used to study the impact of acupuncture on the gut microbiota structure, serum, and testicular metabolites in asthenozoospermic mice. Further validation was obtained by performing a fecal microbiota transplantation (FMT).<br><br>RESULTS: Acupuncture improved the sperm quality; ameliorated testicular pathology; increased serum testosterone (T), follicle-stimulating hormone (FSH), and luteinizing hormone (LH) levels; and repaired gut and blood-testis barrier damage in asthenozoospermic mice. The abundances of Bacteroidota, Firmicutes, Faecalibaculum, and Dubosiella were associated with sperm motility, as shown by a gut microbiome analysis. Serum metabolomics revealed that differentially expressed metabolites (DEMs), such as cytosine and N-oleyl-leucine, were closely related to sperm motility. Testicular metabolomics analysis revealed DEMs, such as 5-fluorouridine and 1-acetylimidazole, were also associated with sperm motility. Furthermore, reproductive function improvements in asthenozoospermic mice through acupuncture were achieved via an FMT.<br><br>CONCLUSION: Acupuncture may alleviate asthenozoospermia symptoms by modulating the gut-testis axis and repairing the gut-testis barrier.}, }
@article {pmid39959235, year = {2025}, author = {Ceccato, HD and Silva, TAOE and Genaro, LM and Silva, JF and de Souza, WM and Oliveira, PSP and de Azevedo, AT and Ayrizono, MLS and Leal, RF}, title = {Artificial intelligence use for precision medicine in inflammatory bowel disease: a systematic review.}, journal = {American journal of translational research}, volume = {17}, number = {1}, pages = {28-46}, pmid = {39959235}, issn = {1943-8141}, abstract = {INTRODUCTION: Inflammatory Bowel Disease (IBD), encompassing Crohn's disease and ulcerative colitis, presents significant clinical challenges due to its heterogeneous nature and complex etiology. Recent advancements in biomedical research have enhanced our understanding of IBD's genetic, microbial, and biochemical aspects. However, persistent issues in clinical management, including treatment non-response, surgical interventions, and diagnostic uncertainties, underscore the need for more targeted approaches. This review examines the convergence of artificial intelligence (AI) and precision medicine (PM) in IBD management. By leveraging AI's capacity to analyze complex, multi-dimensional datasets, this emerging field offers promising applications in improving diagnostic accuracy, predicting treatment responses, and forecasting disease progression, potentially transforming IBD patient care.<br><br>METHOD: The systematic review (SR) was conducted by searching the following databases: PubMed, PubMed PMC, BVS, Scopus, Web of Science, Embase, Cochrane, and ProQuest up to February 2024. Studies that employed AI in IBD applied to precision medicine were included.<br><br>RESULTS: 139 studies on applying AI in precision medicine for IBD were identified. Most studies (>70%) were published after 2020, indicating a recent surge in interest. The AI applications primarily focused on diagnosis, treatment response prediction, and prognosis. Machine learning algorithms were predominantly used, particularly random forest, logistic regression, and support vector machines. Omics data were frequently employed as predictors, especially transcriptomics and microbiome analyses. Studies demonstrated good predictive performance across all three areas, with median AUC values ranging from 0.85 to 0.90.<br><br>CONCLUSION: AI applications in IBD show promising potential to enhance clinical practice, particularly in disease prognosis and predicting treatment response. However, clinical implementation requires further validation through prospective studies. Future research should focus on standardizing protocols, defining clinically significant outcomes, and evaluating the efficacy of these tools.}, }
@article {pmid39958933, year = {2025}, author = {Kuźmycz, O and Kowalczyk, A and Bolanowska, A and Drozdzowska, A and Lach, J and Wierzbińska, W and Kluz, T and Stączek, P}, title = {A comprehensive analysis of the uterine microbiome in endometrial cancer patients - identification of Anaerococcus as a potential biomarker and carcinogenic cofactor.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1511625}, pmid = {39958933}, issn = {2235-2988}, mesh = {Humans ; Female ; *Endometrial Neoplasms/microbiology/genetics ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Uterus/microbiology ; Middle Aged ; Phylogeny ; Biomarkers ; Adult ; Aged ; Reactive Oxygen Species/metabolism ; Carcinogenesis ; Fibroblasts/microbiology ; Biomarkers, Tumor/genetics ; Computational Biology/methods ; Oxidative Stress ; }, abstract = {INTRODUCTION: Endometrial cancer (EC) is a significant gynecological malignancy with increasing incidence worldwide. Emerging evidence highlights the role of the uterine microbiome in the pathogenesis of EC. This study aims to characterize the uterine microbiome in EC patients and identify potential microbial biomarkers, with a focus on Anaerococcus as a differentiating taxon.<br><br>METHODS: The endocervical canal swabs from patients with EC (n=16) and non-cancerous patients (EM, n=13) were collected. The V3-V4 region of the 16S rRNA gene was sequenced using the Illumina platform. Bioinformatic analyses were performed with QIIME2, and statistical comparisons were conducted to assess differences in microbial composition and diversity. In vitro experiments were conducted to assess the functional impact of Anaerococcus on human uterine fibroblasts, including its ability to adhere to the human cells and induce oxidative stress.<br><br>RESULTS: The &#x3b1;-diversity metrics, including Shannon entropy and observed amplicon sequence variants (ASVs), revealed significantly higher microbial diversity in EC samples compared to EM. Anaerococcus was identified as a key taxon differentiating EC from EM groups, showing a higher relative abundance in EC samples. Functional predictions and in vitro assays indicated that Anaerococcus may contribute to carcinogenesis by inducing reactive oxygen species (ROS) production, and has the high ability to adhere to the human endometrial fibroblasts.<br><br>DISCUSSION: The study provides evidence of distinct microbial signatures in EC, with Anaerococcus emerging as a potential biomarker. The in vitro findings suggest its role in endometrial carcinogenesis, underscoring its potential as a target for future diagnostic and therapeutic applications.}, }
@article {pmid39958539, year = {2025}, author = {Qiao, C and Zhang, HX and Tian, XT and Zhang, YJ and Li, DH}, title = {Harnessing multi-omics approaches to elucidate the role of Chinese herbal compounds in chemotherapy-induced gastrointestinal damage.}, journal = {World journal of gastrointestinal oncology}, volume = {17}, number = {2}, pages = {101500}, pmid = {39958539}, issn = {1948-5204}, abstract = {In this editorial, we discuss the findings reported by Wang et al in the latest issue of the World Journal of Gastrointestinal Oncology. Various research methodologies, including microbiome analysis, assert that the Tzu-Chi Cancer-Antagonizing and Life-Protecting II Decoction of Chinese herbal compounds mitigates inflammatory responses by inhibiting the NF-κB signaling pathway. This action helps maintain the dynamic equilibrium of the intestinal microecology and lessens chemotherapy-induced gastrointestinal damage. The efficacy of these compounds is intimately linked to the composition of intestinal microbes. These compounds regulate intestinal microecology by virtue of their specific compatibility and effectiveness, thereby enhancing the overall therapeutic outcomes of cancer chemotherapy. Nonetheless, the exact mechanisms underlying these effects warrant further investigation. Multi-omics technologies offer a systematic approach to elucidate the mechanisms and effectiveness of Chinese herbal compounds in vivo. This manuscript reviews the application of multi-omics technologies to Chinese herbal compounds and explores their potential role in modulating the gastrointestinal microenvironment following cancer chemotherapy, thus providing a theoretical foundation for their continued use in adjunct cancer treatment.}, }
@article {pmid39958467, year = {2025}, author = {Sachse, M and Stellos, K}, title = {Synbiotics and Gut-Heart Axis in Cardiometabolic Disease.}, journal = {JACC. Basic to translational science}, volume = {10}, number = {1}, pages = {16-19}, pmid = {39958467}, issn = {2452-302X}, }
@article {pmid39957996, year = {2025}, author = {Giakomidi, D and Ishola, A and Nus, M}, title = {Targeting gut microbiota to regulate the adaptive immune response in atherosclerosis.}, journal = {Frontiers in cardiovascular medicine}, volume = {12}, number = {}, pages = {1502124}, pmid = {39957996}, issn = {2297-055X}, abstract = {Atherosclerosis, the leading cause of death worldwide, is a chronic inflammatory disease leading to the accumulation of lipid-rich plaques in the intima of large and medium-sized arteries. Accumulating evidence indicates the important regulatory role of the adaptive immune system in atherosclerosis during all stages of the disease. The gut microbiome has also become a key regulator of atherosclerosis and immunomodulation. Whilst existing research extensively explores the impact of the microbiome on the innate immune system, only a handful of studies have explored the regulatory capacity of the microbiome on the adaptive immune system to modulate atherogenesis. Building on these concepts and the pitfalls on the gut microbiota and adaptive immune response interaction, this review explores potential strategies to therapeutically target the microbiome, including the use of prebiotics and vaccinations, which could influence the adaptive immune response and consequently plaque composition and development.}, }
@article {pmid39957783, year = {2024}, author = {Chattaraj, S and Mitra, D and Chattaraj, M and Ganguly, A and Thatoi, H and Mohapatra, PKD}, title = {Brewers' spent grain as fish feed ingredient: Evaluation of bio-safety and analysis of its impact on gut bacteria of Cirrhinus reba by 16S Metagenomic sequencing.}, journal = {Current research in microbial sciences}, volume = {7}, number = {}, pages = {100286}, pmid = {39957783}, issn = {2666-5174}, abstract = {A comprehensive eight week feeding trial was conducted to investigate the potential of brewers' spent grain (BSG) as a sustainable fish feed ingredient. The study assessed both the biosafety of BSG and its impact on the gut microbiome of Cirrhinus reba, utilizing advanced 16S metagenomic sequencing techniques to analyze the composition and diversity of gut bacteria. A total of 90 healthy C. reba juveniles (average weight: 12 ± 1 g) were divided into two dietary groups [for control (C), for BSG meal (tB)] in triplicates. Feed prepared with conventional ingredients was used to feed the control group (C). The group tB was fed with BSG meal. After the feeding trial, the fish in tB group showed significantly higher (p < 0.05) growth parameters as compared to the control group. The results of bio-safety assessment indicated the absence of any pathological symptoms in the BSG meal fed carps. The fish in tB group didn't show any histopathological abnormality. Fish fed the Brewers' Spent Grain exhibited significantly elevated serum biochemical parameters, including alanine transaminase (ALT) and aspartate transaminase (AST), compared to the control group (p < 0.05). 16S Metagenomic sequencing of the fish gut microbiota provides insights into how BSG inclusion affects microbial diversity and composition within the digestive tract of C. reba. The analysis revealed the existence of 240 and 250 diverse bacterial genera in the gastrointestinal tract (GIT) of C. reba in dietary groups C and tB respectively. Importantly, the study found the gut of fish in tB group to be dominated by different beneficial genus including Bacillus, Lactobacillus, Bifidobacterium, Paenibacillus, and Lysinibacillus. Feeding C. reba with BSG meal significantly increased the alpha diversity of the gastrointestinal microbiota, as evidenced by elevated Chao 1 estimator and Shannon index values compared to the control diet (p < 0.05). This study provides comprehensive evidence for the bio-safety of BSG as a sustainable feed ingredient in aquaculture, demonstrating its potential to support healthy fish growth and development. Moreover, the prebiotic potential of BSG in fish has also been highlighted.}, }
@article {pmid39957183, year = {2025}, author = {Weiskirchen, S and Weiskirchen, R}, title = {Unraveling the future: hot topics shaping molecular diagnostics Today.}, journal = {Expert review of molecular diagnostics}, volume = {}, number = {}, pages = {}, doi = {10.1080/14737159.2025.2467969}, pmid = {39957183}, issn = {1744-8352}, abstract = {INTRODUCTION: This special report highlights the transformative potential of advanced diagnostic technologies in modern healthcare, emphasizing their role in enhancing disease detection, treatment personalization, and patient outcomes.<br><br>AREAS COVERED: Innovations such as Next-Generation Sequencing (NGS), liquid biopsy, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) -based diagnostics, Point-of-Care (PoC) testing, microbiome analysis, and Artificial Intelligence are reshaping the diagnostic landscape. These methods facilitate early identification of diseases, enable tailored therapies based on individual genetic profiles, and provide noninvasive monitoring options. Furthermore, telemedicine enhances access to care while reducing costs associated with traditional healthcare delivery. Despite these advancements, challenges remain regarding regulatory compliance, data privacy concerns, and disparities in access to diagnostic services. The report underscores the need for ongoing collaboration among stakeholders to address these limitations effectively.<br><br>EXPERT OPINION: By prioritizing equitable access and continuously evaluating emerging technologies' impact on patient safety and health outcomes, the healthcare system can harness the full potential of modern diagnostics to improve global health.}, }
@article {pmid39957167, year = {2025}, author = {Jiaman, WU and Yan, N and Liya, T and Fei, MA and Yanting, L and Yuanyuan, Z}, title = {Difference of the gut microbiota of premature ovarian insufficiency in two traditional Chinese syndromes.}, journal = {Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan}, volume = {45}, number = {1}, pages = {132-139}, doi = {10.19852/j.cnki.jtcm.2025.01.012}, pmid = {39957167}, issn = {2589-451X}, support = {SZZYSM202311010//Sanming Project of Medicine in Shenzhen: the First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, Luo Songping National Famous Chinese Medicine Practitioner Female Reproductive Disorders Prevention and Treatment Team/ ; 20181229//Guangdong Provincial Administration of Traditional Chinese Medicine: Investigation of the Mechanism of Regulating Ren-Tong-Du Acupuncture on Ovarian Granulosa Cells in Polycystic Ovary Syndrome based on Activin A /Smads Signalling Pathway/ ; 20201294//Guangdong Provincial Administration of Traditional Chinese Medicine: Evaluation of the Efficacy of Menstrual Regulation and Pregnancy Promotion by Acupuncture in the Treatment of Premature Ovarian Insufficiency/ ; JCYJ20210324130001004//Shenzhen Science and Innovation Commission: Investigating the Mechanism of Action of Acupuncture in Regulating the Gut Microbiome to Inhibit Apoptosis of Ovarian Granulosa Cells in Premature Ovarian Insufficiency Mice based on the Rictor/Torepamycin Target Protein C2 Pathway/ ; }, mesh = {Humans ; Female ; *Primary Ovarian Insufficiency/microbiology/blood/genetics ; *Gastrointestinal Microbiome ; Adult ; Young Adult ; Retrospective Studies ; *Bacteria/classification/isolation &amp; purification/genetics ; Medicine, Chinese Traditional ; Anti-Mullerian Hormone/blood ; Estradiol/blood ; RNA, Ribosomal, 16S/genetics ; }, abstract = {PURPOSE: To investigate the differences in gut microbial characteristics between two traditional Chinese syndromes of premature ovarian insufficiency (POI).<br><br>METHODS: Forty women with POI were recruited from the Department of Traditional Chinese Medicine at Shenzhen Maternity and Child Healthcare Hospital between June and December 2020. Women with POI were divided into the kidney deficiency and blood stasis syndrome (SDBS) and Qi and blood deficiency syndrome (QBDS) groups. Gut microbial community profiles were analyzed by 16S rRNA gene sequencing using an Illumina MiSeq system. A retrospective study comparing hormone levels and gut microbiota information was performed between the SDBS and QBDS groups.<br><br>RESULTS: Compared with the QBDS group, the serum levels of estradiol (E2) and anti-M&#xfc;llerian hormone (AMH) were significantly decreased in the SDBS group. The quantities of Adlercreutzia, Eggerthella, Klebsiella, and Paraprevotella significantly increased in the SDBS group, whereas Lactobacillus decreased significantly. Moreover, alterations in the microbiome in the SDBS and QBDS groups were closely related to the levels of E2 and AMH. The area under the receiver operating characteristic curve for the classification of the two syndromes by the gut microbiome was 0.71.<br><br>CONCLUSIONS: There were significant differences in the dominant microbiota between the SDBS and QBDS groups, and the change in Proteobacteria in the QBDS group was more significant. The characteristics of gut microbiota help us differentiate between the SDBS and QBDS groups, which may provide a basis for the objectification of TCM syndrome types.}, }
@article {pmid39956914, year = {2025}, author = {Octaricha, T and Ilmiawati, C and Kasuma, N}, title = {Salivary microbiome profile shifts after scaling in stunted children.}, journal = {BMC research notes}, volume = {18}, number = {1}, pages = {69}, doi = {10.1186/s13104-025-07147-w}, pmid = {39956914}, issn = {1756-0500}, support = {No. 314/UN16.19/PT.01.03/PTM/2024//Skim Penelitian Tesis Magister (PTM) Batch I Universitas Andalas/ ; No. 314/UN16.19/PT.01.03/PTM/2024//Skim Penelitian Tesis Magister (PTM) Batch I Universitas Andalas/ ; No. 314/UN16.19/PT.01.03/PTM/2024//Skim Penelitian Tesis Magister (PTM) Batch I Universitas Andalas/ ; }, mesh = {Humans ; *Saliva/microbiology ; Child ; *Microbiota ; Male ; Female ; *Growth Disorders/microbiology ; Dental Scaling/methods ; Periodontal Index ; }, abstract = {OBJECTIVE: Stunting is a condition of impaired growth in children resulting from chronic malnutrition, characterized by shorter stature compared to peers of the same age. This condition leads to salivary gland dysfunction, which triggers oral dysbiosis and increases the risk of periodontal disease in children. Scaling and root planing (SRP) is the gold standard treatment for periodontal disease, aimed at reducing pathogenic bacterial populations. This study aimed to evaluate the effect of SRP treatment on the oral microbiome profile in the saliva of stunted children. A pre- and post-test study design was employed, involving 10 elementary school children divided into two groups: normal children and stunted children. Each participant underwent scaling, with saliva samples collected before and after the procedure. The oral microbiome profile was analyzed using next-generation sequencing, generating taxonomic data at the phylum, genus, and species level.<br><br>RESULT: Statistical analysis revealed significant changes in the gingival index, a clinical parameter, in the normal group but not in the stunted group. Scaling resulted in shifts in the microbiome profile in both groups, with the dominant phyla identified as Proteobacteria, Bacteroidota, and Firmicutes. Scaling procedure alters the oral microbiome profile in stunted children without affecting the clinical parameter.}, }
@article {pmid39956522, year = {2025}, author = {Altamira-Algarra, B and Garcia, J and Gonzalez-Flo, E}, title = {Cyanobacteria microbiomes for bioplastic production: Critical review of key factors and challenges in scaling from laboratory to industry set-ups.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132231}, doi = {10.1016/j.biortech.2025.132231}, pmid = {39956522}, issn = {1873-2976}, abstract = {Cyanobacteria are photoautotrophic microorganisms capable of accumulating polyhydroxybutyrate (PHB). A novel approach for PHB production involves the exploration of cyanobacterial microbiomes, potentially reducing costs through non-sterile cultivation with non-pure substrates. Although still in its early stages, this approach shows promise for high yields and sustained synthesis. However, managing microbiome population dynamics in non-sterile environments requires effective monitoring and control. This review covers PHB production by cyanobacteria microbiomes, from sample procurement to laboratory-scale production. It highlights recent insights into optimizing cultivation parameters for enhanced biopolymer yield. Strategies to overcome challenges in PHB production are evaluated, emphasizing integrated molecular biology techniques with quantitative and qualitative PHB analysis. Finally, key challenges in scaling up production to industrial-scale scenarios are discussed, along with potential solutions to support the development of sustainable industrial processes. Cyanobacteria microbiomes show promise PHB production but challenges like managing non-sterile conditions and scaling up require optimized strategies and integrated approaches.}, }
@article {pmid39956519, year = {2025}, author = {Bae, I and Rhee, C and Shin, J and Cho, K and Triolo, JM and Shin, SG}, title = {Insights into high ammonia-resistant syntrophic microbiomes and metabolic pathways during continuous anaerobic digestion of cow manure.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {132235}, doi = {10.1016/j.biortech.2025.132235}, pmid = {39956519}, issn = {1873-2976}, abstract = {Understanding microbial responses to ammonia is critical for defining thresholds and ensuring stable operation of anaerobic digestion (AD); however, an understanding of the microbiome's resistance mechanisms to high-total-ammonia-nitrogen (TAN) conditions remains limited. This study determined a TAN threshold of 7 g/L for continuous cow manure AD with increasing TAN levels. TAN was identified as the most critical factor influencing the AD performance, with CH4 production decreasing by > 50 % beyond this level. Additionally, a highly TAN-resistant syntrophic microbiome was identified through network analysis, highlighting key bacteria, Thauera phenolivorans and Fermentimons spp., alongside hydrogenotrophic methanogens. Interestingly, shifts were observed within the hydrogenotrophic methanogen community, transitioning from Methanoculleus bourgensis to Methanoculleus chikugoensis, Methanocorpusculum spp. and Methanobacterium spp. under high-TAN conditions. Significant metabolic pathways specific to high-TAN environments were identified, providing insights into their roles in sustained operation of AD. These findings highlight the performance limitations and functional redundancy under high-TAN conditions.}, }
@article {pmid39956340, year = {2025}, author = {Sharma, M and Pudlo, N and Järvå, MA and Kaur, A and John, A and Burchill, L and Lingford, JP and Epa, R and Abayakoon, P and Scott, NE and Turkenburg, JP and Davies, GJ and Martens, EC and Goddard-Borger, ED and Williams, SJ}, title = {Sulfoglycolysis sustains Eubacterium rectale in low-fiber diets.}, journal = {The Journal of biological chemistry}, volume = {}, number = {}, pages = {108320}, doi = {10.1016/j.jbc.2025.108320}, pmid = {39956340}, issn = {1083-351X}, abstract = {The production of short-chain fatty acids (SCFAs) by Firmicutes (Bacillota) within the human gastrointestinal tract is recognized as critical for gut health and the progression of a range of disease states. Firmicutes are the most diverse phylum of human gut bacteria and are highly studied, and are often specialized to degrade just a few polysaccharide substrates. Members of the Firmicutes include key bacteria that produce butyrate, an SCFA that is generally not produced by members of the other major phyla. Recently, it was shown that Eubacterium rectale, a widespread member of the Firmicutes belonging to the Clostridiales cluster XIVa, can grow on the unusual but ubiquitous plant-derived sugar SQ using a sulfoglycolytic sulfofructose transaldolase pathway. Here, we show that in addition to SQ, E. rectale can also grow on the SQ glycoside sulfoquinovosyl glycerol (SQGro). The 3D structure of the E. rectale sulfoquinovosidase (SftG) shares strong structural conservation with other carbohydrate active enzyme family GH31 SQases. Using sequence-similarity networks, we provide new biological context to a conserved domain of unknown function protein SftX belonging to DUF4867, which is conserved in the sulfoglycolytic sulfofructose transaldolase pathway, and determine its 3D structure. Finally, with the aid of a synthetic mini-human microbiome reconstituted in germ-free mice, we show that an SQ dietary supplement can rescue E. rectale from population crashes that occur upon switching from a high-fiber to a low-fiber, high-fat diet. This suggests that SQ or SQGro has potential as a prebiotic for promoting the maintenance of this important butyrate-producing bacterium within the colonic microbiota.}, }
@article {pmid39956335, year = {2025}, author = {Abreu, MT and Devkota, S and Issokson, K}, title = {A Mediterranean diet for Crohn's disease: Embracing colorful diversity to improve the microbiome.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2025.02.003}, pmid = {39956335}, issn = {1528-0012}, }
@article {pmid39956331, year = {2025}, author = {Yang, D and Sun, X and Wang, H and Wistuba, II and Wang, H and Maitra, A and Chen, Y}, title = {TREM2 depletion in pancreatic cancer elicits pathogenic inflammation and accelerates tumor progression via enriching IL-1β[+] macrophages.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2025.01.244}, pmid = {39956331}, issn = {1528-0012}, abstract = {BACKGROUND &amp; AIMS: Pancreatic ductal adenocarcinoma (PDAC) has a complex tumor microenvironment enriched with tumor-associated macrophages. Triggering receptor expressed on myeloid cells 2 (TREM2) is highly expressed by a subset of macrophages in PDAC. However, the functional role of TREM2 in PDAC progression remains elusive.<br><br>METHODS: We generated a novel transgenic mouse model (KPPC;Trem2[-/-]) that enables the genetic depletion of TREM2 in the context of spontaneous PDAC development. Single-cell RNA-sequencing analysis was utilized to identify changes in the tumor immune microenvironment upon TREM2 depletion. We evaluated the impacts of TREM2 depletion on the tumor immune microenvironment to elucidate the functions of TREM2 in macrophages and PDAC development.<br><br>RESULTS: Unexpectedly, genetic depletion of TREM2 significantly accelerated spontaneous PDAC progression and shortened the survival of KPPC;Trem2[-/-] mice. Single-cell analysis revealed that TREM2 depletion enhanced pro-inflammatory macrophages and exacerbated pathogenic inflammation in PDAC. Specifically, TREM2 functions as a key braking mechanism for the NLRP3/NF-&#x3ba;B/IL-1&#x3b2; inflammasome pathway, opposing to microbial lipopolysaccharide (LPS) as the key activator of this pathway. TREM2 deficiency orchestrated with microbial LPS to trigger IL-1&#x3b2; upregulation and pathogenic inflammation, thereby fueling PDAC development. Notably, IL-1&#x3b2; inhibition or microbiome ablation not only reversed the accelerated PDAC progression caused by TREM2 depletion, but also further inhibited PDAC progression in the TREM2-depleted context.<br><br>CONCLUSIONS: TREM2 depletion accelerates tumor progression by enhancing pro-inflammatory macrophages and IL-1&#x3b2;-mediated pathogenic inflammation in PDAC. The accelerated tumor progression by TREM2 depletion can be reversed by blocking IL-1&#x3b2;-associated pathogenic inflammation.}, }
@article {pmid39956285, year = {2025}, author = {Talwar, S and Harker, JA and Openshaw, PJM and Thwaites, RS}, title = {Autoimmunity in Long-COVID.}, journal = {The Journal of allergy and clinical immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jaci.2025.02.005}, pmid = {39956285}, issn = {1097-6825}, abstract = {Long-COVID (also termed Post-Acute Sequelae of SARS-CoV-2 or PASC) affects up to 10% of people recovering from SARS-CoV-2 infection. Diagnosis is hampered by diffuse symptomatology, lack of biomarkers, an incomplete understanding of pathogenesis, and the lack of validated treatments. In terms of pathogenesis, hypothesised causes include viral persistence, the legacy of endotheliitis and thrombosis, low-grade tissue-based inflammation and/or scarring, perturbation of the host virome/microbiome, or triggering of autoimmunity. Several studies show pre-existing and/or de novo production of autoantibodies after infection with SARS-CoV-2, but the persistence of these antibodies and their role in causing long-COVID is debated. Here, we review the mechanisms through which autoimmune responses can arise during and after viral infection, focusing on the evidence for B-cell dysregulation and autoantibody production in acute and long-COVID.}, }
@article {pmid39957847, year = {2021}, author = {Ferrell, JM and Chiang, JYL}, title = {Bile acid receptors and signaling crosstalk in the liver, gut and brain.}, journal = {Liver research}, volume = {5}, number = {3}, pages = {105-118}, pmid = {39957847}, issn = {2542-5684}, abstract = {Bile acids are physiological detergents derived from cholesterol that aid in digestion and nutrient absorption, and they play roles in glucose, lipid, and energy metabolism and in gut microbiome and metabolic homeostasis. Bile acids mediate crosstalk between the liver and gut through bactericidal modulation of the gut microbiome, while gut microbes influence the composition of the circulating bile acid pool. Recent research indicates bile acids may also be important mediators of neurological disease by acting as peripheral signaling molecules that activate bile acid receptors in the blood-brain barrier and in the brain itself. This review highlights the role of bile acids in maintaining liver and gut microbe homeostasis, as well as their function as mediators of cellular signaling in the liver-gut-brain axis.}, }
@article {pmid39956262, year = {2025}, author = {Wan, M and Wang, W and He, M and Yang, S and Feng, Y and Luo, Y}, title = {Cubebin alleviates chronic stress-induced depression-like behavior in mice by regulating the gut microbiome.}, journal = {European journal of pharmacology}, volume = {}, number = {}, pages = {177384}, doi = {10.1016/j.ejphar.2025.177384}, pmid = {39956262}, issn = {1879-0712}, abstract = {The gut-brain axis is dysregulated as a consequence of alterations in the gut microbiota. These alterations increase toxic microbial metabolites, endotoxemia, and the release of immune mediators and contribute to the development of depression. Cubebin is a dibenzyl butyrolactone lignan, and its stem is also known as Agaru in Tibetan areas, it is commonly used as a sedative and tranquilizing medicine. This study aimed to investigate the effects of cubebin on chronic stress-induced depression-like behavior in mice. Cubebin was observed to mitigate depressive-like behavior in chronic unpredictable mild stress (CUMS) mice, influence the restoration of their cerebral cortex and hippocampal tissue morphology, and enhance the abundance of relevant intestinal flora in depression model mice, particularly by decreasing the abundance of Clostridium, Dorea, and Ruminococcus. The final protein function expression was normalized by regulating depression-related metabolic pathways. Concomitantly, the concentrations of neurotransmitters serotonin (5-HT), norepinephrine (NE), and dopamine (DA) in the brains of mice in the model group were enhanced, and their depressive symptoms were mitigated. Our study findings suggest that cubebin may ameliorate CUMS-induced depression in mice by modulating the microbe-gut-brain axis, elucidating the key effect of gut metabolites on depressive symptoms.}, }
@article {pmid39956110, year = {2025}, author = {Echeveste Medrano, MJ and Smith, GJ and Sánchez-Andrea, I and Jetten, MSM and Welte, CU}, title = {Contrasting Methane, Sulfide and Nitrogen-Loading Regimes in Bioreactors Shape Microbial Communities Originating From Methane-Rich Coastal Sediment of the Stockholm Archipelago.}, journal = {Environmental microbiology}, volume = {27}, number = {2}, pages = {e70056}, doi = {10.1111/1462-2920.70056}, pmid = {39956110}, issn = {1462-2920}, support = {854088//European Commission/ ; 024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; VI.Vidi.223.012//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Bioreactors/microbiology ; *Sulfides/metabolism ; Sweden ; *Nitrogen/metabolism ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Archaea/metabolism/genetics/classification ; Seawater/microbiology ; Bacteria/classification/genetics/metabolism ; Oxidation-Reduction ; Denitrification ; Nitrates/metabolism ; Phylogeny ; Ecosystem ; }, abstract = {Coastal ecosystems are increasingly exposed to high nutrient loads and salinity intrusions due to rising seawater levels. Microbial communities, key drivers of elemental cycles in these ecosystems, consequently, experience fluctuations. This study investigates how the methane-rich coastal sediment microbiome from the Stockholm Archipelago copes with high and low nitrogen and sulfide loading by simulating coastal conditions in two methane-saturated anoxic brackish bioreactors. Over a year, the bioreactors were subjected to the same ratio of nitrate, ammonium and sulfide (2:1:1) under eutrophic or oligotrophic conditions and monitored using 16S rRNA gene amplicon and metagenomic sequencing. Sulfide was depleted in both conditions. Sulfide-dependent denitrification was the predominant process in eutrophic conditions, whereas dissimilatory nitrate reduction to ammonium dominated under oligotrophic conditions. Methane oxidation was driven by Methylobacter and Methylomonas in eutrophic conditions, whereas a more diverse methane-oxidising microbial community developed under oligotrophic conditions, which likely competed for nitrate with anaerobic methanotrophic archaea and the gammaproteobacterial MBAE14. Novel putative copper-dependent membrane-bound monooxygenases (Cu-MMOs) were identified in MBAE14 and co-enriched Rugosibacter genomes, suggesting the need for further physiological and genetic characterisation. This study highlights the importance of understanding coastal anoxic microbiomes under fluctuating conditions, revealing complex interactions and novel pathways crucial for ecosystem functioning.}, }
@article {pmid39955961, year = {2025}, author = {Oanes, C and Alexeeva, M and Søreide, K and Brede, C}, title = {Salting-out assisted liquid-liquid extraction for UPLC-MS/MS determination of bile acids and kynurenine-, indole- and serotonin-pathway metabolites of tryptophan in human serum of healthy probands.}, journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences}, volume = {1255}, number = {}, pages = {124519}, doi = {10.1016/j.jchromb.2025.124519}, pmid = {39955961}, issn = {1873-376X}, abstract = {The bacterial composition of the gut has been found to affect many diseases, including several gastrointestinal cancers. The microbiome appears central in the production of certain metabolites that enter circulation, especially those from bile acids and the essential amino acid tryptophan. The tumor-microenvironment may also produce changes in metabolites, such as those from the tryptophan-kynurenine pathway, of which several compounds may be measured in the blood. As data emerges from large scale metabolomics studies, there will be a need to validate metabolomic biomarkers to confirm their clinical utility. This task also requires knowledge about biological variation of the same metabolites in a healthy population. For this purpose, a novel method was developed for quantification of bile acids and tryptophan metabolites in samples of human serum by ultra-performance liquid chromatography coupled with tandem mass spectrometry. Salting-out assisted liquid-liquid extraction was optimized with the ion-pairing reagent trifluoroacetic acid. In this way, both polar tryptophan metabolites and non-polar bile acids could be extracted with a high recovery, favorable matrix effects, and improved chromatographic focusing, by using straightforward robot pipetting. The instrumental analysis was fast (4 min and 32 s) and with sample injections done directly from the extraction microplate. The method was applied to quantify metabolites in serum from healthy probands, and for investigating inter- and intraindividual variations over six hours.}, }
@article {pmid39955638, year = {2025}, author = {Senavonge, A and Nakphaichit, M and Vongsangnak, W and Roytrakul, S and Patumcharoenpol, P and Kingkaw, A and Wongoutong, C and Weerapakorn, W and Pornputtapong, N and La-Ongkham, O and Poovorawan, Y and Wanlapakorn, N and Kittipongpattana, P and Nitisinprasert, S and Chatchatee, P and Suratannon, N}, title = {Dysbiosis involving methionine and PPAR-γ pathways is associated with early onset atopic dermatitis and food allergy.}, journal = {Asian Pacific journal of allergy and immunology}, volume = {}, number = {}, pages = {}, doi = {10.12932/AP-131223-1749}, pmid = {39955638}, issn = {0125-877X}, abstract = {BACKGROUND: Atopic dermatitis (AD) and food allergy (FA) often originate early in life. Gut microbiota interactions with the host immune system influence allergy development, yet the distinct gut microbiome and functional profiles in individuals with AD, FA, or both AD+FA remain underexplored.<br><br>OBJECTIVE: We investigated microbial colonization and proteomic profiles in infants with AD, FA, and AD+FA compared to age- and sex-matched controls from the Allergy Development in Early Life and Associated Factors in the Thai Birth Cohort (ALICE).<br><br>METHODS: Gut microbiomes from stool samples were analyzed using 16S sequencing, and proteomic analysis was conducted by liquid chromatography-tandem mass spectrometry.<br><br>RESULTS: The study included 16 AD, 5 FA, 5 AD+FA subjects, and 26 controls. AD+FA group exhibited the most severe dysbiosis. Enrichment of proteins involved in methionine biosynthesis in Bifidobacterium scardovii and high Erysipelotrichaceae colonization suggest a link to high-fat diets, known to reduce intestinal short-chain fatty acid and serotonin levels, contributing to allergies. Erysipelotrichaceae in AD+FA groups also expressed proteins related to histidine degradation. Low Bifidobacteriaceae levels were noted in FA and AD+FA, with more pathogenic strains colonized. Increased Bacteroidaceae in FA and AD+FA and Enterobacteriaceae in FA were detected. Pathways involving vitamin B1, a ligand for proliferator-activated receptor-&#x3b3; (PPAR-&#x3b3;) from Enterobacteriaceae could promote TH2 cells, type 2 innate lymphoid cells, and M2 macrophages, likely contribute to allergic inflammation.<br><br>CONCLUSIONS: AD+FA phenotype exhibited the most distinctive gut microbiome alterations, highlighting unique dysbiosis patterns. Microbiome biosynthesis pathways involving metabolism of methionine, histidine, serotonin, and vitamin B1 point to new targets for modifying or treating AD and FA.}, }
@article {pmid39955590, year = {2025}, author = {Lan, W and Lu, Q and Ma, W and Jiang, Z and Chen, Y and Wang, Z and Yao, X and Tang, F}, title = {Investigating the causal relationship between the gut microbiome and rheumatoid arthritis: mediating effects of immune cells.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {187}, pmid = {39955590}, issn = {1479-5876}, support = {[2023]435//Science and Technology Program of Guizhou Province (Guizhou Scientific Foundation-Platform and talent/ ; 82160917//National Natural Science Foundation of China/ ; 2022]004//Guizhou University of Traditional Chinese Medicine National and Provincial Science and Technology Innovation Talent Team Cultivation Project (Guizhou University of Traditional Chinese Medicine TD NO/ ; }, mesh = {*Arthritis, Rheumatoid/microbiology/immunology ; Humans ; *Gastrointestinal Microbiome ; Genome-Wide Association Study ; Mendelian Randomization Analysis ; Causality ; }, abstract = {BACKGROUND: Rheumatoid arthritis (RA) is a complex autoimmune and inflammatory disease that significantly impacts the quality of life for millions worldwide. In recent years, gut microbiota has garnered extensive attention as a potential health-modulating factor, with associations identified between it and various diseases, including RA. This study aims to investigate the causal relationship between gut microbiota and RA using Mendelian Randomization (MR) analysis, and further examines the mediating role of immune cells in this connection.<br><br>METHOD: A MR analytical method was employed by us, integrating genome-wide association study (GWAS) data from FinnGen, MiBioGen, and research led by Valeria Orr&#xf9; and her team to systematically examine the relationships between gut microbiota, immune cells, and RA. Initially, we performed a bidirectional univariable MR analysis to examine the relationship between gut microbiota and RA, consciously avoiding any possible reverse causal influences. Following this, we applied multivariable MR adjustments on gut microbiota that showed positive associations and employed a two-step methodology to examine the overall genetic predictive role of immune cell-mediated gut microbiota in the risk of developing RA.<br><br>RESULT: Our results demonstrate notable causal connections between different gut microbiota and RA. In particular, Mollicutes, Ruminococcaceae UCG002, and Butyricimonas displayed positive associations with RA, while other microbiota, including Rikenellaceae, Lactobacillaceae, and Veillonella, showed negative associations. Additionally, we identified a reduction in the abundance of certain microbiota, including Lachnospiraceae and Ruminococcus1, which were excluded from our study and validated for analytical accuracy using methods such as "leave-one-out." Immune cells, including CD3 found on activated CD4 regulatory T cells that express CD39, serve a mediating function in the development of RA. To summarize, our research focused on the species Butyricimonas id. 945, recognizing immune cells as crucial contributors to the relationship between genetic predictions of gut microbiota and RA.<br><br>CONCLUSION: This research clarifies the intricate causal links between gut microbiota and RA, emphasizing the crucial mediating function of immune cells in this mechanism. These findings not only enhance our understanding of the pathogenesis of RA but also provide new perspectives and potential intervention targets for future prevention and treatment strategies. Future research should further investigate the specific mechanisms underlying the interactions among gut microbiota, immune cells, and RA, while considering the validation of these findings across diverse populations.}, }
@article {pmid39955557, year = {2025}, author = {Hernández, M and Langa, J and Aizpurua, O and Navarro-Noya, YE and Alberdi, A}, title = {Contrasting recovery of metagenome‑assembled genomes and derived bacterial communities and functional profiles from lizard fecal and cloacal samples.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {15}, pmid = {39955557}, issn = {2524-4671}, support = {POS_2022_1_0011//Hezkuntza, Hizkuntza Politika Eta Kultura Saila, Eusko Jaurlaritza/ ; DNRF143//Danmarks Grundforskningsfond/ ; }, abstract = {Genome-resolved metagenomics, based on shotgun sequencing, has become a powerful strategy for investigating animal-associated bacterial communities, due its heightened capability for delivering detailed taxonomic, phylogenetic, and functional insights compared to amplicon sequencing-based approaches. While genome-resolved metagenomics holds promise across various non-lethal sample types, their effectiveness in yielding high-quality metagenome-assembled genomes remains largely unexplored. Our investigation of fecal and cloacal microbiota of the mesquite lizards (Sceloporus grammicus) using genome-resolved metagenomics revealed that fecal samples contributed 97% of the 127 reconstructed bacterial genomes, whereas only 3% were recovered from cloacal swabs, which were largely enriched with host DNA. Taxonomic, phylogenetic and functional alpha bacterial diversity was greater in fecal samples than in cloacal swabs. We also observed significant differences in bacterial community composition between sampling methods, and higher inter-individual variation in cloacal swabs. Bacteroides, Phocaeicola and Parabacteroides (all Bacteroidota) were more abundant in the feces, whereas Hafnia and Salmonella (both Pseudomonadota) increased in the cloaca. Functional analyses showed that metabolic capacities of the microbiota to degrade polysaccharides, sugars and nitrogen compounds were enriched in fecal samples, likely reflecting the role of intestinal bacteria in nutrient metabolism. Overall, our results indicate that fecal samples outperform cloacal swabs in characterizing bacterial assemblages within lizards using genome-resolved metagenomics.}, }
@article {pmid39955550, year = {2025}, author = {Wen, Q and Wang, S and Min, Y and Liu, X and Fang, J and Lang, J and Chen, M}, title = {Associations of the gut, cervical, and vaginal microbiota with cervical cancer: a systematic review and meta-analysis.}, journal = {BMC women's health}, volume = {25}, number = {1}, pages = {65}, pmid = {39955550}, issn = {1472-6874}, support = {2024-YF05-02230-SN//Chengdu Science and Technology Bureau/ ; 2024-803//Health Commission of Sichuan Province/ ; 24QNMP038//Health Commission of Sichuan Province Medical Science and Technology Program/ ; }, mesh = {Humans ; Female ; *Uterine Cervical Neoplasms/microbiology ; *Vagina/microbiology ; *Microbiota/physiology ; *Cervix Uteri/microbiology ; *Gastrointestinal Microbiome/physiology ; }, abstract = {BACKGROUND: An increasing number of studies indicate that the gut, cervical, and vaginal microbiota may play crucial roles in the development of cervical cancer (CC). However, the interactions between the microbiota and the host are yet unknown. To address this gap, a systematic review and meta-analysis were conducted to assess the microbiota alterations in a variety of body locations, including the gut and genital tract.<br><br>METHODS: Electronic searches of PubMed, Embase, Web of Science, and the Cochrane Library were conducted to retrieve eligible papers published from January 1, 2014, to January 1, 2024 (PROSPERO: CRD42024554433). This study was restricted to English-language studies reporting on alpha diversity, beta diversity, and relative abundance, as well as on patients with CC whose microbiota had been analyzed via next-generation sequencing technologies. To assess the risk of bias (RoB), we utilized the Newcastle&#x2012;Ottawa Quality Assessment Scale (NOS) and the ROBINS-I tool. For the meta-analysis, we employed Review Manager 5.4.<br><br>RESULTS: Thirty-six eligible studies were included in this review. The Chao1 index (SMD&#x2009;=&#x2009;0.96, [95% CI: 0.71, 1.21], I[2]&#x2009;=&#x2009;0%) and the Shannon index (SMD&#x2009;=&#x2009;1.02, [95% CI: 0.53, 1.50], I[2]&#x2009;=&#x2009;85%) values from vaginal samples were significantly greater in patients than in the controls. In the cervical samples, the Shannon index value (SMD&#x2009;=&#x2009;1.29, [95% CI: 0.61, 1.97], I[2]&#x2009;=&#x2009;93%) significantly increased, whereas the Chao1 index value did not significantly differ (SMD&#x2009;=&#x2009;0.50, [95% CI: -0.46, 1.46], I[2]&#x2009;=&#x2009;89%). The Shannon index value (SMD&#x2009;=&#x2009;0.25, [95% CI: -0.22, 0.72], I[2]&#x2009;=&#x2009;38%) did not significantly differ across the gut samples. The majority of studies (19/25) indicated that the patients and noncancer controls differed significantly in terms of beta diversity. Cancer-associated changes were observed, with a dramatic decrease in the Lactobacillus genus and significant increases in pathogenic bacteria, including the Anaerococcus, Peptostreptococcus, Porphyromonas, Prevotella, and Sneathia genera. Additionally, the impact of antineoplastic therapies on microbial diversity was inconsistently reported across several studies.<br><br>CONCLUSION: This systematic review elucidates the microbiota alterations associated with the prevalence of CC and its response to anti-tumor therapies, aiming to provide insights for future research directions and precision medicine strategies to enhance women's quality of life.<br><br>PROSPERO REGISTRATION: CRD42024554433.}, }
@article {pmid39955511, year = {2025}, author = {Klomp, K and Alkema, M and Knol, J and Malinowska, AM and Belzer, C}, title = {A randomized controlled study protocol of the TOBBI trial: the effect of a 6 weeks intervention with synbiotics on the recovery speed of the gut microbiota after antibiotic treatment in Dutch toddlers.}, journal = {BMC pediatrics}, volume = {25}, number = {1}, pages = {117}, pmid = {39955511}, issn = {1471-2431}, support = {AF18005//TKI agrifood/ ; AF18005//TKI agrifood/ ; AF18005//TKI agrifood/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Infant ; *Synbiotics/administration &amp; dosage ; *Anti-Bacterial Agents/therapeutic use/administration &amp; dosage ; Child, Preschool ; Netherlands ; Amoxicillin/administration &amp; dosage/therapeutic use ; Amoxicillin-Potassium Clavulanate Combination/therapeutic use ; Feces/microbiology ; Male ; Female ; Bifidobacterium breve ; }, abstract = {BACKGROUND: Antibiotic-induced disruption of the gut microbiome in the first 1000 days of life is linked to an increased risk of the development of immunological, metabolic, and neurobehavioral childhood-onset conditions. Supporting the recovery of the gut microbial community after it has been perturbed by antibiotics might be a promising strategy to reduce these risks. In this clinical study, the effect of a 6 weeks supplementation with synbiotics (Bifidobacterium breve M-16 V, short chain galacto-oligosaccharides and long chain fructo-oligosaccharides) after antibiotic treatment on the recovery speed of the gut microbiota of toddlers will be studied.<br><br>METHODS/DESIGN: A cohort of 126 Dutch toddlers aged 12 to 36&#xa0;months old, who receive an amoxicillin or amoxicillin/clavulanic acid treatment, will be followed for 12&#xa0;weeks. Participants will be randomized into an intervention group, who will consume the study product over a 6&#xa0;weeks period starting at the last day of the antibiotic treatment or into a control group that will continue their usual eating pattern. Stool samples and their characteristics will be collected weekly by both groups. Stool samples will be analyzed for total microbiota and Bifidobacterium spp.. The differences in the proportion of Bifidobacterium out of total gut microbiota, composition of species belonging to Bifidobacterium, and beta diversity overtime will be compared between the two groups to study the effect of the intervention on the gut microbiota after perturbation. Furthermore, the effect of the treatment will also be studied in terms of the gut microbiota metabolic activity and stool characteristics. Additionally, food intake will be recorded to investigate whether diet, especially dietary fibers, may influence the gut microbiota as well. The findings may highlight a potential intervention strategy to support the recovery of the gut community after it has been perturbed by antibiotics in early life.<br><br>TRIAL REGISTRATION: The TOBBI trial was approved by the board of Medical Ethics Review Committee NedMec in June 2022 and registered at&#xa0; https://www.onderzoekmetmensen.nl/en/trial/20358 under the code NL75975.081.20, and at the World Health Organization at https://trialsearch.who.int/Trial2.aspx?TrialID=NL-OMON20358 under NTR-new: NL8996.}, }
@article {pmid39955509, year = {2025}, author = {Li, Z and Yang, X and Zhang, D and Shi, X and Lei, L and Zhou, F and Li, W and Xu, T and Liu, X and Wang, S and Yang, J and Wang, X and Zhong, Y and Yu, L}, title = {Exploration of oral microbiota alteration and AI-driven non-invasive hyperspectral imaging for CAD prediction.}, journal = {BMC cardiovascular disorders}, volume = {25}, number = {1}, pages = {102}, pmid = {39955509}, issn = {1471-2261}, support = {ICRCYG-2022-001//Cross-Innovation Talent Program of Renmin Hospital of Wuhan University/ ; 82270532//National Natural Science Foundation of China/ ; 2021CFA010//Foundation for Innovative Research Groups of Natural Science Foundation of Hubei Province/ ; 2042024kf0041//Central University Basic Research Fund of China/ ; }, mesh = {Humans ; Female ; Male ; *Tongue/microbiology/diagnostic imaging ; *Predictive Value of Tests ; *Coronary Artery Disease/diagnostic imaging/microbiology ; Middle Aged ; *Microbiota ; Prospective Studies ; Aged ; *Hyperspectral Imaging ; Dysbiosis/microbiology ; Machine Learning ; Bacteria/isolation &amp; purification/genetics/classification ; Ribotyping ; Reproducibility of Results ; Coronary Angiography ; Risk Assessment ; Image Interpretation, Computer-Assisted ; }, abstract = {BACKGROUND: Oral microbiome dysbiosis is an important risk factor affecting the occurrence and progression of coronary artery disease (CAD). However, the dysbiosis on the tongue in patients with CAD is still unclear, and whether the oral alteration caused by these disorders can be identified by other tools for CAD diagnosis needs to be further explored. Hyperspectral imaging (HSI) is characterized as high spectral resolution, broad spectral range, and superior spatial resolution. Hyperspectral images contain high-dimensional data that generally require machine learning algorithms for feature identification and model construction. Therefore, this study aims to investigate the variation of tongue microbiota and the effectiveness of HSI models in CAD diagnosis.<br><br>METHODS: Between 2023 and 2024, we prospectively approached 276 patients with chest pain and exhibiting risk for CAD who underwent coronary artery angiography (CAG). And 190 patients were enrolled in this study. Tongue dorsum swabs were collected for subsequent 16sRNA sequencing and microbiome analysis. Tongue dorsum features were extracted from hyperspectral images. The HSI analysis incorporated a total of 4750 hyperspectral images from all patients. All images are divided into training set (N&#x2009;=&#x2009;2555), internal test set (N&#x2009;=&#x2009;1095) and external test set (N&#x2009;=&#x2009;1095). A total of 31 models were constructed. 30 single machine learning algorithms were used to construct and test the CAD prediction models. Furthermore, the best performing fusion model was established. The efficacy of the model was evaluated employing several metrics, including area under the curve (AUC), decision curve analysis (DCA), calibration curve, accuracy (ACC), sensitivity (SE), specificity (SP), positive predictive value (PPV), negative predictive value (NPV) and F1 score.<br><br>RESULTS: The 16sRNA sequencing results indicated significant dysbiosis in the oral microbiota of patients with CAD, with decreased microbial abundance, network complexity and stability. The fusion model (GP-GB-SVM) demonstrated the highest performance, achieving an AUC of 0.92, ACC of 0.82, SE of 0.70, SP of 0.92, PPV of 0.88 and NPV of 0.79 in the internal test set and AUC of 0.86, ACC of 0.70, SE of 0.90, SP of 0.46, PPV of 0.60 and NPV of 0.90 in the external test set.<br><br>CONCLUSION: These findings not only emphasize the significant alteration of microbiome colonized on the tongue dorsum in CAD patients but also demonstrate the tongue features associated with microbiome dysbiosis can be identified in hyperspectral images. Thereby the integration of HSI and machine learning provides novel insights into non-invasive diagnosis of CAD.}, }
@article {pmid39955481, year = {2025}, author = {Wan, Y and Pike, R and Harley, A and Mumin, Z and Potterill, I and Meunier, D and Ganner, M and Getino, M and Coelho, J and Jauneikaite, E and Moganeradj, K and Brown, CS and Holmes, AH and Demirjian, A and Hopkins, KL and Pichon, B}, title = {Complete genome assemblies and antibiograms of 22 Staphylococcus capitis isolates.}, journal = {BMC genomic data}, volume = {26}, number = {1}, pages = {12}, pmid = {39955481}, issn = {2730-6844}, support = {PSN109/WT_/Wellcome Trust/United Kingdom ; NIHR200876//National Institute for Health and Care Research/ ; UGG10057//Price David Evans endowment/ ; }, mesh = {*Staphylococcus capitis/genetics/drug effects/isolation &amp; purification ; *Microbial Sensitivity Tests ; *Genome, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Humans ; Whole Genome Sequencing ; Staphylococcal Infections/microbiology/drug therapy ; Drug Resistance, Multiple, Bacterial/genetics ; }, abstract = {OBJECTIVE: Staphylococcus capitis is part of the human microbiome and an opportunistic pathogen known to cause catheter-associated bacteraemia, prosthetic joint infections, skin and wound infections, among others. Detection of S. capitis in normally sterile body sites saw an increase over the last decade in England, where a multidrug-resistant clone, NRCS-A, was widely identified in blood samples from infants in neonatal intensive care units. To address a lack of complete genomes and antibiograms of S. capitis in public databases, we performed long- and short-read whole-genome sequencing, hybrid genome assembly, and antimicrobial susceptibility testing of 22 diverse isolates.<br><br>DATA DESCRIPTION: We present complete genome assemblies of two S. capitis type strains (subspecies capitis: DSM 20326; subspecies urealyticus: DSM 6717) and 20 clinical isolates (NRCS-A: 10) from England. Each genome is accompanied by minimum inhibitory concentrations of 13 antimicrobials including vancomycin, teicoplanin, daptomycin, linezolid, and clindamycin. These 22 genomes were 2.4-2.7 Mbp in length and had a GC content of 33%. Plasmids were identified in 20 isolates. Resistance to teicoplanin, daptomycin, gentamicin, fusidic acid, rifampicin, ciprofloxacin, clindamycin, and erythromycin was seen in 1-10 isolates. Our data are a resource for future studies on genomics, evolution, and antimicrobial resistance of S. capitis.}, }
@article {pmid39955324, year = {2025}, author = {O' Donovan, CM and Nori, SRC and Shanahan, F and Celentano, G and Murphy, TB and Cotter, PD and Sullivan, OO}, title = {Temporal stability and lack of variance in microbiome composition and functionality in fit recreational athletes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {5619}, pmid = {39955324}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Adult ; *Athletes ; Female ; *Feces/microbiology ; Metagenomics/methods ; Prevotella/genetics/isolation &amp; purification ; Young Adult ; Running ; Faecalibacterium prausnitzii/genetics ; }, abstract = {Human gut microbiome composition and function is influenced by environmental and lifestyle factors, including exercise and fitness. We studied the composition and functionality of the faecal microbiome of recreational (non-elite) runners (n = 62) with serial shotgun metagenomics, at 4 time points over a 7-week period. Gut microbiome composition and function was stable over time. Grouping of samples on the basis of their fitness level (fair, good, excellent, and superior) or habitual training (low (4-6 h/week), medium (7-9 h/week), high (10-12 h/week), and extreme (13 + hours/week)) revealed no significant microbiome-related differences. Overall, the species Faecalibacterium prausnitzii, Blautia wexlerae, and Prevotella copri were the most abundant members of the gut microbiome. Analysis of co-abundance groups (CAGs) revealed no significant relationship between CAGs and fitness levels or training subgroups. Functional pathways were similar across all samples and timepoints with no clustering based on associated metadata. The most abundant genes identified within samples corresponded to pathways for nucleoside and nucleotide biosynthesis, amino acid biosynthesis, and cell wall biosynthesis. Collectively, these results describe the microbiome of active recreational runners and note temporal stability amongst participants.}, }
@article {pmid39955323, year = {2025}, author = {Seco-Hidalgo, V and Witney, AA and Chico, ME and Vaca, M and Arevalo, A and Schuyler, AJ and Platts-Mills, TAE and Ster, IC and Cooper, PJ}, title = {Rurality and relative poverty drive acquisition of a stable and diverse gut microbiome in early childhood in a non-industrialized setting.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {5601}, pmid = {39955323}, issn = {2045-2322}, support = {RO1-AI-20565/NH/NIH HHS/United States ; 088862/Z/09/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; Child, Preschool ; *Rural Population ; Female ; *Poverty ; Male ; Ecuador ; *Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Longitudinal Studies ; Pregnancy ; Infant, Newborn ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {There are limited longitudinal data from non-industrialized settings on patterns and determinants of gut bacterial microbiota development in early childhood. We analysed epidemiological data and stool samples collected from 60 children followed from early infancy to 5 years of age in a rural tropical district in coastal Ecuador. Data were collected longitudinally on a wide variety of individual, maternal, and household exposures. Extracted DNA from stool samples were analysed for bacterial microbiota using 16S rRNA gene sequencing. Both alpha and beta diversity indices suggested stable profiles towards 5 years of age. Greater alpha diversity and lower beta diversity were associated with factors typical of rural poverty including low household incomes, overcrowding, and greater agricultural and animal exposures. Consumption of unpasteurized milk was consistently associated with greater alpha diversity indices. Delivery method and antibiotic exposures during pregnancy and early childhood appeared to have limited effects on developmental trajectories of gut microbiota. Infants living in a non-industrialized setting in conditions of greater poverty and typically rural exposures appeared to acquire more rapidly a stable and diverse gut bacterial microbiome during childhood.}, }
@article {pmid39955207, year = {2025}, author = {Kim, S and Ndwandwe, C and Devotta, H and Kareem, L and Yao, L and O'Mahony, L}, title = {Role of the microbiome in regulation of the immune system.}, journal = {Allergology international : official journal of the Japanese Society of Allergology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.alit.2024.12.006}, pmid = {39955207}, issn = {1440-1592}, abstract = {Immune health and metabolic functions are intimately connected via diet and the microbiota. Immune cells are continuously exposed to a wide range of microbes and microbial-derived compounds, with important mucosal and systemic ramifications. Microbial fermentation of dietary components in vivo generates thousands of molecules, some of which are integral components of the molecular circuitry that regulates immune and metabolic functions. These in turn protect against aberrant inflammatory or hyper-reactive processes and promote effector immune responses that quickly eliminate pathogens, such as SARS-CoV-2. Potent tolerance mechanisms should ensure that these immune cells do not over-react to non-pathogenic factors (e.g. food proteins), while maintaining the ability to respond to infectious challenges in a robust, effective and well controlled manner. In this review we examine the factors and mechanisms that shape microbiota composition and interactions with the host immune system, their associations with immune mediated disorders and strategies for intervention.}, }
@article {pmid39955156, year = {2025}, author = {Xu, M and Liu, X and Chen, T and Zhao, Y and Ma, L and Shi, X and Chen, X and Shi, Y and Adams, JM}, title = {Corrigendum to "Dynamics of wheat rhizosphere microbiome and its impact on grain production across growth stages" [964 (2025) 178524].}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {178834}, doi = {10.1016/j.scitotenv.2025.178834}, pmid = {39955156}, issn = {1879-1026}, }
@article {pmid39955076, year = {2025}, author = {Wang, R and Wang, Z and Zhang, M and Zhong, D and Zhou, M}, title = {Application of photosensitive microalgae in targeted tumor therapy.}, journal = {Advanced drug delivery reviews}, volume = {}, number = {}, pages = {115519}, doi = {10.1016/j.addr.2025.115519}, pmid = {39955076}, issn = {1872-8294}, abstract = {Microalgae present a novel and multifaceted approach to cancer therapy by modulating the tumor-associated microbiome (TAM) and the tumor microenvironment (TME). Through their ability to restore gut microbiota balance, reduce inflammation, and enhance immune responses, microalgae contribute to improved cancer treatment outcomes. As photosynthetic microorganisms, microalgae exhibit inherent anti-tumor, antioxidant, and immune-regulating properties, making them valuable in photodynamic therapy (PDT) and tumor imaging due to their capacity to generate reactive oxygen species (ROS). Additionally, microalgae serve as effective drug delivery vehicles, leveraging their biocompatibility and unique structural properties to target the TME more precisely. Microalgae-based microrobots further expand their therapeutic potential by autonomously navigating complex biological environments, offering a promising future for precision-targeted cancer treatments. We position microalgae as a multifunctional agent capable of modulating TAM, offering novel strategies to enhance TME and improve the efficacy of cancer therapies.}, }
@article {pmid39955022, year = {2025}, author = {Jiao, X and Li, Z}, title = {Impact of Streptozotocin-Induced Type 1 and Type 2 Diabetes on Ocular Surface Microbial Signatures in C57BL/6J Mice.}, journal = {Experimental eye research}, volume = {}, number = {}, pages = {110282}, doi = {10.1016/j.exer.2025.110282}, pmid = {39955022}, issn = {1096-0007}, abstract = {The ocular surface (OS), like other mucosal sites, hosts a diverse microbiome. However, the impact of hyperglycemia associated with diabetes on OS microbial composition remains poorly understood. In this study, we established type 1 diabetes mellitus (T1DM) and type 2 diabetes mellitus (T2DM) models in C57BL/6J mice by administering high-dose streptozotocin (STZ) for T1DM and low-dose STZ combined with a high-fat diet for T2DM. The OS microbiome was characterized and analyzed using 16S rRNA sequencing. The results showed that neither T1DM nor T2DM significantly affected microbial richness compared to normal mice; however, T2DM led to a significant reduction in microbial diversity. This reduction in microbial diversity in T2DM is consistent with known microbial dysbiosis in diabetes, which may contribute to the pathogenesis of ocular complications such as dry eye disease and diabetic retinopathy. Community composition analysis identified Proteobacteria, Pelagibacterium, and Aliihoeflea as the core OS bacteria in normal mice. Diabetes significantly altered the OS microbial composition at various taxonomic levels. Specifically, T1DM was associated with 9 signature bacterial species, including Oceanospirillales, Bacillales, Halomonas, unclassified_f_Lachnospiraceae, and Anoxybacillus. T2DM exhibited 17 bacterial markers, including Firmicutes, Staphylococcus, Corynebacterium, and Parasutterella. Functional prediction of the microbiota using PICRUSt2 indicated potential impairments in carbohydrate metabolism due to diabetes. In conclusion, diabetic mice exhibit severe dysregulation of their OS microbiota, and restoring microbial balance in diabetic patients may represent a promising strategy for preventing and treating diabetic OS pathologies.}, }
@article {pmid39954934, year = {2025}, author = {Martinez, P and Sabatier, JM}, title = {Malignant Tumors in Vagal-innervated Organs: Exploring Its Homeostatic Role.}, journal = {Cancer letters}, volume = {}, number = {}, pages = {217539}, doi = {10.1016/j.canlet.2025.217539}, pmid = {39954934}, issn = {1872-7980}, abstract = {Cancer remains a significant global health challenge, with its progression shaped by complex and multifactorial mechanisms. Recent research suggests that the vagus nerve could play a critical role in mediating communication between the tumor microenvironment and the central nervous system (CNS). This review highlights the diversity of vagal afferent receptors, which could position the vagus nerve as a unique pathway for transmitting immune, metabolic, mechanical, and chemical signals from tumors to the CNS. Such signaling could influence systemic disease progression and tumor-related responses. Additionally, the vagus nerve's interactions with the microbiome and the renin-angiotensin system (RAS)-both implicated in cancer biology-further underscore its potential central role in modulating tumor-related processes. Contradictions in the literature, particularly concerning vagal fibers, illustrate the complexity of its involvement in tumor progression, with both tumor-promoting and tumor-suppressive effects reported depending on cancer type and context. These contradictions often overlook certain experimental biases, such as the failure to distinguish between vagal afferent and efferent fibers during vagotomies or the localized parasympathetic effects that cannot always be extrapolated to the systemic level. By focusing on the homeostatic role of the vagus nerve, understanding these mechanisms could open the door to new perspectives in cancer research related to the vagus nerve and lead to potential therapeutic innovations.}, }
@article {pmid39954909, year = {2025}, author = {Lu, H and Liu, S and Zhang, S and Chen, J and Chen, Q}, title = {Suppression of Alzheimer's disease by Agaricus sinodeliciosus var. Chaidam exopolysaccharide with amyloid-β clearance activity via gut microbiota-metabolite regulation.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {141048}, doi = {10.1016/j.ijbiomac.2025.141048}, pmid = {39954909}, issn = {1879-0003}, abstract = {Amyloid-β (Aβ) aggregation is a hallmark of Alzheimer's disease (AD), characterized by cognitive impairment, and there remains a lack of effective functional compound with Aβ clearance activity. To elucidate the effect of exopolysaccharide (EPS) extracted from Agaricus sinodeliciosus var. Chaidam on Aβ1-42- induced AD rat and uncover the underlying mechanism, the neuroprotective activity of EPS was evaluated using immunofluorescence, immunohistochemistry, western blot, RT-qPCR, microbiomics and metabolomics. The results demonstrated that EPS exhibited significant anti-AD efficacy, as evidenced by improved cognitive function and spatial memory, balanced brain redox status, suppressed neuroinflammatory responses. EPS substantially reduced Aβ1-42 accumulation in the hippocampus by activating Aβ-phagocytic microglia through the mTOR-HIF-1α pathway. Importantly, EPS reconstructed gut microbiota composition by increasing the relative abundance of Ruminococcaceae and reduced Erysipelotrichaceae. The reshaped gut microbiome and the formation of the metabolite serotonin were associated with behavioral alterations, neuroinflammation, and brain oxidative status. Thus, EPS significantly alleviated cognitive deficit and neuroinflammation in Aβ1-42-induced AD rats, potentially by enhancing microglial phagocytosis of Aβ1-42 and modulating the gut microbiome and serotonin production. Collectively, EPS from A. sinodeliciosus var. Chaidam polysaccharide may serve as a novel Aβ1-42-targeted approach for anti-AD therapy.}, }
@article {pmid39954816, year = {2025}, author = {Ladyhina, V and Rajala, E and Sternberg-Lewerin, S and Nazirzadeh, L and Bongcam-Rudloff, E and Dicksved, J}, title = {Methodological aspects of investigating the resistome in pig farm environments.}, journal = {Journal of microbiological methods}, volume = {}, number = {}, pages = {107103}, doi = {10.1016/j.mimet.2025.107103}, pmid = {39954816}, issn = {1872-8359}, abstract = {A typical One Health issue, antimicrobial resistance (AMR) development and its spread among people, animals, and the environment attracts significant research attention. The animal sector is one of the major contributors to the development and dissemination of AMR and accounts for more than 50 % of global antibiotics usage. The use of antibiotics exerts a selective pressure for resistant bacteria in the exposed microbiome, but many questions about the epidemiology of AMR in farm environments remain unanswered. This is connected to several methodological challenges and limitations, such as inconsistent sampling methods, complexity of farm environment samples and the lack of standardized protocols for sample collection, processing and bioinformatical analysis. In this project, we combined metagenomics and bioinformatics to optimise the methodology for reproducible research on the resistome in complex samples from the indoor farm environment. The work included optimizing sample collection, transportation, and storage, as well as DNA extraction, sequencing, and bioinformatic analysis, such as metagenome assembly and antibiotic resistance gene (ARG) detection. Our studies suggest that the current most optimal and cost-effective pipeline for ARG search should be based on Illumina sequencing of sock sample material at high depth (at least 25 M 250 bp PE for AMR gene families and 43 M for gene variants). We present a computational analysis utilizing MEGAHIT assembly to balance the identification of bacteria carrying ARGs with the potential loss of diversity and abundance of resistance genes. Our findings indicate that searching against multiple ARG databases is essential for detecting the highest diversity of ARGs.}, }
@article {pmid39954790, year = {2025}, author = {Mohanakumar, KP and Rendeiro, C and Beart, PM}, title = {Neuro-nutraceuticals: Emerging molecular and functional insights into how natural products improve brain health.}, journal = {Neurochemistry international}, volume = {}, number = {}, pages = {105948}, doi = {10.1016/j.neuint.2025.105948}, pmid = {39954790}, issn = {1872-9754}, abstract = {The editors in assembling this Special Issue, "Neuro-nutraceuticals: Emerging Molecular and Functional Insights into how Natural Products Improve Brain Health", sought to advance our understanding of how such chemical entities alone or in group maintain brain metabolism and homeostasis so that neurons, glia and endothelial cells are healthy during development, ageing and in neuropathologies. The growth of interest in neuro-nutraceuticals and all aspects of their actions relevant to the health of the nervous system continues to amaze all. This Special Issue # 4 contains 39 articles, and we sought to highlight in this Special Issue important new advances and key issues pertinent to future clinical application of neuro-nutraceuticals. The diversity of topics covered is quite broad and includes significant articles on enteric microbiome and brain health. The Editors have tried to provide an up-to-date account of how nutraceuticals work at the molecular and cellular level, and what are the known molecular targets that ultimately can be leveraged clinically to enable the brain to function better. With respect to brain ailments and treatments, single molecule effects, and a therapeutic group of molecules from dietary herbals are discussed in this Special Issue.}, }
@article {pmid39954663, year = {2025}, author = {Shen, J and Xiao, Y and Bi, H and Guo, R and Qu, M and Ding, R and Zhang, X and Li, H and Han, M and Huang, S}, title = {Rotavirus regulates the gut microhabitat immune response through the IL-22/pSTAT3/RegIIIγ signaling pathway, leading to lactose intolerance.}, journal = {International immunopharmacology}, volume = {150}, number = {}, pages = {114275}, doi = {10.1016/j.intimp.2025.114275}, pmid = {39954663}, issn = {1878-1705}, abstract = {Lactose intolerance (LI) is a significant contributor to diarrhea in infants and young children. Recent studies suggest a potential link between rotavirus (RV) infection and alterations in gut microbiota, which may play a role in the mechanism of LI. However, the precise underlying mechanism remains unclear and requires urgent clarification. In this study, we combined insights from immunology and gut microbiome research to propose that the activation of the IL-22/pSTAT3/RegIIIγ signaling pathway, triggered by gut microbiota, may be involved. To investigate this, we established a LI animal model using 7-day-old BALB/c mice, which were infected with RV via oral gavage. The syndromes of mice were carefully recorded and compared during the intervention experiment. Notably, we measured the the expression levels of immunocytokines and phosphorylated signaling proteins, including IL-22, phosphorylated STAT3, and RegIIIγ. Additionally, we assessed the relationships between gut microbiota and these key elements. Our results indicated that RV indeed causes LI, as severe diarrhea was observed in the mice during the first three days of RV infection, subsiding after seven days. ELISA results revealed an increase in IL-22 levels, phosphorylated STAT3, and RegIIIγ, suggesting that the mechanism of LI associated with RV is linked to the classical IL-22/pSTAT3/RegIIIγ signaling pathway. Furthermore, our analysis of the connections between gut microbes and this signaling pathway indicated that "Bacteroidetes" and Firmicutes were significantly positively correlated with IL-22 and lactase, respectively. This finding implies that alterations in gut microbiota may serve as a potential switch for the IL-22/pSTAT3/RegIIIγ signaling pathway, leading to increased lactase levels. In summary, our study demonstrated that the development of LI is associated with the activation of the IL-22/pSTAT3/RegIIIγ signaling pathway alongside changes in gut microbes during RV infection. This provides valuable insights into the mechanisms underlying LI and its clinical treatment through moduLation of the gut microbiome.}, }
@article {pmid39954432, year = {2025}, author = {Zhang, X and Liu, Y and Mo, X and Huang, Z and Zhu, Y and Li, H and Jiang, L and Tan, Z and Yang, Z and Zhu, Y and Huang, J and Zeng, B and Zhuo, R}, title = {Ectomycorrhizal fungi and biochar promote soil recalcitrant carbon increases under arsenic stress.}, journal = {Journal of hazardous materials}, volume = {489}, number = {}, pages = {137598}, doi = {10.1016/j.jhazmat.2025.137598}, pmid = {39954432}, issn = {1873-3336}, abstract = {Globally, vast mining areas (∼31,396.3 km[2]) hold significant potential for soil carbon sequestration. However, the sequestration capacity of mine soils is closely linked to contamination characteristics and restoration strategies. Arsenic, a highly toxic metalloid prevalent in acid mine soils, affects carbon turnover through its interactions with soil compounds. Nevertheless, the underlying mechanisms remain inadequately understood. This study introduces a phytobial remediation approach combining ectomycorrhizal fungus (Suillus luteus) inoculated into Pinus massoniana and biochar as a soil amendment. Results demonstrated that S. luteus extended apoplastic spaces to absorb arsenic into root cell intervals while encapsulating organic matter into aggregates. Biochar further promoted recalcitrant carbon formation, significantly increasing aggregate-carbon, particulate organic carbon (POC), and mineral-associated organic carbon (MAOC) by 3.15-, 1.74-, and 2.33-fold, respectively, compared to controls. Distinct hyphosphere microbiomes were observed in the combined treatment (BS), with enhanced microbial diversity, enzyme activity, carbon-sequestration genes, and necromass production, indicating the pivotal role of soil microorganisms in stable carbon pool formation. These synergistic effects not only facilitated arsenic detoxification but also significantly contributed to carbon stabilization.}, }
@article {pmid39954350, year = {2025}, author = {Dong, Y and Liu, H and Habimana, O}, title = {High risk of Vibrio pathogen and antibiotic resistance transfer in live seafood wet markets of Shantou, China.}, journal = {International journal of food microbiology}, volume = {432}, number = {}, pages = {111098}, doi = {10.1016/j.ijfoodmicro.2025.111098}, pmid = {39954350}, issn = {1879-3460}, abstract = {The global demand for seafood necessitates robust food safety practices, particularly within traditional wet markets. This study investigated the microbiomes of live Japanese mantis shrimp (JMS) and their associated environments (water and biofilm) in local wet markets to assess the risk of pathogen and antibiotic resistance gene (ARG) transfer. Metagenomic analysis showed a significant link between microbiome composition and the type of sample (shrimp, biofilm, and water). While several known human pathogens were associated with shrimp samples, water and biofilm samples exhibited higher abundances of ARGs, suggesting a high risk of pathogen and ARG transfer from the market environment. Notably, this study focused on the diversity and characterization of poorly understood Vibrio species associated with JMS. The prevalence of β-lactam resistance genes in Vibrio isolates, combined with a comparative genomic analysis of several species, highlights this concern. Our study emphasizes the need to improve hygiene practices in wet markets to reduce foodborne illness risks and address antibiotic resistance. This work represents, to our knowledge, the first comparative genomic analysis of Vibrio species in the context of JMS and wet market seafood safety.}, }
@article {pmid39954187, year = {2025}, author = {Zhang, Y and Yuan, S and Wu, Y and Nie, W and You, T and Yang, H and Liu, B}, title = {Advancements in pharmacological interventions for atopic dermatitis current strategies and future directions.}, journal = {Inflammopharmacology}, volume = {}, number = {}, pages = {}, pmid = {39954187}, issn = {1568-5608}, support = {201805010006//Guangzhou key laboratory of construction and application of new drug screening model systems/ ; 2017KSYS002//Key Laboratory of New Drug Discovery and Evaluation of ordinary universities of Guangdong province/ ; Z155080000004//National Key Clinical Specialty Discipline Construction Program of China/ ; }, abstract = {Atopic dermatitis (AD) is a complex chronic inflammatory skin disorder, with its incidence significantly increasing in recent years. The pathogenesis of AD is complex, involving multiple factors such as genetic susceptibility, dysbiosis of the skin microbiome, autoimmune abnormalities, impaired epidermal barrier function, and environmental factors. These factors collectively contribute to the high incidence of the disease and its significant socio-economic burden. This article reviews the pathogenesis of AD and analyzes the current traditional treatment approaches, including topical and systemic therapies, highlighting the issues they face. It focuses on the current status and treatment strategies. Specifically, as the significant heterogeneity of AD, treatment paradigms are gradually shifting from a "one-size-fits-all" approach to personalized treatments. The aim is to achieve more effective management of AD and address the issues arising from individual differences. Through these discussions, this article aims to provide new perspectives and strategies for the clinical treatment of AD, in order to reduce the disease burden on patients.}, }
@article {pmid39954089, year = {2025}, author = {Liu, K and Deng, S and Zhou, Y and Xu, B and Zhang, Y and Li, W and Liu, X and Yao, X}, title = {Crosstalk Between the Skin Environment and Microbial Community in Immune-Related Skin Diseases.}, journal = {Clinical reviews in allergy &amp; immunology}, volume = {68}, number = {1}, pages = {16}, pmid = {39954089}, issn = {1559-0267}, support = {82373489//National Natural Science Foundation of China/ ; 82373489//National Natural Science Foundation of China/ ; 82373489//National Natural Science Foundation of China/ ; 82373489//National Natural Science Foundation of China/ ; 82373489//National Natural Science Foundation of China/ ; 82373489//National Natural Science Foundation of China/ ; 82373489//National Natural Science Foundation of China/ ; 82373489//National Natural Science Foundation of China/ ; 2021-I2M-1-059//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-1-059//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-1-059//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-1-059//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-1-059//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-1-059//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-1-059//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-1-059//CAMS Innovation Fund for Medical Sciences/ ; }, mesh = {Humans ; *Microbiota/immunology ; *Skin/microbiology/immunology ; *Skin Diseases/immunology/etiology/microbiology ; Animals ; Disease Susceptibility ; Cellular Microenvironment/immunology ; }, abstract = {The skin surface hosts diverse skin microbiota, including bacteria, fungi, and viruses. Intricate interactions between the skin microenvironment and microbial community are crucial for maintaining cutaneous homeostasis. This review explores the bidirectional relationship between the skin ecosystem and its microbiota. The skin microenvironment is shaped by a combination of intrinsic factors, dominated by sweat glands and pilosebaceous units, and external factors, such as UV radiation and personal care products, which create distinct niches that influence microbial colonization patterns across different skin regions. The skin microbiome, in turn, modulates the physical, chemical, immunological, and microbial barriers of the skin. We also discuss the alterations in this crosstalk in various immune-related skin conditions such as atopic dermatitis, psoriasis, rosacea, hidradenitis suppurativa, skin cancer, and aging. Understanding these interactions is vital for developing targeted microbiome-based therapies for various skin disorders. Further researches are needed to deepen insights into the microbial roles and their therapeutic potentials in skin health and disease.}, }
@article {pmid39954023, year = {2025}, author = {Garcia, B and Dominguez, MF and Spangenberg, L and Fernandez-Calero, T}, title = {Salivary microbiota characterization of Yerba Mate consumers in Uruguay.}, journal = {Clinical oral investigations}, volume = {29}, number = {2}, pages = {131}, pmid = {39954023}, issn = {1436-3771}, support = {Alicuotas//Programa de Desarrollo de las Ciencias B&#xe1;sicas/ ; Alicuotas//Programa de Desarrollo de las Ciencias B&#xe1;sicas/ ; COF 03/11//FOCEM - Fondo para la Convergencia Estructural del Mercosur/ ; COF 03/11//FOCEM - Fondo para la Convergencia Estructural del Mercosur/ ; }, mesh = {Humans ; *Saliva/microbiology ; Uruguay ; *Microbiota ; Adult ; Female ; Male ; Adolescent ; *Ilex paraguariensis ; RNA, Ribosomal, 16S ; Beverages/microbiology ; }, abstract = {INTRODUCTION: Yerba Mate (YM) is a green-colored infusion, derived from the Ilex paraguariensis plant, very popular and commonly consumed in Latin American countries (southern Brazil, Argentina, Paraguay, and Uruguay), rapidly gaining penetration in global markets, It's a beverage rich in polyphenols, alkaloids, and saponins, making its impact on the oral microbiome particularly interesting.<br><br>OBJECTIVES: This study aimed to characterize the composition of salivary microbiota in Uruguayan YM consumers and non-consumers, exploring potential implications for oral health.<br><br>MATERIALS AND METHODS: Salivary samples were collected from 24 YM consumers and 28 non-consumers in Uruguay (n&#x2009;=&#x2009;52). Participants were dentistry students, aged 18 to 35, with no reported pathologies and who had no oral conditions after visual inspection. 16S rRNA gene metabarcoding Illumina sequencing was employed to analyze their microbial composition. Bioinformatic analysis was conducted to identify and compare microbial taxa between the two groups. Relevant demographic and dietary data were also collected and analyzed.<br><br>RESULTS: The salivary microbiome of YM consumers is not completely different from non-consumers, however, several particular characteristics were found in each group. Both YM consumers and non-consumers exhibited a high relative abundance of Streptococcus species, with Streptococcus oralis being more abundant in a subset of non-consumers suggesting that YM may help maintain a balanced oral microbiota. Although no significant differences were observed in the Shannon diversity index, YM consumers might have a more diverse microbiome than non-consumers (YM consumers showed significantly higher species richness (Chao1 index), a greater number of amplicon sequence variants (ASVs), and broader microbial diversity, as confirmed by multivariate analyses). While the presence of Prevotella spp. in YM consumers aligns with previous research on polyphenol-rich beverages, its role in oral health warrants further investigation.<br><br>CONCLUSIONS: This study highlights the influence of YM consumption on salivary microbiota composition and diversity. YM consumption was associated with increased microbial diversity and species richness, which may contribute to oral microbiome resilience and health. These findings underscore the impact of dietary habits on oral microbial communities and their potential implications for oral health management and disease prevention.}, }
@article {pmid39953749, year = {2025}, author = {Aizpurua, O and Botnen, AB and Eisenhofer, R and Odriozola, I and Santos-Bay, L and Bjørnsen, MB and Gilbert, MTP and Alberdi, A}, title = {Functional Insights Into the Effect of Feralisation on the Gut Microbiota of Cats Worldwide.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17695}, doi = {10.1111/mec.17695}, pmid = {39953749}, issn = {1365-294X}, support = {CF20-0460//Carlsbergfondet/ ; 17417//Villum Fonden/ ; DNRF143//Danmarks Grundforskningsfond/ ; }, abstract = {Successfully adapting to a feral lifestyle with different access to food, shelter and other resources requires rapid physiological and behavioural changes, which could potentially be facilitated by gut microbiota plasticity. To investigate whether alterations in gut microbiota support this transition to a feral lifestyle, we analysed the gut microbiomes of domestic and feral cats from six geographically diverse locations using genome-resolved metagenomics. By reconstructing 229 non-redundant metagenome-assembled genomes from 92 cats, we identified a typical carnivore microbiome structure, with notable diversity and taxonomic differences across regions. While overall diversity metrics did not differ significantly between domestic and feral cats, hierarchical modelling of species communities, accounting for geographic and sex covariates, revealed significantly larger microbial functional capacities among feral cats. The increased capacity for amino acid and lipid degradation corresponds to feral cats' dietary reliance on crude protein and fat. A second modelling analysis, using behavioural phenotype as the main predictor, unveiled a positive association between microbial production of short-chain fatty acids, neurotransmitters and vitamins and cat aggressiveness, suggesting that gut microbes might contribute to heightened aggression and elusiveness observed in feral cats. Functional microbiome shifts may therefore play a significant role in the development of physiological and behavioural traits advantageous for a feral lifestyle, a hypothesis that warrants validation through microbiota manipulation experiments.}, }
@article {pmid39953674, year = {2025}, author = {Schaefer, AS and Nibali, L and Zoheir, N and Moutsopoulos, NM and Loos, BG}, title = {Genetic risk variants implicate impaired maintenance and repair of periodontal tissues as causal for periodontitis-A synthesis of recent findings.}, journal = {Periodontology 2000}, volume = {}, number = {}, pages = {}, doi = {10.1111/prd.12622}, pmid = {39953674}, issn = {1600-0757}, support = {//NIH/ ; }, abstract = {Periodontitis is a complex inflammatory disease in which the host genome, in conjunction with extrinsic factors, determines susceptibility and progression. Genetic predisposition is the strongest risk factor in the first decades of life. As people age, chronic exposure to the periodontal microbiome puts a strain on the proper maintenance of barrier function. This review summarizes our current knowledge on genetic risk factors implicated in periodontitis, derived (i) from hypothesis-free systematic whole genome-profiling studies (genome-wide association studies [GWAS] and quantitative trait loci [QTL] mapping studies), and independently validated through further unbiased approaches; (ii) from monogenic and oligogenic forms of periodontitis; and (iii) from syndromic forms of periodontitis. The genes include, but are not limited to, SIGLEC5, PLG, ROBO2, ABCA1, PF4, and CTSC. Notably, CTSC and PLG gene mutations were also identified in non-syndromic and syndromic forms of prepubertal and early-onset periodontitis. The functions of the identified genes in this review suggest that the pathways affected by the periodontitis-associated gene variants converge in functions involved in the maintenance and repair of structural integrity of the periodontal tissues. Particularly, these genes play a role in the healing of inflamed and ulcerated periodontal tissues, including roles in fibrinolysis, extrusion of cellular debris, extracellular matrix remodeling and angiogenesis. Syndromes that include periodontitis in their phenotype indicate that neutrophils play an important role in the regulation of inflammation in the periodontium. The established genetic susceptibility genes therefore collectively provide new insights into the molecular mechanisms and plausible causal factors underlying periodontitis.}, }
@article {pmid39953673, year = {2025}, author = {Kotsakis, GA and Ganesan, SM}, title = {Microbial Dysbiosis, Titanium Release, and Peri-implantitis.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {220345241307939}, doi = {10.1177/00220345241307939}, pmid = {39953673}, issn = {1544-0591}, abstract = {The peri-implant mucosal barrier is a unique microenvironment where host-microbiome interactions take place on the surface of an implanted biomaterial. Therefore, peri-implant immunity not only is quintessential to oral health but also contributes to the maintenance of the biomaterial-tissue equilibrium in health. This review delves into the intricate interplay between host factors, biomaterial properties, and the microbiome with a focus on the mechanisms underlying peri-implant dysbiosis. Investigations into this complex milieu have led to the emerging understanding of titanium particles released from the implant as significant exposomes. When biomaterial breakdown occurs, implant degradation products form particles that are released in the peri-implant crevice, exerting profound effects on the local immune surveillance. Comparative analyses with natural dentition highlight the distinct immune responses elicited by titanium particles, thereby implicating them as a key modulator of peri-implant dysbiosis that differentiates peri-implant from periodontal inflammation. Nonetheless, disruptions in the homeostatic balance of host-biomaterial interactions are linked to pathogenic shifts of the peri-implant microbiome that are correlated with titanium particles in humans. Collectively, it is now well established that to elucidate the mechanisms governing peri-implant dysbiosis, this triangle of host-microbiome-biomaterial has to be conjointly investigated. This review highlights findings from studies that have underscored the multifaceted nature of peri-implant dysbiosis, emphasizing the intricate crosstalk between host immunity, biomaterial characteristics, and microbial ecology. These findings suggest that the titanium particle exposome may alter key inflammatory cascades in the peri-implant tissues including toll-like receptor activation and inflammasome and complement signaling, which lead to nonresolving destructive inflammation. The presence of abiotic danger signals in the form of implant degradation products in peri-implant tissues may make antimicrobial monotherapies largely ineffective for managing peri-implantitis. In turn, the future of peri-implantitis therapy seems to lie in the development of targeted host modulatory interventions against titanium-mediated inflammatory pathways.}, }
@article {pmid39953591, year = {2025}, author = {Chen, H and Yao, X and Yang, C and Zhang, Y and Dong, H and Zhai, J and Fan, D and Zhou, Q}, title = {Distinctive circulating microbial metagenomic signatures in the plasma of patients with lung cancer and their potential value as molecular biomarkers.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {186}, pmid = {39953591}, issn = {1479-5876}, support = {YCZYPT [2018]06//National Human Genetic Resource Sharing Service Platform/ ; }, mesh = {Humans ; *Lung Neoplasms/blood/microbiology/genetics ; *Metagenomics/methods ; *Biomarkers, Tumor/blood ; Female ; Male ; Middle Aged ; Metagenome/genetics ; Aged ; Case-Control Studies ; ROC Curve ; }, abstract = {Lung cancer (LC) remains the leading cause of cancer death globally. Recent reports have suggested that circulating microbial nucleic acids have potential as promising biomarkers for cancer liquid biopsies. However, circulating microbial profiles and their potential clinical value in LC patients remained unexplored. In this study, plasma samples from 76 LC patients, 9 liver cancer patients, 11 pancreatic cancer patients, and 53 healthy controls (HCs) were collected and underwent metagenomic analyses by whole genome sequencing. The composition and relative abundance of the microbial profiles were significantly different between the LC patients and HCs. A distinct plasma-based microbial profile was observed in LC patients. By differential analysis using MaAslin, 40 significant species between LC patients and HCs were identified. Five species were selected as optimal circulating microbial biomarkers for LC. The constructed classifier based on these five species showed an AUC of 0.9592, 0.9131, and 0.8077 in the discovery, validation, and additional validation cohorts, respectively. Furthermore, metagenomic profiles of 25 lung tumor tissue and plasma paired samples were analyzed and compared. The microbial diversity was significantly increased in plasma compared with the tumor tissue. Among the 13 shared core microbial species, 10 had no difference between the tumor tissue and paired plasma. In conclusion, circulating microbial nucleic acids in the plasma have potential as biomarkers for LC liquid biopsies. The microbiome in the tumor tissue was one of the possible sources of circulating microbial nucleic acids.}, }
@article {pmid39953371, year = {2025}, author = {Vidal, SI and Menta, N and Green, L}, title = {Child and Adult Seborrheic Dermatitis: A Narrative Review of the Current Treatment Landscape.}, journal = {Dermatology and therapy}, volume = {}, number = {}, pages = {}, pmid = {39953371}, issn = {2193-8210}, abstract = {INTRODUCTION: Seborrheic dermatitis (SD) is a common, chronic inflammatory skin condition affecting sebaceous gland-rich areas of the skin. The multifactorial etiology of SD involves sebocyte activity, skin microbiome dysbiosis, and immune factors. Various treatment options exist for management of SD.<br><br>METHODS: A PubMed search conducted on November 1, 2024 using the terms "seborrheic dermatitis" and "treatment" (restricted to 2019-2024) yielded 389 results, from which relevant papers and additional references were included in this review.<br><br>DISCUSSION: Topical antifungals, topical corticosteroids, and topical calcineurin inhibitors are first-line treatments for SD; however, long-term use of each of these may be limited by varying side effects. Roflumilast foam is a newly approved topical with potential to become a first-line treatment. Myriad systemic treatments exist as second- and third-line treatments for cases of moderate-to-severe and/or recalcitrant SD. Procedural interventions of varying efficacy exist.<br><br>CONCLUSIONS: The treatment of SD requires an individualized approach, utilizing a range of topical, systemic, and procedural interventions. The advent of new treatments like roflumilast foam offers novel, well-tolerated, and safer options than what has been available in the past.}, }
@article {pmid39953156, year = {2025}, author = {Dolgin, E}, title = {The researchers on a quest to protect the gut from antibiotics.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {39953156}, issn = {1476-4687}, }
@article {pmid39953141, year = {2025}, author = {Abraham, DJ and Black, CM and Denton, CP and Distler, JHW and Domsic, R and Feghali-Bostwick, C and Gourh, P and Hinchcliff, M and Kolling, F and Kuwana, M and Lafyatis, R and Landegren, U and Mahoney, JM and Martin, J and Matucci-Cerinic, M and McMahan, ZH and Mora, AL and Mouthon, L and Rabinovitch, M and Rojas, M and Rubin, K and Trojanowska, M and Varga, J and Whitfield, ML and Gabrielli, A and Krieg, T}, title = {An international perspective on the future of systemic sclerosis research.}, journal = {Nature reviews. Rheumatology}, volume = {}, number = {}, pages = {}, pmid = {39953141}, issn = {1759-4804}, abstract = {Systemic sclerosis (SSc) remains a challenging and enigmatic systemic autoimmune disease, owing to its complex pathogenesis, clinical and molecular heterogeneity, and the lack of effective disease-modifying treatments. Despite a century of research in SSc, the interconnections among microvascular dysfunction, autoimmune phenomena and tissue fibrosis in SSc remain unclear. The absence of validated biomarkers and reliable animal models complicates diagnosis and treatment, contributing to high morbidity and mortality. Advances in the past 5 years, such as single-cell RNA sequencing, next-generation sequencing, spatial biology, transcriptomics, genomics, proteomics, metabolomics, microbiome profiling and artificial intelligence, offer new avenues for identifying the early pathogenetic events that, once treated, could change the clinical history of SSc. Collaborative global efforts to integrate these approaches are crucial to developing a comprehensive, mechanistic understanding and enabling personalized therapies. Challenges include disease classification, clinical heterogeneity and the establishment of robust biomarkers for disease activity and progression. Innovative clinical trial designs and patient-centred approaches are essential for developing effective treatments. Emerging therapies, including cell-based and fibroblast-targeting treatments, show promise. Global cooperation, standardized protocols and interdisciplinary research are vital for advancing SSc research and improving patient outcomes. The integration of advanced research techniques holds the potential for important breakthroughs in the diagnosis, treatment and care of individuals with SSc.}, }
@article {pmid39953120, year = {2025}, author = {Ammer-Herrmenau, C and Hamm, J and Neesse, A and Günther, K and Besse, M and Zilles-Wegner, D}, title = {Response to electroconvulsive therapy is associated with a more diverse oral microbiome- a prospective longitudinal cohort pilot study.}, journal = {European archives of psychiatry and clinical neuroscience}, volume = {}, number = {}, pages = {}, pmid = {39953120}, issn = {1433-8491}, abstract = {Recently it has been shown that psychiatric disorders are associated with changes in the host microbiome. Little is known about the association of electroconvulsive therapy (ECT) and microbiome alterations. In our pilot-study, 15 patients with severe or treatment resistant depression were prospectively recruited and oral swabs were collected pre- and post-ECT. Compared to a control group, ECT did not lead to a significant microbial shift in longitudinal samples (p = 0.65). However, alpha diversity measurements significantly differed between responders and non-responders before ECT (observed species p = 0.014, Shannon p = 0.03) and after ECT (observed species p = 0.015, Shannon p = 0.13).}, }
@article {pmid39953051, year = {2025}, author = {Lan, LY and Liu, TC and Gao, SM and Li, Q and Yang, L and Fei, HL and Zhong, XK and Wang, YX and Zhu, CY and Abel, C and Kappeler, PM and Huang, LN and Fan, PF}, title = {Comparative study of gut microbiota reveals the adaptive strategies of gibbons living in suboptimal habitats.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {29}, pmid = {39953051}, issn = {2055-5008}, support = {32201269//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Gastrointestinal Microbiome ; Animals ; *Hylobates ; *Ecosystem ; *Bacteria/classification/genetics/isolation &amp; purification ; Adaptation, Physiological ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Biodiversity ; }, abstract = {Wild animals face numerous challenges in less ideal habitats, including the lack of food as well as changes in diet. Understanding how the gut microbiomes of wild animals adapt to changes in food resources within suboptimal habitats is critical for their survival. Therefore, we conducted a longitudinal sampling of three gibbon species living in high-quality (Nomascus hainanus) and suboptimal (Nomascus concolor and Hoolock tianxing) habitats to address the dynamics of gut microbiome assembly over one year. The three gibbon species exhibited significantly different gut microbial diversity and composition. N. hainanus showed the lowest alpha diversity and highest nestedness, suggesting a more specialized and potentially stable microbial community in terms of composition, while H. tianxing displayed high species turnover and low nestedness, reflecting a more dynamic microbial ecosystem, which may indicate greater sensitivity to environmental changes or a flexible response to habitat variability. The gut microbial community of N. concolor was influenced by homogeneous selection in the deterministic process, primarily driven by Prevotellaceae. In contrast, the gut microbial communities of H. tianxing and N. hainanus were influenced by dispersal limitation in the stochastic process, driven by Acholeplasmataceae and Fibrobacterota, respectively. Further, the microbial response patterns to leaf feeding in N. hainanus differed from those of the other two gibbon species. In conclusion, this first cross-species comparative study provides initial insights into the different ecological adaptive strategies of gut microbiomes from a point of community assembly, which could contribute to the long-term conservation of wild primates. In this study, we conducted longitudinal sampling of three gibbon species living in high-quality (Nomascus hainanus) and suboptimal (Nomascus concolor and Hoolock tianxing) habitats to address the dynamics of gut microbiome (composition, alpha diversity, beta diversity and assembly process) over one year.}, }
@article {pmid39952886, year = {2025}, author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW}, title = {Restoring unbalanced rhizosphere: microbiome transplants combatting leaf diseases.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2025.01.011}, pmid = {39952886}, issn = {1878-4372}, abstract = {Similar to humans, plants experience microbiome imbalance, which increases their vulnerability to pathogens. In a recent study, Ketehouli et al. applied a soil microbiome transplant (SMT) to restore the microbiome balance, which potentially reduced the severity of leaf diseases. Here, we examine this approach, highlighting its limitation and offering perspectives on its use for controlling leaf diseases in plants.}, }
@article {pmid39952813, year = {2025}, author = {Gerrick, ER and Howitt, MR}, title = {The Lost Kingdom: commensal protists in the gut microbiota.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2025.01.008}, pmid = {39952813}, issn = {1878-4380}, abstract = {The gut microbiota critically influences many aspects of host biology, from nutrient acquisition to immunological function, and is integral to metazoan life. While most microbiome research has focused on bacteria, the intestinal microbiota encompasses a diverse constellation of microorganisms, including viruses, fungi, archaea, and protists. Among these microbes, commensal protists have been particularly neglected, to the point that their status as true members of the microbiota remained contentious. However, findings over the past decade revealed that commensal protists, particularly those in the Parabasalia phylum (parabasalids), perform keystone roles within the intestinal ecosystem. Emerging evidence highlights how parabasalids dramatically impact host immunity, gut microbiome ecology, and host susceptibility to both infectious and inflammatory diseases. In this review, we discuss the recent discoveries of the varied and powerful roles of commensal parabasalids in the intestinal microbiota and outline the challenges and opportunities in this burgeoning new area of the microbiome field.}, }
@article {pmid39952771, year = {2025}, author = {Cantuti Gendre, J and Le Marrec, C and Chaillou, S and Omhover-Fougy, L and Landaud, S and Dugat-Bony, E}, title = {Exploring viral diversity in fermented vegetables through viral metagenomics.}, journal = {Food microbiology}, volume = {128}, number = {}, pages = {104733}, doi = {10.1016/j.fm.2025.104733}, pmid = {39952771}, issn = {1095-9998}, mesh = {*Metagenomics ; *Vegetables/virology/microbiology ; *Fermentation ; *Bacteriophages/genetics/isolation &amp; purification/classification ; Microbiota ; Brassica/microbiology/virology ; Fermented Foods/microbiology/virology ; Bacteria/genetics/classification/isolation &amp; purification/virology ; Biodiversity ; Daucus carota/microbiology/virology ; Food Microbiology ; Viruses/isolation &amp; purification/classification/genetics ; Enterobacteriaceae/isolation &amp; purification/genetics/virology/classification ; Metagenome ; Lactobacillaceae/isolation &amp; purification/genetics/classification ; }, abstract = {Fermented vegetables are traditionally produced using the endogenous microorganisms present in raw ingredients. While the diversity of bacteria and fungi in fermented vegetables has been relatively well studied, phage communities remain largely unexplored. In this study, we collected twelve samples of fermented cabbage, carrot, and turnip after fermentation and analyzed the microbial and viral communities using shotgun and viral metagenomic approaches. Assessment of the viral diversity also benefited from epifluorescence microscopy to estimate viral load. The viral metagenomics approach targeted dsDNA, ssDNA, and RNA viruses. The microbiome of fermented vegetables was dominated by lactic acid bacteria and varied according to the type of vegetable used as raw material. The analysis of metagenome-assembled-genomes allowed the detection of 22 prophages of which 8 were present as free particles and therefore detected in the metaviromes. The viral community, estimated to range from 5.28 to 7.57 log virus-like particles per gram of fermented vegetables depending on the sample, was mainly composed of dsDNA viruses, although ssDNA and non-bacterial RNA viruses, possibly originating from the phyllosphere, were also detected. The dsDNA viral community, primarily comprising bacteriophages, varied depending on the type of vegetable used for fermentation. The bacterial hosts predicted for these phages mainly belonged to Lactobacillaceae and Enterobacteriaceae families. These results highlighted the complex microbial and viral composition of fermented vegetables, which varied depending on the three types of vegetables used as raw material. Further research is needed to deepen our understanding of the impact of these viruses on the microbial ecology of fermented vegetables and on the quality of the final products.}, }
@article {pmid39952751, year = {2025}, author = {Sequino, G and Cobo-Diaz, JF and Valentino, V and Tassou, C and Volpe, S and Torrieri, E and Nychas, GJ and Álvarez Ordóñez, A and Ercolini, D and De Filippis, F}, title = {Environmental microbiome mapping in poultry processing chain and assessment of microbial dynamics in response to different storage conditions.}, journal = {Food microbiology}, volume = {128}, number = {}, pages = {104734}, doi = {10.1016/j.fm.2025.104734}, pmid = {39952751}, issn = {1095-9998}, mesh = {Animals ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; *Chickens/microbiology ; *Food Storage ; Poultry Products/microbiology ; Food Packaging/methods ; Food Microbiology ; Poultry/microbiology ; Drug Resistance, Bacterial ; Temperature ; Meat/microbiology ; Brochothrix/genetics/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; Environmental Microbiology ; Metagenomics ; }, abstract = {Poultry production chain comprises a complex network involving various stages from rearing to the final distribution of poultry products. This study explores the intricate dynamics within this chain, using shotgun metagenomics, particularly focusing on taxonomic and functional composition of the microbiome, antibiotic resistance and virulence potential. Moreover, the study of the impact of different packaging and storage conditions provides insights into how diverse packaging strategies and storage temperature can impact the shelf-life of chicken meat. Microbiome mapping in poultry processing facility revealed the dominance of Brochothrix thermosphacta, Pseudomonas fragi and Psychrobacter immobilis on poultry-based products and industrial surfaces. Indeed, surfaces of equipment and tools have a significant impact on the microbial composition of the final food products. Furthermore, the study of the microbiome dynamics in chicken meat stored in different packaging (air, modified atmosphere, under vacuum) and temperatures (0, 4 and 10 °C) revealed temperature-dependent microbiota shifts in chicken meat, highlighting specific spoilage organisms (SSOs) in the different packaging methods. Additionally, our results showed that poultry-based products and industrial surfaces belonging to carcasses processing area hosted elevated levels of Antibiotic Resistance Genes, mainly associated with resistance to aminoglycosides, β-lactams, MLSPs (which includes macrolides, lincosamides, streptogramins and pleuromutilins) amphenicols and tetracyclines classes and several Virulence-associated genes related to adherence, biofilm, effector delivery system, motility, nutritional/metabolic factors and regulation. Finally, our findings underscored a notably mobile resistome, showing multiple AR class correlated with mobile elements. This poses a considerable risk, emphasizing the urgent need for proactive measures in addressing potential antibiotic resistance genes dissemination in the poultry chain.}, }
@article {pmid39952648, year = {2025}, author = {Siddiqui, JA and Fan, R and Liu, Y and Syed, AH and Benlin, Y and Chu, Q and Ding, Z and Ghani, MI and Liu, X and Wakil, W and Liu, DD and Chen, X and Cernava, T and Smagghe, G}, title = {The larval gut of Spodoptera frugiperda harbours culturable bacteria with metabolic versatility after insecticide exposure.}, journal = {Insect molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/imb.12983}, pmid = {39952648}, issn = {1365-2583}, support = {32360705//National Natural Science Foundation of China/ ; 31960555//National Natural Science Foundation of China/ ; GCC[2023]070//Guizhou Provincial Science and Technology Program/ ; HZJD[2022]001//Guizhou Provincial Science and Technology Program/ ; 2019-1410//Guizhou Provincial Science and Technology Program/ ; [2023]1-4//Guiyang Science and Technology Program/ ; D20023//Program for Introducing Talents to Chinese Universities/ ; }, abstract = {Spodoptera frugiperda (fall armyworm) poses a substantial risk to crops worldwide, resulting in considerable economic damage. The gut microbiota of insects plays crucial roles in digestion, nutrition, immunity, growth and, sometimes, the degradation of insecticides. The current study examines the effect of synthetic insecticides on the gut microbiome of third instar S. frugiperda larvae using both culture-dependent techniques and 16S rRNA gene sequencing for bacterial community profiling and diversity analysis. In untreated larvae, the sequencing approach revealed a diverse microbiome dominated by the phyla Firmicutes, Proteobacteria and Bacteroidota, with key genera including Bacteroides, Faecalibacterium and Pelomonas. In parallel, 323 bacterial strains were isolated and assigned to the orders Bacillales, Burkholderiales, Enterobacterales, Flavobacteriales, Lactobacillales, Micrococcales, Neisseriaies, Pseudomonadales, Sphingobacteriales and Xanthomonadales. The prevailing culturable species included Serratia marcescens, Klebsiella variicola and Enterobacter quasiroggenkampii. Treatment with sublethal concentrations of three insecticides (broflanilide, spinosad and indoxacarb) caused significant changes in gut microbiome diversity and composition. Treated larvae showed a shift towards increased Proteobacteria abundance and decreased Firmicutes. Specifically, Acinetobacter and Rhodococcus were dominant in treated samples. Functional predictions highlighted significant metabolic versatility involving nutrient processing, immune response, detoxification, xenobiotic metabolism, and stress response, suggesting microbial adaptation to insecticide exposure. Network correlation analysis highlighted disrupted microbial interactions and altered community structures under insecticide treatment. These findings enhance our understanding of how insecticides impact the gut microbiota in S. frugiperda and may inform future strategies for managing pest resistance through microbiome-based approaches.}, }
@article {pmid39952585, year = {2025}, author = {Marizzi Del Olmo, A and López-Doval, JC and Hidalgo, M and Serra, T and Colomer, J and Salvadó, V and Casas, ME and Medina, JS and Matamoros, V}, title = {Holistic Assessment of Chemical and Biological Pollutants in a Mediterranean Wastewater Effluent-Dominated Stream: Interactions and Ecological Impacts.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {125833}, doi = {10.1016/j.envpol.2025.125833}, pmid = {39952585}, issn = {1873-6424}, abstract = {The discharge of treated wastewater from wastewater treatment plants (WWTPs) into river systems is a significant source of pollution, introducing a range of chemical and biological pollutants that impact the chemical and ecological quality status of rivers. This study evaluates the effect of a secondary treated wastewater effluent on the Onyar River, in the northeast Spain. Water and biofilm samples were collected at one upstream and four downstream sampling points (up to 2.8 km from the discharge point) across four seasons. A wide array of pollutants, including metals, pharmaceuticals, microplastics (MPs), per- and polyfluoroalkyl substances (PFAS), antibiotic resistance genes (ARGs), among other emerging pollutants, were detected downstream, with significant differences between upstream and downstream concentrations. Our results show that WWTP discharge also altered biofilm microbiome composition and ARGs presence, being these changes distinguishable from seasonal variations. Nevertheless, a partial recovery further downstream (525 m) was observed for biofilm microbiome and ARGs composition. These findings highlight the value of microbiome analysis in assessing wastewater impacts on river ecosystems and emphasize the need for further research to improve pollutant attenuation and biofilm recovery strategies in river streams.}, }
@article {pmid39952533, year = {2025}, author = {Song, Y and Feng, Y and Liu, G and Duan, Y and Zhang, H}, title = {Research progress on edible mushroom polysaccharides as a novel therapeutic strategy for inflammatory bowel disease.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {140994}, doi = {10.1016/j.ijbiomac.2025.140994}, pmid = {39952533}, issn = {1879-0003}, abstract = {Inflammatory bowel disease (IBD) is a complex condition linked to the gut microbiota, host metabolism, and the immune system. Edible mushroom polysaccharides (EMPs) are gaining attention for their benefits, particularly as prebiotics that help balance gut microbial, a key factor in IBD. With their scalable production, diverse hydrophilic properties, and demonstrated anti-inflammatory effects in both laboratory and animal studies, EMPs show promise for easing IBD symptoms. By supporting a healthy gut microbiome through various mechanisms, EMPs can play an important role in preventing and managing IBD, ultimately benefiting overall health and opening new treatment avenues. This review examines how EMPs affect IBD, focusing on their role in shaping gut microbiota, restoring gut barriers, regulating immune function, and influencing pathways related to colitis. It also explores their impact on the microbiota-gut-multi organ axis and overall host health, as well as the relationship between EMPs preparation, structure, and bioactivity, along with their potential applications in food and medicine. This investigation provides valuable insights into the intricate connections between the gut, immune system, and systemic inflammation system, highlighting how EMPs are key players in this complex interaction.}, }
@article {pmid39952456, year = {2025}, author = {Shi, S and Gan, X and Qian, Y and Cao, Y and Wang, Y and Shi, C and Bi, J and Yu, Q and Han, Q and Qu, J and Li, H}, title = {Metatranscriptomics reveals that plant tannins regulate the expression of intestinal antibiotic resistance genes in Qinghai voles (Neodon fuscus).}, journal = {Environmental research}, volume = {}, number = {}, pages = {121119}, doi = {10.1016/j.envres.2025.121119}, pmid = {39952456}, issn = {1096-0953}, abstract = {Antibiotic resistance genes (ARGs) are a persistent harmful environmental pollutant, epidemic of ARGs thought to be a result of antibiotic misuse. Tannin acid (TA) is a natural plant compounds with bactericidal properties. Nowadays, TA is considered to be a potential replacement of antibiotics. However, the role of TA on ARGs is also not yet clear. To address this knowledge gap, we fed the model plateau animal Qinghai voles (Neodon fuscus) with different concentration TA. We used 16S rDNA sequencing for revealing total bacteria, 16S rRNA sequencing for revealing active bacteria, and metatranscriptomics (active function) sequencing for revealing ARGs and other functions under different TA. Our results showed that although TA reduced macrolide ARGs, TA group enriched 6-fold for tetracycline ARGs, 3-fold for multidrug ARGs, and 5-fold for aminoglycoside ARGs compared with control group. Moreover, TA reduced animal growth performance, and regulated gut microbiome more stable by improving microbial diversity. And TA promoted the production of short-chain fatty acids by gut microbes, such as lactate and acetate. This study reveals modulation of ARGs and gut microbiome by TA and also provides scientific value for the proper use of TA in feed and medical treatment.}, }
@article {pmid39952411, year = {2025}, author = {Chen, L and Wang, X and Wang, S and Liu, W and Song, Z and Liao, H}, title = {The impact of gut microbiota on the occurrence, treatment, and prognosis of ischemic stroke.}, journal = {Neurobiology of disease}, volume = {}, number = {}, pages = {106836}, doi = {10.1016/j.nbd.2025.106836}, pmid = {39952411}, issn = {1095-953X}, abstract = {Ischemic stroke (IS) is a cerebrovascular disease that predominantly affects middle-aged and elderly populations, exhibiting high mortality and disability rates. At present, the incidence of IS is increasing annually, with a notable trend towards younger affected individuals. Recent discoveries concerning the "gut-brain axis" have established a connection between the gut and the brain. Numerous studies have revealed that intestinal microbes play a crucial role in the onset, progression, and outcomes of IS. They are involved in the entire pathophysiological process of IS through mechanisms such as chronic inflammation, neural regulation, and metabolic processes. Although numerous studies have explored the relationship between IS and intestinal microbiota, comprehensive analyses of specific microbiota is relatively scarce. Therefore, this paper provides an overview of the typical changes in gut microbiota following IS and investigates the role of specific microorganisms in this context. Additionally, it presents a comprehensive analysis of post-stroke microbiological therapy and the relationship between IS and diet. The aim is to identify potential microbial targets for therapeutic intervention, as well as to highlight the benefits of microbiological therapies and the significance of dietary management. Overall, this paper seeks to provide key strategies for the treatment and management of IS, advocating for healthy diets and health programs for individuals. Meanwhile, it may offer a new perspective on the future interdisciplinary development of neurology, microbiology and nutrition.}, }
@article {pmid39952304, year = {2025}, author = {Verhey, JT and Boddu, SP and Tarabichi, S and Deckey, DG and Christopher, ZK and Spangehl, MJ and Clarke, HD and Bingham, JS}, title = {Gut-Joint Axis: History of Clostridium Difficile Infection Increases the Risk of Periprosthetic Joint Infection After Total Knee Arthroplasty.}, journal = {The Journal of arthroplasty}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.arth.2025.02.014}, pmid = {39952304}, issn = {1532-8406}, abstract = {INTRODUCTION: Increasing evidence suggests that the gut microbiome is important in immune system function and influences the risk of periprosthetic joint infection (PJI) after total knee arthroplasty (TKA). A C. difficile infection (CDI) is an indicator of poor gut microbiome health. However, no prior studies have evaluated the independent risk of CDI on the rates of PJI after TKA.<br><br>METHODS: Patients undergoing TKA from 2010 to 2021 were identified in a patient claims database (n = 1,416,362). Patients who had a history of CDI within two years prior to TKA (n = 5,170) were propensity-matched on a 1:4 basis to those who did not have a diagnosis of CDI. The exposed CDI cohort was also stratified into four groups by time of CDI before TKA (zero to three months, three to six months, six to 12 months, and one to two years). The risk of PJI within two years following TKA was compared between the exposed and control cohorts. Logistic regression was used to evaluate the association of CDI occurring in each time interval prior to TKA and PJI after TKA.<br><br>RESULTS: A CDI within two years prior to TKA was independently associated with higher odds of PJI (OR [odds ratio], 2.1; 95% CI [confidence interval], 1.91 to 2.36). In addition, we observed a stepwise increase in the risk of PJI by the timing of preoperative CDI infection, with patients who had a diagnosis of CDI within three months of their primary TKA exhibiting the highest odds of developing PJI (OR, 4.19; 95% CI, 3.51 to 5.02). Additionally, patients who had a diagnosis of CDI within two years of undergoing primary TKA were significantly more likely to experience a subsequent episode of CDI at the latest follow-up (OR, 25.9; 95% CI, 22.3 to 30.1).<br><br>CONCLUSION: A CDI prior to TKA is an independent risk factor for PJI. Closer proximity of CDI to surgery is associated with a "dose-dependent" increased PJI risk. Surgeons should consider delaying TKA until a minimum of one year after a diagnosis of CDI.}, }
@article {pmid39952142, year = {2025}, author = {Xu, Y and Huang, Y and Wei, S and Tian, J and Huang, Y and Nie, Q and Zhang, D}, title = {Changes in gut microbiota affect DNA methylation levels and development of chicken muscle tissue.}, journal = {Poultry science}, volume = {104}, number = {3}, pages = {104869}, doi = {10.1016/j.psj.2025.104869}, pmid = {39952142}, issn = {1525-3171}, abstract = {The intestinal microbiome is essential in regulating host muscle growth and development. Antibiotic treatment is commonly used to model dysbiosis of the intestinal microbiota, yet limited research addresses the relationship between gut microbes and muscle growth in yellow-feathered broilers. In this study, Xinghua chickens were administered broad-spectrum antibiotics for eight weeks to induce gut microbiome suppression. We investigated the relationships between the gut microbiome and muscle growth using 16S rRNA sequencing and transcriptomic analysis. Results indicated that antibiotic treatment significantly reduced body weight, dressed weight, eviscerated weight, and breast and leg muscle weight. Microbial diversity and richness in the duodenum, jejunum, ileum, and cecum were significantly decreased. The relative abundances of Firmicutes, Actinobacteria, and Bacteroidetes declined, while Proteobacteria increased. This microbial imbalance led to 298 differentially expressed genes (DEGs) in muscle tissue, of which 67 down-regulated genes were enriched in skeletal muscle development, including MYF6, MYBPC1 and METTL21C genes essential for muscle development. The DEGs were primarily involved in the MAPK signaling pathway, calcium signaling pathway, ECM-receptor interaction, actin cytoskeleton regulation, and nitrogen metabolism. Correlation analysis showed that dysregulation of the cecal microbiome had the most substantial effect on muscle growth and development. Furthermore, intestinal microbiome dysregulation reduced DNMT3b and METTL21C mRNA expression in muscle tissue, lowered overall DNA methylation and SAM levels, and induced methylation changes that impacted skeletal muscle development. This study demonstrates that gut microbiota influence DNA methylation in muscle tissue, thereby associated with muscle growth and development.}, }
@article {pmid39951917, year = {2025}, author = {Tull, S and Saviano, A and Fatima, A and Begum, J and Mansour, AA and Marigliano, N and Schettino, A and Blaising, J and Trenkle, P and Sandrin, V and Maione, F and Regan-Komito, D and Iqbal, AJ}, title = {Dichotomous effects of Galectin-9 in disease modulation in murine models of inflammatory bowel disease.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {184}, number = {}, pages = {117902}, doi = {10.1016/j.biopha.2025.117902}, pmid = {39951917}, issn = {1950-6007}, abstract = {Inflammatory bowel disease (IBD) is a multifaceted disease characterised by compromised integrity of the epithelial barrier, the gut microbiome, and mucosal inflammation. While leukocyte recruitment and infiltration into intestinal tissue are well-studied and targeted in clinical practice, the role of galectins in modulating mucosal immunity remains underexplored. Galectins, a family of lectin-binding proteins, mediate critical interactions between immune cells and the intestinal epithelium. This study investigated the effect of endogenous Galectin-9 (Gal-9), as well as the combined effects with Galectin-3 (Gal-3), in modulating disease progression in murine models of colitis, using global knockout (KO) models for Gal-3, Gal-9, and Gal-3/Gal-9. Global deficiency in both galectins demonstrated improved disease parameters in Dextran sodium sulfate (DSS)-driven colitis. In contrast, in a model of adoptive T cell driven colitis, the addition of recombinant Gal-9 (rGal-9) was associated with reduced intestinal inflammation and an improvement in disease parameters. Further in vitro studies revealed no change in bone marrow-derived macrophage cytokine production in the absence of endogenous Gal-9, whereas the addition of rGal-9 to human macrophages stimulated pro-inflammatory cytokine production. Collectively, these findings demonstrate that Gal-9 plays distinct, context-dependent effects in intestinal inflammation, with both pro-inflammatory and anti-inflammatory effects. The contrasting functions of endogenous and exogenous Gal-9 underscore its complex involvement in IBD pathogenesis and highlight the need to differentiate its physiological function from therapeutic applications.}, }
@article {pmid39951429, year = {2025}, author = {Lee, CY and Bonakdar, S and Arnold, KB}, title = {An in silico framework for the rational design of vaginal probiotic therapy.}, journal = {PLoS computational biology}, volume = {21}, number = {2}, pages = {e1012064}, doi = {10.1371/journal.pcbi.1012064}, pmid = {39951429}, issn = {1553-7358}, abstract = {Bacterial vaginosis (BV) is a common condition characterized by a shift in vaginal microbiome composition that is linked to negative reproductive outcomes and increased susceptibility to sexually transmitted infections. Despite the commonality of BV, standard-of-care antibiotics provide limited control of recurrent BV episodes and development of new biotherapies is limited by the lack of controlled models needed to evaluate new dosing and treatment regimens. Here, we develop an in silico framework to evaluate selection criteria for potential probiotic strains, test adjunctive therapy with antibiotics, and alternative dosing strategies. This computational framework highlighted the importance of resident microbial species on the efficacy of hypothetical probiotic strains, identifying specific interaction parameters between resident non-optimal anaerobic bacteria (nAB) and Lactobacillus spp. with candidate probiotic strains as a necessary selection criterion. Model predictions were able to replicate results from a recent phase 2b clinical trial for the live biotherapeutic product, Lactin-V, demonstrating the relevance of the in silico platform. Results from the computational model support that the probiotic strain in Lactin-V requires adjunctive antibiotic therapy to be effective, and that increasing the dosing frequency of the probiotic could have a moderate impact on BV recurrence at 12 and 24 weeks. Altogether, this framework could provide evidence for the rational selection of probiotic strains and help optimize dosing frequency or adjunctive therapies.}, }
@article {pmid39951402, year = {2025}, author = {Reiss, RA and Guerra, PA and Makhnin, O and Kellom, M}, title = {Whole metagenome sequencing and 16S rRNA gene amplicon analyses reveal the complex microbiome responsible for the success of enhanced in-situ reductive dechlorination (ERD) of a tetrachloroethene-contaminated Superfund site.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0306503}, pmid = {39951402}, issn = {1932-6203}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Biodegradation, Environmental ; *Groundwater/microbiology ; *Metagenome ; *Tetrachloroethylene/metabolism ; Water Pollutants, Chemical/metabolism ; Halogenation ; Metagenomics/methods ; Bacteria/genetics/metabolism/classification ; New Mexico ; }, abstract = {The North Railroad Avenue Plume (NRAP) Superfund site in New Mexico, USA exemplifies successful chlorinated solvent bioremediation. NRAP was the result of leakage from a dry-cleaning that operated for 37 years. The presence of tetrachloroethene biodegradation byproducts, organohalide respiring genera (OHRG), and reductive dehalogenase (rdh) genes detected in groundwater samples indicated that enhanced reductive dechlorination (ERD) was the remedy of choice. This was achieved through biostimulation by mixing emulsified vegetable oil into the contaminated aquifer. This report combines metagenomic techniques with site monitoring metadata to reveal new details of ERD. DNA extracts from groundwater samples collected prior to and at four, 23 and 39 months after remedy implementation were subjected to whole metagenome sequencing (WMS) and 16S rRNA gene amplicon (16S) analyses. The response of the indigenous NRAP microbiome to ERD protocols is consistent with results obtained from microcosms, dechlorinating consortia, and observations at other contaminated sites. WMS detects three times as many phyla and six times as many genera as 16S. Both techniques reveal abundance changes in Dehalococcoides and Dehalobacter that reflect organohalide form and availability. Methane was not detected before biostimulation but appeared afterwards, corresponding to an increase in methanogenic Archaea. Assembly of WMS reads produced scaffolds containing rdh genes from Dehalococcoides, Dehalobacter, Dehalogenimonas, Desulfocarbo, and Desulfobacula. Anaerobic and aerobic cometabolic organohalide degrading microbes that increase in abundance include methanogenic Archaea, methanotrophs, Dechloromonas, and Xanthobacter, some of which contain hydrolytic dehalogenase genes. Aerobic cometabolism may be supported by oxygen gradients existing in aquifer microenvironments or by microbes that produce O2 via microbial dismutation. The NRAP model for successful ERD is consistent with the established pathway and identifies new taxa and processes that support this syntrophic process. This project explores the potential of metagenomic tools (MGT) as the next advancement in bioremediation.}, }
@article {pmid39951399, year = {2025}, author = {Brito, J and Grosicki, GJ and Robinson, AT and Coburn, JW and Costa, PB and Holmes, KE and Lyon, G and Hakonsson, Z and Conti, F and Galpin, AJ}, title = {Hormonal Birth Control Is Associated with Altered Gut Microbiota Beta-Diversity in Physically Active Females Across the Menstrual Cycle: A Pilot Trial.}, journal = {Journal of applied physiology (Bethesda, Md. : 1985)}, volume = {}, number = {}, pages = {}, doi = {10.1152/japplphysiol.00008.2025}, pmid = {39951399}, issn = {1522-1601}, abstract = {Understanding changes to gut microbiota composition in response to hormonal birth control (HBC) may provide insight into the microbial mechanisms underlying the metabolic effects of HBC, for example, altered short-chain fatty acid (SCFA) production. Athletes' unique physiological demands may interact with these microbial mechanisms in distinct ways; however, there is limited research on HBC and gut microbiota diversity and composition across different menstrual cycle phases in physically active females. A pilot cohort of physically active females using HBC (oral contraceptives, hormone-based intrauterine devices, or arm implants) and a control group not using HBC (n=12 per group; 22±2yrs, 24±4kg/m[2] vs. 22±4yrs, 23±4kg/m[2]; Ps≥0.496) provided fecal samples alongside self-reported menstrual phase and circulating sex hormones. Alpha diversity (microbial richness and evenness) was assessed using Shannon Index while beta-diversity (microbial composition differences) was analyzed using PERMANOVA based on Bray-Curtis dissimilarity. Circulating estrogen and luteinizing hormone increased from early (days 1-5) to mid-cycle (days 12-17) in both groups (time effect Ps≤0.01), with greater changes in Control (Ps≤0.046) than HBC (Ps≥0.231). While no menstrual phase effect was observed on either diversity measure (Ps≥0.473), beta-diversity differed between Control and HBC groups (P=0.015), reflecting distinct gut microbiota profiles irrespective of menstrual phase. Seven taxa linked to SCFA production were less abundant in the HBC group (unadjusted Ps≤0.046), though significance was lost after adjusting for multiple comparisons. These findings suggest that in physically active females, hormonal contraception influences gut microbial composition, which may have downstream effects on metabolism and performance.}, }
@article {pmid39951038, year = {2025}, author = {Jacobsen, GE and Gonzalez, EE and Mendygral, P and Faust, KM and Hazime, H and Fernandez, I and Santander, AM and Quintero, MA and Jiang, C and Damas, OM and Deshpande, AR and Kerman, DH and Proksell, S and Sendszichew Shane, M and Sussman, DA and Ghaddar, B and Cickovsk, T and Abreu, MT}, title = {Deep Sequencing of Crohn's Disease Lamina Propria Phagocytes Identifies Pathobionts and Correlates With Pro-Inflammatory Gene Expression.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izae316}, pmid = {39951038}, issn = {1536-4844}, support = {R01DK099076/DK/NIDDK NIH HHS/United States ; T32AI162624//National Institute of Allergy and Infectious Diseases/ ; }, abstract = {BACKGROUND: Crohn's disease (CD) is characterized by an inflammatory response to gut microbiota. Macrophages and dendritic cells play an active role in CD inflammation. Specific microbiota have been implicated in the pathogenesis of ileal CD. We investigated the phagocyte-associated microbiome using an unbiased sequencing approach to identify potential pathobionts and elucidate the host response to these microbes.<br><br>METHODS: We collected ileal and colonic mucosal biopsies from CD patients and controls without inflammatory bowel disease (IBD), isolated lamina propria phagocytes (CD11b+ cells), and performed deep RNA sequencing (n&#x2005;=&#x2005;37). Reads were mapped to the human genome for host gene expression analysis and a prokaryotic database for microbiome taxonomic and metatranscriptomic profiling. Results were confirmed in a second IBD cohort (n&#x2005;=&#x2005;17). Lysed lamina propria cells were plated for bacterial culturing; isolated colonies underwent whole genome sequencing (n&#x2005;=&#x2005;11).<br><br>RESULTS: Crohn's disease ileal phagocytes contained higher relative abundances of Escherichia coli, Ruminococcus gnavus, and Enterocloster spp. than those from controls. CD phagocyte-associated microbes had increased expression of lipopolysaccharide (LPS) biosynthesis pathways. Phagocytes with a higher pathobiont burden showed increased expression of pro-inflammatory and antimicrobial genes, including PI3 (antimicrobial peptide) and BPIFB1 (LPS-binding molecule). E. coli isolated from the CD lamina propria had more flagellar motility and antibiotic resistance genes than control-derived strains.<br><br>CONCLUSIONS: Lamina propria resident phagocytes harbor bacterial strains that may act as pathobionts in CD. Our findings shed light on the role of pathobionts and the immune response in CD pathogenesis and suggest new targets for therapies.}, }
@article {pmid39950834, year = {2025}, author = {Ng, HY and Zhang, L and Tan, JT and Hui, RWH and Yuen, MF and Seto, WK and Leung, WK and Cheung, KS}, title = {Gut Microbiota Predicts Treatment Response to Empagliflozin Among MASLD Patients Without Diabetes Mellitus.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {45}, number = {3}, pages = {e70023}, pmid = {39950834}, issn = {1478-3231}, support = {//General Research Fund, Research Grant Council, The Government of the Hong Kong Special Administrative Region/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Glucosides/therapeutic use ; Middle Aged ; Prospective Studies ; *Benzhydryl Compounds/therapeutic use ; Non-alcoholic Fatty Liver Disease/drug therapy/microbiology ; Treatment Outcome ; Magnetic Resonance Imaging ; Feces/microbiology ; Sodium-Glucose Transporter 2 Inhibitors/therapeutic use ; Logistic Models ; }, abstract = {BACKGROUND AND AIM: We aimed to investigate whether gut microbiota could predict the treatment response to pharmacological agents among metabolic dysfunction-associated steatotic liver disease (MASLD) patients without diabetes mellitus (DM), as data are lacking.<br><br>METHODS: We prospectively followed up non-diabetic MASLD patients who used empagliflozin. Clinical, anthropometric, laboratory assessments and magnetic resonance imaging-proton density fat fraction (MRI-PDFF) were performed from baseline to week 52 (EOT). Baseline stool samples were collected, and shotgun DNA metagenomic sequencing was performed to profile microbiome. The primary outcome was treatment response to empagliflozin at EOT, defined as MRI-PDFF decline &#x2265;&#x2009;30% at EOT from baseline. Linear discriminant analysis [LDA] effect size was used to identify putative bacterial species. Multivariable logistic regression was used to derive adjusted odds ratio (aOR) of outcome with bacterial species by adjusting for clinical factors.<br><br>RESULTS: Twenty-two (48.9%) of 45 patients (median age: 56.9&#x2009;years [IQR: 51.0-63.2]; male: 23 [51.1%]) achieved treatment response at EOT. There was difference in alpha diversity (Shannon index: p&#x2009;<&#x2009;0.001; Simpson index: p&#x2009;=&#x2009;0.001) and beta diversity (p&#x2009;=&#x2009;0.048) in baseline microbiome between treatment response and non-response groups. Faecalibacterium prausnitzii (log10LDAscore&#x2009;=&#x2009;4.27), Lachnospira pectinoschiza (log10LDAscore&#x2009;=&#x2009;3.99), Anaerostipes hadrus (log10LDAscore&#x2009;=&#x2009;3.98), Roseburia faecis (log10LDAscore&#x2009;=&#x2009;3.97), Roseburia inulinivorans (log10LDAscore&#x2009;=&#x2009;3.58) and Agathobaculum butyriciproducens (log10LDAscore&#x2009;=&#x2009;2.77) were enriched in the treatment response group. L. pectinoschiza (aOR: 34.1; p&#x2009;=&#x2009;0.015), A. hadrus (aOR:35.0; p&#x2009;=&#x2009;0.032) and A. butyriciproducens (aOR:22.3; p&#x2009;=&#x2009;0.023) independently predicted treatment response but not clinical factors. These three species collectively predicted treatment response with AUROC of 0.89 (95% CI: 0.80-0.99).<br><br>CONCLUSIONS: Certain gut bacterial species, particularly the combination of A. hadrus, L. pectinoschiza and A. butyriciproducens, may predict treatment response to empagliflozin in MAFLD patients without DM.}, }
@article {pmid39950806, year = {2025}, author = {Hanft, W and Stankiewicz Karita, H and Khorsandi, N and Vohra, P and Plotzker, R}, title = {Sexually transmitted human papillomavirus and related sequelae.}, journal = {Clinical microbiology reviews}, volume = {}, number = {}, pages = {e0008523}, doi = {10.1128/cmr.00085-23}, pmid = {39950806}, issn = {1098-6618}, abstract = {SUMMARYMore than 40 types of sexually transmitted human papillomavirus (HPV) infect the oropharyngeal and anogenital mucosa-high-risk types are associated with precancerous and cancerous lesions of the cervix, vagina, vulva, penis, anus, and oropharynx, and low-risk types cause non-malignant disease, such as anogenital warts. Though most HPV infections resolve spontaneously, immunodeficiencies may result in persistent infection and increased risk of HPV-related sequelae. The mechanism by which HPV results in malignant transformation is multifaceted, involving interactions with numerous cellular pathways, the host immune system, and potentially the host microbiome. Vaccination against HPV is highly efficacious in the prevention of infection and related sequelae, and there now exist several approved formulations that protect against both high- and low-risk types. Despite the advent of vaccination, early detection and treatment of cervical and anal precancerous lesions continues to be integral to secondary prevention-molecular HPV testing, cytology, and tissue biopsy allow for triaging of patients, after which appropriate treatment with close follow-up can avert cancer development.}, }
@article {pmid39950593, year = {2025}, author = {Kiesewetter, KN and Rawstern, AH and Cline, E and Ortiz, GR and Santamaria, F and Coronado-Molina, C and Sklar, FH and Afkhami, ME}, title = {Microbes in reconstructive restoration: Divergence in constructed and natural tree island soil fungi affects tree growth.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {35}, number = {1}, pages = {e70007}, pmid = {39950593}, issn = {1939-5582}, support = {//South Florida Water Management District/ ; 1922521//Division of Environmental Biology/ ; 2030060//Division of Environmental Biology/ ; //National Science Foundation Graduate Research Fellowship Program/ ; //University of Miami Dissertation Year Fellowship/ ; //USDA NIFA Predoctoral Fellowship/ ; }, mesh = {*Soil Microbiology ; *Trees ; *Fungi/physiology ; Environmental Restoration and Remediation/methods ; Microbiota ; Conservation of Natural Resources/methods ; }, abstract = {As ecosystems face unprecedented change and habitat loss, pursuing comprehensive and resilient habitat restoration will be integral to protecting and maintaining natural areas and the services they provide. Microbiomes offer an important avenue for improving restoration efforts as they are integral to ecosystem health and functioning. Despite microbiomes' importance, unresolved knowledge gaps hinder their inclusion in restoration efforts. Here, we address two critical gaps in understanding microbial roles in restoration-fungal microbiomes' importance in "reconstructive" restoration efforts and how management and restoration decisions interactively impact fungal communities and their cascading effects on trees. We combined field surveys, microbiome sequencing, and greenhouse experiments to determine how reconstructing an iconic landscape feature-tree islands-in the highly imperiled Everglades impacts fungal microbiomes and fungal effects on native tree species compared with their natural counterparts under different proposed hydrological management regimes. Constructed islands used in this research were built from peat soil and limestone collected from deep sloughs and levees nearby the restoration sites in 2003, providing 18 years for microbiome assembly on constructed islands. We found that while fungal microbiomes from natural and constructed tree islands exhibited similar diversity and richness, they differed significantly in community composition. These compositional differences arose mainly from changes to which fungal taxa were present on the islands rather than changes in relative abundances. Surprisingly, ~50% of fungal hub taxa (putative keystone fungi) from natural islands were missing on constructed islands, suggesting that differences in community composition of constructed island could be important for microbiome stability and function. The differences in fungal composition between natural and constructed islands had important consequences for tree growth. Specifically, these compositional differences interacted with hydrological regime (treatments simulating management strategies) to affect woody growth across the four tree species in our experiment. Taken together, our results demonstrate that reconstructing a landscape feature without consideration of microbiomes can result in diverging fungal communities that are likely to interact with management decisions leading to meaningful consequences for foundational primary producers. Our results recommend cooperation between restoration practitioners and ecologists to evaluate opportunities for active management and restoration of microbiomes during future reconstructive restoration.}, }
@article {pmid39950509, year = {2025}, author = {Li, M and Wang, L and Peng, Z and Jiang, L and Yan, Y and Xia, Y and Wang, Y and Guo, L and Miao, J and Bian, Y}, title = {Causal Associations of Gut Microbiota Species With Lymphoma: A Two-Sample Mendelian Randomization Study.}, journal = {Hematological oncology}, volume = {43}, number = {2}, pages = {e70046}, doi = {10.1002/hon.70046}, pmid = {39950509}, issn = {1099-1069}, support = {82104671//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome ; Genome-Wide Association Study ; Lymphoma/epidemiology ; }, abstract = {This study aims to focus on GM at species level, exploring the causal associations with different kinds of lymphoma to provide some information on potential intervention directions in lymphoma. Data of GM taxa were extracted from the genome-wide association study conducted by the MiBioGen and Dutch Microbiome Project (DMP), and those of lymphomas were obtained from the FinnGen consortium. Inverse variance weighted (IVW) method and Bonferroni multiple correction were utilized to assess the causal associations of GM species with different kinds of lymphoma. The effect size was expressed by odds ratios (ORs) with 95% confidence intervals (CIs). Reverse causal association analysis has also been performed. Additionally, scatter plots and leave-one-out test were conducted for sensitivity analysis. After correction, the IVW estimates suggested that elevated relative abundance of species Faecalibacterium_prausnitzii had a negatively causal association with increased odds of Hodgkin's lymphoma (HL) (OR = 0.584, 95% CI: 0.516-0.662). Relative abundance of species Gordonibacter_pamelaeae, Holdemania_filiformis, Sutterella_wadsworthensis and Coprococcus_sp_ART55_1 was negatively associated with follicular lymphoma (FL) odds, whereas that of species Bifidobacterium_catenulatum and Coprococcus_comes were positively associated with FL odds (all p < 0.05). Relative abundance of species Akkermansia_muciniphila and Coprococcus_sp_ART55_1 had a negatively causal association with non-follicular lymphoma (NFL) odds, respectively, while that of Bacteroides_uniformis had a positive one (all p < 0.05). Relative abundance of species Flavonifractor_plautii was negatively linked to diffuse large B-cell lymphoma (DLBCL) risk (OR = 0.471, 95% CI: 0.344-0.645). Relative abundance of species Eggerthella_unclassified was positively associated with T/NK cell lymphoma (TNK) risk while that of Ruminococcus_lactaris was negatively associated with TNK risk (all p < 0.05). Elevated relative abundance of Parabacteroides_unclassified was associated with higher risk of non-Hodgkin's lymphoma (NHL) (OR = 1.955, 95% CI: 1.654-2.312). The relative abundance of species Holdemania_filiformis was negatively associated with mantle cell lymphoma (MCL) risk (OR = 0.637, 95% CI: 0.544-0.746). The relative abundance of species Rothia_mucilaginosa and Lachnospiraceae_bacterium_3_1_46FAA had positively causal association with marginal zone lymphoma (MZL) risk, while that of species Alistipes_senegalensis had a negative one (all p < 0.05). This study identified 16 GM species that have potential causal associations with different kinds of lymphoma, which provided some new idea for further exploration on prevention and treatment targets in lymphoma.}, }
@article {pmid39950489, year = {2025}, author = {Singh, S and Abu, Y and Antoine, D and Gomez, D and Tao, J and Truitt, B and Roy, S}, title = {Probiotic supplementation mitigates sex-dependent nociceptive changes and gut dysbiosis induced by prenatal opioid exposure.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2464942}, doi = {10.1080/19490976.2025.2464942}, pmid = {39950489}, issn = {1949-0984}, mesh = {Female ; *Gastrointestinal Microbiome/drug effects ; Animals ; Pregnancy ; Male ; *Dysbiosis/microbiology ; *Probiotics/administration &amp; dosage ; Mice ; *Analgesics, Opioid/adverse effects ; *Mice, Inbred C57BL ; *Prenatal Exposure Delayed Effects/microbiology ; *Nociception/drug effects ; Bacteria/classification/isolation &amp; purification/drug effects/genetics ; Dietary Supplements ; Sex Factors ; }, abstract = {The gut microbiome has emerged as a promising target for modulating adverse effects of opioid exposure due to its significant role in health and disease. Opioid use disorder (OUD) has become increasingly prevalent, specifically in women of reproductive age, contributing to an increased incidence of offspring exposed to opioids in utero. Recent studies have shown that prenatal opioid exposure (POE) is associated with notable changes to the maternal gut microbiome, with subsequent implications for the offspring's microbiome and other adverse outcomes. However, the role of the gut microbiome in mediating sex-based differences in pain sensitivity has not yet been investigated. In this study, both male and female C57BL/6 offspring were used to determine sex-based differences in nociception and gut microbial composition as a result of POE. Our data reveals significant sex-based differences in offspring prenatally exposed to opioids. The gut microbiome of opioid-exposed females showed an enrichment of commensal bacteria including Lactobacillus compared to opioid-exposed males. Additionally, POE females demonstrated decreased nociceptive sensitivity, while males demonstrated increased nociceptive sensitivity. RNA sequencing of the prefrontal cortex showed sex-based differences in several canonical pathways, including an increase in the opioid signaling pathway of opioid-exposed females, which was not observed in males. Microbiome modification via maternal probiotic supplementation attenuated sex-based differences throughout the early stages of life. Together, our study provides further insight on sex-based differences arising from POE and highlights the pivotal role of the gut microbiome as a modifiable target for mitigating its negative effects.}, }
@article {pmid39950378, year = {2025}, author = {Sahil, R and Pal, V and Kharat, AS and Jain, M}, title = {A Multi-Omics Meta-Analysis of Rhizosphere Microbiome Reveals Growth-Promoting Marker Bacteria at Different Stages of Legume Development.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.15429}, pmid = {39950378}, issn = {1365-3040}, support = {//This study is funded by the Department of Biotechnology, Government of India, under the National Network Project scheme./ ; }, abstract = {Plant-microbe interactions have been studied extensively in legumes, but the influence of host developmental stages on its microbiome remains poorly understood. The rhizospheric region enriched with microbial diversity presents an optimal environment to investigate this relationship. We employed a multi-omics meta-analysis approach to identify the rhizospheric bacteria co-existing with legumes at different developmental stages. The data from eight different legume species across various geographical locations, soil conditions and developmental stages (vegetative, reproductive and maturation) were included in the study. A total of 10 developmental stage-specific marker bacteria were identified and found to be positively associated with plant growth phenotypes. The functional profiling elucidated the expression of these marker bacterial genes, indicating the active presence of marker bacteria. Co-expression network analysis revealed the involvement of gene clusters in biological processes such as cobalt and nitrogen metabolism. Further, pathway enrichment analysis illustrated the role of these bacteria in plant metabolic pathways, such as biosynthesis of various plant secondary metabolites, biotin metabolism and carbon fixation in photosynthetic organisms. Our study identified a positive relationship between marker bacteria and the host plant, suggesting their crucial role in legume growth and development that could further aid in crop improvement strategies.}, }
@article {pmid39950272, year = {2025}, author = {Mohammadpour, D and Asadollahi, A and Ozma, MA and Mehramuz, B and Ganbarov, K and Kafil, HS}, title = {Application of Probiotics and Postbiotics in Neurological Disorders.}, journal = {Current pharmaceutical biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113892010336767250128072101}, pmid = {39950272}, issn = {1873-4316}, abstract = {Neurological illnesses encompass a broad spectrum of conditions that affect the brain, spine, and nerves, often impairing daily functioning. The global prevalence of these illnesses is rising, posing significant health challenges. This study investigates the beneficial effects of probiotics and postbiotics in managing various neurological disorders, providing a comprehensive analysis of their use in treating these conditions. The article explores innovative, holistic approaches to neurological care, emphasizing patient-centered therapeutic interventions. Compelling evidence suggests that probiotics and postbiotics positively impact several neurological diseases. Specifically, the findings indicate that these treatments can modulate the gut-brain axis, reduce neuroinflammation, and enhance neuronal protection. The study highlights the potential of specific bacteria and their byproducts to ameliorate neurological disorders. Despite promising results, the current data underscore the challenges in future research on the therapeutic benefits of probiotics and postbiotics for neurological illnesses and underscores the critical role of the gut-brain connection and the microbiome in maintaining neurological health. It also examines the safety and feasibility of using probiotics and postbiotics as adjunct therapies, delving into the mechanisms underlying their beneficial effects. Probiotics and postbiotics demonstrate a capacity to enhance the regenerative potential of the human brain, and recent evaluations provide additional evidence supporting their efficacy and safety. However, further rigorous clinical trials are necessary to validate these findings and establish the most effective therapeutic strategies for treating neurological disorders.}, }
@article {pmid39950103, year = {2024}, author = {Barchi, A and Dell'Anna, G and Massimino, L and Mandarino, FV and Vespa, E and Viale, E and Passaretti, S and Annese, V and Malesci, A and Danese, S and Ungaro, F}, title = {Unraveling the pathogenesis of Barrett's esophagus and esophageal adenocarcinoma: the "omics" era.}, journal = {Frontiers in oncology}, volume = {14}, number = {}, pages = {1458138}, pmid = {39950103}, issn = {2234-943X}, abstract = {Barrett's esophagus (BE) represents a pre-cancerous condition that is characterized by the metaplastic conversion of the squamous esophageal epithelium to a columnar intestinal-like phenotype. BE is the consequence of chronic reflux disease and has a potential progression burden to esophageal adenocarcinoma (EAC). The pathogenesis of BE and EAC has been extensively studied but not completely understood, and it is based on two main hypotheses: "transdifferentiation" and "transcommitment". Omics technologies, thanks to the potentiality of managing huge amounts of genetic and epigenetic data, sequencing the whole genome, have revolutionized the understanding of BE carcinogenesis, paving the way for biomarker development helpful in early diagnosis and risk progression assessment. Genomics and transcriptomics studies, implemented with the most advanced bioinformatics technologies, have brought to light many new risk loci and genomic alterations connected to BE and its progression to EAC, further exploring the complex pathogenesis of the disease. Early mutations of the TP53 gene, together with late aberrations of other oncosuppressor genes (SMAD4 or CKND2A), represent a genetic driving force behind BE. Genomic instability, nonetheless, is the central core of the disease. The implementation of transcriptomic and proteomic analysis, even at the single-cell level, has widened the horizons, complementing the genomic alterations with their transcriptional and translational bond. Increasing interest has been gathered around small circulating genetic traces (circulating-free DNA and micro-RNAs) with a potential role as blood biomarkers. Epigenetic alterations (such as hyper or hypo-methylation) play a meaningful role in esophageal carcinogenesis as well as the study of the tumor micro-environment, which has led to the development of novel immunological therapeutic options. Finally, the esophageal microbiome could be the protagonist to be investigated, deepening our understanding of the subtle association between the host microbiota and tumor development.}, }
@article {pmid39950023, year = {2025}, author = {Dai, W and Fang, Y and Subedi, S}, title = {Mixtures of logistic normal multinomial regression models for microbiome data.}, journal = {Journal of applied statistics}, volume = {52}, number = {3}, pages = {624-655}, pmid = {39950023}, issn = {0266-4763}, abstract = {In the realm of bioinformatics, we frequently encounter discrete data, particularly microbiome taxa count data obtained through 16S rRNA sequencing. These microbiome datasets are commonly characterized by their high dimensionality and the ability to provide insights solely into relative abundance, necessitating their classification as compositional data. Analyzing such data presents challenges due to their confinement within a simplex. Additionally, microbiome taxa counts are subject to influence by various biological and environmental factors like age, gender, and diet. Thus, we have developed a novel approach involving regression-based mixtures of logistic normal multinomial models for clustering microbiome data. These models effectively categorize samples into more homogeneous subpopulations, enabling the exploration of relationships between bacterial abundance and biological or environmental covariates within each identified group. To enhance the accuracy and efficiency of parameter estimation, we employ a robust framework based on variational Gaussian approximations (VGA). Our proposed method's effectiveness is demonstrated through its application to simulated and real datasets.}, }
@article {pmid39949908, year = {2025}, author = {Dămăşaru, MS and Păcurar, M and Mariş, M and Dămăşaru, E and Mariş, M and Tilinca, CM}, title = {Implications of type 1 diabetes mellitus in the etiology and clinic of dento-maxillary anomalies - questionnaire-based evaluation of the dentists' opinion.}, journal = {Medicine and pharmacy reports}, volume = {98}, number = {1}, pages = {135-143}, pmid = {39949908}, issn = {2668-0572}, abstract = {BACKGROUND AND AIMS: Type 1 diabetes is one of the most common chronic childhood diseases, which can be diagnosed at any age, with implications on the general development, but also on the craniofacial structure. It is widely speculated that diabetes occurs when inherited genetic characteristics are triggered by environmental factors. Oral pathology is complex and it includes a series of clinical entities: dental caries, periodontal disease, dento-maxillary anomalies, diseases of the oral mucosa, which implies a significant responsibility for the doctor, but also for society. This study aims to highlight the association of dento-maxillary anomalies with juvenile diabetes, starting from its increased prevalence among children and adolescents, the oral manifestations of diabetes mellitus and its influence on the oral microbiome, the increased incidence of periodontal and dental diseases, by means of a questionnaire.<br><br>METHOD: A cross-sectional study was carried out on a number of 60 dentists, between 01.01.2023 and 01.03.2024, using a questionnaire with 14 items, which was distributed by e-mail and social networks to dentists of different specialties, from various university. Before completing the questionnaire, the doctors were informed about the purpose of the study and that their answers were anonymous and did not imply any responsibility.<br><br>RESULTS: Our results indicated awareness of the association between oral health, the presence of dento-maxillary anomalies and the pathology of type 1 diabetes, among dentists of different specialties. The most frequent changes that occur in the oral cavity in the examined patients are represented by carious lesions, reported by 21 examiners (35.00%), of which 18 (39.13%) are female, aged between 25-35 years.Among the reported dentomaxillary anomalies, those of Angle class II were the most frequent - 17 examiners (28.33%), of which 12 (26.09%) are female reported the presence of these anomalies. The presence of Angle class I anomalies was reported by 13 examiners (21.67%) of which 9 (19.57%) are female, while 6 examiners (10.00%) reported the presence of Angle class III anomalies.<br><br>CONCLUSIONS: The evaluation of modern therapeutic methods through questionnaires distributed online represents a feedback of the tested activity and shows that most doctors know the correlations between diabetes and oro-dental diseases and have an obvious healthy attitude. The possible association between oral diseases and the presence of type 1 diabetes was reported by most of the dentists interviewed, however the information on the correlations between oral health and the presence of type 1 diabetes in children was not sufficiently explored by dentists. The dentist must know the clinical particularities of diabetes mellitus and its implications on the oral status, in order to be able to intervene effectively in reducing the oral and systemic complications of diabetes.}, }
@article {pmid39949904, year = {2025}, author = {Şeulean, EC and Dumitraşcu, DL}, title = {The association between exocrine pancreatic insufficiency and changes in gut microbiota: a narrative review.}, journal = {Medicine and pharmacy reports}, volume = {98}, number = {1}, pages = {5-12}, pmid = {39949904}, issn = {2668-0572}, abstract = {Due to their physical proximity, the healthy pancreas and the gut microbiome are known to interact in a variety of ways. The gut microbiota has been recognized as a potential factor in the development and progression of exocrine pancreatic insufficiency through several mechanisms. Pancreatic diseases like chronic and acute pancreatitis or pancreatic cancer are frequently accompanied by pancreatic exocrine insufficiency which affects the gut microbiota. Firstly, the gut microbes are controlled by antimicrobial pancreatic secretions, while themselves induce the secretion of substances by the pancreas through metabolite production, such as short-chain fatty acids. Secondly, dysbiosis, the alteration in the abundance and diversity of different species, has been observed in patients with pancreatic diseases. Dysbiosis influences carcinogenesis in pancreatic cancer in ways that are either procarcinogenic or anticarcinogenic and finding these connections will have clinical implications. Identifying microbial biomarkers allow for an earlier diagnosis, improved therapy and prognosis in pancreatic cancer. The gut microbiome has a role in the pathogenesis of pancreatitis by either a bacterial translocation or a host immune response mechanism. The disruption of the normal gut barrier is believed to be the primary source of bacteria in acute pancreatitis which leads to infected pancreatic necrosis. In this paper, we review the current data about the association between pancreatic diseases linked to exocrine insufficiency and gut microbiota.}, }
@article {pmid39949868, year = {2024}, author = {Barouei, J and Kable, ME and Moussavi, M and Hsieh, YH}, title = {Editorial: Host-diet-microbiome interactions in obesity prevention and treatment.}, journal = {Frontiers in nutrition}, volume = {11}, number = {}, pages = {1541977}, doi = {10.3389/fnut.2024.1541977}, pmid = {39949868}, issn = {2296-861X}, }
@article {pmid39949799, year = {2025}, author = {Wei, G and Chen, X and Zhang, G and Liang, C and Zhang, Z and Zhang, B and Chen, S and Dong, L}, title = {Assembly and network of Rhei Radix et Rhizoma surface microbiome shaped by processing methods and sampling locations.}, journal = {Chinese herbal medicines}, volume = {17}, number = {1}, pages = {189-199}, pmid = {39949799}, issn = {2589-3610}, abstract = {OBJECTIVE: Rhei Radix et Rhizoma has five types of products, namely, raw rhubarb (RR), wine rhubarb (WR), vinegar rhubarb (VR), cooked rhubarb (CR), and rhubarb charcoal (RC). However, Rhei Radix et Rhizoma is easily contaminated with fungi and mycotoxins if not harvested or processed properly. Here, we intend to analyze how microbiome assemblies and co-occurrence patterns are influenced by sampling locations and processing methods.<br><br>METHODS: High-throughput sequencing and internal transcribed spacer 2 (ITS2) were carried out to study the diversities (&#x3b1;- and &#x3b2;-diversity), composition (dominant taxa and potential biomarkers), and network complexitity of surface fungi on RR, WR, VR, CR, and RC collected from Gansu and Sichuan provinces, China.<br><br>RESULTS: The phyla Ascomycota and Basidiomycota; the genera Kazachstania, Malassezia, and Asterotremella; and the species Kazachstania exigua, Asterotremella pseudolonga, and Malassezia restricta were the dominant fungi and exhibited differences in the two provinces and the five processed products. The &#x3b1;-diversity and network complexity were strongly dependent on processing methods. Chao 1, the Shannon index, and network complexity and connectivity were highest in the CR group. The &#x3b1;-diversity and network complexity were influenced by sampling locations. Chao 1 and network complexity and connectivity were highest in the Gansu Province.<br><br>CONCLUSION: The assembly and network of the surface microbiome on Rhei Radix et Rhizoma were shaped by processing methods and sampling locations. This paper offers a comprehensive understanding of microorganisms, which can provide early warning for potential mycotoxins and ensure the safety of drugs and consumers.}, }
@article {pmid39949692, year = {2024}, author = {Suganya, G and Sahana, NS and Akalya, P and Yadav, ST and Suresh, T and Chandrakala, J}, title = {Detection of porphyromonas gingivalis in oral potentially malignant disorders and oral squamous cell carcinoma using qRT-PCR: A comparative study.}, journal = {Journal of oral and maxillofacial pathology : JOMFP}, volume = {28}, number = {4}, pages = {583-588}, pmid = {39949692}, issn = {0973-029X}, abstract = {BACKGROUND: Recent researches has shown a significant association between microorganisms and oral squamous cell carcinoma (OSCC). Porphyromonas gingivalis, the keystone pathogen in chronic periodontitis, is considered as an important potential etiologic agent of OSCC, but the underlying mechanisms by which P. gingivalis mediates OSCC progression remain poorly understood.<br><br>AIM: The aim of this study was to compare the levels of P. gingivalis in oral potentially malignant disorders, oral squamous cell carcinoma and normal oral mucosa using qRT-PCR.<br><br>METHOD AND MATERIAL: Genomic DNA was extracted and quantified, and the expression of the P. gingivalis levels was done in 16 cases of oral potentially malignant disorders, 16 cases of oral squamous cell carcinoma and 16 cases of normal oral mucosa by quantitative real-time polymerase chain reaction (RT-qPCR).<br><br>RESULTS: It was observed that there was an over expression of P. gingivalis in both oral potentially malignant disorders and oral squamous cell carcinoma with good mean cycle threshold (CT) value of 27.00 and 27.55, respectively. When comparing the levels of P. gingivalis in three groups, oral potentially malignant disorders (OPMD) and oral squamous cell carcinoma (OSCC) showed higher expression than normal mucosa and in between two groups OSCC showed higher expression than OPMD and the difference is statistically significant with P value less than 0.001.<br><br>CONCLUSION: Our findings suggest that there is an over expression of P. gingivalis in oral potentially malignant disorders and oral squamous cell carcinoma, compared to normal mucosa and highly expressed in OSCCs compared to OPMD. Increased levels of P. gingivalis in OPMDs and OSCCs may suggest the early event of tumorigenesis. Hence, it can be used as a valuable marker for early diagnosis, prognosis marker and in the identification of therapeutic targets.}, }
@article {pmid39949674, year = {2024}, author = {Mithradas, N and Sudhakar, U and Shanmugapriya, K and Jeddy, N and Ram, S}, title = {The oral-lung microbiome dysbiosis: Unravelling its role in implications for chronic obstructive pulmonary disease (COPD) pathogenesis.}, journal = {Journal of oral and maxillofacial pathology : JOMFP}, volume = {28}, number = {4}, pages = {619-625}, pmid = {39949674}, issn = {0973-029X}, abstract = {BACKGROUND: The impact of the oral flora on the composition of the microbiome in the lungs is substantial in both healthy and diseased conditions, contributing significantly to its intricacy. There is mounting evidence from microbiological research that suggests a major ecological relationship between periodontitis, Chronic Obstructive Pulmonary Disease (COPD), and oral microecosystems. An association has been established between respiratory diseases and disruptions in the symbiotic equilibrium of the oral microbiome. This study aims to explore the intricate connections between oral health and lung microflora, particularly about the pathogenesis of COPD, and to highlight the implications for future research and clinical practice.<br><br>MATERIALS AND METHODS: Subgingival Plaque samples were collected from a total of 120 participants with 30 healthy Control (H group),30 Periodontitis with no COPD (P group), 30 COPD with periodontally healthy (COPD) and 30 individuals with COPD and Periodontitis (COPD+ P). All participants underwent evaluation of periodontal measurements like Pocket Depth (PD), Clinical loss of Attachment (CAL), Gingival Index (GI), and Plaque Index (PI) Bacterial DNA was extracted and quantified using Real-time polymerase chain reaction. Using the One-dimensional Analysis of Variance (ANOVA) and post-analysis test for multiple comparisons, the mean values of all the clinical parameters were analyzed among the four participant groups. Using the Pearson Correlation coefficient, the parameters were correlated.<br><br>RESULTS: Statistical relevant relation was shown among Probing Depth (PD), Clinical Loss of Attachment (CAL), Plaque Index (PI) and Gingival Index (GI) in the COPD+P group. Increased prevalence of Pa (Pseudomonas aeroginosa) seen among P group and COPD+P. A substantial inverse relationship was seen between the absolute levels of Pa, CAL, PI, and lung function measures (Fev1, Fev1/FVC).<br><br>CONCLUSION: The importance of maintaining dental health in the prevention and treatment of respiratory disorders is highlighted by the relationships that exist between the oral microecosystem, oral hygiene, and respiratory pathologies. There is substantial potential to decrease the occurrence of respiratory illnesses by practicing good oral care and strategically managing the balance of the oral microbial flora. Therefore, future research efforts should prioritize the characterization of the precise impact of the oral microbiota on pulmonary health and use this knowledge towards developing innovative preventive and treatment measures targeted at combating respiratory infections and related diseases.}, }
@article {pmid39949626, year = {2025}, author = {Hou, J and Lv, Z and Wang, Y and Chen, D}, title = {The gut microbiota regulates diabetic retinopathy in adult rats.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1479792}, pmid = {39949626}, issn = {1664-302X}, abstract = {INTRODUCTION: Diabetic retinopathy (DR) is the most common complication of diabetes. Neuronal apoptosis, activated microglia, and microvascular changes are early features of DR. The gut microbiota is critical for the maturation and activation of microglia in the brain, and DR patients exhibit gut dysbiosis. However, the effect of the gut microbiota on retinal microglia under normal or diabetic conditions is still unclear.<br><br>METHODS: Type 2 diabetes (T2D) was established in male adult Brown Norway (BN) rats, and they were treated with gavage of broad-spectrum antibiotic (ABX) suspension. Retinal fundus fluorescein angiography was performed to observe the dynamic growth process and leakage of blood vessels. Retro-orbital injection of FITC-Dextran was performed to observe the changes in blood-retinal barriers. After treatment with ABX and diabetes lasting for more than 6 months, 16S RNA sequencing of stool samples was performed to determine changes in the gut microbiome and mass spectrometry was used to analyze metabolome changes. IBA1, IB4, and Brn3 staining were performed on adult rats' retinal wholemount or sections to observe the changes in microglia, blood vessels and the number of ganglion cells.<br><br>RESULTS: Long-term (6 months) T2D caused gut dysbiosis with increased average taxa numbers. We showed that broad-spectrum antibiotics (ABXs) gavage can reduce the average number of gut microbiota taxa and retinal microglia in adult male BN rats with or without T2D. Interestingly, adult male BN rats with T2D for more than 6 months showed a loss of retinal ganglion cells (RGCs) without significant changes in retinal microglia or retinal vascular vessels. However, ABX gavage reduced retinal microglia and alleviated RGC damage in these T2D rats.<br><br>CONCLUSION: Our data suggests that ABX gavage-induced gut dysbiosis can reduce retinal microglia in adult rats and alleviate RGC loss in long-term T2D rats. Targeting the gut microbiota may be a future therapeutic strategy for DR management.}, }
@article {pmid39949622, year = {2025}, author = {Qiu, R and Pan, C and Qin, Y and Wei, Q and Yu, Y and Zhang, Y and Xie, X and Li, J and Chen, S and Li, K and Fouad, D and Wu, Y and Zhong, Q}, title = {Polygonatum kingianum polysaccharide alleviated intestinal injuries by mediating antioxidant ability and microbiota.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1492710}, pmid = {39949622}, issn = {1664-302X}, abstract = {INTRODUCTION: Polygonatum kingianum is a well-known medicinal herb with proven bioactivities; however, little is known about the effects of its polysaccharide on intestinal injuries in animals induced by lipopolysaccharide (LPS).<br><br>METHODS: A total of 30 Institute of Cancer Research (ICR) mice were divided into control (CH), induced (MH), and treated (H) groups. Mice in group H were supplemented with 100 mg/kg Polygonatum kingianum polysaccharides, while groups C and M were treated with the same amount of normal saline by gavage for 18 days. On the 18[th] day animals in groups M and H were induced by LPS (10 mg/kg).<br><br>RESULTS: The results showed the weight of mice in group MH significantly dropped (P < 0.0001), while mice in the PK group had a higher weight (P < 0.01). Pathological analysis found that the majority of the villi in mice induced by LPS were broken and short, while PK-treated animals had longer and considerably integrated villi. The villi length in groups CH (P < 0.0001) and H (P < 0.0001) was longer than that in group M, and the value of villi length/crypt depth in group MH was smaller than that in groups CH (P < 0.0001) and H (P < 0.0001), while the crypt depth in group MH was higher than in groups CH (P < 0.0001) and H (P < 0.0001). Serum inspection showed that MAD (P < 0.05), IL-1&#x3b2; (P < 0.05), IL-6 (P < 0.05), and TNF-&#x3b1; (P < 0.01) were significantly higher in group MH, while SOD (P < 0.001), T-AOC (P < 0.01), and GSH-Px (P < 0.01) were notably higher in groups CH and H. Microbiome sequencing of mice obtained 844,477 raw and 725,469 filtered reads. There were 2,407 ASVs detected in animals, and there were 312 and 328 shared ASVs between CH and MH, and CH and H, respectively. There were 5 phyla and 20genera of remarkable bacteria found among mice groups including genera of Escherichia, Pseudomonas_E, Mailhella, Paramuribaculum, NM07-P-09, Odoribacter, Nanosyncoccus, SFM01, Onthenecus, Clostridium_Q, UBA6985, Ructibacterium, UBA946, Lachnoclostridium_B, Evtepia, CAG-269, Limivicinus, Formimonas, Dehalobacterium, Dwaynesavagella, and UBA6985. We revealed that Polygonatum kingianum polysaccharide could alleviate intestinal injuries by promoting oxidation resistance, decreasing inflammatory responses, and accommodating the intestinal microbiota of mice.<br><br>DISCUSSION: Our results suggest the possibility of developing novel therapies for intestinal diseases.}, }
@article {pmid39949573, year = {2024}, author = {Shi, X and Hua, S and Chen, Z and Cao, W and Xiao, M and Pei, W and Cao, Z and Zhang, Z and Yang, H and Shao, X and Xia, Y}, title = {Characterization of serum metabolome and respiratory microbiota in children with influenza A virus infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1478876}, pmid = {39949573}, issn = {2235-2988}, mesh = {Humans ; *Influenza, Human/blood ; *Metabolome ; *Microbiota ; Female ; Male ; Child, Preschool ; Child ; RNA, Ribosomal, 16S/genetics ; Influenza A virus ; Infant ; Influenza A Virus, H1N1 Subtype ; Influenza A Virus, H3N2 Subtype ; Serum/chemistry ; Adolescent ; Mass Spectrometry ; }, abstract = {The risk of children being infected with Influenza A virus (IAV) is high, and if not treated promptly, it can lead to serious illness. Compared with control group, IAV infection decreased the contents of platelet, white blood cell, lymphocyte, eosinophil, basophil, CD3[+] T cells, CD4[+] T cells, CD8[+] T cells, and B cells, while increasing the number of red blood cell. Additionally, IAV infection increased serum concentrations of total protein, albumin and lipase, while decreasing the contents of calcium, triglyceride, total bilirubin, direct bilirubin, indirect bilirubin and gamma-glutamyltransferase. However, the interactions between the respiratory microbiome and metabolites and their impact on IAV in children remains unclear. Ultra performance liquid chromatography quadrupole time of flight mass spectrometry (UPLC-QTOF/MS) and 16S rRNA gene sequencing were employed to analysis the respiratory microbiome and serum metabolic characteristics of 85 patients with IAV infection and age-matched 55 controls with respiratory disease who tested negative for 13 types of respiratory pathogens. The serum metabolic profile of IAV patients was significantly changed, and the purine metabolism was destroyed. Purine metabolism was also enriched in H3N2 patients compared to H1N1, with increased xanthine, deoxyguanosine, and inosine. The respiratory microbiome structure in children with IAV, including H1N1 and H3N2, was significantly different from that of the control, with significantly increased Chao index. The Mantel test revealed the correlation and consistency in the trends of Haemophilus, Ureaplasma and Inosine. This study revealed the characteristics of the respiratory microbiome and serum metabolites in pediatric patients with IAV, providing a new direction for exploring the pathogenesis of IAV in children.}, }
@article {pmid39949360, year = {2025}, author = {Lawson, R and Chen, Y and Zhang, J and Chiasson, MA and Ellis, J and Bureau, D and Moccia, RD and Huyben, D}, title = {Effects of Dietary Protein to Lipid Ratio and Insect Meal on Growth Performance, Feed Utilization, and the Gut Microbiome of Lake Whitefish (Coregonus clupeaformis).}, journal = {Aquaculture nutrition}, volume = {2025}, number = {}, pages = {5511161}, pmid = {39949360}, issn = {1365-2095}, abstract = {Wild stocks of lake whitefish (Coregonus clupeaformis) are declining in the Great Lakes, and there is a lack of information on their nutritional requirements and gut health indicators to effectively culture them in an aquaculture setting. The aim of this study was to evaluate the growth performance, nutrient utilization, and gut microbiome of lake whitefish fed varying protein:lipid ratios with and without the inclusion of insect meal from black soldier fly (BSF). In total, 450 lake whitefish (301 ± 10 g) were fed one of five diets with differing protein-to-lipid ratios (high-protein 54%, low-protein 48%, high-lipid 18%, or low-lipid 12%), and an additional commercial control rainbow trout diet (Bluewater commercial control [BCC]). High-protein diets included 5% BSF meal to explore its potential to partially replace fishmeal in the diet. After 16 weeks at 8.5°C, growth performance and nutrient digestibility were the highest for lake whitefish fed the high-protein-high-lipid (HPHL) and BCC diets, while the feed conversion ratio (FCR) was numerically lowest for the HPHL. Protein and energy retention, and lipid digestibility were highest for fish fed the HPHL and BCC diets, while the BCC diet had the highest lipid retained, concomitant with high viscerosomatic index (VSI). High lipid in fish, especially in the viscera that is removed during processing, is not desirable, thus the HPHL diet is recommended. The gut microbiome was dominated by Proteobacteria, specifically by the genera of Shewanella and Aeromonas, although feeding high-lipid diets resulted in the lowest alpha diversity, but was not significant. These results are novel for this species, and we recommend that lake whitefish diets should be formulated to have a minimum 54:18 protein-to-lipid ratio. The results from this study provide baseline information on the nutrition and gut microbiome of lake whitefish, which can be used to develop a species-specific feed rather than feeding them rainbow trout feed. However, further work on targeted breeding and genetic selection of broodstock, together with diet optimization, is needed to improve the growth performance and nutrient utilization in order to enable an effective, economical, and environmentally sustainable culture of lake whitefish.}, }
@article {pmid39949350, year = {2024}, author = {Lee, DB and Hwang, IS}, title = {Macronutrient balance determines the human gut microbiome eubiosis: insights from in vitro gastrointestinal digestion and fermentation of eight pulse species.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1512217}, pmid = {39949350}, issn = {1664-302X}, abstract = {The interactions between macronutrients, the human gut microbiome, and their metabolites (short-chain fatty acids) were comprehensively investigated via an in vitro digestion and fermentation model subjected to eight pulse species. 16S rRNA sequencing and taxonomic analysis of pulse digesta fermented for up to 24 h revealed an increase in the relative abundance of gut health-detrimental genera represented by Escherichia-Shigella in kidney bean, soybean, cowpea, chickpea, and black bean samples. In contrast, the relative abundance of health-positive genera, including Bacteroides, Eubacterium, and Akkermansia, was elevated in red bean, mung bean, and Heunguseul. At the same time, the proportion of the pathogenic Escherichia-Shigella decreased. Concurrently, these three species exhibited an increase in microbial diversity as evidenced by the calculation of α-diversity (Shannon index) and β-diversity (Bray-Curtis distance). Despite the lower nutrient contents in the three pulses, represented by carbohydrates, amino acids, and fatty acids, network analysis revealed that the nutrient contents in the pulse digesta possess complex positive or negative correlations with a variety of bacteria, as well as their metabolites. These correlations were more pronounced in red bean, mung bean, and Heunguseul than in the other pulses. It was postulated that the overall potential to nourish gut environments in these species was due to the balance of their nutritional components. The linear regression analysis demonstrated that there was a negative association between carbohydrate and amino acid contents and the increase in Shannon indices. Furthermore, the ratio of carbohydrates to fatty acids and amino acids to fatty acids displayed negative correlations with the diversity increase. The ratio of carbohydrates to amino acids showed a weak positive correlation. It is noteworthy that a diet comprising foods with a balanced nutritional profile supports the growth of beneficial gut microbes, thereby promoting microbial eubiosis. Consistent work on different ingredients is essential for precise insight into the interplay between food and the human microbiome in complex dietary patterns.}, }
@article {pmid39949286, year = {2025}, author = {Wagner, CL}, title = {Convergence of Two Fields-Breastfeeding and Lifestyle Medicine: Integrating Early Nutrition and Wellness for Lifelong Outcomes: A Tribute to Dr. Ruth Lawrence, A Pioneer in Both Fields.}, journal = {Breastfeeding medicine : the official journal of the Academy of Breastfeeding Medicine}, volume = {}, number = {}, pages = {}, doi = {10.1089/bfm.2025.0003}, pmid = {39949286}, issn = {1556-8342}, abstract = {Breastfeeding medicine and lifestyle medicine are grounded in preventive health and holistic care, emphasizing early interventions that foster long-term wellness. Dr. Ruth Lawrence, a pioneer in breastfeeding medicine, recognized breastfeeding as a cornerstone of preventive care, advocating for its profound impact on maternal and infant health. Her seminal work, Breastfeeding: A Guide for the Medical Profession, and her role in founding the journal Breastfeeding Medicine have been instrumental in shaping the field, emphasizing both the nutritional and psychosocial benefits of breastfeeding. Breastfeeding provides optimal nutrition, immune protection, and metabolic programming, reducing the risk of acute infections, chronic diseases, and maternal conditions such as postpartum depression and cancer. Similarly, lifestyle medicine focuses on modifiable factors-nutrition, physical activity, stress management, and sleep hygiene-to improve lifelong health outcomes. These fields converge in their shared emphasis, for example, on the gut microbiome, a critical determinant of immune and metabolic health. Breastfed infants have more diverse and beneficial gut microbiota, which reduce the risk of obesity and metabolic disorders, a focus paralleled by lifestyle medicine's advocacy for plant-based, fiber-rich diets. This review explores the parallels between breastfeeding and lifestyle medicine, advocating for research that moves beyond isolated nutrient analysis to examining whole dietary patterns in breastfeeding mothers. Maternal diet during lactation enhances the bioactive components of breast milk, including prebiotics, probiotics, and immune factors, amplifying its preventive effects. By integrating Dr. Lawrence's forward-thinking principles with insights from lifestyle medicine, breastfeeding medicine can advance its understanding of how maternal nutrition and modifiable lifestyle factors optimize health outcomes for both mother and infant, underscoring the transformative potential of early interventions in shaping lifelong health.}, }
@article {pmid39949270, year = {2025}, author = {Zhu, C and Zhang, Y and Pan, Y and Zhang, Z and Liu, Y and Lin, X and Cai, J and Xiong, Z and Pan, Y and Nie, H}, title = {Clinical correlation between intestinal flora profiles and the incidence of postmenopausal osteoporosis.}, journal = {Gynecological endocrinology : the official journal of the International Society of Gynecological Endocrinology}, volume = {41}, number = {1}, pages = {2465587}, doi = {10.1080/09513590.2025.2465587}, pmid = {39949270}, issn = {1473-0766}, mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; *Osteoporosis, Postmenopausal/epidemiology/microbiology ; Aged ; Incidence ; Bone Density ; Feces/microbiology ; Postmenopause ; }, abstract = {PURPOSE: This study aimed to explore the characteristics of intestinal microflora polymorphism in postmenopausal women, and to determine the pathophysiological changes of gene polymorphism of intestinal flora and bone metabolism in postmenopausal osteoporosis (PMOP) patients.<br><br>METHODS: A total of 104 postmenopausal women with PMOP or normal bone density were included. Lifestyle, hip T-score, bone metabolism indexes (25(OH)D, PTH, &#x3b2;-CTX, PINP), intestinal mucous membrane barrier function (diamine oxidase, D-lactic acid, LPS), gene polymorphisms, and characteristics of gut microbiota were examined.<br><br>RESULTS: Women with PMOP had reduced physical activity, less dietary protein and calcium intake, lower levels of 25(OH)D, hip T-score, and BMD, but PMOP group had increased total energy and fat intake, and higher levels of PTH, &#x3b2;-CTX, diamine oxidase, D-lactic acid, and LPS (p&#x2009;<&#x2009;.05 for all), as compared with normal subjects. Analyses of the &#x3b1;- and &#x3b2;-diversity of fecal microbiota indicated remarkably differences in postmenopausal women with or without PMOP. In details, individuals with PMOP had increased abundances of some genera (e.g. Roseburia and Bacteroides), but decreased abundances of some genera (e.g. Streptococcus and Dorea). Furthermore, use of a random forest model based on differential abundant taxa and ROC analysis could efficiently identify women with PMOP in the present cohort (AUC = 0.93).<br><br>CONCLUSION: The incidence of PMOP was closely associated with fecal microbial compositions and intestinal functional changes. The present findings supported potential applications of gut microbiome analysis for early diagnosis of PMOP, and provided potential therapeutic targets.}, }
@article {pmid39949247, year = {2025}, author = {Gilbert-Eckman, AR and Gao, M and Blaustein, RA and Tikekar, RV}, title = {Cold atmospheric plasma treatment induces oxidative stress and alters microbial community profile in the leaves of sweet basil (Ocimum basilicum var. Kiera) plant.}, journal = {Journal of food science}, volume = {90}, number = {2}, pages = {e70066}, doi = {10.1111/1750-3841.70066}, pmid = {39949247}, issn = {1750-3841}, support = {//University of Maryland/ ; }, mesh = {*Ocimum basilicum/chemistry ; *Plant Leaves ; *Oxidative Stress/drug effects ; *Reactive Oxygen Species/metabolism ; *Microbiota/drug effects ; *Plasma Gases/pharmacology ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/drug effects ; }, abstract = {The oxidative species generated by cold atmospheric plasma (CAP) treatment can impact the plant stress response system. We hypothesized that this response is not limited to the site of CAP application and it is transmitted through the plant. The resulting stress response can influence the plant microbiome on the intact plant. These hypotheses were tested by the application of CAP to live sweet basil (Ocimum basilicum var. Kiera). A single upper leaf of the plant underwent a 60 s CAP treatment at three different wattage intensity levels. Reactive oxygen species (ROS) generation in directly treated leaves and leaves in the vicinity of the treatment site (i.e., one, two, or three nodes away) was measured using the fluorescein degradation assay (ex/em: 485/525). Leaves directly exposed to CAP showed a marked increase in ROS production. Interestingly, basil leaves not directly treated by CAP also showed a significant (p < 0.05) increase in ROS generation compared to untreated control, extending to the two nearest nodes from the treatment site in all plants tested. The leaf microbiomes were evaluated using 16S rRNA gene sequencing. CAP appeared to drive restructuring of the leaf microbiota profiles, despite maintaining a similar α-diversity. CAP treatment intensity led to significant differences (p < 0.05) in the relative abundances of a variety of dominant bacterial families (e.g., Psuedomonadaceae and Streptomycetaceae) and phyla, and the effects on certain taxa were dependent on leaf distance from the treatment site. CAP's ability to restructure plant microbiota may have applications to improve produce microbial safety and shelf-life. PRACTICAL APPLICATION: Cold atmospheric plasma induces a stress response in a living plant beyond the site of application. This response includes an increase in the production of reactive oxygen species that can trigger pathways to enhance the production of phytochemicals. CAP treatment also alters the microbial community profile, possibly through plant stress response. Results from this study can be useful in developing CAP treatment of intact plant for improved growth, production of health-benefiting phytochemicals, and managing its microbiota.}, }
@article {pmid39949184, year = {2025}, author = {Kabir, F and Yung, DBY and da Cruz Nizer, WS and Allison, KN and Zigic, S and Russell, E and DeZeeuw, KG and Marek, JE and Cassol, E and Pletzer, D and Overhage, J}, title = {Pressure injuries and biofilms: Microbiome, model systems and therapies.}, journal = {Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society}, volume = {33}, number = {1}, pages = {e70005}, doi = {10.1111/wrr.70005}, pmid = {39949184}, issn = {1524-475X}, support = {//Bruy&#xe8;re Academic Medical Organization (BAMO) Innovation Grant/ ; //Carleton University International Research Seed Grant/ ; //Carleton University Research Development Grant/ ; }, mesh = {*Biofilms ; Humans ; *Pressure Ulcer/microbiology/therapy ; *Microbiota/physiology ; *Wound Healing/physiology ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Wound Infection/microbiology/therapy ; }, abstract = {Chronic wounds have emerged as significant clinical problems owing to their increasing incidence and greater recognition of associated morbidity and socio-economic burden. They are defined as wounds that do not progress normally through the stages of healing in a timely and/or orderly manner. Pressure injuries, in particular, represent a serious problem for patients who are elderly or have limited mobility, such as wheelchair users or those who spend most of the day in bed. These injuries often result from prolonged pressure exerted on the skin over the bone. Treatment of pressure injuries is complex and costly. Emerging evidence suggests that the pressure injury microbiome plays a vital role in chronic wound formation and delaying wound healing. Additionally, antibiotics often fail due to the formation of resistant biofilms and the emergence of antimicrobial-resistant bacteria. In this review, we will summarise the current knowledge on: (a) biofilms and microbiomes in pressure injuries; (b) in vitro and in vivo model systems to study pressure injuries, and (c) current therapies and novel treatment approaches. Understanding the complex interactions between microbes and the host immune system in pressure injuries will provide valuable insights to improve patient outcomes.}, }
@article {pmid39949153, year = {2025}, author = {An, S and Kong, J and Ghorbani, A and Dehghani, A and Alizadeh, S}, title = {Effect of Pro-, Pre- and Synbiotic Supplementation on the Growth of Infants and Children: An Umbrella Systematic Review and Meta-Analysis.}, journal = {Journal of paediatrics and child health}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpc.16789}, pmid = {39949153}, issn = {1440-1754}, abstract = {BACKGROUND: In recent years, pro-, pre- and synbiotics have been suggested to positively influence the growth outcomes of infants and children. However, the findings have been inconsistent. This umbrella meta-analysis was conducted to evaluate this effect.<br><br>METHODS: The PubMed, Web of Science and Scopus databases were systematically searched until June 2024 to identify relevant studies. Weight gain, length gain, head circumstance (HC) gain, body mass index (BMI) as well as weight-for-height (WHZ), height-for-age (HAZ), weight-for-age (WAZ) and BMI-for-age (BMIAZ) Z-scores were considered as the outcomes. Standardised mean differences (SMD) along with the 95% confidence interval (CI) were utilised to estimate the overall effect size. Subgroup analyses were conducted to identify the sources of heterogeneity among the studies.<br><br>RESULTS: We included 26 meta-analyses, which encompassed a total of 72&#x2009;285 participants. The pooled umbrella analysis revealed positive effects of pro-, pre- and synbiotics on weight gain (SMD&#x2009;=&#x2009;0.17, 95% CI: 0.09-0.25) and height gain (SMD&#x2009;=&#x2009;0.10, 95% CI: 0.01-0.19) in both healthy individuals and preterm infants, although significant heterogeneity was observed across the studies (p&#x2009;<&#x2009;0.001). Furthermore, the subgroup analyses indicated very weak evidence for an increase in BMI and WAZ following microbiome-based interventions.<br><br>CONCLUSION: Supplementation with pro-, pre- and synbiotics has the potential to enhance weight and height gain in infants and children. Additional large-scale studies are needed to confirm their clinical applications.}, }
@article {pmid39949145, year = {2025}, author = {Prout, AJ and Meert, KL and Al-Ahmadi, M and Dickson, RP}, title = {Alterations in the intestinal microbiome and immune dysregulation in infants with CHD undergoing cardiopulmonary bypass: a scoping review.}, journal = {Cardiology in the young}, volume = {}, number = {}, pages = {1-6}, doi = {10.1017/S1047951125000332}, pmid = {39949145}, issn = {1467-1107}, abstract = {BACKGROUND: Infants who require cardiopulmonary bypass for surgical repair of CHD are at high risk for secondary infections, which cause significant death and disability. The risk of secondary infection is increased by immune dysfunction. The intestinal microbiome calibrates immune function. Infants with CHD have substantial changes in their intestinal microbiome. We performed this scoping review to describe the current understanding of the relationship between the intestinal microbiome and immune function after pediatric cardiac surgery with cardiopulmonary bypass.<br><br>METHODS: We searched the PubMed, Cumulative Index to Nursing and Allied Health Literature, Cochrane, and Scopus databases with the assistance of a medical librarian. We included trials that analysed intestinal microbiome composition and immune function after cardiac surgery with cardiopulmonary bypass in infants.<br><br>RESULTS: We found two observational cohorts and two interventional trials describing composition of intestinal microbiome and some measures of immune function after heart surgery with cardiopulmonary bypass in infants. A total of 114 children were analysed. Three trials were exclusively in infants, and one was in older children and infants. All trials found a differential composition of the intestinal microbiome in infants with CHD compared to those without CHD, and one described a robust correlation between composition of the intestinal microbiome with cytokine profile and adverse outcomes.<br><br>CONCLUSIONS: Despite robust preclinical data and data from other disease states, there is minimal data about the correlation between immune function and intestinal microbiome composition in infants with CHD after cardiopulmonary bypass.}, }
@article {pmid39949097, year = {2025}, author = {Bhandari, V}, title = {Twins and Necrotizing Enterocolitis: Genetic Relevance.}, journal = {Current pediatric reviews}, volume = {}, number = {}, pages = {}, doi = {10.2174/0115733963369969250212072155}, pmid = {39949097}, issn = {1875-6336}, abstract = {In preterm infants, necrotizing enterocolitis (NEC) is one of the most devastating complications seen in the neonatal intensive care unit (NICU), with both short- and long-term sequelae. Outcomes reported for mono- (versus di-) chorionic twins suggest an increased incidence in the monochorionic twins, usually attributed to abnormal placental vascular connections. Same sex concordance and zygosity data suggest shared genetic and environmental factors as important contributing factors to the pathogenesis of NEC. This concept is further supported by fecal microbiome data from preterm twins. However, there is also some uncertainty in these observations because studies that controlled for gestational age did not show significant differences between singletons and twins in the occurrence of NEC. This mini-review was undertaken as a critical appraisal of the published literature in terms of twin studies to establish the genetic relevance vis-àvis NEC. There is a need for further evaluation of genetic and confounding factors arising from the environment and the gut microbiome in these infants using cohorts with larger sample sizes.}, }
@article {pmid39949039, year = {2025}, author = {Maldarelli, GA and Metz, M and Oguntunmibi, S and Tran, N and Xiang, G and Lukin, D and Scherl, EJ and Longman, RS}, title = {IgG-seq identifies immune-reactive enteric bacteria in Crohn's disease with spondyloarthritis.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2464221}, doi = {10.1080/19490976.2025.2464221}, pmid = {39949039}, issn = {1949-0984}, mesh = {Humans ; *Crohn Disease/microbiology/immunology ; *Gastrointestinal Microbiome ; *Spondylarthritis/microbiology/immunology ; Female ; Male ; Adult ; *Immunoglobulin G/blood ; *Feces/microbiology ; Middle Aged ; Bacteria/classification/genetics/isolation &amp; purification/immunology ; Clostridiales/isolation &amp; purification/genetics ; Young Adult ; Case-Control Studies ; }, abstract = {Joint inflammation is the most common extraintestinal manifestation of Crohn's disease (CD). Although alterations in the enteric microbiota are described in CD with spondyloarthritis (CD-SpA), it is not known whether distinct taxa serve as markers for clinical subtypes of axial (AxSpA) or peripheral SpA (pSpA) in CD. Moreover, it is not yet known whether these taxa generate a specific systemic IgG response. Here, we sequenced the fecal microbiome from 106 individuals (44 CD, 39 CD-SpA, 14 CD-AxSpA, and 9 healthy controls [HC]). This unique cohort revealed distinct taxonomic compositions of CD and CD-SpA compared to HC and demonstrates that the composition of the CD-AxSpA microbiome is distinct from that of CD-pSpA. Using autologous serum, we identified enteric bacteria recognized by serum IgG and demonstrate differences in the IgG coating index of specific bacterial genera associated with CD-SpA. The IgG coating index of Mediterraneibacter gnavus differentiated patients with CD-pSpA and is positively associated with joint disease activity. This work illustrates divergent microbiome compositions in CD-SpA subtypes, as well as the recognition of distinct enteric bacteria by serum IgG with the potential to serve as a marker of joint inflammation in CD.}, }
@article {pmid39948823, year = {2025}, author = {Abid, H and Maheshwari, P and Abid, A}, title = {The Crucial Role of Gut Microbiome in Cardiovascular Health.}, journal = {JPMA. The Journal of the Pakistan Medical Association}, volume = {75}, number = {2}, pages = {373}, doi = {10.47391/JPMA.21392}, pmid = {39948823}, issn = {0030-9982}, }
@article {pmid39948759, year = {2025}, author = {Abdolmaleky, HM and Nohesara, S and Zhou, JR and Thiagalingam, S}, title = {Epigenetics in evolution and adaptation to environmental challenges: pathways for disease prevention and treatment.}, journal = {Epigenomics}, volume = {}, number = {}, pages = {1-17}, doi = {10.1080/17501911.2025.2464529}, pmid = {39948759}, issn = {1750-192X}, abstract = {Adaptation to challenging environmental conditions is crucial for the survival/fitness of all organisms. Alongside genetic mutations that provide adaptive potential during environmental challenges, epigenetic modifications offer dynamic, reversible, and rapid mechanisms for regulating gene expression in response to environmental changes in both evolution and daily life, without altering DNA sequences or relying on accidental favorable mutations. The widespread conservation of diverse epigenetic mechanisms - like DNA methylation, histone modifications, and RNA interference across diverse species, including plants - underscores their significance in evolutionary biology. Remarkably, environmentally induced epigenetic alterations are passed to daughter cells and inherited transgenerationally through germline cells, shaping offspring phenotypes while preserving adaptive epigenetic memory. Throughout anthropoid evolution, epigenetic modifications have played crucial roles in: i) suppressing transposable elements and viral genomes intruding into the host genome; ii) inactivating one of the X chromosomes in female cells to balance gene dosage; iii) genetic imprinting to ensure expression from one parental allele; iv) regulating functional alleles to compensate for dysfunctional ones; and v) modulating the epigenome and transcriptome in response to influence from the gut microbiome among other functions. Understanding the interplay between environmental factors and epigenetic processes may provide valuable insights into developmental plasticity, evolutionary dynamics, and disease susceptibility.}, }
@article {pmid39948579, year = {2025}, author = {Guo, J and Wang, C and Li, H and Ding, C}, title = {Exploring the causal associations of the gut microbiota and plasma metabolites with ovarian cancer: an approach of mendelian randomization analysis combined with network pharmacology and molecular docking.}, journal = {Journal of ovarian research}, volume = {18}, number = {1}, pages = {27}, pmid = {39948579}, issn = {1757-2215}, support = {82174135//National Natural Science Foundation of China/ ; YC-2023-0610//Specialized Discipline of Chinese Medicine and Liver Disease in Summit Plateau, Pudong New Area/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; *Mendelian Randomization Analysis ; *Molecular Docking Simulation ; *Ovarian Neoplasms/blood/microbiology/genetics ; *Genome-Wide Association Study ; Network Pharmacology ; Risk Factors ; Carcinoma, Ovarian Epithelial/blood/microbiology/genetics ; Metabolome ; }, abstract = {BACKGROUND: While increasing evidence suggests that alterations in the gut microbiota and metabolites are associated with ovarian cancer (OC) risk, whether these associations imply causation remains to be identified.<br><br>METHODS: We conducted a two-sample Mendelian randomization (MR) study utilizing a large-scale genome-wide association study (GWAS) to explore the causal effects of the gut microbiota of 196/220 individuals and 1,400 plasma metabolites on OC and epithelial ovarian cancer (EOC) subtypes. Data on the gut microbiota were obtained from the MiBioGen consortium of 18,340 subjects and the Dutch Microbiome Project of 7,738 volunteers. Data on plasma metabolites were derived from a GWAS of plasma metabolites in 8,299 participants. Ovarian cancer (n&#x2009;=&#x2009;25,509) and EOC subtypes were obtained from the Ovarian Cancer Association Consortium (OCAC). Metabolites and associated targets were analyzed via network pharmacology and molecular docking.<br><br>RESULTS: At the genus and species levels, we identified seven risk factors for the gut microbiota: the genus Dialister (P&#x2009;=&#x2009;0.024), genus Ruminiclostridium5 (P&#x2009;=&#x2009;0.0004), genus Phascolarctobacterium (P&#x2009;=&#x2009;0.0217), species Bacteroides massiliensis (P&#x2009;=&#x2009;0.011), species Phascolarctobacterium succinatutens (P&#x2009;=&#x2009;0.0212), species Paraprevotella clara (P&#x2009;=&#x2009;0.0247) and species Bacteroides dorei (P&#x2009;=&#x2009;0.0054). In addition, five gut microbes at the genus and species levels were found to be protective: genus Family XIII AD3011 group (P&#x2009;=&#x2009;0.006), genus Butyrivibrio (P&#x2009;=&#x2009;0.0095), genus Oscillibacter (P&#x2009;=&#x2009;0.0206), species Roseburia hominis (P&#x2009;=&#x2009;0.0241), and species Bifidobacterium bifidum (P&#x2009;=&#x2009;0.0224). For plasma metabolites, we revealed five positive and four negative correlations with OC. Among these, caffeic acid and caffeine metabolites and sphingomyelin and ceramide metabolites were identified as risk factors, whereas phenylalanine metabolites, butyric acid metabolites, and some lipid metabolites were recognized as protective factors. A series of sensitivity analyses revealed no abnormalities, including pleiotropy and heterogeneity analyses.<br><br>CONCLUSION: Our MR analysis demonstrated that the gut microbiota and metabolites are causally associated with OC, which has significant potential for the early detection and diagnosis of OC and EOC subtypes, providing valuable insights into this area of research.}, }
@article {pmid39948576, year = {2025}, author = {Ma, L and Shi, M and Zhang, X and Liu, Y and Jin, H and Li, D and Zhang, H and Feng, L and Zuo, J and Wang, Y and Liu, J and Han, J}, title = {Circulating microbiome DNA features and its effect on predicting clinicopathological characteristics of patients with colorectal cancer.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {178}, pmid = {39948576}, issn = {1479-5876}, support = {GZ20250078//the Medical Science Research Project of Hebei: Medical Applicable Technology Tracking Project/ ; }, mesh = {Humans ; Female ; Male ; Middle Aged ; *Colorectal Neoplasms/microbiology/blood/pathology ; *Microbiota ; Case-Control Studies ; Aged ; Prognosis ; Adult ; DNA, Bacterial/blood/genetics ; Neoplasm Metastasis ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) presents a complex tumor microenvironment influenced by genetic and microbial factors. Microbial DNA from the gut and tumor microenvironment can translocate into the bloodstream, forming a circulating microbiome associated with prognosis and clinicopathological features. This study investigates the peripheral venous blood microbiome in CRC patients using 2bRAD-M sequencing and evaluates its clinical significance.<br><br>METHODS: Peripheral venous blood samples from 29 CRC patients (19 males, 10 females; mean age 57 years) and 10 healthy controls were analyzed to assess microbial diversity. Additionally, 20 tumor tissue samples from CRC patients were examined via RT-qPCR to validate blood-tumor microbial correlations. Statistical analyses evaluated associations between microbial abundance and clinical features, including metastasis and PD-L1 Combined Positive Score (CPS). Comparative analyses between CRC patients and healthy controls were performed to identify disease-specific microbial signatures.<br><br>RESULTS: A total of 270 microbial species were identified, with dominant phyla including Actinomycetota, Bacillota, Bacteroidota, and Pseudomonadota. Bosea lupini was significantly associated with metastasis stage (p&#x2009;=&#x2009;0.034), while Mycobacterium tuberculosis (p&#x2009;=&#x2009;0.022), Porphyromonas pasteri (p&#x2009;=&#x2009;0.017), and Bosea lupini (p&#x2009;=&#x2009;0.045) correlated with CPS. Microbes such as Bosea lupini, Ralstonia mannitolilytica, and Porphyromonas pasteri suggested potential tumor-derived translocation into the bloodstream.<br><br>CONCLUSION: This study identifies a distinct peripheral venous blood microbiome in CRC patients, highlighting specific microbes associated with clinicopathological features and disease progression. These findings suggest the potential of blood microbiomes as noninvasive biomarkers for CRC prognosis and therapeutic targets, warranting further investigation in larger cohorts.}, }
@article {pmid39948426, year = {2025}, author = {Zang, T and Zhang, Z and Liu, W and Yin, L and Zhao, S and Liu, B and Ma, L and Li, Z and Tang, X}, title = {Structural and functional changes in the oral microbiome of patients with craniofacial microsomia.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {5400}, pmid = {39948426}, issn = {2045-2322}, support = {2021-I2M-1-068//Chinese Academy of Medical Science Innovation Fund for Medical Sciences/ ; }, mesh = {Humans ; Male ; *Microbiota ; Female ; *Mouth/microbiology ; *Saliva/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; Child ; Goldenhar Syndrome/microbiology ; Dysbiosis/microbiology ; Adolescent ; Adult ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Young Adult ; Metagenomics/methods ; Child, Preschool ; Case-Control Studies ; }, abstract = {Craniofacial microsomia (CFM) is the second most common congenital craniofacial deformity, presenting diverse clinical manifestations and treatments that may influence oral bacteria dysbiosis (OBD). However, research linking CFM to OBD is limited. Saliva samples were collected from 20 patients with CFM and 24 controls. We compared oral microflora and gene function using 16 S ribosomal RNA sequencing and metagenomics. We also evaluated the correlation between CFM clinical phenotypes and microbiota community structure. Patients with CFM demonstrated greater richness and evenness in their oral microflora. The dominant genera included several pathogenic species, such as Actinomyces, Fusobacterium, and Prevotella. Notably, the severity of CFM correlated positively with the abundance of Neisseria and Porphyromonas. Upregulated pathways were primarily linked to biotin and amino acid metabolism, such as Tryptophan metabolism and Lysine degradation, and further underscored the need for focused oral health interventions in this population. This study is the first to indicate that CFM patients exhibit unique oral bacterial dysbiosis, marked by a higher presence of opportunistic pathogens and increased pathways related to oral and systemic health. These findings highlight the importance of monitoring oral health in patients with CFM.}, }
@article {pmid39948421, year = {2025}, author = {Richter, KM and Wrage, M and Krekeler, C and De Oliveira, T and Conradi, LC and Menck, K and Bleckmann, A}, title = {Model systems to study tumor-microbiome interactions in early-onset colorectal cancer.}, journal = {EMBO molecular medicine}, volume = {}, number = {}, pages = {}, pmid = {39948421}, issn = {1757-4684}, support = {01KD2101F//Bundesministerium f&#xfc;r Bildung und Forschung (BMBF)/ ; 493624047//Deutsche Forschungsgemeinschaft (DFG)/ ; }, abstract = {Colorectal cancer (CRC) is a major health problem, with an alarming increase of early-onset CRC (EO-CRC) cases among individuals under 50 years of age. This trend shows the urgent need for understanding the underlying mechanisms leading to EO-CRC development and progression. There is significant evidence that the gut microbiome acts as a key player in CRC by triggering molecular changes in the colon epithelium, leading to tumorigenesis. However, a comprehensive collection and comparison of methods to study such tumor-microbiome interactions in the context of EO-CRC is sparse. This review provides an overview of the available in vivo, ex vivo as well as in vitro approaches to model EO-CRC and assess the effect of gut microbes on tumor development and growth. By comparing the advantages and limitations of each model system, it highlights that, while no single model is perfect, each is suitable for studying specific aspects of microbiome-induced tumorigenesis. Taken together, multifaceted approaches can simulate the human body's complexity, aiding in the development of effective treatment and prevention strategies for EO-CRC.}, }
@article {pmid39948085, year = {2025}, author = {Du, Y and Zhang, L and Yang, Y and Cheng, K and Li, K and Zhou, Y and Li, L and Jin, Y and He, X}, title = {Assembly, network and functional compensation of specialists and generalists in poplar rhizosphere under salt stress.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {28}, pmid = {39948085}, issn = {2055-5008}, mesh = {*Populus/microbiology ; *Rhizosphere ; *Soil Microbiology ; *Salt Stress ; *Microbiota ; Bacteria/classification/genetics ; Plant Roots/microbiology ; Salinity ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Salinity is a major challenge for plant growth, but Populus euphratica, a species native to desert regions, has a remarkable ability to tolerate salt stress. This study aimed to explore how salinity affects the rhizosphere microbiome of P. euphratica, focusing on diversity patterns, assembly mechanisms, network characterization, and the functional roles of specialists and generalists under salt stress conditions. The findings revealed that increased salinity enhances the complexity of the rhizosphere microbial network and the diversity of bacterial specialists. Specialists demonstrated a wider range of environmental adaptation and played a pivotal role in species interactions within the microbial network. Notably, salinity stress altered the structure and assembly of plant rhizosphere specialists, facilitating functional compensation and potentially augmenting the health of P. euphratica. This research offers critical insights into the microbiome dynamics of P. euphratica under salinity stress, advancing the understanding of specialists and generalists in the rhizosphere.}, }
@article {pmid39948046, year = {2025}, author = {Syal, A and Martell, M and Sikdar, R and Dietz, M and Ziegert, Z and Jahansouz, C and Elias, MH and Staley, C}, title = {Quorum quenching enzymes disrupt bacterial communication in a sex- and dose-dependent manner.}, journal = {Animal models and experimental medicine}, volume = {}, number = {}, pages = {}, doi = {10.1002/ame2.12520}, pmid = {39948046}, issn = {2576-2095}, support = {//Biotechnology Institute and the MnDrive initiative (to MHE)/ ; }, abstract = {BACKGROUND: Over the past 50 years, the incidence of obesity has gradually increased, necessitating investigation into the multifactorial contributors to this disease, including the gut microbiota. Bacteria within the human gut microbiome communicate using a density-dependent process known as quorum sensing (QS), in which autoinducer (AI) molecules (e.g., N-acyl-homoserine lactones [AHLs]) are produced to enable bacterial interactions and regulate gene expression.<br><br>METHODS: We aimed to disrupt QS using quorum quenching (QQ) lactonases GcL and SsoPox, which cleave AHL signaling molecules in a taxa-specific manner based on differing enzyme affinities for different substrates. We hypothesized that QQ hinders signals from obesity-associated pathobionts, thereby slowing or preventing obesity.<br><br>RESULTS: In a murine model of diet-induced obesity, we observed GcL and SsoPox treatments have separate sex-dependent and dose-dependent effects on intestinal community composition and diversity. Notably, male mice given 2&#x2009;mg/mL SsoPox exhibited significant changes in the relative abundances of gram-negative taxa, including Porphyromonadaceae, Akkermansiaceae, Muribaculaceae, and Bacteroidales (Kruskal-Wallis p&#x2009;<&#x2009;0.001). Additionally, we used covariance matrix network analysis to model bacterial taxa co-occurrence due to QQ enzyme administration. There were more associations among taxa in control mice, particularly among gram-negative bacteria, whereas mice receiving SsoPox had the fewest associations.<br><br>CONCLUSIONS: Overall, our study establishes proof of concept that QQ is a targetable strategy for microbial control in&#xa0;vivo. Further characterization and dosage optimization of QQ enzymes are necessary to harness their therapeutic capability for the treatment of chronic microbial-associated diseases.}, }
@article {pmid39948020, year = {2025}, author = {Oscullo, G and Bekki, A and Martinez-Garcia, MA}, title = {Microbiome, Metabolome and Complexity in Bronchiectasis: The Future is Here.}, journal = {Archivos de bronconeumologia}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.arbres.2025.01.009}, pmid = {39948020}, issn = {1579-2129}, }
@article {pmid39947675, year = {2025}, author = {Wei, X and Feng, X}, title = {DS0384 Alleviates Necrotizing Enterocolitis: Secretes N-carbamyl glutamic Acid and Participates in Lipid Metabolism and Lipid Peroxidation Processes.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2410040}, doi = {10.4014/jmb.2410.10040}, pmid = {39947675}, issn = {1738-8872}, mesh = {Animals ; Mice ; *Enterocolitis, Necrotizing/metabolism/microbiology/drug therapy/pathology ; *Lipid Peroxidation/drug effects ; Rats ; *Lipid Metabolism/drug effects ; *Toll-Like Receptor 4/metabolism/genetics ; *Disease Models, Animal ; *Limosilactobacillus reuteri/metabolism ; Gastrointestinal Microbiome/drug effects ; Cell Line ; Ileum/metabolism/pathology ; NF-kappa B/metabolism ; Apoptosis/drug effects ; Mice, Inbred C57BL ; Lipopolysaccharides ; Male ; }, abstract = {Necrotizing enterocolitis (NEC) is a life-threatening inflammatory bowel disease linked to gut microbiome dysbiosis. This study evaluates the efficacy of Limosilactobacillus reuteri strain DS0384, which secretes N-carbamyl glutamic acid (NCG), in modulating lipid peroxidation and inflammatory pathways in NEC. After pretreatment with DS0384, NEC mouse model was induced by gavage with bacteria-containing formula. NCG levels in the ileum were measured via CE-TOFMS metabolomic analysis. Additionally, rat small intestinal epithelial IEC-6 cells were exposed to lipopolysaccharide (LPS), treated with DS0384 DNA (D-DNA), and/or transfected to overexpress fatty acid synthase (FASN) and Toll-like receptor 4 (TLR4). Lipid peroxidation, peroxidation and inflammatory factors and NF-κB pathways were analysed. Immunofluorescence was used to measure the expression levels of ZO-1 and TLR4 in the ileum. DS0384 treatment significantly reduced more histological abnormalities, apoptosis, and TLR4 expression in NEC mice, while restoring NCG levels, downregulating FASN and inhibiting lipid peroxidation and inflammation. Pre-treatment with D-DNA maintained cell vitality, reduced apoptosis, and suppressed TLR4/NF-κB-mediated inflammasome activation. Overexpression of FASN or TLR4 reversed these effects. DS0384 is a promising therapeutic against NEC, enhancing gut barrier integrity and modulating inflammatory and oxidative responses, suggesting potential clinical benefits in preventing NEC progression.}, }
@article {pmid39947314, year = {2025}, author = {Zhang, X and Chen, Y and Xia, Y and Lin, S and Zhou, X and Pang, X and Yu, J and Sun, L}, title = {Oral microbiota in colorectal cancer: Unraveling mechanisms and application potential.}, journal = {Life sciences}, volume = {}, number = {}, pages = {123462}, doi = {10.1016/j.lfs.2025.123462}, pmid = {39947314}, issn = {1879-0631}, abstract = {Colorectal cancer (CRC), with a rising prevalence, is the third most commonly diagnosed cancer and the third leading cause of cancer-related death. Studies have shown that a complex interplay between the development of CRC and alterations in the oral microbiome. Recent advancements in genomics and metagenomics have highlighted the significant roles of certain oral microbes, particularly Porphyromonas gingivalis (P. gingivalis) and Fusobacterium nucleatum (F. nucleatum), in the progression of CRC. However, the detailed mechanisms by which the oral microbiota influence CRC development remain unclear. This review aims to elucidate the role of oral microbiota in CRC progression, evaluate their potential as biomarkers, and explore therapeutic strategies targeting these microbes. This review offers insights into the mechanisms underlying the interaction between oral microbiota and CRC, underscoring the potential of oral microbes as diagnostic and prognostic biomarkers, as well as therapeutic targets. Future research should focus on clarifying the exact pathways and developing innovative therapeutic strategies to enhance the diagnosis and treatment.}, }
@article {pmid39947272, year = {2025}, author = {Yuan, X and Wang, J and Wang, W and Song, Y and Wu, J and Du, R}, title = {Microbiome alterations in primary Sjögren's syndrome: Regional dysbiosis and microbiome-targeted therapeutic strategies.}, journal = {Clinical immunology (Orlando, Fla.)}, volume = {}, number = {}, pages = {110444}, doi = {10.1016/j.clim.2025.110444}, pmid = {39947272}, issn = {1521-7035}, abstract = {Primary Sjögren's syndrome (pSS) is a complex autoimmune disease characterized by diverse clinical manifestations. While xerophthalmia and xerostomia are hallmark symptoms, the disease often involves multiple organ systems, including the kidneys, lungs, nervous system, and gastrointestinal tract, leading to systemic morbidity in severe cases. Despite extensive research, the precise pathogenesis of pSS remains unclear, likely involving infectious, hormonal, and genetic factors. Emerging evidence highlights the microbiome as a key contributor to autoimmune diseases, including pSS. Dysbiosis in the oral, ocular, gut, and genital microbiomes plays a critical role in disease onset, progression, and variability. This review summarizes current findings on microbiome alterations in pSS, emphasizing their role in pathogenesis and clinical features, and explores microbiome-targeted therapies. Understanding the role of the microbiome in pSS pathophysiology could advance disease management and inspire targeted therapeutic strategies.}, }
@article {pmid39947184, year = {2025}, author = {Heinken, A and Hulshof, TO and Nap, B and Martinelli, F and Basile, A and O'Brolchain, A and O'Sullivan, NF and Gallagher, C and Magee, E and McDonagh, F and Lalor, I and Bergin, M and Evans, P and Daly, R and Farrell, R and Delaney, RM and Hill, S and McAuliffe, SR and Kilgannon, T and Fleming, RMT and Thinnes, CC and Thiele, I}, title = {A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites.}, journal = {Cell systems}, volume = {}, number = {}, pages = {101196}, doi = {10.1016/j.cels.2025.101196}, pmid = {39947184}, issn = {2405-4720}, abstract = {Genome-scale modeling of microbiome metabolism enables the simulation of diet-host-microbiome-disease interactions. However, current genome-scale reconstruction resources are limited in scope by computational challenges. We developed an optimized and highly parallelized reconstruction and analysis pipeline to build a resource of 247,092 microbial genome-scale metabolic reconstructions, deemed APOLLO. APOLLO spans 19 phyla, contains >60% of uncharacterized strains, and accounts for strains from 34 countries, all age groups, and multiple body sites. Using machine learning, we predicted with high accuracy the taxonomic assignment of strains based on the computed metabolic features. We then built 14,451 metagenomic sample-specific microbiome community models to systematically interrogate their community-level metabolic capabilities. We show that sample-specific metabolic pathways accurately stratify microbiomes by body site, age, and disease state. APOLLO is freely available, enables the systematic interrogation of the metabolic capabilities of largely still uncultured and unclassified species, and provides unprecedented opportunities for systems-level modeling of personalized host-microbiome co-metabolism.}, }
@article {pmid39947133, year = {2025}, author = {Elmassry, MM and Sugihara, K and Chankhamjon, P and Kim, Y and Camacho, FR and Wang, S and Sugimoto, Y and Chatterjee, S and Chen, LA and Kamada, N and Donia, MS}, title = {A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules.}, journal = {Cell host &amp; microbe}, volume = {33}, number = {2}, pages = {218-234.e12}, doi = {10.1016/j.chom.2025.01.002}, pmid = {39947133}, issn = {1934-6069}, mesh = {*Gastrointestinal Microbiome ; Humans ; Mice ; Animals ; *Inflammatory Bowel Diseases/microbiology ; Feces/microbiology ; Crohn Disease/microbiology ; Disease Models, Animal ; Multigene Family ; Colitis/microbiology ; Metagenomics ; Clostridium/genetics ; Mice, Inbred C57BL ; Female ; }, abstract = {Gut microbiome changes have been associated with several human diseases, but the molecular and functional details underlying these associations remain largely unknown. Here, we performed a meta-analysis of small molecule biosynthetic gene clusters (BGCs) in metagenomic samples of the gut microbiome from inflammatory bowel disease (IBD) patients and matched healthy subjects and identified two Clostridia-derived BGCs that are significantly associated with Crohn's disease (CD), a main IBD type. Using synthetic biology, we discovered and solved the structures of six fatty acid amides as the products of the CD-enriched BGCs, which we subsequently detected in fecal samples from IBD patients. Finally, we show that the discovered molecules disrupt gut permeability and exacerbate disease in chemically or genetically susceptible mouse models of colitis. These findings suggest that microbiome-derived small molecules may play a role in the etiology of IBD and represent a generalizable approach for discovering molecular mediators of disease-relevant microbiome-host interactions.}, }
@article {pmid39947132, year = {2025}, author = {Wittmers, F and Poirier, C and Bachy, C and Eckmann, C and Matantseva, O and Carlson, CA and Giovannoni, SJ and Goodenough, U and Worden, AZ}, title = {Symbionts of predatory protists are widespread in the oceans and related to animal pathogens.}, journal = {Cell host &amp; microbe}, volume = {33}, number = {2}, pages = {182-199.e7}, doi = {10.1016/j.chom.2025.01.009}, pmid = {39947132}, issn = {1934-6069}, mesh = {*Symbiosis ; Animals ; *Choanoflagellata/physiology ; *Oceans and Seas ; *Phylogeny ; Humans ; Bacteria/genetics/classification ; Gene Transfer, Horizontal ; Genome, Bacterial ; Fishes/microbiology ; Eukaryota/physiology/genetics ; Microbiota ; }, abstract = {Protists are major predators of ocean microbial life, with an ancient history of entanglements with prokaryotes, but their delicate cell structures and recalcitrance to culturing hinder exploration of marine symbioses. We report that tiny oceanic protistan predators, specifically choanoflagellates-the closest living unicellular relatives of animals-and uncultivated MAST-3 form symbioses with four bacterial lineages related to animal symbionts. By targeting living phagotrophs on ship expeditions, we recovered genomes from physically associated uncultivated Legionellales and Rickettsiales. The evolutionary trajectories of Marinicoxiellaceae, Cosmosymbacterales, Simplirickettsiaceae, and previously named Gamibacteraceae vary, including host-engagement mechanisms unknown in marine bacteria, horizontally transferred genes that mediate pathogen-microbiome interactions, and nutritional pathways. These symbionts and hosts occur throughout subtropical and tropical oceans. Related bacteria were detected in public data from freshwater, fish, and human samples. Symbiont associations with animal-related protists, alongside relationships to animal pathogens, suggest an unexpectedly long history of shifting associations and possibilities for host expansion as environments change.}, }
@article {pmid39947040, year = {2025}, author = {Kang, H and Lee, UJ and Park, BY and Kim, M and Yang, M}, title = {Effects of deep ocean-derived magnesium-enhanced water on metabolic diseases with microbiome changes.}, journal = {Diabetes &amp; metabolic syndrome}, volume = {19}, number = {2}, pages = {103203}, doi = {10.1016/j.dsx.2025.103203}, pmid = {39947040}, issn = {1878-0334}, abstract = {AIMS: To investigate the effects of magnesium (Mg) from deep ocean sources, we conducted a randomized clinical trial involving adults with hypertension, diabetes, or hyperlipidemia.<br><br>METHODS: Subjects consumed either Mg-enriched water (MEW) or a placebo (80 or 6&#xa0;mg of Mg per 2&#xa0;L/day, respectively) for 4 weeks. We examined the detoxifying effects of MEW on environmental toxicants, including polycyclic aromatic hydrocarbons (PAHs) and oxidative stress, and its impact on gut microbiome composition (N&#xa0;=&#xa0;30; 49.26&#xa0;&#xb1;&#xa0;9.55&#xa0;yrs).<br><br>RESULTS: Most subjects consumed less Mg than the RDA, enabling their participation in the trial. Despite limitations in serum Mg measurement to assess Mg intake, MEW intake led to improvements in body mass index (BMI), insulin levels, triglycerides, glucose-BMI, and fatigue. Regardless of Mg content, water consumption reduced urinary levels of 1-hydroxypyrene, a major PAH metabolite, and malondialdehyde, an oxidative stress biomarker. Moreover, the MEW group exhibited greater diversity in gut microbiome composition than the placebo group. Notably, MEW kept the abundance of Clostridium, Dorea, or Desulfovibrio, indicating a balanced Mg intake.<br><br>CONCLUSION: MEW (80&#xa0;mg of Mg/day) appears safe for RDA and effective for preventing CVD or T2DM, as evidenced by gut microbiome and biomarker outcomes.}, }
@article {pmid39946873, year = {2025}, author = {Feng, Y and Li, L and Ma, Q and Liu, S and Wang, P and Li, X and Ma, J}, title = {Effect of microcystin-LR on intestinal microbiota, metabolism, and health of zebrafish (Danio rerio).}, journal = {The Science of the total environment}, volume = {967}, number = {}, pages = {178838}, doi = {10.1016/j.scitotenv.2025.178838}, pmid = {39946873}, issn = {1879-1026}, abstract = {Microcystin-LR (MC-LR) is typically produced along with the occurrence of cyanobacterial blooms, potentially exerting deleterious effects on intestinal microbiota and health in aquatic animals. To date, the underlying mechanism by which MC-LR affects intestinal health remains elusive. In this study, adult male zebrafish were exposed to MC-LR to assess its impact on the microbiome and metabolome. Histopathological and biochemical results indicated that MC-LR damaged intestinal villi and epithelial cells, induced intestinal barrier injury and inflammatory response. Metabolomics results revealed that MC-LR induced amino acid, carbohydrate, lipid, energy metabolisms dysbiosis, and specifically promoted glycine, serine and threonine metabolism. Metagenomics results demonstrated that MC-LR altered the composition of intestinal microbiota, and microbial function prediction suggested that MC-LR promoted the functions associated with amino acid, lipid, carbohydrate and energy metabolisms. Multiomics and Metorigin analyses jointly confirmed that glycine, serine and threonine metabolism was predominantly regulated by dominant Proteobacteria, Firmicutes, Fusobacteriota and Bacteroidota under MC-LR stress. This study offers a comprehensive perspective on the toxicity of microbiota and microbiota-derived metabolism in fish intestines induced by MC-LR and deepens our comprehension of the disruptive influence of MC-LR on intestinal homeostasis in organisms.}, }
@article {pmid39946872, year = {2025}, author = {Wang, Z and Yang, Y and Kümmel, S and Richnow, HH and Nijenhuis, I and Vogt, C}, title = {Heterotrophic nitrate reduction potential of an aquifer microbial community from psychrophilic to thermophilic conditions.}, journal = {The Science of the total environment}, volume = {967}, number = {}, pages = {178716}, doi = {10.1016/j.scitotenv.2025.178716}, pmid = {39946872}, issn = {1879-1026}, abstract = {High temperature-aquifer thermal energy storage (HT-ATES) aims at the seasonal storage and extraction of large quantities of heat in the subsurface. However, the impacts of temperature fluctuations caused by HT-ATES toward biodiversity and ecosystem services in the subsurface environment with respect to the nitrogen cycle remain unclear. Hence, understanding possible temperature adaptation mechanisms of aquifer microbial communities is crucial to assess potential environmental risks associated with HT-ATES. In this study, we investigated the effects of temperatures between 12 °C and 80 °C on a pristine aquifer microbial community and its capacity to reduce nitrate, a common global groundwater contaminant. [13]C-labeled acetate was used as easily consumable carbon and energy source for nitrate reduction, allowing precise activity measurement by analysis of released [13]CO2. We observed nitrate reduction coupled to acetate mineralization at 12 °C, 25 °C, 38 °C, 45 °C and 60 °C but not at 80 °C. The rates of acetate mineralization at 12 °C to 38 °C were significantly higher than rates at 45 °C and 60 °C. Temperature significantly affected the composition of the acetate-mineralizing, nitrate-reducing microbial communities. Members of the families Pseudomonadaceae and Comamonadaceae mainly developed in enrichments incubated at 12 °C and 25 °C, whereas phylotypes affiliated to Rhizobiaceae dominated at 38 °C. At 45 °C and 60 °C, phylotypes belonging to Symbiobacteriaceae, Paenibacillaceae and Planococcaceae mainly developed. These findings indicate that the indigenous aquifer microbiome can maintain the ability to reduce nitrate over a wide temperature range, providing support that HT-ATES may allow thermal energy storage while simultaneously attenuating nitrate pollution.}, }
@article {pmid39946810, year = {2025}, author = {Wnuk, E and Szafranek-Nakonieczna, A and Goraj, W and Wiącek, D and Wolińska, A and Łopucki, R}, title = {Evaluation of vanadium effect on methane oxidation and the microbiome composition in soil.}, journal = {Journal of environmental management}, volume = {376}, number = {}, pages = {124529}, doi = {10.1016/j.jenvman.2025.124529}, pmid = {39946810}, issn = {1095-8630}, abstract = {Carbon transformations in the environment are extremely important due to observed climate changes. Various types of pollution resulting from human activity are a factor that modifies the occurrence of these natural processes in the environment. One of these pollutants is vanadium, the presence of which is constantly increasing in the environment. For this reason, the aim of the study was to investigate the influence of vanadium (the most toxic form, pentavalent) on the efficiency of methane oxidation in Leptosol soil. Our research allowed us to identify methanotrophs of the genera Methylobacter and Methylomicrobium in the soil. The presence of these methanotrophs was negatively correlated with the doses of vanadium tested. A decrease in Methylobacter abundance was observed with increased vanadium doses of 188 and 500 mg kg[-1], which was reflected in the methanotrophic activity. A decrease in Methylomicrobium abundance was observed starting from the lower vanadium dose (18.39 mg kg[-1]). The presence of both genera was positively correlated with methanotrophic activity, suggesting that both genera may be involved in methane oxidation in this soil. Our research also indicated the genera of microorganisms whose presence was stimulated by the addition of vanadium, including: Nocardioides, Rubrobacter, Bacillus, Paenibacillus, Streptomyces, which indicates that they have defense mechanisms against vanadium and may participate in lowering its concentration in the environment. There were also those whose presence was clearly reduced, such as Acidobacter, Pseudomonas, Hassallia, Gemmatimonas, Methylotenera. This research provides new insight into how vanadium contamination regulates the methanotrophy process in the soil environment.}, }
@article {pmid39946793, year = {2025}, author = {Chen, C and Xiao, Q and Wen, Z and Gong, F and Zhan, H and Liu, J and Li, H and Jiao, Y}, title = {Gut microbiome-derived indole-3-carboxaldehyde regulates stress vulnerability in chronic restraint stress by activating aryl hydrocarbon receptors.}, journal = {Pharmacological research}, volume = {213}, number = {}, pages = {107654}, doi = {10.1016/j.phrs.2025.107654}, pmid = {39946793}, issn = {1096-1186}, abstract = {Chronic stress constitutes a major precipitating factor for Major Depressive Disorder (MDD), and comprehending individual differences in stress responses is crucial for the development of effective intervention strategies for MDD. Recent studies indicate that an individual's vulnerability to chronic stress is closely associated with gut microbiota composition, but the underlying mechanisms remain unclear. This study aims to investigate whether the gut microbiota and its metabolites can serve as gut-brain signaling molecules and explores how the gut microbiota affects stress sensitivity. Here, we showed that gut microbiome-derived indole-3-carboxaldehyde (I3C) can act as a gut-brain signaling molecule that links tryptophan metabolism by gut microbes to stress vulnerability in the host. First, we identified a specific reduction in gut microbiome-derived I3C levels in the hippocampus and colon through untargeted and targeted metabolomic analyses. Then, the study of gut microbiota suggested that the relative abundance of lactobacillus was reduced significantly in stress-susceptible rats, whereas fecal microbiota transplantation regulates stress vulnerability. Furthermore, supplementation with I3C and the representative I3C-producing strain, Lactobacillus reuteri, was shown to alleviate depression-like behaviors induced by chronic stress. Further research confirms that I3C can inhibit neuroinflammation and promote hippocampal neurogenesis through the aryl hydrocarbon receptors (AhR) signal pathway, thereby mitigating the host's susceptibility to stress. In conclusion, our findings elucidate that the gut microbiome-derived-I3C can help buffer the host's stress through the AhR/SOCS2/NF-κB/NLRP3 pathway, providing a gut-brain signaling basis for emotional behavior.}, }
@article {pmid39946531, year = {2025}, author = {Wyllie, RM and Jensen, PA}, title = {The MutRS quorum-sensing system controls lantibiotic mutacin production in the human pathogen Streptococcus mutans.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {7}, pages = {e2421164122}, doi = {10.1073/pnas.2421164122}, pmid = {39946531}, issn = {1091-6490}, support = {GM138210//HHS | National Institutes of Health (NIH)/ ; }, mesh = {*Streptococcus mutans/metabolism/genetics/drug effects ; *Bacteriocins/metabolism/biosynthesis/pharmacology ; *Quorum Sensing ; *Bacterial Proteins/metabolism/genetics ; Humans ; Gene Expression Regulation, Bacterial/drug effects ; }, abstract = {Microbes use quorum-sensing systems to respond to ecological and environmental changes. In the oral microbiome, the pathogenic bacterium Streptococcus mutans uses quorum-sensing to control the production of bacteriocins. These antimicrobial peptides kill off ecological competitors and allow S. mutans to dominate the microenvironment of dental plaques and form dental caries. One class of bacteriocins produced by S. mutans, the lantibiotic mutacins, are particularly effective at killing due to their broad spectrum of activity. Despite years of study, the regulatory mechanisms governing production of lantibiotic mutacins I, II, and III in S. mutans have never been elucidated. We identified a distinct class of quorum-sensing system, MutRS, that regulates mutacins and is widespread among the streptococci. We demonstrate that MutRS systems are activated by a short peptide pheromone (Mutacin Stimulating Peptide) and show that MutRS controls production of three separate lantibiotic mutacins in three different strains of S. mutans. Finally, we show that paralogous MutRS systems participate in inter- and intrastrain crosstalk, providing further evidence of the interplay between quorum-sensing systems in the oral streptococci.}, }
@article {pmid39946165, year = {2025}, author = {Wang, J and Skalkos, Z and Grueber, C and Whittington, CM}, title = {Changes to the reproductive microbiome of the brood pouch during male pregnancy in seahorses (Hippocampus abdominalis).}, journal = {Reproduction (Cambridge, England)}, volume = {}, number = {}, pages = {}, doi = {10.1530/REP-24-0159}, pmid = {39946165}, issn = {1741-7899}, abstract = {Seahorses demonstrate an unusual reproductive strategy in which males incubate embryos inside a complex "brood pouch" until parturition, analogous to mammalian viviparity. In many species, a "normal" reproductive microbiome ensures successful embryogenesis and enables parents (usually mothers) to provide their offspring with their initial microbiome. In male-pregnant seahorses, embryos may receive microbiomes from both parents: from the paternal brood pouch and from the maternal eggs. Using the pot-bellied seahorse (Hippocampus abdominalis), we employed 16S rRNA sequencing to explore the reproductive microbiome. We aimed to compare the microbiome of the male pregnant pouch to the male non-pregnant pouch and external skin, and to identify bacterial taxa found exclusively in the pregnant pouch that could be derived maternally, from the microbiome of eggs. Our findings demonstrate that the pregnant brood pouch microbiome is compositionally distinct from the non-pregnant pouch and external skin. The pouch microbiome also has characteristics of resistance to colonisation by pathogens, including a low species richness, high species evenness and diversity, and very low abundance of Vibrio, a genus that includes fish skin pathogens. Thirteen bacterial taxa appear exclusively in the pregnant pouch, relative to the non-pregnant pouch, and seven of these overlapped with taxa present in or on the eggs. The possible supplementation of brood pouch microbiome with egg-associated micro-organisms hints at a maternal microbial contribution to male pregnancy. This characterisation of the pregnant seahorse pouch microbiome provides a platform for further research into its function and possible adaptive value during male pregnancy.}, }
@article {pmid39946159, year = {2025}, author = {Trigg, NA and Zhou, SK and Harris, JC and Lamonica, MN and Nelson, MA and Silverman, MA and Kambayashi, T and Conine, CC}, title = {A lack of commensal microbiota influences the male reproductive tract intergenerationally in mice.}, journal = {Reproduction (Cambridge, England)}, volume = {}, number = {}, pages = {}, doi = {10.1530/REP-24-0204}, pmid = {39946159}, issn = {1741-7899}, abstract = {The microbiome encompasses the array of microorganisms inhabiting various niches in the body and is necessary for numerous physiological processes, including normal metabolism and a functioning immune system. Not only does the absence of a microbiome in mice impact the exposed animals but also inherited phenotypes in successive generations of progeny, suggesting that the absence of a microbiome impacts the germline and gametes. Indeed, recent research has identified a role of the gut microbiome in contributing to male fertility, in both healthy and disease states. While this link is beginning to be established, the impact of the microbiome on the male reproductive tract remains understudied. Here, we utilized a germ-free mouse model to examine the influence of the absence of microbes on the male reproductive tract. In contrast to mice with an established microbiome, germ-free mice display decreased testicular weight and the prevalence of an epididymitis-like inflammation phenotype. These histopathological changes are accompanied by transcriptomic dysregulation in the reproductive tract of germ-free mice, particularly in the cauda epididymis. Moreover, such transcriptomic changes are transmitted to the next generation with high correlation of gene expression in the cauda epididymis between germ-free mice and their conventionalized (microbiome-restored) male offspring, when compared to control mice. Ultimately, our findings identify the reproductive sequalae of males without a functional microbiome and additionally in their conventionalized offspring, suggesting that the paternal microbiota is an underappreciated contributor to male reproductive function.}, }
@article {pmid39946032, year = {2025}, author = {Karam, F and El Deghel, Y and Iratni, R and Dakroub, AH and Eid, AH}, title = {The Gut Microbiome and Colorectal Cancer: An Integrative Review of the Underlying Mechanisms.}, journal = {Cell biochemistry and biophysics}, volume = {}, number = {}, pages = {}, pmid = {39946032}, issn = {1559-0283}, abstract = {Colorectal cancer (CRC) is the second leading cause of cancer-related mortality worldwide. While the incidence and mortality of CRC have decreased overall due to better screening, rates in adults under 50 have risen. CRC can manifest as inherited syndromes (10%), familial clustering (20%), or sporadic forms (70%). The gut microbiota, comprising mainly firmicutes and bacteroidetes, play a key role in CRC development and prevention. Indeed, CRC progression is influenced by the dynamic interaction between the gut microbiota, the intestinal barrier, the immune system, and the production of short-chain fatty acids. Not surprisingly, imbalance in the gut microbiota, termed dysbiosis, has been linked to CRC due to ensuing chronic inflammation, DNA damage, and oxidative stress. This may explain the notion that probiotics and fecal microbiota transplantation offer potential strategies for CRC prevention and treatment by restoring microbial balance and enhancing anti-cancer immune responses. This review appraises the roles of gut microbiota in promoting or preventing CRC. It also discusses the mechanistic interplay between microbiota composition, the intestinal barrier, and the immune system, with the hope of developing potential therapeutic strategies.}, }
@article {pmid39945759, year = {2025}, author = {Law, JD and Gao, Y and Kovvali, S and Thirugnanasambantham, P and Wysocki, VH and Ahmer, BMM and Gopalan, V}, title = {Identification of inhibitors of the Salmonella FraB deglycase, a drug target.}, journal = {FEBS open bio}, volume = {}, number = {}, pages = {}, doi = {10.1002/2211-5463.70001}, pmid = {39945759}, issn = {2211-5463}, support = {R01AI116119//National Institute of Allergy and Infectious Diseases/ ; R01AI140541//National Institute of Allergy and Infectious Diseases/ ; T32-GM086252/GM/NIGMS NIH HHS/United States ; P41GM128577/GM/NIGMS NIH HHS/United States ; RM1GM149374/GM/NIGMS NIH HHS/United States ; 1R43GM140749/GM/NIGMS NIH HHS/United States ; //Ohio State University College of Medicine/ ; //Ohio State University Comprehensive Cancer Center/ ; P30 CA016058/NH/NIH HHS/United States ; }, abstract = {Nontyphoidal Salmonella is one of the most prevalent causes of human foodborne illnesses worldwide, with no narrow-spectrum antibiotics or vaccines available. Here, we seek to address this gap. During the host inflammatory response, Salmonella metabolizes fructose-asparagine as a nutrient using proteins encoded in the fra operon. Deletion of fraB leads to a build-up of 6-phosphofructose-aspartate, the substrate of FraB, and intoxicates Salmonella. Because fra genes are absent in mammals and most members of the human gut microbiome, FraB inhibitors are expected to have limited off-target effects and offer prospects as potential therapeutics. To identify such inhibitors, we conducted a high-throughput screening of small-molecule libraries using a FraB activity-based biochemical assay. We screened 131,165 compounds and identified 126 hits that could be obtained commercially for further characterization. When tested at 25 μm inhibitor in the presence of 1 mm 6-phosphofructose-aspartate, FraB activity was reduced ~ 30-100% by 65 compounds. Guided by preliminary cell-based data, we further characterized six compounds (one triazolidine, two thiadiazolidines, and three triazolothiadiazoles) and found them to exhibit IC50 values from ~ 3 to 100 μm and KI (inhibitor constant) values from ~ 1 to 29 μm. Native mass spectrometry revealed that all three triazolothiadiazoles were capable of binding FraB; we also obtained evidence that one of the triazolothiadiazoles binds FraB even in the presence of substrate. The recurrence of multiple pharmacophores bolsters prospects for farming more hits from compound libraries and for designing therapeutics against nontyphoidal Salmonella.}, }
@article {pmid39945579, year = {2025}, author = {Sun, F and Zhang, Y and Tan, CP and Gu, Y and Liu, Y and Xu, YJ}, title = {Analytical Capabilities and Future Perspectives of Chemometrics in Omics for Food Microbial Investigation.}, journal = {Critical reviews in analytical chemistry}, volume = {}, number = {}, pages = {1-14}, doi = {10.1080/10408347.2025.2463430}, pmid = {39945579}, issn = {1547-6510}, abstract = {Microbiomes significantly impact food flavor, food quality and human health. The development of omics technologies has revolutionized our understanding of the microbiome, the generated complex datasets, as well as their processing and interpretation need to be taken seriously. Currently, chemometrics has shown huge potential in omics data analysis, which is crucial to reveal the functional attributes and mechanisms of microbiomes in food nutrition and safety. However, various chemometric tools have their own characteristics, selecting appropriate technologies and performing multiomics data fusion analysis to improve the precision and reliability of food microbial investigations is still a huge challenge. In this review, we summarized the omics technologies used in food microbiome studies, overviewed the principle and applicability of chemometrics in omics, and discussed the challenges and prospects of chemometrics. The urgent need for chemometrics is to integrate deep learning (DL) and artificial intelligence algorithms to enhance its analytical capabilities and prediction accuracy. We hope this review will provide valuable insights of the integration of multiomics and bioinformatics combined with various chemometric techniques in data analysis for food microbial investigation. In the future, chemometrics combined with modern technologies for multiomics data analysis will further deepen our understanding of food microbiology and improve food safety.}, }
@article {pmid39945558, year = {2025}, author = {Zhang, L and Liu, ZX and Liu, YH and Chen, Y and Chen, J and Lu, CH}, title = {Auricularia auriculaPolysaccharides Exert Anti-inflammatory Effects in Hepatic Fibrosis by the Gut-Liver Axis and Enhancing SCFA Metabolism.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.4c07952}, pmid = {39945558}, issn = {1520-5118}, abstract = {Auricularia auricula, esteemed in Chinese culture for their culinary and medicinal properties, exhibits notable metabolic and immunomodulatory effects. The principal active constituents are indigestible fermentable polysaccharides, which not only exhibit anti-inflammatory activities but also facilitate the proliferation of beneficial gut microbiota. However, the influence of gut-derived components on liver-regulated metabolic products remains insufficiently understood. This item offers insights into the therapeutic potential of wood ear mushrooms for treating hepatic fibrosis and the associated mechanisms. Following 8 weeks of treatment, a substantial reduction in ECM deposition was recorded, linked to modulation of the NLRP3 inflammasome activation. This study aims to reveal the potential microbiome-mediated mechanisms behind its therapeutic effects. Insights from antibiotic combination treatments indicate that the protective effects against ECM deposition rely on the presence of specific gut microbiota. This fecal microbiota intervention enhances key physiological mechanisms, underscoring the contributions of Lactobacillales, Rikenellaceae, and Bacteroidaceae in potentially mitigating fibrosis. Collectively, these findings suggest that interventions utilizing wood ear mushrooms may reduce inflammation and ECM deposition, mediated by the TLR4/NF-κB pathway.}, }
@article {pmid39945545, year = {2025}, author = {Verster, AJ and Salerno, P and Valls, R and Barrack, K and Price, CE and McClure, EA and Madan, JC and O'Toole, GA and Sanville, JL and Ross, BD}, title = {Persistent delay in maturation of the developing gut microbiota in infants with cystic fibrosis.}, journal = {mBio}, volume = {}, number = {}, pages = {e0342024}, doi = {10.1128/mbio.03420-24}, pmid = {39945545}, issn = {2150-7511}, abstract = {The healthy human infant gut microbiome undergoes stereotypical changes in taxonomic composition between birth and maturation to an adult-like stable state. During this time, extensive communication between microbiota and the host immune system contributes to health status later in life. Although there are many reported associations between microbiota compositional alterations and disease in adults, less is known about how microbiome development is altered in pediatric diseases. One pediatric disease linked to altered gut microbiota composition is cystic fibrosis (CF), a multi-organ genetic disease involving impaired chloride secretion across epithelia and heightened inflammation both in the gut and at other body sites. Here, we use shotgun metagenomics to profile the strain-level composition and developmental dynamics of the infant fecal microbiota from several CF and non-CF longitudinal cohorts spanning from birth to greater than 36 months of life. We identify a set of keystone species that define microbiota development in early life in non-CF infants but are missing or decreased in relative abundance in infants with CF, resulting in a delayed pattern of microbiota maturation, persistent entrenchment in a transitional developmental phase, and subsequent failure to attain an adult-like stable microbiota. Delayed maturation is strongly associated with cumulative antibiotic treatments, and we also detect the increased relative abundance of oral-derived bacteria and higher levels of fungi in infants with CF, features that are associated with decreased gut bacterial density. These findings suggest the potential for future directed therapies targeted at overcoming developmental delays in microbiota maturation for infants with CF.IMPORTANCEThe human gastrointestinal tract harbors a diversity of microbes that colonize upon birth and collectively contribute to host health throughout life. Infants with the disease cystic fibrosis (CF) harbor altered gut microbiota compared to non-CF counterparts, with lower levels of beneficial bacteria. How this altered population is established in infants with CF and how it develops over the first years of life is not well understood. By leveraging multiple large non-CF infant fecal metagenomic data sets and samples from a CF cohort collected prior to highly effective modulator therapy, we define microbiome maturation in infants up to 3 years of age. Our findings identify conserved age-diagnostic species in the non-CF infant microbiome that are diminished in abundance in CF counterparts that instead exhibit an enrichment of oral-derived bacteria and fungi associated with antibiotic exposure. Together, our study builds toward microbiota-targeted therapy to restore healthy microbiota dynamics in infants with CF.}, }
@article {pmid39945541, year = {2025}, author = {Lapid, R and Motro, Y and Craddock, H and Salah, I and King, R and Winner, K and Kahila Bar-Gal, G and Moran-Gilad, J}, title = {Abundance of clinically relevant antimicrobial resistance genes in the golden jackal (Canis aureus) gut.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0081924}, doi = {10.1128/msphere.00819-24}, pmid = {39945541}, issn = {2379-5042}, abstract = {UNLABELLED: The spread of antimicrobial resistance (AMR) is a critical One Health issue. Wildlife could act as reservoirs or vehicles of AMR bacteria (ARBs) and AMR genes (ARGs) but are relatively understudied. We sought to investigate clinically relevant ARGs in golden jackals (Canis aureus) thriving near human settlements in Israel. Fecal samples were collected from 111 jackals across four regions over a 10-month period. Various animal and spatio-temporal metadata were collected. Samples were analyzed by quantitative PCR (qPCR) for beta-lactamases (blaTEM, blaCTX-M15, and blaSHV), qnrS and int1. A subset of samples was subject to shotgun metagenomic sequencing followed by resistome and microbiome analyses. qPCR detected a high prevalence of ARGs, including beta-lactamases (blaTEM-1, 96.4%; blaCTX-M-15, 51.4%, blaSHV, 15.3%), fluoroquinolone resistance (qnrS, 87.4%), and class 1 integrons (Int1, 94.6%). The blaTEM-1 gene was found to be more prevalent in adult jackals compared to younger ones. Metagenomic analysis of a subset of samples revealed a diverse gut microbiome harboring a rich resistome with tetracycline resistance genes being the most prevalent. Metagenome-assembled genome analysis further identified several ARGs associated with clinically relevant bacteria. These findings highlight the potential role of golden jackals as reservoirs for AMR and emphasize the need for ongoing surveillance to better understand AMR transmission dynamics at the wildlife-human interface.<br><br>IMPORTANCE: The research highlights the potential role of the golden jackals as reservoirs for antimicrobial resistance (AMR). The high prevalence of clinically relevant AMR genes in these jackals emphasizes the need for ongoing surveillance and monitoring to better understand AMR transmission dynamics at the wildlife-human interface.}, }
@article {pmid39945538, year = {2025}, author = {Zhang, L and Zhang, T and Xu, Y-R and Sun, J-M and Pan, X-R and Gu, K-Z and Zhang, K-Q and Zhang, Z-G and Liang, L-M}, title = {Induction of conidial traps in the nematode-trapping fungus Drechslerella dactyloides by soil microbes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0129124}, doi = {10.1128/msystems.01291-24}, pmid = {39945538}, issn = {2379-5077}, abstract = {UNLABELLED: Nematode-trapping fungi, renowned for their specialized predatory structures that ensnare nematodes, offer a promising biological approach to managing plant-parasitic nematodes. However, the efficacy of these fungi is frequently hampered by biotic and abiotic factors within the soil, which can significantly impede fungal germination (fungistasis). To counteract these environmental challenges, certain nematode-trapping fungi have evolved to produce traps from their conidia, referred to as conidial traps. This adaptation allows them to bypass the inhibitory effects of their surroundings, enhancing their predatory capabilities. In this study, we explored how soil affects conidial trap formation in Drechslerella dactyloides. Our findings revealed that Acinetobacter spp. and Pantoea spp. present in soil extracts play pivotal roles in triggering the development of these traps. Using metagenomic sequencing, we mapped the shifts in bacterial communities and their relative abundances before and after incubation for up to 24 hours to optimize soil induction effects. This analysis highlighted the enrichment of specific functional genes in soil microbes and provided insights into the mechanisms driving conidial trap formation, based on changes in soil characteristics. Furthermore, through bacterial isolation procedures, we successfully cultured and characterized the bacteria responsible for this phenomenon, confirming their potent ability to stimulate the production of conidial traps in nematode-trapping fungi. This study not only underscores the critical role of bacterial diversity in modulating the life cycle transitions of nematode-trapping fungi but also sets the stage for the development of more effective and sustainable strategies to harness these fungi in the battle against pathogenic nematodes.<br><br>IMPORTANCE: Predatory nematode-trapping fungi are important microbial antagonists of nematodes and can be developed into biocontrol agents. However, microbial biocontrol agents often suffer from inconsistent efficacy, primarily due to biotic and abiotic stresses in the rhizosphere soil. Drechslerella dactyloides, a nematode-trapping fungus, produces conidial traps in soil, serving as a survival strategy to overcome these stresses. In this study, we optimized soil suspensions to efficiently induce the formation of conidial traps. We found that bacteria in the soil directly trigger this formation. Metagenomic sequencing revealed bacterial enrichment during optimization, and we isolated and purified these bacteria with inducible activity. Our research deepens the understanding of this survival strategy of nematode-trapping fungi in nature, laying the foundation for enhancing the effectiveness of nematode biocontrol using this mechanism.}, }
@article {pmid39945519, year = {2025}, author = {Roach, SN and Phillips, W and Pross, LM and Sanders, AE and Pierson, MJ and Hunter, RC and Langlois, RA}, title = {Virus-induced perturbations in the mouse microbiome are impacted by microbial experience.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0056324}, doi = {10.1128/msphere.00563-24}, pmid = {39945519}, issn = {2379-5042}, abstract = {The bacterial microbiome has a major impact on health and can shape metabolism, host tolerance, immune responses, and the outcome of future infections. The bacterial microbiome is highly variable between individuals. Specific pathogen-free animals have reduced microbiome diversity, making it difficult to evaluate the impact of infection-induced microbiome disruption that would be observed in free-living animals, including people. Mice are commonly used as a preclinical model but unfortunately often fail to predict translation success or failure, particularly for immune and infectious disease-targeting therapies. Here, we utilize pet store mouse cohoused "dirty" mice with diverse microbial experience to explore how host variability and infection may be interacting to drive unique microbiome changes. We found that cohoused animals had significantly increased bacterial diversity in the small intestine and cecum but not in the large intestine. There were differentially abundant taxa between clean and dirty animals in all three tissues. After infection with influenza A virus, samples clustered by both housing condition and infection status in the cecum and large intestine, while small intestine samples clustered predominantly by infection. Altogether, these results highlight the differential impact of housing, infection, and interaction between the two in dictating community composition across the gastrointestinal microbiome.IMPORTANCETraditionally housed pathogen-free mouse models do not fully capture the natural variability observed among human microbiomes, which may underlie their poor translationally predictive value. Understanding the difference between pathogen-induced shifts in the bacterial microbiome and natural microbiome variance is a major hurdle to determining bacterial biomarkers of disease. It is also critical to understand how diverse baseline microbiomes may be differentially impacted by infection and contribute to disease. Pet store cohoused "dirty" mice have diverse microbial experiences and microbiomes, allowing us to evaluate how baseline variation, infection, and interaction between the two impact the microbiome.}, }
@article {pmid39945201, year = {2025}, author = {Berard, AR and Brubaker, DK and Nemecio, DX and Farr Zuend, C}, title = {Understanding the Associations of Urogenital Microbiomes With Fertility and In Vitro Fertilization.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {93}, number = {2}, pages = {e70035}, doi = {10.1111/aji.70035}, pmid = {39945201}, issn = {1600-0897}, support = {R01HD110367//Eunice Kennedy Shriver National Institute of Child Health &amp; Human Development of the National Institutes of Health/ ; }, mesh = {Humans ; *Fertilization in Vitro ; Female ; Male ; *Microbiota ; *Fertility ; Pregnancy ; Urogenital System/microbiology ; Infertility, Female/microbiology ; }, abstract = {Infertility, defined as the inability to establish a clinical pregnancy after a year of regular, unprotected sexual intercourse, impacts 8%-12% of couples worldwide. Many of these couples turn to in vitro fertilization (IVF) to build their families. The success rate of IVF procedures is variable, with estimates of up to 40% of embryo transfers being unsuccessful. Herein we review the existing literature on the role of the female and male urogenital microbiomes and genital inflammation on fertility and IVF outcomes. We discuss the microbiome across the female reproductive tract (FRT) and identify associations with female infertility, female genital tract inflammation, and success of IVF procedures. We also discuss the male urogenital microbiome and the associations between microbial taxa, genital inflammation, and male fertility parameters. Finally, we consider microbial transfer within couples and the impact this may have on fertility and the success of IVF procedures.}, }
@article {pmid39944910, year = {2025}, author = {Liu, Y and Li, X and Li, Y and Li, H and Li, J}, title = {The Assembly of Fish Gut Microbiomes Through Habitat Variation Provides Insight Into Redbelly Tilapia Invading a Large Subtropical River.}, journal = {Ecology and evolution}, volume = {15}, number = {2}, pages = {e70945}, pmid = {39944910}, issn = {2045-7758}, abstract = {The environment in which fish reside markedly shapes the composition of their gut microbiome. However, the precise mechanisms by which the assembly process of fish gut microbiota adapts to diverse habitat conditions remain largely uncharted, especially in the case of invasive tilapia, renowned for its remarkable adaptability to environmental changes. In this study, we employed high-throughput 16S rRNA gene sequencing to explore the gut microbiome of redbelly tilapia from three distinct habitats. Our results showed substantial disparities in both the composition and diversity (alpha and beta) of the gut microbiome between wild and pond-cultured redbelly tilapia. Notably, stochastic processes emerged as the dominant forces governing the assembly of the gut microbial community in redbelly tilapia. As the habitat shifted from pond-cultured to wild, the influence of undominated processes in gut microbial community assembly waned, while the effect of dispersal limitation intensified. Co-occurrence network analysis suggested that habitat variation contributed to the enhanced complexity of the gut microbial network in invasive tilapia during their transition from pond to wild environments. Across the three distinct habitats, variations were observed in the influence of environmental factors on the gut microbiota of tilapia. Moreover, our findings demonstrated that the gut microbiome of wild tilapia possessed unique characteristics, such as higher alpha diversity and a relatively greater abundance of genes encoding putative cellulolytic enzymes crucial for digesting the preferred food source of tilapia (hydrophytes), particularly in fragmented habitats with well-developed cascade dams. Additionally, we identified that OTU8895 (Clostridum_sensu_stricto_1) and OTU11387 (unclassified Bacilli) were core biomarkers of the gut bacterial community in wild redbelly tilapia, offering valuable insights for the monitoring and management of invasive tilapia populations.}, }
@article {pmid39944872, year = {2025}, author = {Zhai, L and Kong, J and Zhao, C and Xu, Y and Sang, X and Zhu, W and Yao, N}, title = {Global trends and challenges in childhood caries: a 20-year bibliometric review.}, journal = {Translational pediatrics}, volume = {14}, number = {1}, pages = {139-152}, pmid = {39944872}, issn = {2224-4344}, abstract = {Childhood caries is a prevalent condition affecting nearly 50% of children globally across various age groups under 12 years, posing serious implications for their health and development. Understanding global research trends is essential for identifying knowledge gaps and guiding future studies aimed at developing effective intervention strategies. This study provides a comprehensive bibliometric review of childhood caries research from 2003 to 2023. Using CiteSpace, we analyzed 2,178 publications from the Web of Science (WOS) to map research trends, identify key challenges, and examine collaborative networks. The analysis revealed a threefold increase in research output, with the United States and Brazil leading contributions. Key challenges include persistent socioeconomic disparities influencing caries prevalence, limited access to effective treatments like silver diamine fluoride, and the complex role of the oral microbiome. International collaborations across 108 countries indicate a growing global effort to address these issues. Despite advancements, significant disparities in disease burden persist, especially in low- and middle-income countries, highlighting the urgent need to translate research into practice and develop targeted interventions. This review highlights the steady increase in research output on childhood caries over the past two decades, with the United States and Brazil leading contributions. Persistent disparities in disease burden and limited access to effective treatments remain critical challenges, particularly in low- and middle-income countries. These findings underscore the need for targeted research and policy efforts to address these inequities.}, }
@article {pmid39944755, year = {2024}, author = {Melograna, F and Sudhakar, P and Yousefi, B and Caenepeel, C and Falony, G and Vieira-Silva, S and Krishnamoorthy, S and Fardo, D and Verstockt, B and Raes, J and Vermeire, S and Van Steen, K}, title = {Individual-network based predictions of microbial interaction signatures for response to biological therapies in IBD patients.}, journal = {Frontiers in molecular biosciences}, volume = {11}, number = {}, pages = {1490533}, pmid = {39944755}, issn = {2296-889X}, abstract = {Inflammatory Bowel Disease (IBD), which includes Ulcerative Colitis (UC) and Crohn's Disease (CD), is marked by dysbiosis of the gut microbiome. Despite therapeutic interventions with biological agents like Vedolizumab, Ustekinumab, and anti-TNF agents, the variability in clinical, histological, and molecular responses remains significant due to inter-individual and inter-population differences. This study introduces a novel approach using Individual Specific Networks (ISNs) derived from faecal microbial measurements of IBD patients across multiple cohorts. These ISNs, constructed from baseline and follow-up data post-treatment, successfully predict therapeutic outcomes based on endoscopic remission criteria. Our analysis revealed that ISNs characterised by core gut microbial families, including Lachnospiraceae and Ruminococcaceae, are predictive of treatment responses. We identified significant changes in abundance levels of specific bacterial genera in response to treatment, confirming the robustness of ISNs in capturing both linear and non-linear microbiota signals. Utilising network topological metrics, we further validated these findings, demonstrating that critical microbial features identified through ISNs can differentiate responders from non-responders with respect to various therapeutic outcomes. The study highlights the potential of ISNs to provide individualised insights into microbiota-driven therapeutic responses, emphasising the need for larger cohort studies to enhance the accuracy of molecular biomarkers. This innovative methodology paves the way for more personalised and effective treatment strategies in managing IBD.}, }
@article {pmid39944752, year = {2024}, author = {Little, RD and Jayawardana, T and Koentgen, S and Zhang, F and Connor, SJ and Boussioutas, A and Ward, MG and Gibson, PR and Sparrow, MP and Hold, GL}, title = {Pathogenesis and precision medicine for predicting response in inflammatory bowel disease: advances and future directions.}, journal = {eGastroenterology}, volume = {2}, number = {1}, pages = {e100006}, pmid = {39944752}, issn = {2976-7296}, abstract = {The pathogenesis of inflammatory bowel disease (IBD) is complex and multifactorial. Undertreated disease has substantial individual and societal consequences. Current patient classification and subsequent positioning of IBD therapy are based on crude, readily accessible clinical data. These broad parameters are unlikely to reflect underlying molecular profiles and may account for the observed heterogeneity in treatment response. Precision medicine offers identification and integration of molecular profiles into clinical decision-making. Despite several promising scientific and technological advances, the pathogenesis and targetable molecular drivers of IBD remain incompletely understood. Precision medicine therefore remains aspirational. This comprehensive narrative review describes our current understanding of IBD pathophysiology, highlights preliminary genetic, immunological and microbial predictors of treatment response and outlines the role of 'big data' and machine learning in the path towards precision medicine.}, }
@article {pmid39944722, year = {2025}, author = {Saravanan, C and Gopinath, NK and Ganesan, R and Thirumurugan, D}, title = {Challenges and limitations in using bacterial metabolites as immunomodulators.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1535394}, pmid = {39944722}, issn = {2235-2988}, mesh = {Humans ; *Bacteria/metabolism ; *Immunologic Factors/metabolism ; *Gastrointestinal Microbiome ; Animals ; Metabolomics ; Immunomodulating Agents/metabolism ; Metagenomics ; }, abstract = {Harnessing the immunomodulatory potential of bacterial metabolites opens up exciting possibilities for treating various immune-related disorders. However, turning this potential into a reality presents significant challenges. This review investigates these challenges, focusing on discovery, production, characterization, stability, formulation, safety, and individual variability limitations. The limited bioavailability of many metabolites, as well as potential improvements along with the potential for off-target effects and the importance of precise targeting, are emphasized. Furthermore, the complex interactions between gut bacterial metabolites and the microbiome are investigated, highlighting the importance of personalized approaches. We conclude by discussing promising advances in metagenomics, metabolomics, synthetic biology, and targeted delivery systems, which hold out hope for overcoming these limitations and paving the way for the clinical translation of bacterial metabolites as effective immunomodulators.}, }
@article {pmid39944650, year = {2025}, author = {Rabee, AE and Abou-Souliman, I and Yousif, AI and Lamara, M and El-Sherbieny, MA and Elwakeel, EA and Sallam, AM}, title = {Variations in rumen microbiota and host genome impacted feed efficiency in goat breeds.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1492742}, pmid = {39944650}, issn = {1664-302X}, abstract = {INTRODUCTION: Improving feed efficiency (FE) is a significant goal in animal breeding programs. Variations in FE and its relationship with rumen microbiota remain poorly understood across different goat breeds.<br><br>METHODS: This study assessed the influence of the rumen microbiome and host genome on FE in 10 Shami (SH) goats and 10 Zaraibi (ZA) goats, all of which were fed the same diet. The animals were genotyped using the Illumina 65KSNP chip arrays v2, and their rumen bacteria and archaea were investigated using PCR-amplicon sequencing of the 16S rRNA gene.<br><br>RESULTS: The results showed that the ZA goats exhibited higher FE than the SH goats (p < 0.05) and a greater relative abundance (p < 0.05) of rumen bacterial groups that are involved in the degradation of cellulose and hemicelluloses, such as Bacteroidota and Fibrobacterota, along with genera such as Prevotella, Lachnospiraceae AC2044 group, Lachnospiraceae NK3A20 group, and Succiniclasticum, which are linked to carbohydrate and nitrogen metabolism pathways. In addition, breed differences were found to affect the proportions of milk fatty acids. The association analysis identified 26 genome windows containing several putative candidate genes, such as TMEM241, AP4S1, FTO, HYAL2, BBS2, CD52, CRYBG2, PIGV, WDTC1, EEF1A2, GBA2, FNIP1, ACSL6, STARD10, VPS26B, ACAD8, GLB1L3, NRN1L, LCAT, and SLC7A6. These genes contributed to FE traits in Egyptian goats, as they are involved in obesity, metabolism, and the transport of energy, vitamins, fatty acids, proteins, and lipids through diverse biological pathways.<br><br>DISCUSSION: This study suggests that specific genetic markers and rumen microbial traits could be used to identify high-efficient individuals in Egyptian goat breeds, and improving breeding strategies for FE.}, }
@article {pmid39944648, year = {2025}, author = {Lu, J and Jiang, M and Chai, D and Sun, Y and Wu, L}, title = {Integrative analysis of intestinal flora and untargeted metabolomics in attention-deficit/hyperactivity disorder.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1452423}, pmid = {39944648}, issn = {1664-302X}, abstract = {Attention Deficit Hyperactivity Disorder (ADHD) is a clinically common neurodevelopmental disorder of the brain. In addition to genetic factors, an imbalance in gut flora may also play a role in the development of ADHD. Currently, it is critical to investigate the function of gut flora and related metabolites, which may form the fundamental basis of bidirectional cross-linking between the brain and the gut, in addition to focusing on the changed gut flora in ADHD. This study aimed to investigate the possible relationship between changes in gut flora and metabolites and ADHD by analyzing metagenome and untargeted metabolomics of fecal samples from ADHD patients. Specifically, we attempted to identify key metabolites and the metabolic pathways they are involved in, as well as analyze in detail the structure and composition of the gut flora of ADHD patients. In order to further investigate the relationship between gut flora and ADHD symptoms, some behavioral studies were conducted following the transplantation of gut flora from ADHD patients into rats. The results of the metagenome analysis revealed several distinct strains, including Bacteroides cellulosilyticus, which could be important for diagnosing ADHD. Additionally, the ADHD group showed modifications in several metabolic pathways and metabolites, including the nicotinamide and nicotinic acid metabolic pathways and the metabolite nicotinamide in this pathway. The behavioral results demonstrated that rats with ADHD gut flora transplants displayed increased locomotor activity and interest, indicating that the onset of behaviors such as ADHD could be facilitated by the flora associated with ADHD. This research verified the alterations in gut flora and metabolism observed in ADHD patients and provided a list of metabolites and flora that were significantly altered in ADHD. Simultaneously, our findings revealed that modifications to the microbiome could potentially trigger behavioral changes in animals, providing an experimental basis for comprehending the function and influence of gut flora on ADHD. These results might provide new perspectives for the development of novel treatment strategies.}, }
@article {pmid39944640, year = {2025}, author = {Shao, C and Chen, S and Yang, H and Li, M and Liu, Y and Wen, S and Xiao, J and Tang, L}, title = {Age and diet affect self-resilience of intestinal microbiome in mice.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1507396}, pmid = {39944640}, issn = {1664-302X}, abstract = {BACKGROUND: Gut microbiota contributes to human health. Little is known about the self-resilience of the gut microbiota after dysbiosis. This study aimed to investigate the self-resilience of the gut microbiome at different ages and the effects of diet on its recovery capacity in adulthood.<br><br>METHODS: A rodent model of antibiotic-induced dysbiosis was used. Microscopy was used to observe morphological changes in the mucosa. In addition, 16S rRNA sequencing and polymerase chain reaction-denaturing gradient gel electrophoresis were performed to identify the bacterial taxa and microbiome structure, respectively.<br><br>RESULTS: The diversity of the gut microbiota in infant mice was recovered by the sixth week, while relative abundance of Ruminococcaceae_UCG_014 was low and did not return to normal levels. Gut microbiota in young adult mice recovered in the fourth week. Prevotellaceae and Alloprevotella were significantly higher in the high-fat-diet group than those in the control group. The elderly mice had three, two, four, and seven statistically different genera between the dysbiosis and control groups at weeks 6, 8, 10, and 12, respectively. Intestinal epithelial structure and cecum index are restored with microbiota repaired.<br><br>DISCUSSION: The gut microbiota in infant and adult mice is more capable of self- resilience, the composition of the microbiota and mucosal morphology of the intestine can be largely restored. Adding protein and fat to the diet accelerated colony recovery in young adult mice in the short term. In elderly mice, the resilience of the gut microbiota was reduced, and the occurrence of dysbiosis at this stage may accelerate organismal aging and affect the lifespan. A limitation of this study is that all data were derived from mice. Therefore, we must be cautious about translating the microbiome results from mice to humans.}, }
@article {pmid39944638, year = {2025}, author = {Sarsaiya, S and Jain, A and Singh, R and Gong, Q and Wu, Q and Chen, J and Shi, J}, title = {Unveiling the rhizosphere microbiome of Dendrobium: mechanisms, microbial interactions, and implications for sustainable agriculture.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1531900}, pmid = {39944638}, issn = {1664-302X}, abstract = {The rhizosphere microbiome plays a critical role in plant health and productivity by fostering beneficial microbial interactions that support nutrient cycling, stress tolerance, and disease suppression. In the context of Dendrobium, understanding its interactions is essential for optimizing cultivation and promoting sustainable agricultural practices. This review explores the rhizosphere microbiome of Dendrobium, focusing on the mechanisms and microbial interactions that contribute to plant health, stress tolerance, and growth and their implications for sustainable agriculture. This study highlights the diverse composition of microbial communities in the Dendrobium rhizosphere, including key bacteria (e.g., Pseudomonas fluorescens and Bacillus subtilis), fungi (e.g., Glomus spp.), and biocontrol agents (Trichoderma spp.), and discusses their roles in nutrient cycling, disease suppression, and plant growth promotion. This review emphasizes the significance of plant-microbe signaling, such as the production of flavonoids, phytohormones, and strigolactones, in shaping the microbial environment and enhancing plant resilience. Additionally, it addresses modern techniques for analyzing microbial communities, including metagenomics and next-generation sequencing, and their applications in advancing precision agriculture. Future research should focus on bridging knowledge gaps related to genotype-microbiome interactions, exploring emerging microbial consortia and enhancing the integration of microbiome management in precision agriculture systems to improve plant health and productivity.}, }
@article {pmid39944596, year = {2025}, author = {Brizola Toscan, R and Lesiński, W and Stomma, P and Subramanian, B and Łabaj, PP and Rudnicki, WR}, title = {Antimicrobial resistance in diverse urban microbiomes: uncovering patterns and predictive markers.}, journal = {Frontiers in genetics}, volume = {16}, number = {}, pages = {1460508}, pmid = {39944596}, issn = {1664-8021}, abstract = {Antimicrobial resistance (AMR) is a growing global health concern, driven by urbanization and anthropogenic activities. This study investigated AMR distribution and dynamics across microbiomes from six U.S. cities, focusing on resistomes, viromes, and mobile genetic elements (MGEs). Using metagenomic data from the CAMDA 2023 challenge, we applied tools such as AMR++, Bowtie, AMRFinderPlus, and RGI for resistome profiling, along with clustering, normalization, and machine learning techniques to identify predictive markers. AMR++ and Bowtie outperformed other tools in detecting diverse AMR markers, with binary normalization improving classification accuracy. MGEs were found to play a critical role in AMR dissemination, with 394 genes shared across all cities. Removal of MGE-associated AMR genes altered resistome profiles and reduced model performance. The findings reveal a heterogeneous AMR landscape in urban microbiomes, particularly in New York City, which showed the highest resistome diversity. These results underscore the importance of MGEs in AMR profiling and provide valuable insights for designing targeted strategies to address AMR in urban settings.}, }
@article {pmid39944558, year = {2024}, author = {Hornikova, T and Jelinkova, A and Jiraskova Zakostelska, Z and Thon, T and Coufal, S and Polouckova, A and Kopelentova, E and Kverka, M and Makovicky, P and Tlaskalova-Hogenova, H and Sediva, A and Schwarzer, M and Srutkova, D}, title = {Genetic background and microbiome drive susceptibility to epicutaneous sensitization and food allergy in adjuvant-free mouse model.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1509691}, pmid = {39944558}, issn = {1664-3224}, mesh = {Animals ; *Food Hypersensitivity/immunology/microbiology ; Mice ; *Gastrointestinal Microbiome/immunology ; *Mice, Inbred BALB C ; *Disease Models, Animal ; *Ovalbumin/immunology ; *Skin/immunology/microbiology ; *Th2 Cells/immunology ; *Allergens/immunology ; Genetic Background ; Mast Cells/immunology/metabolism ; Female ; Mice, Inbred C57BL ; Genetic Predisposition to Disease ; Chymases/genetics/metabolism ; Cytokines/metabolism ; Germ-Free Life ; Immunization ; }, abstract = {BACKGROUND: The dual allergen exposure hypothesis states that sensitization to food antigens occurs through a damaged skin barrier in individuals with no previous oral tolerance to certain foods. However, the resulting allergic reaction could depend on factors such as the host's genetic predisposition as well as the skin and gut microbiota.<br><br>METHODS: Specific-pathogen-free BALB/c and C57BL/6 and germ-free (GF) BALB/c mice were epicutaneously sensitized with ovalbumin (OVA) via dorsal tape-stripped skin and challenged with OVA by intragastric gavage. The development of food allergy (FA) symptoms, the Th2 and mast cell immune response and differences in the skin and gut microbiota were investigated.<br><br>RESULTS: BALB/c mice, but not C57BL/6 mice, showed severe clinical signs of FA (hypothermia, diarrhea) as well as a stronger serum antibody response and Th2 cytokine secretion in the spleen and jejunum after OVA-treatment. The increased mast cell count correlated with higher MCPT-1 production and histidine decarboxylase mRNA expression in the jejunum of these mice. The 16S rRNA sequencing analysis revealed lower abundance of short-chain fatty acids producing bacteria in the gut microbiome of OVA-treated BALB/c mice. Changes in the &#x3b2;-diversity of the gut microbiome reflect both the genetic background as well as the OVA treatment of experimental mice. Compared to SPF mice, GF mice developed more severe anaphylactic hypothermia but no diarrhea, although they had a higher mast cell count, increased MCPT-1 production in the jejunum and serum, and increased arachidonate 5-lipoxygenase mRNA expression.<br><br>CONCLUSIONS: We show that the BALB/c mice are a mouse strain of choice for model of adjuvant-free epicutaneous sensitization through the disrupted skin barrier and following food allergy development. Our results highlight the significant influence of genetic background and microbiota on food allergy susceptibility, emphasizing the complex interplay between these factors in the allergic response.}, }
@article {pmid39944521, year = {2024}, author = {Langgartner, D and Weiss, AJ and Amoroso, M and Sterrett, JD and Lowry, CA and Reber, SO}, title = {Effects of repeated intragastric administrations with heat-inactivated Mycobacterium aurum DSM 33539 on the stress-induced aggravation of dextran sulfate sodium (DSS) colitis in C57BL/6N mice.}, journal = {Frontiers in neuroscience}, volume = {18}, number = {}, pages = {1488603}, pmid = {39944521}, issn = {1662-4548}, abstract = {Stress-protective effects have been reported for M. vaccae NCTC 11659 and M. vaccae ATCC 15483[T]. However, it remains to be investigated whether also closely related rapidly growing environmental saprophytic non-tuberculous mycobacteria (NTM) species have protective effects against the negative consequences of chronic psychosocial stress. Therefore, the aim of the current study was to assess whether repeated i.g. administrations of a heat-inactivated preparation of Mycobacterium aurum DSM 33539 prior to 19 days of chronic subordinate colony housing (CSC) are able to ameliorate the negative effects of this preclinically validated mouse model for chronic psychosocial stress on subsequent dextran sulfate sodium (DSS) colitis in male C57BL/6N mice. The results of the present study show that repeated i.g. administrations of M. aurum DSM 33539 have stabilizing effects on the composition of the gut microbiome, indicated by the findings that M. aurum DSM 33539 prevented CSC-induced increases in the relative abundances of the colitogenic phyla Desulfobacterota and Deferribacterota. Indeed, the relative abundance of Deferribacterota on day 19 was strongly correlated with histological damage to the colon. In line with the latter, M. aurum DSM 33539 was further protective against the aggravating effects of stress on subsequent DSS colitis. Collectively, our findings confirm and extend previous findings from our group and suggest that the stress-protective effects reported for M. vaccae NCTC 11659 and M. vaccae ATCC 15483[T] are generalizable also to other NTM species.}, }
@article {pmid39944472, year = {2024}, author = {Ariaee, A and Koentgen, S and Wardill, HR and Hold, GL and Prestidge, CA and Armstrong, HK and Joyce, P}, title = {Prebiotic selection influencing inflammatory bowel disease treatment outcomes: a review of the preclinical and clinical evidence.}, journal = {eGastroenterology}, volume = {2}, number = {2}, pages = {e100055}, pmid = {39944472}, issn = {2976-7296}, abstract = {Inflammatory bowel disease (IBD) is characterised by chronic inflammation in the gastrointestinal tract, with unclear aetiology but with known factors contributing to the disease, including genetics, immune responses, environmental factors and dysbiosis of the gut microbiota. Existing pharmacotherapies mainly target the inflammatory symptoms of disease, but recent research has highlighted the capacity for microbial-accessible carbohydrates that confer health benefits (ie, prebiotics) to selectively stimulate the growth of beneficial gut bacteria for improved IBD management. However, since prebiotics vary in source, chemical composition and microbiota effects, there is a clear need to understand the impact of prebiotic selection on IBD treatment outcomes. This review subsequently explores and contrasts the efficacy of prebiotics from various sources (β-fructans, galacto-oligosaccharides, xylo-oligosaccharides, resistant starch, pectin, β-glucans, glucomannans and arabinoxylans) in mitigating IBD symptomatology, when used as either standalone or adjuvant therapies. In preclinical animal colitis models, prebiotics have revealed type-dependent effects in positively modulating gut microbiota composition and subsequent attenuation of disease indicators and proinflammatory responses. While prebiotics have demonstrated therapeutic potential in animal models, clinical evidence for their precise efficacy remains limited, stressing the need for further investigation in human patients with IBD to facilitate their widespread clinical translation as microbiota-targeting IBD therapies.}, }
@article {pmid39944364, year = {2024}, author = {Prosty, C and Katergi, K and Papenburg, J and Lawandi, A and Lee, TC and Shi, H and Burnham, P and Swem, L and Routy, B and Yansouni, CP and Cheng, MP}, title = {Causal role of the gut microbiome in certain human diseases: a narrative review.}, journal = {eGastroenterology}, volume = {2}, number = {3}, pages = {e100086}, pmid = {39944364}, issn = {2976-7296}, abstract = {Composed of an elaborate ecosystem of bacteria, fungi, viruses and protozoa residing in the human digestive tract, the gut microbiome influences metabolism, immune modulation, bile acid homeostasis and host defence. Through observational and preclinical data, the gut microbiome has been implicated in the pathogenesis of a spectrum of chronic diseases ranging from psychiatric to gastrointestinal in nature. Until recently, the lack of unequivocal evidence supporting a causal link between gut microbiome and human health outcomes incited controversy regarding its significance. However, recent randomised controlled trial (RCT) evidence in conditions, such as Clostridioides difficile infection, cancer immunotherapy and ulcerative colitis, has supported a causal relationship and has underscored the potential of the microbiome as a therapeutic target. This review delineates the RCT evidence substantiating the potential for a causal relationship between the gut microbiome and human health outcomes, the seminal observational evidence that preceded these RCTs and the remaining knowledge gaps.}, }
@article {pmid39944355, year = {2024}, author = {Li, S and Li, R and Lee, JR and Zhao, N and Ling, W}, title = {ZINQ-L: a zero-inflated quantile approach for differential abundance analysis of longitudinal microbiome data.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1494401}, pmid = {39944355}, issn = {1664-8021}, abstract = {BACKGROUND: Identifying bacterial taxa associated with disease phenotypes or clinical treatments over time is critical for understanding the underlying biological mechanism. Association testing for microbiome data is already challenging due to its complex distribution that involves sparsity, over-dispersion, heavy tails, etc. The longitudinal nature of the data adds another layer of complexity - one needs to account for the within-subject correlations to avoid biased results. Existing longitudinal differential abundance approaches usually depend on strong parametric assumptions, such as zero-inflated normal or negative binomial. However, the complex microbiome data frequently violate these distributional assumptions, leading to inflated false discovery rates. In addition, the existing methods are mostly mean-based, unable to identify heterogeneous associations such as tail events or subgroup effects, which could be important biomedical signals.<br><br>METHODS: We propose a zero-inflated quantile approach for longitudinal (ZINQ-L) microbiome differential abundance test. A mixed-effects quantile rank-score-based test was proposed for hypothesis testing, which consists of a test in mixed-effects logistic model for the presence-absence status of the investigated taxon, and a series of mixed-effects quantile rank-score tests adjusted for zero inflation given its presence. As a regression method with minimal distributional assumptions, it is robust to the complex microbiome data, controlling false discovery rate, and is flexible to adjust for important covariates. Its comprehensive examination of the abundance distribution enables the identification of heterogeneous associations, improving the testing power.<br><br>RESULTS: Extensive simulation studies and an application to a real kidney transplant microbiome study demonstrate the improved power of ZINQ-L in detecting true signals while controlling false discovery rates.<br><br>CONCLUSION: ZINQ-L is a zero-inflated quantile-based approach for detecting individual taxa associated with outcomes or exposures in longitudinal microbiome studies, providing a robust and powerful option to improve and complement the existing methods in the field.}, }
@article {pmid39944304, year = {2025}, author = {Newton, C and Fichera, A}, title = {Anastomosis after Bowel Resection for Crohn's Disease: State of the Art Review.}, journal = {Clinics in colon and rectal surgery}, volume = {38}, number = {2}, pages = {104-112}, pmid = {39944304}, issn = {1531-0043}, abstract = {Recurrence after surgically induced remission in Crohn's disease remains a topic of research and debate with significant clinical implications for overall quality of life and intestinal and defecatory functions. While the surgeon continues to play a critical role in surgical prophylaxis of recurrence, optimal results will only be obtained in the setting of a true multidisciplinary team approach, following the principles of "the right surgery, on the right patient, at the right time, performed by the right surgeon, supported by the right team." The centerpiece of surgical prophylaxis is the intestinal anastomosis. The ideal anastomosis after resection for Crohn's disease should be safe and reliable, as postoperative septic complications have been shown to increase the risk of recurrence; result in a wide lumen and a configuration that would not impede enteric flow; exclude or excise the mesentery, a known culprit in primary and recurrent disease; and preserve vascularization and innervation. This article will review the evidence supporting the above-mentioned surgical principles and the long-term results of the different anastomotic configurations.}, }
@article {pmid39944265, year = {2024}, author = {Ye, ZN and Eslick, GD and Huang, SG and He, XX}, title = {Faecal microbiota transplantation for eradicating Helicobacter pylori infection: clinical practice and theoretical postulation.}, journal = {eGastroenterology}, volume = {2}, number = {4}, pages = {e100099}, pmid = {39944265}, issn = {2976-7296}, abstract = {The sustained increase in antibiotic resistance leads to a declining trend in the eradication rate of Helicobacter pylori (H. pylori) infection with antibiotic-based eradication regimens. Administration of a single probiotic shows limited efficacy in eradicating H. pylori infection. This review indicates that faecal microbiota transplantation (FMT), a novel therapeutic approach, either as a monotherapy or adjunctive therapy, exhibits beneficial effects in terms of the eradication of H. pylori infection and the prevention of adverse events. The role of FMT in H. pylori eradication may be associated directly or indirectly with some therapeutic constituents within the faecal suspension, including bacteria, viruses, antimicrobial peptides and metabolites. In addition, variations in donor selection, faecal suspension preparation and delivery methods are believed to be the main factors determining the effectiveness of FMT for the treatment of H. pylori infection. Future research should refine the operational procedures of FMT to achieve optimal efficacy for H. pylori infection and explore the mechanisms by which FMT acts against H. pylori.}, }
@article {pmid39944118, year = {2025}, author = {Yang, J and Song, I and Saito, M and Hartanto, T and Ichinohe, T and Fukuda, S}, title = {Partially hydrolyzed guar gum attenuates symptoms and modulates the gut microbiota in a model of SARS-CoV-2 infection.}, journal = {Gut microbiome (Cambridge, England)}, volume = {6}, number = {}, pages = {e1}, pmid = {39944118}, issn = {2632-2897}, abstract = {The coronavirus disease 2019 (COVID-19) pandemic has caused health issues worldwide. Studies have suggested that modulation of the gut microbiota could attenuate the severity of COVID-19 symptoms. In light of this, we explored the effects of the prebiotic dietary fibre partially hydrolyzed guar gum (PHGG) on SARS-CoV-2 infection in a Syrian hamster model, hypothesizing that modulation of the gut microbiome and intestinal metabolites through PHGG administration would improve COVID-19 disease outcomes. Eight hamsters each were assigned to the PHGG administration and control groups. The PHGG group was given a diet supplemented with 5% PHGG for two weeks. Consequently, PHGG improved the host survival rate to 100% compared to 25% of the control group (P = 0.003) and attenuated morbid weight loss. Another non-infected set of hamsters was used for the analysis of the gut microbiome composition with 16S rRNA amplicon sequencing, serum, and faecal metabolites with GC-MS and LC-MS. PHGG altered the gut microbiome composition and increased the relative abundances of Ileibacterium, Bifidobacterium, and Prevotella. Furthermore, it elevated the concentrations of faecal valeric acid, propionic acid, ursodeoxycholic acid, and serum deoxycholic acid. Taken together, our data suggest that the prebiotic PHGG modulates gut metabolites and has the potential to reduce COVID-19 morbidity.}, }
@article {pmid39944117, year = {2025}, author = {Longwani, U and Sharma, AK and Malwe, AS and Jaiswal, SK and Sharma, VK}, title = {GutBugDB: a web resource to predict the human gut microbiome-mediated biotransformation of biotic and xenobiotic molecules.}, journal = {Gut microbiome (Cambridge, England)}, volume = {6}, number = {}, pages = {e3}, pmid = {39944117}, issn = {2632-2897}, abstract = {There has been a growing recognition of the significant role played by the human gut microbiota in altering the bioavailability as well as the pharmacokinetic and pharmacodynamic aspects of orally ingested xenobiotic and biotic molecules. The determination of species-specific contributions to the metabolism of biotic and xenobiotic molecules has the potential to aid in the development of new therapeutic and nutraceutical molecules that can modulate human gut microbiota. Here we present "GutBugDB," an open-access digital repository that provides information on potential gut microbiome-mediated biotransformation of biotic and xenobiotic molecules using the predictions from the GutBug tool. This database is constructed using metabolic proteins from 690 gut bacterial genomes and 363,872 protein enzymes assigned with their EC numbers (with representative Expasy ID and domains present). It provides information on gut microbiome enzyme-mediated metabolic biotransformation for 1439 FDA-approved drugs and nutraceuticals. GutBugDB is publicly available at https://metabiosys.iiserb.ac.in/gutbugdb/.}, }
@article {pmid39943435, year = {2025}, author = {Kosinski, L and Engen, PA and Swanson, B and Villanueva, M and Shaikh, M and Green, SJ and Naqib, A and Hamaker, B and Cantu-Jungles, TM and Keshavarzian, A}, title = {Use of a Novel Passive E-Nose to Monitor Fermentable Prebiotic Fiber Consumption.}, journal = {Sensors (Basel, Switzerland)}, volume = {25}, number = {3}, pages = {}, doi = {10.3390/s25030797}, pmid = {39943435}, issn = {1424-8220}, mesh = {Humans ; *Electronic Nose ; *Dietary Fiber/analysis/metabolism ; *Volatile Organic Compounds/analysis ; *Feces/microbiology/chemistry ; *Prebiotics/analysis ; Male ; Female ; *RNA, Ribosomal, 16S/genetics ; Adult ; Fermentation ; Gastrointestinal Microbiome/physiology ; }, abstract = {We developed a home-based electronic nose (E-Nose) to passively monitor volatile organic compounds (VOCs) emitted following bowel movements and assessed its validity by correlating the output with prebiotic fiber intake. Healthy, non-overweight participants followed a three-week protocol which included the following: (1) installing the E-Nose in their bathroom; (2) activating the device following each bowel movement; (3) recording their dietary intake; (4) consuming a fiber bar (RiteCarbs) containing a blend of 10 g of prebiotic fiber daily during weeks two and three; and (5) submit stool specimens at the beginning and end of the study for 16S rRNA gene sequencing and analysis. Participants' fecal microbiome displayed significantly increased relative abundance of putative total SCFA-producing genera (p = 0.0323) [total acetate-producing genera (p = 0.0214), total butyrate-producing genera (p = 0.0131)] and decreased Gram-negative proinflammatory genera (p = 0.0468). Prebiotic intervention significantly increased the participants' fiber intake (p = 0.0152), E-Nose Min/Max (p = 0.0339), and area over the curve in VOC-to-fiber output (p = 0.0044). Increased fiber intake was negatively associated (R[2] = 0.53, p = 0.026) with decreased relative abundance of putative Gram-negative proinflammatory genera. This proof-of-concept study demonstrates that a prototype E-Nose can noninvasively detect a direct connection between fiber intake and VOC outputs in a home-based environment.}, }
@article {pmid39943210, year = {2025}, author = {Kim, EB and Choi, S and Park, J and Xuan, B}, title = {Effects of Increased Housing Space Without Altering Stocking Density on Body Weight, Stress, and Gut Microbiome in Broiler Chickens.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/ani15030441}, pmid = {39943210}, issn = {2076-2615}, support = {RS-2024-00344849//National Research Foundation of Korea/ ; }, abstract = {Effective poultry management practices that promote chicken health are crucial for producing higher-quality chicken meat at a lower cost. This study examined the hypothesis that increasing space while maintaining stocking density may positively impact poultry health. We evaluated body weight (BW) as an indicator of growth, stress markers, and the composition of the gut microbiome by comparing two housing sizes: smaller (control) and larger (treatment) spaces, with 10 birds per space and a stocking density of 12.3 birds/m[2]. Chickens in the larger space had 15% higher BW (p = 0.06) compared to those in the smaller space when significance was evaluated at p < 0.10. Stress indicators such as blood cortisol (acute) and brain FKBP51 did not differ significantly. Faith's phylogenetic diversity was marginally higher in the larger space (p = 0.05), and microbial communities differed significantly between the two groups. The relative abundance of several genera, including Clostridium_sensu_stricto_1 (p = 0.02), Lactobacillus (p = 0.03), and Paracoccus (p < 0.01), was greater in the larger space, whereas Turicibacter (p = 0.02), Escherichia-Shigella (p = 0.01), and Lysinibacillus (p = 0.01) were more abundant in the smaller space. The larger and smaller spaces were associated with a significant (p < 0.05) increase in the abundance of 39 and 25 MetaCyc pathways, respectively, involved in amino acid and nitrogen metabolisms. These findings suggest that increasing housing space without altering stocking density or additional treatments may improve both growth and gut microbiome health in broilers. Our results provide insights into the relationship between chicken housing environments and the gut microbiome.}, }
@article {pmid39943180, year = {2025}, author = {Tadee, P and Khaodang, P and Patchanee, P and Buddhasiri, S and Eiamsam-Ang, T and Kittiwan, N and Tadee, P}, title = {Characterization of Lung Microbiome in Subclinical Pneumonic Thai Pigs Using 16S rRNA Gene Sequencing.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/ani15030410}, pmid = {39943180}, issn = {2076-2615}, support = {R67IN00549//Faculty of Veterinary Medicine, Chiang Mai University/ ; }, abstract = {Bacterial respiratory disease is one of the major concerns in the modern pig industry. To address the limitations of culture-based methods, 16S rRNA sequencing was employed to characterize the pig lung microbiome to gain a better understanding of microbial physiology and their population genetics. A batch of 510 slaughtered pigs from a farm located in Lampang province, Thailand, was selected. Individual pig weight was recorded. A total of 24 lungs (10 normal and 14 pneumonic lungs) were sampled for gross lesion examination and lung microbial communities were investigated. Poor growth performance and weight uniformity were denoted in this batch. Several pathogenic bacteria were detected in both normal and pneumonic lungs. Microbial diversity was decreased in the pneumonic group. PCoA and NMDS analysis showed a clear separation between the groups. Stenotrophomonas spp. (42.12%) was the dominant genus identified in normal lungs, while Mycoplasma hyopneumoniae (71.97%) was the most abundant in pneumonic lungs, correlating with the commonly observed consolidation lesions. The slaughterhouse serves as a key checkpoint for gathering comprehensive information on pig respiratory health, and lung is representative of the lower respiratory tract for microbiomics. Monitoring of lung lesions should be implemented routinely to gain a better understanding of regional pig respiratory health.}, }
@article {pmid39943163, year = {2025}, author = {Du, H and Li, K and Guo, W and Na, M and Zhang, J and Na, R}, title = {Maternal Roughage Sources Influence the Gastrointestinal Development of Goat Kids by Modulating the Colonization of Gastrointestinal Microbiota.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/ani15030393}, pmid = {39943163}, issn = {2076-2615}, support = {BR22-13-02//Basic scientific research business fee project for universities directly under the Inner Mongolia Autonomous Region/ ; NMGIRT2322//Innovative Research Team in Universities of Inner Mongolia Autonomous Region/ ; }, abstract = {During pregnancy and lactation, maternal nutrition is linked to the full development of offspring and may have long-term or lifelong effects. However, the influence of the doe's diet on the gastrointestinal (GI) tract of young kids remains largely unexplored. Therefore, we investigated the effects of doe roughage sources (alfalfa hay, AH, or corn straw, CS) during pregnancy and lactation on kid growth, GI morphology, barrier function, metabolism, immunity, and microbiome composition. The results indicate that, compared with the CS group, does fed an AH diet had significantly higher feed intake (p < 0.01). However, CS-fed does exhibited higher neutral detergent fiber (NDF) digestibility (p < 0.05). There were no significant differences in animal (doe or kid) weight among the groups (p > 0.05). In the rumen of goat kids, the AH group exhibited a higher papillae width and increased levels of interleukin-10 (IL-10) compared with the CS group (p < 0.05). In the jejunum of goat kids, the AH group showed a higher villus-height-to-crypt-depth (VH/CD) ratio, as well as elevated levels of secretory immunoglobulin A (SIgA), immunoglobulin G (IgG), IL-10, acetate, and total volatile fatty acids (TVFAs), when compared with the CS group (p < 0.05). Transcriptome analysis revealed that the source of roughage in does was associated with changes in the GI transcriptome of the kids. Differentially expressed genes (DEGs) in the rumen were mainly associated with tissue development and immune regulation, while the DEGs in the jejunum were mainly associated with the regulation of transferase activity. Spearman correlation analyses indicated significant associations between GI DEGs and phenotypic indicators related to GI development, immunity, and metabolism. LEfSe analysis identified 14 rumen microbial biomarkers and 6 jejunum microbial biomarkers. Notably, these microorganisms were also enriched in the rumen or day 28 milk of the does. Further microbial composition analysis revealed significant correlations between the rumen and milk microbiomes of does and the rumen or jejunum microbiomes of kids. Association analyses indicated that microbial biomarkers interact with host genes, thereby affecting the development and function of the GI system. Additionally, correlation analyses revealed significant association between milk metabolites and the rumen and jejunum microbiomes of kids. This study demonstrated that maternal diet significantly influences the development of microbial ecosystems in offspring by modulating microbial communities and metabolite composition. The early colonization of GI microorganisms is crucial for the structural development, barrier function, immune capacity, and microbial metabolic activity of the GI system.}, }
@article {pmid39943131, year = {2025}, author = {Frazier, AN and Ferree, L and Belk, AD and Al-Lakhen, K and Cramer, MC and Metcalf, JL}, title = {Stochasticity Highlights the Development of Both the Gastrointestinal and Upper-Respiratory-Tract Microbiomes of Neonatal Dairy Calves in Early Life.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/ani15030361}, pmid = {39943131}, issn = {2076-2615}, abstract = {The microbiome of dairy calves undergoes extensive change due to various forces during the first weeks of life. Importantly, diseases such as bovine respiratory disease (BRD) and calf diarrhea can have profound impacts on the early-life microbiome. Therefore, a longitudinal, repeated-measures pilot study was designed to characterize the establishment of nasal and fecal microbiomes of dairy calves, assess the governing forces of microbial assembly, and evaluate how disease states impact these microbial ecologies. Dairy calves (n = 19) were clinically evaluated for gastrointestinal and respiratory disease across three weeks beginning at age ≤ seven days old. Fecal (n = 57) and nasal (n = 57) microbial samples were taken for paired-end 16S rRNA gene amplicon sequencing. Taxonomy and diversity analyses were used to characterize early-life nasal and fecal microbiomes. Stochasticity and determinism were measured using normalized stochasticity testing (NST) and Dirichlet multinomial model (DMM). All analyses were tested for statistical significance. Clinical diarrhea was observed in 11 of the 19 calves. Clinical BRD was not independently observed among the cohort; however, two calves presented clinical signs of both BRD and diarrhea. Taxonomic analysis revealed that fecal samples were highlighted by Bacteroidaceae (40%; relative abundance), Ruminococcaceae (13%), and Lachnospiraceae (10%), with changes in diversity (Kruskal-Wallis; p < 0.05) and composition (PERMANOVA; p < 0.05). Clinical diarrhea reduced diversity in the fecal microbiome but did not impact composition. Nasal samples featured Moraxellaceae (49%), Mycoplasmataceae (16%), and Pasteurellaceae (3%). While no diversity changes were seen in nasal samples, compositional changes were observed (p < 0.05). NST metrics (Kruskal-Wallis; p > 0.01) and DMM (PERMANOVA; p < 0.01) revealed that stochastic, neutral theory-based assembly dynamics govern early-life microbial composition and that distinct microbial populations drive community composition in healthy and diarrheic calves.}, }
@article {pmid39943124, year = {2025}, author = {François, AC and Cesarini, C and Taminiau, B and Renaud, B and Kruse, CJ and Boemer, F and van Loon, G and Palmers, K and Daube, G and Wouters, CP and Lecoq, L and Gustin, P and Votion, DM}, title = {Unravelling Faecal Microbiota Variations in Equine Atypical Myopathy: Correlation with Blood Markers and Contribution of Microbiome.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/ani15030354}, pmid = {39943124}, issn = {2076-2615}, support = {D65-1418-projet SAMA//Service Public de Wallonie/ ; }, abstract = {Hypoglycin A and methylenecyclopropylglycine are protoxins responsible for atypical myopathy in equids. These protoxins are converted into toxins that inhibit fatty acid β-oxidation, leading to blood accumulation of acylcarnitines and toxin conjugates, such as methylenecyclopropylacetyl-carnitine. The enzymes involved in this activation are also present in some prokaryotic cells, raising questions about the potential role of intestinal microbiota in the development of intoxication. Differences have been noted between the faecal microbiota of cograzers and atypical myopathy-affected horses. However, recent blood acylcarnitines profiling revealed subclinical cases among cograzers, challenging their status as a control group. This study investigates the faecal microbiota of horses clinically affected by atypical myopathy, their cograzers, and a control group of toxin-free horses while analysing correlations between microbiota composition and blood parameters. Faecal samples were analysed using 16S amplicon sequencing, revealing significant differences in α-diversity, evenness, and β-diversity. Notable differences were found between several genera, especially Clostridia_ge, Bacteria_ge, Firmicutes_ge, Fibrobacter, and NK4A214_group. Blood levels of methylenecyclopropylacetyl-carnitine and C14:1 correlated with variations in faecal microbial composition. The theoretical presence of enzymes in bacterial populations was also investigated. These results underscore the critical need to investigate the potential role of intestinal microbiota in this poisoning and may provide insights for developing prevention and treatment strategies.}, }
@article {pmid39943093, year = {2025}, author = {Odu-Onikosi, SG and Momoh, TA and Abarra, ST and Wood, NE and Amulejoye, FD and Emery, M and Harper, GM and Eynon, B and Kuri, V and Kühlwein, H and Merrifield, DL}, title = {Impact of Autolysed Brewer's Yeast and Soluble Dried Yeast Extract on Growth Performance and Mucosal Health of Atlantic Salmon (Salmo salar) Parr.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/ani15030323}, pmid = {39943093}, issn = {2076-2615}, support = {N/A//Tertiary Education Trust Fund/ ; N/A//Lagos State University of Science and Technology, Nigeria/ ; N/A//Leiber (Germany)/ ; }, abstract = {Yeast-based feed additives have emerged as promising functional feed additives (FFAs) to promote sustainable aquaculture development through enhanced gut health and immune modulation in fish. The present study evaluated the impact of autolysed brewer's yeast (ABY) and soluble dried yeast extract (SDYE) in improving the intestinal and skin histology, immune response, and intestinal microbiome of Atlantic salmon parr (Salmo salar) over a 9-week feeding trial. Three experimental diets were produced: a control diet, a diet supplemented with ABY at 2.5 g/kg, and a diet supplemented with SDYE at 2.5 g/kg. These diets were administered to triplicate tanks of Atlantic salmon. The yeast-supplemented diets, especially ABY, improved intestinal mucosal fold length, lamina propria width, microvilli density, and intestinal goblet cell counts, as well as skin goblet cell counts. The yeast additives had no detrimental effects on the fish haematology, with no significant differences in haemoglobin concentration, red blood cell counts, and white blood cell counts among the treatment groups. Gene expression analysis revealed upregulation of il-1β and muc-2 in fish fed the ABY diet, indicating enhanced immune function and potentially mucosal protection. Intestinal microbiota analysis revealed Firmicutes as the most dominant phylum in all groups, followed by Actinobacteriota. Distinct bacterial community shifts were observed between the treatment groups, with a significant increase in the relative abundance of taxa such as Staphylococcus in yeast-supplemented diets and a significant decrease in Streptococcus and Weissella. Collectively, these findings suggest that the yeast additives, especially ABY, enhance gut health and immune function without compromising growth performance.}, }
@article {pmid39943086, year = {2025}, author = {Küçükoflaz, M and Özbek, V and Güçlü, BK and Sarıözkan, S and Zaman, C&#x130; and Aydın, E and Makav, M and Beyzi, SB and Öztaş, SY and Akın, MA}, title = {Effects of Bacillus amyloliquefaciens FD777 and Macleaya cordata Extract on Performance, Immunity, Gastrointestinal System Microbiome, and Profitability in Holstein Calves.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/ani15030313}, pmid = {39943086}, issn = {2076-2615}, abstract = {This study was performed to determine the effects of dietary supplementation of Bacillus amyloliquefaciens FD777 (BA) and Macleaya cordata extract (MCE) on the performance, morbidity and mortality rates, body measurements, immunity, rumen parameters, antioxidant parameters, microbiome level, and profitability of calves during the pre-weaning period. In the study, 51 calves were divided into three groups as one control and two treatment groups considering their age (1 day old), gender (nine females and eight males in each group), and birth weight (37.7 ± 0.4 kg). The calves in the control group (CON) were fed milk without supplements whereas the first treatment group (BA) was fed milk containing 10 mL/day/head of Bacillus amyloliquefaciens FD777 and the second treatment group (MCE) was fed milk containing 2 g/day/head of MCE. As a result, supplementing BA and MCE to calf milk had no significant effect on body weight (BW), dry matter intake (DMI), feed efficiency (FE), morbidity and mortality rates, rumen pH, IgG, IgA, and IgM values, and gastrointestinal microbiota (p > 0.05). On the other hand, it was determined that body weight gain (BWG), body length, body depth, rump width, withers height change, rump height change, rump width change, and serum GSH level increased significantly in the BA group compared to the control group (p < 0.05). According to the partial budget analysis, despite the additional cost of supplementing BA to the calf milk, no calf deaths and lower disease were observed in this group, unlike the other groups, resulting in a lowest calf rearing cost and highest profit. In calves receiving MCE, withers height, rump height, body length, rump width, body depth, chest circumference change, withers height change, rump height change, and rump width change values increased significantly compared with the control group (p < 0.05). In conclusion, the results obtained not only reveal the positive effects of BA and MCE on calves during the pre-weaning period, but also encourage the necessity of investigating their effects on the long-term performance of animals and farm economies.}, }
@article {pmid39943041, year = {2025}, author = {de Haas, B and Dhooghe, E and Geelen, D}, title = {Root Exudates in Soilless Culture Conditions.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/plants14030479}, pmid = {39943041}, issn = {2223-7747}, abstract = {Root metabolite secretion plays a critical role in increasing nutrient acquisition, allelopathy, and shaping the root-associated microbiome. While much research has explored the ecological functions of root exudates, their relevance to horticultural practices, particularly soilless cultivation, remains underexplored. Steering root exudation could help growers enhance the effectiveness of plant growth-promoting bacteria. This review summarizes current knowledge on root exudation in soilless systems, examining its process and discussing environmental influences in the context of soilless cultivation. Plants in soilless systems exhibit higher total carbon exudation rates compared to those in natural soils, with exudation profiles varying across systems and species. Root exudation decreases with plant age, with most environmental adaptations occurring during early growth stages. Several environmental factors unique to soilless systems affect root exudation. For instance, nutrient availability has a major impact on root exudation. Light intensity reduces exudation rates, and light quality influences exudation profiles in a species- and environment-dependent manner. Elevated CO2 and temperature increase exudation. Factors related to the hydroponic nutrient solution and growing media composition remain insufficiently understood, necessitating further research.}, }
@article {pmid39942939, year = {2025}, author = {Mamaeva, A and Makeeva, A and Ganaeva, D}, title = {The Small Key to the Treasure Chest: Endogenous Plant Peptides Involved in Symbiotic Interactions.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/plants14030378}, pmid = {39942939}, issn = {2223-7747}, support = {23-66-10013//Russian Science Foundation/ ; }, abstract = {Plant growth and development are inextricably connected with rhizosphere organisms. Plants have to balance between strong defenses against pathogens while modulating their immune responses to recruit beneficial organisms such as bacteria and fungi. In recent years, there has been increasing evidence that regulatory peptides are essential in establishing these symbiotic relationships, orchestrating processes that include nutrient acquisition, root architecture modification, and immune modulation. In this review, we provide a comprehensive summary of the peptide families that facilitate beneficial relationships between plants and rhizosphere organisms.}, }
@article {pmid39942836, year = {2025}, author = {Chen, J and Zhang, X and Zhao, J and Ding, W and Zhang, X and Pan, L and Xu, H}, title = {Study of the Correlation Between Endophyte Abundances and Metabolite Levels in Different Parts of the Tissue of Cultivated and Wild Arnebia euchroma (Royle) Johnst. Based on Microbiome Analysis and Metabolomics.}, journal = {Molecules (Basel, Switzerland)}, volume = {30}, number = {3}, pages = {}, doi = {10.3390/molecules30030734}, pmid = {39942836}, issn = {1420-3049}, support = {No. 2024D01E18//the Outstanding Youth Science Fund of Xinjiang Uygur Autonomous Region Natural Science Foundation/ ; No. 82060696//the National Natural Science Foundation of China/ ; B202205//the Xinjiang Medical University Doctoral Research Initiation Fund Project/ ; }, mesh = {*Endophytes/metabolism ; *Metabolomics/methods ; *Microbiota ; *Boraginaceae/chemistry/metabolism/microbiology ; *Plant Roots/microbiology/metabolism/chemistry ; *Plant Leaves/microbiology/metabolism/chemistry ; Metabolome ; Bacteria/metabolism/classification ; }, abstract = {Arnebia euchroma (Royle) Johnst. has high medicinal and economic value, but in recent years, wild resources of this species have been depleted and the quality of artificially cultivated A. euchroma has been poor. The endophyte community of medicinal plants is rich, serving as an internal resource that promotes the growth of medicinal plants and the accumulation of secondary metabolites, and has important potential application value in improving the quality of medicinal materials. A. euchroma cultivars and wild varieties contain abundant endophyte communities and metabolites in different tissues. However, the relationships between A. euchroma endophytes and metabolites with different growth patterns and different tissue sites remain unclear. In this study, microbiome analysis and metabolomics were used to analyze the diversity of endophytes in the root and leaf tissues of cultivated and wild A. euchroma and their correlations with metabolites. The results revealed that the diversity of endophytes in A. euchroma was different from that in wild A. euchroma and that there was tissue specificity among different tissues. A species composition analysis revealed that the dominant endophytic fungi belonged to Ascomycota and Basidiomycota, and the dominant endophytic bacteria belonged to Proteobacteria and Cyanobacteria. A total of 248 metabolites, including quinones, flavonoids, alkaloids, organic acids, sugars, amino acids, coumarins, sterols, terpenoids, polyphenols, fatty ketones, and their derivatives, were identified in positive ion mode via LC-MS/MS. According to their different growth patterns and associated tissue parts, 9 differentially abundant metabolites were screened between AEZ-L (cultivated leaf tissue of A. euchroma) and AEY-L (wild leaf tissue of A. euchroma), 6 differentially abundant metabolites were screened between AEZ-R (cultivated root tissue of A. euchroma) and AEY-R (wild root tissue of A. euchroma), and 104 differentially abundant metabolites were screened between AEZ-R and AEZ-L. Eighty-two differentially abundant metabolites were screened between AEY-R and AEY-L. The contents of eight naphthoquinones in AEZ-R and AEY-R were determined via HPLC. The contents of β,β'-dimethylacrylylakanin in wild A. euchroma were greater than those in cultivated A. euchroma. A correlation analysis revealed that the dominant endophytes in the four groups were significantly correlated with a variety of metabolites, and the eight naphthoquinones in the root tissue were also significantly correlated with the dominant endophytes. The diversity of the A. euchroma endophyte community differed across different growth patterns and different tissue parts. There were significant differences in the relative contents of A. euchroma metabolites in different tissues. A correlation analysis verified the correlation between A. euchroma endophytes and metabolites.}, }
@article {pmid39942104, year = {2025}, author = {Zhang, X and Zhao, S and Yuan, J and Feng, L}, title = {Microbiome Flora and Metabolomics Analysis of Mung Bean Sour Liquid in Luoyang, China.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/foods14030511}, pmid = {39942104}, issn = {2304-8158}, support = {13480068//Doctor Scientific Research Start-up Fund of Henan University of Science and Technology/ ; }, abstract = {In order to reveal the fermentation microflora and fermentation metabolites of traditional mung bean sour liquid (MBSL) in Luoyang area, China, this experiment was sampled from four administrative districts of Luoyang, and volatile metabolites and non-targeted metabolites were detected and analyzed by HS-SPME-GC-MS and LC-MS, and bacterial and fungal sequencing were analyzed by Illumina MiSeq high-throughput sequencing technology. And the correlation between microorganisms and metabolites was conducted. The results showed that 42 volatiles were detected in four MBSL samples named Jianxi (JX), Liujia (Liu), LiJia (LJ), Majia (MJ), with 11 identical volatile flavor subtances, and the highest content of esters was found in JX, Liu, and LJ, and the highest content of acids was found in MJ. A total of 1703 non-targeted metabolites were identified, and there were more types of amino acids, carbohydrates, fatty acids and their complexes, flavonoids, carbonyl compounds, and organic acids, accounting for 40.93%. High-throughput sequencing results showed that there were nine bacterial and fungal genera with an average abundance of more than 1%, and the dominant genera mainly belonged to lactic acid bacteria and yeast. The composition of dominant genera was different in different workshop samples, and the abundance of fungal genera differed greatly. Among the volatile substances, Methyleugenol, a volatile component, was related to more bacteria, and ketones and hydrocarbons may be more closely associated with bacteria. Acetic acid and Oxalic acid may be more closely related to fungi, while some esters were more closely related to both fungal and bacterial genera. For non-target metabolites, amino acid and alcohol metabolites may be more influenced by bacteria, and organic acids and flavonoids may be more influenced by fungi.}, }
@article {pmid39942099, year = {2025}, author = {Zhao, Z and Zhong, L and Wu, J and Zeng, G and Liu, S and Deng, Y and Zhang, Y and Tang, X and Zhang, M}, title = {Modulation of Gut Mycobiome and Serum Metabolome by a MUFA-Rich Diet in Sprague Dawley Rats Fed a High-Fructose, High-Fat Diet.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/foods14030506}, pmid = {39942099}, issn = {2304-8158}, support = {32101970//National Natural Science Foundation of China/ ; R2021YJ-YB2001, R2023PY-QF002//the Special Fund for Scientific Innovation Strategy-Construction of high level academy of Agriculture Science/ ; }, abstract = {The intake of oleic acid-rich fats, a hallmark of the Mediterranean diet, has well-documented beneficial effects on human metabolic health. One of the key mechanisms underlying these effects is the regulation of gut microbiota structure and function. However, most existing studies focus on gut bacteria, while gut fungi, as a vital component of the gut microbiota, remain largely unexplored. This study compared the effects of regular peanut oil (PO) and high-oleic acid peanut oil (HOPO) on the gut mycobiome and serum metabolome employing ITS high-throughput sequencing and UPLC-MS/MS metabolomics to explore how dietary fatty acid composition influences gut microecology. Both HOPO and PO effectively reversed high-fat, high-fructose diet (HFFD)-induced reductions in gut fungal diversity, with HOPO showing superior efficacy in restoring gut microbiome balance, as reflected by an improved fungal-to-bacterial diversity ratio and reduced abundance of pathogenic fungi such as Aspergillus, Penicillium, and Candida. Furthermore, HOPO demonstrated a greater ability to normalize serum bile acid levels, including taurochenodesoxycholic acid, and to reverse elevated pantothenol levels, suggesting its potential role in maintaining bile acid metabolism and CoA biosynthesis. In summary, HOPO is more effective than PO in maintaining the normal structure and function of gut mycobiome in HFFD-fed SD rats.}, }
@article {pmid39942000, year = {2025}, author = {Wu, J and Wang, X and Aga, L and Tang, L and Tan, S and Zhang, D and Li, H and Yang, L and Zhang, N and Su, S and Xiao, M and Min, R and Li, A and Wang, X}, title = {Lacticaseibacillus casei JS-2 from 'Jiangshui' Reduces Uric Acid and Modulates Gut Microbiota in Hyperuricemia.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/foods14030407}, pmid = {39942000}, issn = {2304-8158}, support = {81773841//the National Natural Science Foundation of China/ ; }, abstract = {Lacticaseibacillus casei (JS-2) is a novel probiotic isolated from "Jiangshui", a kind of traditional folk fermented food, which has a significant effect on hyperuricemia (HUA). In vitro experimental results showed that JS-2 has a high degradation ability and selectivity for uric acid (UA). The animal test results indicated that after two weeks of treatment, JS-2 could significantly reduce the level of UA in the serum of HUA quails (p < 0.01), and its effect is almost equivalent to that of the positive drug control group, benzbromarone. Further, after JS-2 treatment, the level of xanthine oxidase in quail serum decreased significantly. Analysis data of quail fecal metabolomics results showed that JS-2-altering metabolites were involved in amino acid, purine, and lipid metabolism. To investigate the mechanism underlying JS-2-mediated UA degradation in the quail model of HUA, 16S rRNA gene sequencing was conducted. It was found that the structure and function of the gut microbiota were restored after JS-2 intervention, and the abundance of short-chain fatty acid (SCFA)-producing bacteria (g__Ruminococcus_torques_group and g__Butyricicoccus) and bacteria with UA degradation capacity (g__unclassified_f__Lachnospiraceae and g__Negativibacillus) increased significantly; intestinal SCFAs, especially propionic acid, increased accordingly. These experimental data suggest that the beneficial effects of JS-2 may derive from changes in the gut microbiome, altering host-microbiota interactions, reducing UA levels by increasing UA excretion, and reducing absorption. These findings provided new evidence that JS-2 has the potential to be used as a naturally functional food for the prevention of HUA.}, }
@article {pmid39941980, year = {2025}, author = {Li, J and Jia, J and Teng, Y and Wang, X and Xia, X and Song, S and Zhu, B and Xia, X}, title = {Polysaccharides from Sea Cucumber (Stichopus japonicus) Synergize with Anti-PD1 Immunotherapy to Reduce MC-38 Tumor Burden in Mice Through Shaping the Gut Microbiome.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/foods14030387}, pmid = {39941980}, issn = {2304-8158}, support = {Dljswgj202403//Dalian Jinshiwan Laboratory Project/ ; 81972692//National Natural Science of Foundation of China/ ; 2022YFD2100104//National Key Research and Development Program of China/ ; }, abstract = {Immune checkpoint inhibitors (ICIs) have revolutionized cancer treatment and significantly improved outcomes for patients with certain malignancies. However, immunotherapy with ICIs is only effective in a subset of patients and the gut microbiota have been identified as an important factor associated with response to ICI therapy. Polysaccharides from sea cucumber (Stichopus japonicus) (SCP) have been shown to modulate the gut microbiota and exhibit beneficial health functions, but whether SCP could synergize with anti-PD1 immunotherapy remains unexplored. In this study, mice with ICI-sensitive MC38 tumors were treated with anti-PD1 antibody after supplementation with or without SCP to examine the potential impact of SCP on the efficacy of immunotherapy. SCP strongly amplified the anti-tumor activity of anti-PD1 in MC38 tumor-bearing mice. Flow cytometry and immunohistological staining demonstrated that SCP treatment increased cytotoxic CD8[+] T lymphocytes while decreasing regulatory Foxp3[+] CD4[+] T lymphocytes. Gut microbiota and metabolomic analysis revealed that SCP modulated the microbiota and increased the abundance of certain metabolites such as indole-3-carboxylic acid. Furthermore, fecal microbiota transplantation experiments justified that the synergistic effect of SCP with anti-PD1 was partially mediated through the gut microbiota. Mice receiving microbiota from SCP-treated mice showed a boosted response to anti-PD1, along with enhanced anti-tumor immunity. These findings indicate that SCP could be utilized as a dietary strategy combined with anti-PD1 therapy to achieve improved outcomes in patients.}, }
@article {pmid39941819, year = {2025}, author = {Mougeot, JL and Beckman, M and Kooshki, M and Neuberger, J and Shukla, K and Furdui, C and Bahrani Mougeot, F and Porosnicu, M}, title = {Salivary Microbiome Profiling of HPV+ and HPV- Oropharyngeal Head and Neck Cancer Patients Undergoing Durvalumab Immunotherapy Suggests Prevotella melaninogenica and Veillonella atypica as Key Players: A Pilot Study.}, journal = {Cancers}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/cancers17030452}, pmid = {39941819}, issn = {2072-6694}, abstract = {OBJECTIVE: Head and neck cancer (HNC) is a common cancer represented by nearly 80% oral cavity (OC) and oropharyngeal cancers (OPCs). Seventy percent of OPCs are associated with the Human Papilloma Virus (HPV). Immunotherapy holds the promise of future improvements in treating HNC patients. The study objective was to determine whether durvalumab immunotherapy alone, prior to curative surgery, would significantly impact the oral salivary microbiome in a pilot cohort of HPV negative and positive OC and OPC patients.<br><br>METHODS: Early stage OPC patients with squamous cell carcinoma were recruited: 5 HPV+ and 12 HPV-, and treated with two or three administrations of durvalumab given every two weeks, prior to surgery. Unstimulated saliva was collected and processed for bacterial DNA Isolation and V1-V3 16S rRNA gene next generation sequencing, taxa identification, and determination of relative abundance at four time points: baseline prior to surgery (A) and weekly durvalumab treatment timepoints (B, C, and D). Alpha- and beta-diversity differences for the time series were determined in Primerv7. MaAsLin2 in R was used to identify potential associations with the time series and/or HPV status. Linear decomposition model (LDM) R-package was used to investigate the relationship of salivary microbiome with HPV status. ROC curves were plotted for significant species in common between MaAsLin2 analysis and FDR-corrected Mann-Whitney U-test using XLSTAT.<br><br>RESULTS: Longitudinal microbiome data across four timepoints (A, B, C, D) were obtained (HPV+: n = 18 samples; HPV-: n = 46 samples). A total of 416 taxa were detected across all time points, ranging from 336 to 373 per group. There were no differences in &#x3b1;- and &#x3b2;-diversities for all longitudinal comparisons (C vs. BCD, AB vs. CD, or A vs. B, C, or D). However, comparison A vs. D showed a significant increase in Prevotella melaninogenica relative abundance, a potentially pathogenic species able to evade the immune system, after three weeks treatment. Moreover, differences in beta-diversity based on HPV status were found. LDM analysis identified Veillonella atypica, overrepresented in HPV+ group, as the top species accounting for HPV status.<br><br>CONCLUSIONS: The results are consistent with findings from previous studies investigating HNC patients treated with chemoradiotherapy. More research is needed to understand possible impact of immunotherapy on opportunistic bacterial species, although negligible impact from durvalumab treatment on salivary microbiome was observed.}, }
@article {pmid39941749, year = {2025}, author = {Vega, AA and Shah, PP and Rouchka, EC and Clem, BF and Dean, CR and Woodrum, N and Tanwani, P and Siskind, LJ and Beverly, LJ}, title = {E. coli Biomolecules Increase Glycolysis and Invasive Potential in Lung Adenocarcinoma.}, journal = {Cancers}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/cancers17030380}, pmid = {39941749}, issn = {2072-6694}, support = {1R01CA193220-05A1/NH/NIH HHS/United States ; }, abstract = {Introduction: Recent studies have discovered that lung cancer subtypes possess distinct microbiome profiles within their tumor microenvironment. Additionally, the tumor-associated microbiome exhibits altered bacterial pathways, suggesting that certain bacterial families are more capable of facilitating tumor progression than others. We hypothesize that there exists a crosstalk between lung adenocarcinoma (LUAD) cells and bacterial cells. Methods and Materials: RNA sequencing (RNA-seq) was performed on LUAD cell lines to explore the paracrine signaling effects of bacterial biomolecules. Based on our RNA-seq data, we investigated glycolysis by measuring glucose uptake and lactate production, invasive potential through invasion assays, and epithelial-to-mesenchymal transition (EMT) markers. Since lipopolysaccharides (LPS), abundant on the cell walls of Gram-negative bacteria, can activate toll-like receptor 4 (TLR4), we inhibited TLR4 with C34 to assess its relationship with the observed phenotypic changes. To identify the bacterial biomolecules responsible for these changes, we treated the media with RNAse enzyme, charcoal or dialyzed away molecules larger than 3 kDa. Results and Discussion: RNA-seq revealed 948 genes upregulated in the presence of E. coli biomolecules. Among these, we observed increased expression of Hexokinase II (HKII), JUN proto-oncogene, and Snail Family Transcriptional Repressor 1. We verified the elevation of glycolytic enzymes through Western blot and saw elevation of 2-deoxyglucose uptake and lactate production in LUAD cell lines incubated in E. coli biomolecules. In addition to E. coli elevating glycolysis in LUAD cell lines, E. coli exposure enhanced invasive potential as demonstrated by Boyden chamber assays. Notably, inhibition of TLR4 did not reduce the impact of E. coli biomolecules on glycolysis or the invasive potential of LUAD. Modulating the E. coli-supplemented media with RNAse enzyme or dextran-coated charcoal or using a spin column to remove biomolecules smaller than 3 kDa resulted in changes in HKII and Claudin protein expression. These findings suggest a direct relationship between E. coli and LUAD, wherein several cancer hallmarks are upregulated. Future studies should further investigate these bacterial biomolecules and their role in the tumor microenvironment to fully understand the impact of microbial shifts on cancer progression.}, }
@article {pmid39941737, year = {2025}, author = {Galasso, L and Termite, F and Mignini, I and Esposto, G and Borriello, R and Vitale, F and Nicoletti, A and Paratore, M and Ainora, ME and Gasbarrini, A and Zocco, MA}, title = {Unraveling the Role of Fusobacterium nucleatum in Colorectal Cancer: Molecular Mechanisms and Pathogenic Insights.}, journal = {Cancers}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/cancers17030368}, pmid = {39941737}, issn = {2072-6694}, abstract = {Fusobacterium nucleatum, a gram-negative anaerobic bacterium, has emerged as a significant player in colorectal cancer (CRC) pathogenesis. The bacterium causes a persistent inflammatory reaction in the colorectal mucosa by stimulating the release of pro-inflammatory cytokines like IL-1β, IL-6, and TNF-α, creating an environment conducive to cancer progression. F. nucleatum binds to and penetrates epithelial cells through adhesins such as FadA, impairing cell junctions and encouraging epithelial-to-mesenchymal transition (EMT), which is associated with cancer advancement. Additionally, the bacterium modulates the host immune system, suppressing immune cell activity and creating conditions favorable for tumor growth. Its interactions with the gut microbiome contribute to dysbiosis, further influencing carcinogenic pathways. Evidence indicates that F. nucleatum can inflict DNA damage either directly via reactive oxygen species or indirectly by creating a pro-inflammatory environment. Additionally, it triggers oncogenic pathways, especially the Wnt/β-catenin signaling pathway, which promotes tumor cell growth and longevity. Moreover, F. nucleatum alters the tumor microenvironment, impacting cancer cell behavior, metastasis, and therapeutic responses. The purpose of this review is to elucidate the molecular mechanisms by which F. nucleatum contributes to CRC. Understanding these mechanisms is crucial for the development of targeted therapies and diagnostic strategies for CRC associated with F. nucleatum.}, }
@article {pmid39941602, year = {2025}, author = {Bessa, LJ and Egas, C and Botelho, J and Machado, V and Alcoforado, G and Mendes, JJ and Alves, R}, title = {Unveiling the Resistome Landscape in Peri-Implant Health and Disease.}, journal = {Journal of clinical medicine}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/jcm14030931}, pmid = {39941602}, issn = {2077-0383}, support = {2022.01430.PTDC//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; }, abstract = {Background: The human oral microbiome is a critical reservoir for antibiotic resistance; however, subgingival peri-implant biofilms remain underexplored in this context. We aimed to explore the prevalence and distribution of antibiotic resistance genes (ARGs) in metagenomes derived from saliva and subgingival peri-implant biofilms. Methods: A total of 100 metagenome datasets from 40 individuals were retrieved from the Sequence Read Archive (SRA) database. Of these, 20 individuals had exclusively healthy implants and 20 had both healthy and affected implants with peri-implantitis. ARGs and their taxonomic assignments were identified using the ABRicate tool, and plasmid detection was performed with PlasmidFinder. Results: Four plasmid replicons were identified in 72 metagenomes, and 55 distinct ARGs from 13 antibiotic classes were detected in 89 metagenomes. ARGs conferring resistance to macrolides-lincosamides-streptogramins, tetracyclines, beta-lactams, and fluoroquinolones were the most prevalent. The msr(D) and mef(A) genes showed the highest prevalence, except in saliva samples from individuals with healthy implants, where mef(A) ranked fourth. A pairwise PERMANOVA of principal coordinate analysis based on Jaccard distances revealed that saliva samples exhibited significantly greater ARG diversity than subgingival biofilm samples (p < 0.05). However, no significant differences were observed between healthy and peri-implantitis-affected subgingival biofilm groups (p > 0.05). The taxonomic origins of ARGs were also analyzed to understand their distribution and potential impact on oral microbial communities. Conclusions: Resistome profiles associated with both peri-implant health and disease showed no significant differences and higher salivary abundance of ARGs compared to subgingival biofilm samples.}, }
@article {pmid39941458, year = {2025}, author = {Baldin, A and Nucibella, C and Manera, C and Bacci, C}, title = {Efficacy of Tocopherol vs. Chlorhexidine in the Management of Oral Biopsy Site: A Randomized Clinical Trial.}, journal = {Journal of clinical medicine}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/jcm14030788}, pmid = {39941458}, issn = {2077-0383}, abstract = {Background/Objectives: Chlorhexidine digluconate (CHX) is widely regarded as the gold standard for oral mucosa antiseptic treatments but has been associated with delayed healing, scar formation, microbiome alterations, and fibroblast toxicity. Tocopherol, with its ability to accelerate tissue healing and minimal side effects, has emerged as a potential alternative. This randomized clinical trial aimed to compare the efficacy of topical tocopherol acetate and 0.2% chlorhexidine in managing postoperative pain and wound healing following oral cavity biopsies. Methods: Seventy-seven patients undergoing oral biopsies were divided into two groups: the test group (tocopherol acetate) and the control group (0.2% chlorhexidine). Pain was assessed using VAS (Visual Analogue Scale) scores on days 1 and 6 postoperatively, and wound healing was evaluated through measurements of the biopsy site's height and width from standardized photographs analyzed with ImageJ. Painkiller use was also documented. The study followed CONSORT (Consolidated Standards of Reporting Trials) guidelines, with ethical approval from the Padua Ethics Committee and registration on ISRCTN. Results: No significant differences were found between the groups in VAS scores, wound dimensions, or painkiller use (p > 0.05). However, significant pain reduction within each group was observed (p < 0.0001). Conclusions: Tocopherol acetate showed comparable efficacy to chlorhexidine, suggesting it could be a viable alternative for postoperative care in oral surgery.}, }
@article {pmid39941170, year = {2025}, author = {Farah, A and Assaf, T and Hindy, J and Abboud, W and Mahamid, M and Savarino, EV and Mari, A}, title = {The Dynamic Evolution of Eosinophilic Esophagitis.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/diagnostics15030240}, pmid = {39941170}, issn = {2075-4418}, abstract = {Eosinophilic esophagitis (EoE) is a chronic, immune-mediated inflammatory condition of the esophagus characterized by eosinophilic infiltration, and hallmark symptoms of esophageal dysfunction such as dysphagia and food impaction. Over the past three decades, EoE has been recognized as a distinct clinical entity, distinguished from gastroesophageal reflux disease (GERD) through advancements in diagnostic techniques, particularly endoscopy with biopsy. The rising global prevalence of EoE reflects enhanced diagnostic awareness, evolving criteria, and environmental along with lifestyle changes. The etiology of EoE is multifactorial, involving genetic predispositions, immune dysregulation, the gut microbiome, and environmental triggers, including dietary allergens and aeroallergens. Key mechanisms include a type 2 helper T-cell (Th2)-driven immune response, epithelial barrier dysfunction, and genetic variants such as CAPN14 and TSLP. Chronic inflammation leads to tissue remodeling, fibrosis, and esophageal narrowing, contributing to disease progression and complications. Management strategies have evolved to include dietary elimination, proton pump inhibitors, topical corticosteroids, biologics, and endoscopic interventions for fibrostenotic complications. Emerging therapies targeting cytokines such as interleukin (IL)-4, IL-5, and IL-13, alongside novel diagnostic tools like the esophageal string test and Cytosponge, offer promising avenues for improved disease control and non-invasive monitoring. Long-term surveillance combining endoscopic and histological evaluations with biomarkers and non-invasive tools is critical to optimizing outcomes and preventing complications. Future research should address gaps in understanding the role of the esophageal microbiome, refine therapeutic approaches, and develop personalized strategies to improve disease management and patient quality of life.}, }
@article {pmid39941161, year = {2025}, author = {Sunamoto, M and Morohoshi, K and Sato, B and Mihashi, R and Inui, M and Yamada, M and Miyado, K and Kawano, N}, title = {Complement Factor B Deficiency Is Dispensable for Female Fertility but Affects Microbiome Diversity and Complement Activity.}, journal = {International journal of molecular sciences}, volume = {26}, number = {3}, pages = {}, doi = {10.3390/ijms26031393}, pmid = {39941161}, issn = {1422-0067}, support = {24K12568, 23K17435, 21K18298//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; Female ; *Complement Factor B/genetics/metabolism/deficiency ; *Mice, Knockout ; Mice ; *Fertility ; *Microbiota ; Male ; Gastrointestinal Microbiome ; Complement Pathway, Alternative ; Vagina/microbiology ; Complement Activation ; Mice, Inbred C57BL ; }, abstract = {Complement factor B (CFB) is a crucial component for the activation of the alternative pathway due to the formation of the C3 convertase with C3b, which further produces C3b to enhance the overall complement activity. Although Cfb is expressed not only in the immune tissues, but also in the reproductive tract, the physiological role of the alternative complement pathway in reproduction remains unclear. In this study, we addressed this issue by producing Cfb-knockout (KO) mice and analyzing their phenotypes. Sperm function, number of ovulated oocytes, and litter size were normal in KO mice. In contrast, the diversity of microbiomes in the gut and vaginal tract significantly increased in KO mice. Some serine protease activity in the serum from KO mice was lower than that of wild-type mice. Since the serum from KO mice showed significantly lower activity of the alternative complement pathway, CFB was found to be essential for this pathway. Our results indicate that although the alternative pathway is dispensable for normal fertility and development, it maintains the gut and vaginal microbiomes by suppressing their diversity and activating the alternative complement pathway.}, }
@article {pmid39941139, year = {2025}, author = {Enache, RM and Roşu, OA and Profir, M and Pavelescu, LA and Creţoiu, SM and Gaspar, BS}, title = {Correlations Between Gut Microbiota Composition, Medical Nutrition Therapy, and Insulin Resistance in Pregnancy-A Narrative Review.}, journal = {International journal of molecular sciences}, volume = {26}, number = {3}, pages = {}, doi = {10.3390/ijms26031372}, pmid = {39941139}, issn = {1422-0067}, mesh = {Humans ; Pregnancy ; *Gastrointestinal Microbiome ; *Insulin Resistance ; Female ; *Diabetes, Gestational/diet therapy/microbiology/metabolism ; *Nutrition Therapy/methods ; }, abstract = {Many physiological changes accompany pregnancy, most of them involving metabolic perturbations. Alterations in microbiota composition occur both before and during pregnancy and have recently been correlated with an important role in the development of metabolic complications, such as insulin resistance and gestational diabetes mellitus (GDM). These changes may be influenced by physiological adaptations to pregnancy itself, as well as by dietary modifications during gestation. Medical nutritional therapy (MNT) applied to pregnant women at risk stands out as one of the most important factors in increasing the microbiota's diversity at both the species and genus levels. In this review, we discuss the physiological changes during pregnancy and their impact on the composition of the intestinal microbiota, which may contribute to GDM. We also discuss findings from previous studies regarding the effectiveness of MNT in reducing insulin resistance. In the future, additional studies should aim to identify specific gut microbial profiles that serve as early indicators of insulin resistance during gestation. Early diagnosis, achievable through stool analysis or metabolite profiling, may facilitate the timely implementation of dietary or pharmaceutical modifications, thereby mitigating the development of insulin resistance and its associated sequelae.}, }
@article {pmid39941107, year = {2025}, author = {Nemzer, BV and Al-Taher, F and Kalita, D and Yashin, AY and Yashin, YI}, title = {Health-Improving Effects of Polyphenols on the Human Intestinal Microbiota: A Review.}, journal = {International journal of molecular sciences}, volume = {26}, number = {3}, pages = {}, doi = {10.3390/ijms26031335}, pmid = {39941107}, issn = {1422-0067}, mesh = {Humans ; *Polyphenols/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Dietary Fiber/pharmacology/metabolism ; Antioxidants/pharmacology ; Diet ; }, abstract = {Dietary polyphenols are garnering attention in the scientific community due to their potential health-beneficial properties and preventative effects against chronic diseases, viz. cardiovascular diseases, diabetes, obesity, and neurodegenerative diseases. Polyphenols are antioxidants that change microbial composition by suppressing pathogenic bacteria and stimulating beneficial bacteria. The interaction of polyphenols with dietary fibers affects their bioaccessibility in the upper and lower parts of the digestive tract. Dietary fibers, polyphenols, their conjugates, and their metabolites modulate microbiome population and diversity. Consuming polyphenol-rich dietary fibers such as pomegranate, cranberry, berries, and tea improves gut health. A complex relationship exists between polyphenol-rich diets and gut microbiota for functioning in human health. In this review, we provide an overview of the interactions of dietary polyphenols, fibers, and gut microbiota, improving the understanding of the functional properties of dietary polyphenols.}, }
@article {pmid39940959, year = {2025}, author = {Matsumura, M and Fujihara, H and Maita, K and Miyakawa, M and Sakai, Y and Nakayama, R and Ito, Y and Hasebe, M and Kawaguchi, K and Hamada, Y}, title = {Combinatorial Effects of Cisplatin and PARP Inhibitor Olaparib on Survival, Intestinal Integrity, and Microbiome Modulation in Murine Model.}, journal = {International journal of molecular sciences}, volume = {26}, number = {3}, pages = {}, doi = {10.3390/ijms26031191}, pmid = {39940959}, issn = {1422-0067}, support = {18K09543//Japan Society for the Promotion of Science/ ; 20K10196//Japan Society for the Promotion of Science/ ; 24K14764//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; *Phthalazines/pharmacology ; *Cisplatin/pharmacology ; *Piperazines/pharmacology ; *Poly(ADP-ribose) Polymerase Inhibitors/pharmacology ; Mice ; *Gastrointestinal Microbiome/drug effects ; Intestines/microbiology/drug effects/pathology ; Disease Models, Animal ; Male ; }, abstract = {This study investigated the effects of the poly (ADP-ribose) polymerase (PARP) inhibitor Olaparib, alone and in combination with cisplatin, on intestinal integrity, survival, and microbiome composition using a murine model. Statistical analyses were conducted using one-way analysis of variance with Bonferroni correction for multiple comparisons, considering p-values of <0.05 as statistically significant. Microbiome profiling was performed using Qiime 2 software. Histopathological and microbiome analyses revealed Olaparib's protective effects on intestinal integrity, mitigating cisplatin-induced damage. The single administration of cisplatin caused significant histological damage, biochemical disruptions, and dysbiosis, characterized by an increase in pro-inflammatory microbiome, such as Clostridium_sensu_stricto_1, and a decrease in beneficial short-chain fatty acid (SCFA)-producing microbiome. Conversely, the single administration of Olaparib was associated with an increase in SCFA-producing microbiome, such as Lachnospiraceae NK4A136, and exhibited minimal toxicity. The combination administration showed complicated outcomes, as follows: reduced cisplatin-induced cytotoxicity and increased SCFA-producing microbiome ratios, yet the long-term effects revealed reduced survival rates in the cisplatin group and sustained weight gain suppression. These findings emphasize Olaparib's potential in enhancing intestinal barrier integrity, reducing inflammation, and positively modulating microbiome diversity. However, the entangled pharmacodynamic interactions in the combination administration underscore the need for further investigation. The study highlights the potential of microbiome-targeted interventions in improving therapeutic outcomes for both cancer treatment and inflammatory bowel disease management.}, }
@article {pmid39940948, year = {2025}, author = {Rastegari, F and Driscoll, M and Riordan, JD and Nadeau, JH and Johnson, JS and Weinstock, GM}, title = {Comparison of Lysis and Amplification Methodologies for Optimal 16S rRNA Gene Profiling for Human and Mouse Microbiome Studies.}, journal = {International journal of molecular sciences}, volume = {26}, number = {3}, pages = {}, doi = {10.3390/ijms26031180}, pmid = {39940948}, issn = {1422-0067}, support = {HG01244/GF/NIH HHS/United States ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; Humans ; Animals ; Mice ; *Microbiota/genetics ; *Feces/microbiology ; Bacteria/genetics/classification ; Polymerase Chain Reaction/methods ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {When conducting sequence-based analysis of microbiome samples, it is important to accurately represent the bacterial communities present. The aim of this study was to compare two commercially available DNA isolation and PCR amplification approaches to determine their impact on the taxonomic composition of microbiome samples following 16S rRNA gene sequencing. A well-established 16S rRNA gene profiling approach, which was widely used in the Human Microbiome Project (HMP), was compared with a novel alkaline degenerative technique that utilizes alkaline cell lysis in combination with a degenerate pool of primers for nucleic acid extraction and PCR amplification. When comparing these different approaches for the microbiome profiling of human and mouse fecal samples, we found that the alkaline-based method was able to detect greater taxonomic diversity. An in silico analysis of predicted primer binding against a curated 16S rRNA gene reference database further suggested that this novel approach had the potential to reduce population bias found with traditional methods, thereby offering opportunities for improved microbial community profiling.}, }
@article {pmid39940777, year = {2025}, author = {Han, EJ and Ahn, JS and Choi, YJ and Kim, DH and Chung, HJ}, title = {Changes in Gut Microbiota According to Disease Severity in a Lupus Mouse Model.}, journal = {International journal of molecular sciences}, volume = {26}, number = {3}, pages = {}, doi = {10.3390/ijms26031006}, pmid = {39940777}, issn = {1422-0067}, support = {A439111, C430000 and C442400//Korea Basic Science Institute/ ; No. RS-2023-00224099//National Research Foundation (NRF) funded by the Korean government (MSIT)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Lupus Erythematosus, Systemic/microbiology/immunology ; Mice ; *Disease Models, Animal ; *Dysbiosis/microbiology/immunology ; Female ; Severity of Illness Index ; Mice, Inbred MRL lpr ; Immunoglobulin G/immunology ; }, abstract = {Systemic lupus erythematosus (SLE) is a multifaceted autoimmune disease driven by immune dysregulation. This study investigated the relationship between gut microbiota and lupus severity using the MRL/lpr lupus mouse model. Mice were grouped based on total immunoglobulin (Ig)G, IgG2a levels, and urine albumin-to-creatinine ratio (ACR), allowing for the comparison of gut microbiota profiles across different disease severities. Interestingly, severe lupus mice exhibited significant reductions in Ruminiclostridium cellulolyticum, Lactobacillus johnsonii, and Kineothrix alysoides, while Clostridium saudiense, Pseudoflavonifractor phocaeensis, and Intestinimonas butyriciproducens were enriched. These microbial shifts correlated with elevated IgG, IgG2a, and ACR levels, indicating that changes in the gut microbiome may directly influence key immunological markers associated with lupus severity. The depletion of beneficial species and the enrichment of potentially pathogenic bacteria appear to contribute to immune activation and disease progression. This study suggests that gut microbiota dysbiosis plays a critical role in exacerbating lupus by modulating immune responses, reinforcing the link between microbial composition and lupus pathogenesis. Our findings provide the first evidence identifying these distinct gut microbial species as potential contributors to lupus severity, highlighting their role as key factors in disease progression.}, }
@article {pmid39940760, year = {2025}, author = {Sipos, L and Banczerowski, P and Juhász, J and Fedorcsák, I and Berényi, G and Makra, N and Dunai, ZA and Szabó, D and Erőss, L}, title = {Brain Tumors and Beyond: Multi-Compartment Microbiome and Mycobiome Analysis.}, journal = {International journal of molecular sciences}, volume = {26}, number = {3}, pages = {}, doi = {10.3390/ijms26030991}, pmid = {39940760}, issn = {1422-0067}, support = {Human Microbiota Study 0272//Hungarian Research Network/ ; }, mesh = {Humans ; *Brain Neoplasms/microbiology/pathology ; *Mycobiome ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; *Fungi/classification/genetics/isolation &amp; purification ; Male ; Female ; Bacteria/classification/genetics/isolation &amp; purification ; Middle Aged ; Microbiota/genetics ; Tumor Microenvironment ; Adult ; }, abstract = {Brain tumors are frequently diagnosed diseases in which etiology and progression largely depend on mutations and genetic factors. Additionally, recent reports document that the microbiome may influence tumor growth, tumor microenvironment, and response to therapy. Our goal was to examine the extent to which the bacterial composition-microbiota-and fungal composition-mycobiota-characteristic of the tumor and its microenvironment correlate with the composition of the gut and blood microbiota and mycobiota in five randomly selected brain tumor patients. The bacterial composition of the tumor, tumor-adjacent tissue (TAT), blood, and gut samples of the five patients were analyzed by 16S rRNA and ITS-based sequencing in order to determine the bacterial and fungal composition. The gut microbiome and mycobiome composition showed individual and tissue-specific signatures in each patient. The microbiome composition of the blood, TAT, and tumor tissue was very similar in each patient, dominated by Klebsiella, Enterococcus, Blautia, and Lactobacillus spp. In contrast, the mycobiome composition of the blood, TAT, and tumor showed a diverse, individual picture. The most common fungal species in the blood and TAT were Tomentella, Didymosphaeria, Alternaria, Penicillium, Mycosphaerella, and Discosia. The blood and TAT mycobiome were similar to each other but unique and characteristic of the patients. In contrast, in the tumor tissues, Alternaria, Malassezia, Schizophyllum, and Tomentella genus were the most common fungi genus. Our results showed that the presence of fungi in tumors shows a unique pattern that is independent of the pattern observed in the gut, blood, and tumor environment and that the effects of the mycobiome are distinct and cannot be associated with those of the microbiome. Elucidating the role of fungi in tumors and exploring the relationship between fungi and brain tumor types may open up further therapeutic options.}, }
@article {pmid39940744, year = {2025}, author = {Polyák, H and Galla, Z and Rajda, C and Monostori, P and Klivényi, P and Vécsei, L}, title = {Plasma and Visceral Organ Kynurenine Metabolites Correlate in the Multiple Sclerosis Cuprizone Animal Model.}, journal = {International journal of molecular sciences}, volume = {26}, number = {3}, pages = {}, doi = {10.3390/ijms26030976}, pmid = {39940744}, issn = {1422-0067}, support = {NKFIH 138125//National Research, Development and Innovation Office/ ; Neuroscience Research Group//HUN-REN-SZTE/ ; &#xda;NKP-23-3//New National Excellence Program of the Ministry for Culture and Innovation from the source of the National Research, Development and Innovation Fund/ ; Helga Poly&#xe1;k Ph.D is a member of the Preventive Health Sciences Research Group.//the Incubation Competence Centre of the Life Sciences Cluster of the Centre of Excellence for Interdisciplinary Research, Development and Innovation of the University of Szeged/ ; }, mesh = {Animals ; *Kynurenine/metabolism/blood ; *Multiple Sclerosis/metabolism/chemically induced/blood/pathology ; *Cuprizone/toxicity ; Mice ; *Disease Models, Animal ; *Tryptophan/metabolism/blood ; *Serotonin/metabolism/blood ; Kynurenic Acid/blood/metabolism ; 5-Hydroxytryptophan/metabolism ; Indoleacetic Acids/metabolism/blood/urine ; Xanthurenates/metabolism/blood ; Male ; Mice, Inbred C57BL ; Female ; }, abstract = {The cuprizone (CPZ) model of multiple sclerosis (MS) is excellent for studying the molecular differences behind the damage caused by poisoning. Metabolic differences in the kynurenine pathway (KP) of tryptophan (TRP) degradation are observed in both MS and a CPZ mouse model. Our goal was to analyze the kynurenine, serotonin, and indole pathways of TRP degradation on the periphery, in the neurodegenerative processes of inflammation. In our study, mice were fed with 0.2% CPZ toxin for 5 weeks. We examined the metabolites in the three pathways of TRP breakdown in urine, plasma, and relevant visceral organs with bioanalytical measurements. In our analyses, we found a significant increase in plasma TRP, 5-hydroxytryptophan (5-HTP), and indole-3-acetic acid (IAA) levels, while a decrease in the concentrations of 3-hydroxy-L-kynurenine (3-HK), xanthurenic acid (XA), kynurenic acid (KYNA), and quinaldic acid in the plasma of toxin-treated group was found. A marked decrease in the levels of 3-HK, XA, KYNA, quinaldic acid, and indole-3-lactic acid was also observed in the visceral organs by the end of the poisoning. Furthermore, we noticed a decrease in the urinary levels of the TRP, KYNA, and XA metabolites, while an increase in serotonin and 5-hydroxyindoleacetic acid in the CPZ group was noticed. The toxin treatment resulted in elevated tryptamine and indoxyl sulfate levels and reduced IAA concentration. Moreover, the urinary para-cresyl sulfate concentration also increased in the treated group. In the present study, we showed the differences in the three main metabolic pathways of TRP degradation in the CPZ model. We confirmed the relationship and correlation between the content of the kynurenine metabolites in the plasma and the tissues of the visceral organs. We emphasized the suppression of the KP and the activity of the serotonin and indole pathways with a particular regard to the involvement of the microbiome by the indole pathway. Consequently, this is the first study to analyze in detail the distribution of the kynurenine, serotonin, and indole pathways of TRP degradation in the periphery.}, }
@article {pmid39940450, year = {2025}, author = {Zhang, X and Hu, H and Zhang, Y and Hu, S and Lu, J and Peng, W and Luo, D}, title = {Dietary Capsaicin Exacerbates Gut Microbiota Dysbiosis and Mental Disorders in Type 1 Diabetes Mice.}, journal = {Nutrients}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/nu17030593}, pmid = {39940450}, issn = {2072-6643}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Capsaicin/pharmacology ; *Dysbiosis ; *Diabetes Mellitus, Type 1/microbiology/complications ; Male ; *Anxiety ; *Diabetes Mellitus, Experimental/complications/microbiology ; *Depression ; Brain-Gut Axis/drug effects ; Mice, Inbred C57BL ; Behavior, Animal/drug effects ; Hippocampus/metabolism/drug effects ; Mental Disorders ; Diet ; }, abstract = {Background/Objectives: Diabetes mellitus is often accompanied by mental health complications, including anxiety, depression, and cognitive decline. Recent research suggested that capsaicin, the active component of chili peppers, may influence mental health. This study aimed to determine the effect of dietary capsaicin on mental disorders in a type 1 diabetes (T1D) mouse model, while also exploring the potential involvement of the microbiota-gut-brain axis. Methods: We induced T1D in mice using streptozotocin (STZ) and administered a diet supplemented with 0.005% capsaicin for five weeks. Behavioral assessments, including the open field test (OFT), tail suspension test (TST), forced swimming test (FST), elevated plus maze (EPM) test, and Morris water maze (MWM) test, were conducted to evaluate depressive and anxiety-like behaviors as well as cognitive function. Targeted and untargeted metabolomics analyses were performed to assess neurotransmitter levels in the hippocampus and serum metabolites, while 16S rRNA sequencing was utilized to analyze gut microbiota composition. Intestinal barriers were determined using western blot detection of the tight junction proteins ZO-1 and occludin. Results: Dietary capsaicin exacerbated anxiety and depressive-like behaviors along with cognitive declines in T1D mice. Capsaicin reduced gut microbiota diversity and levels of beneficial bacteria, while broad-spectrum antibiotic treatment further intensified anxiety and depression behaviors. Metabolomic analysis indicated that capsaicin disrupted metabolic pathways related to tryptophan and phenylalanine, leading to decreased neuroprotective metabolites, such as kynurenic acid, hippurate, and butyric acid. Additionally, capsaicin diminished the expression of ZO-1 and occludin, indicating increased intestinal permeability. Conclusions: Dietary capsaicin aggravates gut microbiota and metabolic disturbances in diabetic mice, thereby worsening anxiety, depression, and cognitive decline.}, }
@article {pmid39940425, year = {2025}, author = {Chen, E and Ajami, NJ and White, DL and Liu, Y and Gurwara, S and Hoffman, K and Graham, DY and El-Serag, HB and Petrosino, JF and Jiao, L}, title = {Dairy Consumption and the Colonic Mucosa-Associated Gut Microbiota in Humans-A Preliminary Investigation.}, journal = {Nutrients}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/nu17030567}, pmid = {39940425}, issn = {2072-6643}, support = {RP#140767//Cancer Prevention and Research Institute of Texas/ ; DK56338/DK/NIDDK NIH HHS/United States ; 001//Gillson Longenbaugh Foundation/ ; 001//Gillson Longenbaugh Foundation/ ; CX001430//U.S. Department of Veterans Affairs/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Cross-Sectional Studies ; *Dairy Products/microbiology ; Middle Aged ; *Colon/microbiology ; *Intestinal Mucosa/microbiology ; Adult ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Diet ; Aged ; Yogurt/microbiology ; }, abstract = {BACKGROUND: Dairy consumption has been associated with various health outcomes that may be mediated by changes in gut microbiota.<br><br>METHODS: This cross-sectional study investigated the association between the colonic mucosa-associated gut microbiota and the self-reported intake of total dairy, milk, cheese, and yogurt. A total of 97 colonic mucosal biopsies collected from 34 polyp-free individuals were analyzed. Dairy consumption in the past year was assessed using a food frequency questionnaire. The 16S rRNA gene V4 region was amplified and sequenced. Operational taxonomic unit (OTU) classification was performed using the UPARSE and SILVA databases. OTU diversity and relative abundance were compared between lower vs. higher dairy consumption groups. Multivariable negative binomial regression models for panel data were used to estimate the incidence rate ratio and 95% confidence interval for bacterial counts and dairy consumption. False discovery rate-adjusted p values (q value) < 0.05 indicated statistical significance.<br><br>RESULTS: Higher total dairy and milk consumption and lower cheese consumption were associated with higher alpha microbial diversity (adjusted p values < 0.05). Higher total dairy and milk consumption was also associated with higher relative abundance of Faecalibacterium. Higher milk consumption was associated with higher relative abundance of Akkermansia. Higher total dairy and cheese consumption was associated with lower relative abundance of Bacteroides.<br><br>CONCLUSIONS: Dairy consumption may influence host health by modulating the structure and composition of the colonic adherent gut microbiota.}, }
@article {pmid39940405, year = {2025}, author = {Fan, R and Kim, J and Kim, YC and Chung, S}, title = {Effects of Fish Oil with Heat Treatment on Obesity, Inflammation, and Gut Microbiota in Ovariectomized Mice.}, journal = {Nutrients}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/nu17030549}, pmid = {39940405}, issn = {2072-6643}, support = {MAS00587//USDA/NIFA Hatch project/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Female ; *Fish Oils/pharmacology ; *Ovariectomy ; *Mice, Inbred C57BL ; *Inflammation ; *Obesity/therapy/metabolism/microbiology ; Mice ; Dietary Supplements ; Hyperthermia, Induced/methods ; Insulin Resistance ; Menopause ; Hot Temperature ; }, abstract = {Background/Objectives: Menopause induces substantial metabolic changes, including a reduction in metabolic rate and an elevated risk of developing metabolic diseases. Fish oil (FO) supplementation has been shown to ameliorate menopause-associated metabolic risks. Hyperthermia treatment (HT) has recently gained attention for its potential to improve metabolic and immune health. However, it remains to be determined whether HT can confer metabolic benefits comparable to those of FO supplementation or enhance the metabolic benefits of FO supplementation. This study aims to delineate the distinctive and collaborative effects of HT and FO supplementation in mitigating menopause-associated metabolic dysfunction. Methods: Female C57BL/6 ovariectomized (OVX) mice were randomly assigned to four groups (n = 12/group) to evaluate the individual and combined effects of FO supplementation (5% w/w) and HT treatment. For HT, whole-body heat exposure was conducted at 40-41 °C for 30 min, 5 days per week. After 12 weeks, animals were used to evaluate the changes in glucose and lipid metabolism, obesity outcome, and inflammatory markers. The gut microbiome analysis was conducted from cecal content by 16S rRNA sequencing. Acute inflammation was induced by lipopolysaccharide (LPS) injection to evaluate inflammatory responses. Results: HT alone distinctively reduced weight gain, lowered core body temperature, and attenuated insulin resistance comparable to FO supplement in OVX mice. The collaborative effect of FO and HT was not evident in metabolic parameters but more prominent in attenuating proinflammatory responses and microbiota modulation. Conclusions: Our findings suggest that the combined treatment of FO supplementation and HT may serve as an effective strategy to mitigate menopause-associated immune susceptibility and metabolic dysfunction. These benefits are likely mediated, at least in part, through the reduction in inflammation and modulation of the gut microbiota.}, }
@article {pmid39940404, year = {2025}, author = {Zhang, H and Su, Q}, title = {Low-FODMAP Diet for Irritable Bowel Syndrome: Insights from Microbiome.}, journal = {Nutrients}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/nu17030544}, pmid = {39940404}, issn = {2072-6643}, support = {CUHK14104124//Research Grants Council of the Hong Kong Special Administrative Region/ ; }, mesh = {*Irritable Bowel Syndrome/diet therapy/microbiology ; Humans ; *Gastrointestinal Microbiome/physiology ; *Oligosaccharides/administration &amp; dosage ; *Monosaccharides ; Disaccharides ; Fermentation ; Probiotics/administration &amp; dosage ; Diet, Carbohydrate-Restricted/methods ; Diet/methods ; FODMAP Diet ; Polymers ; }, abstract = {Irritable bowel syndrome (IBS) is a prevalent gastrointestinal disorder characterized by chronic abdominal pain, bloating, and altered bowel habits. Low-FODMAP diets, which involve restricting fermentable oligosaccharides, disaccharides, monosaccharides, and polyols, have emerged as an effective dietary intervention for alleviating IBS symptoms. This review paper aims to synthesize current insights into the impact of a low-FODMAP diet on the gut microbiome and its mechanisms of action in managing IBS. We explore the alterations in microbial composition and function associated with a low-FODMAP diet and discuss the implications of these changes for gut health and symptom relief. Additionally, we examine the balance between symptom improvement and potential negative effects on microbial diversity and long-term gut health. Emerging evidence suggests that while a low-FODMAP diet can significantly reduce IBS symptoms, it may also lead to reductions in beneficial microbial populations. Strategies to mitigate these effects, such as the reintroduction phase and the use of probiotics, are evaluated. This review highlights the importance of a personalized approach to dietary management in IBS, considering individual variations in microbiome responses. Understanding the intricate relationship between diet, the gut microbiome, and IBS symptomatology will guide the development of more effective, sustainable dietary strategies for IBS patients.}, }
@article {pmid39940370, year = {2025}, author = {Öneş, E and Zavotçu, M and Nisan, N and Baş, M and Sağlam, D}, title = {Effects of Kefir Consumption on Gut Microbiota and Athletic Performance in Professional Female Soccer Players: A Randomized Controlled Trial.}, journal = {Nutrients}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/nu17030512}, pmid = {39940370}, issn = {2072-6643}, support = {TDK-2023-91//Ac&#x131;badem University Scientific Research Projects Coordination Office (ABAPKO)/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Adult ; Young Adult ; *Soccer/physiology ; *Kefir/microbiology ; *Athletic Performance/physiology ; Adolescent ; Athletes ; Diet ; Body Composition ; RNA, Ribosomal, 16S/genetics ; Dietary Fiber/administration &amp; dosage ; }, abstract = {BACKGROUND/OBJECTIVES: This study aimed to determine the impact of the daily consumption of kefir on the gut microbiome, body composition, and athletic performance of professional female soccer players.<br><br>METHODS: The participants encompassed 21 females aged 18-29 years who were assigned to one of the two groups: the experimental group, which comprised females who consumed 200 mL of kefir daily for 28 days, and the control group, which comprised females who continued with their normal diet. Anthropometric measurements, dietary intake, the composition of the gut microbiome through 16S rRNA gene sequencing, and an athletic performance test known as the 30-15 Intermittent Fitness Test were performed before and after the intervention.<br><br>RESULTS: The results of this study revealed that the consumption of kefir increased the microbial diversity (Shannon and Chao1 indices), wherein a significant increase was noted in the abundance of Akkermansia muciniphila and Faecalibacterium prausnitzii, microorganisms that regulate energy metabolism and have anti-inflammatory effects. Furthermore, the athletic performance variables, including VO2max (mL.kg[-1].min[-1]) and finishing speed (km/h), were strongly related to the abundance of these short-chain fatty acid-producing bacteria. A link between the microbiota profile and the dietary intake of fiber and protein as well as the body composition measurements was also established.<br><br>CONCLUSIONS: This study indicated that kefir consumption can positively affect the gut microbiota, which could in turn affect the athletes' performance. Therefore, to determine the effects of kefir as a functional food in sports nutrition over a longer period, more research should be conducted.}, }
@article {pmid39940363, year = {2025}, author = {Han, AL and Ryu, MS and Yang, HJ and Jeong, DY and Choi, KH}, title = {The Efficacy of Cheonggukjang in Alleviating Menopausal Syndrome and Its Effects on the Gut Microbiome: A Randomized, Double-Blind Trial.}, journal = {Nutrients}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/nu17030505}, pmid = {39940363}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Female ; Double-Blind Method ; Middle Aged ; *Menopause ; Glycine max ; Fermented Foods ; Feces/microbiology ; Republic of Korea ; Postmenopause ; Treatment Outcome ; }, abstract = {Background/Objectives: Menopause is associated with various symptoms. Although hormone replacement therapy (HRT) is commonly used, concerns regarding its side effects have led to the development of alternative treatments. This study evaluated the potential health benefits of Cheonggukjang, a traditional Korean fermented soybean product in alleviating menopausal symptoms and improving metabolic parameters in postmenopausal women. Additionally, the effect of Cheonggukjang on the gut microbiome was assessed using stool analysis. Methods: In this randomized, double-blind clinical trial, 60 postmenopausal women were assigned to three groups: high-beneficial-microorganism content Cheonggukjang (HTC), low-beneficial-microorganism content Cheonggukjang (LTC), and commercially available Cheonggukjang (CC). Participants consumed 3.3 g of Cheonggukjang tablets daily for 8 weeks. We assessed menopausal symptom relief using the Kupperman index, metabolic parameters, and changes in the gut microbiome using stool analysis. Results: The Kupperman index scores significantly decreased across all three groups, with the HTC group showing the greatest improvement. No significant changes were observed in body mass index, weight, or lipid profiles. Blood glucose levels decreased significantly only in the HTC group. Microbiome analysis revealed an increase in beneficial bacteria in the HTC and CC groups and a decrease in harmful bacteria. The Firmicutes-to-Bacteroidetes ratio decreased in both HTC and CC groups, though this change was not significant. Conclusions: Cheonggukjang supplementation significantly alleviated menopausal symptoms, particularly in the HTC group, and improved the gut microbiota composition. These findings suggest that Cheonggukjang, particularly with its high beneficial microorganism content, may offer a promising alternative for managing menopausal symptoms and improving metabolic health in postmenopausal women.}, }
@article {pmid39940343, year = {2025}, author = {Tomaszek, N and Urbaniak, AD and Bałdyga, D and Chwesiuk, K and Modzelewski, S and Waszkiewicz, N}, title = {Unraveling the Connections: Eating Issues, Microbiome, and Gastrointestinal Symptoms in Autism Spectrum Disorder.}, journal = {Nutrients}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/nu17030486}, pmid = {39940343}, issn = {2072-6643}, support = {B.SUB.25.445//Medical University of Bialystok/ ; }, mesh = {Humans ; *Autism Spectrum Disorder/microbiology ; *Gastrointestinal Microbiome/physiology ; *Gastrointestinal Diseases/microbiology ; *Brain-Gut Axis/physiology ; Feeding and Eating Disorders ; Child ; Feeding Behavior/physiology ; }, abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by challenges in social communication, restricted interests, and repetitive behaviors. It is also associated with a high prevalence of eating disorders, gastrointestinal (GI) symptoms, and alterations in gut microbiota composition. One of the most pressing concerns is food selectivity. Various eating disorders, such as food neophobia, avoidant/restrictive food intake disorder (ARFID), specific dietary patterns, and poor-quality diets, are commonly observed in this population, often leading to nutrient deficiencies. Additionally, gastrointestinal problems in children with ASD are linked to imbalances in gut microbiota and immune system dysregulation. The aim of this narrative review is to identify previous associations between the gut-brain axis and gastrointestinal problems in ASD. We discuss the impact of the "microbiome-gut-brain axis", a bidirectional connection between gut microbiota and brain function, on the development and symptoms of ASD. In gastrointestinal problems associated with ASD, a 'vicious cycle' may play a significant role: ASD symptoms contribute to the prevalence of ARFID, which in turn leads to microbiota degradation, ultimately worsening ASD symptoms. Current data suggest a link between gastrointestinal problems in ASD and the microbiota, but the amount of evidence is limited. Further research is needed, targeting the correlation of a patient's microbiota status, dietary habits, and disease course.}, }
@article {pmid39940329, year = {2025}, author = {Naik, RG and Purcell, SA and Gold, SL and Christiansen, V and D'Aloisio, LD and Raman, M and Haskey, N}, title = {From Evidence to Practice: A Narrative Framework for Integrating the Mediterranean Diet into Inflammatory Bowel Disease Management.}, journal = {Nutrients}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/nu17030470}, pmid = {39940329}, issn = {2072-6643}, mesh = {Humans ; *Diet, Mediterranean ; *Inflammatory Bowel Diseases/diet therapy ; *Gastrointestinal Microbiome ; Quality of Life ; }, abstract = {Emerging evidence underscores the pivotal role of diet in preventing and managing inflammatory bowel disease (IBD). As our comprehension of the microbiome's role in IBD expands, dietary modifications are increasingly recognized as potential adjuncts or primary therapeutic strategies. Key components of the Mediterranean diet (MD)-including microbiota-accessible carbohydrates, omega-3 fatty acids, polyphenols, and antioxidants-have demonstrated promise in enhancing gut microbiota diversity and reducing intestinal inflammation, making it a practical approach for managing IBD. Moreover, the MD offers additional benefits considering the rising prevalence of comorbid chronic inflammatory conditions such as diabetes, cardiovascular disease, and obesity in IBD patients. The purpose of this narrative review was to provide an overview of the feasibility and clinical outcomes of the MD and offer evidence-based guidance for researchers and practitioners on how to adapt the MD to patients with IBD. According to several cross-sectional and interventional studies, the MD is feasible for patients with IBD and confers several benefits, such as reduced inflammation, improved disease activity, and enhanced quality of life, with a strong adherence rate and minimal adverse effects. To facilitate knowledge translation, we provide a practical framework for integrating the MD as a nutritional therapy for IBD, including specific recommendations and messaging that researchers, practitioners, and patients can use. By synthesizing current evidence and offering actionable insights, the aim is to facilitate the integration of the MD into IBD management, with the potential to improve patient outcomes.}, }
@article {pmid39940326, year = {2025}, author = {Srivastava, G and Brylinski, M}, title = {A Data-Driven Approach to Enhance the Prediction of Bacteria-Metabolite Interactions in the Human Gut Microbiome Using Enzyme Encodings and Metabolite Structural Embeddings.}, journal = {Nutrients}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/nu17030469}, pmid = {39940326}, issn = {2072-6643}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Bacteria/classification/metabolism ; *Machine Learning ; Principal Component Analysis ; }, abstract = {Background: The human gut microbiome is critical for host health by facilitating essential metabolic processes. Our study presents a data-driven analysis across 312 bacterial species and 154 unique metabolites to enhance the understanding of underlying metabolic processes in gut bacteria. The focus of the study was to create a strategy to generate a theoretical (negative) set for binary classification models to predict the consumption and production of metabolites in the human gut microbiome. Results: Our models achieved median balanced accuracies of 0.74 for consumption predictions and 0.95 for production predictions, highlighting the effectiveness of this approach in generating reliable negative sets. Additionally, we applied a kernel principal component analysis for dimensionality reduction. The consumption model with a polynomial kernel, and the production model with a radial basis function with 32 reduced features, showed median accuracies of 0.58 and 0.67, respectively. This demonstrates that biological information can still be captured, albeit with some loss, even after reducing the number of features. Furthermore, our models were validated on six previously unseen cases, achieving five correct predictions for consumption and four for production, demonstrating alignment with known biological outcomes. Conclusions: These findings highlight the potential of integrating data-driven approaches with machine learning techniques to enhance our understanding of gut microbiome metabolism. This work provides a foundation for creating bacteria-metabolite datasets to enhance machine learning-based predictive tools, with potential applications in developing therapeutic methods targeting gut microbes.}, }
@article {pmid39940323, year = {2025}, author = {Koudonas, A and Tsiakaras, S and Tzikoulis, V and Papaioannou, M and de la Rosette, J and Anastasiadis, A and Dimitriadis, G}, title = {Lifestyle Factors and the Microbiome in Urolithiasis: A Narrative Review.}, journal = {Nutrients}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/nu17030465}, pmid = {39940323}, issn = {2072-6643}, mesh = {Humans ; *Urolithiasis/microbiology/prevention &amp; control ; *Life Style ; *Microbiota ; Vitamin D/administration &amp; dosage ; Dietary Supplements ; }, abstract = {Urolithiasis represents one of the most common urologic diseases, and its incidence demonstrates, globally, an increasing trend. The application of preventive measures is an established strategy to reduce urolithiasis-related morbidity, and it is based mostly on the adaptation of lifestyle factors and pharmacotherapy. Furthermore, other research areas demonstrate promising results, such as the research on the microbiome. In the current review, we searched for the latest data on lifestyle-based prevention and microbiome alterations in urolithiasis patients. The majority of the proposed lifestyle measures are already included in the urological guidelines, while additional factors, such as vitamin D supplementation, seem to have a putative positive effect. From the microbiome studies, several microbial composition patterns and metabolic pathways demonstrated an inhibiting or promoting role in lithogenesis. Up to the present, stone prevention has not shown satisfying results, which suggests that lifestyle measures are not adequate. Moreover, microbiome studies are prone to bias, since microbes are strongly affected by numerous clinical factors, while the analysis procedures are not standardized yet. Analysis standardization and data pooling from extensive registration of clinical and microbiome data are essential steps in order to improve the existing prevention strategy with targeted microbiome manipulations.}, }
@article {pmid39940316, year = {2025}, author = {Sardaro, MLS and Grote, V and Baik, J and Atallah, M and Amato, KR and Ring, M}, title = {Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition.}, journal = {Nutrients}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/nu17030458}, pmid = {39940316}, issn = {2072-6643}, support = {IM AWARE Advisory Council Research Pilot Grants//Osher Center for Integrative Medicine/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Fruit ; Male ; Female ; *Vegetables ; Adult ; *Saliva/microbiology ; *Fruit and Vegetable Juices ; *Diet ; Dietary Fiber/administration &amp; dosage/pharmacology ; Mouth/microbiology ; Microbiota/drug effects ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Young Adult ; Feces/microbiology ; Bacteria/classification/genetics ; }, abstract = {BACKGROUND: In recent years, juicing has often been promoted as a convenient way to increase fruit and vegetable intake, with juice-only diets marketed for digestive cleansing and overall health improvement. However, juicing removes most insoluble fiber, which may diminish the health benefits of whole fruits and vegetables. Lower fiber intake can alter the microbiota, affecting metabolism, immunity, and mental health, though little is known about juicing's specific effects on the microbiota. This study addresses this gap by exploring how juicing impacts gut and oral microbiome composition in an intervention study.<br><br>METHODS: Fourteen participants followed one of three diets-exclusive juice, juice plus food, or plant-based food-for three days. Microbiota samples (stool, saliva, and inner cheek swabs) were collected at baseline, after a pre-intervention elimination diet, immediately after juice intervention, and 14 days after intervention. Moreover, 16S rRNA gene amplicon sequencing was used to analyze microbiota taxonomic composition.<br><br>RESULTS: The saliva microbiome differed significantly in response to the elimination diet (unweighted UniFrac: F = 1.72, R = 0.06, p < 0.005; weighted UniFrac: F = 7.62, R = 0.23, p-value = 0.0025) with a significant reduction in Firmicutes (p = 0.004) and a significant increase in Proteobacteria (p = 0.005). The juice intervention diets were also associated with changes in the saliva and cheek microbiota, particularly in the relative abundances of pro-inflammatory bacterial families, potentially due to the high sugar and low fiber intake of the juice-related products. Although no significant shifts in overall gut microbiota composition were observed, with either the elimination diet or the juice intervention diets, bacterial taxa associated with gut permeability, inflammation, and cognitive decline increased in relative abundance.<br><br>CONCLUSIONS: These findings suggest that short-term juice consumption may negatively affect the microbiota.}, }
@article {pmid39940300, year = {2025}, author = {Farmakioti, I and Stylianopoulou, E and Siskos, N and Karagianni, E and Kandylas, D and Vasileiou, AR and Fragkiskatou, F and Somalou, P and Tsaroucha, A and Ypsilantis, P and Panas, P and Kourkoutas, Y and Skavdis, G and Grigoriou, ME}, title = {Enhancing Gut Microbiome and Metabolic Health in Mice Through Administration of Presumptive Probiotic Strain Lactiplantibacillus pentosus PE11.}, journal = {Nutrients}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/nu17030442}, pmid = {39940300}, issn = {2072-6643}, support = {MIS 5047291//Operational Programme "Competitiveness, Entrepreneurship and Innovation" (NSRF 2014-2020) and co-financed by Greece and the EU (European Regional Development Fund)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Probiotics/administration &amp; dosage ; Mice ; *Feces/microbiology ; Male ; Lactobacillaceae ; Mice, Inbred C57BL ; Cecum/microbiology/metabolism ; }, abstract = {Background: Over the past decade, probiotics have gained increasing recognition for their health benefits to the host. While most research has focused on the therapeutic effects of probiotics in the treatment of various diseases, recent years have seen a shift towards exploring their role in enhancing and supporting overall health. Methods: In this work, we have studied the effects of a novel potential probiotic strain, Lactiplantibacillus pentosus PE11, in healthy mice following a six-week dietary intervention. The assessment included monitoring the general health of the animals, biochemical analyses, profiling of the gut and fecal microbial communities, and gene expression analysis. Results: Our results showed that the administration of Lactiplantibacillus pentosus PE11 led to changes in the composition of the fecal microbiome, specifically an increase in the Firmicutes/Bacteroidetes ratio and in the relative abundance of the Lachnospiraceae, Ruminococcaceae, and Rikenellaceae families. Reduced Tnf expression and elevated Zo1 expression were also observed in the cecum, pointing to anti-inflammatory properties and improved intestinal barrier integrity. Additionally, a significant reduction in triglycerides and alanine aminotransferase levels-within physiological ranges-was observed, along with a trend toward decreased total cholesterol levels. Conclusions: These findings suggest that in healthy mice, Lactiplantibacillus pentosus PE11 has the potential to positively influence gut microbiome structure and metabolism, thereby supporting improved overall health.}, }
@article {pmid39940268, year = {2025}, author = {Raimundo, M and Rodrigues, P and Esteban, S and Espinosa-Martos, I and Jiménez, E}, title = {Ligilactobacillus salivarius PS11610 Enhances the Fertilization Success of IVF: A Preliminary Retrospective Analysis.}, journal = {Nutrients}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/nu17030410}, pmid = {39940268}, issn = {2072-6643}, mesh = {Humans ; Female ; *Fertilization in Vitro/methods ; Pregnancy ; Retrospective Studies ; *Probiotics/administration &amp; dosage ; Adult ; *Ligilactobacillus salivarius ; *Embryo Transfer/methods ; Pregnancy Rate ; Pregnancy Outcome ; }, abstract = {BACKGROUND/OBJECTIVES: Infertility affects couples at reproductive age, with in vitro fertilization (IVF) being the most effective treatment. Success rates of IVF are influenced by several factors, including a healthy female reproductive system microbiome, which can improve implantation rates and pregnancy outcomes. This study evaluated the impact of Ligilactobacillus salivarius PS11610 on IVF outcomes. This strain showed antimicrobial activity against pathogens related to dysbiosis, commonly observed in women undergoing assisted reproductive treatment.<br><br>RESULTS: The administration of L. salivarius PS11610 at a dose of 1 &#xd7; 10[9] CFU every 12 h for at least one month before IVF procedures, particularly in the frozen embryo transfer (FET) group, appears to enhance the success rate of IVF. IVF procedures without embryo transfer showed no significant differences between the groups. However, there were statistically significant differences in the quality of embryos, specifically in category 2, which were higher in the group without L. salivarius PS11610 supplementation (p = 0.042). Similar results were seen in the IVF with embryo transfer group, where the quality of embryos in categories 2 and 3 was higher in the group without L. salivarius PS11610 (p = 0.019 and p = 0.05, respectively). IVF with FET showed notable improvements, where intake of L. salivarius PS11610 was associated with a significant increase in live birth infants (26.4% with L. salivarius PS11610 vs. 17.9% without, p = 0.034) and higher biochemical pregnancy rates (42.6% vs. 34%, p = 0.071).<br><br>CONCLUSIONS: Despite some differences in embryo quality, the overall positive impact on pregnancy and birth outcomes highlights L. salivarius PS11610 as a promising supplement in assisted reproductive treatments.}, }
@article {pmid39940254, year = {2025}, author = {Barata, P and Oliveira, A and Soares, R and Fernandes, A}, title = {Gut Microbiota Is Not Significantly Altered by Radioiodine Therapy.}, journal = {Nutrients}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/nu17030395}, pmid = {39940254}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/radiation effects ; Female ; Middle Aged ; Male ; *Feces/microbiology ; *Iodine Radioisotopes ; *Hyperthyroidism/radiotherapy/microbiology ; Adult ; Prospective Studies ; Thyroid Neoplasms/radiotherapy/microbiology ; Aged ; Bacteria/classification/radiation effects/genetics/isolation &amp; purification ; Metagenomics/methods ; }, abstract = {Purpose: Radiotherapy treatments are known to alter the gut microbiota. However, little is known regarding the effect of nuclear medicine treatments on gut microbiota, and it is established that nuclear medicine is inherently different from radiotherapy. To address this knowledge gap, we conducted a prospective study to identify changes in the gut microbiota of patients treated with [[131]I]NaI by comparing fecal samples before and after RAIT. Methods: Fecal samples of 64 patients (37 with thyroid cancer and 27 with hyperthyroidism) with indication for RAIT were collected 2 to 3 days before treatment and 8 to 10 days post-treatment. After DNA extraction, the gut microbiota's richness, diversity, and composition were analyzed by shotgun metagenomics. In addition, LEfSe was performed to compare compositional changes in specific bacteria. Results: Gut microbiome richness and diversity remained unchanged after RAIT, with few changes in its composition identified, especially in patients with hyperthyroidism. Conclusions: This study provides a conceptual and analytical basis for increasing our understanding of the effects of radiopharmaceuticals on gut microbiota. Our preliminary results indicate that RAIT, contrary to radiotherapy, does not cause major disruptions to the human gut microbiota.}, }
@article {pmid39940253, year = {2025}, author = {Isolauri, E and Laitinen, K}, title = {Resilience to Global Health Challenges Through Nutritional Gut Microbiome Modulation.}, journal = {Nutrients}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/nu17030396}, pmid = {39940253}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Pregnancy ; Female ; *Global Health ; Noncommunicable Diseases/prevention &amp; control ; Nutritional Status ; Infant ; Obesity/microbiology/prevention &amp; control/etiology ; }, abstract = {As the world faces an escalating challenge of non-communicable diseases (NCDs), with phenotypes ranging from allergic chronic immuno-inflammatory diseases to neuropsychiatric disorders, it becomes evident that their seeds are sown during the early stages of life. Furthermore, within only a few decades, human obesity has reached epidemic proportions and now represents the most serious public health challenge of our time. Recent demonstrations that a growing number of these conditions are linked to aberrant gut microbiota composition and function have evoked active scientific interest in host-microbe crosstalk, characterizing and modulating the gut microbiota in at-risk circumstances. These efforts appear particularly justified during the most critical period of developmental plasticity when the child's immune, metabolic, and microbiological constitutions lend themselves to long-term adjustment. Pregnancy and early infancy epitomize an ideal developmental juncture for preventive measures aiming to reduce the risk of NCDs; by promoting the health of pregnant and lactating women today, the health of the next generation(s) may be successfully improved. The perfect tools for this initiative derive from the earliest and most massive source of environmental exposures, namely the microbiome and nutrition, due to their fundamental interactions in the function of the host immune and metabolic maturation.}, }
@article {pmid39940246, year = {2025}, author = {Redruello-Requejo, M and Del Mar Blaya, M and González-Reguero, D and Robas-Mora, M and Arranz-Herrero, J and Partearroyo, T and Varela-Moreiras, G and Penalba-Iglesias, D and Jiménez-Gómez, P and Reche-Sainz, P}, title = {Cross-Sectional Comparative Analysis of Gut Microbiota in Spanish Adolescents with Mediterranean and Western Diets.}, journal = {Nutrients}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/nu17030388}, pmid = {39940246}, issn = {2072-6643}, mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; Adolescent ; *Diet, Mediterranean ; Cross-Sectional Studies ; Male ; Female ; Spain ; *Diet, Western ; Bacteria/classification/genetics ; RNA, Ribosomal, 16S/genetics ; Anti-Bacterial Agents/pharmacology ; Feces/microbiology ; Fast Foods/microbiology ; }, abstract = {UNLABELLED: Dietary patterns, such as the Mediterranean diet (MD) and the Western diet (WD), influence gut microbiota composition and functionality, which play important roles in energy metabolism and nutrient absorption.<br><br>OBJECTIVES: A descriptive cross-sectional study was designed to evaluate the gut microbiota of 19 Spanish adolescents and to investigate the association of MD and ultra-processed food (UPF) intake with microbial diversity and community structure.<br><br>METHODS: Functional diversity of gut microbiota was evaluated using Biolog EcoPlates, taxonomic composition was assessed with 16S rRNA sequencing via MinION, and phenotypic responses to antibiotics were analyzed using the cenoantibiogram technique under aerobic and anaerobic conditions.<br><br>RESULTS: Adolescents with higher adherence to the MD exhibited greater functional diversity, as per the Shannon-Weaver index. In addition, this group showed higher abundance of bacterial genera previously described as beneficial, such as Paraclostridium, Anaerobutyricum, Romboutsia, and Butyricicoccus. In contrast, adolescents reporting greater UPF intakes had a microbiota composition similar to those with low adherence to the MD, characterized by decreased abundance of beneficial genera. Regarding antibiotic resistance, significant differences were only observed under anaerobic conditions, with individuals with low adherence to the MD showing more sensitivity for most antibiotics tested.<br><br>CONCLUSIONS: These results suggest that the MD promotes a healthier and more balanced gut environment, potentially improving metabolic functions in adolescents. Despite the lack of differences in &#x3b1;-diversity, comparisons of microbial community structure between adolescents following the MD and those with high UPF (characteristic of the WD) showed clear differences in terms of &#x3b2;-diversity. These findings suggest that dietary patterns influence the composition of the gut microbiota in a more complex manner, beyond just taxonomic richness. The outcomes of this exploratory study highlight opportunities for future research to deepen understanding of the long-term health implications of these dietary patterns, as well as the mechanisms regulating the composition, functionality, and phenotypic responses to antibiotics of gut microbial communities.}, }
@article {pmid39940045, year = {2025}, author = {Schropp, N and Bauer, A and Stanislas, V and Huang, KD and Lesker, TR and Bielecka, AA and Strowig, T and Michels, KB}, title = {The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {52}, pmid = {39940045}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Cross-Over Studies ; Male ; Female ; Adult ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fatty Acids, Volatile/metabolism ; *Fermented Foods/microbiology ; Middle Aged ; Feces/microbiology ; Metagenomics/methods ; Young Adult ; Metabolome ; Healthy Volunteers ; }, abstract = {BACKGROUND: Sauerkraut is a fermented food that has been suspected to have a beneficial impact on the gut microbiome, but scientific evidence is sparse. In this crossover intervention trial with 87 participants (DRKS00027007), we investigated the impact of daily consumption of fresh or pasteurized sauerkraut for 4 weeks on gut microbial composition and the metabolome in a healthy study population.<br><br>RESULTS: Using shotgun metagenomic sequencing, we observed changes in single bacterial species following fresh and pasteurized sauerkraut consumption. More pronounced changes were observed in the pasteurized sauerkraut intervention arm. Only pasteurized sauerkraut consumption increased serum short-chain fatty acids (SCFAs).<br><br>CONCLUSIONS: The gut microbiome of healthy individuals is rather resilient to short-term dietary&#xa0;interventions even though single species might be affected by sauerkraut consumption. Video Abstract.}, }
@article {pmid39940033, year = {2025}, author = {Ajileye, OD and Verocai, GG and Light, JE}, title = {A review of filarial nematodes parasitizing tick vectors: unraveling global patterns in species diversity, host associations, and interactions with tick-borne pathogens.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {50}, pmid = {39940033}, issn = {1756-3305}, mesh = {Animals ; *Ticks/parasitology/physiology ; *Filarioidea/genetics/physiology ; Humans ; Host-Parasite Interactions ; Arachnid Vectors/parasitology ; Tick-Borne Diseases/transmission/parasitology ; Filariasis/transmission/parasitology ; }, abstract = {Ticks are well-known vectors of pathogens, including filarial nematodes, which can affect animal and human health. This review synthesizes current knowledge of filarial nematodes that utilize ticks as vectors, focusing on the Onchocercidae. Five genera of onchocercid filarial nematodes (Cercopithifilaria, Cherylia, Cruorifilaria, Monanema, and Yatesia) have demonstrated vector-parasite relationships with ticks, while Acanthocheilonema has only demonstrated molecular detection without confirmed vector competence. Vector competence has been experimentally proven for several species through documented development to infective stages. However, our understanding of tick-borne filarial nematodes remains limited owing to insufficient detection efforts and methodological challenges. Detection methods include traditional dissection, advanced imaging techniques such as microcomputed tomography (micro-CT), and molecular approaches, each with distinct advantages and limitations. To address knowledge gaps, future research should focus on conducting large-scale surveys of tick populations and wildlife to investigate vector competence, health impacts, and coinfection dynamics. Multi-disciplinary collaboration and community involvement in tick surveillance will advance our understanding of tick-borne filarial nematode ecology and epidemiology. Future research priorities include confirming vector competence where only molecular detection exists, investigating natural transmission patterns, and understanding the mechanisms influencing successful development in tick vectors. By addressing these knowledge gaps through systematic surveillance and experimental studies, we can better understand these complex host-parasite-vector relationships and their implications for animal health.}, }
@article {pmid39939954, year = {2025}, author = {Swarup, S and Gupta, A and Chung, M and Radhakrishnan, V and Davis, V and Lynch, MDJ and Charles, TC and Cheng, J and Mendoza, G}, title = {Rapid shift of gut microbiome and enrichment of beneficial microbes during arhatic yoga meditation retreat in a single-arm pilot study.}, journal = {BMC complementary medicine and therapies}, volume = {25}, number = {1}, pages = {51}, pmid = {39939954}, issn = {2662-7671}, mesh = {Humans ; *Yoga ; Pilot Projects ; *Gastrointestinal Microbiome ; *Meditation ; Male ; Adult ; Female ; Diet, Vegetarian ; Middle Aged ; Feces/microbiology ; }, abstract = {BACKGROUND: The human microbiome plays a vital role in human health, mediated by the gut-brain axis, with a large diversity of functions and physiological benefits. The dynamics and mechanisms of meditations on oral and gut microbiome modulations are not well understood. This study investigates the short-term modulations of the gut and oral microbiome during an Arhatic Yoga meditation retreat as well as on the role of microbiome in improving well-being through a possible gut-brain axis.<br><br>METHODS: A single-arm pilot clinical trial was conducted in a controlled environment during a 9-day intensive retreat of Arhatic Yoga meditation practices with vegetarian diet. Oral and fecal samples of 24 practitioners were collected at the start (Day0: T1), middle (Day3: T2), and end (Day9:T3) of the retreat. Targeted 16S rRNA gene amplicon sequencing was performed for both oral and gut samples. Functional pathway predictions was identified using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2). DESeq2 was used to identify the differential abundant taxa. Various statistical analyses were performed to assess the significant changes in the data.<br><br>RESULTS: Our findings revealed that Arhatic Yoga meditation together with a vegetarian diet led to changes in the oral and gut microbiome profiles within the 9-day retreat. Oral microbiome profile showed a significant (p&#x2009;<&#x2009;0.05) difference in the species richness and evenness at the end of study, while non-metric multidimensional scaling (NMDS) confirmed the shift in the gut microbiome profile of the practitioners by T2 timepoint, which was further supported by PERMANOVA analysis (p&#x2009;<&#x2009;0.05). Health-benefiting microbes known to improve the gastrointestinal and gut-barrier functions, immune modulation, and gut-brain axis were enriched. Gut microbiome of both beginner and advanced Arhatic Yoga practitioners showed similar trends of convergence by the end of study. This implies a strong selection pressure by Arhatic Yoga meditation together with a vegetarian diet on the beneficial gut microbiome.<br><br>CONCLUSION: This pilot study demonstrates that Arhatic Yoga meditation practices combined with a vegetarian diet during a short intensive retreat resulted in enrichment of known health-promoting microbes. Such microbial consortia may be developed for potential health benefits and used as probiotics to improve the gastrointestinal and immune systems, as well as functions mediated by the gut-brain axis.<br><br>TRIAL REGISTRATION: Study was submitted in https://clinicaltrials.gov/on28-02-2024 . Retrospective registered.}, }
@article {pmid39939889, year = {2025}, author = {Albracht, C and Buscot, F and Eisenhauer, N and Gebler, A and Herrmann, S and Schmidt, A and Tarkka, M and Goldmann, K}, title = {Invertebrate Decline Has Minimal Effects on Oak-Associated Microbiomes.}, journal = {Environmental microbiology}, volume = {27}, number = {2}, pages = {e70051}, doi = {10.1111/1462-2920.70051}, pmid = {39939889}, issn = {1462-2920}, support = {677232/ERC_/European Research Council/International ; DFG-FZT 118//German Research Foundation/ ; 202548816//German Research Foundation/ ; DFG-FOR 5000//German Research Foundation/ ; }, mesh = {*Quercus/microbiology ; Animals ; *Microbiota ; *Invertebrates/microbiology ; *Plant Leaves/microbiology ; *Soil Microbiology ; Rhizosphere ; Bacteria/genetics/classification/metabolism ; Mycorrhizae/physiology ; Plant Roots/microbiology ; Biomass ; Herbivory ; Fungi/genetics/classification ; Biodiversity ; Grassland ; Ecosystem ; }, abstract = {Recently, biomass of invertebrates has declined substantially at many locations with the implications of this biodiversity loss for ecosystems yet unknown. Through multitrophic interactions, plant- and soil-associated microbiomes might be altered, causing a cascade of changes on diverse ecosystem processes. We simulated aboveground invertebrate decline in grassland ecosystems with two levels of invertebrate biomass (36% and 100% of current ambient conditions), plus a control with no invertebrates present. Each standardised grassland mesocosm additionally contained one clonal Quercus robur L. sapling to investigate the extent of invertebrate decline effects exceeding grasslands. We investigated oak biomass partitioning and mycorrhiza formation, oak leaf transcriptome and microbiome composition of leaves, roots and rhizosphere. While invertebrate decline did not significantly affect oak performance and herbivory-related gene expression, fungal communities presented an increase of saprotrophs and pathogens, especially in leaves. Among leaf-inhabiting bacteria, Proteobacteria and Actinobacteria increased under invertebrate decline. The belowground microbiome was only little affected. But, invertebrate decline came along with a reduced influence on predators leading to an elevated aphids infestation that proofed able to alter microbiota. Our findings establish a strong difference between above- and belowground, with the impacts of invertebrate decline being more pronounced in the leaf microbiome.}, }
@article {pmid39939643, year = {2025}, author = {Tandoro, Y and Chiu, HF and Tan, CL and Hsieh, MH and Huang, YW and Yu, J and Wang, LS and Chan, CH and Wang, CK}, title = {Black raspberry supplementation on overweight and Helicobacter pylori infected mild dementia patients a pilot study.}, journal = {NPJ science of food}, volume = {9}, number = {1}, pages = {9}, pmid = {39939643}, issn = {2396-8370}, abstract = {Alzheimer's disease (AD) is the most common form of dementia. H. pylori infection and overweight have been implicated in AD via the gut-brain axis (GBA). This study aimed to determine whether supplementation of BRBs has a meaningful effect on H. pylori infection, overweight, and AD development in a clinical trial setting. We conducted a randomized placebo-controlled clinical trial in patients with mild clinical dementia who also had H. pylori infection and were overweight. The study was conducted over 10 weeks, consisting of an 8-week intervention period (25 g powder of black raspberries, BRBs, or placebo twice daily, morning and evening) and a 2-week follow-up. The primary outcomes were changes in Clinical Dementia Rating (CDR), Urea Breath Test (UBT), and Body Mass Index (BMI). Consumption of BRBs improved cognitive functions (p < 0.00001), compared to the placebo group (p > 0.05). Besides, BRBs ingestion decreased H. pylori infection and BMI (p < 0.00001 and p < 0.05 respectively) while the placebo group stayed statistically the same (p = 0.98 and p = 0.25 respectively). BRBs significantly decreased inflammatory markers, improved oxidative index, and adiponectin (p < 0.05) compared to the placebo group, while adenosine monophosphate-activated protein kinase (AMPK) and leptin did not significantly change. BRBs modulated the abundance of several fecal probiotics, particularly, Akkermansia muciniphila. Our results provided that BRBs suppressed H. pylori infection, decreased BMI, and rebalanced the gut microbiome, which could improve cognitive functions in mild dementia patients. Longer and larger randomized clinical trials of BRB interventions targeting H. pylori infection, overweight, or mild dementia are warranted to confirm the results from this pilot trial. Trial Registration: ClinicalTrials.gov identifier: NCT05680532.}, }
@article {pmid39939570, year = {2025}, author = {Nieto, EE and Festa, S and Colman, D and Macchi, M and Morelli, IS and Coppotelli, BM}, title = {Challenging the impact of consortium diversity on bioaugmentation efficiency and native bacterial community structure in an acutely PAH-contaminated soil.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {39939570}, issn = {1614-7499}, support = {PICT 2019-1805//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; PICT 2019-2540//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/ ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are priority pollutants. We studied the effect of bioaugmentation using three allochthonous bacterial consortia with increasing diversity: SC AMBk, SC1, and SC4, on the structure and functionality of an artificially and acutely PAH-contaminated soil microbiome. The PAH supplementation increased substrate availability, allowing the inocula to efficiently degrade the supplemented PAHs after 15 days of incubation, become temporarily established, and modify the number of total interactions with soil residents. Sphingobium and Burkholderia, both members of the inoculants, were the major contributors to functional KOs (KEGG orthologs) linked to degradation and were differentially abundant genera in inoculated microcosms, indicating their competitiveness in the soil. Hence, bioaugmentation efficiency relied on them, while further degradation could be carried out by native microorganisms. This is one of the first studies to apply three inocula, designed from naturally occurring bacteria, and to study their effect on the soil's native community through ANCOM-BC. We revealed that when a resource that can be used by the inoculant is added to the soil, a high-diversity inoculant is not necessary to interact with the native community and establish itself. This finding is crucial for the design of microbiome engineering in bioremediation processes.}, }
@article {pmid39939548, year = {2025}, author = {Ballerini, M and Galiè, S and Tyagi, P and Catozzi, C and Raji, H and Nabinejad, A and Macandog, ADG and Cordiale, A and Slivinschi, BI and Kugiejko, KK and Freisa, M and Occhetta, P and Wargo, JA and Ferrucci, PF and Cocorocchio, E and Segata, N and Vignati, A and Morgun, A and Deleidi, M and Manzo, T and Rasponi, M and Nezi, L}, title = {A gut-on-a-chip incorporating human faecal samples and peristalsis predicts responses to immune checkpoint inhibitors for melanoma.}, journal = {Nature biomedical engineering}, volume = {}, number = {}, pages = {}, pmid = {39939548}, issn = {2157-846X}, support = {22-0402/AICR_/Worldwide Cancer Research/United Kingdom ; 22-0402/AICR_/Worldwide Cancer Research/United Kingdom ; IG 26406//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; StartUp Grant 21474//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; 860715//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 860715//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 860715//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, abstract = {Patient responses to immune checkpoint inhibitors can be influenced by the gastrointestinal microbiome. Mouse models can be used to study microbiome-host crosstalk, yet their utility is constrained by substantial anatomical, functional, immunological and microbial differences between mice and humans. Here we show that a gut-on-a-chip system mimicking the architecture and functionality of the human intestine by including faecal microbiome and peristaltic-like movements recapitulates microbiome-host interactions and predicts responses to immune checkpoint inhibitors in patients with melanoma. The system is composed of a vascular channel seeded with human microvascular endothelial cells and an intestinal channel with intestinal organoids derived from human induced pluripotent stem cells, with the two channels separated by a collagen matrix. By incorporating faecal samples from patients with melanoma into the intestinal channel and by performing multiomic analyses, we uncovered epithelium-specific biomarkers and microbial factors that correlate with clinical outcomes in patients with melanoma and that the microbiome of non-responders has a reduced ability to buffer cellular stress and self-renew. The gut-on-a-chip model may help identify prognostic biomarkers and therapeutic targets.}, }
@article {pmid39939451, year = {2025}, author = {O'Leary, K}, title = {Reversing the effects of industrialization on the gut microbiome.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41591-025-00010-2}, pmid = {39939451}, issn = {1546-170X}, }
@article {pmid39838923, year = {2025}, author = {Mah, JC and Lohmueller, KE and Garud, NR}, title = {Inference of the Demographic Histories and Selective Effects of Human Gut Commensal Microbiota Over the Course of Human History.}, journal = {Molecular biology and evolution}, volume = {42}, number = {2}, pages = {}, doi = {10.1093/molbev/msaf010}, pmid = {39838923}, issn = {1537-1719}, support = {T32 5T32GM008185//NIGMS NIH/ ; //Paul Allen Research Foundation/ ; //UC Hellman Fellows/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Symbiosis ; Genetic Fitness ; Selection, Genetic ; Phylogeny ; Genetic Drift ; }, abstract = {Despite the importance of gut commensal microbiota to human health, there is little knowledge about their evolutionary histories, including their demographic histories and distributions of fitness effects (DFEs) of mutations. Here, we infer the demographic histories and DFEs for amino acid-changing mutations of 39 of the most prevalent and abundant commensal gut microbial species found in Westernized individuals over timescales exceeding human generations. Some species display contractions in population size and others expansions, with several of these events coinciding with several key historical moments in human history. DFEs across species vary from highly to mildly deleterious, with differences between accessory and core gene DFEs largely driven by genetic drift. Within genera, DFEs tend to be more congruent, reflective of underlying phylogenetic relationships. Together, these findings suggest that gut microbes have distinct demographic and selective histories.}, }
@article {pmid39944248, year = {2023}, author = {El-Omar, EM}, title = {Future directions in the microbiome field: an editor's perspective.}, journal = {eGastroenterology}, volume = {1}, number = {1}, pages = {e100003}, doi = {10.1136/egastro-2023-100003}, pmid = {39944248}, issn = {2976-7296}, }
@article {pmid39939365, year = {2025}, author = {Soares, KO and Da Rocha, TF and Hale, VL and Vasconcelos, PC and do Nascimento, LJ and da Silva, NMV and Rodrigues, AE and de Oliveira, CJB}, title = {Comparing the impact of landscape on the gut microbiome of Apis mellifera in Atlantic Forest and Caatinga Biomes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {5293}, pmid = {39939365}, issn = {2045-2322}, support = {001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 88881.311776/2018-01//CAPES-PrInt Project "Omic sciences applied to the prevention of antimicrobial resistance at the human-animal-environment interface-a one health approach/ ; 88881.311776/2018-01//CAPES-PrInt Project "Omic sciences applied to the prevention of antimicrobial resistance at the human-animal-environment interface-a one health approach/ ; 3136678/2020-0//Conselho Nacional de Pesquisa e Desenvolvimento/ ; 3136678/2020-0//Conselho Nacional de Pesquisa e Desenvolvimento/ ; }, mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome ; *Forests ; Brazil ; *RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Ecosystem ; }, abstract = {The composition of the gut microbiota in animals can be influenced by a variety of intrinsic and extrinsic factors in the host, such as diet, physiological state, and genetics. This study aimed to compare the structural composition of the gut microbiota of Apis mellifera bees from two distinct Brazilian biomes, the Atlantic Forest and the Caatinga, using high throughput 16 S rRNA sequencing. We identified a core microbiota composed of seven genera present in all samples: Lactobacillus, Commensalibacter, Rhizobiaceae, Snodgrassella, Gilliamella, Orbaceae and Bifidobacterium. These taxa accounted for 63% of all bacterial genera in the dataset. Interestingly, we observed a significantly differential abundance of the genus Apibacter between bees from the two biomes, with a marked increase in bees from Atlantic Forest. However, the overall variance in the gut structural composition attributable to landscape type, while significant, was relatively low. Notably, none of the members of the core microbiota were differently abundant between the biomes. Understanding the magnitude of landscape-associated effects on the microbiota of bees in different biomes is crucial for the accurate assessment of the impact of anthropogenic factors. These findings provide important insights into the resilience and adaptability of the honey bee gut microbiome across contrasting environments, contributing to the development of conservation and sustainable management strategies for these essential pollinators.}, }
@article {pmid39939328, year = {2025}, author = {Markus, MRP and Weiss, FU and Hertel, J and Weiss, S and Rühlemann, M and Bang, C and Franke, A and Völker, U and Homuth, G and Kocher, T and Völzke, H and Lerch, MM and Ittermann, T and Felix, SB and Ewert, R and Bahls, M and Dörr, M and Frost, F}, title = {Lower cardiorespiratory fitness is associated with an altered gut microbiome. The Study of Health in Pomerania (SHIP).}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {5171}, pmid = {39939328}, issn = {2045-2322}, mesh = {*Gastrointestinal Microbiome ; Humans ; *Cardiorespiratory Fitness/physiology ; Male ; Female ; Middle Aged ; Adult ; Feces/microbiology ; Cross-Sectional Studies ; Germany/epidemiology ; RNA, Ribosomal, 16S/genetics ; Exercise Test ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Sedentarism is characterized by low levels of physical activity, a risk factor for obesity and cardio-metabolic diseases. It can also adversely affect the composition and diversity of the gut microbiome which may result in harmful consequences for human health. While cardiorespiratory fitness (CRF) is inversely and independently associated with cardiovascular risk factors and diseases and all-cause mortality, the relationship between low CRF and the gut microbiome is not well known. A total of 3,616 individuals from two independent population-based cohorts of the Study of Health in Pomerania (SHIP-START and SHIP-TREND) performed standardized, symptom-limited cardiopulmonary exercise testing (CPET) and had faecal samples collected to determine gut microbiota profiles (16S rRNA gene sequencing). We analysed cross-sectional associations of CRF with the gut microbiome composition controlling for confounding factors. Lower CRF was associated with reduced microbial diversity, loss of beneficial short-chain fatty acid producing bacteria (i.e. Butyricoccus, Coprococcus, unclassified Ruminococcaceae or Lachnospiraceae) and an increase in opportunistic pathogens such as Escherichia/Shigella, or Citrobacter. Decreased cardiorespiratory performance was associated with a gut microbiota pattern that has been previously related to a proinflammatory state. These associations were independent of body weight or glycemic control.}, }
@article {pmid39939193, year = {2025}, author = {Kijpaisalratana, N and Phuah, CL and Ament, Z and Bhave, VM and Garcia-Guarniz, AL and Duskin, J and Couch, CA and Irvin, MR and Kimberly, WT and ,  and , }, title = {White matter hyperintensity severity modifies gut metabolite association with cognitive outcomes.}, journal = {The journal of prevention of Alzheimer's disease}, volume = {}, number = {}, pages = {100086}, doi = {10.1016/j.tjpad.2025.100086}, pmid = {39939193}, issn = {2426-0266}, abstract = {BACKGROUND: Gut microbiome-associated metabolites and white matter hyperintensities (WMH) are independently associated with cognitive impairment. However, it is unclear if gut metabolites and WMH interact to influence dementia.<br><br>OBJECTIVES: To examine the association between gut microbial metabolites and cognitive outcomes and assess whether the severity of baseline WMH would impact associations between gut microbial metabolites and cognitive outcomes.<br><br>DESIGN: Cross-sectional design.<br><br>SETTING: Cohort of individuals who are clinically normal, mild cognitive impairment, or Alzheimer's Disease in the Alzheimer's Disease Neuroimaging Initiative (ADNI).<br><br>PARTICIPANTS: A total of 578 participants with available baseline 3.0T 2D-Fluid Attenuation Inversion Recovery (FLAIR) Magnetic Resonance Imaging (MRI) scans and baseline gut microbial metabolite measurement were included in the analysis.<br><br>MEASUREMENTS: Gut metabolite measurements and automated WMH volume estimations were obtained from FLAIR MRI and were used to assess the association and interaction with cognitive impairment.<br><br>RESULTS: Of 104 metabolites studied, glycodeoxycholic acid (GDCA) surpassed the false discovery rate and was associated the Alzheimer's Disease Assessment Scale-Cognitive Subscale version 13 (ADAS-Cog13) score (&#x3b2; = 0.12, 95 % CI = 0.05-0.20, p = 0.001) and cognitive impairment determined by mini-mental status exam (MMSE) (OR = 2.11, 95 % CI = 1.41-3.15, p < 0.001). GDCA was associated with higher ADAS-Cog13 in participants with low WMH burden (&#x3b2; = 0.21, 95% CI = 0.10-0.32, p < 0.001) but not in participants with high WMH burden (&#x3b2; = 0.04, 95 % CI = -0.07 to 0.14, p = 0.48; interaction p = 0.02).<br><br>CONCLUSION: An elevated level of GDCA was associated with worse cognition. WMH severity modified the association between GDCA and cognitive outcomes.}, }
@article {pmid39939191, year = {2025}, author = {Liss, MA}, title = {Is the Microbiome Enough: Role of Diet and Metabolites in Our Interventions.}, journal = {European urology focus}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.euf.2025.01.017}, pmid = {39939191}, issn = {2405-4569}, abstract = {The gut microbiome may represent a new pillar in human health. As we move beyond the small data sets used for comparison, we will need to consider the bidirectional implications of interactions between diet/lifestyle (inputs) and metabolites (outputs) in interventional clinical trials to maximize the beneficial impact in health and disease.}, }
@article {pmid39938947, year = {2025}, author = {Rogowska-van der Molen, MA and Manzano-Marín, A and Postma, JL and Coolen, S and van Alen, T and Jansen, RS and Welte, CU}, title = {From Eggs to Guts: Symbiotic Association of Sodalis nezarae sp. nov. with the Southern Green Shield Bug Nezara viridula.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf017}, pmid = {39938947}, issn = {1574-6941}, abstract = {Phytophagous insects engage in symbiotic relationships with bacteria that contribute to digestion, nutrient supplementation, and development of the host. The analysis of shield bug microbiomes has been mainly focused on the gut intestinal tract predominantly colonized by Pantoea symbionts, and other microbial community members in the gut or other organs have hardly been investigated. In this study, we reveal that the Southern green shield bug Nezara viridula harbours a Sodalis symbiont in several organs, with a notable prevalence in salivary glands, and anterior regions of the midgut. Removing external egg microbiota via sterilization profoundly impacted insect viability but did not disrupt the vertical transmission of Sodalis and Pantoea symbionts. Based on the dominance of Sodalis in testes, we deduce that N. viridula males could be involved in symbiont vertical transmission. Genomic analyses comparing Sodalis species revealed that Sodalis sp. Nvir shares characteristics with both free-living and obligate insect-associated Sodalis spp. Sodalis sp. Nvir also displays genome instability typical of endosymbiont lineages, which suggests ongoing speciation to an obligate endosymbiont. Together, our study reveals that shield bugs harbour unrecognized symbionts that might be paternally transmitted.}, }
@article {pmid39938754, year = {2025}, author = {Fernandes, M and Palmieri, O and Castellana, S and Spanetta, M and Latiano, T and Lupo, C and Masi, C and Cardile, C and Calvello, C and Izzi, F and Placidi, F and Mazza, T and Mercuri, NB and Latiano, A and Liguori, C}, title = {Gut microbiome composition changes in obstructive sleep apnoea syndrome also in relation to excessive daytime sleepiness.}, journal = {Brain research bulletin}, volume = {}, number = {}, pages = {111251}, doi = {10.1016/j.brainresbull.2025.111251}, pmid = {39938754}, issn = {1873-2747}, abstract = {INTRODUCTION: Obstructive sleep apnoea syndrome (OSAS) is considered a risk factor for several comorbidities. Alteration in gut microbiome was documented in OSAS animal models and in paediatric patients. This study analysed gut microbiome composition in adult patients with OSAS and compared to controls. Further, the effect of excessive daytime sleepiness (EDS) on gut microbiome was evaluated.<br><br>METHODS: Adult patients with OSAS underwent polysomnographic recording and completed the Epworth Sleepiness Scale (ESS) to assess EDS. Faecal samples were collected and compared between patients and healthy controls. Composition, community diversity, differences in taxa abundance profiles and sample dysbiosis were evaluated through 16S metagenomics and multiple bioinformatics algorithms. OSAS patients were distributed in two groups according to EDS (ESS score&#x2265;10) to assess differences in clinical, polysomnographic and faecal data.<br><br>RESULTS: Twenty-three OSAS patients were compared to 44 controls. Patients presented significant differences of gut microbiome biodiversity, specifically in qualitative alpha diversity metrics (Faith's PD Kruskal-Wallis test, p-value=0.003; Number_of_Observed_Features, p value =0.001). OSAS patients tend to cluster together, at least for Jaccard and Unweighted UniFrac distance-based PERMANOVA tests (q-values=0.02 and =0.003, respectively). Several taxa were detected as different in abundance between OSAS patients and controls, although, globally, OSAS patients cannot be considered as "dysbiotic". Differences in bacteria composition were evident between OSAS patients with and those without EDS.<br><br>CONCLUSIONS: OSAS is associated with gut microbiome alteration in adult patients. EDS in OSAS seems to characterize a different gut microbiome composition, although it can be only hypothesized a gut-mediated effect on EDS in OSAS.}, }
@article {pmid39938496, year = {2025}, author = {Holtmann, G and Moniruzzaman, MD and Shah, A}, title = {Decoding the Gut-Brain Axis: A Journey Towards Targeted Interventions for Disorders-of-Gut-Brain Interaction.}, journal = {Digestive diseases (Basel, Switzerland)}, volume = {}, number = {}, pages = {1-14}, doi = {10.1159/000543845}, pmid = {39938496}, issn = {1421-9875}, abstract = {BACKGROUND: The gut-brain axis is a bidirectional communication pathway connecting the gastrointestinal tract and the brain. Disorders of Gut-Brain Interaction (DGBI) manifest as highly prevalent gastrointestinal disorders such as irritable bowel syndrome (IBS) or Functional Dyspepsia (FD).<br><br>SUMMARY: The initial focus of DGBI research was on the effects of psychological stress on digestive functions like gastrointestinal motility, or secretion of gastric acid and pancreatic enzymes. Concepts related to DGBI have expanded in recent decades. Activation of mucosal or systemic immune functions has been observed in DGBI, and it is established that the gastrointestinal microbiome can alter mucosal integrity and permeability, leading to proinflammatory cytokine release that affects brain function. Pharmacologic treatments (e.g., tricyclic antidepressants), and non-pharmacologic interventions (e.g., cognitive behavioral therapy), are now standard for DGBI patients. Advances in culture-independent methods to study gastrointestinal microbes reveal new insights into DGBI and gut microbiota appear to play a crucial role in modulating the gut-brain axis and regulating various bodily functions.}, }
@article {pmid39938307, year = {2025}, author = {Kempe, M and Haverinen-Shaughnessy, U and Tuoresmäki, P and Täubel, M}, title = {Effects of energy retrofits on the indoor microbiota in Northern European apartments.}, journal = {International journal of hygiene and environmental health}, volume = {265}, number = {}, pages = {114538}, doi = {10.1016/j.ijheh.2025.114538}, pmid = {39938307}, issn = {1618-131X}, abstract = {While the urgent need for energy saving is triggering energy retrofit measures in buildings, there are still large gaps in our understanding of how these measures may impact indoor environmental quality, including particle, chemical, and microbial exposure, and ultimately human health. Here, we explore the effects of energy retrofits on the indoor microbiota characteristics of 193 apartments in 40 apartment buildings in two Northern European countries, Finland and Lithuania. Amplicon sequencing was used to characterise fungal and bacterial microbiota compositions in airborne, settled dust samples collected from apartments before and after energy retrofits, mostly targeting upgrades in insulation, heating and/or ventilation systems, and windows. Pairwise pre versus post testing of the most abundant fungal and bacterial taxa and diversity metrics, (generalized) linear mixed modelling ((G)LMM), and Analysis of Composition of Microbiomes (ANCOM) differential abundance testing were used to explore the effects of retrofits on indoor microbiota while accounting for confounding factors. The results indicated significant, country-dependent changes in the relative abundances of individual bacterial and fungal taxa, and a smaller proportion of human-sourced bacteria in Finnish buildings after compared to before retrofits. As in previous studies, factors such as outdoor temperature and type of ventilation were found to influence both bacterial and fungal composition indoors. To the best of our knowledge, this is the first dedicated, multi-country study on impacts of energy retrofits on indoor microbiota. Our novel findings offer a foundation for future research into this topic, including studies on the potential health relevance of energy retrofit associated indoor microbiome changes.}, }
@article {pmid39938296, year = {2025}, author = {Tan, L and Liang, J and Qin, Z and Ning, T and Wei, X and Yang, B and Wang, Q and Xu, Y and Shen, F}, title = {Unveiling the sustained effects of plant root exudates on soil microbiome and resistome and the related functional traits.}, journal = {Journal of environmental management}, volume = {376}, number = {}, pages = {124485}, doi = {10.1016/j.jenvman.2025.124485}, pmid = {39938296}, issn = {1095-8630}, abstract = {Investigating the transmission mechanisms and influencing factors of antibiotic resistance genes (ARGs) in the soil-plant continuum is vital for mitigating ARG contamination and safeguarding plant and human health. Rhizosphere soil serves as a crucial interface for ARG propagation and transmission; however, it is unclear whether and how plant involved in regulating ARGs in their rhizosphere environment. Root exudates acting as vital links in the plant-soil-microbe interaction. Here, we examined the fluctuating patterns of the resistome and mobile genetic elements (MGEs) following exposure to four types of common root exudates: amino acids (AAs), sugars, long-chain organic acids (LCOAs), and short-chain organic acids (SCOAs). AAs exerted a rapid and pronounced effect, leading to a significant elevation in total ARG and MGE abundance by 3.18-fold and 21.06-fold, respectively, compared to the control group by day 7. Conversely, the impact of sugars manifested gradually over time. The influence of AAs and sugars persisted beyond 240 days post-treatment cessation. Importantly, the proliferation of ARGs was closely linked to the enrichment of plant growth-promoting bacteria (PGPBs) such as Pseudomonas, Cupriavidus, Azospirillum, Variovorax, and Ensifer. Functional analysis revealed that the potential features of ARGs and MGEs were associated with cell wall/membrane/envelope biogenesis, cell motility, and inorganic ion transport. This study offers novel insights into the factors influencing the dynamics of ARGs in the plant rhizosphere and may contribute to ecologically sustainable agricultural practices.}, }
@article {pmid39937126, year = {2025}, author = {Ugai, S and Liu, L and Kosumi, K and Kawamura, H and Hamada, T and Mima, K and Arima, K and Okadome, K and Yao, Q and Matsuda, K and Zhong, Y and Mizuno, H and Chan, AT and Garrett, WS and Song, M and Giannakis, M and Giovannucci, EL and Zhang, X and Ogino, S and Ugai, T}, title = {Long-term yogurt intake and colorectal cancer incidence subclassified by Bifidobacterium abundance in tumor.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2452237}, doi = {10.1080/19490976.2025.2452237}, pmid = {39937126}, issn = {1949-0984}, mesh = {*Yogurt/microbiology ; Humans ; *Colorectal Neoplasms/microbiology/epidemiology ; Male ; Incidence ; Female ; *Bifidobacterium/isolation &amp; purification ; Middle Aged ; Prospective Studies ; Aged ; Adult ; Gastrointestinal Microbiome ; }, abstract = {Evidence suggests a tumor-suppressive effect of the intake of yogurt, which typically contains Bifidobacterium. We hypothesized that long-term yogurt intake might be associated with colorectal cancer incidence differentially by tumor subgroups according to the amount of tissue Bifidobacterium. We utilized the prospective cohort incident-tumor biobank method and resources of two prospective cohort studies. Inverse probability weighted multivariable Cox proportional hazards regression was used to assess differential associations of yogurt intake with the incidence of colorectal carcinomas subclassified by the abundance of tumor tissue Bifidobacterium. During follow-up of 132,056 individuals, we documented 3,079 incident colorectal cancer cases, including 1,121 with available tissue Bifidobacterium data. The association between long-term yogurt intake and colorectal cancer incidence differed by Bifidobacterium abundance (P heterogeneity = 0.0002). Multivariable-adjusted hazard ratios (HRs) (with 95% confidence intervals) in individuals who consumed ≥2 servings/week (vs. <1 serving/month) of yogurt were 0.80 (0.50-1.28) for Bifidobacterium-positive tumor and 1.09 (0.81-1.46) for Bifidobacterium-negative tumor. This differential association was also observed in a subgroup analysis of proximal colon cancer (P heterogeneity = 0.018). Long-term yogurt intake may be differentially associated with the incidence of proximal colon cancer according to Bifidobacterium abundance, suggesting the antitumor effect of yogurt intake on the specific tumor subgroup.}, }
@article {pmid39936902, year = {2025}, author = {Lin, X and Xu, M and Lan, R and Hu, D and Zhang, S and Zhang, S and Lu, Y and Sun, H and Yang, J and Liu, L and Xu, J}, title = {Gut commensal Alistipes shahii improves experimental colitis in mice with reduced intestinal epithelial damage and cytokine secretion.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0160724}, doi = {10.1128/msystems.01607-24}, pmid = {39936902}, issn = {2379-5077}, abstract = {The commensal bacterium Alistipes shahii is a core microbe of the human gut microbiome and its abundance is negatively correlated with inflammatory bowel diseases (IBDs). However, its fundamental role in regulating inflammatory response remains unknown. Using a dextran sulfate sodium (DSS)-induced colitis mouse model, we examined the effect of A. shahii strain As360 intervention on host inflammatory response and found that A. shahii As360 alleviated disease activity index, colon shortening, and colonic histopathological lesion. The levels of tight junction proteins (mainly ZO1 and claudin-1) were decreased in DSS-induced colitis mice, whereas the levels of these proteins were elevated in colitis mice with A. shahii As360 treatment. In addition, A. shahii As360 treatment led to alterations in cytokine release, especially an increase of IL10. It also led to reduced expressions of mtor and Nlrp3 and increased expression of mTOR inhibitor Ddit4 at the transcriptional level. 16S rRNA amplicon sequencing found that Bacteroides, a producer of short-chain fatty acids (SCFAs), was enriched in the fecal samples of mice with A. shahii treatment. Metabolic analyses found that, following A. shahii As360 treatment, the SCFAs in the fecal content was increased whereas lactic acid was decreased in the cecal content. These findings suggest that supplementation with A. shahii As360 is a promising strategy to prevent colitis.IMPORTANCEAs one of the core microbes and keystone species in the human gut, Alistipes shahii has the potential to inhibit inflammation and improve inflammatory bowel diseases (IBDs) conditions. In this study, we experimentally demonstrated that oral administration of A. shahii As360 alleviated symptoms of colitis, altered the release of cellular inflammatory factors, reduced the intestinal epithelial barrier damage, and changed gut microbiota and fecal metabolites. These findings provide a deeper understanding of the beneficial effects of A. shahii and its perspective for better strategies to prevent IBD.}, }
@article {pmid39936895, year = {2025}, author = {Paez-Diaz, JA and Nieves-Morales, R and Melendez-Martinez, G and Rivera-Lopez, EO and Rodríguez-Ramos, J and Rios-Velazquez, C}, title = {Characterization of intestinal fungal communities through ITS amplicon from metagenomic libraries of sea cucumber (Holothuria glaberrima).}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0132024}, doi = {10.1128/mra.01320-24}, pmid = {39936895}, issn = {2576-098X}, abstract = {The brown rock sea cucumber (Holothuria glaberrima) microbiome is vital for understanding its ecological dynamics. This study focuses on the microbial composition and abundance of fungi across different intestinal regions of H. glaberrima, giving insights into host-microbe interactions and supporting future ecological and comparative studies on their regeneration capabilities.}, }
@article {pmid39936816, year = {2025}, author = {Schweitzer, M and Wassermann, B and Abdelfattah, A and Cernava, T and Berg, G}, title = {Microbiome Literacy: Enhancing Public and Academic Understanding Through the 'Microbiome &amp; Health' Online Course.}, journal = {Microbial biotechnology}, volume = {18}, number = {2}, pages = {e70094}, doi = {10.1111/1751-7915.70094}, pmid = {39936816}, issn = {1751-7915}, support = {//Bundesministerium f&#xfc;r Bildung, Wissenschaft und Forschung/ ; //University of Vienna, Graz University of Technology/ ; }, mesh = {*Microbiota ; Humans ; }, abstract = {Microorganisms are fundamental to life on Earth, influencing biogeochemical processes, soil fertility, and the health of humans, animals and plants. Human activities have left a remarkable footprint on the environment, including global microbiomes. Enhancing awareness and improving education about microbiome functions can contribute to a sustainable economy and resilient systems. However, public understanding of microbiome science is hindered by misinformation and limited accessible educational resources. To address this, we developed the massive open online course (MOOC) 'Microbiome &amp; Health', available on iMooX.at and YouTube. The course, structured into six units, covers microbiome concepts, methodologies, human and plant microbiomes, antibiotic resistance, and environmental impacts, aligning with the One Health concept and the Sustainable Development Goals of the United Nations. Initial results show that the MOOC provides the means to increase microbiology literacy, with 73.2% external participation and above-average completion rates. Integration as a mandatory component in university courses has improved student performance, halting declining grades and pass rates. This highlights the MOOC's potential to enhance public and academic understanding of microbiome science, fostering informed decisions for sustainable health and environmental stewardship as well as paving the way for new microbiome-based solutions in biotechnology.}, }
@article {pmid39936794, year = {2025}, author = {Tleuova, KZ and Shingisov, AU and Khamitova, BM and Kanseitova, ET and Tulekbaeva, AK}, title = {Isolation and molecular characterization of Lactobacillus delbrueckii subsp based on bulgaricus strain 1 from kefir shows probiotic and antimicrobial properties: Linking probiotics to UNSDG (United Nations Sustainable Development Goals) agenda: 2030.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {84}, number = {}, pages = {e286969}, doi = {10.1590/1519-6984.286969}, pmid = {39936794}, issn = {1678-4375}, mesh = {*Probiotics ; *Lactobacillus delbrueckii/physiology/metabolism ; *Kefir/microbiology ; Sustainable Development ; Microbial Sensitivity Tests ; United Nations ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The global population increase necessitates the dire need for ample food as medicine. Good health and well-being are stressed on probiotic functional foods. The present study characterizes biochemical and molecular identification of potential lactic acid bacteria. The potent antimicrobial properties also affirm Lactobacillus delbrueckii subsp. bulgaricus strain 3286. Biochemical analysis comprises carbohydrate fermentation, tolerance to acids and bile salts, production of bioactive compounds, lecithinase production, gelatinase production, and strain ripening ability. Antibiotic sensitivity to various antibiotics was assessed employing minimum inhibitory concentration (MIC) and E-test. Strain resistance to increased salt concentrations coherently concludes the positive impact of gut microbiome and gut-brain axis health management. The preliminary assessment requires further in vitro, in vivo, and in silico analysis for commercialization, market strategy and utility as functional food supplementation. The study can be rationalized for sustainable development goals regarding SDG 3: good health and well-being. Further, the UNSDG agenda 2030 also ascertains the role of probiotic foods in life longevity and public health management systems.}, }
@article {pmid39936619, year = {2025}, author = {Smith, W and Azevedo, EP}, title = {Hunger Games: A Modern Battle Between Stress and Appetite.}, journal = {Journal of neurochemistry}, volume = {169}, number = {2}, pages = {e70006}, doi = {10.1111/jnc.70006}, pmid = {39936619}, issn = {1471-4159}, support = {//Foundation for Prader-Willi Research/ ; //Whitehall Foundation/ ; P20-GM148302//NIH COBRE in Neurodevelopment and its Disorders/ ; }, mesh = {Humans ; Animals ; *Hunger/physiology ; *Stress, Psychological/physiopathology/metabolism ; Appetite/physiology ; Feeding and Eating Disorders/physiopathology/metabolism ; Gastrointestinal Microbiome/physiology ; Hypothalamo-Hypophyseal System/metabolism ; Pituitary-Adrenal System/metabolism ; }, abstract = {Stress, an evolutionarily adaptive mechanism, has become a pervasive challenge in modern life, significantly impacting feeding-relevant circuits that play a role in the development and pathogenesis of eating disorders (EDs). Stress activates the hypothalamic-pituitary-adrenal (HPA) axis, disrupts specific neural circuits, and dysregulates key brain regions, including the hypothalamus, hippocampus, and lateral septum. These particular structures are interconnected and key in integrating stress and feeding signals, modulating hunger, satiety, cognition, and emotional coping behaviors. Here we discuss the interplay between genetic predispositions and environmental factors that may exacerbate ED vulnerability. We also highlight the most commonly used animal models to study the mechanisms driving EDs and recent rodent studies that emphasize the discovery of novel cellular and molecular mechanisms integrating stress and feeding signals within the hippocampus-lateral septum-hypothalamus axis. In this review, we discuss the role of gut microbiome, an emerging area of research in the field of EDs and unanswered questions that persist and hinder the scientific progress, such as why some individuals remain resilient to stress while others become at high risk for the development of EDs. We finally discuss the need for future research delineating the impact of specific stressors on neural circuits, clarifying the relevance and functionality of hippocampal-septal-hypothalamic connectivity, and investigating the role of key neuropeptides such as CRH, oxytocin, and GLP-1 in human ED pathogenesis. Emerging tools like single-cell sequencing and advanced human imaging could uncover cellular and circuit-level changes in brain areas relevant for feeding in ED patients. Ultimately, by integrating basic and clinical research, science offers promising avenues for developing personalized, mechanism-based treatments targeting maladaptive eating behavior for patients suffering from EDs.}, }
@article {pmid39936592, year = {2025}, author = {Negishi, H and Ichikawa, A and Takahashi, S and Kano, H and Makino, S}, title = {Targeted prebiotic application of gluconic acid-containing oligosaccharides promotes Faecalibacterium growth through microbial cross-feeding networks.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf027}, pmid = {39936592}, issn = {1751-7370}, abstract = {The gut microbiome plays a crucial role in human health, and certain bacterial species, such as Faecalibacterium prausnitzii, are particularly beneficial. This study conducted a comprehensive investigation of prebiotic compounds that showed potential for specifically promoting beneficial gut bacteria. Using in vitro fecal cultures and a human intervention study, we identified maltobionic acid and lactobionic acid as compounds that specifically promoted Faecalibacterium growth both in vitro and in vivo without significantly affecting Bifidobacterium, which is typically increased by traditional prebiotics. In a human intervention study (n = 27), a significant increase was observed in Faecalibacterium abundance following maltobionic acid supplementation, with effectiveness correlating with the initial Parabacteroides abundance. Mechanistic investigations revealed a cross-feeding pathway between gut bacteria. In this pathway, Parabacteroides species converted the gluconic acid moiety of maltobionic and lactobionic acids to glucuronic acid, which was then preferentially utilized by Faecalibacterium. These findings suggest that gluconic acid-containing oligosaccharides are promising prebiotics for the targeted enhancement of beneficial Faecalibacterium and underscore the importance of microbial interactions in prebiotic research, offering new avenues for personalized microbiome modulation strategies.}, }
@article {pmid39936174, year = {2025}, author = {Leyrer, V and Blum, J and Marhan, S and Kandeler, E and Zimmermann, T and Berauer, BJ and Schweiger, AH and Canarini, A and Richter, A and Poll, C}, title = {Drought Impacts on Plant-Soil Carbon Allocation-Integrating Future Mean Climatic Conditions.}, journal = {Global change biology}, volume = {31}, number = {2}, pages = {e70070}, doi = {10.1111/gcb.70070}, pmid = {39936174}, issn = {1365-2486}, support = {//Anton and Petra Ehrmann-Stiftung/ ; }, mesh = {*Droughts ; *Soil Microbiology ; *Climate Change ; *Soil/chemistry ; *Carbon/metabolism/analysis ; Triticum/physiology/metabolism ; Biomass ; }, abstract = {Droughts affect soil microbial abundance and functions-key parameters of plant-soil carbon (C) allocation dynamics. However, the impact of drought may be modified by the mean climatic conditions to which the soil microbiome has previously been exposed. In a future warmer and drier world, effects of drought may therefore differ from those observed in studies that simulate drought under current climatic conditions. To investigate this, we used the field experiment 'Hohenheim Climate Change,' an arable field where predicted drier and warmer mean climatic conditions had been simulated for 12 years. In April 2021, we exposed this agroecosystem to 8 weeks of drought with subsequent rewetting. Before drought, at peak drought, and after rewetting, we pulse-labelled winter wheat in situ with [13]CO2 to trace recently assimilated C from plants to soil microorganisms and back to the atmosphere. Severe drought decreased soil respiration (-35%) and abundance of gram-positive bacteria (-15%) but had no effect on gram-negative bacteria, fungi, and total microbial biomass C. This pattern was not affected by the mean precipitation regime to which the microbes had been pre-exposed. Reduced mean precipitation had, however, a legacy effect by decreasing the proportion of recently assimilated C allocated to the microbial biomass C pool (-50%). Apart from that, continuous soil warming was an important driver of C fluxes throughout our experiment, increasing plant biomass, root sugar concentration, labile C, and respiration. Warming also shifted microorganisms toward utilizing soil organic matter as a C source instead of recently assimilated compounds. Our study found that moderate shifts in mean precipitation patterns can impose a legacy on how plant-derived C is allocated in the microbial biomass of a temperate agroecosystem during drought. The overarching effect of soil warming, however, suggests that how temperate agroecosystems respond to drought will mainly be affected by future temperature increases.}, }
@article {pmid39936170, year = {2025}, author = {Michl, K and Kanasugi, M and Förster, A and Wuggenig, R and Issifu, S and Hrynkiewicz, K and Emmerling, C and David, C and Dumont, B and Mårtensson, LD and Rasche, F and Berg, G and Cernava, T}, title = {The microbiome of a perennial cereal differs from annual winter wheat only in the root endosphere.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycae165}, pmid = {39936170}, issn = {2730-6151}, abstract = {The intensification of agriculture has led to environmental degradation, including the loss of biodiversity. This has prompted interest in perennial grain cropping systems to address and mitigate some of these negative impacts. In order to determine if perennial grain cultivation promotes a higher microbial diversity, we assessed the endophytic microbiota of a perennial grain crop (intermediate wheatgrass, Thinopyrum intermedium L.) in comparison to its annual counterpart, wheat (Triticum aestivum L.). The study covered three sampling sites in a pan-European gradient (Sweden, Belgium, and France), two plant genotypes, three plant compartments (roots, stems, and leaves), and two sampling time points. We observed that the host genotype effect was mainly evident in the belowground compartment, and only to a lesser extent in the aboveground tissues, with a similar pattern at all three sampling sites. Moreover, intermediate wheatgrass roots harbored a different bacterial community composition and higher diversity and richness compared to their annual counterparts. The root bacterial diversity was influenced by not only several soil chemical parameters, such as the carbon:nitrogen ratio, but also soil microbial parameters, such as soil respiration and dehydrogenase activity. Consistent findings across time and space suggest stable mechanisms in microbiota assembly associated with perennial grain cropping, underscoring their potential role in supporting biodiversity within sustainable agricultural systems.}, }
@article {pmid39936163, year = {2025}, author = {Wang, X and Zhang, B and Jiang, R}, title = {Microbiome interplays in the gut-liver axis: implications for liver cancer pathogenesis and therapeutic insights.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1467197}, pmid = {39936163}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Liver Neoplasms/microbiology/therapy/etiology/metabolism ; *Liver/metabolism/pathology ; Animals ; Dysbiosis ; Fatty Liver/microbiology ; }, abstract = {Globally, primary liver cancer (PLC) ranks the most fatal malignancy. Most of the patients are in advanced stage of PLC at the very time they are diagnosed with it, accounting much for its poor prognosis. With the advancement of modern medical research and care system, the main etiology of PLC more and more switches from hepatitis viruses such as HAV, HBV, HCV, HEV to other causes like metabolism-associated steatohepatitis (MASH) and metabolic-associated fatty liver disease (MAFLD). As a result, it is of great necessity to find out new ways for treatment and early diagnosis to cope with this problem. Nowadays, as the mechanism of the Gut-Liver Axis in the formation of MAFLD, MASH and PLC has been gradually elucidated. The association between gut microbiome and the formation of PLC is of great significance to take an insight into. In this review, we present the concept of Gut-Liver Axis and its function in the mutual influence between gut microbiota and PLC from several aspects in which we will focus on the structure of gut barrier and the functional influences the gut microbiota have on the immune response and metabolic changes on human liver. Furthermore, we conclude the potential association of gut microbiota constitution with the PLC. Eventually, we hope this review can offer novel instructions for early diagnosis and treatment for liver cancer.}, }
@article {pmid39936028, year = {2024}, author = {Clark-Boucher, D and Coull, BA and Reeder, HT and Wang, F and Sun, Q and Starr, JR and Lee, KH}, title = {Group-wise normalization in differential abundance analysis of microbiome samples.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {39936028}, issn = {2331-8422}, abstract = {A key challenge in differential abundance analysis of microbial samples is that the counts for each sample are compositional, resulting in biased comparisons of the absolute abundance across study groups. Normalization-based differential abundance analysis methods rely on external normalization factors that account for the compositionality by standardizing the counts onto a common numerical scale. However, existing normalization methods have struggled at maintaining the false discovery rate in settings where the variance or compositional bias is large. This article proposes a novel framework for normalization that can reduce bias in differential abundance analysis by re-conceptualizing normalization as a group-level task. We present two normalization methods within the group-wise framework: group-wise relative log expression (G-RLE) and fold-truncated sum scaling (FTSS). G-RLE and FTSS achieve higher statistical power for identifying differentially abundant taxa than existing methods in model-based and synthetic data simulation settings, while maintaining the false discovery rate in challenging scenarios where existing methods suffer. The best results are obtained from using FTSS normalization with the differential abundance analysis method MetagenomeSeq. Code for implementing the methods and replicating the analysis can be found at our GitHub page (https://github.com/dclarkboucher/microbiome_groupwise_normalization).}, }
@article {pmid39935961, year = {2025}, author = {Leardini, D and Gambuti, G and Muratore, E and Baccelli, F and Gottardi, F and Venturelli, F and Belotti, T and Prete, A and Fabbrini, M and Brigidi, P and Turroni, S and Masetti, R}, title = {Levofloxacin Prophylaxis in Pediatric and Young Adult Allogeneic Hematopoietic Stem Cell Transplantation Recipients Does not Prevent Infective Complications and Infections-related Deaths.}, journal = {Open forum infectious diseases}, volume = {12}, number = {2}, pages = {ofae707}, pmid = {39935961}, issn = {2328-8957}, abstract = {BACKGROUND: The prophylactic use of quinolones in the setting of allogeneic hematopoietic stem cell transplantation (allo-HCT) is controversial and solid evidence is missing, particularly in children.<br><br>METHODS: In this single-center retrospective study, we compared outcomes in patients receiving (n = 74) or not receiving (n = 70) levofloxacin (LVX) prophylaxis, assessing overall survival, event-free survival, acute graft-versus-host disease (aGvHD) and bloodstream infection incidence, and infection-related mortality. Gut microbiota composition was analyzed in a subgroup using 16S rRNA sequencing of stool samples collected pre-HCT and at engraftment.<br><br>RESULTS: We analyzed 144 allo-HCT in 143 patients performed for any indication. No differences were found in the 2 groups regarding main HCT outcomes, namely, cumulative incidence of aGvHD (37.9% vs 43.5%; P = .733), grade III-IV aGvHD (12.2% vs 8.7%; P = .469), gut aGVHD (12.2% vs 17.5%; P = .451), bloodstream infections (25.6% vs 34.1%; P = .236) and death from bacterial infection (9.5% vs 4.3%; P = 0.179). In patients experiencing bacterial infections, those receiving prophylaxis showed higher incidence of quinolone-resistant strains (P = .001). On a subgroup of 50 patients, we analyzed the gut microbiota composition, showing a lower abundance of Blautia (P = .015), Enterococcus (P = .011), and Actinomyces (P = .07) at neutrophil engraftment in patients receiving LVX prophylaxis.<br><br>CONCLUSIONS: LVX prophylaxis in the setting of allo-HCT does not prevent infective complications and increases the prevalence of antibiotic-resistant strains.}, }
@article {pmid39935646, year = {2025}, author = {Yang, W and Si, SC and Wang, WH and Li, J and Ma, YX and Zhao, H and Liu, J}, title = {Gut dysbiosis in primary sarcopenia: potential mechanisms and implications for novel microbiome-based therapeutic strategies.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1526764}, pmid = {39935646}, issn = {1664-302X}, abstract = {Primary sarcopenia is characterized by a progressive loss of skeletal muscle mass, strength, and physical function that occurs with aging. Despite the related adverse or even serious health outcomes, no medications are currently available for treating primary sarcopenia. Here, we discuss recent advancements in understanding the mechanistic role of gut microbiota-muscle cross-talk in primary sarcopenia, and the therapeutic implications. The mechanistic insights encompass a causal role of gut dysbiosis in primary sarcopenia, potentially mediated through gut microbiota-derived bioactive metabolites, such as short-chain fatty acids (SCFAs), secondary bile acids, and their associated signaling pathways, which may be translated into the development of new microbiome-based treatment and diagnostic approaches. Furthermore, we identify challenges that need addressing in future studies to facilitate the translation into potential novel treatment and differential diagnosis for older individuals with sarcopenia.}, }
@article {pmid39934908, year = {2025}, author = {Wang, L and Simopoulos, CMA and Serrana, JM and Ning, Z and Li, Y and Sun, B and Yuan, J and Figeys, D and Li, L}, title = {PhyloFunc: phylogeny-informed functional distance as a new ecological metric for metaproteomic data analysis.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {50}, pmid = {39934908}, issn = {2049-2618}, support = {201906015034//China Scholarship Council/ ; TECHNOMISE Program//Natural Sciences and Engineering Research Council of Canada/ ; TECHNOMISE Program//Natural Sciences and Engineering Research Council of Canada/ ; 32370050//National Natural Science Foundation of China/ ; }, mesh = {*Phylogeny ; *Gastrointestinal Microbiome/genetics ; Animals ; *Proteomics/methods ; Mice ; Humans ; *Bacteria/classification/genetics ; Data Analysis ; Microbiota/genetics ; }, abstract = {BACKGROUND: Beta-diversity is a fundamental ecological metric for exploring dissimilarities between microbial communities. On the functional dimension, metaproteomics data can be used to quantify beta-diversity to understand how microbial community functional profiles vary under different environmental conditions. Conventional approaches to metaproteomic functional beta-diversity often treat protein functions as independent features, ignoring the evolutionary relationships among microbial taxa from which different proteins originate. A more informative functional distance metric that incorporates evolutionary relatedness is needed to better understand microbiome functional dissimilarities.<br><br>RESULTS: Here, we introduce PhyloFunc, a novel functional beta-diversity metric that incorporates microbiome phylogeny to inform on metaproteomic functional distance. Leveraging the phylogenetic framework of weighted UniFrac distance, PhyloFunc innovatively utilizes branch lengths to weigh between-sample functional distances for each taxon, rather than differences in taxonomic abundance as in weighted UniFrac. Proof of concept using a simulated toy dataset and a real dataset from mouse inoculated with a synthetic gut microbiome and fed different diets show that PhyloFunc successfully captured functional compensatory effects between phylogenetically related taxa. We further tested a third dataset of complex human gut microbiomes treated with five different drugs to compare PhyloFunc's performance with other traditional distance methods. PCoA and machine learning-based classification algorithms revealed higher sensitivity of PhyloFunc in microbiome responses to paracetamol. We provide PhyloFunc as an open-source Python package (available at https://pypi.org/project/phylofunc/), enabling efficient calculation of functional beta-diversity distances between a pair of samples or the generation of a distance matrix for all samples within a dataset.<br><br>CONCLUSIONS: Unlike traditional approaches that consider metaproteomics features as independent and unrelated, PhyloFunc acknowledges the role of phylogenetic context in shaping the functional landscape in metaproteomes. In particular, we report that PhyloFunc accounts for the functional compensatory effect of taxonomically related species. Its effectiveness, ecological relevance, and enhanced sensitivity in distinguishing group variations are demonstrated through the specific applications presented in this study. Video Abstract.}, }
@article {pmid39934899, year = {2025}, author = {Chandrasekaran, P and Krausz, M and Han, Y and Mitsuiki, N and Gabrysch, A and Nöltner, C and Proietti, M and Heller, T and Grou, C and Calderon, V and Subramanian, P and Jones, DR and Siu, Y and Deming, C and Conlan, S and Holland, SM and Segre, JA and Uzel, G and Grimbacher, B and Falcone, EL}, title = {The intestinal microbiome and metabolome discern disease severity in cytotoxic T-lymphocyte-associated protein 4 deficiency.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {51}, pmid = {39934899}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolome ; Female ; Male ; Adult ; *Severity of Illness Index ; *Biomarkers/metabolism ; *Dysbiosis/microbiology ; Young Adult ; Adolescent ; Child ; Streptococcus/immunology ; CTLA-4 Antigen/metabolism/genetics ; Middle Aged ; Feces/microbiology ; Child, Preschool ; Case-Control Studies ; }, abstract = {BACKGROUND: Cytotoxic T-lymphocyte-associated protein 4 deficiency (CTLA4-D) is an inborn error of immunity (IEI) caused by heterozygous mutations, and characterized by immune cell infiltration into the gut and other organs, leading to intestinal disease, immune dysregulation and autoimmunity. While regulatory T-cell dysfunction remains central to CTLA4-D immunopathogenesis, mechanisms driving disease severity and intestinal pathology are unknown but likely involve intestinal dysbiosis. We determined whether the intestinal microbiome and metabolome could distinguish individuals with severe CTLA4-D and identify biomarkers of disease severity.<br><br>RESULTS: The genera Veillonella and Streptococcus emerged as biomarkers that distinguished CTLA4-D from healthy cohorts from both the National Institutes of Health (NIH) Clinical Center, USA (NIH; CTLA-D, n&#x2009;=&#x2009;32; healthy controls, n&#x2009;=&#x2009;16), and a geographically distinct cohort from the Center for Chronic Immunodeficiency (CCI) of the&#xa0;Medical Center&#xa0;-&#xa0;University of&#xa0;Freiburg, Germany (CCI; CTLA4-D, n&#x2009;=&#x2009;25; healthy controls, n&#x2009;=&#x2009;24). Since IEIs in general may be associated with perturbations of the microbiota, a disease control cohort of individuals with common variable immunodeficiency (CVID, n&#x2009;=&#x2009;20) was included to evaluate for a CTLA4-D-specific microbial signature. Despite common IEI-associated microbiome changes, the two bacterial genera retained their specificity as biomarkers for CTLA4-D. We further identified intestinal microbiome and metabolomic signatures that distinguished patients with CTLA4-D having severe vs. mild disease. Microbiome changes were associated with distinct stool metabolomic profiles and predicted changes in metabolic pathways. These differences were impacted by the presence of gastrointestinal manifestations and were partially reversed by treatment with abatacept and/or sirolimus.<br><br>CONCLUSIONS: Loss of intestinal&#xa0;microbial diversity and dysbiosis causing metabolomic changes was observed in CTLA4-D. Albeit some of these features were shared with CVID, the distinct changes associated with CTLA4-D highlight the fact that IEI-associated microbiome changes likely reflect the underlying immune dysregulation. Identified candidate intestinal microbial and metabolic biomarkers distinguishing individuals with CTLA4-D based on severity should be studied prospectively to determine their predictive value, and investigated as potential therapeutic ta. Video Abstract.}, }
@article {pmid39934569, year = {2025}, author = {Sun, M and Liu, H and Ju, H and Chen, H and Yang, R and Yan, D and Shen, L and Cai, A and Zhi, Y and Xiao, L and Tang, Q and Wang, Y}, title = {Metformin suppresses gammadelta T17 cell differentiation alleviating DSS-induced colitis.}, journal = {Immunologic research}, volume = {73}, number = {1}, pages = {49}, pmid = {39934569}, issn = {1559-0755}, support = {2023JZ020//Clinical Medicine Special Research Foundation of Nantong University/ ; 2023JZ020//Clinical Medicine Special Research Foundation of Nantong University/ ; 2023JZ020//Clinical Medicine Special Research Foundation of Nantong University/ ; 2023JZ020//Clinical Medicine Special Research Foundation of Nantong University/ ; 2023JZ020//Clinical Medicine Special Research Foundation of Nantong University/ ; 2023JZ020//Clinical Medicine Special Research Foundation of Nantong University/ ; 2023JZ020//Clinical Medicine Special Research Foundation of Nantong University/ ; 202490101//Collaborative Innovation Research Project of Jiangsu Vocational College of Medicine/ ; 202490101//Collaborative Innovation Research Project of Jiangsu Vocational College of Medicine/ ; 202490101//Collaborative Innovation Research Project of Jiangsu Vocational College of Medicine/ ; 202490101//Collaborative Innovation Research Project of Jiangsu Vocational College of Medicine/ ; 202490101//Collaborative Innovation Research Project of Jiangsu Vocational College of Medicine/ ; 202490101//Collaborative Innovation Research Project of Jiangsu Vocational College of Medicine/ ; YCBK2024019//The Natural Science Foundation of Yancheng City/ ; YCBK2024019//The Natural Science Foundation of Yancheng City/ ; YCBK2024019//The Natural Science Foundation of Yancheng City/ ; SBK20241852//The Natural Science Foundation of Jiangsu Province/ ; SBK20241852//The Natural Science Foundation of Jiangsu Province/ ; SBK20241852//The Natural Science Foundation of Jiangsu Province/ ; SBK20241852//The Natural Science Foundation of Jiangsu Province/ ; 81902906//Natural Science Foundation of China/ ; }, mesh = {*Metformin/pharmacology ; Animals ; *Cell Differentiation/drug effects ; Mice ; *Dextran Sulfate ; *Colitis/chemically induced/drug therapy/immunology ; Disease Models, Animal ; Receptors, Antigen, T-Cell, gamma-delta/metabolism ; Mice, Inbred C57BL ; Th17 Cells/immunology/drug effects ; Colitis, Ulcerative/drug therapy/immunology/chemically induced ; TOR Serine-Threonine Kinases/metabolism ; Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism ; Male ; Humans ; }, abstract = {Ulcerative colitis (UC) is a chronic, nonspecific, relapsing inflammatory bowel disease. Metformin has pleiotropic effects including anti-inflammatory properties and a notable impact on the gut microbiome. γδT17 cells play crucial role in initiating and maintaining intestinal inflammation. The effect of metformin on γδT17 cells remains unclear. This study aims to explore the connection between metformin-mediated ameliorated response in colitis mice and γδT17 cell activity. The role of γδT17 cell inhibition in metformin-mediated colitis amelioration was evaluated in mice. The effect of metformin on γδT17 differentiation and the possible mechanism were evaluated in a set of in vitro experiments. Results showed that the accumulation of γδT17 cells was negatively correlated with metformin treatment in DSS-induced colitis mice. Exogenous γδT17 cells blocked metformin-mediated colitis inhibition. Furthermore, metformin inhibited γδT17 differentiation, which was related to the inhibition of mTOR/RORγt activity. Our results reveal that metformin ameliorates colitis symptoms by suppressing γδT17 differentiation, suggesting a viable strategy against UC, although the mechanism of metformin in inhibiting γδT17 differentiation remains to be further studied.}, }
@article {pmid39934561, year = {2025}, author = {Mohsen, E and Haffez, H and Ahmed, S and Hamed, S and El-Mahdy, TS}, title = {Multiple Sclerosis: A Story of the Interaction Between Gut Microbiome and Components of the Immune System.}, journal = {Molecular neurobiology}, volume = {}, number = {}, pages = {}, pmid = {39934561}, issn = {1559-1182}, abstract = {Multiple sclerosis (MS) is defined as an inflammatory disorder that chronically affects the central nervous system of young people mostly and is distributed globally. It is associated with degeneration and demyelination of the myelin sheath around the nerves, resulting in multiple neurological disability symptoms ranging from mild to severe cases that end with paralysis sometimes. MS is one of the rising diseases globally that is unfortunately associated with reduced quality of life and adding national economic burdens. The definite MS mechanism is not clearly defined; however, all the previous researches confirm the role of the immune system as the master contributor in the pathogenesis. Innate and adaptive immune cells are activated peripherally then attracted toward the central nervous system (CNS) due to the breakdown of the blood-brain barrier. Recently, the gut-brain axis was shown to depend on gut metabolites that are produced by different microorganisms in the colon. The difference in microbiota composition between individuals is responsible for diversity in secreted metabolites that affect immune responses locally in the gut or systemically when reach blood circulation to the brain. It may enhance or suppress immune responses in the central nervous system (CNS) (repeated short forms); consequently, it may exacerbate or ameliorate MS symptoms. Recent data showed that some metabolites can be used as adjuvant therapy in MS and other inflammatory diseases. This review sheds light on the nature of MS and the possible interaction between gut microbiota and immune system regulation through the gut-brain axis, hence contributing to MS pathogenesis.}, }
@article {pmid39934474, year = {2025}, author = {Yoshimura, Y and Wakabayashi, H and Nagano, F and Matsumoto, A and Shimazu, S and Shiraishi, A and Kido, Y and Bise, T and Hamada, T and Yoneda, K and Maeda, K}, title = {Systemic inflammation is associated with gut microbiota diversity in post-stroke patients.}, journal = {European geriatric medicine}, volume = {}, number = {}, pages = {}, pmid = {39934474}, issn = {1878-7649}, support = {23K21639//Japan Society for the Promotion of Science/ ; 22-4//Research Funding of Longevity Sciences/ ; }, abstract = {BACKGROUND: There is growing interest in gut microbiota and health outcomes. However, the relationship between systemic inflammation and gut microbiota diversity in hospitalized patients remains unclear. This study aimed to investigate the association in post-stroke rehabilitation patients.<br><br>METHODS: A cross-sectional study was conducted on post-stroke patients admitted to a rehabilitation hospital. Systemic inflammation was assessed using the modified Glasgow Prognostic Score (mGPS). Gut microbiota diversity was evaluated using three indices: Shannon index, Operational Taxonomic Unit (OTU) richness, and Faith's Phylogenetic Diversity (PD). Multiple linear regression analyses were performed to examine the relationship between mGPS and gut microbiota diversity indices, adjusting for potential confounders.<br><br>RESULTS: A total of 156 patients (mean age 78.4&#xa0;years; 55.7% men) were analyzed. The median mGPS was 0 (interquartile range: 0-1), with GPS distribution: 61.8% scored 0, 25.7% scored 1, and 12.5% scored 2. After adjusting for confounders, mGPS was significantly and negatively associated with the Shannon index (B&#x2009;=&#x2009;-0.143, 95% CI -0.288 to -0.002, &#x3b2;&#x2009;=&#x2009;-0.177) and OTU richness (B&#x2009;=&#x2009;-17.832, 95% CI -24.349 to -3.951, &#x3b2;&#x2009;=&#x2009;-0.208). However, no significant association was observed between mGPS and Faith's PD (B&#x2009;=&#x2009;-1.155, 95% CI -2.464 to 0.189, &#x3b2;&#x2009;=&#x2009;-0.155).<br><br>CONCLUSION: This study demonstrates a significant negative association between systemic inflammation and both quantitative and qualitative gut microbiota diversity in post-stroke patients.}, }
@article {pmid39934405, year = {2025}, author = {Richardson, M and Zhao, S and Lin, L and Sheth, RU and Qu, Y and Lee, J and Moody, T and Ricaurte, D and Huang, Y and Velez-Cortes, F and Urtecho, G and Wang, HH}, title = {Publisher Correction: SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41564-025-01951-7}, pmid = {39934405}, issn = {2058-5276}, }
@article {pmid39934389, year = {2025}, author = {Ailer, E and Müller, CL and Kilbertus, N}, title = {Instrumental variable estimation for compositional treatments.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {5158}, pmid = {39934389}, issn = {2045-2322}, mesh = {*Microbiota ; Humans ; }, abstract = {Many scientific datasets are compositional in nature. Important biological examples include species abundances in ecology, cell-type compositions derived from single-cell sequencing data, and amplicon abundance data in microbiome research. Here, we provide a causal view on compositional data in an instrumental variable setting where the composition acts as the cause. First, we crisply articulate potential pitfalls for practitioners regarding the interpretation of compositional causes from the viewpoint of interventions and warn against attributing causal meaning to common summary statistics such as diversity indices in microbiome data analysis. We then advocate for and develop multivariate methods using statistical data transformations and regression techniques that take the special structure of the compositional sample space into account while still yielding scientifically interpretable results. In a comparative analysis on synthetic and real microbiome data we show the advantages and limitations of our proposal. We posit that our analysis provides a useful framework and guidance for valid and informative cause-effect estimation in the context of compositional data.}, }
@article {pmid39933914, year = {2025}, author = {Marette, A and Pilon, G}, title = {Host-microbiome determinants of insulin resistance in obesity: alone we go faster, together we go further!.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2024-333855}, pmid = {39933914}, issn = {1468-3288}, }
@article {pmid39933500, year = {2025}, author = {Liu, M and Wang, H and Huang, J and Huai, Y and Yu, C and Fang, G and Zhang, M and Bo, R and Fan, K and Li, J}, title = {Dynamic Observation of Colonic Lesions, Commensal Microbiome and Mycobiome Variations in Trinitrobenzene Sulfonic Acid -Induced Experimental Crohn's Disease in Rats.}, journal = {Digestion}, volume = {}, number = {}, pages = {1-17}, doi = {10.1159/000543337}, pmid = {39933500}, issn = {1421-9867}, abstract = {Crohn's disease (CD) is an inflammatory bowel disease characterized by chronic inflammation of the entire digestive lining. Although the pathogenesis of CD remains unclear, multiple factors especially altered microbiota are among its causes. In this study, an experimental CD model was established by TNBS-enema. Then the dynamic changes of colonic tissue lesions, tight junctions, inflammation response, and oxidative stress are respectively tested by H&amp;E staining, immunofluorescence staining, and commercial kits. 16S rRNA and ITS sequencing of colonic feces were applied to analyze the composition and diversity of the microbiome and mycobiome for lasting 5 weeks. As a result, despite TNBS being applied only once time, the stimuli-caused injury reached a peak in the second week (the most severe period), after which symptoms began to gradually return to the normal stage. Additionally, consistent with the TNBS-caused colonic damage, deaths were also concentrated within two weeks after modeling, with only one death occurring in the subsequent period despite ongoing inflammation and other typical symptoms. In terms of gut bacteria, microbiome diversity decreased significantly while mycobiome diversity increased, along with the enrichment of harmful microbiota and shrinkage of probiotic microorganisms. Therefore, the data suggested that TNBS-induced CD can be roughly divided into two phases: the acute inflammatory phase (weeks 1 to 2) and the chronic inflammatory phase (weeks 3 to 5). However, the microbiome and mycobiome dysbiosis did not return to normal within the trial period. Hence, our findings may facilitate a better comprehension of the dynamic progress of experimental TNBS-induced CD.}, }
@article {pmid39933444, year = {2025}, author = {Rob, M and Yousef, M and Lakshmanan, AP and Mahboob, A and Terranegra, A and Chaari, A}, title = {Microbial signatures and therapeutic strategies in neurodegenerative diseases.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {184}, number = {}, pages = {117905}, doi = {10.1016/j.biopha.2025.117905}, pmid = {39933444}, issn = {1950-6007}, abstract = {Neurodegenerative diseases (NDs), including Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), and multiple sclerosis (MS), arise from complex interactions between genetic factors, environmental exposures, and aging. Additionally, gut dysbiosis has been linked to systemic inflammation and neurodegeneration. Advances in microbiome and metabolome profiling techniques have provided deeper insights into how alterations in gut microbiota and dietary patterns affect metabolic pathways and contribute to the progression of NDs. This review explores the profiles of gut microbiome and metabolome derived biomarkers and their roles in NDs. Across phyla, families, and genera, we identified 55 microbial alterations in PD, 24 in AD, 4 in ALS, and 17 in MS. Some notable results include an increase in Akkermansia in PD, AD, and MS and a decrease in short-chain fatty acids (SCFAs) in PD and AD. We examined the effects of probiotics, prebiotics, fecal microbiota transplants (FMT), sleep, exercise, and diet on the microbiota, all of which contributed to delayed onset and alleviation of symptoms. Further, artificial intelligence (AI) and machine learning (ML) algorithms applied to omics data have been crucial in identifying novel therapeutic targets, diagnosing and predicting prognosis, and enabling personalized medicine using microbiota-modulating therapies in NDs patients.}, }
@article {pmid39933397, year = {2025}, author = {Wu, X and Yu, Q and Hou, Y and Zhang, X and Ocholi, SS and Wang, L and Yan, Z and Li, J and Han, L}, title = {Emodin-8-O-β-D-glucopyranoside alleviates cholestasis by maintaining intestinal homeostasis and regulating lipids and bile acids metabolism in mice.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {258}, number = {}, pages = {116734}, doi = {10.1016/j.jpba.2025.116734}, pmid = {39933397}, issn = {1873-264X}, abstract = {Cholestatic liver disease(CLD) is caused by impaired bile flow due to obstruction of the biliary tract, and long-term exposure to bile acids in the liver triggers inflammation, eventually leading to liver toxicity and liver fibrosis. Emodin-8-O-β-D-glucopyranoside(EG) is anthraquinone compound that is widely found in traditional Chinese medicine. It possessed antioxidative and anti-inflammatory activities. However, the effect of EG on cholestatic liver injury(CLI) has not been explored. In this study, Alpha-naphthyl isothiocyanate(ANIT)-induced CLI mice were used to investigate the anti-cholestasis and hepatoprotective effects of EG through serum biochemical index detection, non-targeted metabolomics, lipidomics, and intestinal flora 16S rRNA sequencing. The results suggested that EG restores homeostasis of the gut microbiome while regulating bile acids metabolism and lipid-related metabolic pathways to reduce liver damage in ANIT-induced cholestasis. This study provides a new perspective on the mechanism of EG, and help offer a more natural approach to managing liver damage.}, }
@article {pmid39933372, year = {2025}, author = {Zhu, G and Yang, S and He, W and Han, X and Chen, L and Chen, G and Lin, T}, title = {Simulated nitrogen deposition enhances resistance of female poplars over males to Pestalotiopsis microspora infection through the recruitment of antagonistic microbes in phyllosphere.}, journal = {Journal of environmental management}, volume = {376}, number = {}, pages = {124484}, doi = {10.1016/j.jenvman.2025.124484}, pmid = {39933372}, issn = {1095-8630}, abstract = {Atmospheric nitrogen deposition has globally increased due to human activities and has strongly interfered with plant growth and resistance to biotic stressors. Dioecious plant species have shown secondary dimorphism in growth and development between male and female individuals in response to increased nitrogen deposition. However, the extent to whether these sexual differences influence variations in phyllosphere microbial communities and the associated pathogen resistance between male and female conspecifics remains unclear. To address this knowledge gap, female and male full-sibs of a poplar species were exposed to simulated nitrogen deposition and then artificially infected with a leaf pathogenic fungus, Pestalotiopsis microspora. The findings revealed that simulated nitrogen deposition promoted the growth of both sexes, with male plants exhibiting superior growth. Following P. microspora infection, female control plants displayed a greater leaf lesion area compared to males, but simulated nitrogen deposition reversed this difference. Further phyllosphere microbiome analysis and toxicity test indicated that the sexual differences in pathogen resistance between male and female conspecifics were likely attributable to alterations in the composition and structure of epiphytic microbes as the phyllosphere of female plants harbored a higher abundance of ecologically beneficial microbes with potential biological control capabilities, whereas males exhibited an increase abundance in the phytopathogens genera in response to simulated nitrogen deposition. Confirmatively, two bacterial strains were successfully isolated from the epiphytic phyllosphere of female plants that exhibited strong antagonistic effect against the pathogenic fungus P. microspora in both in vitro and in vivo conditions. The findings have significant implications for the selection of suitable poplar sexes for landscaping and reforestation efforts in areas experienced severe atmospheric nitrogen deposition.}, }
@article {pmid39933292, year = {2025}, author = {He, H and Huo, L and Oosthuizen-Vosloo, S and Pieper, KJ and Stubbins, A and Yoon, B and Pinto, AJ}, title = {Building plumbing influences the microdiversity and community assembly of the drinking water microbiome.}, journal = {Water research}, volume = {276}, number = {}, pages = {123244}, doi = {10.1016/j.watres.2025.123244}, pmid = {39933292}, issn = {1879-2448}, abstract = {Building plumbing microbial communities can significantly influence water quality at the point of use, particularly during periods of stagnation. Thus, a fine-scale understanding of factors governing community membership and structure, as well as environmental and ecological factors shaping building plumbing microbial communities is critical. In this study, we utilized full-length 16S ribosomal RNA (rRNA) gene sequencing to investigate the microdiversity and spatial-temporal dynamics of microbial communities in institutional and residential building plumbing systems. Bacterial operational taxonomic units (OTUs) within institutional buildings exhibited much lower microdiversity relative to the same OTUs in residential buildings. Higher microdiversity was associated with higher persistence and relative abundance of OTUs. Interestingly, amplicon sequencing variants within the same OTUs exhibited habitat preferences based on the building type while also demonstrating varying temporal turnover patterns. Dispersal limitation disproportionately governed community assembly in institutional buildings, whereas heterogeneous selection was the dominant ecological mechanism shaping the microbial community in residential buildings. Dispersal limitation in institutional buildings is consistent with larger building sizes and greater periods of water stagnation. Interestingly, the inability to explain the extent of heterogeneous selection-driven community assembly in residential locations using measured water chemistry may suggest a disproportionately large effect of fine-scale variation in plumbing characteristics on community assembly in residential locations.}, }
@article {pmid39933221, year = {2025}, author = {Cao, Y and Fan, X and Zang, T and Li, Y and Tu, Y and Wei, Y and Bai, J and Liu, Y}, title = {Gut microbiota causes depressive phenotype by modulating glycerophospholipid and sphingolipid metabolism via the gut-brain axis.}, journal = {Psychiatry research}, volume = {346}, number = {}, pages = {116392}, doi = {10.1016/j.psychres.2025.116392}, pmid = {39933221}, issn = {1872-7123}, abstract = {Emerging evidence suggests that changes in the gut microbiota (GM) are related to prenatal depression onset, but the underlying molecular mechanisms remain obscure. This study was conducted to explore how disordered GM is involved in the onset of prenatal depression through the microbiome-gut-brain (MGB) axis. We transplanted fecal microbiota from women with and without prenatal depression into germ-free mice. Fecal metagenomic sequencing and LC-MS untargeted metabolomics analysis were performed to identify the GM composition, function, and metabolites in mice. Lipid metabolomics analysis was then used to characterize the lipid metabolism of brain tissue in mice. We found that mice transplanted with fecal microbiota from women with prenatal depression exhibited depressive-like behaviors as well as characteristic disorders of the phylum Firmicutes. Weighted Gene Correlation Network Analysis identified three microbial and one metabolic module in the gut, alongside two lipid metabolic modules in the brain, as significantly related to all depressive-like behaviors. These modules were enriched for glycerophospholipid and sphingolipid metabolism. In addition, the GM of mice with depressive-like behaviors were enriched and deficient in relevant functions and enzymes in the glycerophospholipid (mainly phosphatidylethanolamine) and sphingolipid (mainly hexosyl-ceramide) metabolic pathways, respectively. Consistently, glycerophospholipid and sphingolipid metabolites in the brains of depressive-like mice were up- and down-regulated. Increased phosphatidylethanolamine and decreased hexosyl-ceramide were significantly related to differential genera in the gut. Collectively, our findings provide a novel microbial and metabolic framework for understanding the role of the MGB axis in prenatal depression, indicating that the GM may be involved in the onset of depressive phenotypes by modulating central glycerophospholipid and sphingolipid metabolic homeostasis.}, }
@article {pmid39932999, year = {2025}, author = {Tepekule, B and Barcik, W and Staiger, WI and Bergadà-Pijuan, J and Scheier, T and Brülisauer, L and Hall, AR and Günthard, HF and Hilty, M and Kouyos, RD and Brugger, SD}, title = {Computational and in vitro evaluation of probiotic treatments for nasal Staphylococcus aureus decolonization.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {7}, pages = {e2412742122}, doi = {10.1073/pnas.2412742122}, pmid = {39932999}, issn = {1091-6490}, support = {1449 M//Promedica Stiftung/ ; GRS-09420//Gebert R&#xfc;f Stiftung (Gebert R&#xfc;f Foundation)/ ; GRS-09420//Gebert R&#xfc;f Stiftung (Gebert R&#xfc;f Foundation)/ ; BSSGI0_155851//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; K-84804 - 01 - 01//UZH | Foundation for Research in Science and the Humanities (Stiftung f&#xfc;r wissenschaftliche Forschung)/ ; }, mesh = {*Probiotics/administration &amp; dosage/pharmacology ; *Staphylococcus aureus/drug effects ; Humans ; *Staphylococcal Infections/microbiology/drug therapy ; *RNA, Ribosomal, 16S/genetics ; Anti-Bacterial Agents/pharmacology ; Microbiota/drug effects ; Nose/microbiology ; Computer Simulation ; Adult ; }, abstract = {Despite the rising challenge of antibiotic resistance, current approaches to eradicate nasal pathobionts Staphylococcus aureus and Streptococcus pneumoniae rely on antibacterials. An alternative is the artificial inoculation of commensal bacteria, i.e., probiotic treatment, supported by the increasing evidence for commensal-mediated inhibition of pathogens. To systematically investigate the potential of this approach, we developed a quantitative framework simulating the nasal microbiome dynamics by combining mathematical modeling with longitudinal microbiota data. By inferring community parameters using 16S ribosomal RNA (rRNA) amplicon sequencing data and simulating the nasal microbial dynamics of patients colonized with S. aureus, we compared the decolonization performance of probiotic and antibiotic treatments under different assumptions on patients' community composition and susceptibility profile. To further compare the robustness of these treatments, we simulated an S. aureus challenge and quantified the recolonization probability. Through in vitro experiments using nasal swabs of adults colonized with S. aureus, we confirmed that after antibiotic treatment, recolonization of S. aureus was inhibited in samples treated with a probiotic mixture compared to the nontreated control. Our results suggest that probiotic treatment outperforms antibiotics in terms of decolonization performance, recolonization robustness, and leads to less collateral reduction in the microbiome diversity. Thus, probiotic treatment may provide a promising alternative to combat antibiotic resistance, with the additional advantage of personalized treatment options via using the patient's own metagenomic data. The combination of an in silico framework with in vitro experiments using clinical samples reported in this work is an important step forward to further investigate this alternative in clinical trials.}, }
@article {pmid39932953, year = {2025}, author = {Chen, MY and Fulton, LM and Huang, I and Liman, A and Hossain, SS and Hamilton, CD and Song, S and Geissmann, Q and King, KC and Haney, CH}, title = {Order among chaos: High throughput MYCroplanters can distinguish interacting drivers of host infection in a highly stochastic system.}, journal = {PLoS pathogens}, volume = {21}, number = {2}, pages = {e1012894}, doi = {10.1371/journal.ppat.1012894}, pmid = {39932953}, issn = {1553-7374}, mesh = {*Host-Pathogen Interactions/physiology ; *Arabidopsis/microbiology ; *Plant Diseases/microbiology ; Microbiota/physiology ; Stochastic Processes ; }, abstract = {The likelihood that a host will be susceptible to infection is influenced by the interaction of diverse biotic and abiotic factors. As a result, substantial experimental replication and scalability are required to identify the contributions of and interactions between the host, the environment, and biotic factors such as the microbiome. For example, pathogen infection success is known to vary by host genotype, bacterial strain identity and dose, and pathogen dose. Elucidating the interactions between these factors in vivo has been challenging because testing combinations of these variables quickly becomes experimentally intractable. Here, we describe a novel high throughput plant growth system (MYCroplanters) to test how multiple host, non-pathogenic bacteria, and pathogen variables predict host health. Using an Arabidopsis-Pseudomonas host-microbe model, we found that host genotype and bacterial strain order of arrival predict host susceptibility to infection, but pathogen and non-pathogenic bacterial dose can overwhelm these effects. Host susceptibility to infection is therefore driven by complex interactions between multiple factors that can both mask and compensate for each other. However, regardless of host or inoculation conditions, the ratio of pathogen to non-pathogen emerged as a consistent correlate of disease. Our results demonstrate that high-throughput tools like MYCroplanters can isolate interacting drivers of host susceptibility to disease. Increasing the scale at which we can screen drivers of disease, such as microbiome community structure, will facilitate both disease predictions and treatments for medicine and agricultural applications.}, }
@article {pmid39932940, year = {2025}, author = {Van Renne, N and Vanwolleghem, T}, title = {Detection of hepatitis B virus mRNA from single cell RNA sequencing data without prior knowledge.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0314060}, doi = {10.1371/journal.pone.0314060}, pmid = {39932940}, issn = {1932-6203}, mesh = {Humans ; *Hepatitis B virus/genetics ; *Single-Cell Analysis/methods ; *RNA, Messenger/genetics ; *RNA, Viral/genetics ; *Sequence Analysis, RNA/methods ; Liver/virology/metabolism ; Female ; Hepatitis B, Chronic/virology/genetics ; Male ; Adult ; Hepatocytes/virology/metabolism ; }, abstract = {The ability to detect microbial reads from sequencing data has significantly advanced microbiome and infectious disease research. Recently, INVADEseq introduced a technique to extract microbial reads from single-cell RNA sequencing (scRNA-seq) data following 16S rRNA amplification. We hypothesized that this approach could be leveraged to detect viruses in eukaryotic cells without such amplification or prior knowledge, provided they produce viral mRNAs containing poly-A tails. To test this, we aimed to detect Hepatitis B Virus (HBV) reads from liver samples of patients with chronic HBV infection, both with and without HBsAg loss. We successfully detected HBV reads in the liver of viraemic patients, predominantly in hepatocytes and, to a lesser extent, in Kupffer cells. Functionally cured HBV patients with HBsAg loss had undetectable HBV mRNA in the liver. This study demonstrates the ability to extract and identify viral reads from scRNA-seq data without prior knowledge and without specific amplification. This approach can be used for screening scRNA-seq data for the presence of viral reads at single-cell resolution, potentially enhancing our understanding of the cellular distribution of viruses and virus-host interactions.}, }
@article {pmid39932930, year = {2025}, author = {Silamiķele, L and Silamiķelis, I and Kotoviča, PP and Kloviņš, J}, title = {Bacterial targets of fecal host miRNAs in high-fat diet-fed mice.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0315871}, doi = {10.1371/journal.pone.0315871}, pmid = {39932930}, issn = {1932-6203}, mesh = {Animals ; *MicroRNAs/genetics/metabolism ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Mice ; Male ; *Metformin/pharmacology ; *Diet, High-Fat/adverse effects ; *Diabetes Mellitus, Type 2/microbiology/genetics/metabolism ; Mice, Inbred C57BL ; Bacteria/genetics/classification ; }, abstract = {The gut microbiome composition is intricately linked to the host's health status, yet the mechanisms underlying its interaction with the host are not fully understood. MicroRNAs (miRNAs), facilitating intercellular communication, are found in bodily fluids, including the intestinal content, where they may affect the microbiome. However, their role in type 2 diabetes (T2D)-associated microbiome and treatment implications are not explored. Our study investigated how host miRNAs may influence gut microbiome changes related to metformin treatment in a T2D mouse model. Analyzing fecal and gut mucosal samples via small RNA sequencing, we correlated results with microbiome sequencing data, identifying miRNA-microbiome correlations, bacterial targets, and proteins targeted in these bacteria. Significant differences in miRNA expression based on diet and intestinal location were noted, with minor effects from metformin treatment in the proximal small intestine of non-diabetic male mice. Key fecal miRNAs targeting bacteria included mmu-miR-5119, mmu-miR-5126, mmu-miR-6538, and mmu-miR-2137, primarily affecting Oscillospiraceae_NOV, Lachnospiraceae_NOV, and Bacteroides. Our analysis of targeted proteins revealed diverse biological and molecular effects. Further research into miRNA-bacteria interactions could lead to new strategies for manipulating the gut microbiome in T2D and beyond.}, }
@article {pmid39932806, year = {2025}, author = {Tian, Y and Jin, M and Li, H and Li, D and Pei, Y}, title = {Advancements in rheumatoid arthritis immunotherapy: a comprehensive bibliometric analysis of research trends and hotspots (2003-2023).}, journal = {Clinical and experimental rheumatology}, volume = {}, number = {}, pages = {}, doi = {10.55563/clinexprheumatol/xo2fjd}, pmid = {39932806}, issn = {0392-856X}, abstract = {OBJECTIVES: To analyse research trends and developments in rheumatoid arthritis (RA) immunotherapy through a comprehensive bibliometric analysis of literature from 2003 to 2023.<br><br>METHODS: Publications related to RA immunotherapy were retrieved from Web of Science Core Collection database using specified search terms. Bibliometric analysis was performed with VOSviewer, CiteSpace, Pajek, and R packages to examine publication patterns, international collaborations, research hotspots, and emerging trends. Analysis covered publication outputs, country contributions, institutional networks, and keyword evolution patterns.<br><br>RESULTS: Analysis based on a total of 940 publications showcased that the associated researches featured exponential growth (R&#xb2;=0.885) over the study period. The United States led with 285 publications (30.3%), followed by China (187, 19.9%) and Germany (156, 16.6%). International collaboration intensity increased, with average collaborating countries per paper rising from 1.8 to 2.7. Research focus evolved through three phases: fundamental immunology (2003-2010), therapeutic development (2011-2017), and precision medicine (2018-2023). Current hotspots encompassed immunomodulation mechanisms (38% of keywords), immune-related adverse events management, as well as cancer immunity interactions. Emerging trends highlighted nanotechnology applications and microbiome research, with respective growth rates of 218% and 245% in recent years.<br><br>CONCLUSIONS: This analysis revealed significant evolution in RA immunotherapy research, characterised by increasing international collaboration and methodological sophistication. The involved fields displayed a clear transition from basic immunological research to precision medicine approaches. Emerging hotspots in nanotechnology and microbiome studies suggested promising therapeutic innovations. These findings were seen to provide valuable guidance for future research fields and resource allocation in RA immunotherapy.}, }
@article {pmid39932663, year = {2025}, author = {da Silva Pereira, M and Alcantara, LM and de Freitas, LM and de Oliveira Ferreira, AL and Leal, PL}, title = {Microbial Rumen proteome analysis suggests Firmicutes and Bacteroidetes as key producers of lignocellulolytic enzymes and carbohydrate-binding modules.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {39932663}, issn = {1678-4405}, support = {Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado da Bahia//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado da Bahia/ ; Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, abstract = {Lignocellulosic biomass, rich in cellulose, hemicellulose, and lignin, offers a sustainable source for biofuels and and production of other materials such as polymers, paper, fabrics, bioplastics and biofertilizers. However, its complex structure hinders efficient conversion. Chemical, enzymatic, and microbial methods aim to unlock the trapped sugars and phenols. The rumen microbiome, a fascinating ecosystem within ruminant animals, holds particular promise. The Hungate 1000 project sequenced 410 microbial genomes from the rumen, enabling in silico screening for lignocellulolytic enzymes. This approach saves time and resources, supporting the development of sustainable bioconversion technologies aligned with the UN's 2030 agenda goals. Analysis of these 410 predicted proteomes revealed diverse carbohydrate-active enzymes (CAZymes) and carbohydrate-binding modules (CBMs) across various microorganisms. Notably, Firmicutes and Bacteroidetes dominated CAZyme and CBM production, suggesting collaborative efforts among different phyla during degradation. The presence of CBM50 and chitinases hints at the ability to utilize chitin from fungal cell walls. Interestingly, the absence of ligninolytic auxiliary activity enzymes reaffirms the rumen microbiome's incapability of directly degrading lignin. However, enzymes facilitating the loosening of the cell wall by cleaving lignin-hemicellulose linkages were identified. This suggests a strategy for making cellulose more accessible to hydrolytic enzymes. This study highlights the intricate relationship between rumen microbes, contributing necessary enzymes for plant cell wall deconstruction in this unique environment. Additionally, it underlines the power of in silico techniques for analyzing big data, paving the way for advancements in sustainable bioconversion.}, }
@article {pmid39932658, year = {2025}, author = {Ramirez, GA and Cardamone, C and Lettieri, S and Fredi, M and Mormile, I}, title = {Clinical and Pathophysiological Tangles Between Allergy and Autoimmunity: Deconstructing an Old Dichotomic Paradigm.}, journal = {Clinical reviews in allergy &amp; immunology}, volume = {68}, number = {1}, pages = {13}, pmid = {39932658}, issn = {1559-0267}, mesh = {Humans ; *Hypersensitivity/immunology ; *Autoimmunity ; Animals ; Th17 Cells/immunology ; Immunoglobulin E/immunology ; Autoimmune Diseases/immunology/etiology ; Th2 Cells/immunology ; Mast Cells/immunology ; B-Lymphocytes/immunology ; Eosinophils/immunology ; Disease Susceptibility ; }, abstract = {Allergic and autoimmune disorders are characterised by dysregulation of the immune responses to otherwise inert environmental substances and autoantigens, leading to inflammation and tissue damage. Their incidence has constantly increased in the last decades, and their co-occurrence defies current standards in patient care. For years, allergy and autoimmunity have been considered opposite conditions, with IgE and Th2 lymphocytes cascade driving canonical allergic manifestations and Th1/Th17-related pathways accounting for autoimmunity. Conversely, growing evidence suggests that these conditions not only share some common inciting triggers but also are subtended by overlapping pathogenic pathways. Permissive genetic backgrounds, along with epithelial barrier damage and changes in the microbiome, are now appreciated as common risk factors for both allergy and autoimmunity. Eosinophils and mast cells, along with autoreactive IgE, are emerging players in triggering and sustaining autoimmunity, while pharmacological modulation of B cells and Th17 responses has provided novel clues to the pathophysiology of allergy. By combining clinical and therapeutic evidence with data from mechanistic studies, this review provides a state-of-the-art update on the complex interplay between allergy and autoimmunity, deconstructing old dichotomic paradigms and offering potential clues for future research.}, }
@article {pmid39932617, year = {2025}, author = {Sivalingam, AM}, title = {Emerging Mechanisms and Biomarkers Associated with T-Cells and B-Cells in Autoimmune Disorders.}, journal = {Clinical reviews in allergy &amp; immunology}, volume = {68}, number = {1}, pages = {14}, pmid = {39932617}, issn = {1559-0267}, mesh = {Humans ; *Autoimmune Diseases/immunology/diagnosis/etiology ; *Biomarkers ; *B-Lymphocytes/immunology ; *T-Lymphocytes/immunology ; Female ; Animals ; Gastrointestinal Microbiome/immunology ; Child ; }, abstract = {Autoimmune diseases are characterized by the dysregulation of B-cells, which are responsible for antibody production against pathogens, and T-cells, which play a crucial role in cell-mediated immunity, including both helper and cytotoxic T-cells. These disorders frequently present with abnormal responses from both B- and T-cells, which can have a significant impact on cardiovascular health, particularly among the female patients. Key mechanisms contributing to these diseases include the activation of the NLRP3 inflammasome impaired efferocytosis is the process by which phagocytes clear apoptotic cells to maintain immune and developmental balance. Defects in this process can lead to inflammatory and autoimmune disorders. The gut microbiota helps defend against pathogens and signals immune cells, playing a vital role in human health and is involved in many aspects of the body. Novel therapeutic strategies such as nanomedicine and targeted treatments are being developed to restore immune balance. The significance of thymic homeostasis the influence of viral infections and the presence of tertiary lymphoid structures highlight the need for multidisciplinary approaches in the management of these conditions. A case study of a 9-year-old girl diagnosed with seronegative autoimmune encephalitis, who displayed severe obsessive-compulsive disorder (OCD) and aggressive behavior, exemplifies the complexities involved in treatment. Promising interventions, including CAR-T-cell therapy and nanomedicine, are under development for various autoimmune diseases, such as vitiligo and refractory autoimmune rheumatic diseases (ARDs). Furthermore, emerging therapies, including CAR-T-cell therapy, mRNA-based strategies, and microbiome modulation, are being explored alongside advancements in personalized medicine and early diagnostic techniques to improve patient outcomes for individuals affected by autoimmune diseases.}, }
@article {pmid39932508, year = {2025}, author = {Ramos-López, C and García-Rodrigo, L and Sánchez-Tirado, E and González-Cortés, A and Agüí, L and Yáñez-Sedeño, P and Pingarrón, JM}, title = {Nanocellulose-modified electrodes for simultaneous biosensing of microbiome-related oral diseases biomarkers.}, journal = {Mikrochimica acta}, volume = {192}, number = {3}, pages = {141}, pmid = {39932508}, issn = {1436-5073}, mesh = {Humans ; *Biomarkers/blood ; *Electrodes ; *Biosensing Techniques/methods ; *Cellulose/chemistry ; *Graphite/chemistry ; Microbiota ; Pulmonary Disease, Chronic Obstructive/diagnosis ; Saliva/chemistry/microbiology ; Immunoassay/methods ; Matrix Metalloproteinase 9/blood ; Limit of Detection ; Electrochemical Techniques/methods ; Antibodies, Immobilized/immunology ; Arthritis, Rheumatoid/diagnosis/blood ; Nanostructures/chemistry ; Periodontitis/microbiology/diagnosis/blood ; }, abstract = {The preparation of a dual immunosensor for the simultaneous determination of two important microbiome-related oral disease biomarker matrix metalloproteinases MMP-9 and MMP-13 is reported. Screen-printed dual carbon electrodes (SPdCEs) modified with reduced graphene oxide and crystalline nanocellulose (rGO/CNC) were used for the immobilization of specific capture antibodies and the implementation of sandwich-type immunoassays using biotinylated secondary antibodies. Amperometric detection through the hydroquinone HQ/H2O2 system was employed. The limits of detection (LOD) achieved were 0.25 and 0.30 ng mL[-1] for MMP-9 and MMP-13, respectively. The developed immunosensor proved to be useful for the determination of both MMPs in saliva from healthy individuals and patients of periodontitis as well as in serum from patients diagnosed with rheumatoid arthritis (RA) and chronic obstructive pulmonary disease (COPD). The obtained results agreed with those provided by commercial ELISA kits, and the developed dual immunosensor proved to be competitive versus this methodology, requiring less than 2 h for the simultaneous determination of both biomarkers.}, }
@article {pmid39932495, year = {2025}, author = {Feng, T and Chen, X and Wu, S and Tang, W and Zhou, H and Fang, Z}, title = {Predicting the bacterial host range of plasmid genomes using the language model-based one-class support vector machine algorithm.}, journal = {Microbial genomics}, volume = {11}, number = {2}, pages = {}, doi = {10.1099/mgen.0.001355}, pmid = {39932495}, issn = {2057-5858}, mesh = {*Plasmids/genetics ; *Support Vector Machine ; *Host Specificity ; *Bacteria/genetics/classification ; *Genome, Bacterial ; Algorithms ; Machine Learning ; }, abstract = {The prediction of the plasmid host range is crucial for investigating the dissemination of plasmids and the transfer of resistance and virulence genes mediated by plasmids. Several machine learning-based tools have been developed to predict plasmid host ranges. These tools have been trained and tested based on the bacterial host records of plasmids in related databases. Typically, a plasmid genome in databases such as the National Center for Biotechnology Information is annotated with only one or a few bacterial hosts, which does not encompass all possible hosts. Consequently, existing methods may significantly underestimate the host ranges of mobile plasmids. In this work, we propose a novel method named HRPredict, which employs a word vector model to digitally represent the encoded proteins on plasmid genomes. Since it is difficult to confirm which host a particular plasmid definitely cannot enter, we developed a machine learning approach for predicting whether a plasmid can enter a specific bacterium as a no-negative samples learning task. Using multiple one-class support vector machine (SVM) models that do not require negative samples for training, HRPredict predicts the host range of plasmids across 45 families, 56 genera and 56 species. In the benchmark test set, we constructed reliable negative samples for each host taxonomic unit via two indirect methods, and we found that the area under the curve (AUC), F1-score, recall, precision and accuracy of most taxonomic unit prediction models exceeded 0.9. Among the 13 broad-host-range plasmid types, HRPredict demonstrated greater coverage than HOTSPOT and PlasmidHostFinder, thus successfully predicting the majority of hosts previously reported. Through feature importance calculation for each SVM model, we found that genes closely related to the plasmid host range are involved in functions such as bacterial adaptability, pathogenicity and survival. These findings provide significant insight into the mechanisms through which bacteria adjust to diverse environments through plasmids. The HRPredict algorithm is expected to facilitate in-depth research on the spread of broad-host-range plasmids and enable host-range predictions for novel plasmids reconstructed from microbiome sequencing data.}, }
@article {pmid39932403, year = {2025}, author = {Momo Cabrera, P and Bokulich, NA and Zimmermann, P}, title = {Evaluating stool microbiome integrity after domestic freezer storage using whole-metagenome sequencing, genome assembly, and antimicrobial resistance gene analysis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0227824}, doi = {10.1128/spectrum.02278-24}, pmid = {39932403}, issn = {2165-0497}, abstract = {UNLABELLED: The gut microbiome is crucial for host health. Early childhood is a critical period for the development of a healthy gut microbiome, but it is particularly sensitive to external influences. Recent research has focused on using advanced techniques like shotgun metagenome sequencing to identify key microbial signatures and disruptions linked to disease. For accurate microbiome analysis, samples need to be collected and stored under specific conditions to preserve microbial integrity and composition, with -80°C storage considered the gold standard for stabilization. This study investigates the effect of domestic freezer storage on the microbial composition of stool samples obtained from 20 children under 4 years of age with the use of shotgun metagenome sequencing. Fresh stool samples were aliquoted into sterile tubes, with one aliquot stored at 4°C and analyzed within 24 hours, while others were frozen in domestic freezers (below -18°C) and analyzed after 1 week, 2 months, and 6 months. Assessments of contig assembly quality, microbial diversity, and antimicrobial resistance genes revealed no significant degradation or variation in microbial composition.<br><br>IMPORTANCE: Most prior studies on sample storage have relied on amplicon sequencing, which is less applicable to metagenome sequencing-given considerations of contig quality and functional gene detection-and less reliable in representing microbial composition. Moreover, the effects of domestic freezer storage for at-home stool collection on microbiome profiles, contig quality, and antimicrobial resistance gene profiles have not been previously investigated. Our findings suggest that stool samples stored in domestic freezers for up to 6 months maintain the integrity of metagenomic data. These findings indicate that domestic freezer storage does not compromise the integrity or reproducibility of metagenomic data, offering a reliable and accessible alternative for temporary sample storage. This approach enhances the feasibility of large-scale at-home stool collection and citizen science projects, even those focused on the more easily perturbed early life microbiome. This advancement enables more inclusive research into the gut microbiome, enhancing our understanding of its role in human health.}, }
@article {pmid39932300, year = {2025}, author = {Gerbec, ZJ and Serapio-Palacios, A and Metcalfe-Roach, A and Krekhno, Z and Bar-Yoseph, H and Woodward, SE and Pena-Díaz, J and Nemirovsky, O and Awrey, S and Moreno, SH and Beatty, S and Kong, E and Radisavljevic, N and Cirstea, M and Chafe, S and McDonald, PC and Aparicio, S and Finlay, BB and Dedhar, S}, title = {Identification of intratumoral bacteria that enhance breast tumor metastasis.}, journal = {mBio}, volume = {}, number = {}, pages = {e0359524}, doi = {10.1128/mbio.03595-24}, pmid = {39932300}, issn = {2150-7511}, abstract = {UNLABELLED: The central, mortality-associated hallmark of cancer is the process of metastasis. It is increasingly recognized that bacteria influence multiple facets of cancer progression, but the extent to which tumor microenvironment-associated bacteria control metastasis in cancer is poorly understood. To identify tumor-associated bacteria and their role in metastasis, we utilized established murine models of non-metastatic and metastatic breast tumors to identify bacteria capable of driving metastatic disease. We found several species of the Bacillus genus that were unique to metastatic tumors, and found that breast tumor cells cultured with a Bacillus bacterium isolated from metastatic tumors, Bacillus thermoamylovorans, produced nearly 3× the metastatic burden as control cells or cells cultured with bacteria from non-metastatic breast tumors. We then performed targeted metabolomics on tumor cells cultured with different bacterial species and found that B. thermoamylovorans differentially regulated tumor cell metabolite profiles compared to bacteria isolated from non-metastatic tumors. Using these bacteria, we performed de novo sequencing and tested for the presence of genes that were unique to the bacterium isolated from metastatic tumors in a patient population to provide a proof-of-concept for identifying how specific bacterial functions are associated with the metastatic process in cancer independent of bacterial species. Together, our data directly demonstrate the ability of specific bacteria to promote metastasis through interaction with cancer cells.<br><br>IMPORTANCE: Metastasis is a major barrier to long-term survival for cancer patients, and therapeutic options for patients with aggressive, metastatic forms of breast cancer remain limited. It is therefore critical to understand the differences between non-metastatic and metastatic disease to identify potential methods for slowing or even stopping metastasis. In this work, we identify a bacterial species present with metastatic breast tumors capable of increasing the metastatic capabilities of tumor cells. We isolated and sequenced this bacteria, as well as a control species which failed to promote metastasis, and identified specific bacterial genes that were unique to the metastasis-promoting species. We tested for the presence of these bacterial genes in patient tumor samples and found they were more likely to be associated with mortality. We also identified enrichment of specific bacterial functions, providing insight into possible sources of bacteria-driven increases in the metastatic potential of multiple cancer types.}, }
@article {pmid39931947, year = {2025}, author = {Liu, Y and Zhao, T and Wang, Z and Zhang, Y and Shen, J and Lu, B}, title = {The microbiome- and metabolome-modulating activity of dietary cholesterol: insights from the small and large intestines.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4fo03049d}, pmid = {39931947}, issn = {2042-650X}, abstract = {Cholesterol is an important lipid molecule that affects the gut microbiome upon ingestion. We systematically investigated the effects of cholesterol on the microbiota of the large and small intestines using ex vivo and in vivo models, combining flow cytometry, metabolomics, and metagenomics. The results showed that cholesterol directly causes a loss of bacterial membrane polarity and integrity, as well as a reduction in microbial metabolic activity. Cholesterol directly affected the global metabolism of the large and small intestinal microbiota, including amino acid, carbohydrate, and nucleotide metabolism. Ex vivo and in vivo studies shared similar results, showing that cholesterol increased the abundance of the primary bile acid-metabolizing bacteria Clostridium and Dorea in the large intestinal microbiota, confirming the enrichment effect of cholesterol on these bacteria. In the in vivo model, increased conjugated bile acids in the small intestine and decreased abundance of BSH-containing Bifidobacterium were observed due to cholesterol. Only in vivo models have demonstrated that cholesterol increases phosphatidylcholine levels in both the small and large intestines, which may be related to the effects of cholesterol on host metabolism. The pro-inflammatory capacity of the intestinal microbiota was enhanced by cholesterol, as evidenced by the increased levels of IL-1β and TNF-α in THP-1 cells upon stimulation with cholesterol-treated microbiota. This study comprehensively elucidates the effects of cholesterol on the composition and metabolic functions of the microbiota in both the large and small intestines. It offers a novel perspective on the ways in which cholesterol affects host metabolism via the gut microbiome.}, }
@article {pmid39931688, year = {2025}, author = {He, X and Yuan, X and Shu, Q and Gao, Y and Chen, Y and Liu, Y and Xu, J and Zhang, Y and Cao, G}, title = {Therapeutic effects of traditional Chinese medicine Hua-Feng-Dan in a rat model of ischemic stroke involve renormalization of gut microbiota.}, journal = {Frontiers in pharmacology}, volume = {16}, number = {}, pages = {1485340}, pmid = {39931688}, issn = {1663-9812}, abstract = {Hua-Feng-Dan is a traditional Chinese medicine used to treat ischemic stroke, but little is known about its therapeutic mechanism. This study explored whether and how the mechanism involves readjustment of gut microbiota. Rats were subjected to middle cerebral artery occlusion as a model of ischemic stroke or to sham surgery, then treated or not with Hua-Feng-Dan. The different groups of animals were compared in terms of neurological score, cerebral infarct volume, brain edema, brain and gut histopathology to assess stroke severity. They were also compared in terms of indices of intestinal barrier permeability, inflammation and oxidative stress, brain metabolites as well as composition of the gut microbiota and their metabolites. Hua-Feng-Dan significantly reduced cerebral infarct volume and brain water content and improved neurological score, ischemic brain histopathology, and gut histopathology. It partially reversed stroke-induced intestinal barrier disruption and leakage, inflammation, dyslipidemia and oxidative stress, as well as the stroke-induced increase in pathogenic gut microbiota (e.g., Escherichia-Shigella, Enterococcus, Clostridium_innocuum_group) and decrease in beneficial microbiota (e.g., Lachnospiraceae, unclassified__f__Lachnospiracea and Ruminococcus_torques_group). The treatment altered levels of 39 and 38 metabolites produced during gut microbial and brain tissue metabolism respectively, mainly of amino acids, nucleosides, short-chain fatty acids, and essential fatty acids. Levels of factors related to inflammation and intestinal barrier permeability correlated positively with relative abundance of Escherichia-Shigella and Clostridium_innocuum_group, and negatively with 4-(glutamylamino) butanoate, 2-hydroxy-3-methylbutyric acid, dihomo-α-linolenic acid, dihomolinoleic acid, and 10-nitrolinoleic acid. Conversely, levels of 4-(glutamylamino) butanoate, 2-hydroxy-3-methylbutyric acid, and 10-nitrolinoleic acid correlated positively with relative abundance of unclassified__f__Lachnospiracea. Our results suggest that Hua-Feng-Dan may mitigate ischemic stroke injury by renormalizing gut microbiota and restoring gut barrier function, gut metabolism, thereby helping to alleviate inflammatory, neurological damage, and brain metabolic disorders.}, }
@article {pmid39931275, year = {2024}, author = {Skoulakis, A and Skoufos, G and Ovsepian, A and Hatzigeorgiou, AG}, title = {Machine learning models reveal microbial signatures in healthy human tissues, challenging the sterility of human organs.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1512304}, pmid = {39931275}, issn = {1664-302X}, abstract = {BACKGROUND: The presence of microbes within healthy human internal organs still remains under question. Our study endeavors to discern microbial signatures within normal human internal tissues using data from the Genotype-Tissue Expression (GTEx) consortium. Machine learning (ML) models were developed to classify each tissue type based solely on microbial profiles, with the identification of tissue-specific microbial signatures suggesting the presence of distinct microbial communities inside tissues.<br><br>METHODS: We analyzed 13,871 normal RNA-seq samples from 28 tissues obtained from the GTEx consortium. Unaligned sequencing reads with the human genome were processed using AGAMEMNON, an algorithm for metagenomic microbial quantification, with a reference database comprising bacterial, archaeal, and viral genomes, alongside fungal transcriptomes. Gradient-boosting ML models were trained to classify each tissue against all others based on its microbial profile. To validate the findings, we analyzed 38 healthy living tissue samples (samples from healthy tissues obtained from living individuals, not deceased) from an independent study, as the GTEx samples were derived from post-mortem biopsies.<br><br>RESULTS: Tissue-specific microbial signatures were identified in 11 out of the 28 tissues while the signatures for 8 tissues (Muscle, Heart, Stomach, Colon tissue, Testis, Blood, Liver, and Bladder tissue) demonstrated resilience to in silico contamination. The models for Heart, Colon tissue, and Liver displayed high discriminatory performance also in the living dataset, suggesting the presence of a tissue-specific microbiome for these tissues even in a living state. Notably, the most crucial features were the fungus Sporisorium graminicola for the heart, the gram-positive bacterium Flavonifractor plautii for the colon tissue, and the gram-negative bacterium Bartonella machadoae for the liver.<br><br>CONCLUSION: The presence of tissue-specific microbial signatures in certain tissues suggests that these organs are not devoid of microorganisms even in healthy conditions and probably they harbor low-biomass microbial communities unique to each tissue. The discoveries presented here confront the enduring dogma positing the sterility of internal tissues, yet further validation through controlled laboratory experiments is imperative to substantiate this hypothesis. Exploring the microbiome of internal tissues holds promise for elucidating the pathophysiology underlying both health and a spectrum of diseases, including sepsis, inflammation, and cancer.}, }
@article {pmid39931170, year = {2025}, author = {Wang, H and Huang, W and Pan, X and Tian, M and Chen, J and Liu, X and Li, Q and Qi, J and Ye, Y and Gao, L}, title = {Quzhou Aurantii Fructus Flavonoids Ameliorate Inflammatory Responses, Intestinal Barrier Dysfunction in DSS-Induced Colitis by Modulating PI3K/AKT Signaling Pathway and Gut Microbiome.}, journal = {Journal of inflammation research}, volume = {18}, number = {}, pages = {1855-1874}, pmid = {39931170}, issn = {1178-7031}, abstract = {PURPOSE: To explore the protective effect and underlying mechanism of Quzhou Aurantii Fructus flavonoids (QAFF) on Ulcerative colitis (UC).<br><br>METHODS: The constituents of QAFF were accurately determined by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The therapeutic impacts of QAFF were assessed in dextran sulfate sodium (DSS)-induced UC mice, focusing on the changes in body weight, disease activity index (DAI), colon length, histological assessment of colonic tissues, levels of pro-inflammatory cytokines, and expression of tight junction proteins. Western blotting confirmed key regulatory proteins within the differential signaling pathways, guided by transcriptome analysis. Additionally, the influence of QAFF on the gut microbiome was explored through 16S ribosomal RNA (rRNA) sequencing. The alterations in endogenous metabolites were detected by untargeted metabolomics, and their potential correlation with intestinal flora was then examined utilizing Spearman correlation analysis. Subsequently, the regulation of gut microbiome by QAFF was validated by fecal microbiota transplantation (FMT).<br><br>RESULTS: Eleven flavonoids, including Naringin and hesperidin, were initially identified from QAFF. In vivo experiments demonstrated that QAFF effectively ameliorated colitis symptoms, reduced IL-6, IL-1&#x3b2;, and TNF-&#x3b1; levels, enhanced intestinal barrier integrity, and downregulated PI3K/AKT pathway activation. Furthermore, QAFF elevated the levels of beneficial bacteria like Lachnospiraceae_NK4A136_group and Alloprevotella and concurrently reduced the pathogenic bacteria such as Escherichia-Shigella, [Eubacterium]_siraeum_group, and Parabacteroides. Metabolomics analysis revealed that 34 endogenous metabolites exhibited significant alterations, predominantly associated with Glycerophospholipid metabolism. These metabolites were significantly correlated with those differential bacteria modulated by QAFF. Lastly, the administration of QAFF via FMT ameliorated the colitis symptoms.<br><br>CONCLUSION: QAFF could ameliorate inflammatory responses and intestinal barrier dysfunction in DSS-induced UC mice probably by modulating the PI3K/AKT signaling pathway and gut microbiome, offering promising evidence for the therapeutic potential of QAFF in UC treatment.}, }
@article {pmid39930789, year = {2025}, author = {Jiang, H and Lv, M and He, T and Xie, M and Zhao, Z and He, J and Luo, S and Guo, Y and Chen, J}, title = {Effects of ex situ conservation on commensal bacteria of crocodile lizard and conservation implications.}, journal = {The veterinary quarterly}, volume = {45}, number = {1}, pages = {1-14}, doi = {10.1080/01652176.2025.2463704}, pmid = {39930789}, issn = {1875-5941}, mesh = {Animals ; *Lizards/microbiology ; *Conservation of Natural Resources ; *Skin/microbiology ; *Microbiota ; Bacteria/classification/isolation &amp; purification/genetics ; Endangered Species ; Symbiosis ; }, abstract = {Ex situ conservation is an important wildlife conservation strategy, but endangered wildlife in captivity often exhibit high disease rates. Commensal microorganisms are vital for homeostasis, immunity, and linked to diseases. This study analyzed the structure, assembly, variations of the symbiotic microbiota of the endangered crocodile lizard, and their relationship with environment, as well as the effects of captivity on them, to explore why captive reptiles face high dermatosis rates. Results showed that the reptile's microbiota significantly differ from that of its habitat, demonstrating niche specificity. While species richness among organs showed no significant differences, microbial diversity varied considerably. Skin microbiota showed no site-specific clustering. The assembly of skin, oral, and intestinal bacterial communities was dominated by homogeneous selection. The gut and oral bacterial networks were resilient to disturbances, while the skin bacterial network was sensitive. Captivity primarily affected the skin microbiota, reducing its diversity and stability, thereby increasing disease risk, and these effects were not solely attributable to environmental changes. These findings suggested that skin microbial changes in captive reptiles may be responsible for their increased susceptibility to dermatosis in ex situ conservation. This study underscored the importance of understanding reptile-associated microbes for effective conservation strategies and offers potential solutions.}, }
@article {pmid39930533, year = {2025}, author = {Chiarenza, A and Aluisio, GV and Parrinello, NL and Marino, S and Corsale, AM and Privitera, GF and Azgomi, M and La Spina, E and Cambria, D and Curtopelle, A and Isola, G and Botta, C and Di Raimondo, F and Romano, A and Santagati, M}, title = {BNT162b2 mRNA vaccination affects the gut microbiome composition of patients with follicular lymphoma and chronic lymphocytic leukemia.}, journal = {Biomarker research}, volume = {13}, number = {1}, pages = {25}, pmid = {39930533}, issn = {2050-7771}, support = {cod. CINECA 202254FLSB, CUP: E53D23001220006//Ministero dell'Istruzione e del Merito/ ; cod 2022FN7ANE, CUP E53D23001300006//Ministero dell'Istruzione e del Merito/ ; programma ricerca di ateneo UNICT 2020-22 linea 2 cod MICROCOSM//Universit&#xe0; di Catania/ ; programma ricerca di ateneo UNICT 2020-22 linea 2 cod MICROCOSM//Universit&#xe0; di Catania/ ; programma ricerca di ateneo UNICT 2020-22 linea 2 cod MICROCOSM//Universit&#xe0; di Catania/ ; }, abstract = {BACKGROUND: In both chronic lymphatic leukemia (CLL) and follicular lymphoma (FL) immunotherapy determines B-depletion that leads to temporary suppression of humoral immunity, which is clinically relevant especially during the COVID-19 pandemic, when most patients in the first wave received the BNT162b2 vaccine during anti-neoplastic treatment.<br><br>METHODS: To capture changes in the immunome and microbiome composition in CLL and FL patients upon mRNA-based vaccination, we designed a prospective, longitudinal study to profile both the humoral and the cellular response after exposure to the BNT162b2 COVID-19 vaccine.<br><br>RESULTS: In both CLL patients and FL patients, the second and third administrations of the BNT162b2 vaccine increased the titer of specific antibodies against SARS-CoV-2. In FL patients, vaccination induced expansion of central memory CD8&#x2009;+&#x2009;CD57dim CD279&#x2009;+&#x2009;T cells and reduction of the neutrophil subset myeloid 1 (CD14[-]CD15[+]CD16[dim]CD64[+]CD33[-]CD38[+]PDL1[+]HLA-DR[-]); in both cohorts, CD45RA&#x2009;+&#x2009;CD27&#x2009;+&#x2009;CD279&#x2009;+&#x2009;NK cells were expanded after a full cycle of vaccination. After vaccination, the genera Collinsella, Gemmiger, Lachnospiraceae, Blautia, Ruminococcus and Lactobacillus increased in both CLL patients and FL patients, whereas Faecalibacterium, Enterobacteriacae, and Enterococcus decreased. Multivariate analysis failed to identify factors associated with changes in microbiome communities among the CLL and FL cohorts, considering age, sex, exposure to anti-CD20 therapy and disease activity. Only in FL patients, alpha diversity was negatively correlated with neutrophil subsets myeloid 1 e 5 at baseline and positively correlated with neutrophil subset 6 after vaccination. PICRUSt2 analysis showed how microbiome can also affect the host health promoting chronic inflammation. The L-lysine biosynthesis pathway was more represented in CLL patients, whereas the L-valine degradation pathway and the anaerobic degradation of purine nucleobases were overrepresented in the FL cohort.<br><br>CONCLUSIONS: Taken together, our findings reveal the effect of the BNT162b2 vaccine in shaping the microbiome composition in CLL and FL patients, despite receiving treatment for their underlying active disease, and highlight the importance of a comprehensive analysis of the immunome and microbiome profiling to understand immune function in these cohorts of patients.}, }
@article {pmid39930446, year = {2025}, author = {Dong, L and Ji, Z and Hu, J and Jiang, Q and Wei, W}, title = {Oral microbiota shifts following tooth loss affect gut health.}, journal = {BMC oral health}, volume = {25}, number = {1}, pages = {213}, pmid = {39930446}, issn = {1472-6831}, support = {YSP202314//Young Scientist Program of Beijing Stomatological Hospital, Capital Medical University/ ; }, mesh = {Animals ; *Tooth Loss/microbiology ; Mice ; *Gastrointestinal Microbiome ; *Mice, Inbred C57BL ; RNA, Ribosomal, 16S ; Saliva/microbiology ; Feces/microbiology ; Microbiota ; Mouth/microbiology ; Male ; }, abstract = {BACKGROUND: Tooth loss not only impairs oral function but also affects gut health by altering the host microbiota. Understanding the oral-gut axis can provide insights into systemic health implications following tooth loss.<br><br>METHODS: Using an animal model, we extracted the molars of C57 mice. Saliva and fecal samples were collected for 16S rRNA and metagenomic sequencing to analyze changes in the oral and gut microbiota. Pearson correlation analysis assessed the relationship between altered microbial communities.<br><br>RESULTS: The study found a significant reduction in oral microbiota diversity following tooth loss, with increased Proteobacteria and decreased Muribacter. Gut microbiota showed increased Firmicutes and decreased Bacteroidota. Correlations between oral and gut microbiota changes were observed, indicating a potential link between tooth loss and alterations in intestinal microbial balance.<br><br>CONCLUSION: In the mouse model, tooth loss disrupted the balance of the oral-gut microbiota, with potential implications for intestinal health. Although these findings are from a murine model, considering the existence of the oral-gut axis balance in the human body, it is reasonable to postulate that following tooth loss in humans, the health of the intestinal microecology may also warrant attention.}, }
@article {pmid39930324, year = {2025}, author = {Mitra, D and Armijo, GK and Ober, EH and Baker, SM and Turner, HC and Broustas, CG}, title = {MIIST305 mitigates gastrointestinal acute radiation syndrome injury and ameliorates radiation-induced gut microbiome dysbiosis.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2458189}, doi = {10.1080/19490976.2025.2458189}, pmid = {39930324}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/radiation effects ; *Dysbiosis/microbiology ; *Acute Radiation Syndrome/drug therapy/microbiology ; Male ; Mice ; *Mice, Inbred C57BL ; *Bacteria/classification/isolation &amp; purification/radiation effects ; Gastrointestinal Tract/microbiology/radiation effects ; Radiation Injuries, Experimental/prevention &amp; control/microbiology/pathology ; Radiation-Protective Agents/pharmacology/therapeutic use ; Humans ; }, abstract = {High-dose radiation exposure results in gastrointestinal (GI) acute radiation syndrome identified by the destruction of mucosal layer, intestinal growth barrier dysfunction, and aberrant inflammatory responses. Further, radiation causes gut microbiome dysbiosis characterized by diminished microbial diversity, mostly commensal bacteria, and the spread of bacterial pathogens that trigger the recruitment of immune cells and the production of pro-inflammatory factors that lead to further GI tissue damage. Currently, there are no U.S. Food and Drug Administration (FDA) approved countermeasures that can treat radiation-induced GI injuries. To meet this critical need, Synedgen Inc. has developed a glycopolymer radiomitigator (MIIST305) that is specifically targeted to the GI tract, which acts by intercalating into the mucus layer and the glycocalyx of intestinal epithelial cells that could potentially ameliorate the deleterious effects of radiation. Male C57BL/6J adult mice were exposed to 13 Gy partial body X-irradiation with 5% bone marrow shielding and MIIST305 was administered on days 1, 3, and 5 post-irradiation. Approximately 85% of the animals survived the irradiation exposure and were apparently healthy until the end of the 30-day study period. In contrast, no control, Vehicle-treated animals survived past day 10 at this radiation dose. We show that MIIST305 improved intestinal epithelial barrier function and suppressed systemic inflammatory responses mediated by radiation-induced pro-inflammatory cytokines. Taxonomic profiling and community structure of the fecal and colonic mucosa microbiota demonstrated that MIIST305 treatment increased microbial diversity and restored abundance of beneficial commensal bacteria, including Lactobacillus and Bifidobacterium genera while suppressing potentially pathogenic bacteria Enterococcus and Staphylococcus compared with Vehicle-treated animals. In summary, MIIST305 is a novel GI-targeted therapeutic that greatly enhances survival in mice exposed to lethal radiation and protects the GI tract from injury by restoring a balanced gut microbiota and reducing pro-inflammatory responses. Further development of this drug as an FDA-approved medical countermeasure is of critical importance.}, }
@article {pmid39930249, year = {2025}, author = {Wang, JG and Dou, HH and Liang, QY}, title = {Gut microbiota, inflammatory cytokines, and Kawasaki disease: a Mendelian randomization study and mediation analysis.}, journal = {Pediatric research}, volume = {}, number = {}, pages = {}, pmid = {39930249}, issn = {1530-0447}, abstract = {OBJECTIVE: This study investigates the causal relationship between gut microbiota, inflammatory cytokines, and Kawasaki disease (KD), and whether cytokines mediate the effect of gut microbiota on KD.<br><br>METHODS: A Mendelian randomization analysis using the inverse-variance weighted method assessed the causal effects of gut microbiota and inflammatory cytokines on KD and explored potential mediation.<br><br>RESULTS: The study found causal links between 20 types of gut microbiota and KD. Ten types increased KD risk, notably Francisellales (OR&#x2009;=&#x2009;27.82, P&#x2009;=&#x2009;0.0309). Ten types provided protection, with Fusobacteriaceae showing the strongest effect (OR&#x2009;=&#x2009;0.0424, P&#x2009;=&#x2009;0.002). Five inflammatory cytokines were significantly associated with KD; adenosine deaminase was most protective (OR&#x2009;=&#x2009;0.7447, P&#x2009;=&#x2009;0.0037), while Fractalkine indicated higher risk (OR&#x2009;=&#x2009;2.0448, P&#x2009;=&#x2009;0.0315). Mediation analysis revealed that the Interleukin-10 receptor subunit beta mediates the effect of Bifidobacterium adolescentis on KD, with a mediation effect of -0.0237 (4.75% ratio). Interleukin-20 mediates the effect of Faecalicatena lactaris on KD, with a mediation effect of -0.1168 (15.30% ratio).<br><br>CONCLUSION: The findings indicate a causal relationship among gut microbiota, inflammatory cytokines, and KD, suggesting that the gut microbiome influences KD through specific cytokines.<br><br>IMPACT: The study confirmed a causal relationship between 20 types of gut microbiota and Kawasaki disease, finding that 10 types increase the risk of Kawasaki disease, particularly Francisellales. Five inflammatory cytokines were significantly associated with Kawasaki disease, with adenosine deaminase showing a protective effect, while Fractalkine increased the risk. Mediation analysis indicated that specific inflammatory cytokines (such as Interleukin-10 receptor subunit beta and Interleukin-20) play a significant mediating role between gut microbiota and Kawasaki disease.}, }
@article {pmid39930163, year = {2025}, author = {Kahraman Ilıkkan, &#xd6;}, title = {Lactobacillomics as a new notion in lactic acid bacteria research through omics integration.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {41}, number = {2}, pages = {68}, pmid = {39930163}, issn = {1573-0972}, mesh = {*Lactobacillales/genetics/metabolism ; *Probiotics ; *Metabolomics ; *Genomics/methods ; *Proteomics ; Fermentation ; Metagenomics ; Humans ; Genome, Bacterial ; }, abstract = {Omics technologies are a set of disciplines that analyze large-scale molecular data to understand biological systems in a holistic way. These technologies aim to reveal the structure, functions and interactions of organisms by studying processes at many levels of biomolecules, from the genome to metabolism. Lactobacillomics is introduced as an interdisciplinary field that integrates multiple "omics" technologies-including genomics, transcriptomics, proteomics, metabolomics, and metagenomics- to provide a comprehensive insight into "lactic acid bacteria" species. Lactobacillomics aims to elucidate the genetic, metabolic, and functional characteristics of lactic acid bacteria (LAB) species, providing insights into the mechanisms underlying their probiotic effects and contributions to the host microbiome. By analyzing genomes and metabolic pathways, researchers can identify specific genes responsible for health-promoting functions and desirable fermentation characteristics, which can guide the development of targeted probiotic strains with optimized health benefits. The integration of these omics data allows facilitating the discovery of biomarkers for health and disease states, the development of new probiotics tailored to specific populations or health conditions, and the optimization of fermentation processes to enhance the safety, flavor, and nutritional profile of fermented foods. A comprehensive review and bibliometric analysis were conducted to provide an overview of this promising field between 2005 and 2025 by examining Web of Science Core Collection data. Research results reveal trending topics, future perspectives, and key areas of growth within lactic acid bacteria (LAB) studies, particularly as they intersect with omics technologies.}, }
@article {pmid39930064, year = {2025}, author = {Eriksen, AMH and Rodríguez, JA and Seersholm, F and Hollund, HI and Gotfredsen, AB and Collins, MJ and Grønnow, B and Pedersen, MW and Gilbert, MTP and Matthiesen, H}, title = {Exploring DNA degradation in situ and in museum storage through genomics and metagenomics.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {210}, pmid = {39930064}, issn = {2399-3642}, mesh = {*Museums ; *Metagenomics/methods ; *Genomics/methods ; Animals ; *Archaeology ; Greenland ; Bone and Bones ; DNA/genetics ; }, abstract = {Understanding the environmental and microbial processes involved in DNA degradation from archaeological remains is a fundamental part of managing bone specimens. We investigated the state of DNA preservation in 33 archaeozoological caribou (Rangifer tarandus) ribs excavated from the same excavation trench at a former Inuit hunting camp in West Greenland, separated by 43 years: 1978 and 2021. Our findings show that DNA is better preserved in the most recently excavated samples, indicating a detrimental effect of museum storage on DNA integrity. Additionally, our data reveals a diverse microbiome in these bones, encoding genes relevant for bone degradation, such as enzymatic families relating to collagenases, peptidases and glycosidases. Microbes associated with bone degradation were present in both new and historical samples, with museum-stored bones showing significantly more DNA damage. Overall, our research sheds light on the nuanced dynamics governing the preservation of genomic material in archaeological contexts, underscoring the vital importance of careful considerations in museum curation practices for the sustainable conservation of invaluable skeletal records in museum repositories and in situ.}, }
@article {pmid39930028, year = {2025}, author = {Rook, O and Zwart, H}, title = {Awareness of human microbiome may promote healthier lifestyle and more positive environmental attitudes.}, journal = {Communications medicine}, volume = {5}, number = {1}, pages = {39}, pmid = {39930028}, issn = {2730-664X}, support = {No 964590//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; No 964590//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, abstract = {BACKGROUND: The human microbiome is an essential factor of physical and mental health, yet the general population has little knowledge about it. This survey explores public familiarity with the human microbiome and (potential) public preferences related to monitoring and improving one's microbiome health. The study also examines whether recognizing the importance of one's microbiome may promote a more ecosystem-aware perspective towards microorganisms.<br><br>METHODS: We conducted an online survey with nationally representative samples from France, Germany, South Korea, and Taiwan (N&#x2009;=&#x2009;2860). The results were interpreted using descriptive statistics and network analysis. We also performed a t-test to compare perceptions of microorganisms before and after a short reflection on the role of human microbiome for one's body and health.<br><br>RESULTS: In our data, most respondents express willingness to monitor the health of their microbiome (especially, in the European countries) and to adjust their lifestyle such as diet and exercise to improve it. A paired samples t-test shows a slight positive shift in perceptions of microorganisms and the microbial world after the reflection exercise compared to baseline.<br><br>CONCLUSIONS: The study shows that the public recognize the essential role of the human microbiome in health and are willing to take care of it, which may have implications for public health policy. Our findings also suggest that stronger awareness of the human microbiome may promote lifestyle change and a more encompassing environmental outlook.}, }
@article {pmid39930009, year = {2025}, author = {Potel, CM and Burtscher, ML and Garrido-Rodriguez, M and Brauer-Nikonow, A and Becher, I and Le Sueur, C and Typas, A and Zimmermann, M and Savitski, MM}, title = {Uncovering protein glycosylation dynamics and heterogeneity using deep quantitative glycoprofiling (DQGlyco).}, journal = {Nature structural &amp; molecular biology}, volume = {}, number = {}, pages = {}, pmid = {39930009}, issn = {1545-9985}, abstract = {Protein glycosylation regulates essential cellular processes such as signaling, adhesion and cell-cell interactions; however, dysregulated glycosylation is associated with diseases such as cancer. Here we introduce deep quantitative glycoprofiling (DQGlyco), a robust method that integrates high-throughput sample preparation, highly sensitive detection and precise multiplexed quantification to investigate protein glycosylation dynamics at an unprecedented depth. Using DQGlyco, we profiled the mouse brain glycoproteome, identifying 177,198 unique N-glycopeptides-25 times more than previous studies. We quantified glycopeptide changes in human cells treated with a fucosylation inhibitor and characterized surface-exposed glycoforms. Furthermore, we analyzed tissue-specific glycosylation patterns in mice and demonstrated that a defined gut microbiota substantially remodels the mouse brain glycoproteome, shedding light on the link between the gut microbiome and brain protein functions. Additionally, we developed a novel strategy to evaluate glycoform solubility, offering new insights into their biophysical properties. Overall, the in-depth profiling offered by DQGlyco uncovered extensive complexity in glycosylation regulation.}, }
@article {pmid39930007, year = {2025}, author = {Taglialegna, A}, title = {A gut microbiome-restoring diet.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {39930007}, issn = {1740-1534}, }
@article {pmid39929976, year = {2025}, author = {Sardar, P and Beresford-Jones, BS and Xia, W and Shabana, O and Suyama, S and Ramos, RJF and Soderholm, AT and Tourlomousis, P and Kuo, P and Evans, AC and Imianowski, CJ and Conti, AG and Wesolowski, AJ and Baker, NM and McCord, EAL and Okkenhaug, K and Whiteside, SK and Roychoudhuri, R and Bryant, CE and Cross, JR and Pedicord, VA}, title = {Gut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {39929976}, issn = {2058-5276}, support = {206245/Z/17/Z//Wellcome Trust (Wellcome)/ ; 302351/Z/23/Z//Wellcome Trust (Wellcome)/ ; A2194//Rosetrees Trust/ ; EP/X024709/1//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, abstract = {The gut microbiome modulates immunotherapy treatment responses, and this may explain why immune checkpoint inhibitors, such as anti-PD-1, are only effective in some patients. Previous studies correlated lipopolysaccharide (LPS)-producing gut microbes with poorer prognosis; however, LPS from diverse bacterial species can range from immunostimulatory to inhibitory. Here, by functionally analysing faecal metagenomes from 112 patients with melanoma, we found that a subset of LPS-producing bacteria encoding immunostimulatory hexa-acylated LPS was enriched in microbiomes of clinical responders. In an implanted tumour mouse model of anti-PD-1 treatment, microbiota-derived hexa-acylated LPS was required for effective anti-tumour immune responses, and LPS-binding antibiotics and a small-molecule TLR4 antagonist abolished anti-PD-1 efficacy. Conversely, oral administration of hexa-acylated LPS to mice significantly augmented anti-PD-1-mediated anti-tumour immunity. Penta-acylated LPS did not improve anti-PD-1 efficacy in vivo and inhibited hexa-acylated LPS-induced immune activation in vitro. Microbiome hexa-acylated LPS therefore represents an accessible predictor and potential enhancer of immunotherapy responses.}, }
@article {pmid39929955, year = {2025}, author = {Ruijiao, Z and Tianyuan, L and Shiyin, W and Sihui, M and Shumei, D and Lei, X and Liqin, C and Zhangjie, J and Qinghua, P and Liangchao, Q}, title = {One lung ventilation during thoracoscopic lobectomy alters lung microbiome miversity and composition.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {4937}, pmid = {39929955}, issn = {2045-2322}, support = {82260382//National Natural Science Foundation of China/ ; 20242BAB25497//Natural Science Foundation of Jiangxi Province/ ; }, mesh = {Humans ; Male ; Female ; *Microbiota ; *Lung/microbiology ; *One-Lung Ventilation/methods ; Middle Aged ; Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; Pneumonectomy/adverse effects ; Thoracoscopy/methods ; Postoperative Complications/microbiology/etiology ; }, abstract = {Current research indicates that the lungs are not sterile and maintain their own unique microecological balance, which can be disrupted by mechanical ventilation.One-lung ventilation (OLV) induces ischemia-reperfusion (IR) injury in the non-ventilated lung, a common contributor to acute lung injury during the perioperative period. This study investigates alterations in the pulmonary microbiome following one-lung ventilation during thoracoscopic lobectomy and evaluates the impact of differential microbiota on inflammatory responses. Approved by the Hospital Ethics Committee, this study involved 65 patients undergoing thoracoscopic lobectomy from April 2024 to June 2024. An internally controlled paired analysis was implemented to compare bronchoalveolar lavage fluid(BALF) collected from the operative side lung before and after one-lung ventilation. Key outcomes included changes in lung microbiota composition, levels of IL-1β and TNF-α, and the incidence of postoperative complications, with samples preserved for future analysis. Our research revealed significant changes in the abundances of Veillonella, Rothia, Ralstonia, and Melittanglum following one-lung ventilation during thoracoscopic lobectomy. However, there were no notable changes in overall microbial diversity, and alpha diversity remained unchanged. Correspondingly, the levels of IL-1β and TNF-α in the bronchoalveolar lavage fluid significantly increased post-OLV, positively correlating with Ralstonia abundance. The operational taxonomic units and species abundances significantly decreased following one-lung ventilation; nevertheless, overall microbial diversity remained stable. In BALF, levels of IL-1β and TNF-α were markedly elevated, with Ralstonia identified as a key pulmonary microbiome agent influencing inflammatory responses after one-lung ventilation.}, }
@article {pmid39929809, year = {2025}, author = {Feng, JN and Shao, W and Yang, L and Pang, J and Ling, W and Liu, D and Wheeler, MB and He, HH and Jin, T}, title = {Hepatic fibroblast growth factor 21 is required for curcumin or resveratrol in exerting their metabolic beneficial effect in male mice.}, journal = {Nutrition &amp; diabetes}, volume = {15}, number = {1}, pages = {4}, pmid = {39929809}, issn = {2044-4052}, mesh = {Animals ; *Fibroblast Growth Factors/metabolism/blood ; *Resveratrol/pharmacology ; Male ; *Curcumin/pharmacology ; *Liver/metabolism/drug effects ; Female ; Mice ; *Mice, Knockout ; *Diet, High-Fat ; *Obesity/metabolism ; Triglycerides/blood ; Diet, Fat-Restricted ; Mice, Inbred C57BL ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism ; }, abstract = {BACKGROUND: Our mechanistic understanding on metabolic beneficial effects of dietary polyphenols has been hampered for decades due to the lack of functional receptors for those compounds and their extremely low plasma concentrations. Recent studies by our team and others suggest that those dietary polyphenols target gut microbiome, and gut-liver axis and that hepatic fibroblast factor 21 (FGF21) serves as a common target for various dietary interventions.<br><br>METHODS: Utilizing liver-specific FGF21 null mice (lFgf21[-/-]), we are asking a straightforward question: Is hepatic FGF21 required for curcumin or resveratrol, two typical dietary polyphenols, in exerting their metabolic beneficial effect in obesogenic diet-induced obesity mouse models.<br><br>RESULTS: On low-fat diet feeding, no appreciable defect on glucose disposal was observed in male or female lFgf21[-/-] mice, while fat tolerance was moderately impaired in male but not in female lFgf21[-/-] mice, associated with elevated random and fasting serum triglyceride (TG) levels, and reduced hepatic expression of Ehhadh and Ppargc1a, which encodes the two downstream effectors of FGF21. On high-fat-high-fructose (HFHF) diet challenge, Fgf21[fl/fl] but not lFgf21[-/-] mice exhibited response to curcumin intervention on reducing fasting serum TG, and on improving fat tolerance. Resveratrol intervention also affected FGF21 expression or its downstream effectors. Metabolic beneficial effects of resveratrol intervention observed in HFHF diet-challenged Fgf21[fl/fl] mice were either absent or attenuated in lFgf21[-/-] mice.<br><br>CONCLUSION AND SIGNIFICANCE: We conclude that hepatic FGF21 is required for curcumin or resveratrol in exerting their major metabolic beneficial effect. The recognition that FGF21 as the common target of dietary intervention, demonstrated in current as well as previous investigations, brings us a novel angle in understanding metabolic disease treatment and prevention. It remains to be further explored how various dietary interventions regulate FGF21 expression and function, via certain common or unique gut-liver or gut-brain-liver axis.}, }
@article {pmid39929718, year = {2025}, author = {Zhu, W and Chang, L and Zhao, C and Cai, B and Sui, L and Shen, C and Li, H and Wang, B and Jiang, J}, title = {Phylosymbiosis and Parallel Geographical Patterns in the Gut Microbiota of Desert-Dwelling Amphibians and Reptiles.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.12963}, pmid = {39929718}, issn = {1749-4877}, abstract = {Variation patterns in gut microbial diversity among host species and populations offer valuable insights into the mechanisms underlying environment-host-microbiome interactions. However, the extent to which host phylogeny and geography drive these variation patterns in animal gut microbiota remains an open question. Amphibians and reptiles are important models to address this issue. Using 194 gut microbial samples of three amphibian and four reptile species inhabiting the Tarim Desert, we demonstrated phylosymbiosis in these animals, which was associated with heterogeneous selection and dispersal limitation. In interpopulation comparisons, Bufotes pewzowi and Teratoscincus przewalskii exhibited geography-dependent variations in their gut microbiota, particularly in relation to longitude and annual precipitation. These geographical patterns were linked to the heterogeneous selection of microbiota. Interestingly, the microbiota of B. pewzowi and T. przewalskii showed parallel variations with longitude, suggesting common selective pressures on amphibian and reptile microbiota. Finally, we found host genetic background did not account for the geographical pattern in their gut microbiota, even though it was also associated with geographical factors. This suggested environment-microbe interaction as a potential and independent ecological pathway mediating the associations between the environment and animals. Overall, these findings extend our understanding of variation patterns in gut microbiota and shed light on the underlying mechanisms.}, }
@article {pmid39929522, year = {2025}, author = {Morcilio, M and Reibel, YG and Theis-Mahon, N and Thelen, RM and Arnett, MC}, title = {Oral and General Health Implications of Alcoholism: A review of the literature.}, journal = {Journal of dental hygiene : JDH}, volume = {99}, number = {1}, pages = {41-54}, pmid = {39929522}, issn = {1553-0205}, mesh = {Humans ; *Alcoholism/complications ; *Oral Health ; Periodontal Diseases ; Neoplasms ; Oral Hygiene ; Health Status ; }, abstract = {Purpose The purpose of this narrative review of the literature was to examine the current evidence on alcoholism and the consequences on oral and general health, in addition to implications to enhance dental hygiene practice for individuals with alcohol use disorder (AUD).Methods The search was developed for Medline (via Ovid) and then translated to Cinahl, Scopus, and Web of Science Core Collection. Search results were limited to 2016-present, humans, and English language. Results were exported to EndNote 21 (Clarivate Analytics) for deduplication and uploaded to Rayyan for screening. Two reviewers independently screened titles and abstracts against the inclusion criteria and conflicts were discussed until consensus. A second set of reviewers independently screened titles and abstracts, conflicts were discussed until consensus.Results Of the 406 articles, 383 were excluded. A total of 23 articles were included and categorized into five domains: general health (n=6), screening tools and education (n=5), oral health (n=4), periodontal diseases and conditions (n=4), and cancer (n=4). General health conditions identified included: cardiovascular events, ischemic stroke, hemorrhagic stroke, liver cirrhosis, pancreatitis, injuries sustained from traffic accidents, and secondary cancers. Microbial dysbiosis was identified in the gut microbiome, respiratory tract and oral/gut. Oral conditions included: AUD risk of poor oral hygiene, bruxism symptoms/tooth wear, necrotizing periodontal diseases and peri-implant disease. The AUDIT-C was found to be a reliable screening tool to identify patients at risk of hazardous alcohol consumption in the dental setting.Conclusion Excessive alcohol consumption increases morbidity and mortality risk due to the association of chronic health conditions, inflammation and secondary cancers.}, }
@article {pmid39929417, year = {2025}, author = {Ur Rahman Shah, SA and Hao, Y and Tang, B and Ahmad, M and He, D and Nabi, G and Zheng, J and Wan, X and Wang, C and Wang, K}, title = {The Association of Seasonal Dietary Shift with Fecal Metabolome and Microbiota in the Captive Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis).}, journal = {Environmental research}, volume = {}, number = {}, pages = {121082}, doi = {10.1016/j.envres.2025.121082}, pmid = {39929417}, issn = {1096-0953}, abstract = {The gut microbiota can act as a buffer against changes in energy and food availability and adapt plastically to fluctuations in the host's diet. However, it is unknown how changes in the gut microbiome with the seasons impact microbial metabolism and the accessibility of nutrients to hosts. The study utilized 16S rRNA and UHPLC-MS/MS approaches to examine seasonal fecal metabolome variations in the captive Yangtze finless porpoises (YFPs) to determine if these variations are linked to nutrient intake or gut microbiome composition changes. The YFPs were mostly fed a frozen and live fish diet, with different food intakes yearly. We found that gut microbial diversity remained constant, but community structure varied seasonally. Firmicutes and Cyanobacteria were higher in winter, Actinobacteria in spring and fall, and proteobacteria in summer. The genus Paeniclostridium was significantly higher in the spring season, Romboutsia and Clostridium_sensu_stricto_13 were significantly higher in the summer, while Terrisporobacter and Macrococcus were significantly higher in the fall group. The study reported that seasonal dietary variation significantly impacted the fecal metabolome by affecting the metabolism, including energy, amino acid, carbohydrate, and nucleotide metabolism of the captive YFP. Moreover, significant correlations between metabolome and microbiome were found, and these correlations may indicate that the captive YFP has adapted to cope with dietary variations and enhance energy acquisition. These findings improve our knowledge of the link between microbiota, diet, metabolites, and the physiology of the host and suggest that gut microbial populations may adapt continuously to changes in diet.}, }
@article {pmid39929240, year = {2025}, author = {Ramchandar, N and Bradley, JS}, title = {Clinical Application of Bacteriophage Therapy in Children.}, journal = {Pediatrics}, volume = {}, number = {}, pages = {}, doi = {10.1542/peds.2024-068838}, pmid = {39929240}, issn = {1098-4275}, abstract = {Bacteriophages are highly specific in targeting single pathogens in the treatment of bacterial infections and thus offer a promising alternative to antibiotic therapies with the potential for essentially no impact to the child's own microbiome. Bacteriophages have been evaluated by investigators for several pathogens and tissue site infections in adults, but data in children are lacking. The application of this therapy in pediatrics provides an extraordinary opportunity to redesign our approach to directed, precision medicine antimicrobial therapy for infants and children for both acute infections and for chronic infections, particularly those caused by multidrug-resistant pathogens. In this therapeutic approach, a bacteriophage preparation would be selected exclusively for and limited to the patient's specific pathogen, thus minimizing the collateral damage to the child's microbiome, as often demonstrated with antibiotic therapy. In the following article, we describe these novel anti-infective biological agents, review the recent literature, discuss practical considerations and limitations, and share potential applications for both topical and systemic administration of bacteriophages, either as primary therapy or in combination with traditional antibiotics. Additionally, important areas of interest for pediatric research are discussed.}, }
@article {pmid39929003, year = {2025}, author = {Bakir-Gungor, B and Temiz, M and Canakcimaksutoglu, B and Yousef, M}, title = {Prediction of colorectal cancer based on taxonomic levels of microorganisms and discovery of taxonomic biomarkers using the Grouping-Scoring-Modeling (G-S-M) approach.}, journal = {Computers in biology and medicine}, volume = {187}, number = {}, pages = {109813}, doi = {10.1016/j.compbiomed.2025.109813}, pmid = {39929003}, issn = {1879-0534}, abstract = {Colorectal cancer (CRC) is one of the most prevalent forms of cancer globally. The human gut microbiome plays an important role in the development of CRC and serves as a biomarker for early detection and treatment. This research effort focuses on the identification of potential taxonomic biomarkers of CRC using a grouping-based feature selection method. Additionally, this study investigates the effect of incorporating biological domain knowledge into the feature selection process while identifying CRC-associated microorganisms. Conventional feature selection techniques often fail to leverage existing biological knowledge during metagenomic data analysis. To address this gap, we propose taxonomy-based Grouping Scoring Modeling (G-S-M) method that integrates biological domain knowledge into feature grouping and selection. In this study, using metagenomic data related to CRC, classification is performed at three taxonomic levels (genus, family and order). The MetaPhlAn tool is employed to determine the relative abundance values of species in each sample. Comparative performance analyses involve six feature selection methods and four classification algorithms. When experimented on two CRC associated metagenomics datasets, the highest performance metric, yielding an AUC of 0.90, is observed at the genus taxonomic level. At this level, 7 out of top 10 groups (Parvimonas, Peptostreptococcus, Fusobacterium, Gemella, Streptococcus, Porphyromonas and Solobacterium) were commonly identified for both datasets. Moreover, the identified microorganisms at genus, family, and order levels are thoroughly discussed via refering to CRC-related metagenomic literature. This study not only contributes to our understanding of CRC development, but also highlights the applicability of taxonomy-based G-S-M method in tackling various diseases.}, }
@article {pmid39928944, year = {2025}, author = {Kim, J and Choi, Y and Song, Y and Park, W}, title = {Smartphone-Based Telemonitoring for Better Oral Health With Toothbrushes: 6-Month Randomized Controlled Trial.}, journal = {Journal of medical Internet research}, volume = {27}, number = {}, pages = {e65128}, doi = {10.2196/65128}, pmid = {39928944}, issn = {1438-8871}, mesh = {Humans ; *Smartphone ; *Toothbrushing/instrumentation/methods ; Female ; Male ; *Oral Health ; Adult ; Middle Aged ; Telemedicine/instrumentation ; Republic of Korea ; Oral Hygiene/methods/instrumentation ; Prospective Studies ; Halitosis/prevention &amp; control ; }, abstract = {BACKGROUND: A toothbrush device that telemonitors toothbrushing is a technologically advanced solution providing personalized feedback on toothbrushing habits and oral hygiene. These devices integrate smartphone apps to enhance oral health compliance through dental professional feedback.<br><br>OBJECTIVE: This 6-month prospective randomized controlled trial aimed to compare the clinical effectiveness, defined as improved oral hygiene measured by plaque reduction and halitosis control, of an interactive telemonitoring toothbrush (ITT), an oscillating-rotating power toothbrush (ORT), and a manual toothbrush (MT).<br><br>METHODS: Participants were recruited offline from the Department of Advanced General Dentistry at Yonsei University Dental Hospital, South Korea. A total of 150 participants were randomly assigned to 3 groups (50 participants each): (1) an ITT connected to a smartphone app providing real-time feedback and weekly dental professional reviews, (2) an ORT with smartphone-based guidance requiring participants to send weekly brushing records via screenshots, and (3) an MT with a brushing diary for review. Data collection occurred in clinical settings. Primary outcomes included plaque reduction measured using the Simple Hygiene Score (SHS), while secondary outcomes included plaque reduction measured using the Turesky modification of the Quigley-Hein plaque index (QHI), reductions in halitosis, and changes in oral microbiota. All outcomes were assessed at baseline and 1 month, 3 months, and 6 months.<br><br>RESULTS: A total of 150 participants completed the study. Over 6 months, the SHS increased in the MT group (mean 3.16, SD 4.86 to mean 5.66, SD 5.20) but significantly decreased in the ITT group (mean 3.47, SD 5.50 to mean 2.27, SD 3.82; P=.004). Similarly, QHI decreased more in the ITT group (mean 1.79, SD 0.72 to mean 0.85, SD 0.63) than in the ORT (P<.001) and MT (P<.001) groups. Regarding microbiota, there were no significant differences in high-risk periodontal microbiota or the ratio of caries-risk to anticaries microbiota between the ITT and ORT groups. However, in the MT group, the ratio of caries-risk microbiota was significantly higher at the 3-month (P<.001) and 6-month (P=.005) recalls than at baseline and at the 3-month (P=.048) and 6-month (P=.03) recalls than at the 1-month recall. Poststudy questionnaires indicated that 45 of 50 ITT participants (92%) and 37 of 50 ORT participants (76%) reported improved brushing ability. The most effective feature in the ITT group was brushing training, while participants in the ORT group cited the brushing guide as most useful (P<.001). Satisfaction scores were higher in the ORT group (mean 7.90, SD 1.21) than in the ITT group (mean 7.15, SD 1.66; P=.004). The number of brushing events decreased significantly in the ORT group (P=.02), while brushing duration increased in the MT group (P=.01).<br><br>CONCLUSIONS: ITTs enable better oral hygiene management than MTs through dental professional feedback. However, further studies are needed to optimize feedback intervals and improve long-term adherence.<br><br>TRIAL REGISTRATION: Clinical Research Information Service (CRIS), Republic of Korea, KCT0009094; https://cris.nih.go.kr/cris/search/detailSearch.do?seq=26110&amp;search_page=L.}, }
@article {pmid39928757, year = {2025}, author = {Cherwin, CH and Hoang, J and Roberts, EK and Mangalam, A}, title = {Gut Microbiome and Symptom Burden in Obese and Non-Obese Women Receiving Chemotherapy for Breast Cancer.}, journal = {Biological research for nursing}, volume = {}, number = {}, pages = {10998004251318397}, doi = {10.1177/10998004251318397}, pmid = {39928757}, issn = {1552-4175}, abstract = {Purpose: Obese women with breast cancer experience high symptom burden, poor quality of life, and increased mortality compared to non-obese women with breast cancer. Obesity-related changes to the bacteria of the gut, the GI microbiome, may be one such mechanism for these differences in outcomes. The purpose of this work is to report symptom burden and GI microbiome composition between obese and non-obese women with breast cancer to identify potential microbial influences for symptom severity. Methods: 59 women with breast cancer (26 obese, 33 non-obese) provided symptom reports using the Memorial Symptom Assessment Scale and stool samples for 16S analysis one week after receiving chemotherapy. Symptom reports were summarized and examined for differences based on obesity. Fecal microbiome analysis was compared between groups using alpha-diversity (Shannon index), beta-diversity (Principal Coordinate Analysis with weighted UniFrac distances), and LASSO analysis of abundance of bacterial species. Results: While symptom burden was high, it did not differ based on obesity status. Alpha- and beta-diversity did not find significant differences based on obesity, but LASSO analysis identified eight bacteria to be significantly enriched in obese participants: Collinsella aerofacien, Prevotella 7, Coprobacillus cateniformis, Ruminococcus torques group, Agathobacter, Frisingicoccus, Roseburia inulinivorans, and Monoglobus pectinilyticus. Conclusions: Identifying biologic mechanisms driving symptoms is necessary for the development of therapies to reduce cancer-related symptom burden. While obesity may alter the GI microbiome and influence symptom burden in women with breast cancer, these effects may be outweighed by the effects of chemotherapy on the gut.}, }
@article {pmid39928508, year = {2025}, author = {Bae, J and Campbell, A and Hein, M and Hillis, SL and Grice, E and Rakel, BA and Gardner, SE}, title = {Relationship of opioid tolerance to patient and wound factors, and wound micro-environment in patients with open wounds.}, journal = {Journal of wound care}, volume = {34}, number = {Sup2}, pages = {S6-S16}, doi = {10.12968/jowc.2023.0215}, pmid = {39928508}, issn = {0969-0700}, mesh = {Humans ; Male ; Female ; Cross-Sectional Studies ; Middle Aged ; *Analgesics, Opioid/therapeutic use ; *Wounds and Injuries ; Adult ; *Drug Tolerance ; Aged ; Microbiota/drug effects ; Pain Measurement ; Depression ; }, abstract = {OBJECTIVE: Opioid tolerance is a criterion for opioid use disorder, which is currently an epidemic in the US. Individuals with open wounds are frequently administered opioids; however, the phenomenon of opioid tolerance has not been examined in the context of wounds. The purpose of this exploratory study was to compare patient/wound factors, wound microbiome and inflammatory mediators between individuals who were opioid-tolerant versus those who were not opioid-tolerant.<br><br>METHOD: Patients with acute open wounds were enrolled in this cross-sectional study. All study data were collected before and during a one-time study dressing change.<br><br>RESULTS: The study included a total of 385 participants. Opioid-tolerant participants were significantly younger (p<0.0001); had higher levels of depression (p=0.0055) and anxiety (p=0.0118); had higher pain catastrophising scores (p=0.0035); reported higher resting wound pain (p<0.0001); had a higher number of wounds of <30 days' duration (p=0.0486); and had wounds with lower bacterial richness (p=0.0152) than participants who were not opioid-tolerant. A backward elimination logistic regression model showed that four predictors-resting wound pain, age, bacterial richness and depression-were the most important variables in predicting opioid-tolerance status.<br><br>CONCLUSION: These findings provide the first insights into the phenomenon of opioid tolerance in the context of open wounds. This study provides findings from which to guide hypothesis-driven research in the future.}, }
@article {pmid39928324, year = {2025}, author = {Hourigan, SK and Mueller, NT and Dominguez-Bello, MG}, title = {Can Vaginal Seeding Improve Health Outcomes of Infants Born by Cesarean Delivery?.}, journal = {JAMA pediatrics}, volume = {}, number = {}, pages = {}, doi = {10.1001/jamapediatrics.2024.6893}, pmid = {39928324}, issn = {2168-6211}, }
@article {pmid39928205, year = {2025}, author = {Clerici, L and Bottari, D and Bottari, B}, title = {Gut Microbiome, Diet and Depression: Literature Review of Microbiological, Nutritional and Neuroscientific Aspects.}, journal = {Current nutrition reports}, volume = {14}, number = {1}, pages = {30}, pmid = {39928205}, issn = {2161-3311}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Probiotics ; *Depression/diet therapy ; *Diet ; *Brain-Gut Axis/physiology ; Prebiotics ; Mental Health ; Tryptophan/metabolism ; }, abstract = {PURPOSE OF REVIEW: This review explores the intricate relationships among the gut microbiota, dietary patterns, and mental health, focusing specifically on depression. It synthesizes insights from microbiological, nutritional, and neuroscientific perspectives to understand how the gut-brain axis influences mood and cognitive function.<br><br>RECENT FINDINGS: Recent studies underscore the central role of gut microbiota in modulating neurological and psychological health via the gut-brain axis. Key findings highlight the importance of dietary components, including probiotics, prebiotics, and psychobiotics, in restoring microbial balance and enhancing mood regulation. Different dietary patterns exhibit a profound impact on gut microbiota composition, suggesting their potential as complementary strategies for mental health support. Furthermore, mechanisms like tryptophan metabolism, the HPA axis, and microbial metabolites such as SCFAs are implicated in linking diet and microbiota to depression. Clinical trials show promising effects of probiotics in alleviating depressive symptoms. This review illuminates the potential of diet-based interventions targeting the gut microbiota to mitigate depression and improve mental health. While the interplay between microbial diversity, diet, and brain function offers promising therapeutic avenues, further clinical research is needed to validate these findings and establish robust, individualized treatment strategies.}, }
@article {pmid39927989, year = {2025}, author = {Zhang, Y and Hu, T and Wang, X and Sun, N and Cai, Q and Kim, HY and Fan, Y and Liu, D and Guan, X}, title = {Profiles of gut microbiota and metabolites for high risk of transgenerational depression-like behavior by paternal methamphetamine exposure.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {39}, number = {3}, pages = {e70386}, doi = {10.1096/fj.202402839R}, pmid = {39927989}, issn = {1530-6860}, support = {82271531//MOST | National Natural Science Foundation of China (NSFC)/ ; 82211540400//MOST | National Natural Science Foundation of China (NSFC)/ ; BK20240726//JST | Natural Science Foundation of Jiangsu Province (Jiangsu Natural Science Foundation)/ ; ZD202302//Traditional Chinese Medicine Technology Development Project of Jiangsu Province/ ; }, mesh = {Animals ; *Methamphetamine/toxicity/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice ; Male ; *Depression/metabolism/chemically induced ; *Paternal Exposure/adverse effects ; Behavior, Animal/drug effects ; Mice, Inbred C57BL ; Central Nervous System Stimulants/pharmacology/toxicity ; Female ; }, abstract = {Parental substance abuse increases the risk of neurological and psychiatric disorders in offsprings. However, its underlying mechanism remains elusive. Our previous study demonstrated that long-term exposure to methamphetamine (Meth), a psychostimulant drug with high addiction potential, remarkably alters the gut microbiome and metabolites in male mice, which contribute to Meth-induced anxiety-like behaviors. The current study aimed to investigate whether gut microbiota and metabolism serve as potential peripheral targets for transgenerational mental problems by paternal Meth exposure. We found that paternal Meth exposure induced depression-like behaviors both in the first (F1) and the second (F2) generations of male mice. Further, the depletion of gut bacteria through antibiotic treatments normalized the depression-like behaviors to normal levels in both F1 and F2 male mice. Then, alterations in gut bacterial composition were observed in both F1 and F2 male mice. Specifically, Eubacterium_ruminantium_group, Enterorhabdus, Alloprevotella, and Parabacteroides were the commonly affected bacterial taxa in F1 and F2 male mice. In addition, the results of alterations in gut metabolism showed that LPC 14:1-SN1 emerged as the consistently altered metabolite in the colons of F1 and F2 male mice. Taken together, our findings provide the first evidence that paternal Meth exposure enhances depression-like behaviors in F1 and F2 male mice, potentially mediated by the gut microbiome and metabolism.}, }
@article {pmid39927883, year = {2025}, author = {Rout, S and Dash, R and Satish, V and Venugopal, G and Rao, BN and Bandhyopadhyay, D and Bhoi, SK and Ramadass, B}, title = {Exploring the role of acylated ghrelin and gut microbiome in delineating cognitive health in the elderly.}, journal = {Aging}, volume = {null}, number = {}, pages = {}, doi = {10.18632/aging.206200}, pmid = {39927883}, issn = {1945-4589}, abstract = {INTRODUCTION: With increased life expectancy, there is an increase in aging population and prevalence of dementia. Ghrelin is a key regulator of spatial memory and cognition. The gut microbiome may affect the circulating levels of unacylated ghrelin (UAG) and acylated ghrelin (AG). Thus, we explore the potential association of the gut microbiome, AG, and cognitive health in the aging dementia patient.<br><br>METHODS: 40 dementia patients and 40 controls were recruited. Fecal Microbiome analysis using 16S rRNA sequencing was performed on 18 samples. A mixed-method approach was employed for robust interpretation.<br><br>RESULTS: Dementia patients had an increased serum AG and AG/UAG ratio. With the increase in AG among dementia subjects, a significant decrease in species richness was observed. Bifidobacterium longum, Eubacterium biforme, Fecalibacterium prausnitzii, Lactobacillus ruminis, and Prevotella copri contributed to substantial differences in beta-diversity. Blautia obeum was associated with Mini-Mental State Examination (MMSE), and Fecalibacterium prausnitzii was associated with Montreal Cognitive Assessment (MoCA) Scale.<br><br>DISCUSSION: This pilot study indicates a complex interaction between AG, gut microbiome, and cognitive scores. Increased AG corresponds to both dementia and gut dysbiosis, intricately interconnecting the gut-brain axis. The circulating AG and associated gut microbiome might be a putative biomarker for dementia.}, }
@article {pmid39927868, year = {2025}, author = {Zouiouich, S and Wan, Y and Vogtmann, E and Porras, C and Abnet, CC and Shi, J and Sinha, R}, title = {Sample size estimations based on human microbiome temporal stability over six months: a shallow shotgun metagenome sequencing analysis.}, journal = {Cancer epidemiology, biomarkers &amp; prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology}, volume = {}, number = {}, pages = {}, doi = {10.1158/1055-9965.EPI-24-0839}, pmid = {39927868}, issn = {1538-7755}, abstract = {BACKGROUND: Biological factors impact the human microbiome, highlighting the need for reasonably estimating sample sizes in future population studies.<br><br>METHODS: We assessed the temporal stability of fecal microbiome diversity, species composition, and genes and functional pathways through shallow shotgun metagenome sequencing. Using intraclass correlation coefficients (ICC), we measured biological variability over six months. We estimated case numbers for 1:1 or 1:3 matched case-control studies, considering significance levels of 0.05 and 0.001 with 80% power, based on the collected fecal specimens per participant.<br><br>RESULTS: The fecal microbiome's temporal stability over six months varied (ICC <0.6) for most alpha and beta diversity metrics. Heterogeneity was seen in species, genes, and pathways stability (ICC 0.0-0.9). Detecting an odds ratio of 1.5 per standard deviation required 1,000-5,000 cases (0.05 significance for alpha and beta; 0.001 for species, genes, pathways) with equal cases and controls. Low-prevalent species needed 15,102 cases; high-prevalent species required 3,527. Similar needs applied to genes and pathways. In a 1:3 matched case-control study with one fecal specimen, 10,068 cases were needed for low-prevalent species; 2,351 for high-prevalent species. For odds ratios of 1.5 with multiple specimens, cases needed for low-prevalent species were 15,102 (one specimen), 8,267 (two specimens), and 5,989 (three specimens).<br><br>CONCLUSIONS: Detecting disease associations requires a large number of cases. Repeating prediagnostic samples and matching cases to more controls could decrease the needed number of cases for such detections.<br><br>IMPACT: Our results will help future epidemiologic studies design and implement well-powered microbiome studies.}, }
@article {pmid39927858, year = {2024}, author = {Sankaran, K and Kodikara, S and Li, JJ and Cao, KL}, title = {Semisynthetic simulation for microbiome data analysis.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, doi = {10.1093/bib/bbaf051}, pmid = {39927858}, issn = {1477-4054}, support = {R01GM152744//National Institutes of Health/National Institutes for General Medical Sciences/ ; GM112625/NH/NIH HHS/United States ; DBI-1846216//National Science Foundation/ ; GNT2025648//National Health and Medical Research Council/ ; //Maurice H. Belz Fund/ ; }, mesh = {*Microbiota ; Humans ; Computer Simulation ; High-Throughput Nucleotide Sequencing ; Computational Biology/methods ; Data Analysis ; Software ; }, abstract = {High-throughput sequencing data lie at the heart of modern microbiome research. Effective analysis of these data requires careful preprocessing, modeling, and interpretation to detect subtle signals and avoid spurious associations. In this review, we discuss how simulation can serve as a sandbox to test candidate approaches, creating a setting that mimics real data while providing ground truth. This is particularly valuable for power analysis, methods benchmarking, and reliability analysis. We explain the probability, multivariate analysis, and regression concepts behind modern simulators and how different implementations make trade-offs between generality, faithfulness, and controllability. Recognizing that all simulators only approximate reality, we review methods to evaluate how accurately they reflect key properties. We also present case studies demonstrating the value of simulation in differential abundance testing, dimensionality reduction, network analysis, and data integration. Code for these examples is available in an online tutorial (https://go.wisc.edu/8994yz) that can be easily adapted to new problem settings.}, }
@article {pmid39927795, year = {2025}, author = {Huang, D and Chen, Y and Li, C and Yang, S and Lin, L and Zhang, X and Su, X and Liu, L and Zhao, H and Luo, T and Cai, S and Ren, Q and Dong, H}, title = {Variations in salivary microbiome and metabolites are associated with immunotherapy efficacy in patients with advanced NSCLC.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0111524}, doi = {10.1128/msystems.01115-24}, pmid = {39927795}, issn = {2379-5077}, abstract = {Lung cancer is a leading cause of cancer mortality, with non-small cell lung cancer (NSCLC) comprising the majority of cases. Despite the advent of immune checkpoint inhibitors (ICIs), a significant number of patients fail to achieve a durable response, highlighting the need to understand the factors influencing treatment efficacy. Saliva samples and tumor samples were collected from 20 NSCLC patients. The salivary microbiota was profiled using metagenomic next-generation sequencing, and metabolites were analyzed via liquid chromatography-mass spectrometry to identify correlations among bacteria, metabolites, and immunotherapy responses. Immunohistochemistry (IHC) analysis of tissue samples verified the result. Besides, in vitro experiments and tumor tissue microarray, including 70 NSCLC patients, were utilized to further explore the potential mechanism linking the oral microbiome and immunotherapy efficacy. The study revealed several differential species and distinct metabolite compositions between responders and non-responders to ICI therapy in NSCLC and explored correlations and mechanisms between microbiota metabolites and immunotherapy resistance. Notably, it was found that several Neisseria and Actinomyces species were significantly enriched in responders and identified lipids and lipid-like molecules associated with PD-L1 expression levels and treatment outcomes. Importantly, several differential lipid molecules were associated with differential species. Further, in vitro experiments and IHC experiments indicated that abnormal fat metabolism linked to dysbiosis is correlated with immunotherapy resistance through regulation of CD8[+] T cell activity/infiltration and PD-L1 expression. Specific saliva microbiome and its associated lipids metabolites are significantly associated with the efficacy of ICI-based therapy in lung cancer. Our findings suggest that oral microbiome modulation and targeting lipid metabolism could improve immunotherapy responses, offering new avenues for personalized treatment strategies.IMPORTANCEIn non-small cell lung cancer, our study links specific salivary microbiome profiles and related lipid metabolites to the efficacy of immune checkpoint inhibitor (ICI) therapies. Responders showed enrichment of certain Neisseria and Actinomyces species and distinct lipid compositions. These lipids correlate with PD-L1 expression and CD8[+] T cell activity, affecting treatment outcomes. Our results imply that modulating the oral microbiome and targeting lipid metabolism may enhance ICI effectiveness, suggesting novel personalized therapeutic approaches.}, }
@article {pmid39927763, year = {2025}, author = {Dandeu, LNR and Lachovsky, J and Sidlik, S and Marenco, P and Orschanski, D and Aguilera, P and Vázquez, M and Carballo, MdP and Fernández, E and Penas-Steinhardt, A and Chasseing, NA and Labovsky, V}, title = {Relevance of oncobiome in breast cancer evolution in an Argentine cohort.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0059724}, doi = {10.1128/msphere.00597-24}, pmid = {39927763}, issn = {2379-5042}, abstract = {UNLABELLED: Breast cancer is the leading cause of cancer deaths in women worldwide, with about 20,000 cases annually in Argentina. While age, diet, and genetics are known risk factors, most breast cancer cases have unknown causes, necessitating the discovery of new risk factors. The aim of this study was the analysis of the prognostic relevance of the oncobiome in Argentinean breast cancer patients. Sequencing of the V4 region 16S rRNA gene was performed on 34 primary breast tumor samples, using bioinformatic and statistical analyses to identify bacteria and hypothetical pathways. Each sample presented a unique microbial profile, with Proteobacteria being the most abundant phylum. Tumors >2 cm showed greater alpha diversity with increased nucleotide biosynthesis. Moreover, progesterone-receptor tumors showed differences in beta diversity, being progesterone receptor-positive tumors that had the highest expression of Acinetobacter and Moraxella. In disease progression, the phylum Chloroflexi was prevalent in tumors of surviving patients. Acinetobacter and Cloacibacterium genera were significantly higher in patients without events and those without metastasis. We found that nucleotide and cell-structure biosynthesis, and lipid metabolism pathways were enriched in tumors with poor progression, whereas amino-acid degradation was increased in tumors of surviving patients. This finding is an indication that tumor cells are taking advantage of this effect of the microbiome during tumor progression. We conclude that oncobiome is dysbiotic in these patients, with distinct patterns in those with poor progression. Suggesting a link between the oncobiome and cancer progression, paving the way for new therapies to improve patient quality of life and survival.<br><br>IMPORTANCE: This is the first study to investigate the relevance of the oncobiome in the evolution of breast cancer in a cohort of Argentine patients. It also highlights the need for further research in this area to improve our understanding of the role of the microbiome in this disease and potentially identify new therapeutic targets or prognostic indicators. Understanding the complex interaction between the microbiome, the tumor microenvironment, and the pathogenesis of breast cancer holds the promise of more personalized and effective treatment approaches in the future.}, }
@article {pmid39927761, year = {2025}, author = {Frame, LA}, title = {Fiber, microbiomes, and SCFAs: insights from companion animal models to inform personalized nutrition.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0145424}, doi = {10.1128/msystems.01454-24}, pmid = {39927761}, issn = {2379-5077}, abstract = {A recent study by A. Bhosle, M. I. Jackson, A. M. Walsh, E. A. Franzosa, et al. (mSystems 10:e00452-24, 2024, https://doi.org/10.1128/msystems.00452-24) enhances our understanding of dietary fiber's impact on the gut microbiome and metabolome in companion animals, uncovering individual variations in microbial and metabolic responses. By examining short-chain fatty acid (SCFA) profiles in response to fiber, the authors reveal potential therapeutic benefits of tailored dietary interventions, such as enhanced gut and immune health. These findings resonate with human microbiome research, where dietary fiber has shown health benefits through microbial diversity and SCFA production. The study emphasizes the potential for breed-specific responses to fiber, given the variation in microbiome composition and physiology across breeds. Such insights align with emerging concepts of personalized nutrition, offering an opportunity to develop precision dietary strategies that address specific health needs in both veterinary and human contexts. This foundational research positions dietary fiber as a valuable tool in preventive health, providing a roadmap for future studies to refine individualized approaches for gut microbiome modulation.}, }
@article {pmid39927333, year = {2024}, author = {Safika, S and Indrawati, A and Hidayat, R and Puarada, ARR}, title = {Characterizing the gut microbiome of birds-of-paradise in the northwest lowland of Papua Island.}, journal = {Open veterinary journal}, volume = {14}, number = {12}, pages = {3345-3354}, pmid = {39927333}, issn = {2218-6050}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteria/isolation &amp; purification/classification/genetics ; Indonesia ; Feces/microbiology ; Passeriformes/microbiology ; }, abstract = {BACKGROUND: Birds-of-paradise, renowned for their stunning plumage and intricate mating rituals, have been extensively studied for their external characteristics. However, the microbial communities inhabiting their digestive tracts remain largely unexplored. The gut microbiome plays a vital role in host health and physiology, influencing digestion, nutrient absorption, and immune function. Understanding the microbiome of birds-of-paradise, particularly in their unique tropical rainforest habitats, may offer valuable insights into their adaptation and overall health.<br><br>AIM: This study aims to characterize the gut microbiome of birds-of-paradise and to explore the relationship between microbiome and host.<br><br>METHODS: Fecal samples were collected from Jayapura Regency, Indonesia, with non-invasive sampling methods. DNA was extracted using the DNeasy PowerSoil Pro Kit. Shotgun metagenomic sequencing was performed on the MGI DNBSEQ-G400 platform to obtain DNA sequences. DNA sequences were analyzed using DIAMOND followed by MEGAN6 to provide insights into the relative abundance of bacterial taxa within the microbiome.<br><br>RESULTS: Using Operational Taxonomy Unit analysis we identified 1,398,117 sequences from 5,048,280 initial sequences. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Acidobacteria were the dominant phyla, with other phyla present in smaller amounts. Burkholderiales, Hyphomicrobiales, Sphingobacteriales, and Enterobacterales were dominant orders, each with specific functional roles. Family and Genus-Level Abundance: Flavobacteriaceae, Comamonadaceae, and Sphingobacteriaceae were dominant families, while Flavobacterium, Delftia, and Pedobacter were dominant genera. Delftia sp., Pedobacter sp., Klebsiella pneumoniae, Achromobacter sp., Bacillus pumilus, Rhizobium sp., and Brevundimonas sp. were among the most abundant species.<br><br>CONCLUSION: The microbiome in the gut of birds-of-paradise is characterized by a diverse community of bacteria, fungi, and other microorganisms. The abundance of specific orders, families, and genera varies between samples, suggesting that differences in diet, habitat, or host genetics may influence microbiome composition. The findings reveal a diverse and complex microbial community that likely plays a crucial role in host health and physiology.}, }
@article {pmid39927261, year = {2025}, author = {Hou, S and Jiang, Y and Zhang, F and Cheng, T and Zhao, D and Yao, J and Wen, P and Jin, L and Huang, S}, title = {Unveiling early-life microbial colonization profile through characterizing low-biomass maternal-infant microbiomes by 2bRAD-M.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1521108}, pmid = {39927261}, issn = {1664-302X}, abstract = {INTRODUCTION: The microbial composition of human breast milk and infant meconium offers critical insights into the early microbial colonization profile, and it greatly contributes to the infant's immune system and long-term health outcomes. However, analyzing these samples often faces technical challenges and limitations of low-resolution using conventional approaches due to their low microbial biomass.<br><br>METHODS: Here, we employed the type IIB restriction enzymes site-associated DNA sequencing for microbiome (2bRAD-M) as a reduced metagenomics method to address these issues and profile species-level microbial composition. We collected breast milk samples, maternal feces, and infant meconium, comparing the results from 2bRAD-M with those from both commonly used 16S rRNA amplicon sequencing and the gold-standard whole metagenomics sequencing (WMS).<br><br>RESULTS: The accuracy and robustness of 2bRAD-M were demonstrated through its consistently high correlation of microbial individual abundance and low whole-community-level distance with the paired WMS samples. Moreover, 2bRAD-M enabled us to identify clinical variables associated with infant microbiota variations and significant changes in microbial diversity across different lactation stages of breast milk.<br><br>DISCUSSION: This study underscores the importance of employing 2bRAD-M in future large-scale and longitudinal studies on maternal and infant microbiomes, thereby enhancing our understanding of microbial colonization in early life stages and demonstrating further translational potential.}, }
@article {pmid39927188, year = {2025}, author = {Scharf, E and Schlattmann, P and Stallhofer, J and Stallmach, A}, title = {Do Antibiotics Cause Inflammatory Bowel Disease? A Systematic Review and Meta-Analysis.}, journal = {Visceral medicine}, volume = {41}, number = {1}, pages = {32-47}, pmid = {39927188}, issn = {2297-4725}, abstract = {INTRODUCTION: Inflammatory bowel disease (IBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), exhibits a multifactorial pathogenesis influenced by genetic and environmental factors. Antibiotic usage has been implicated in modifying the gut microbiome, potentially leading to dysbiosis and contributing to IBD risk. Despite existing literature, the relationship remains inconclusive. This meta-analysis aimed to evaluate the association between prior antibiotic use and the onset of IBD.<br><br>METHODS: A systematic literature search in PubMed was conducted to identify studies exploring the link between antibiotic use and subsequent IBD diagnosis. Studies reporting CD, UC, or both as primary outcomes were included. The meta-analysis, performed according to PRISMA guidelines, summarized risk estimates, represented as odds ratios (ORs), and corresponding confidence intervals (CIs). Subgroup analyses involved the categorization of antibiotics and the determination of the minimum number of antibiotic therapy courses administered.<br><br>RESULTS: Out of 722 publications, 31 studies comprising 102,103 individuals met eligibility criteria. The pooled OR for IBD in those with prior antibiotic exposure was 1.40 (95% CI: 1.25-1.56). Antibiotic use was associated with an increased risk of IBD (OR: 1.52, 95% CI: 1.19-1.94). Notably, this association was confined to CD (OR: 1.50, 95% CI: 1.27-1.77), while no significant association was observed with UC (OR: 1.21, 95% CI: 1.00-1.47). Risk augmentation for IBD correlated positively with the number of antibiotic courses (OR: 1.08, 95% CI: 1.05-1.12).<br><br>CONCLUSION: Previous antibiotic use is associated with the later development of CD. A positive dose-response effect was also observed. Against this background, antibiotics should be used rationally.}, }
@article {pmid39927182, year = {2025}, author = {Takeuchi, S and Kawada, JI and Suzuki, A and Sakamoto, K and Fukuda, Y and Horiba, K and Suzuki, T and Torii, Y and Shindo, Y and Ito, Y}, title = {Metagenomic Analysis of Lung Microbiome in Patients With Interstitial Lung Diseases and Sarcoidosis: An Experimental Study.}, journal = {Health science reports}, volume = {8}, number = {2}, pages = {e70328}, pmid = {39927182}, issn = {2398-8835}, abstract = {BACKGROUND AND AIMS: Interactions between the lung microbiome and pulmonary epithelium plays a pivotal role in shaping immunity in the lung. Idiopathic pulmonary fibrosis (IPF) is the most common interstitial lung disease (ILD). Some patients with IPF develop episodic acute exacerbations often associated with microbial dysbiosis in the lungs. This study aimed to investigate etiologic agents as well as the lung microbiome in patients with ILDs and sarcoidosis.<br><br>METHODS: This study analyzed 31 patients divided into the IPF (IPF-stable, n&#x2009;=&#x2009;12), acute exacerbation of ILDs (AE-ILDs, n&#x2009;=&#x2009;6), and sarcoidosis (n&#x2009;=&#x2009;13) groups. Bronchoalveolar lavage fluid (BALF) samples were analyzed by RNA-based metagenomic next-generation sequencing (NGS) on an Illumina platform.<br><br>RESULTS: In total, 87 pathogens were detected using metagenomic NGS at the genus level. Prevotella, Streptococcus, and Veillonella dominated the BALF microbial communities, and sequence reads of these bacteria were abundant, especially in the sarcoidosis group. Conversely, only a small number of bacterial reads were detected in the AE-ILDs group, and the overall proportion of microbial composition differed from that of the other groups. No significant difference was found in community diversity (&#x3b1;-diversity) among the groups, whereas the structural similarity of the microflora (&#x3b2;-diversity) differed significantly between the AE-ILDs and sarcoidosis groups.<br><br>CONCLUSIONS: Bacterial sequence reads in BALF were smaller in both the IPF-stable and AE-ILD groups than in the sarcoidosis group. Dysbiosis in the lung microbiome has been observed in patients with AE-ILD and may be related to the progression of inflammation.}, }
@article {pmid39927018, year = {2024}, author = {Abdul, NS and Odeh, LG and Alenazi, AA and Alzahrani, JA and Almutib, AT and Soman, C}, title = {Probiotics in the Prevention and Treatment of Periodontal Diseases: A Systematic Review.}, journal = {Journal of pharmacy &amp; bioallied sciences}, volume = {16}, number = {Suppl 4}, pages = {S3302-S3307}, pmid = {39927018}, issn = {0976-4879}, abstract = {INTRODUCTION: Periodontal diseases (PDs) pose a significant challenge to dental health, leading to a growing interest in probiotics as potential therapeutic and prophylactic agents. Literature evidence has shown conflicting results on the use of probiotics in the management of PDs. Hence, this systematic review was performed to explore the effectiveness of probiotics in both the prevention and treatment of PDs by synthesizing data from relevant studies.<br><br>METHODOLOGY: Various databases were searched using appropriate MeSH keywords as per the PRISMA protocol. Studies were included only if they met certain criteria. Two reviewers independently extracted data variables from the included literature. The risk of bias 2.0 tool was employed to assess the methodological quality of the included studies.<br><br>RESULTS: In total, 21 studies were considered eligible and included in the review. It was observed that 17 studies reported a statistically significant improvement in both periodontitis and gingivitis among the probiotic group compared to control cohorts. The synthesized evidence from the review suggests that probiotics play a favourable role in both the prevention and treatment of PDs.<br><br>CONCLUSION: It also supports the incorporation of probiotics as a potential adjunctive therapy in PD management. However, further research is warranted to explore the specific probiotic strains, dosages, and treatment durations for optimized outcomes.}, }
@article {pmid39926803, year = {2024}, author = {Bhuvaneswarri, J and Amaldas, J and Umapathy, VR and Ramya, V}, title = {Role of TM7 in the Oral Microbiome and its Implications for Periodontal Disease: A Systematic Review.}, journal = {Journal of pharmacy &amp; bioallied sciences}, volume = {16}, number = {Suppl 4}, pages = {S3060-S3063}, pmid = {39926803}, issn = {0976-4879}, abstract = {Periodontal disease, a prevalent oral health condition, involves a complex microbial community. Advanced sequencing technologies have enabled in-depth studies of the oral microbiome, focusing on specific bacterial taxa like TM7. This systematic review analyzes the role of TM7 in the oral microbiome and its implications for periodontal disease. This review underscores TM7's importance in the oral microbiome and its potential as a target for future research on periodontal disease pathogenesis.}, }
@article {pmid39926318, year = {2025}, author = {Rågård, N and Baumwall, SMD and Paaske, SE and Hansen, MM and Høyer, KL and Mikkelsen, S and Erikstrup, C and Dahlerup, JF and Hvas, CL}, title = {Validation methods for encapsulated faecal microbiota transplantation: a scoping review.}, journal = {Therapeutic advances in gastroenterology}, volume = {18}, number = {}, pages = {17562848251314820}, pmid = {39926318}, issn = {1756-283X}, abstract = {Faecal microbiota transplantation (FMT) is increasingly used for diseases associated with a disrupted intestinal microbiome, mainly Clostridioides difficile infection. Encapsulated FMT is a patient-friendly application method that improves accessibility and convenience. Capsule processing may be standardised, but validation protocols are warranted. This review aimed to describe published validation methods for encapsulated FMT. Original studies reporting using encapsulated faecal formulations were included, regardless of indication. Studies were excluded if they did not address processing and validation or used non-donor-derived content. We conducted a comprehensive scoping review, implementing a systematic search strategy in PubMed, Embase and Web of Science. Processing data and validation methods were registered during full-text analysis and combined to create an overview of approaches for assessing quality in encapsulated FMT processing. The searches identified 324 unique studies, of which 44 were included for data extraction and analysis. We identified eight validation covariables: donor selection, pre-processing, preservation, oxygen-sparing processing, microbial count, viability, engraftment and clinical effect outcomes, from which we constructed a model for quality assessment of encapsulated FMT that exhaustively categorised processing details and validation measures. Our model comprised three domains: (1) Processing (donor selection and processing protocol), (2) Content analysis (microbiota measures and dose measures) and (3) Clinical effect (engraftment and clinical outcomes). No studies presented a reproducible capsule protocol; their validation strategies were sparse and divergent. The validation of FMT capsules is heterogeneous, and processing requires relevant standardisation protocols, mainly focusing on capsule content. Future studies should report validation covariables to enable accurate comparative assessments of clinical effects.}, }
@article {pmid39926224, year = {2025}, author = {Paul, JK and Azmal, M and Haque, ASNB and Meem, M and Talukder, OF and Ghosh, A}, title = {Unlocking the secrets of the human gut microbiota: Comprehensive review on its role in different diseases.}, journal = {World journal of gastroenterology}, volume = {31}, number = {5}, pages = {99913}, pmid = {39926224}, issn = {2219-2840}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology/physiology ; *Dysbiosis/immunology/microbiology ; *Probiotics/therapeutic use ; *Prebiotics/administration &amp; dosage ; *Fecal Microbiota Transplantation ; Neoplasms/microbiology/immunology/therapy ; Bacteria/immunology ; Autoimmune Diseases/microbiology/immunology ; Metabolic Diseases/microbiology/immunology/therapy ; }, abstract = {The human gut microbiota, a complex and diverse community of microorganisms, plays a crucial role in maintaining overall health by influencing various physiological processes, including digestion, immune function, and disease susceptibility. The balance between beneficial and harmful bacteria is essential for health, with dysbiosis - disruption of this balance - linked to numerous conditions such as metabolic disorders, autoimmune diseases, and cancers. This review highlights key genera such as Enterococcus, Ruminococcus, Bacteroides, Bifidobacterium, Escherichia coli, Akkermansia muciniphila, Firmicutes (including Clostridium and Lactobacillus), and Roseburia due to their well-established roles in immune regulation and metabolic processes, but other bacteria, including Clostridioides difficile, Salmonella, Helicobacter pylori, and Fusobacterium nucleatum, are also implicated in dysbiosis and various diseases. Pathogenic bacteria, including Escherichia coli and Bacteroides fragilis, contribute to inflammation and cancer progression by disrupting immune responses and damaging tissues. The potential for microbiota-based therapies, such as probiotics, prebiotics, fecal microbiota transplantation, and dietary interventions, to improve health outcomes is examined. Future research directions in the integration of multi-omics, the impact of diet and lifestyle on microbiota composition, and advancing microbiota engineering techniques are also discussed. Understanding the gut microbiota's role in health and disease is essential for formulating personalized, efficacious treatments and preventive strategies, thereby enhancing health outcomes and progressing microbiome research.}, }
@article {pmid39926158, year = {2025}, author = {Marangi, M and Boughattas, S}, title = {Genetic diversity of single-celled microorganism Blastocystis sp. and its associated gut microbiome in free-ranging marine mammals from North-Western Mediterranean Sea.}, journal = {Current research in microbial sciences}, volume = {8}, number = {}, pages = {100349}, pmid = {39926158}, issn = {2666-5174}, abstract = {Blastocystis sp. is frequently identified in humans and several animal hosts exhibiting a wide genetic diversity. Within One Health perspective, data on Blastocystis sp. distribution and its circulating subtypes (STs) from the terrestrial environment are available, while those from the marine environment remain still scare. A genetic and 16S rRNA gene sequencing analysis were conducted over the period 2022-2024 by screening fecal samples from four different species of free-ranging marine mammals (sperm, fin, long-finned pilot and Cuvier's beaked whales) circulating within North-Western Mediterranean Sea. 10 out of 43 fecal samples (23.2 %) were found positive to Blastocystis sp. using molecular tools. A predominance of zoonotic subtype ST3 among different species of marine mammals as well as the presence of ST1 allele 4 subtype and even untypable subtype within the fin whale specimen was reported. Moreover, Firmicutes, Bacteroidetes and Proteobacteria within the different Blastocystis-carrier marine mammal species as well the identification of Archaebacteria from Methanomethylophilaceae family within the fin whale isolate were detected by Illumina V3-V4 generated data. The present survey presents new insights regarding Blastocystis sp. prevalence and its circulating zoonotic ST1-ST3 subtypes from the marine environment, as well as its associated gut microbiome, providing hence baseline data for a better understanding of the associated risk and to prevent human and marine ecosystem exposure to these anthropogenic microorganisms.}, }
@article {pmid39926112, year = {2024}, author = {Guo, H}, title = {Interactions between the tumor microbiota and breast cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1499203}, pmid = {39926112}, issn = {2235-2988}, mesh = {*Breast Neoplasms/microbiology ; Humans ; Female ; *Gastrointestinal Microbiome ; Microbiota ; Prognosis ; }, abstract = {Breast cancer is the most common malignancy in women worldwide. Changes in the microbiota and their metabolites affect the occurrence and development of breast cancer; however, the specific mechanisms are not clear. Gut microbes and their metabolites influence the development of breast cancer by regulating the tumor immune response, estrogen metabolism, chemotherapy, and immunotherapy effects. It was previously thought that there were no microorganisms in breast tissue, but it is now thought that there are microorganisms in breast cancer that can affect the outcome of the disease. This review builds on existing research to comprehensively analyze the role of gut and intratumoral microbiota and their metabolites in the development and metastasis of breast cancer. We also explore the potential function of the microbiota as biomarkers for prognosis and therapeutic response, highlighting the need for further research to clarify the causal relationship between the microbiota and breast cancer. We hope to provide new ideas and directions for the development of new methods for breast cancer treatment.}, }
@article {pmid39926039, year = {2025}, author = {Yu, P and Xu, W and Li, Y and Xie, Z and Shao, S and Liu, J and Wang, Y and Wang, L and Yang, H}, title = {Ginsenosides 20R-Rg3 and Rg5 enriched black ginseng inhibits colorectal cancer tumor growth by activating the Akt/Bax/caspase-3 pathway and modulating gut microbiota in mice.}, journal = {Current research in food science}, volume = {10}, number = {}, pages = {100978}, pmid = {39926039}, issn = {2665-9271}, abstract = {Black ginseng (BG) is of great interest for its anti-cancer property. Its detailed mechanism, however, is still lacking. This study aims to evaluate the effectiveness of ginsenosides 20R-Rg3 and Rg5 enriched BG (Rg3/Rg5-BG), innovatively prepared by low temperature steam-heating process, against colorectal cancer (CRC), and elucidate its potential molecular mechanism. Interestingly, much higher concentrations of rare ginsenosides were detected in this unique BG than those in red ginseng, especially 20R-Rg3 and Rg5, which may contribute to treatment of CRC. As expected, Rg3/Rg5-BG demonstrated a dose-dependent reduction in cancer cell viability, along with the induction of cell apoptosis and cell cycle arrest. Moreover, Rg3/Rg5-BG retarded tumor growth in the model mice, as evidenced by downregulation of anti-apoptotic Bcl-2 protein and phosphatidyl Akt, and upregulation of the apoptotic proteins Bax, caspase-8, and cleaved caspase-3, enhancing apoptosis of tumor cells. Additionally, Rg3/Rg5-BG treatment improved the gut microbiota and intervened with bacteria associated with cancer development, including increasing beneficial probiotics such as Candidatus_Saccharibacteria and Saccharibacteria_genera_incertae_sedis and decreasing pernicious bacteria (Vampirovibrio, Clostridium_XlVb, etc.). Our results manifested for the first time that Rg3/Rg5-BG exerted its anti-cancer effects: through activation of the caspase-3/Bax/Bcl-2 pathway and by altering the gut microbiome composition, thus paving the way for new therapeutic strategies that incorporate natural products in cancer treatment.}, }
@article {pmid39926032, year = {2025}, author = {Akhavan, SR and Kelley, ST}, title = {PyBootNet: a python package for bootstrapping and network construction.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18915}, pmid = {39926032}, issn = {2167-8359}, mesh = {Animals ; Mice ; *Software ; Female ; *Gastrointestinal Microbiome ; Polycystic Ovary Syndrome/genetics/metabolism ; Computational Biology/methods ; Gene Regulatory Networks ; }, abstract = {BACKGROUND: Network analysis has emerged as a tool for investigating interactions among species in a community, interactions among genes or proteins within cells, or interactions across different types of data (e.g., genes and metabolites). Two aspects of networks that are difficult to assess are the statistical robustness of the network and whether networks from two different biological systems or experimental conditions differ.<br><br>METHODS: PyBootNet is a user-friendly Python package that integrates bootstrapping analysis and correlation network construction. The package offers functions for generating bootstrapped network metrics, statistically comparing network metrics among datasets, and visualizing bootstrapped networks. PyBootNet is designed to be accessible and efficient with minimal dependencies and straightforward input requirements. To demonstrate its functionality, we applied PyBootNet to compare correlation networks derived from study using a mouse model to investigate the impacts of Polycystic Ovary Syndrome (PCOS) on the gut microbiome. PyBootNet includes functions for data preprocessing, bootstrapping, correlation matrix calculation, network statistics computation, and network visualization.<br><br>RESULTS: We show that PyBootNet generates robust bootstrapped network metrics and identifies significant differences in one or more network metrics between pairs of networks. Our analysis of the previously published PCOS gut microbiome data also showed that our network analysis uncovered patterns and treatment effects missed in the original study. PyBootNet provides a powerful and extendible Python bioinformatics solution for bootstrapping analysis and network construction that can be applied to microbes, genes, metabolites and other biological data appropriate for network correlation comparison and analysis.}, }
@article {pmid39925933, year = {2025}, author = {Wu, D and Yin, M and Cao, D and Zhang, X and Zhu, Y and Wei, Y and Li, Y and Wen, C and Zhou, J}, title = {Disruption of Gut Microbiota and Associated Fecal Metabolites in Collagen-Induced Arthritis Mice During the Early Stage.}, journal = {Journal of inflammation research}, volume = {18}, number = {}, pages = {1703-1717}, pmid = {39925933}, issn = {1178-7031}, abstract = {BACKGROUND: Rheumatoid arthritis (RA) is a chronic autoimmune disease and increasing evidence suggests that disturbances in the composition and function of gut microbiota are potentially implicated in the progression of RA. Further revealing the microbiota and related metabolic disorders in the preclinical stage of RA (pre-RA) is of great significance for exploration of disease mechanisms.<br><br>METHODS: DBA/1 mice were injected with type II collagen on days 0 and 21 to establish collagen-induced arthritis (CIA) mouse model. Footpad thickness, serum autoantibodies, and joint histopathology were used to assess the progression of RA. A combination of 16S rRNA sequencing, untargeted metabolomics and targeted short-chain fatty acids (SCFAs) analysis were employed to comprehensively investigate the alterations of gut microbiota and fecal metabolites in CIA during the pre-RA stage.<br><br>RESULTS: 20 days after the initial collagen immunization, CIA mice showed immune responses without joint symptoms, alongside gut microbiota disruption. Alterations were observed in 20 microbial taxa, including Oscillospira, Bifidobacterium, Ruminococcus, Allobaculum, Alistipes, Lactobacillus, and Candidatus_Arthromitus, etc. Untargeted and targeted metabolomics identified 33 altered fecal metabolites, mainly including sugars and their derivatives, amino acids, long-chain fatty acids and SCFAs, etc. Correlation analysis showed significant correlations between specific gut microbial abundances and fecal metabolite levels. Especially, SCFAs were strongly associated with Bifidobacterium, Alistipes, Ruminococcus, Anaerotruncus, and Allobaculum.<br><br>CONCLUSION: These findings suggest that collagen immunization leads to disruption of gut microbiome and induces changes of fecal metabolites in mice, which may play a key role in early development of RA in CIA mice.}, }
@article {pmid39925886, year = {2024}, author = {Yang, Y and Zhou, HY and Zhou, GM and Chen, J and Ming, R and Zhang, D and Jiang, HW}, title = {The impact of different gastrointestinal reconstruction techniques on gut microbiota after gastric cancer surgery.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1494049}, pmid = {39925886}, issn = {1664-302X}, abstract = {INTRODUCTION: Gastric cancer is one of the common malignant tumors in the digestive tract, characterized by high incidence and mortality rates. This is particularly significant in China, where a large proportion of global new cases of gastric cancer and related deaths occur. In recent years, with the continuous development of molecular biology technology, people have gained a deeper understanding of the gastrointestinal microbiome, and studies have shown that it is closely related to the occurrence, development, and therapeutic response of gastric cancer. Although surgical intervention is crucial in significantly extending the survival of gastric cancer patients, the disruption of the balance of the intestinal microbiota caused by surgery itself should not be overlooked, as it may affect postoperative recovery.<br><br>METHODS: This study was approved by the Biomedical Ethics Committee of Sichuan Mianyang 404 Hospital. A random sampling method was used to select patients who underwent gastric cancer surgery at the hospital from January 2023 to December 2023. All patients signed written informed consent forms. Standardized perioperative management was conducted for the patients in the study, including preoperative preparation, intraoperative handling, and postoperative treatment. Fecal samples were collected from patients before surgery (before bowel preparation) and around one week after surgery for 16S rRNA sequencing analysis, through which differential biomarkers and related functional genes were sought.<br><br>RESULTS: The study results indicated that there was no significant difference in the diversity of the gut microbiota between the two groups. Compared with the R-Y group, the DTR surgical method significantly altered the structure of the gut microbiota, affecting the types, quantities, and proportions of intestinal bacteria. Furthermore, the DTR group exhibited poorer postoperative nutritional absorption capacity compared to the R-Y group, as indicated by a lower F/B ratio. The R-Y group showed a richer abundance of Bacteroidetes and a lower abundance of Proteobacteria, as well as a higher F/B ratio after surgery. These findings provide new insights into the changes in the gut microbiota following gastric cancer surgery, which may be of significant importance for postoperative recovery and long-term health management.<br><br>DISCUSSION: This study reveals the impact of different gastrointestinal reconstruction techniques on the postoperative gut microbiota of gastric cancer patients, providing new insights into the physiological changes during the postoperative recovery period. Although there was no significant difference in microbial diversity between the DTR group and the R-Y group, the DTR group showed more pronounced changes in microbial structure postoperatively, which may be associated with an increased risk of postoperative infection. These findings emphasize the importance of considering the impact on the gut microbiota when selecting gastric cancer surgery methods. However, the study had a limited sample size and did not delve into changes in metabolites. Future studies should expand the sample size and conduct metabolomic analyses to further validate these preliminary findings.}, }
@article {pmid39925695, year = {2025}, author = {Clougher, SB and Niedziela, D and Versura, P and Mulcahy, G}, title = {Best practices for the experimental design of one health studies on companion animal and owner microbiomes - From data collection to analysis.}, journal = {One health (Amsterdam, Netherlands)}, volume = {20}, number = {}, pages = {100977}, pmid = {39925695}, issn = {2352-7714}, abstract = {The relationship between owner and companion animal represents an underestimated opportunity for the studying of One Health relationships between humans, animals, and the environment they share. Microbiome exchanges between owner and pet have been documented for the gut, skin, oral, and nasal microbiomes. These studies give a unique insight into bacterial flows between humans and animals, but come with their specific challenges. This review discusses the data and sample collection challenges, as well as laboratory, bioinformatic and data analysis challenges specific to One Health studies on companion animal and owner microbiomes. We provide an overview of possible data to be collected and pitfalls to avoid during sample collection and conservation, DNA extraction, and library preparation. We present the main bioinformatics pipelines in sequencing-data microbiome analysis, as well as data analysis specific to pet-owner microbiome comparison. We review and compare three beta-diversity measures (Bray-Curtis dissimilarity, unweighted, and weighted UniFrac distances) for pet-owner distances and the tests to compare them. Finally, we propose a framework with key considerations to bear in mind when designing and carrying out owner-companion animal studies, as well as best practices to implement them. Although these studies come with additional difficulties compared to species-specific microbiome studies, they offer the opportunity to identify biomarkers, environmental triggers, and impacts of pet-owner interactions across species.}, }
@article {pmid39925382, year = {2025}, author = {Mcgonigal, M and Ito, K}, title = {From Soil to Surface: Exploring the Impact of Green Infrastructure on Microbial Communities in the Built Environment.}, journal = {Journal of genomics}, volume = {13}, number = {}, pages = {10-23}, pmid = {39925382}, issn = {1839-9940}, abstract = {High microbial diversity offers extensive benefits to both the environment and human health, contributing to ecosystem stability, nutrient cycling, and pathogen suppression. In built environments, factors such as building design, human activity, and cleaning protocols influence microbial communities. This study investigates the impact of landscape design on microbial diversity and function within the "Visionary Lab" exhibition in Tokyo, Japan, using 16S rRNA gene amplicon sequencing and shallow shotgun sequencing. Despite the limited sample size, the study suggests that the Visionary Lab samples may exhibit higher microbial diversity compared to other museum areas. Potential distinct microbial community structures may be correlated with sampling locations. However, despite this, no consistent patterns were observed in virulence factors or antimicrobial resistance genes across the samples. Metabolic function analysis showed varied profiles, suggesting diverse ecological interactions influenced that may be by the curated landscape. This suggest that the curated landscape design may have the potential to enhance microbial diversity, highlighting a possible avenue to create healthier and more sustainable built environments. However, the lack of consistent patterns in virulence factors and antimicrobial resistance genes underscores the complexity of microbial community dynamics.}, }
@article {pmid39925335, year = {2025}, author = {Li, L and Hayashi-Okada, Y and Falkner, KL and Shimizu, Y and Zambon, JJ and Kirkwood, KL and Schifferle, RE and Genco, RJ and Diaz, PI}, title = {Effect of an intensive antiplaque regimen on microbiome outcomes after nonsurgical periodontal therapy.}, journal = {Journal of periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1002/JPER.24-0141}, pmid = {39925335}, issn = {1943-3670}, support = {//Sunstar Inc., Osaka, Japan,/ ; }, abstract = {BACKGROUND: It has been well documented that periodontal treatment decreases the levels of certain disease-associated species in subgingival plaque. Few studies, however, investigate to which extent periodontal therapy restores a health-like subgingival community. Here, we conducted a secondary analysis to evaluate microbiome outcomes of nonsurgical periodontal therapy alone or followed by an intensive antiplaque regimen, analyzing microbiome trajectories at the community level with respect to health.<br><br>METHODS: Eighty-six subjects with periodontitis stages II/III were evaluated at baseline and 6 months after receiving scaling and root planing alone (SRP, n&#xa0;=&#xa0;41) or followed by an antiplaque regimen consisting of use of 0.12% chlorhexidine for 3 months and interdental cleaners for 6 months (SRP + P + S, n&#xa0;=&#xa0;45). Thirty periodontally healthy subjects served as reference. The subgingival microbiome was characterized by 16S rRNA gene sequencing, and longitudinal within-subject changes were quantified with respect to a healthy plane (HPL) modeled from the reference group.<br><br>RESULTS: Evaluation of individual microbiome trajectories showed that only the SRP + P + S group had a statistically significant reduction in distance to the HPL. However, responses were variable in both groups, with only a fraction of individuals changing in the direction of health. Random forest analysis revealed baseline microbiome composition as a greater predictor of microbiome response than type of treatment rendered.<br><br>CONCLUSION: An adjunct antiplaque regimen resulted in a greater approximation of the microbiome to the healthy state. However, responses varied greatly among subjects highlighting the need for robust and personalized approaches to restore eubiosis.<br><br>PLAIN LANGUAGE SUMMARY: This study looked at how different treatments for gum disease change the bacteria in the gums of people with moderate to severe gum problems. Eighty-six people received standard gum treatments, and some also used a mouthwash and special tools to clean between their teeth at home. After 6 months, more people in the group that added the extra cleaning steps had healthier bacteria in their gums than people who received the standard treatment. However, not everyone responded the same way. The study found that the types of bacteria someone had at the start were better at predicting how well the treatment would work, more than the type of treatment itself. This means gum disease treatments may need to be personalized for better results.}, }
@article {pmid39924996, year = {2025}, author = {Muhammad, M and Wahab, A and Waheed, A and Hakeem, KR and Mohamed, HI and Basit, A and Toor, MD and Liu, YH and Li, L and Li, WJ}, title = {Navigating Climate Change: Exploring the Dynamics Between Plant-Soil Microbiomes and Their Impact on Plant Growth and Productivity.}, journal = {Global change biology}, volume = {31}, number = {2}, pages = {e70057}, doi = {10.1111/gcb.70057}, pmid = {39924996}, issn = {1365-2486}, mesh = {*Climate Change ; *Soil Microbiology ; *Microbiota ; *Plant Development ; Agriculture/methods ; Crops, Agricultural/growth &amp; development/microbiology ; Plants/microbiology ; Rhizosphere ; }, abstract = {Understanding the intricate interplay between plant and soil microbiomes and their effects on plant growth and productivity is vital in a rapidly changing climate. This review explores the interconnected impacts of climate change on plant-soil microbiomes and their profound effects on agricultural productivity. The ongoing rise in global temperatures, shifting precipitation patterns and extreme weather events significantly affect the composition and function of microbial communities in the rhizosphere. Changes in microbial diversity and activity due to rising temperatures impact nutrient cycling, microbial enzyme synthesis, soil health and pest and disease management. These changes also influence the dynamics of soil microbe communities and their capability to promote plant health. As the climate changes, plants' adaptive capacity and microbial partners become increasingly crucial for sustaining agriculture. Mitigating the adverse effects of climate change on plant growth and agricultural productivity requires a comprehensive understanding of the interconnected mechanisms driving these processes. It highlights various strategies for mitigating and adapting to environmental challenges, including soil management, stress-tolerant crops, cover cropping, sustainable land and water management, crop rotation, organic amendments and the development of climate-resilient crop varieties. It emphasises the need for further exploration of plant-soil microbiomes within the broader context of climate change. Promising mitigation strategies, including precision agriculture and targeted microbiome modifications, offer valuable pathways for future research and practical implementation of global food security and climate change.}, }
@article {pmid39924716, year = {2024}, author = {Yao, R and Sun, L and Gao, R and Mei, Y and Xue, G and Yu, D}, title = {PTTM: dissecting the profile of tumor tissue microbiome to reveal microbiota features and associations with host transcriptome.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, doi = {10.1093/bib/bbaf057}, pmid = {39924716}, issn = {1477-4054}, support = {81971402//National Natural Science Foundation of China/ ; 14DZ2272300//Shanghai Key Laboratory of Cell Engineering Program/ ; 20YF1458100//Shanghai Science and Technology Commission Sailing Program/ ; }, mesh = {Humans ; *Microbiota/genetics ; *Neoplasms/genetics/microbiology/metabolism ; *Transcriptome ; Computational Biology/methods ; Tumor Microenvironment/genetics ; Databases, Genetic ; }, abstract = {Microbiota is present in the human tissue microenvironment and closely related to tumorigenesis and treatment. However, the landscape of tissue microbiome and its relationship with tumors remain less understood. In this study, we re-analyzed the omics data from the 7104 samples (94 projects for 15 cancers) in the NCBI database to obtain microbial profiles. After normalization and decontamination processing, we established classification models to distinguish between different tumors and tumor with adjacent normal tissues. The models had excellent performances, indicating that tissue microbiome had significant tumor specificity. Moreover, a series of key bacteria and bacteria-gene association pairs were screened out based on bioinformatic analysis, such as the tumor-promoting bacteria Fusobacterium, the tumor-suppressing bacteria Actinomyces, and the significant Rhodopseudomonas-COL1A1 association pair. In addition, we created a visual website, PTTM (http://198.46.152.196:7080/), for users to query and download the results. The identified key bacteria and association pairs provide candidate targets for further exploration of the molecular mechanisms of microbial action on tumorigenesis and the development of cancer therapy.}, }
@article {pmid39924644, year = {2025}, author = {Li, X and Xiao, X and Wang, S and Wu, B and Zhou, Y and Deng, P}, title = {Uncovering de novo polyamine biosynthesis in the gut microbiome and its alteration in inflammatory bowel disease.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2464225}, doi = {10.1080/19490976.2025.2464225}, pmid = {39924644}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome ; Humans ; Animals ; Mice ; *Feces/microbiology ; *Inflammatory Bowel Diseases/microbiology/metabolism ; *Polyamines/metabolism ; Metabolomics ; Putrescine/metabolism/biosynthesis ; Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Spermidine/metabolism/biosynthesis ; Bacteroides/metabolism/genetics ; Mice, Inbred C57BL ; Male ; Female ; }, abstract = {Polyamines are important gut microbial metabolites known to affect host physiology, yet the mechanisms behind their microbial production remain incompletely understood. In this study, we developed a stable isotope-resolved metabolomic (SIRM) approach to track polyamine biosynthesis in the gut microbiome. Viable microbial cells were extracted from fresh human and mouse feces and incubated anaerobically with [U-[13]C]-labeled inulin (tracer). Liquid chromatography-high resolution mass spectrometry analysis revealed distinct [13]C enrichment profiles for spermidine (SPD) and putrescine (PUT), indicating that the arginine-agmatine-SPD pathway contributes to SPD biosynthesis in addition to the well-known spermidine synthase pathway (PUT aminopropylation). Species differences were observed in the [13]C enrichments of polyamines and related metabolites between the human and mouse microbiome. By analyzing the fecal metabolomics and metatranscriptomic data from an inflammatory bowel disease (IBD) cohort, we found significantly higher polyamine levels in IBD patients compared to healthy controls. Further investigations using single-strain SIRM and in silico analyses identified Bacteroides spp. as key contributors to polyamine biosynthesis, harboring essential genes for this process and potentially driving the upregulation of polyamines in IBD. Taken together, this study expands our understanding of polyamine biosynthesis in the gut microbiome and will facilitate the development of precision therapies to target polyamine-associated diseases.}, }
@article {pmid39924593, year = {2025}, author = {Wang, H and You, W and Zhu, Z and Zhang, Y and Hu, C and Lu, J and Huang, Y and Peng, R and Shan, R and Li, R and Chen, Y and Qi, F and Yan, F and Zhan, Q}, title = {Streptococcus lutetiensis inhibits CD8[+] IL17A[+] TRM cells and leads to gastric cancer progression and poor prognosis.}, journal = {NPJ precision oncology}, volume = {9}, number = {1}, pages = {43}, pmid = {39924593}, issn = {2397-768X}, abstract = {In many solid tumours, including gastric cancer (GC), the beginning and progression of the tumour are closely correlated with the tumour microbiome. Here, we show the changes in the gastric microbiota and their influence on immune regulation and the promotion of GC progression through 16s rRNA sequencing and single cell RNA sequencing. Streptococcus lutetiensis (S. lutetiensis) was found to be enriched in the tumour tissues of GC patients. Further analysis using single-cell sequencing and flow cytometry showed that S. lutetiensis notably affects the antitumour immunity by suppressing IL17 signalling and reducing the population of CD8[+]IL17A[+] tissue-resident memory T (TRM) cells by activating Nrf2-mediated oxidative stress response. Mouse models confirm S. lutetiensis promotes GC progression by impairing immune responses in CD8[+]IL17A[+]TRM cells, suggesting it as a potential GC prognosis indicator and immunotherapy target, highlighting the microbiome's role in cancer progression.}, }
@article {pmid39924526, year = {2025}, author = {Díez López, C and Van Herreweghen, F and De Pessemier, B and Minnebo, Y and Taelman, S and Judge, K and Ransley, K and Hammond, C and Batson, M and Stock, M and Van Criekinge, W and Van de Wiele, T and Macmaster, A and Callewaert, C}, title = {Unravelling the hidden side of laundry: malodour, microbiome and pathogenome.}, journal = {BMC biology}, volume = {23}, number = {1}, pages = {40}, pmid = {39924526}, issn = {1741-7007}, support = {HBC.2020.2292//Agentschap Innoveren en Ondernemen/ ; FWO19/PSD/084//Fonds Wetenschappelijk Onderzoek/ ; }, mesh = {*Microbiota ; Humans ; *Odorants/analysis ; Laundering/methods ; Volatile Organic Compounds/analysis ; Clothing ; Skin/microbiology ; }, abstract = {BACKGROUND: Recent trends towards lower washing temperatures and a reduction in the use of bleaching agents in laundry undoubtedly benefit our environment. However, these conditions impair microbial removal on clothes, leading to malodour generation and negative impacts on consumer well-being. Clothing undergoes cycles of wearing, washing and drying, with variable exposure to microorganisms and volatilomes originating from the skin, washing machine, water and laundry products. Laundry malodour is therefore a complex problem that reflects its dynamic ecosystem. To date, comprehensive investigations that encompass the evaluation of both microbial community and malodorous volatile organic compounds throughout all stages of the wash-wear-dry cycle are scarce. Furthermore, the microbial and malodour profiles associated with extended humid-drying conditions are poorly defined.<br><br>RESULTS: Here we present olfaction-directed chemical and microbiological studies of synthetic T-shirts after wearing, washing and drying. Results show that although washing reduces the occurrence of known malodour volatile organic compounds, membrane-intact bacterial load on clothing is increased. Skin commensals are displaced by washing machine microbiomes, and for the first time, we show that this shift is accompanied by an altered pathogenomic profile, with many genes involved in biofilm build-up. We additionally highlight that humid-drying conditions are associated with characteristic malodours and favour the growth of specific Gram-negative bacteria.<br><br>CONCLUSIONS: These findings have important implications for the development of next-generation laundry products that enhance consumer well-being, while supporting environmentally friendly laundry practices.}, }
@article {pmid39924167, year = {2025}, author = {Vinay, G and Seppen, J and Setlow, P and Brul, S}, title = {Bile acids as germinants for Clostridioides difficile spores, evidence of adaptation to the gut?.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuaf005}, pmid = {39924167}, issn = {1574-6976}, abstract = {Bacterial spores formed upon metabolic stress have minimal metabolic activity and can remain dormant for years. Nevertheless, they can sense the environment and germinate quickly upon exposure to various germinants. Germinated spores can then outgrow into vegetative cells. Germination of spores of some anaerobes, especially Clostridioides difficile, is triggered by cholic acid and taurocholic acid. Elevated levels of these bile acids are thought to correlate with a perturbed gut microbiome, which cannot efficiently convert primary bile acids into secondary bile acids. That bile acids are germination-triggers suggests these bacteria have a life cycle taking place partially in the mammalian digestive tract where bile acids are plentiful; notably bile acids can be made by all vertebrates. Thus, spores survive in the environment until taken up by a host where they encounter an environment suitable for germination and then proliferate in the largely anaerobic large intestine; some ultimately sporulate there, regenerating environmentally resistant spores in the C. difficile life cycle. This review summarizes current literature on effects of bile acids and their metabolites on spore germination in the gut and evidence that adaptation to bile acids as germinants is a consequence of a life cycle both inside and outside the digestive tract.}, }
@article {pmid39924079, year = {2025}, author = {Ballarò, R and Wasylishen, AR and Pieterman, CRC and Olsen, C and Irajizad, E and Wu, R and Katayama, H and Liu, H and Cai, Y and León-Letelier, RA and Dennison, JB and Waguespack, S and Do, KA and Agarwal, SK and Walter, M and Welch, J and Weinstein, L and Blau, JE and Jha, S and Nilubol, N and Vriens, MR and van Leeuwaarde, RS and van Treijen, MJC and Valk, GD and Perrier, ND and Hanash, SM and Fahrmann, JF}, title = {Elevated levels of circulating microbial-associated uremic toxins are associated with metastatic duodenopancreatic neuroendocrine tumors in patients with Multiple Endocrine Neoplasia Type 1.}, journal = {Cancer letters}, volume = {}, number = {}, pages = {217537}, doi = {10.1016/j.canlet.2025.217537}, pmid = {39924079}, issn = {1872-7980}, abstract = {Metastatic duodenopancreatic neuroendocrine tumors (dpNETs) are the primary cause of mortality among patients with Multiple Endocrine Neoplasia Type 1 (MEN1). Emerging evidence implicates the microbiome and microbial-derived secreted factors in promoting cancer development and progression. In the current study, we report that the circulating microbial-associated uremic toxins trimethylamine N-oxide (TMAO), indoxyl sulfate (IS), cresol sulfate (CS), cresol glucuronide (CG), and phenol sulfate (PS) are elevated in MEN1 patients with metastatic dpNETs. Proteomic- and metabolomic-based analysis of resected dpNET tissues from MEN1 patients also revealed detectable levels of uremic toxins that positively correlated with peptide-based signatures corresponding to Fusobacterium nucleatum, Faecalibacterium prausnitzii, and Klebsiella pneumoniae and negatively correlated with Streptococcus pneumoniae and Streptococcus thermophilus. A microbial-associated uremic toxin panel (MUTP) was developed and, in an independent case-control validation cohort, the panel yielded an area under the receiver operating characteristic curve (AUC) of 0.94 (95% CI: 0.85-1.00) with 67% sensitivity at 95% specificity for identifying MEN1 patients with metastatic dpNETS. Increases in circulating microbial-associated uremic toxins during early stages of neoplasia were also found to be associated with poor overall survival in an Men1[fl/fl]Pdx1-Cre[Tg] mouse model of MEN1 pancreatic NETs. Our findings suggest that microbial dysbiosis is associated with disease aggressiveness and that increases in circulating microbial-associated uremic toxins may be a prognostic indication for MEN1 individuals who are at risk of having metastatic dpNETs.}, }
@article {pmid39924004, year = {2025}, author = {Corona-Cervantes, K and Sánchez-Salguero, E and Zárate-Segura, PB and Krishnakumar, A and Piña-Escobedo, A and Rangel-Calvillo, MN and Ramírez-Lozada, T and Acosta-Altamirano, G and Lázaro-Pérez, NDS and Sierra-Martínez, M and Santos-Argumedo, L and García-Mena, J}, title = {Maternal immunoglobulins differentially bind a diverse bacterial community in human colostrum and the stool of breastfed neonates.}, journal = {Immunology letters}, volume = {}, number = {}, pages = {106978}, doi = {10.1016/j.imlet.2025.106978}, pmid = {39924004}, issn = {1879-0542}, abstract = {In the early days, maternal immunoglobulins are essential for sustaining a balanced gut environment by influencing the interaction between the host and the microbiome. The successional establishment of the pioneer strains is an interesting topic of research where maternal immunoglobulins appear to be important. This proof-of-concept study explored the binding pattern of IgA1, IgA2, IgM, and IgG classes to a commensal bacterial in human colostrum and the stool of breastfed neonates. We used flow cytometry coupled with 16S rRNA gene sequencing in human colostrum and neonatal feces samples to characterize this Ig-microbiota association. We observed that in human colostrum samples, IgA2 and IgM bind alfa and beta Proteobacteria, which can potentially stimulate neonatal immune system development in the gut. Other immunoglobulins like IgG predominantly bind facultative anaerobes belonging to the Firmicutes phylum, reported as part of human milk microbiota and pioneer colonizers of the neonatal gut. Maternal immunoglobulins also bind a wide diversity of bacteria in the neonatal stool. For instance, IgA2 and IgM bound more members of the phylum Bacteroidetes in comparison to IgG, these Bacteroidetes and some firmicutes have been reported as late colonizers of the neonatal gut, and their presence is important due to their ability to produce important short chain fatty acids like propionate and butyrate. Our results support the current view that microbial and immunoglobulin transference is crucial for developing the neonate's immune system and individual gut microbiota.}, }
@article {pmid39923913, year = {2025}, author = {Scala, M and Del Rocio Gonzalez Soltero, M and Esteban, AB and Fernandez, JMB and Ferreiro, VR and Serretti, A and Fanelli, G and Jimenez, RR}, title = {Oropharyngeal microbiota in patients with psychotic disorders: A scoping review on compositional and functional alterations.}, journal = {Progress in neuro-psychopharmacology &amp; biological psychiatry}, volume = {}, number = {}, pages = {111288}, doi = {10.1016/j.pnpbp.2025.111288}, pmid = {39923913}, issn = {1878-4216}, abstract = {BACKGROUNDS: Oropharyngeal microbiota may be implicated in the onset and progression of psychotic disorders. This scoping review aims to map the existing evidence concerning the composition, diversity, and metabolic pathways of the oropharyngeal microbiota in patients aged 18 to 65 with a main diagnosis of a psychotic disorder, including individuals at clinical high-risk for psychosis (CHRP) or experiencing first episode psychosis (FEP).<br><br>METHODS: The scoping review was performed according to the PRISMA-ScR checklist. The systematic literature search was conducted using PubMed, Web of Science, and CINAHL until February 2024.<br><br>RESULTS: Seven cross-sectional studies were included, comprising 43 individuals at CHRP, 13 with FEP, 85 with first-episode of schizophrenia (FES), 171 with schizophrenia, and 8 with another schizophrenia spectrum disorder. The oropharyngeal microbiota showed an increase in Lactobacillus gasseri abundance in schizophrenia, and in Firmicutes/Proteobacteria phylum ratio in patients experiencing CHR-P and FES. In schizophrenia, an altered &#x3b2;-diversity was observed alongside increased metabolic pathways related to metabolite transporters. In FES, higher &#x3b1;-diversity and disruptions in amino acid, carbohydrate, and xenobiotic metabolism pathways were found. Hydrogen sulfide (H2S)-producing bacteria were generally enriched in all the stages of disease. Correlations were observed between oropharyngeal microbiota and psychotic symptom domains.<br><br>CONCLUSIONS: Potential microbial signatures, such as Lactobacillus gasseri and H2S-producing bacteria, were identified in the oropharyngeal microbiota. Alterations in the oropharyngeal microbiota composition and function may be associated with different stages of psychotic disorders, with some overlap between CHR-P and FES.}, }
@article {pmid39923866, year = {2025}, author = {Simpson, A and Pilotto, AM and Brocca, L and Mazzolari, R and Rosier, BT and Carda-Diéguez, M and Casas-Agustench, P and Bescos, R and Porcelli, S and Mira, A and Easton, C and Henriquez, FL and Burleigh, M}, title = {Eight Weeks of High-Intensity Interval Training Alters the Tongue Microbiome and Impacts Nitrate and Nitrite Levels in Previously Sedentary Men.}, journal = {Free radical biology &amp; medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.freeradbiomed.2025.02.006}, pmid = {39923866}, issn = {1873-4596}, abstract = {Nitric oxide (*NO) is a key signalling molecule, produced enzymatically via *NO synthases (NOS) or following the stepwise reduction of nitrate to nitrite via oral bacteria. Exercise training upregulates NOS expression and improves systemic health, but its effect on oral health, and more particularly the oral microbiome, has not been investigated. We used an exercise training study design to investigate changes in the tongue dorsum microbiome, and in nitrate and nitrite levels in the saliva, plasma and muscle, before, during and after an exercise training period. Eleven untrained males (age 25 ± 5 years, mass 64.0 ± 11.2 kg, stature 171 ± 6 cm, O2peak 2.25 ± 0.42 l·min[-1]) underwent 8-weeks of high-intensity interval training (HIIT), followed by 12-weeks of detraining. The tongue dorsum microbiome was examined using Pac-Bio long-read 16S rRNA sequencing. Nitrate and nitrite levels were quantified with high-performance liquid chromatography. Grouped nitrite-producing species did not change between any timepoints. However, HIIT led to changes in the microbiome composition, increasing the relative abundance of some, but not all, nitrite-producing species. These changes included a decrease in the relative abundance of nitrite-producing Rothia and a decrease in Neisseria, alongside changes in 6 other bacteria at the genus level (all p≤0.05). At the species level, the abundance of 9 bacteria increased post-training (all p≤0.05), 5 of which have nitrite-producing capacity, including Rothia mucilaginosa and Streptococcus salivarius. Post-detraining, 6 nitrite-producing species remained elevated relative to baseline. Nitrate increased in plasma (p=0.03) following training. Nitrite increased in the saliva after training (p=0.02) but decreased in plasma (p=0.03) and muscle (p=0.002). High-intensity exercise training increased the abundance of several nitrite-producing bacteria and altered nitrate and nitrite levels in saliva, plasma, and muscle. Post-detraining, several nitrite-producing bacteria remained elevated relative to baseline, but no significant differences were detected in nitrate or nitrite levels. Switching from a sedentary to an active lifestyle alters both the microbiome of the tongue and the bioavailability of nitrate and nitrite, with potential implications for oral and systemic health.}, }
@article {pmid39923847, year = {2025}, author = {Xie, Y and Irwin, S and Nelson, B and van Daelen, M and Fontenot, L and Jacobs, JP and Cappelletti, M and Feng, H and Li, Y and Koon, HW}, title = {Citrulline inhibits Clostridioides difficile infection with anti-inflammatory effects.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {}, number = {}, pages = {101474}, doi = {10.1016/j.jcmgh.2025.101474}, pmid = {39923847}, issn = {2352-345X}, abstract = {BACKGROUND AND AIMS: Clostridioides difficile infection (CDI) causes colitis and diarrhea. C. difficile bacterium produces toxins A and B, which cause intestinal inflammation. A metabolomics analysis discovered fecal metabolites with anti-inflammatory effects in CDI. We aimed to identify an anti-CDI metabolite that can inhibit CDI-mediated colitis and prevent recurrence.<br><br>METHODS: Fresh human colonic tissues and primary human cells were used to determine metabolite effects. Humanized C. difficile-infected HuCD34-NCG mice and antibiotics-treated human gut microbiota-treated (ABX+HGM) hamsters were used to simulate the human environment.<br><br>RESULTS: High-throughput screening and fecal metabolomics analysis identified anti-inflammatory metabolites. Compared to other tested metabolites, citrulline preserved the mucosal integrity of toxin-exposed fresh human colonic tissues with reduced macrophage inflammatory protein 1 alpha (MIP-1&#x3b1;) and increased interleukin-10 (IL-10) expression. Oral citrulline treatment alleviated cecal inflammation in hamsters infected with C. difficile ribotype 027. This was accomplished by the augmented expression of cecal IL-10 and the diminished level of cecal MIP-1&#x3b1;. Citrulline and vancomycin synergistically prevented recurrence in the infected ABX+HGM hamsters. In C57BL/6J mice infected with C. difficile VPI10463, citrulline ameliorated colitis by reducing colonic Ccl3 mRNA expression. In immunologically humanized HuCD34-NCG mice infected with toxin B-expressing C. difficile ribotype 017, citrulline ameliorated colitis with increased human IL-10 expression in colonic macrophages. Citrulline suppressed MIP-1&#x3b1; secretion and GSK3&#x3b1;/&#x3b2; dephosphorylation in the toxin A-exposed human colonic epithelial cells and promoted IL-10 expression in toxin B-exposed human macrophages and heat shock protein 27 phosphorylation.<br><br>CONCLUSION: Citrulline exerts anti-inflammatory effects in the intestines against C. difficile toxins and inhibits CDI recurrence in mice and hamsters.}, }
@article {pmid39923740, year = {2025}, author = {Krause-Kyora, B and da Silva, NA and Kaplan, E and Kolbe, D and ,  and Wohlers, I and Busch, H and Ellinghaus, D and Caliebe, A and Sezgin, E and Nebel, A and Schreiber, S}, title = {Neolithic introgression of IL23R-related protection against chronic inflammatory bowel diseases in modern Europeans.}, journal = {EBioMedicine}, volume = {113}, number = {}, pages = {105591}, doi = {10.1016/j.ebiom.2025.105591}, pmid = {39923740}, issn = {2352-3964}, abstract = {BACKGROUND: The hypomorphic variant rs11209026-A in the IL23R gene provides significant protection against immune-related diseases in Europeans, notably inflammatory bowel diseases (IBD). Today, the A-allele occurs with an average frequency of 5% in Europe.<br><br>METHODS: This study comprised 251 ancient genomes from Europe spanning over 14,000 years. In these samples, the investigation focused on admixture-informed analyses and selection scans of rs11209026-A and its haplotypes.<br><br>FINDINGS: rs11209026-A was found at high frequencies in Anatolian Farmers (AF, 18%). AF later introduced the allele into the ancient European gene-pool. Subsequent admixture caused its frequency to decrease and formed the current southwest-to-northeast allele frequency cline in Europe. The geographic distribution of rs11209026-A may influence the gradient in IBD incidence rates that are highest in northern and eastern Europe.<br><br>INTERPRETATION: Given the dramatic changes from hunting and gathering to agriculture during the Neolithic, AF might have been exposed to selective pressures from a pro-inflammatory lifestyle and diet. Therefore, the protective A-allele may have increased survival by reducing intestinal inflammation and microbiome dysbiosis. The adaptively evolved function of the variant likely contributes to the high efficacy and low side-effects of modern IL-23 neutralisation therapies for chronic inflammatory diseases.<br><br>FUNDING: German Research Foundation (EXC 2167 390884018 and EXC 2150 390870439).}, }
@article {pmid39923616, year = {2025}, author = {Cui, L and Wang, B and Luo, K and Liu, Y and Xie, Y and Liu, L and Chen, J and Fan, G and Liu, S and Tian, X}, title = {The diversity, composition, network characteristics and community assembly of intestinal microbiome in sea cucumber reflect the differences in habitats and aquaculture practices.}, journal = {Journal of environmental management}, volume = {376}, number = {}, pages = {124487}, doi = {10.1016/j.jenvman.2025.124487}, pmid = {39923616}, issn = {1095-8630}, abstract = {The possible differentiation of microbiomes in various habitats and aquaculture practices has rarely been studied until now. Here, the microbiomes of five different culture systems for sea cucumber Apostichopus japonicus were compared, including outdoor pond, indoor workshop, net cage, suspension cage, marine ranching. Samples of intestinal contents from sea cucumber, surrounding water and sediment were collected from these culture systems. Significant differentiations in microbial diversity, composition, function were found in various culture systems. Microbial source-tracking analysis indicated that intestinal microbiomes of sea cucumber were more similar to sediment than to surrounding water. Totally, 23 shared core operational taxonomic units (OTUs) were identified in intestinal microbiome of sea cucumber in these systems, belong to following orders: Rhodobacterales (15), Rhizobiales (3), Flavobacteriales (2), Verrucomicrobiales (1), Campylobacterales (1), unclassified (1). Meanwhile, unique core OTUs in various systems tended to aggregate toward oligotrophic, potentially beneficial, or pathogenic bacteria. Microbial network characteristics in marine ranching and suspension cage systems were consistent with those in high-stress habitats, exhibiting lower diversity, complexity, modularity, dominated by positive interactions. Conversely, opposite trends were observed in indoor workshop, outdoor pond, net cage systems. Strong diffusion limitations on intestinal microbial community of sea cucumber, particularly in marine ranching system, were elucidated. Distinct characteristics of microbiome in various culture systems reflected differences in habitats and aquaculture practices. These findings provide new insights into impact of aquaculture systems on microbial community in aquatic animals, could contribute to healthy aquaculture practices for sea cucumber industry.}, }
@article {pmid39923579, year = {2025}, author = {Fan, Y and Meng, S and Song, Y and Zhang, Y and Song, Y and Chen, Z and Xie, K}, title = {Interaction, diagnosis, and treatment of lung microbiota-NLRP3 inflammasome-target organ axis in sepsis.}, journal = {International immunopharmacology}, volume = {149}, number = {}, pages = {114222}, doi = {10.1016/j.intimp.2025.114222}, pmid = {39923579}, issn = {1878-1705}, abstract = {Sepsis is defined as a life-threatening condition caused by a dysregulated host response to infection, leading to multi-organ dysfunction, and representing a significant global health burden. The progression of sepsis is closely linked to disruptions in lung microbiota, including bacterial translocation, impaired barrier function, and local microenvironmental disturbances. Conversely, the worsening of sepsis exacerbates lung microbiota imbalances, contributing to multi-organ dysfunction. Recent culture-independent microbiological techniques have unveiled the complexity of the respiratory tract microbiome, necessitating a reassessment of the interactions between the host, microbes, and pathogenesis in sepsis. This review synthesizes current insights into the causes of microbiota dysbiosis and the regulatory mechanisms of the NOD-like receptor pyrin domain containing 3 (NLRP3) inflammasome, as well as their interactions during sepsis and sepsis-induced organ dysfunction. In addition, we summarize novel diagnostic and therapeutic approaches from the current study that may offer promising prospects for the management of sepsis.}, }
@article {pmid39923562, year = {2025}, author = {Solazzo, G and Rovelli, S and Iodice, S and Chung, M and Frimpong, M and Bollati, V and Ferrari, L and Ghedin, E}, title = {The microbiome of Total Suspended Particles and its influence on the respiratory microbiome of healthy office workers.}, journal = {Ecotoxicology and environmental safety}, volume = {291}, number = {}, pages = {117874}, doi = {10.1016/j.ecoenv.2025.117874}, pmid = {39923562}, issn = {1090-2414}, abstract = {Air particulate matter (PM) is widely recognized for its potential to negatively affect human health, including changes in the upper respiratory microbiome. However, research on PM-associated microbiota remains limited and mostly focused on PM (e.g., PM2.5 and PM10). This study aims to characterize for the first time the microbiome of Total Suspended Particles (TSP) and investigate the correlations of indoor TSP with the human upper respiratory microbiome. Biological and environmental samples were collected over three collection periods lasting three weeks each, between May and July 2022 at the University of Milan and the University of Insubria Como. TSP were sampled using a filter-based technique, while respiratory samples from both anterior nares (AN) and the nasopharynx (NP) were collected using swabs. Microbiome analysis of both human (N = 145) and TSP (N = 51) samples was conducted on metagenomic sequencing data. A comparison of indoor and outdoor TSP microbiomes revealed differences in microbial diversity and taxonomic composition. The indoor samples had higher relative abundance of environmental bacteria often associated with opportunistic infections like Paracoccus sp., as well as respiratory bacteria such as Staphylococcus aureus and Klebsiella pneumoniae. Additionally, both indoor and outdoor TSP samples contained broad spectrum antibiotic resistance genes. Indoor TSP exposure was negatively associated with commensal bacteria and positively associated with Staphylococcus aureus relative abundance. Finally, a correlation between the relative abundance of respiratory bacteria identified in the indoor TSP and the upper respiratory microbiome was found, suggesting a potential interaction between TSP and the upper airways.}, }
@article {pmid39923452, year = {2025}, author = {Gulizia, JP and Khalid, Z and Terra-Long, MT and Vargas, JI and Hernandez, JR and Pacheco, WJ and Krehling, JT and Macklin, KS and Dozier, WA and McCafferty, KW and Hauck, R}, title = {Response of YPM x Ross 708 male broilers to diets containing varying inclusions of phytase, calcium butyrate, and bacitracin methylene disalicylate during the grower and finisher periods-part 2: Intestinal health and physiology.}, journal = {Poultry science}, volume = {104}, number = {3}, pages = {104862}, doi = {10.1016/j.psj.2025.104862}, pmid = {39923452}, issn = {1525-3171}, abstract = {This study evaluated the effects of calcium butyrate (CB) and bacitracin methylene disalicylate 50 (BMD) combined with different phytase concentrations on broiler intestinal health and physiology. Day-old YPM x Ross 708 male broilers (2,880) were distributed in 72 floor pens and assigned to 1 of 9 treatments (8 replicates/treatment). This experiment was a factorial arrangement including 2 phytase concentrations (500 or 1,500 FTU/kg) and 4 microbiota modulating feed additive levels (MMFA; (1) none, (2) only CB (0.5 g/kg of diet), (3) only BMD (55 mg/kg of diet), or (4) both CB and BMD). Additionally, a negative control without phytase and MMFA was included. Intestinal permeability was assessed on d 27. Jejunum wall and cecal content samples were collected on d 28 and 42 to assess jejunum villus height (VH), crypt depth, tight-junction and mucin gene expression, cecal microbiome diversity, and predicted bacterial metabolic pathways. Phytase and MMFA did not influence intestinal permeability (P > 0.05). Combining both CB and BMD with 1,500 FTU/kg of phytase compared to 500 FTU/kg lowered d 28 VH (P ≤ 0.05). Jejunal expression of CL-1, CL-4, CL-5, and ZO-2 on d 28 as well as CL-2 on d 42 changed between MMFA when combined with 1,500 FTU/kg of phytase but not 500 FTU/kg (P ≤ 0.05). Day 42 Pielou's evenness increased when 1,500 FTU/kg of phytase was combined with both CB and BMD compared to no MMFA (P ≤ 0.05). The cecal microbial beta diversity was not influenced by phytase, MMFA, or their interaction (P > 0.05). Overall, broiler intestinal health and physiology were influenced by CB and BMD depending on phytase concentration, demonstrating the complex interactions between these feed additives.}, }
@article {pmid39923290, year = {2025}, author = {Wang, S and Wu, M}, title = {Decoding the link between microbial secondary metabolites and colorectal cancer.}, journal = {Computational biology and chemistry}, volume = {115}, number = {}, pages = {108372}, doi = {10.1016/j.compbiolchem.2025.108372}, pmid = {39923290}, issn = {1476-928X}, abstract = {Colorectal cancer (CRC) is a prevalent form of cancer in humans, with the gut microbiota playing a significant role in its pathogenesis. Although previous research has primarily focused on the role of primary metabolites produced by gut microbes in CRC development, the role of secondary metabolites remains largely unexplored. Secondary metabolites are known to mediate crucial interactions between the microbiota and the host, potentially influencing CRC progression. However, their specific relationship to CRC pathogenesis is poorly understood. To address this gap, we performed a meta-analysis using fecal metagenomic data from a cohort of CRC patients and healthy controls, aiming to identify CRC-associated microbial secondary metabolite biosynthetic gene clusters (BGCs). Our findings not only provide valuable insights into the pathogenicity and carcinogenicity of CRC but also shed light on the potential mechanisms underlying its development.}, }
@article {pmid39923152, year = {2024}, author = {Ting-Ting, L and Pi-Hong, L and Cai-Liang, P and Nai-Zhi, G}, title = {Chinese medicine to regulate intestinal bacteria in the treatment of atherosclerosis: A review.}, journal = {Pakistan journal of pharmaceutical sciences}, volume = {37}, number = {6}, pages = {1599-1607}, pmid = {39923152}, issn = {1011-601X}, mesh = {*Atherosclerosis/microbiology/drug therapy/metabolism ; Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; *Drugs, Chinese Herbal/therapeutic use/pharmacology ; *Medicine, Chinese Traditional/methods ; Animals ; Dysbiosis ; }, abstract = {In recent years, several studies have shown that the stability of intestinal bacteria, which acts as a natural barrier, plays a key role fighting against cardiovascular disease. Dysbiosis of the gut microbiome can trigger inflammatory responses and oxidative stress damage, cause abnormal cholesterol metabolism and disrupt the levels of short-chain fatty acids, oxidized trimethylamine and bile acids, thus influencing the occurrence and development of atherosclerosis. Chinese medicine believes that the formation of atherosclerosis is related to the malfunction of the spleen in transportation and transformation, with the interplay of phlegm and blood stagnation being the primary pathogenesis. In addition, the gut micro biome is inextricably linked to the spleen. Ancient medical books recorded "the spleen is the source of phlegm production" and "the heart and small intestine are in close proximity to each other", exploring its TCM pathogenesis from the perspective of phlegm and stasis. Therefore, this review explores the mechanisms by which intestinal micro biota affects atherosclerosis and summarizes the role of Chinese herbal medicine in modulating intestinal microbes in the treatment of AS, providing new ideas for the prevention and treatment of cardiovascular disease.}, }
@article {pmid39922995, year = {2025}, author = {Xu, W and Li, L and Kang, H and Wang, M and Liu, Y and Wang, G and Yu, P and Liang, J and Liu, Z}, title = {Amniotic fluid microbiota and metabolism with non-syndromic congenital heart defects: a multi-omics analysis.}, journal = {BMC pregnancy and childbirth}, volume = {25}, number = {1}, pages = {130}, pmid = {39922995}, issn = {1471-2393}, support = {2023NSFSC1642//the National Natural Science Foundation of Sichuan Province for Young Scholars/ ; 2014FY110700//the Special Project for Basic Work of Science &amp; Technology/ ; 82103858//the National Natural Science Foundation of China/ ; 2021YJ0212//the Applied Basic Research Program of Sichuan Province/ ; 21PJ057//the Popularization Application Project of Sichuan Province/ ; }, mesh = {Humans ; Female ; *Amniotic Fluid/microbiology/metabolism ; Case-Control Studies ; *Heart Defects, Congenital/microbiology/metabolism ; Pregnancy ; *Microbiota ; Adult ; *Metabolomics/methods ; RNA, Ribosomal, 16S ; Pregnancy Trimester, Third/metabolism ; Pregnancy Trimester, Second/metabolism ; Metabolome ; Multiomics ; }, abstract = {BACKGROUND AND AIMS: Recent studies have indicated possible links between the microbiota and the fetal heart, while the relevant mechanism is still unknown. This study is aims to investigate whether analyzing the microbiota and metabolic profiles of amniotic fluid collected from pregnant women whose fetuses with or without non-syndromic congenital heart defects (CHDs), during the second and third trimester of pregnancy, could offer valuable insights into CHDs.<br><br>METHODS AND RESULTS: A case-control study was conducted with 17 cases diagnosed with non-syndromic CHDs (CHDs group) and 34 controls without congenital anomalies (control group) at a ratio of 1:2. The 16&#xa0;S rDNA gene sequencing and metabolomics methods were employed to assess 51 amniotic fluid samples. The amniotic fluid microbiome from the CHDs group exhibited significantly higher Shannon and Simpson indices compared to the control group. At the genus level, 240 bacterial taxa were substantially enriched in the two groups, with 93 of those taxa being highly enriched in the case group. Compared to the control group, the case group exhibited 177 metabolites that were significantly increased and 480 metabolites that were down-regulated. The differential metabolites were primarily enriched in the steroid hormone biosynthesis, bile secretion and ovarian steroidogenesis, according to KEGG analysis. The observed variations in nine metabolites could attributed to fifty-eight distinct bacterial taxa. The nine differential metabolites were mainly associated with pathways involving steroid hormone biosynthesis, bile secretion, glycolysis, tricarboxylic acid (TCA) cycle, NADPH metabolism, and acyl transfer pathways.<br><br>CONCLUSION: The CHDs group has disturbed amniotic fluid microbiota and metabolites, and more research was required to elucidate the mechanism.}, }
@article {pmid39922984, year = {2025}, author = {Xu, R and Chen, W and Chen, S and Wang, X and Xu, J and Zhang, Y and Ma, Y}, title = {Unraveling the Rhubarb (Rheum officinale Baill.) Root and Rhizosphere Microbial Communities in Response to Pathogen Exposure.}, journal = {Molecular biotechnology}, volume = {}, number = {}, pages = {}, pmid = {39922984}, issn = {1559-0305}, support = {2024QCY-KXJ-105//Department of Science and Technology of Shaanxi Province and the Bureau of Science/ ; L2023-ZDKJ-QCY-SXGG-GY-013//Collaborative Innovation Center for Water Treatment Technology and Materials/ ; }, abstract = {This study investigated the microbial community composition and structure in healthy and diseased rhubarb (Rheum rhabarbarum) root systems, examining both root tissue and rhizosphere environments. Alpha diversity analysis revealed significantly higher microbial abundance in the rhizosphere compared to root tissues, with notable differences between healthy and diseased plants. Principal coordinate analysis demonstrated that bacterial community composition was primarily influenced by ecological niches (47.5% variation explained), whereas fungal communities segregated based on plant health status. Network analysis revealed increased bacterial community complexity in diseased plants rhizosphere (579 nodes, 13,016 edges) compared to healthy plants (542 nodes, 8700 edges), while fungal networks showed opposite trends with significant reduction in diseased conditions (147 nodes, 30 edges vs. 205 nodes, 418 edges). Correlation analysis identified significant associations between specific microbial taxa and soil properties, with notable positive correlations between certain bacteria (Oscillospirales) and fungi (Barnettozyma, Mortierella) with soil organic matter and nutrient availability. Pathogenic taxa, including Fusarium and members of Burkholderiales, showed negative correlations with beneficial microorganisms, suggesting potential antagonistic relationships. These findings provide crucial insights into the complex interactions within the rhubarb root microbiome and their implications for plant health, contributing to our understanding of root rot disease dynamics and potential management strategies.}, }
@article {pmid39922818, year = {2025}, author = {Gutierrez, MW and van Tilburg Bernardes, E and Ren, E and Kalbfleisch, KN and Day, M and Lameu, EL and Glatthardt, T and Mercer, EM and Sharma, S and Zhang, H and Al-Azawy, A and Chleilat, F and Hirota, SA and Reimer, RA and Arrieta, MC}, title = {Early-life gut mycobiome core species modulate metabolic health in mice.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1467}, pmid = {39922818}, issn = {2041-1723}, support = {RGPIN-2018-04305//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Mycobiome ; Mice ; *Obesity/microbiology/metabolism ; Mice, Inbred C57BL ; Male ; Diet, High-Fat/adverse effects ; Candida albicans ; Germ-Free Life ; Adiposity ; }, abstract = {The gut microbiome causally contributes to obesity; however, the role of fungi remains understudied. We previously identified three core species of the infant gut mycobiome (Rhodotorula mucilaginosa, Malassezia restricta and Candida albicans) that correlated with body mass index, however their causal contributions to obesity development are unknown. Here we show the effects of early-life colonization by these fungal species on metabolic health in gnotobiotic mice fed standard (SD) or high-fat-high-sucrose (HFHS) diets. Each species resulted in bacterial microbiome compositional and functional differences. R. mucilaginosa and M. restricta increased adiposity in mice fed SD, while only R. mucilaginosa exacerbated metabolic disease. In contrast, C. albicans resulted in leanness and resistance to diet-induced obesity. Intestinal nutrient transporter expression was unaffected by the presence of fungi in jejunal enteroids, yet the immune landscape in white adipose tissue was distinctly impacted by each fungal species, suggesting that these phenotypes may be a result of fungal immune regulation. This work revealed that three common fungal colonizers have distinct causal influences on obesity and metabolic inflammation and justifies the consideration of fungi in microbiome research on host metabolism.}, }
@article {pmid39922591, year = {2025}, author = {Osagie, E and Akhigbe, P and Idemudia, N and Obuekwe, O and Adebiyi, R and Schlecht, N and Liu, J and Bromberg, Y and Eki-Udoko, FE and Osazuwa-Peters, N and Coker, MO}, title = {Human Papillomavirus, Human Immunodeficiency Virus, and Oral Microbiota Interplay in Nigerian Youth (HOMINY): A Prospective Cohort Study Protocol.}, journal = {BMJ open}, volume = {15}, number = {2}, pages = {e091017}, doi = {10.1136/bmjopen-2024-091017}, pmid = {39922591}, issn = {2044-6055}, mesh = {Humans ; Prospective Studies ; Adolescent ; Nigeria/epidemiology ; *HIV Infections/microbiology/epidemiology ; *Papillomavirus Infections/epidemiology ; *Microbiota ; Female ; Child ; Male ; Mouth/microbiology/virology ; Research Design ; Adult ; Saliva/microbiology/virology ; Human Papillomavirus Viruses ; }, abstract = {INTRODUCTION: Persistent oral infections with high-risk human papillomavirus (HR-HPV) are a potential cause of most oropharyngeal cancers (OPCs). Oral HR-HPV infection and persistence are significantly higher in people living with HIV (PLWH). Most data on oral HR-HPV in PLWH come from developed countries or adult cohorts. This study aims to investigate oral HR-HPV susceptibility and persistence among children and adolescents living with HIV (CALHIV) and to understand the roles of perinatal HIV exposure, infection, antiretroviral treatment, and the oral microbiome.<br><br>METHODS AND ANALYSIS: This prospective cohort study is ongoing at the University of Benin Teaching Hospital (UBTH), Nigeria, involving mother-child pairs followed at 6-month intervals for 2 years. Participants include children aged 9-18 and their mothers aged 18 and above. The study targets 690 adolescents in three groups: 230 CALHIV, 230 HIV-exposed but uninfected and 230 HIV-unexposed and uninfected. Oral rinse, saliva, buccal swabs and supragingival plaque samples are collected at each visit. Blood samples are tested for HIV, Hepatitis B virus (HBV) and Hepatitis C virus (HCV), with CD4, CD8 and full blood counts performed. Oral HPV is assessed for incidence, persistence, and clearance. Statistical analyses to look for associations between cohort baseline characteristics and findings will be conducted using univariable and multivariable models for repeated data and high-dimensional microbiome data. All statistical tests will be two-sided; a p value <0.05&#x2009;will indicate significance. Multiple comparisons will be adjusted using the False Discovery Rate (FDR) correction to control for Type I error.<br><br>ETHICS AND DISSEMINATION: The study was approved by Rutgers State University (Pro2022000949) and the UBTH (ADM/E22/A/VOL. VII/14813674). Informed consent was obtained from all parents/guardians.}, }
@article {pmid39922090, year = {2025}, author = {Wei, C and Ye, L and Tang, S and Chen, P and Huang, J and Zhi, Z}, title = {The association between preoperative vaginal dysbiosis and endometrial polyp recurrence after hysteroscopic polypectomy: A retrospective-prospective cohort study.}, journal = {European journal of obstetrics, gynecology, and reproductive biology}, volume = {307}, number = {}, pages = {148-153}, doi = {10.1016/j.ejogrb.2025.02.002}, pmid = {39922090}, issn = {1872-7654}, abstract = {AIM: To explore whether preoperative vaginal dysbiosis influences the recurrence of endometrial polyps after hysteroscopic polypectomy.<br><br>DESIGN: Retrospective-prospective observational cohort study.<br><br>METHODS: A total of 679 patients from our university-affiliated hospital were included in this study. All patients underwent hysteroscopic polypectomy and were subsequently monitored for endometrial polyp recurrence through transvaginal ultrasonography at six-month intervals. Comprehensive clinical data were collected, encompassing preoperative vaginal dysbiosis, parity, polyp size, polyp number, the presence of uterine fibroids, polycystic ovary syndrome, endometriosis, and body mass index. The cohort was categorized into recurrence and non-recurrence groups, with comparative analyses conducted to assess the impact of these factors.<br><br>RESULTS: Preoperative vaginal dysbiosis and endometriosis were significantly associated with endometrial polyp recurrence (P&#xa0;<&#xa0;0.05). The odds ratio (OR) for preoperative vaginal dysbiosis was 3.286 (95&#xa0;% confidence interval [CI]: 2.675-3.786), and for endometriosis, it was 3.328 (95&#xa0;% CI: 2.567-3.643). Further analysis revealed that bacterial density, bacterial diversity, and the Lactobacillus detection rate were significantly higher in the non-recurrence group compared to the recurrence group (P&#xa0;<&#xa0;0.05). In contrast, increased leukocyte esterase activity, Gardnerella vaginalis presence, and Candida detection were significantly more prevalent in the recurrence group than in the non-recurrence group (P&#xa0;<&#xa0;0.05).<br><br>CONCLUSION: This study identifies preoperative vaginal dysbiosis as an independent risk factor for Endometrial Polyp recurrence after Hysteroscopic Polypectomy. Endometriosis is also associated with recurrence. Close monitoring of preoperative vaginal microecological parameters and targeted interventions could help manage dysbiosis and reduce recurrence.<br><br>IRB APPROVAL: The First Affiliated Hospital of Guangxi Medical University Ethical Review Committee. Approval number: 2024-E817-01.}, }
@article {pmid39921918, year = {2025}, author = {Favaron, A and Abdalla, Y and Basit, A and Orlu, M}, title = {Ai's role in colon-targeted drug delivery.}, journal = {Expert opinion on drug delivery}, volume = {}, number = {}, pages = {}, doi = {10.1080/17425247.2025.2465769}, pmid = {39921918}, issn = {1744-7593}, }
@article {pmid39921821, year = {2025}, author = {Zhang, S and Huang, J and Jiang, Z and Tong, H and Ma, X and Liu, Y}, title = {Tumor microbiome: roles in tumor initiation, progression, and therapy.}, journal = {Molecular biomedicine}, volume = {6}, number = {1}, pages = {9}, pmid = {39921821}, issn = {2662-8651}, support = {1.3.5 project for disciplines of excellence//West China Hospital, Sichuan University/ ; }, mesh = {Humans ; *Neoplasms/microbiology/therapy/immunology/pathology ; *Microbiota/physiology ; *Tumor Microenvironment/immunology ; *Disease Progression ; Animals ; }, abstract = {Over the past few years, the tumor microbiome is increasingly recognized for its multifaceted involvement in cancer initiation, progression, and metastasis. With the application of 16S ribosomal ribonucleic acid (16S rRNA) sequencing, the intratumoral microbiome, also referred to as tumor-intrinsic or tumor-resident microbiome, has also been found to play a significant role in the tumor microenvironment (TME). Understanding their complex functions is critical for identifying new therapeutic avenues and improving treatment outcomes. This review first summarizes the origins and composition of these microbial communities, emphasizing their adapted diversity across a diverse range of tumor types and stages. Moreover, we outline the general mechanisms by which specific microbes induce tumor initiation, including the activation of carcinogenic pathways, deoxyribonucleic acid (DNA) damage, epigenetic modifications, and chronic inflammation. We further propose the tumor microbiome may evade immunity and promote angiogenesis to support tumor progression, while uncovering specific microbial influences on each step of the metastatic cascade, such as invasion, circulation, and seeding in secondary sites. Additionally, tumor microbiome is closely associated with drug resistance and influences therapeutic efficacy by modulating immune responses, drug metabolism, and apoptotic pathways. Furthermore, we explore innovative microbe-based therapeutic strategies, such as engineered bacteria, oncolytic virotherapy, and other modalities aimed at enhancing immunotherapeutic efficacy, paving the way for microbiome-centered cancer treatment frameworks.}, }
@article {pmid39921778, year = {2025}, author = {Ros, M and Lidon, P and Carrascosa, A and Muñoz, M and Navarro, MV and Orts, JM and Pascual, JA}, title = {Polyurethane foam degradation combining ozonization and mealworm biodegradation and its exploitation.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {39921778}, issn = {1614-7499}, abstract = {The biodegradation of polyurethane foam (PU foam) using a combination of oxidative pre-treatment (ozonization) and Tenebrio molitor (T. molitor) mealworms was conducted in this study. Different degrees of ozone oxidation (0%, 25%, and 50%) were applied to PU foam, which was subsequently fed to mealworms. The mealworms' survival and growth were then compared to mealworms receiving a normal diet (bran). Results showed that mealworms fed with non-oxidized PU foam (PUF0) exhibited a higher consumption rate (11.8%) than those fed with 25% (PUF25) and 50% (PUF50) oxidized PU foam (7.7% and 5.7%, respectively). The survival rate was similar across all the PU foam diets and the bran diet. Fourier transform infrared (FTIR) spectroscopy and differential scanning calorimetry (DSC) analyses revealed minor structural changes in the PU foam. The gut microbiota analysis showed a significant correlation between the PU foam and bran diets. Among the different oxidized PU, distinct microbial community profiles were also observed, with the genus Klebsiella consistently present across the PU foam diets. The ozone pre-treatment altered the palatability and degradation of the PU foam by mealworms, while the mealworm frass and chitin obtained could potentially be used as resources for agricultural and industrial applications that would close the circular bio-economy cycle.}, }
@article {pmid39921663, year = {2025}, author = {Kramer, J and Maréchal, S and Figueiredo, ART and Kümmerli, R}, title = {Strain identity effects contribute more to Pseudomonas community functioning than strain interactions.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf025}, pmid = {39921663}, issn = {1751-7370}, abstract = {Microbial communities can shape key ecological services, but the determinants of their functioning often remain little understood. While traditional research predominantly focuses on effects related to species identity (community composition and species richness), recent work increasingly explores the impact of species interactions on community functioning. Here, we conducted experiments with replicated small communities of Pseudomonas bacteria to quantify the relative importance of strain identity versus interaction effects on two important functions, community productivity and siderophore production. By combining supernatant and competition assays with an established linear model method, we show that both factors have significant effects on functioning, but identity effects generally outweigh strain interaction effects. These results hold irrespective of whether strain interactions are inferred statistically or approximated experimentally. Our results have implications for microbiome engineering, as the success of approaches aiming to induce beneficial (probiotic) strain interactions will be sensitive to strain identity effects in many communities.}, }
@article {pmid39921560, year = {2025}, author = {Matos, GA and Nunes-Costa, D and Pinto, DV and Martins, CS and Silva, JL and Leocadio, PCL and Andrade, MER and Raposo, RS and Tiago, I and Alarico, S and Santos, EA and Cardoso, VN and Santos, FA and Alvarez-Leite, JI and Empadinhas, N and Oriá, RB}, title = {Methylmercury Chronic Exposure and a High-Fat Diet Induce Gut Microbiome Alterations and Intestinal Barrier Disruption in Mice.}, journal = {Environmental toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1002/tox.24469}, pmid = {39921560}, issn = {1522-7278}, support = {071/2013 # 144494//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 402738/2021-7//Funda&#xe7;&#xe3;o Cearense de Apoio ao Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; CNPq/MCTI/FNDCT call n&#xba; 18/2021//Funda&#xe7;&#xe3;o Cearense de Apoio ao Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, abstract = {Methylmercury (MeHg) is markedly toxic to humans. Our study explores whether MeHg and high-fat diet (HFD) can impair the intestinal barrier with microbiota dysbiosis in mice. Weanling mice were fed to HFD or standard diet for 40 days. In the last 20 days of diets, mice received either MeHg (20 mg/L) or drinking water. Proximal small intestine, cecum, and hair samples were collected. Villus length, crypt depth, villus/crypt length, mucin2 and lysozyme-positive cell counts, ZO-1 and occludin gene expression, and intestinal functional permeability were analyzed to assess the intestinal barrier. Blood samples were drawn to assess lipid parameters. Gut microbiome profiling was conducted with DNA from fecal/cecal samples. In addition, we analyzed ZO-1 immunofluorescence in the colon and small intestine. HFD increased MDA, Mucin2, and reduced villus height, crypt depth, villus/crypt length, lysozyme(+)-cell count, and increased intestinal permeability, regardless of MeHg intoxication. MeHg-HFD combination affected the intestinal barrier, decreasing ZO-1, occludin, and Nrf2 transcription, and increased permeability. HFD increased total plasma cholesterol and triglycerides. Only MeHg-HFD reduced microbiome alpha-diversity along with colonic ZO-1 immunolabeling loss compared to non-intoxicated mice fed a control diet. Regardless of diet, the genera Streptococcus, Psychrobacter, Facklamia, and Corynebacterium were severely depleted following MeHg intoxication. Other groups, such as Atopostipes and Jeotgalicoccus, were not altered by MeHg or HFD alone, but were significantly reduced by the combined HFD-MeHg. Synergistic effects of MeHg-HFD on the mucosa-associated microbiota are more pronounced than their individual effects. Our findings suggest that MeHg intoxication does not cause extensive dysbiosis but led to intestinal barrier disruption.}, }
@article {pmid39921114, year = {2025}, author = {Farooq, S and Talat, A and Dhariwal, A and Petersen, FC and Khan, AU}, title = {Transgenerational Gut Dysbiosis: Unveiling the Dynamics of Antibiotic Resistance through Mobile Genetic Elements from Mothers to Infants.}, journal = {International journal of antimicrobial agents}, volume = {}, number = {}, pages = {107458}, doi = {10.1016/j.ijantimicag.2025.107458}, pmid = {39921114}, issn = {1872-7913}, abstract = {The initial microbial colonization of the gut is seeded by microbes transmitted from the mother's gut, skin, and vaginal tract. As the gut microbiome evolves, a few transmitted microbes persist throughout life. Understanding the impact of mother-to-neonate gut microbiome and antibiotic resistance genes (ARGs) transmission is crucial for establishing its role in infants' immunity against pathogens. This study primarily explores mother-neonate ARG transmission through 125 publicly available fecal metagenomes, isolated from eighteen mother-neonate pairs. The core ARGs, detected in both mothers and their respective infants at all stages (birth, 1[st], 2[nd], 3[rd], 4[th], 8[th] and 12[th] months) included aminoglycosidases APH(3')-IIIa, Bifidobacterium adolescentis rpoB mutants conferring resistance to rifampicin, β-lactamases CblA-1, CfxA2, multi-drug resistance gene CRP, diaminopyrimidine resistance gene dfrF, fluoroquinolone-resistance gene emrR, macrolide; lincosamide; streptogramin resistance gene ErmB, ErmG, macrolide resistance gene Mef(En2), nucleosidase SAT-4, and tetracycline-resistance genes tet(O), tet(Q), and tet(W). Most of these infants and mothers were not administered any antibiotics. In infants, ARGs were predominantly carried by Bacillota, Pseudomonadota, and Actinomycetota, similar to the mothers. The dominant ARG-carrying opportunistic pathogens were Escherichia coli, Klebsiella, and Streptococcus, found across all infant cohorts. All the core ARGs were associated with mobile genetic elements, signifying the role of horizontal gene transfer(HGT). We detected 132 virulence determinants, mostly Escherichia coli-specific, including pilus chaperones, general secretion pathway proteins, type III secretion system effectors, and heme-binding proteins. Maternal-neonate transmission of ARGs along with possible nosocomial infections, mode of delivery, breastfeeding versus formula feeding, and gestation period, must be considered for mother-neonate health.}, }
@article {pmid39921084, year = {2025}, author = {Karched, M and Alyahya, A and Khalaf, ME and Bhardwaj, RG and Al-Sane, M and Qudeimat, MA}, title = {Comparative Analysis of Salivary Cytokine Profiles and Oral Microbial Composition in Caries-Active and Caries-Free Children.}, journal = {Journal of dentistry}, volume = {}, number = {}, pages = {105611}, doi = {10.1016/j.jdent.2025.105611}, pmid = {39921084}, issn = {1879-176X}, abstract = {AIM: This study aimed to evaluate salivary cytokine levels and the prevalence of cariogenic bacterial species in children with active dental caries compared to caries-free peers.<br><br>METHODS: This cross-sectional study involved forty randomly selected children aged 7-9 years, who were divided into caries-active or caries-free groups. DNA was extracted from supragingival plaque using the DNeasy kit and analysed. Microbial profiling was conducted using HOMINGS 16S rRNA gene sequencing. Saliva samples were also collected and analysed using multiplex cytokine bead assays on the Luminex system to assess cytokine levels.<br><br>RESULTS: The caries-active group exhibited significantly higher relative abundance of genera Leptotrichia, Veillonella, and Kingella (p<0.05). At the species level, Streptococcus sanguinis, Leptotrichia shahii, Streptococcus mutans, Leptotrichia sp. HOT_498, TM7[G-1] sp. HOT_346, Rothia dentocariosa were significantly enriched in the caries-active group. In females, IL-15 and IL-1&#x3b2; were significantly elevated in the caries-active group, with no cytokine differences observed in males or overall levels. The relative abundance of Leptotrichia shahii, Streptococcus mutans, Streptococcus sanguinis, TM7[G-1] sp. HOT_346, Abiotrophia defectiva, and Rothia dentocariosa significantly correlated with cytokines, including Aggrecan, BAFF, CD-40L, IL-1&#x3b2;, IL-5, IL-8, IL-11, IL-15, IL-17, IL-23, IL-28A, MIP-3&#x3b1;, Pentraxin 3, and TNF-&#x3b1;. In the caries-free group, only Leptotrichia hongkongensis showed a significant association with IL-10.<br><br>CONCLUSION: Distinct microbiome differences at both the genus and species levels were observed between caries-active and caries-free groups. Salivary cytokine levels were similar between the groups, except for higher IL-15 and IL-1&#x3b2; in females from the caries-active group. Correlations between bacteria and cytokines in the caries-active group highlight the need for further research on the microbiome-immune interaction in caries development.<br><br>CLINICAL SIGNIFICANCE: Microbiome profiles, cytokine levels, and their potential correlation in caries-active children suggest that further study and understanding of these factors could help identify individuals at higher risk for caries and guide preventive care.}, }
@article {pmid39921042, year = {2025}, author = {Bhosale, VB and Koparde, AA and Thorat, VM}, title = {Vulvovaginal Candidiasis-An Overview of Current Trends and the Latest Treatment Strategies.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {107359}, doi = {10.1016/j.micpath.2025.107359}, pmid = {39921042}, issn = {1096-1208}, abstract = {Vulvovaginal candidiasis (VVC) is becoming more common, mostly affecting hospitalized and immunocompromised people. Candida albicans, among other species, is a significant causal agent, accounting for 90% of infections. VVC, which affects up to 75% of women, causes physical and psychological problems, with Candida albicans being associated in 85-95% of cases(Dantas-Medeiros et al., 2023, Tomas et al., 2021, Dantas-Medeiros et al., 2021). Its physical symptoms include genital discomfort, decreased sexual pleasure, and psychological suffering. According to comparative research, pregnant women had a greater VVC prevalence, which can be ascribed to hormonal changes, poor hygiene, and diabetes. Antifungal medicines, which are widely used for therapy, have resulted in resistance issues, demanding a rethinking of therapeutic techniques. There are still diagnostic hurdles, with symptoms overlapping with other illnesses necessitating rigorous examination and laboratory tests. Recurrent Vulvovaginal Candidiasis (RVVC) affects 138 million women each year, causing morbidity and lowering quality of life. Financial constraints highlight the importance of novel, well-tolerated medicines. Resistance to antifungal drugs, notably azoles, complicates therapy. Probiotics, which focus on vaginal microbiome balance, appear as viable preventative strategies. From menarche to menopause, hormonal changes increase susceptibility to VVC, with estrogen playing a critical role. The growing resistance and limited antifungal alternatives, translating research in to clinical practice is critical. Current care is based on antifungals, but problems continue, necessitating the investigation of new drugs. Oteseconazole and ibrexafungerp show promise and have the potential to change RVVC therapy. While useful, probiotics generally supplement standard antifungal methods. In conclusion, tackling the growing difficulties of VVC necessitates ongoing research, novel therapeutics, and possible vaccine development in order to reduce the significant worldwide burden presented by this common fungal illness.}, }
@article {pmid39920996, year = {2025}, author = {Jiao, X and Li, Y and Hu, Y and Yan, R and Fu, T and Liu, J and Li, Z}, title = {Antibiotic-Induced dysbiosis of the ocular microbiome affects corneal circadian rhythmic activity in mice.}, journal = {Mucosal immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.mucimm.2025.01.010}, pmid = {39920996}, issn = {1935-3456}, abstract = {The ocular surface microbiota plays a critical role in maintaining corneal homeostasis, but its disruption and subsequent effects on corneal functions remain poorly understood. This study investigates how antibiotic-induced microbial depletion affects the corneal circadian transcriptome in C57BL/6J mice. Dysbiosis was induced using a topical antibiotic cocktail, and RNA sequencing was employed to analyze gene expression across eight time points over 24 h. Antibiotic treatment disrupted corneal circadian rhythms, eliminating rhythmicity in 1,812 genes and introducing rhythmicity in 1,928 previously arrhythmic genes. Furthermore, epithelial adhesion was impaired, inflammation was elevated, and neural sensitivity was reduced. More than 50 % of ocular microbial genera exhibited daily oscillations, with six genera showing significant correlations with corneal rhythmic transcripts. Additionally, the administration of TLR agonists restored circadian gene expression patterns, with partial recovery of corneal barrier function and immune homeostasis, further highlighting the potential of microbiota-targeted therapies in treating ocular surface disorders. These findings underscore the critical role of the ocular microbiota in regulating corneal health and suggest that restoring microbial balance via TLR activation may offer new therapeutic avenues for eye diseases.}, }
@article {pmid39920966, year = {2025}, author = {Yang, J and Xu, Z and Wang, X and Zhang, X and Zhu, Y and Guo, J}, title = {Parents greater influenced the fecal microbiome and resistome of ibis nestlings than artifical breeding environment contamination.}, journal = {Environmental research}, volume = {}, number = {}, pages = {121057}, doi = {10.1016/j.envres.2025.121057}, pmid = {39920966}, issn = {1096-0953}, abstract = {The trajectory and dynamics of gut resistome development in the early life of the endangered birds, as well as how they are acquired remain largely unclear. Here, we present a longitudinal study of the fecal microbiome and resistome of crested ibis (Nipponia nippon) chicks in the first three months of life. In addition, the microbiome and resistome in their parental and living environmental samples were also determined for further exploring the possible factors that could affecting their gut resistome. The gut microbiome of ibis chicks contained diverse antibiotic resistance genes (ARGs), dominated by β-lactam, tetracycline, aminoglycoside and macrolide. Novel to this study were the significant, the ARG abundances of ibis chicks were significantly higher than their parents, which would decrease with age. In addition, significant negative correlation between the ARG abundance and microbiome diversity, speculating that the ARG abundances were possibly associated with the gut microbial maturity. Finally, the SourceTracker analysis showed that the microbiota of the ibis parent gut and food were the main sources of ibis chicks microbiota. Collectively, our study showed a trajectory of the resistome and microbiome and the possible influencing factors in the early stage of life in ibises, which would advance our understanding of ARG dynamics in young crested ibis and provide valuable insights into the direction of conservation efforts.}, }
@article {pmid39920864, year = {2025}, author = {Kennedy, EA and Weagley, JS and Kim, AH and Antia, A and DeVeaux, AL and Baldridge, MT}, title = {Bacterial community assembly of specific pathogen-free neonatal mice.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {46}, pmid = {39920864}, issn = {2049-2618}, support = {DGE-1745038//National Science Foundation/ ; F31AI167499/NH/NIH HHS/United States ; T32AI007172/NH/NIH HHS/United States ; T32AI007163/NH/NIH HHS/United States ; R01AI139314/NH/NIH HHS/United States ; 1065897//Crohn's and Colitis Foundation/ ; }, mesh = {Animals ; Mice ; *Feces/microbiology ; *Animals, Newborn/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Female ; Specific Pathogen-Free Organisms ; *Mice, Inbred C57BL ; *Mice, Inbred BALB C ; Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Microbiota ; }, abstract = {BACKGROUND: Neonatal mice are frequently used to model diseases that affect human infants. Microbial community composition has been shown to impact disease progression in these models. Despite this, the maturation of the early-life murine microbiome has not been well-characterized. We address this gap by characterizing the assembly of the bacterial microbiota of C57BL/6 and BALB/c litters from birth to adulthood across multiple independent litters.<br><br>RESULTS: The fecal microbiome of young pups is dominated by only a few pioneering bacterial taxa. These taxa are present at low levels in the microbiota of multiple maternal body sites, precluding a clear identification of maternal source. The pup microbiota begins diversifying after 14&#xa0;days, coinciding with the beginning of coprophagy and the consumption of solid foods. Pup stool bacterial community composition and diversity are not significantly different from dams from day 21 onwards. Short-read shotgun sequencing-based metagenomic profiling of young pups enabled the assembly of metagenome-assembled genomes for strain-level analysis of these pioneer Ligilactobacillus, Streptococcus, and Proteus species.<br><br>CONCLUSIONS: Assembly of the murine microbiome occurs over the first weeks of postnatal life and is largely complete by day 21. This detailed view of bacterial community development across multiple commonly employed mouse strains informs experimental design, allowing researchers to better target interventions before, during, or after the maturation of the bacterial microbiota. The source of pioneer bacterial strains appears heterogeneous, as the most abundant taxa identified in young pup stool were found at low levels across multiple maternal body sites, suggesting diverse routes for seeding of the murine microbiome. Video Abstract.}, }
@article {pmid39920859, year = {2025}, author = {Zhang, C and Liu, H and Jiang, X and Zhang, Z and Hou, X and Wang, Y and Wang, D and Li, Z and Cao, Y and Wu, S and Huws, SA and Yao, J}, title = {Correction: An integrated microbiome- and metabolome-genome-wide association study reveals the role of heritable ruminal microbial carbohydrate metabolism in lactation performance in Holstein dairy cows.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {47}, pmid = {39920859}, issn = {2049-2618}, }
@article {pmid39920776, year = {2025}, author = {Han, Y and Teng, TM and Han, J and Kim, HS}, title = {Antibiotic-associated changes in Akkermansia muciniphila alter its effects on host metabolic health.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {48}, pmid = {39920776}, issn = {2049-2618}, support = {NRF-2018M3A9F3055923 and NRF-2015M3C9A4053393//The national research foundation of the Republic of Korea/ ; }, mesh = {*Akkermansia/genetics ; Mice ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; Humans ; *Obesity/microbiology ; Penicillins ; Verrucomicrobia/genetics/drug effects ; Mice, Inbred C57BL ; Mutation ; beta-Lactamases/genetics/metabolism ; Disease Models, Animal ; Male ; }, abstract = {BACKGROUND: Altered gut microbiota has emerged as a major contributing factor to the etiology of chronic conditions in humans. Antibiotic exposure, historically dating back to the mass production of penicillin in the early 1940s, has been proposed as a primary contributor to the cumulative alteration of microbiota over generations. However, the mechanistic link between the antibiotics-altered microbiota and chronic conditions remains unclear.<br><br>RESULTS: In this study, we discovered that variants of the key beneficial gut microbe, Akkermansia muciniphila, were selected upon exposure to penicillin. These variants had mutations in the promoter of a TEM-type &#x3b2;-lactamase gene or pur genes encoding the de novo purine biosynthesis pathway, and they exhibited compromised abilities to mitigate host obesity in a murine model. Notably, variants of A. muciniphila are prevalent in the human microbiome worldwide.<br><br>CONCLUSIONS: These findings highlight a previously unknown mechanism through which antibiotics influence host health by affecting the beneficial capacities of the key gut microbes. Furthermore, the global prevalence of A. muciniphila variants raises the possibility that these variants contribute to global epidemics of chronic conditions, warranting further investigations in human populations. Video Abstract.}, }
@article {pmid39920623, year = {2025}, author = {Blirup-Plum, SA and Jensen, HE and Hartmann, KT and Nielsen, SS and Pankoke, K and Hansen, MS and Pedersen, KS and Larsen, I and Nielsen, JP and Olsen, JE and Kudirkiene, E and Braunstein, TH and Barington, K}, title = {Can infectious omphalitis in piglets be clinically diagnosed during the first three days of life?.}, journal = {BMC veterinary research}, volume = {21}, number = {1}, pages = {58}, pmid = {39920623}, issn = {1746-6148}, mesh = {Animals ; Swine ; *Swine Diseases/pathology/microbiology/diagnosis ; *Animals, Newborn ; Denmark/epidemiology ; Umbilicus/pathology/microbiology ; Female ; Male ; }, abstract = {BACKGROUND: Globally, the increase in antimicrobial resistance is of great concern. In Denmark, the pig sector is accountable for the majority of antimicrobial usage in animals. As new-born piglets are at risk of developing infectious omphalitis, and many pigs are treated by antimicrobials within the first days of life, an early and accurate diagnosis of the disease is imperative to maintain animal welfare and reduce the antimicrobial usage. The aim of the present study was to compare histopathological and microbiological findings in piglets clinically diagnosed with and without omphalitis during the first three days after birth.<br><br>RESULTS: A total of 98 case piglets with omphalitis and 98 control piglets without omphalitis, based on clinical examinations during the first three days of life, were included. Of the 196 piglets, 79 (38 cases and 41 controls) presented histopathological omphalitis. Post mortem, the volume of the umbilicus was significantly enlarged in cases compared to controls (p&#x2009;=&#x2009;0.01). Except for a group of bacteria unidentified by matrix-assisted laser desorption ionisation time-of-flight (MALDI-TOF) (p&#x2009;=&#x2009;0.02), no apparent association was found between histopathologically diagnosed omphalitis and the prevalence of specific pathogens (p&#x2009;>&#x2009;0.05). The frequency of histopathologically diagnosed omphalitis tended to increase with increasing age in both cases and controls. The frequency of piglets with both histopathological omphalitis and arthritis/synovitis was significantly different among cases and controls (p&#x2009;=&#x2009;0.05). This was due to all controls, and none of the cases, with arthritis/synovitis presented histopathological omphalitis.<br><br>CONCLUSION: The clinical differentiation between omphalitis cases and controls did not correspond to the histological diagnosis of omphalitis in zero-to-three days old piglets. An inaccurate clinical diagnosis complicates prudent use of antimicrobials in pig herds. In addition, animal welfare may be hampered in infected piglets due to lack of treatment and in healthy piglets due to the antimicrobial effect on the gut microbiome.}, }
@article {pmid39920446, year = {2025}, author = {Ledford, H}, title = {Engineered nose bacteria sneak drugs into the brain.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {39920446}, issn = {1476-4687}, }
@article {pmid39920217, year = {2025}, author = {Szoke, Z and Fauszt, P and Mikolas, M and David, P and Szilagyi-Tolnai, E and Pesti-Asboth, G and Homoki, JR and Kovacs-Forgacs, I and Gal, F and Stundl, L and Czegledi, L and Stagel, A and Biro, S and Remenyik, J and Paholcsek, M}, title = {Comprehensive analysis of antimicrobial resistance dynamics among broiler and duck intensive production systems.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {4673}, pmid = {39920217}, issn = {2045-2322}, mesh = {Animals ; *Ducks/microbiology ; *Chickens/microbiology ; *Anti-Bacterial Agents/pharmacology ; Poultry Diseases/microbiology/drug therapy ; Drug Resistance, Bacterial ; Drug Resistance, Multiple, Bacterial/genetics ; Bacteria/drug effects/genetics/classification ; Animal Husbandry/methods ; Microbial Sensitivity Tests ; }, abstract = {Antimicrobial resistance (AMR) is a global health challenge requiring cross-sector action, with research largely focused on chickens, leaving ducks underexplored. This study examines AMR dynamics in Ross 308 broilers and Cherry Valley ducks over 15 months and 15 stocking periods under consistent rearing conditions. A total of 96 pooled samples were collected: 50 from broiler farms (26 biological, 24 environmental) and 46 from duck farms (24 biological, 22 environmental). Using next-generation shotgun sequencing, 3,665 distinct AMR types were identified: 1,918 in broilers and 1,747 in ducks. Host-specific AMRs comprised 25.3% in broilers and 18% in ducks, while 56.7% were shared. AMR diversity declined across production phases, with broilers losing 641 types and ducks losing 308, yet AMR frequencies increased significantly by the finisher phase (p < 0.0001). Based on in silico data, prophylactic antibiotic use significantly reduced the prevalence of multidrug-resistant bacteria in both poultry species (p < 0.05). Hospital-acquired infection-associated AMRs were higher in broilers than in ducks at the start of production but declined significantly by the end of the rearing period (p < 0.0001). Above-average resistance markers accounted for approximately 10% of all detected resistance determinants. Tetracycline and phenicol resistances emerged as the most prevalent. 13 high-resistance carrier (HRC) species were shared between both hosts. Broiler-specific HRCs exhibited significantly higher abundances (relative frequency: 0.08) than duck-specific HRCs (relative frequency: 0.003, p = 0.035). The grower phase emerged as a critical intervention point. In farm environments 15 broiler-specific and 9 duck-specific biomarker species were identified, each strongly correlated with poultry-core HRCs (correlation coefficient > 0.7). Broiler exhibited higher abundances of key resistance genes, with tetracycline resistance predominantly associated with Bacteroides coprosuis, Pasteurella multocida, and Acinetobacter baumannii. Despite its limitations, this research provides key insights into AMR trends in two major poultry types, guiding targeted interventions and sustainable management strategies.}, }
@article {pmid39920171, year = {2025}, author = {Li, J and Xu, J and Jin, J and Xu, C and Gan, Y and Wang, Y and Feng, R and Fan, W and Li, Y and Zhao, X and Li, Y and Gong, S and Su, L and Cai, Y and Shi, L and Sun, X and Xiang, Y and Wang, Q and Li, R and Zhao, J and Liu, Y and Qin, J and Li, Z and He, J}, title = {A Comprehensive Dataset on Microbiome Dynamics in Rheumatoid Arthritis from a Large-Scale Cohort Study.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {232}, pmid = {39920171}, issn = {2052-4463}, mesh = {*Arthritis, Rheumatoid/microbiology ; Humans ; *Gastrointestinal Microbiome ; *RNA, Ribosomal, 16S/genetics ; Cohort Studies ; Female ; Male ; }, abstract = {Alterations in intestinal microbiota have been identified as a key risk factor in rheumatoid arthritis (RA). This study presents a multidimensional gut microbiota profile from a large cohort of RA patients, stratified by disease stage and treatment regimens, and compared to healthy controls. Our dataset comprises gut microbiota profiles from 2,238 individuals, including 1,034 RA patients (Ascia Pacific RA cohort, APRAC) and 1,204 healthy controls. This dataset is enriched with detailed clinical metadata, including patient profiles, treatment histories, and environmental factors, providing a comprehensive "disease exposome" for RA. By integrating 16S rRNA gene sequencing with demographic, clinical, and environmental data, we offer a valuable resource to explore the complex relationships between gut microbiota and RA progression. This large-scale dataset is expected to be a foundation for collaborative research, advancing our understanding of the microbiome's systemic effects in RA and other autoimmune diseases and potentially guiding new therapeutic approaches.}, }
@article {pmid39920168, year = {2025}, author = {Du, Y and Fan, Y and Li, X and Chen, F}, title = {Novel anti-inflammatory properties of mannose oligosaccharides in the treatment of inflammatory bowel disease via LGALS3 modulation.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {26}, pmid = {39920168}, issn = {2055-5008}, support = {2023012150-JH3/4600//Natural Science Foundation of Liaoning Province (Liaoning Provincial Natural Science Foundation)/ ; }, mesh = {*Gastrointestinal Microbiome/drug effects ; *Inflammatory Bowel Diseases/drug therapy ; *Oligosaccharides/pharmacology ; Animals ; Mice ; Humans ; *Mannose/pharmacology ; *Anti-Inflammatory Agents/pharmacology ; Dysbiosis ; Galectins ; Bacteria/classification/drug effects/genetics ; Mice, Inbred C57BL ; Disease Models, Animal ; Cytokines/metabolism ; Male ; }, abstract = {This study investigates the role of Gum Arabic Mannose Oligosaccharides (GA-MOS) in modulating gut microbiota and alleviating symptoms of Inflammatory Bowel Disease (IBD). Employing both in vitro and in vivo models, we explored how GA-MOS influences microbial communities, particularly focusing on their capacity to enhance health-associated bacteria and reduce pathogenic species within the gut environment. Our findings reveal that GA-MOS treatment significantly altered the gut microbiota composition, increasing the abundance of anti-inflammatory bacteria while decreasing pro-inflammatory species, thus contributing to a reduction in gut inflammation and an improvement in intestinal barrier function. Detailed molecular analyses further demonstrated that these changes in microbiota were associated with modifications in the host's immune response, particularly through the suppression of key inflammatory pathways and cytokines involved in IBD progression. These results underscore the potential of dietary polysaccharides like GA-MOS as therapeutic agents in managing dysbiosis and inflammatory conditions in the gut, offering a promising approach for enhancing microbial health and overall disease management in IBD. This study provides novel insights into the bioactive properties of MOS and their interactions with gut microbiota, suggesting broader implications for their use in microbiome-centered therapies.}, }
@article {pmid39920128, year = {2025}, author = {Popova, PV and Isakov, AO and Rusanova, AN and Sitkin, SI and Anopova, AD and Vasukova, EA and Tkachuk, AS and Nemikina, IS and Stepanova, EA and Eriskovskaya, AI and Stepanova, EA and Pustozerov, EA and Kokina, MA and Vasilieva, EY and Vasilyeva, LB and Zgairy, S and Rubin, E and Even, C and Turjeman, S and Pervunina, TM and Grineva, EN and Koren, O and Shlyakhto, EV}, title = {Personalized prediction of glycemic responses to food in women with diet-treated gestational diabetes: the role of the gut microbiota.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {25}, pmid = {39920128}, issn = {2055-5008}, support = {075-15-2022-301//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-301//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-301//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-301//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-301//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-301//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-301//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-301//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-301//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-301//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-301//Ministry of Science and Higher Education of the Russian Federation/ ; 075-15-2022-301//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {Humans ; Female ; Pregnancy ; *Diabetes, Gestational/microbiology ; *Gastrointestinal Microbiome ; Adult ; *Blood Glucose ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; Postprandial Period ; Machine Learning ; Blood Glucose Self-Monitoring/methods ; Diet/methods ; Glycemic Index ; }, abstract = {We developed a prediction model for postprandial glycemic response (PPGR) in pregnant women, including those with diet-treated gestational diabetes mellitus (GDM) and healthy women, and explored the role of gut microbiota in improving prediction accuracy. The study involved 105 pregnant women (77 with GDM, 28 healthy), who underwent continuous glucose monitoring (CGM) for 7 days, provided food diaries, and gave stool samples for microbiome analysis. Machine learning models were created using CGM data, meal content, lifestyle factors, biochemical parameters, and microbiota data (16S rRNA gene sequence analysis). Adding microbiome data increased the explained variance in peak glycemic levels (GLUmax) from 34 to 42% and in incremental area under the glycemic curve (iAUC120) from 50 to 52%. The final model showed better correlation with measured PPGRs than one based only on carbohydrate count (r = 0.72 vs. r = 0.51 for iAUC120). Although microbiome features were important, their contribution to model performance was modest.}, }
@article {pmid39920117, year = {2025}, author = {Wu, J and Liu, S and Zhang, H and Chen, S and Si, J and Liu, L and Wang, Y and Tan, S and Du, Y and Jin, Z and Xie, J and Zhang, D}, title = {Flavones enrich rhizosphere Pseudomonas to enhance nitrogen utilization and secondary root growth in Populus.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1461}, pmid = {39920117}, issn = {2041-1723}, support = {32371906//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Populus/microbiology/growth &amp; development/genetics/metabolism ; *Plant Roots/microbiology/growth &amp; development/metabolism ; *Rhizosphere ; *Nitrogen/metabolism ; *Pseudomonas/genetics/metabolism ; *Soil Microbiology ; Gene Expression Regulation, Plant ; Microbiota ; Flavonoids/metabolism ; Plant Proteins/metabolism/genetics ; }, abstract = {Plant growth behavior is a function of genetic network architecture. The importance of root microbiome variation driving plant functional traits is increasingly recognized, but the genetic mechanisms governing this variation are less studied. Here, we collect roots and rhizosphere soils from nine Populus species belonging to four sections (Leuce, Aigeiros, Tacamahaca, and Turanga), generate metabolite and transcription data for roots and microbiota data for rhizospheres, and conduct comprehensive multi-omics analyses. We demonstrate that the roots of vigorous Leuce poplar enrich more Pseudomonas, compared with the poorly performing poplar. Moreover, we confirm that Pseudomonas is strongly associated with tricin and apigenin biosynthesis and identify that gene GLABRA3 (GL3) is critical for tricin secretion. The elevated tricin secretion via constitutive transcription of PopGL3 and Chalcone synthase (PopCHS4) can drive Pseudomonas colonization in the rhizosphere and further enhance poplar growth, nitrogen acquisition, and secondary root development in nitrogen-poor soil. This study reveals that plant-metabolite-microbe regulation patterns contribute to the poplar fitness and thoroughly decodes the key regulatory mechanisms of tricin, and provides insights into the interactions of the plant's key metabolites with its transcriptome and rhizosphere microbes.}, }
@article {pmid39920009, year = {2025}, author = {Portela, ND and Mena, C and Martín, MG and Burstein, VL and Chiapello, LS and Pesoa, SA}, title = {Effect of DNA extraction method in gut fungal community assessment.}, journal = {Revista Argentina de microbiologia}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ram.2024.12.005}, pmid = {39920009}, issn = {0325-7541}, abstract = {Understanding the gut mycobiota composition and its impact on health requires reliable methods for fungal community assessment. This study explores the influence of DNA extraction methods in GM analysis. Three protocols were evaluated: Qiagen DNeasy blood and tissue kit with mechanical glass bead lysis (DNgb), Thermofisher MagMax Microbiome ultra-nucleic isolation kit automated method (MM), and MM combined with glass beads lysis (MMgb). Fecal samples from healthy volunteers were collected, DNA extracted and ITS2 amplicon library preparation and sequencing performed. Results showed that DNA yields did not significantly differ among methods and the addition of glass bead beating favored the recovery of DNA more appropriate for fungal analysis. Beta diversity revealed distinct clusters, with MMgb showing the most pronounced variation in mycobiota composition, exposing particularly the low abundance taxa. LEfSe analysis identified significant differences in the abundance of fungal species among the extraction methods. Samples extracted with bead beating were enriched in filamentous species, while those without this step showed higher relative abundance of yeast fungi. This study underscores the importance of selecting appropriate DNA extraction methods for accurate characterization of the gut mycobiota, emphasizing the need for standardized methodologies to ensure reproducibility and reliability in microbial data acquisition.}, }
@article {pmid39919958, year = {2025}, author = {Condori-Catachura, S and Ahannach, S and Ticlla, M and Kenfack, J and Livo, E and Anukam, KC and Pinedo-Cancino, V and Collado, MC and Dominguez-Bello, MG and Miller, C and Vinderola, G and Merten, S and Donders, GGG and Gehrmann, T and ,  and Lebeer, S}, title = {Diversity in women and their vaginal microbiota.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2024.12.012}, pmid = {39919958}, issn = {1878-4380}, abstract = {Women's health is essential to global societal and economic wellbeing, yet health disparities remain prevalent. The vaginal microbiota plays a critical role in health, with research indicating that reduced levels of core bacteria, such as lactobacilli, are associated with conditions like bacterial vaginosis (BV) and increased infection susceptibility. Lower levels of vaginal lactobacilli are reported more frequently in women of African and Latin American descent compared with women of European and Asian descent. However, geographical and other study inclusion and analysis biases influence current research. This opinion highlights the need for a more comprehensive understanding of a 'healthy' vaginal microbiome. It underscores efforts to broaden global research on microbiome diversity in socially relevant contexts, avoiding inappropriate applications of terms such as race and ethnicity.}, }
@article {pmid39919878, year = {2025}, author = {Peñalver Bernabé, B and Oliveira, ML and Wolf, PG and McLeod, A and Gabel, K and Cares, K and Robinson, N and DiPiazza, B and Varady, K and Tussing-Humphreys, L}, title = {Intermittent Fasting: Implications for Obesity-Related Colorectal Tumorigenesis.}, journal = {Endocrinology and metabolism clinics of North America}, volume = {54}, number = {1}, pages = {61-83}, doi = {10.1016/j.ecl.2024.10.007}, pmid = {39919878}, issn = {1558-4410}, mesh = {Humans ; *Colorectal Neoplasms/etiology/prevention &amp; control ; *Obesity ; *Fasting/physiology ; *Carcinogenesis/immunology ; *Gastrointestinal Microbiome/physiology ; Intermittent Fasting ; }, abstract = {Obesity is associated with metabolic and immune perturbations (ie, insulin resistance, increased inflammation, and oxidative stress), circadian rhythm dysregulation, and gut microbial changes that can promote colorectal tumorigenesis. Colorectal cancer (CRC) is the third most incident cancer in the United States. This narrative review examines the effects of intermittend fasting on factors influencing colon tumorigenesis, such as body weight, metabolic and immune markers, circadian rythm, and the gut microbiota in humans. Findings suggest that intermittent fasting regimens can lead to weight loss and shifts in metabolic markers, which could be preventive for CRC but effects on the gut microbiota composition and functions still remains elusive.}, }
@article {pmid39919749, year = {2025}, author = {Nevot, G and Santos-Moreno, J and Campamà-Sanz, N and Toloza, L and Parra-Cid, C and Jansen, PAM and Barbier, I and Ledesma-Amaro, R and van den Bogaard, EH and Güell, M}, title = {Synthetically programmed antioxidant delivery by a domesticated skin commensal.}, journal = {Cell systems}, volume = {}, number = {}, pages = {101169}, doi = {10.1016/j.cels.2025.101169}, pmid = {39919749}, issn = {2405-4720}, abstract = {Bacteria represent a promising dynamic delivery system for the treatment of disease. In the skin, the relevant location of Cutibacterium acnes within the hair follicle makes this bacterium an attractive chassis for dermal biotechnological applications. Here, we provide a genetic toolbox for the engineering of this traditionally intractable bacterium, including basic gene expression tools, biocontainment strategies, markerless genetic engineering, and dynamic transcriptional regulation. As a proof of concept, we develop an antioxidant-secreting strain capable of reducing oxidative stress in a UV stress model.}, }
@article {pmid39919718, year = {2025}, author = {Huang, C and Lim, AI}, title = {Pre-birth stem cell education: A gift from mother's bugs.}, journal = {Cell stem cell}, volume = {32}, number = {2}, pages = {175-176}, doi = {10.1016/j.stem.2025.01.009}, pmid = {39919718}, issn = {1875-9777}, mesh = {Humans ; Female ; Animals ; Pregnancy ; *Gastrointestinal Microbiome ; Stem Cells ; TOR Serine-Threonine Kinases/metabolism ; }, abstract = {The maternal gut microbiota undergoes significant changes during pregnancy and plays a pivotal role in offspring development. In this issue, Dang et al. demonstrate that modifying the maternal gut microbiome during pregnancy shapes offspring neural and intestinal stem cells via the mTOR pathway, with long-lasting effects on their functions.}, }
@article {pmid39919593, year = {2025}, author = {Zhang, H and Feng, Y and Yang, H and Li, Y and Ma, Z and Li, L and Chen, L and Zhao, Y and Shan, L and Xia, Y}, title = {The interaction between genetic predicted gut microbiome abundance and particulate matter on the risk of incident asthma in adults.}, journal = {Ecotoxicology and environmental safety}, volume = {291}, number = {}, pages = {117848}, doi = {10.1016/j.ecoenv.2025.117848}, pmid = {39919593}, issn = {1090-2414}, abstract = {Air pollution and gut microbial abundance (GMA) are both closely related with asthma incidence. This study aims to explore significant interact on the risk of incident asthma in adult exist between GMA and PM2.5 exposure based on a prospective cohort of UK Biobank. Polygenic score of GMA was calculated using 19 distinct single nucleotide polymorphisms. PM2.5 exposure was predicted using a validated Land Use Regression model. Incident asthma was identified by linking with medical encounters or first occurrence source. Cox proportional hazards regression models were used to evaluate the associations. Hazard ratios (HRs) and 95 % confidence intervals (CIs) were calculated. During an average follow-up of 11.4 years within 390,054 participants, a total of 11,312 asthma cases occurred with an incidence density of 2.54 per 1000 person years. Participants with the highest PM2.5 and GMA exposure were associated with a 13 % (HR = 1.13, 95 % CI: 1.05, 1.22; Pfor trend < 0.001) higher and 16 % (HR = 0.84, 95 %CI: 0.74, 0.94; Pfor trend < 0.01) lower risk of incident asthma, respectively. A significant negative additive interaction between GMA and PM2.5 exposure with the risk of incident asthma in adult was found (Relative Excess Risk due to Interaction = -0.08, 95 % CI, -0.16, -0.002). Participants with very high GMA and lowest PM2.5 exposure level were associated with a 26 % (HR = 0.74, 95 % CI: 0.57, 0.96) lower risk of incident asthma. A higher level of GMA has the potential to alleviate the detrimental effect of PM2.5 exposure on the risk of asthma in adults. Strategies targeting GMA, such as modifying diet and using probiotics supplement may be helpful for preventing asthma derived from PM2.5 exposure.}, }
@article {pmid39919573, year = {2025}, author = {Yu, C and Li, H and Hua, L and Che, L and Feng, B and Fang, Z and Xu, S and Zhuo, Y and Li, J and Wu, D and Zhang, J and Lin, Y}, title = {Deciphering the microbiome, lipopolysaccharides, and metabolome interplay: Unveiling putrescine's mechanism for enhancing sperm quality in heat-stressed boars.}, journal = {Theriogenology}, volume = {236}, number = {}, pages = {60-73}, doi = {10.1016/j.theriogenology.2025.01.027}, pmid = {39919573}, issn = {1879-3231}, abstract = {Global warming has added to concerns regarding declining male fertility due to high temperatures. As a metabolite of arginine, putrescine improves gut health and promotes testicular development in boar; however, its action in improving semen quality under heat stress is unknown. Therefore, we assessed the effect of putrescine on the semen quality of boars in a heat stress model. Results showed that putrescine ameliorated the heat stress-induced decline in semen quality and testosterone levels in boars, confirmed by sperm viability, immobility rate, and apoptosis levels. Fecal microbial 16S rRNA sequencing showed that heat stress induces intestinal microecological dysregulation triggering an increase in the serum lipopolysaccharide (LPS) levels and reducing boar semen quality. A negative correlation between the Lachnospiraceae_XPB1014_group and LPS-binding protein (LBP) levels was observed. The Lachnospiraceae_XPB1014_group was reduced significantly under heat stress, and its relative abundance significantly increased after putrescine diet, which reduced both LPS and LBP in the serum of heat-stressed boars. Heat stress also affected plasma amino acid metabolism, and the regulation of plasma metabolism by putrescine can be attributed to its effects on LPS and the LBP owing to the significantly correlation of both with multiple plasma differential metabolites. Putrescine is thus considered to inhibit the increased serum LPS by acting on intestinal microorganisms, particularly by increasing the relative abundance of the Lachnospiraceae_XPB1014_group, and further modulate plasma amino acid metabolism to improve the semen quality in heat-stressed boars.}, }
@article {pmid39919466, year = {2025}, author = {Wang, X and Lyu, Y and Cheng, SW and Tsang, TF and Chong, KC and Boon, SS and Yang, X and Lai, CK and Chan, PK and Zuo, Z}, title = {Inter-individual variability in the metabolism of psychotropic drugs by the enzyme activities from the human gut microbiome.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {258}, number = {}, pages = {116717}, doi = {10.1016/j.jpba.2025.116717}, pmid = {39919466}, issn = {1873-264X}, abstract = {The interaction between marketed drugs and the gut microbiome is increasingly being recognized, and it is now known that enzymes produced by the bacteria in the human gut can degrade psychotropic drugs. However, the degree of inter-individual variation in their metabolism remains largely unknown. Here, we present a simple model for detecting individual drug-microbiome interaction using fecalase. We incubated fecalase prepared from freshly collected stool samples from healthy volunteers (n = 18) and incubated with nine selected psychotropic medications. We proved fecalase retained enzymatic activities and showed the degree of drug degradation differed significantly for different psychotropic drugs, and there was significant inter-individual variation in the metabolism of phenytoin, amitriptyline, and chlorpromazine with the inter-individual point difference between the strongest and weakest metabolizer of 85 %, 39 %, and 30 % respectively. These findings highlight the potential of fecalase as a model for studying personalized drug metabolism and underscore the importance of considering gut microbiome variability in pharmacological research.}, }
@article {pmid39919372, year = {2025}, author = {Swain, S and Sahoo, P and Biswal, S and Sethy, K and Panda, AN and Sahoo, N}, title = {Fecal bacterial microbiota diversity characterized for dogs with atopic dermatitis: its alteration and clinical recovery after meat-exclusion diet.}, journal = {American journal of veterinary research}, volume = {}, number = {}, pages = {1-9}, doi = {10.2460/ajvr.24.09.0274}, pmid = {39919372}, issn = {1943-5681}, abstract = {OBJECTIVE: To achieve clinical recovery in canine atopic dermatitis affected pet dogs via alteration of the gut microbiome, following a meat and egg exclusion diet for 60 days.<br><br>METHODS: 24 atopic dermatitis-affected pet dogs, all fed poultry meat and egg, and another 48 apparently healthy controls fed both poultry meat and egg (n = 24) or vegetable diet (24) were included in the study. The study was undertaken in the Bhubaneswar Smart City, Odisha, India, from July to December 2023. Fecal samples were collected at 2 points for DNA analysis, ie, on day 0 and day 60 of the change from a meat/egg-based diet to a vegetable-based diet. Extracted DNA samples were pooled category-wise and subjected to the gut microbiome analysis in the Nanopore sequencer targeting the 16S rRNA gene. Burrows-Wheeler Transform, Ferragina-Manzini index, and Krona charts were used for taxonomical classification and visualization of relative abundances of bacterial species within the metagenome. Alpha- and beta-diversity analyses were performed.<br><br>RESULTS: Atopic pets at day 0 showed elevation in the gut microbiome population with an adequate concentration of pathogens like Escherichia coli and Clostridiodes difficile with lower amounts of the beneficial bacteria like Lactobacillus sp, while the pets at 60 days after dietary intervention showed a significant decline in bacterial species like E coli and C difficile with higher amount of Lactobacillus sp. Both control groups showed variations of microbiome between them as well as from the atopic pets.<br><br>CONCLUSIONS: We found a close association of poultry meat/egg diet with gut microbiome population and atopic symptoms as well in dogs, and elimination of such diet could be helpful in clinical recovery.<br><br>CLINICAL RELEVANCE: Dietary intervention with the exclusion of potential allergens from poultry meat and egg sources can be an effective approach for the management of canine atopic dermatitis.}, }
@article {pmid39919360, year = {2025}, author = {Lemons, JMS and Narrowe, AB and Firrman, J and Mahalak, KK and Liu, L and Higgins, S and Moustafa, AM and Baudot, A and Deyaert, S and Van den Abbeele, P}, title = {The food additive butylated hydroxyanisole minimally affects the human gut microbiome ex vivo.}, journal = {Food chemistry}, volume = {473}, number = {}, pages = {143037}, doi = {10.1016/j.foodchem.2025.143037}, pmid = {39919360}, issn = {1873-7072}, abstract = {Butylated hydroxyanisole (BHA) continues to raise consumer concerns. All previous evaluations of this additive have failed to consider its effect on the gut microbiome, even though it enters the colon. An ex vivo model was used to assess the effect of BHA on microbial communities from 24 donors, aged infants to older adults. A dose of 0.35 g/L BHA elicited no statistically significant changes in the functional outputs or community structure for any age group. Although not large enough to affect community diversity, there were some significant decreases at the phylum level. Among the genes most significantly affected by treatment with BHA across age groups are those involved in lipopolysaccharide synthesis and bacterial electron transport encoded by Bacteroidota, Proteobacteria, and Verrucomicrobiota. Given what is known about the intracellular activity of BHA, these genes may hint at a mechanism behind BHA's evident, but minimally detrimental effect on the gut microbiota.}, }
@article {pmid39919201, year = {2025}, author = {Liu, C and Chen, Z and Wang, X and Deng, Y and Tao, L and Zhou, X and Deng, J}, title = {Response of Soil Phage Communities and Prokaryote-Phage Interactions to Long-Term Drought.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c08448}, pmid = {39919201}, issn = {1520-5851}, abstract = {Soil moisture is a fundamental factor affecting terrestrial ecosystem functions. In this study, microscopic enumeration and joint metaviromic and metagenomic sequencing were employed together to investigate the impact of prolonged drought on soil phage communities and their interactions with prokaryotes in a subtropical evergreen forest. Our findings revealed a marked reduction in the abundances of prokaryotic and viral-like particles, by 73.1% and 75.2%, respectively, and significantly altered the structure of prokaryotic and phage communities under drought. Meanwhile, drought substantially increased the fraction of prokaryotic communities containing lysogenic phages by 163%, as well as the proportion of temperate phages. Nonetheless, drought likely amplified negative prokaryote-phage interactions given the nearly doubled proportion of negative links in the prokaryote-phage co-occurrence network, as well as the higher frequency and diversity of antiphage defense systems found in prokaryotic genomes. Under drought, soil phages exerted greater top-down control on typical soil k-strategists including Acidobacteria and Chloroflexi. Moreover, phage-encoded auxiliary metabolic genes may impact host metabolism in biosynthesis-related functions. Collectively, the findings of this study underscore the profound impact of drought on soil phages and prokaryote-phage interactions. These results also emphasize the importance of managing soil moisture levels during soil amendment and microbiome manipulation to account for the influence of soil phages.}, }
@article {pmid39918873, year = {2025}, author = {Chhabra, KH and Shoemaker, R and Herath, CB and Thomas, MC and Filipeanu, CM and Lazartigues, E}, title = {Molecular Dissection of the Role of ACE2 in Glucose Homeostasis.}, journal = {Physiological reviews}, volume = {}, number = {}, pages = {}, doi = {10.1152/physrev.00027.2024}, pmid = {39918873}, issn = {1522-1210}, support = {HL150592//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; HL150592//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; BX004294//U.S. Department of Veterans Affairs (VA)/ ; }, abstract = {Angiotensin Converting Enzyme 2 (ACE2) was discovered 25 years ago as a negative regulator of renin-angiotensin system, opposing the effects of angiotensin-II. Beyond its well-demonstrated roles in cardiovascular regulation and Covid-19 pathology, ACE2 is involved in a plethora of physio-pathological processes. In this review, we summarize the latest discoveries on the role of ACE2 in glucose homeostasis and regulation of metabolism. In the endocrine pancreas, ACE2 is expressed at low levels in β cells, but loss of its expression inhibits glucose-stimulated insulin secretion and impairs glucose tolerance. Conversely, overexpression of ACE2 improved glycemia and suggests that recombinant ACE2 might be a future therapy for diabetes. In the skeletal muscle of ACE2-deficient mice, a progressive triglyceride accumulation was observed, whereas in diabetic kidney the initial increase in ACE2 is followed by a chronic reduction of expression in kidney tubules and impairment of glucose metabolism. At the intestinal level, dysregulation of the enzyme alters the amino acid absorption and intestinal microbiome, while at the hepatic level, ACE2 protects against diabetic fatty liver disease. Not least, ACE2 is upregulated in adipocytes in response to nutritional stimuli and administration of recombinant ACE2 decreased body weight and increased thermogenesis. In addition to tissue-specific regulation of ACE2 function, the enzyme undergoes complex cellular posttranslational modifications which are changed during diabetes evolution, with at least proteolytic cleavage and ubiquitination leading to modifications in ACE2 activity. Detailed characterization of ACE2 in specific cellular- and tissue-manner holds promise for improving therapeutic outcomes in diabetes and metabolic disorders.}, }
@article {pmid39918827, year = {2025}, author = {Silva, CBP and Nascimento-Silva, EA and Zaramela, LS and da Costa, BRB and Rodrigues, VF and De Martinis, BS and Carlos, D and Tostes, RC}, title = {Drinking pattern and sex modulate the impact of ethanol consumption on the mouse gut microbiome.}, journal = {Physiological genomics}, volume = {}, number = {}, pages = {}, doi = {10.1152/physiolgenomics.00031.2024}, pmid = {39918827}, issn = {1531-2267}, support = {2020/11339-2//Funda&#x00E7;&#x00E3;o de Amparo &#x00E0; Pesquisa do Estado de S&#x00E3;o Paulo (FAPESP)/ ; 2013/08216-2//Funda&#x00E7;&#x00E3;o de Amparo &#x00E0; Pesquisa do Estado de S&#x00E3;o Paulo (FAPESP)/ ; 2020/08554-9//Center for Research in Inflammatory Diseases/ ; }, abstract = {Background: Gut microbiota impacts host homeostasis and diseases. Chronic plus binge ethanol consumption has been linked to increased injuries than chronic or binge ethanol intake alone. We hypothesized that distinct shapes in gut microbiota composition are induced by chronic, binge and the association of these treatments, thereby affecting host functions and contributing to sex-based differences in alcohol use disorders. Methods: Male and female C57BL/6J mice were submitted to chronic, binge or chronic plus binge ethanol feeding. DNA was extracted from fecal microbiota, followed by analysis of the V3-V4 region of the 16S rRNA gene and sequencing on an Illumina platform. Gut microbiome analysis was performed using QIIME v2022.2.0. Functional profiling of the gut microbiome was performed using PICRUSt2. Results: Ethanol differentially affected the gut microbiota of female and male mice. Decreased alpha diversity was observed in male and female mice from the chronic plus binge and chronic groups, respectively. The genera Faecalibaculum, Lachnospiraceae and Alistipes were identified as major potential biomarkers for gut dysbiosis induced by ethanol consumption. In addition, ethanol-induced gut dysbiosis altered several metabolic pathways. Conclusion: Ethanol consumption modifies the mouse gut microbiome in a drinking pattern- and sex-dependent manner, potentially leading to different susceptibility to ethanol-related diseases. Chronic plus binge ethanol intake induces a more pronounced gut dysbiosis in male mice. Conversely, chronic ethanol is linked to a greater degree of gut dysbiosis in female mice. The changed gut microbiome may be potentially targeted to prevent, mitigate, or treat alcohol use disorders.}, }
@article {pmid39918275, year = {2025}, author = {Rodrigues, CS and Gaifem, J and Pereira, MS and Alves, MF and Silva, M and Padrão, N and Cavadas, B and Moreira-Barbosa, C and Alves, I and Marcos-Pinto, R and Torres, J and Lavelle, A and Colombel, JF and Sokol, H and Pinho, SS}, title = {Alterations in mucosa branched N-glycans lead to dysbiosis and downregulation of ILC3: a key driver of intestinal inflammation.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2461210}, doi = {10.1080/19490976.2025.2461210}, pmid = {39918275}, issn = {1949-0984}, mesh = {Animals ; *Dysbiosis/microbiology/immunology ; *Polysaccharides/metabolism ; Mice ; *Gastrointestinal Microbiome ; *Intestinal Mucosa/immunology/microbiology/metabolism ; Humans ; *Inflammatory Bowel Diseases/immunology/microbiology ; Down-Regulation ; Lymphocytes/immunology ; Mice, Inbred C57BL ; Inflammation/immunology/metabolism ; Bacteria/classification/isolation &amp; purification ; Glycosylation ; Immunity, Innate ; Female ; Nod2 Signaling Adaptor Protein/metabolism/genetics ; Male ; }, abstract = {The perturbation of the symbiotic relationship between microbes and intestinal immune system contributes to gut inflammation and Inflammatory Bowel Disease (IBD) development. The host mucosa glycans (glycocalyx) creates a major biological interface between gut microorganisms and host immunity that remains ill-defined. Glycans are essential players in IBD immunopathogenesis, even years before disease onset. However, how changes in mucosa glycosylation shape microbiome and how this impact gut immune response and inflammation remains to be clarified. Here, we revealed that alterations in the expression of complex branched N-glycans at gut mucosa surface, modeled in glycoengineered mice, resulted in dysbiosis, with a deficiency in Firmicutes bacteria. Concomitantly, this mucosa N-glycan switch was associated with a downregulation of type 3 innate lymphoid cells (ILC3)-mediated immune response, leading to the transition of ILC3 toward an ILC1 proinflammatory phenotype and increased TNFα production. In addition, we demonstrated that the mucosa glycosylation remodeling through prophylactic supplementation with glycans at steady state was able to restore microbial-derived short-chain fatty acids and microbial sensing (by NOD2 expression) alongside the rescue of the expression of ILC3 module, suppressing intestinal inflammation and controlling disease onset. In a complementary approach, we further showed that IBD patients, often displaying dysbiosis, exhibited a tendency of decreased MGAT5 expression at epithelial cells that was accompanied by reduced ILC3 expression in gut mucosa. Altogether, these results unlock the effects of alterations in mucosa glycome composition in the regulation of the bidirectional crosstalk between microbiota and gut immune response, revealing host branched N-glycans/microbiota/ILC3 axis as an essential pathway in gut homeostasis and in preventing health to intestinal inflammation transition.}, }
@article {pmid39918056, year = {2025}, author = {Roby, RK and Wiscovitch-Russo, RA and Hart, R and Appel, AE and Kazmi, MA and Huber, T and Åberg, KC and Sakmar, TP and Lorente, JA and Gonzalez-Juarbe, N}, title = {Sampling techniques and genomic analysis of biological material from artworks.}, journal = {Journal of forensic sciences}, volume = {}, number = {}, pages = {}, doi = {10.1111/1556-4029.15701}, pmid = {39918056}, issn = {1556-4029}, support = {//Richard Lounsbery Foundation/ ; //Achelis and Bodman Foundation/ ; }, abstract = {The genomic analysis of biological material from artworks can be used to guide curation, preservation, and restoration. Additionally, human DNA recovered from artworks may provide other insights. However, the recovery of biological samples from artworks is dependent on the sampling technique used and the media from which the biological materials are recovered. The ideal sampling method should be noninvasive, yet robust. We studied five artworks on paper and compared three sampling methods, each with increasing degrees of invasiveness. Minimally invasive swabbing techniques collect samples from the surface, whereas more aggressive techniques such as wet vacuuming were expected to yield more biological material from within the support media and more likely to produce authentic DNA from the artwork. We report a comparison of collection techniques to generate microbial DNA sequence data, the conserved human gene RNase P, and Y-STRs from artworks on paper. We observed that wet vacuuming resulted in higher DNA recovery than double swabbing and core punches. Diverse microbial populations existed on the corners and centers of the five artworks studied, but the distribution of the total biomass was relatively even across the surfaces of the works sampled. Studies of peripheral regions, where sampling is less likely to cause alterations to the artwork, could thus yield useful results in microbiome and human DNA studies. These results provide a framework for sampling artworks on paper to obtain biological material. The methods described may provide microbiome identification to facilitate restoration and preservation, and might also contribute to the determination of provenance.}, }
@article {pmid39917835, year = {2025}, author = {Hoffbeck, C and Middleton, DMRL and Wallbank, JA and Boey, JS and Taylor, MW}, title = {Culture-Independent Species-Level Taxonomic and Functional Characterisation of Bacteroides, the Core Bacterial Genus Within Reptile Guts.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17685}, doi = {10.1111/mec.17685}, pmid = {39917835}, issn = {1365-294X}, support = {//University of Auckland Doctoral Scholarship/ ; }, abstract = {The genus Bacteroides is a widespread and abundant bacterial taxon associated with gut microbiotas. Species within Bacteroides fill many niches, including as mutualists, commensals and pathogens for their hosts. Within many reptiles, Bacteroides is a dominant, 'core' gut bacterium that sometimes exhibits increased abundance in times of food scarcity, such as during hibernation. Here, we take a two-pronged approach to better characterise Bacteroides populations in reptile guts. Firstly, we leverage published 16S rRNA gene sequence datasets to determine the species-level distributions of Bacteroides members in reptile hosts. Secondly, we mine publicly available metagenomes to extract data for Bacteroides from reptiles, birds, amphibians and mammals, to compare the functional potential of Bacteroides in different host taxa. The 16S rRNA gene analyses revealed that B. acidifaciens is the most common Bacteroides species in reptile guts, and that different orders of reptiles differ in which Bacteroides species they harbour. The taxonomy of Bacteroides species recovered from metagenomic assembly did not differ between reptile orders or substantially across birds, amphibians and mammals. Metagenome-assembled genomes for Bacteroides species were marginally more related when their hosts were more closely related, with reptile hosts in particular harbouring markedly more unique Bacteroides MAGs compared to other hosts. Our findings indicate that hosts harbour similar profiles of Bacteroides species across broad comparisons, but with some differences between reptile groups, and that Bacteroides appears to perform largely similar roles in vertebrate host guts regardless of host relatedness.}, }
@article {pmid39917692, year = {2024}, author = {Loewy, ZG}, title = {Editorial: Cross-kingdom interactions in oral dysbiosis and host response.}, journal = {Frontiers in dental medicine}, volume = {5}, number = {}, pages = {1398868}, pmid = {39917692}, issn = {2673-4915}, }
@article {pmid39916938, year = {2024}, author = {Liu, Y and Yang, B and Qi, Q and Liu, S and Du, Y and Ye, L and Zhou, Q}, title = {Metagenomic next-generation sequencing for lung cancer low respiratory tract infections diagnosis and characterizing microbiome features.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1518199}, pmid = {39916938}, issn = {2235-2988}, mesh = {Humans ; *Lung Neoplasms/microbiology/diagnosis ; *Respiratory Tract Infections/microbiology/diagnosis/virology ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; *Microbiota/genetics ; Male ; *Bacteria/genetics/classification/isolation &amp; purification ; Female ; Middle Aged ; Aged ; Sputum/microbiology ; Fungi/isolation &amp; purification/classification/genetics ; Coinfection/microbiology/diagnosis/virology ; Adult ; Metagenome ; Aged, 80 and over ; }, abstract = {BACKGROUND: The capability of mNGS in diagnosing suspected LRTIs and characterizing the respiratory microbiome in lung cancer patients requires further evaluation.<br><br>METHODS: This study evaluated mNGS diagnostic performance and utilized background microbial sequences to characterize LRT microbiome in these patients. GSVA was used to analyze the potential functions of identified genera.<br><br>RESULTS: Bacteria were the most common pathogens (n=74) in LRTIs of lung cancer patients, and polymicrobial infections predominated compared to monomicrobial infections (p<0.001). In diagnosing LRTIs in lung cancer patients, the pathogen detection rate of mNGS (83.3%, 70/84) was significantly higher than that of sputum culture (34.5%, 29/84) (p<0.001). This result was consistent with that of non-lung cancer patients (p<0.001). Furthermore, in the specific detection of bacteria (95.7% vs. 22.6%) and fungi (96.0% vs. 22.2%), the detection rate of mNGS was also significantly higher than that of CMTs mainly based on culture (p<0.001, p<0.001). However, in the detection of CMV/EBV viruses, there was no significant difference between the detection rate of mNGS and that of viral DNA quantification (p = 1.000 and 0.152). mNGS analysis revealed Prevotella, Streptococcus, Veillonella, Rothia, and Capnocytophaga as the most prevalent genera in the LRT of lung cancer patients. GSVA revealed significant correlations between these genera and tumor metabolic pathways as well as various signaling pathways including PI3K, Hippo, and p53.<br><br>CONCLUSION: mNGS showed a higher pathogen detection rate than culture-based CMTs in lung cancer patients with LRTIs, and also characterizing LRT microbiome composition and revealing potential microbial functions linked to lung carcinogenesis.}, }
@article {pmid39916659, year = {2025}, author = {Borrego-Ruiz, A and Borrego, JJ}, title = {The role of the gut microbiome in Alzheimer's disease pathophysiology.}, journal = {Current opinion in neurology}, volume = {}, number = {}, pages = {}, doi = {10.1097/WCO.0000000000001352}, pmid = {39916659}, issn = {1473-6551}, abstract = {PURPOSE OF REVIEW: The present review aims to provide an overview of the existing understanding of the role of the gut microbiome in the Alzheimer's disease pathophysiology.<br><br>RECENT FINDINGS: Recent research has highlighted the significant role of the gut microbiome in the pathogenesis of Alzheimer's disease via the gut-brain axis. However, the precise mechanisms by which gut microbiome and its microbial metabolites influence brain function are not clearly understood. Various factors, such as diet, drugs, lifestyle, stress, and microbial infections can provoke an imbalance in the gut microbiome homeostasis, known as dysbiosis. This dysbiosis impacts intestinal and blood-brain barrier permeability, elevating pro-inflammatory cytokines and contributing to neurodegeneration. Moreover, the gut microbiome generates neurotransmitters, amyloids, neurotoxins, and metabolites, which may play a role in systemic inflammation and in the disruption of physiological barriers.<br><br>SUMMARY: In the past decade, advancements in microbiome analysis technologies and bioinformatics have significantly enhanced our understanding of the role of the gut microbiome in Alzheimer's disease. The gut microbiome plays a pivotal regulatory role in the progression of Alzheimer's disease, and closely interacts with its pathogenesis, encompassing inflammation, amyloidosis, neurodegeneration, tauopathy, and co-pathologies.}, }
@article {pmid39916634, year = {2025}, author = {Sanaei, E and de Roode, JC}, title = {The role of host plants in driving pathogen susceptibility in insects through chemicals, immune responses and microbiota.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {}, number = {}, pages = {}, doi = {10.1111/brv.70003}, pmid = {39916634}, issn = {1469-185X}, support = {2202255//United States National Science Foundation/ ; }, abstract = {In this comprehensive exploration, we delve into the pivotal role of host plants in shaping the intricate interactions between herbivorous insects and their pathogens. Recent decades have seen a surge in studies that demonstrate that host plants are crucial drivers of the interactions between insects and pathogens, providing novel insights into the direct and indirect interactions that shape tri-trophic interactions. These studies have built on a wide range of pathogens, from viruses to bacteria, and from protozoans to fungi. We summarise these studies, and discuss the mechanisms of plant-mediated insect resistance to infection, ranging from the toxicity of plant chemicals to pathogens to enhancement of anti-pathogen immune responses, and modulation of the insect's microbiome. Although we provide evidence for the roles of all these mechanisms, we also point out that the majority of existing studies are phenomenological, describing patterns without addressing the underlying mechanisms. To further our understanding of these tri-trophic interactions, we therefore urge researchers to design their studies to enable them specifically to distinguish the mechanisms by which plants affect insect susceptibility to pathogens.}, }
@article {pmid39916516, year = {2025}, author = {Nunez, H and Nieto, PA and Mars, RA and Ghavami, M and Sew Hoy, C and Sukhum, K}, title = {Early life gut microbiome and its impact on childhood health and chronic conditions.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2463567}, doi = {10.1080/19490976.2025.2463567}, pmid = {39916516}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Chronic Disease ; Animals ; Infant ; Child Health ; Child, Preschool ; Bacteria/classification/genetics/isolation &amp; purification ; Infant, Newborn ; Feces/microbiology ; Child ; }, abstract = {The development of the gut microbiome is crucial to human health, particularly during the first three years of life. Given its role in immune development, disturbances in the establishment process of the gut microbiome may have long term consequences. This review summarizes evidence for these claims, highlighting compositional changes of the gut microbiome during this critical period of life as well as factors that affect gut microbiome development. Based on human and animal data, we conclude that the early-life microbiome is a determinant of long-term health, impacting physiological, metabolic, and immune processes. The early-life gut microbiome field faces challenges. Some of these challenges are technical, such as lack of standardized stool collection protocols, inconsistent DNA extraction methods, and outdated sequencing technologies. Other challenges are methodological: small sample sizes, lack of longitudinal studies, and poor control of confounding variables. To address these limitations, we advocate for more robust research methodologies to better understand the microbiome's role in health and disease. Improved methods will lead to more reliable microbiome studies and a deeper understanding of its impact on health outcomes.}, }
@article {pmid39915906, year = {2025}, author = {Wang, Y and Matangkasombut, O and Kemoli, AM and John-Stewart, G and Benki-Nugent, S and Slyker, J and Aldrovandi, GM and Seminario, AL}, title = {Oral Microbiome and Dental Caries in Kenyan Children and Adolescents Living with HIV.}, journal = {JDR clinical and translational research}, volume = {}, number = {}, pages = {23800844241311862}, doi = {10.1177/23800844241311862}, pmid = {39915906}, issn = {2380-0852}, abstract = {OBJECTIVE: This cross-sectional study evaluates the association between the oral microbiome and the presence of untreated dental caries among Kenyan children and adolescents living with HIV (CALHIV).<br><br>METHODS: We collected 83 oral swab samples from CALHIV receiving medical care at Kenyatta National Hospital. We used the 16S rRNA sequencing technique on oral swab samples to profile bacterial composition. Only CALHIV with results of oral microbiome and dental examinations simultaneously were included in the further analysis. We compared the alpha and beta diversity of the oral microbiome between individuals with and without dental caries. Log-ratio LASSO regression with 2-stage estimation, 10-fold cross-validation, and adjustment for the false discovery rate was applied to select the best features that can predict caries status at the phylum level.<br><br>RESULTS: Of the 70 participants with both oral health data and oral microbiome data available, 66% had dental caries. The group with dental caries had higher Chao 1 alpha diversity (P = 0.046) but not beta diversity. Log-ratio LASSO regression had a higher ratio of paired features proteobacteria/SR1 (P = 0.0067), Euryarchaeota/SR1 (P = 0.0074), Acidobacteria/SR1 (P = 0.0079), and Fusobacteria/SR1 (P = 0.0125) at the phylum level and was significantly associated with a lower prevalence of untreated dental caries. A higher abundance of SR1 together with certain bacteria was associated with a higher prevalence of untreated dental caries.<br><br>CONCLUSIONS: This is the first study to analyze the oral microbiome of CALHIV and untreated dental caries in a cohort that had received medical care since their first years of life. While this study provides information about the paired feature selection for dental caries in CALHIV on ART using cross-validation, SR1 may interact with other bacteria to increase the prevalence of untreated dental caries. Longitudinal microbiome data and samples from multiple sites in the oral cavity will be essential for understanding and confirming these findings.<br><br>KNOWLEDGE TRANSFER STATEMENT: The results of this study can help clinicians understand how SR1 interacts with other bacteria that may increase the prevalence of untreated dental caries in children and adolescents living with HIV and on long-term antiretroviral therapy. Furthermore, these findings may provide valuable insights for future research, informing longitudinal microbiome data and sampling from various sites in the oral cavity.}, }
@article {pmid39915884, year = {2025}, author = {He, R and Qi, P and Shu, L and Ding, Y and Zeng, P and Wen, G and Xiong, Y and Deng, H}, title = {Dysbiosis and extraintestinal cancers.}, journal = {Journal of experimental &amp; clinical cancer research : CR}, volume = {44}, number = {1}, pages = {44}, pmid = {39915884}, issn = {1756-9966}, support = {82160546//National Science Foundation of China/ ; 82460116//National Science Foundation of China/ ; 20202BBG73027//Science Foundation of Jiangxi Province/ ; 20242BAB26116//Science Foundation of Jiangxi Province/ ; JXSQ2023201020//Foundation of Jiangxi Province for Distinguished Scholars/ ; 20183021//Science and Technology Plan Fund of Jiangxi Health Commission/ ; 20202ACBL206017//Science and Technology Department of Jiangxi Province/ ; GJJ210185//Education Department of Jiangxi Province/ ; }, mesh = {Humans ; *Dysbiosis/microbiology ; *Neoplasms/microbiology/pathology ; Gastrointestinal Microbiome ; Animals ; }, abstract = {The gut microbiota plays a crucial role in safeguarding host health and driving the progression of intestinal diseases. Despite recent advances in the remarkable correlation between dysbiosis and extraintestinal cancers, the underlying mechanisms are yet to be fully elucidated. Pathogenic microbiota, along with their metabolites, can undermine the integrity of the gut barrier through inflammatory or metabolic pathways, leading to increased permeability and the translocation of pathogens. The dissemination of pathogens through the circulation may contribute to the establishment of an immune-suppressive environment that promotes carcinogenesis in extraintestinal organs either directly or indirectly. The oncogenic cascade always engages in the disruption of hormonal regulation and inflammatory responses, the induction of genomic instability and mutations, and the dysregulation of adult stem cell proliferation. This review aims to comprehensively summarize the existing evidence that points to the potential role of dysbiosis in the malignant transformation of extraintestinal organs such as the liver, breast, lung, and pancreas. Additionally, we delve into the limitations inherent in current methodologies, particularly the challenges associated with differentiating low loads gut-derived microbiome within tumors from potential sample contamination or symbiotic microorganisms. Although still controversial, an understanding of the contribution of translocated intestinal microbiota and their metabolites to the pathological continuum from chronic inflammation to tumors could offer a novel foundation for the development of targeted therapeutics.}, }
@article {pmid39915883, year = {2025}, author = {O'Rourke, JA and Vincent, SA and Williams, IEI and Gascoyne, EL and Devlin, PF}, title = {Phytochrome-mediated shade avoidance responses impact the structure and composition of the bacterial phyllosphere microbiome of Arabidopsis.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {20}, pmid = {39915883}, issn = {2524-6372}, support = {BB/M011178/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; NE/S007229/1//Natural Environment Research Council/ ; }, abstract = {The shade avoidance response triggers a dramatic promotion of elongation growth, accompanied by a significant reprogramming of metabolic pathways as plants seek to prevent overtopping and adapt to vegetative shade. Here we demonstrate that simulated vegetative shade results in significant changes in the structure and composition of the phyllosphere bacterial microbiome. Our study uncovered significant shifts in the diversity, occurrence, abundance and activity of bacteria within the phyllosphere microbiome. A comparison of responses in both wild-type plants and phytochrome mutants, which inherently exhibit a shade-avoidance phenotype, revealed both indirect responses to host plant physiology and direct responses to light among the microbiota. Hierarchical clustering of response patterns further suggested that over a third of the taxa constituting the core phyllosphere microbiome in our assay show some degree of response to vegetative shade. Bacteria that increased in abundance on plants with a shade-avoidance phenotype corresponded to genera associated with beneficial traits such as enhanced disease resistance and growth promotion. Our findings suggests that plants manipulate their phyllosphere microbiome under shade conditions as a strategy to optimise fitness when competing for light. We discuss the implications of our findings in terms of furthering our understanding of plant-microbe signalling in the shaping of the phyllosphere microbiome and the possibility of manipulating the phyllosphere microbiome for plant health in an agricultural setting at high planting densities.}, }
@article {pmid39915809, year = {2025}, author = {Zhang, Y and Li, HZ and Breed, M and Tang, Z and Cui, L and Zhu, YG and Sun, X}, title = {Soil warming increases the active antibiotic resistome in the gut of invasive giant African snails.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {42}, pmid = {39915809}, issn = {2049-2618}, support = {2022T150635//fellowship of China Postdoctoral Science Foundation/ ; 42407166//National Natural Science Foundation of China/ ; 42307165//National Natural Science Foundation of China/ ; 32361143523//National Natural Science Foundation of China/ ; 2021-DST-004//Ningbo S&amp;T project/ ; 2021-DST-004//Ningbo S&amp;T project/ ; 2021-DST-004//Ningbo S&amp;T project/ ; 2023YFF1304601//National Key Research and Development Program of China/ ; 322GJHZ2022028FN//International Partnership Program of Chinese Academy of Sciences/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics/drug effects ; *Snails/microbiology/genetics ; *Global Warming ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/classification/drug effects ; Soil/chemistry ; Soil Microbiology ; beta-Lactamases/genetics ; Metagenomics ; Metagenome ; Drug Resistance, Microbial/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {BACKGROUND: Global warming is redrawing the map for invasive species, spotlighting the globally harmful giant African snail as a major ecological disruptor and public health threat. Known for harboring extensive antibiotic resistance genes (ARGs) and human pathogens, it remains uncertain whether global warming exacerbates these associated health risks.<br><br>METHODS: We use phenotype-based single-cell Raman with D2O labeling (Raman-D2O) and genotype-based metagenomic sequencing to investigate whether soil warming increases active antibiotic-resistant bacteria (ARBs) in the gut microbiome of giant African snails.<br><br>RESULTS: We show a significant increase in beta-lactam phenotypic resistance of active ARBs with rising soil temperatures, mirrored by a surge in beta-lactamase genes such as SHV, TEM, OCH, OKP, and LEN subtypes. Through a correlation analysis between the abundance of phenotypically active ARBs and genotypically ARG-carrying gut microbes, we identify species that contribute to the increased activity of antibiotic resistome under soil warming. Among 299 high-quality ARG-carrying metagenome-assembled genomes (MAGs), we further revealed that the soil warming enhances the abundance of "supercarriers" including human pathogens with multiple ARGs and virulence factors. Furthermore, we identified elevated biosynthetic gene clusters (BGCs) within these ARG-carrying MAGs, with a third encoding at least one BGC. This suggests a link between active ARBs and secondary metabolism, enhancing the environmental adaptability and competitive advantage of these organisms in warmer environments.<br><br>CONCLUSIONS: The study underscores the complex interactions between soil warming and antibiotic resistance in the gut microbiome of the giant African snail, highlighting a potential escalation in environmental health risks due to global warming. These findings emphasize the urgent need for integrated environmental and health strategies to manage the rising threat of antibiotic resistance in the context of global climate change. Video Abstract.}, }
@article {pmid39915668, year = {2025}, author = {Madroñero, LJ and Calvo, EP and Coronel-Ruiz, C and Velandia-Romero, ML and Calderón-Peláez, MA and Arturo, JA and Franco-Rodríguez, AP and Gutiérrez-Pérez, R and López, LS and Delgado, FG and Camacho-Ortega, SJ and Bernal-Cepeda, LJ and Bohórquez, SP and Castellanos, JE}, title = {Pathogenic and periodontal bacteria may contribute to the fatal outcome of critically ill elderly COVID-19 patients.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {4490}, pmid = {39915668}, issn = {2045-2322}, support = {Contract 377-2020; Grant 1308101577416//Colombian Ministry of Sciences and Technology/ ; }, mesh = {Humans ; *COVID-19/mortality/microbiology/complications/virology ; Female ; Male ; Aged ; *Critical Illness ; *Microbiota ; Aged, 80 and over ; SARS-CoV-2/isolation &amp; purification ; Bacteria/classification/isolation &amp; purification/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Some studies suggest that the respiratory microbiome of COVID-19 patients differs from that of healthy individuals, infected patients may have reduced diversity and increased levels of opportunistic bacteria, however, the role of the microbiome in fatal SARS-CoV-2 infection remains poorly understood. Our study aimed to determine whether there are differences in the respiratory microbiome between patients who recovered from COVID-19 and those who died, by characterizing the bacterial communities of both groups. A total of 24 patients who recovered from COVID-19 and 24 who died were included in the study, patient data were analyzed for signs, symptoms and clinical variables. Airway samples were collected and the 16 S rRNA variable regions V3-V4 were amplified and sequenced using the Illumina MiSeq platform. Elevated levels of blood urea nitrogen, creatinine and lactate dehydrogenase, and higher frequencies of cardiovascular disease, diabetes mellitus and renal disease were observed in patients with a fatal outcome. Compared to patients who recovered from COVID-19, patients who died exhibited a microbiome enriched in periodontal and pathogenic bacteria such as Klebsiella pneumoniae. Our results highlighted a dual relationship between SARS CoV-2 infection and an exacerbated periodontopathogen-induced immune response.}, }
@article {pmid39915534, year = {2025}, author = {Yang, F and Jia, X and Ma, Z and Liu, S and Liu, C and Chen, D and Wang, X and Qian, N and Ma, H}, title = {Exploring the prognostic role of microbial and genetic markers in lung squamous cell carcinoma.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {4499}, pmid = {39915534}, issn = {2045-2322}, mesh = {Humans ; *Lung Neoplasms/genetics/microbiology/diagnosis ; Prognosis ; *Carcinoma, Squamous Cell/genetics/microbiology/diagnosis ; *Biomarkers, Tumor/genetics ; *Microbiota/genetics ; Male ; Genetic Markers ; Female ; Middle Aged ; RNA, Messenger/genetics ; Gene Expression Regulation, Neoplastic ; }, abstract = {Despite advances in diagnostic and therapeutic strategies, the prognosis of lung squamous cell carcinoma (LUSC) patients remains poor, and the potential of microbiome-based prognostic biomarkers and therapeutic targets remains largely unexplored. LUSC patient data from The Cancer Genome Atlas (TCGA), including microbial genus level abundance data and RNA sequencing (RNA-Seq) data, were used as a training dataset. Two other independent datasets GSE19188 and GSE157009 serve as validation datasets. A microbiome-based risk score (RS) model was constructed by univariate Cox regression analysis combined with the least absolute contraction and selection operator (LASSO) regression. 18 microbial genera were found to be significantly associated with RFS in LUSC patients. The microbial signature built with these microbial genera, exhibited robust predictive accuracy in both the training and validation datasets. Furthermore, hub mRNA between high- and low-risk groups were selected by XGBOOST and intersect with mRNAs screened by univariate Cox regression analysis, finally identifying four mRNA significantly associated with LUSC prognosis. This study reveals a complex interplay between the lung microbiome and genetic biomarkers, and identifies specific microbial-based and mRNA associated with prognosis in LUSC. These findings provide a basis for future studies aimed to elucidate the mechanisms underlying these associations and provide potential biomarkers for guiding treatment decisions and improving patient outcomes.}, }
@article {pmid39916928, year = {2023}, author = {Punnanitinont, A and Kramer, JM}, title = {Sex-specific differences in primary Sjögren's disease.}, journal = {Frontiers in dental medicine}, volume = {4}, number = {}, pages = {1168645}, pmid = {39916928}, issn = {2673-4915}, abstract = {Many autoimmune diseases show a striking female sex predilection, including primary Sjögren's disease (pSD). Patients with pSD display exocrine gland pathology, such as salivary hypofunction and salivary and lacrimal gland inflammation. Moreover, many serious systemic disease manifestations are well-documented, including interstitial nephritis, hypergammaglobulinemia and neuropathies. Of note, women and men with pSD display distinct clinical phenotypes. While the underlying reasons for these clinical observations were poorly understood for many years, recent studies provide mechanistic insights into the specific regulatory landscapes that mediate female susceptibility to autoimmunity. We will review factors that contribute to the female sex bias, with an emphasis on those that are most relevant to pSD pathogenesis. Specifically, we will focus on sex hormones in disease, genetic alterations that likely contribute to the significant disease prevalence in females, and studies that provide evidence for the role of the gut microbiota in disease. Lastly, we will discuss therapeutics that are in clinical trials for pSD that may be particularly efficacious in targeting signaling networks that mediate inflammation in a sex-specific manner.}, }
@article {pmid39915510, year = {2025}, author = {Rabbani, G and Afiq-Rosli, L and Lee, JN and Waheed, Z and Wainwright, BJ}, title = {Effects of life history strategy on the diversity and composition of the coral holobiont communities of Sabah, Malaysia.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {4459}, pmid = {39915510}, issn = {2045-2322}, mesh = {*Anthozoa/microbiology ; Animals ; Malaysia ; *Microbiota ; *Symbiosis ; Biodiversity ; Bacteria/genetics/classification ; Climate Change ; Coral Reefs ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Coral-associated microbes have essential roles in promoting and regulating host function and health. As climate change advances and other environmental perturbations increasingly impact corals, it is becoming ever more important that we understand the composition of the microbial communities hosted. Without this baseline it is impossible to assess the magnitude and direction of any future changes in microbial community structure. Here, we characterised both the bacterial and Symbiodiniaceae communities in four coral species (Diploastrea heliopora, Porites lutea, Pachyseris speciosa, and Pocillopora acuta) collected from Sabah, Malaysia. Our findings reveal distinct microbial communities associated with different coral species tending to reflect the varied life history strategies of their hosts. Microbial communities could be differentiated by collection site, with shifts in Symbiodiniaceae communities towards more stress tolerant types seen in samples collected on the shallow Sunda Shelf. Additionally, we identified a core microbiome within species and a more discrete core between all species. We show bacterial and Symbiodiniaceae communities are structured by host species and appear to be influenced by host life history characteristics. Furthermore, we identified a core microbiome for each species finding that several amplicon sequence variants were shared between hosts, this suggests a key role in coral health regardless of species identity. Given the paucity of work performed in megadiverse regions such as the Coral Triangle, this research takes on increased importance in our efforts to understand how the coral holobiont functions and how it could be altered as climate change advances.}, }
@article {pmid39915243, year = {2025}, author = {Zhao, S and Lin, H and Li, W and Xu, X and Wu, Q and Wang, Z and Shi, J and Chen, Y and Ye, L and Xi, L and Chen, L and Yuan, M and Su, J and Gao, A and Jin, J and Ying, X and Wang, X and Ye, Y and Sun, Y and Zhang, Y and Deng, X and Shen, B and Gu, W and Ning, G and Wang, W and Hong, J and Wang, J and Liu, R}, title = {Post sleeve gastrectomy-enriched gut commensal Clostridia promotes secondary bile acid increase and weight loss.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2462261}, doi = {10.1080/19490976.2025.2462261}, pmid = {39915243}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Bile Acids and Salts/metabolism ; *Weight Loss ; Mice ; *Gastrectomy ; Humans ; Male ; *Clostridium/metabolism/genetics ; *Mice, Inbred C57BL ; *Obesity/microbiology/metabolism/surgery ; Receptors, G-Protein-Coupled/metabolism/genetics ; Fecal Microbiota Transplantation ; Female ; Adult ; Feces/microbiology ; Symbiosis ; Bariatric Surgery ; Adipose Tissue/metabolism ; }, abstract = {The gut microbiome is altered after bariatric surgery and is associated with weight loss. However, the commensal bacteria involved and the underlying mechanism remain to be determined. We performed shotgun metagenomic sequencing in obese subjects before and longitudinally after sleeve gastrectomy (SG), and found a significant enrichment in microbial species in Clostridia and bile acid metabolizing genes after SG treatment. Bile acid profiling further revealed decreased primary bile acids (PBAs) and increased conjugated secondary bile acids (C-SBAs) after SG. Specifically, glycodeoxycholic acid (GDCA) and taurodeoxycholic acid (TDCA) were increased at different follow-ups after SG, and were associated with the increased abundance of Clostridia and body weight reduction. Fecal microbiome transplantation with post-SG feces increased SBA levels, and alleviated body weight gain in the recipient mice. Furthermore, both Clostridia-enriched spore-forming bacteria and GDCA supplementation increased the expression of genes responsible for lipolysis and fatty acid oxidation in adipose tissue and reduced adiposity via Takeda G-protein-coupled receptor 5 (TGR5) signaling. Our findings reveal post-SG gut microbiome and C-SBAs as contributory to SG-induced weight loss, in part via TGR5 signaling, and suggest SBA-producing gut microbes as a potential therapeutic target for obesity intervention.}, }
@article {pmid39914821, year = {2025}, author = {Kord-Parijaee, E and Ferdosi-Shahandashti, E and Hafezi, N}, title = {Interactions Between Mesenchymal Stem Cells and Microorganisms: Unraveling the Paradox for Enhanced Mesenchymal Stem Cell-Based Therapy.}, journal = {Tissue engineering. Part B, Reviews}, volume = {}, number = {}, pages = {}, doi = {10.1089/ten.teb.2024.0334}, pmid = {39914821}, issn = {1937-3376}, abstract = {Mesenchymal stem cells (MSCs) have emerged as a promising therapeutic tool in stem cell-based therapy due to their immunomodulatory or regenerative characteristics. Nowadays, controlled application of nonpathogenic bacterial cells and their derivatives has shown promise in preconditioning and manipulating MSC behavior. This approach is being explored in various fields, including immunotherapy, tissue engineering, and cell therapy. However, recent discoveries have elucidated the complex interactions between MSCs and microorganisms, especially bacteria and viruses, raising concerns regarding the utility of MSCs in clinical applications. In this review, we discussed the interactions between MSCs and microorganisms and highlighted both positive and negative aspects. We also examined the use of bacterial-derived compounds in MSCs-mediated interventions. The balanced colonization of the microbiome in organs, such as the oral cavity, not only does not hinder therapeutic interventions but also could be crucial for achieving desirable outcomes. On the contrary, disturbances in the microbiome have been found to disturb the biological potential of MSCs, such as migration, osteogenic differentiation, and cell proliferation. Evidence also suggests that commensal bacteria, following certain interventions, can transition to a pathogenic state when interacting with MSCs, leading to acute inflammation. Indeed, the maintenance of homeostasis through various approaches, such as probiotic application, results in an optimal equilibrium during MSCs-based therapies. However, further investigation into this matter is imperative to identify efficacious interventions.}, }
@article {pmid39914553, year = {2025}, author = {Tanabe, N and Matsumoto, H and Morimoto, C and Hirai, T}, title = {Sputum short-chain fatty acids, microbiome, inflammation, and mucus plugging in obstructive airway disease.}, journal = {The Journal of allergy and clinical immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jaci.2025.01.031}, pmid = {39914553}, issn = {1097-6825}, abstract = {BACKGROUND: Short-chain fatty acids (SCFAs), produced by anaerobic bacteria through fermentation in the gut, may suppress eosinophilic inflammation while potentially promoting neutrophilic inflammation. However, the role of local SCFAs in airway microbiome, inflammation, and mucus plugging in type 2 dominant obstructive airway diseases remains unclear.<br><br>OBJECTIVE: To investigate associations between sputum SCFAs and the relative abundance of anaerobic bacteria, neutrophil and eosinophil counts in sputum, and mucus plug scores on computed tomography (CT) in patients with obstructive airway diseases.<br><br>METHODS: Sputum samples and chest CT were prospectively collected in stable patients with asthma with fixed airflow limitation, chronic obstructive pulmonary disease (COPD), and asthma-COPD overlap (ACO). Sputum samples were analyzed for SCFAs concentrations, including n-butyrate, acetate, and propionate, microbiome composition using 16S rRNA sequencing, and inflammatory cell differentials.<br><br>RESULTS: In 46 patients, enriched for ACO with relatively high type 2 markers, higher SCFA levels were associated with higher relative abundance of phylum Bacteroidetes and lower relative abundance of phylum Proteobacteria. Hierarchical clustering identified a severe eosinophil-dominant inflammation cluster characterized by lower SCFAs levels and higher mucus plug scores. In the two neutrophilic clusters, one characterized by higher SCFAs levels and the other by lower SCFAs levels, lower butyrate levels were significantly associated with higher mucus plug scores.<br><br>CONCLUSION: Local SCFA concentrations may be closely associated with the airway microbiome and influence mucus plugging in ACO-enriched populations. Understanding these interactions could inform therapeutic strategies targeting SCFAs or the microbiome to manage type 2 dominant obstructive airway diseases.}, }
@article {pmid39914464, year = {2025}, author = {Turpin, W and Lee, SH and Croitoru, K}, title = {Gut Microbiome Signature in Predisease Phase of Inflammatory Bowel Disease: Prediction to Pathogenesis to Prevention.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2025.01.004}, pmid = {39914464}, issn = {1528-0012}, abstract = {Advances in understanding the pathogenesis of inflammatory bowel disease (IBD) point toward a key role of the gut microbiome. We review the data describing the changes in the gut microbiome from IBD case-control studies and compare these findings with emerging data from studies of the preclinical phase of IBD. What is apparent is that assessing changes in the composition and function of the gut microbiome during the preclinical phase helps address confounding factors, such as disease activity and drug therapy, which can directly influence the gut microbiome. Understanding these changes in the predisease phase provides a means of predicting IBD in high-risk populations and offers insights into possible mechanisms involved in disease pathogenesis. Finally, we discuss strategies to use this information to design interventions aimed at modulating the microbiome as a means of preventing or delaying the onset of IBD.}, }
@article {pmid39914389, year = {2025}, author = {Ji, P and Wang, N and Yu, Y and Zhu, J and Zuo, Z and Zhang, B and Zhao, F}, title = {Single-cell delineation of the microbiota-gut-brain axis: Probiotic intervention in Chd8 haploinsufficient mice.}, journal = {Cell genomics}, volume = {}, number = {}, pages = {100768}, doi = {10.1016/j.xgen.2025.100768}, pmid = {39914389}, issn = {2666-979X}, abstract = {Emerging research underscores the gut microbiome's impact on the nervous system via the microbiota-gut-brain axis, yet comprehensive insights remain limited. Using a CHD8-haploinsufficient model for autism spectrum disorder (ASD), we explored host-gut microbiota interactions by constructing a single-cell transcriptome atlas of brain and intestinal tissues in wild-type and mutant mice across three developmental stages. CHD8 haploinsufficiency caused delayed development of radial glial precursors and excitatory neural progenitors in the E14.5 brain, inflammation in the adult brain, immunodeficiency, and abnormal intestinal development. Selective CHD8 knockdown in intestinal epithelial cells generated Chd8[ΔIEC] mice, which exhibited normal sociability but impaired social novelty recognition. Probiotic intervention with Lactobacillus murinus selectively rescued social deficits in Chd8[ΔIEC] mice, with single-cell transcriptome analysis revealing underlying mechanisms. This study provides a detailed single-cell transcriptomic dataset of ASD-related neural and intestinal changes, advancing our understanding of the gut-brain axis and offering potential therapeutic strategies for ASD.}, }
@article {pmid39914371, year = {2025}, author = {Dinleyici, EC}, title = {Breastfeeding and Health Benefits for the Mother-Infant Dyad: A Perspective on Human Milk Microbiota.}, journal = {Annals of nutrition &amp; metabolism}, volume = {}, number = {}, pages = {1-13}, doi = {10.1159/000541711}, pmid = {39914371}, issn = {1421-9697}, abstract = {BACKGROUND: Current scientific research on breastfeeding provides substantial evidence of its numerous positive impacts, not only for children in both the short and long term but also for mothers who engage in breastfeeding.<br><br>SUMMARY: In addition to the gold standard effect of human milk on infant nutrition, breastfeeding is associated with a lower incidence of infections, reduced infant/childhood mortality, necrotizing enterocolitis, and obesity during childhood and later in life, better cognitive performance, and a higher IQ score. For mothers, breastfeeding prolongs lactational amenorrhea, may facilitate postpartum weight loss, and may reduce breast and ovarian cancers and cardiovascular diseases. Breastfeeding can also play a beneficial role in preventing antibiotic resistance, which is a global concern across all age groups. Implementing exclusive breastfeeding for all infants has the potential to enhance child development and decrease healthcare expenses, leading to economic savings for both individual families and society. Human milk is a biologically active food that functions as both prebiotic and probiotic because of its oligosaccharides and the composition of its microbiota, which act as synergistic synbiotics.}, }
@article {pmid39913420, year = {2025}, author = {Jumbam, B and Toro, M and Hu, M}, title = {Comparative analysis of grape berry microbiota uncovers sour rot associates from a Maryland vineyard.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0314397}, doi = {10.1371/journal.pone.0314397}, pmid = {39913420}, issn = {1932-6203}, mesh = {*Vitis/microbiology ; *Microbiota/drug effects ; *Fruit/microbiology ; *Plant Diseases/microbiology ; Maryland ; Fungi/genetics/isolation &amp; purification/classification ; Farms ; Insecticides/pharmacology ; Bacteria/genetics/classification/isolation &amp; purification/drug effects ; }, abstract = {Grape sour rot (GSR) is a disease complex involving fungi and bacteria that can cause significant yield losses of susceptible varieties. It is widely spread in the eastern U.S. and other grape-growing regions globally. Previous studies suggest that damaged fruit skin and feeding insects like Drosophila spp. are required for the disease to occur. Current control strategies for the management of sour rot are not sustainable, and research on the implications of chemical management of the disease on microbiome diversity is scarce. Our aim was to: i) investigate the effect of insecticide application and netting treatment on the microbiota of GSR-susceptible and tolerant grape varieties; and ii) identify the core microbial assemblages potentially associated with grape sour rot development in Maryland. Using a combined analysis of culture-dependent and independent data, we found that microbiota diversity of healthy grape berries did not change with netting, insecticide application, and between varieties. There was a significant difference in bacterial diversity between healthy and sour rot-affected berries. Komagataeibacter was consistently associated with infected berries followed by Acetobacter and Gluconobacter. This is the first study to report the association of Komagataeibacter with GSR-infected berries. It is thus imperative to investigate its role alongside that of other identified core microbiomes in sour rot development. Candida and Pichia were also consistent genera in infected berries. Several unidentified Candida, Pichia, and other fungal species from infected berries formed the core mycobiomes and it would be worth investigating their involvement in GSR development in Mid-Atlantic vineyards.}, }
@article {pmid39913363, year = {2025}, author = {Davidov, K and Itzahri, S and Sinberger, LA and Oren, M}, title = {Unveiling microbial succession dynamics on different plastic surfaces using WGCNA.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0318843}, doi = {10.1371/journal.pone.0318843}, pmid = {39913363}, issn = {1932-6203}, mesh = {*Microbiota/genetics ; *Plastics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; Seawater/microbiology ; DNA Barcoding, Taxonomic ; }, abstract = {Over recent decades, marine microorganisms have increasingly adapted to plastic debris, forming distinct plastic-attached microbial communities. Despite this, the colonization and succession processes on plastic surfaces in marine environments remain poorly understood. To address this knowledge gap, we conducted a microbiome succession experiment using four common plastic polymers (PE, PP, PS, and PET), as well as glass and wood, in a temperature-controlled seawater system over a 2- to 90-day period. We employed long-read 16S rRNA metabarcoding to profile the prokaryotic microbiome's taxonomic composition at five time points throughout the experiment. By applying Weighted Gene Co-expression Network Analysis (WGCNA) to our 16S metabarcoding data, we identified unique succession signatures for 77 bacterial genera and observed polymer-specific enrichment in 39 genera. Our findings also revealed that the most significant variations in microbiome composition across surfaces occurred during the initial succession stages, with potential intra-genus relationships that are linked to surface preferences. This research advances our understanding of microbial succession dynamics on marine plastic debris and introduces a robust statistical approach for identifying succession signatures of specific bacterial taxa.}, }
@article {pmid39913342, year = {2025}, author = {Martin, H and Rogers, LA and Moushtaq, L and Brindley, AA and Forbes, P and Quintion, AR and Murphy, ARJ and Hipperson, H and Daniell, TJ and Ndeh, D and Amsbury, S and Hitchcock, A and Lidbury, IDEA}, title = {Metabolism of hemicelluloses by root-associated Bacteroidota species.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf022}, pmid = {39913342}, issn = {1751-7370}, abstract = {Bacteroidota species are enriched in the plant microbiome and provide several beneficial functions for their host, including disease suppression. Determining the mechanisms that enable bacteroidota to colonise plant roots may therefore provide opportunities for enhancing crop production through microbiome engineering. By focusing on nutrient acquisition mechanisms, we discovered Bacteroidota species lack high affinity ATP-binding cassette transporters common in other plant bacteria for capturing simple carbon exudates. Instead, bacteroidota possess TonB-dependent transporters predicted to import glycans produced by plant polysaccharide breakdown. Metatranscriptomics (oat rhizosphere) identified several TonB-dependent transporters genes that were highly expressed in Flavobacterium (phylum Bacteroidota). Using Flavobacterium johnsoniae as the model, we experimentally validated the function of one highly expressed TonB-dependent transporters, identifying a conserved Xyloglucan Utilisation Loci conferring an ability to import xyloglucan, the major hemicellulose secreted from plant roots. Xyloglucan utilisation loci harbour an endoxyloglucanase related to family 5 subfamily 4 subclade 2D glycoside hydrolases carrying a mutation that we demonstrate is required for full activity towards xyloglucan. Based on analysing 700 soil metagenomes, subclade 2D glycoside hydrolases have radiated in soil and are prevalent among plant-associated bacteroidota and certain taxa affiliated with Gammaproteobacteria. In bacteroidota, particularly Flavobacterium species, xyloglucan utilisation loci organisation was highly conserved, which may increase their competitive ability to utilise xyloglucan. Given bacteroidota lack high-affinity nutrient transporters for simple carbon, instead possessing xyloglucan utilisation loci and similar gene clusters, our data suggests hemicellulose exudates provide them with an important carbon source in the rhizosphere.}, }
@article {pmid39913324, year = {2025}, author = {Huang, H and Mani, J and Vetter, TR and Gan, TJ}, title = {Examining the Impact of the Human Microbiome in the Perioperative Setting.}, journal = {Anesthesia and analgesia}, volume = {}, number = {}, pages = {}, pmid = {39913324}, issn = {1526-7598}, }
@article {pmid39913235, year = {2025}, author = {Hordinsky, M and Andriessen, A and Day, D and McMichael, A and Mesinkovska, N and Woolery-Lloyd, H}, title = {INDIVIDUAL ARTICLE: Etiology, Treatment Challenges, and the Role of Scalp and Haircare in Managing Dandruff.}, journal = {Journal of drugs in dermatology : JDD}, volume = {24}, number = {2}, pages = {s8-s14}, doi = {10.36849/JDD.32712}, pmid = {39913235}, issn = {1545-9616}, mesh = {Humans ; *Dandruff/diagnosis/therapy ; *Dermatitis, Seborrheic/therapy/diagnosis ; *Scalp ; Hair ; Quality of Life ; Consensus ; Pruritus/therapy/etiology/diagnosis ; Scalp Dermatoses/therapy/diagnosis ; }, abstract = {Dandruff and seborrheic dermatitis are associated with a disrupted scalp barrier that contributes to irritation, pruritus, and flaking of the scalp. The flaking and itch associated with dandruff can significantly impact an individual's self-esteem and quality of life. While the exact pathogenesis of dandruff is still not completely understood, scalp barrier health and its microbiome are thought to play significant roles in disease propagation. Five expert dermatologists with extensive experience in hair, dandruff, and seborrheic dermatitis were selected to participate in discussions that would result in five consensus statements focused on scalp barrier health and dandruff. Results of a systematic literature search and expert panel discussion are presented. These consensus statements aim to reflect expert opinions on the current understanding of scalp health in the context of dandruff and seborrheic dermatitis. The panel addressed challenges to promote scalp health, improve patient comfort, and prevent flares during dandruff management and maintenance. The presented consensus statements urge reframing our current understanding of dandruff and seborrheic dermatitis treatment by refocusing attention on global scalp and hair health. J Drugs Dermatol. 2025;24:2(Suppl 1):s8-14.}, }
@article {pmid39913178, year = {2025}, author = {Yao, Y and Chen, J and Cao, H and Lu, Z and Shen, H and Ji, J and Jiao, Q}, title = {Causal Effect Between Gut Microbiota, Gut Bacterial Pathway, and Chronic Spontaneous Urticaria: A Large-Scale Bidirectional Mendelian Randomization Analysis.}, journal = {Journal of investigational allergology &amp; clinical immunology}, volume = {}, number = {}, pages = {0}, doi = {10.18176/jiaci.1054}, pmid = {39913178}, issn = {1018-9068}, abstract = {BACKGROUND: To analyze causality between gut microbiota and chronic spontaneous urticaria (CSU) and to investigate the mediating effect of metabolic pathways.<br><br>METHODS: We extracted genome-wide association study summary statistics for 211 microbiota taxa from the MiBioGen consortium (N=18 340), 205 microbiota metabolic pathways from the Dutch Microbiome Project (N=7738), and CSU from the FinnGen genomics initiative (N=450). Bidirectional Mendelian randomization (MR) was performed to detect genetic causality between gut microbiota, gut bacterial pathways, and CSU. Sensitivity analyses were performed to validate the robustness of the results. Mediation MR investigated mediators in the association between gut microbiota and CSU.<br><br>RESULTS: MR analysis suggested that the family Peptococcaceae and its child taxon, the genus Peptococcus, were risk factors for CSU. In addition, the genera Collinsella, Lachnospiraceae UCG004, Ruminococcaceae UCG004, and Sellimonas were also risk factors for CSU, whereas Family XIII UCG001, Lachnospiraceae UCG010, and Methanobrevibacter had protective effects on CSU. As for metabolic pathways, NONMEVIPP-PWY, PWY-5022, and PWY-7221 were positively associated with CSU, although others, such as KDO-NAGLIPASYN-PWY, PWY- 6353, and PWY-7400 presented a suggestive association with CSU. Moreover, PWY-7400 was a mediator in causality between the family Peptococcaceae and CSU. These results were based on nominal significance (P<.05). None of the Bonferroni corrected P values were <.05.<br><br>CONCLUSIONS: Our study confirmed a causal association between gut microbiota and CSU, with the metabolic pathway being a potential mediator. Our findings provide new insights for further mechanistic and clinical studies in CSU.}, }
@article {pmid39912928, year = {2025}, author = {Yu, C and Yan, W and Shucheng, H and Huang, Y and Jiang, X}, title = {Roles of skin microbiota in hidradenitis suppurativa: insights from a two-sample mendelian randomization analysis.}, journal = {Archives of dermatological research}, volume = {317}, number = {1}, pages = {346}, pmid = {39912928}, issn = {1432-069X}, support = {82273559//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Hidradenitis Suppurativa/microbiology/genetics ; *Mendelian Randomization Analysis ; *Microbiota/genetics ; *Skin/microbiology ; *Corynebacterium/isolation &amp; purification/genetics ; Cross-Sectional Studies ; Genome-Wide Association Study ; Germany/epidemiology ; }, abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease associated with unique lesional dysbiotic features. However, the role of the microbiology in the pathogenesis of HS remains in dispute. We aimed to conduct a two-sample Mendelian randomization study to investigate the relationship between skin microbiota and HS. A two-sample Mendelian randomization study was performed using the summary statistics of skin microbiota from summary GWAS data of the European descent from two cross-sectional, population-based German cohorts, KORA FF4 (n = 324) and PopGen (n = 273). The summary statistics of hidradenitis suppurativa were obtained from the FinnGen DF10 (1,070 cases and 394,105 controls). Inverse variance weighted (IVW), MR-Egger regression, weighted median, simple mode, weighted mode, and MRPRESSO were used to examine the causal association between skin microbiota and hidradenitis suppurativa. Cochran's Q statistics were used to quantify the heterogeneity of instrumental variables. Our study suggested that genus Corynebacterium in dry skin is significantly associated with HS after false discovery rate (FDR) correction (odds ratio (OR) = 1.04, 95% confidence interval (CI): 1.02-1.06, P = 0.0002, FDR adjusted P = 0.035). Additionally, we found genus Micrococcus in moist skin (OR = 1.10, 95% CI: 1.03-1.18, P = 0.0060, FDR adjusted P = 0.360), species Streptococcus salivarius in dry skin (OR = 1.03, 95% CI: 1.01-1.05, P = 0.0070, FDR adjusted P = 0.360), and species Propionibacterium granulosum (OR = 1.02, 95% CI: 1.00-1.04, P = 0.0460, FDR adjusted P = 0.970) are potentially associated with HS before FDR adjustment. No evidence of the effect in the reverse direction for HS on skin microbial features. This two-sample Mendelian randomization study found that genus Corynebacterium was causally associated with HS. Further studies are needed to clarify the protective effect of prebiotics, probiotics or microbiome transplants on HS.}, }
@article {pmid39912727, year = {2025}, author = {Ma, X and Li, M and Zhang, Y and Xu, T and Zhou, X and Qian, M and Yang, Z and Han, X}, title = {Akkermansia muciniphila identified as key strain to alleviate gut barrier injury through Wnt signaling pathway.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, doi = {10.7554/eLife.92906}, pmid = {39912727}, issn = {2050-084X}, support = {32172765//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Wnt Signaling Pathway ; *Akkermansia/physiology ; *Gastrointestinal Microbiome/physiology ; Mice ; Swine ; *Enterotoxigenic Escherichia coli/physiology ; *Fecal Microbiota Transplantation ; Intestinal Mucosa/microbiology/metabolism ; Escherichia coli Infections/microbiology/therapy ; Disease Models, Animal ; Bacteroides fragilis/physiology ; Organoids ; }, abstract = {As the largest mucosal surface, the gut has built a physical, chemical, microbial, and immune barrier to protect the body against pathogen invasion. The disturbance of gut microbiota aggravates pathogenic bacteria invasion and gut barrier injury. Fecal microbiota transplantation (FMT) is a promising treatment for microbiome-related disorders, where beneficial strain engraftment is a significant factor influencing FMT outcomes. The aim of this research was to explore the effect of FMT on antibiotic-induced microbiome-disordered (AIMD) models infected with enterotoxigenic Escherichia coli (ETEC). We used piglet, mouse, and intestinal organoid models to explore the protective effects and mechanisms of FMT on ETEC infection. The results showed that FMT regulated gut microbiota and enhanced the protection of AIMD piglets against ETEC K88 challenge, as demonstrated by reduced intestinal pathogen colonization and alleviated gut barrier injury. Akkermansia muciniphila (A. muciniphila) and Bacteroides fragilis (B. fragilis) were identified as two strains that may play key roles in FMT. We further investigated the alleviatory effects of these two strains on ETEC infection in the AIMD mice model, which revealed that A. muciniphila and B. fragilis relieved ETEC-induced intestinal inflammation by maintaining the proportion of Treg/Th17 cells and epithelial damage by moderately activating the Wnt/β-catenin signaling pathway, while the effect of A. muciniphila was better than B. fragilis. We, therefore, identified whether A. muciniphila protected against ETEC infection using basal-out and apical-out intestinal organoid models. A. muciniphila did protect the intestinal stem cells and stimulate the proliferation and differentiation of intestinal epithelium, and the protective effects of A. muciniphila were reversed by Wnt inhibitor. FMT alleviated ETEC-induced gut barrier injury and intestinal inflammation in the AIMD model. A. muciniphila was identified as a key strain in FMT to promote the proliferation and differentiation of intestinal stem cells by mediating the Wnt/β-catenin signaling pathway.}, }
@article {pmid39912651, year = {2025}, author = {Zvonareva, T and Courson, DS and Purcell, EB}, title = {Clostridioides difficile infection study models and prospectives for probing the microbe-host interface.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0040724}, doi = {10.1128/jb.00407-24}, pmid = {39912651}, issn = {1098-5530}, abstract = {Clostridioides difficile infection (CDI) is an urgent public health threat with a high rate of recurrence and limited treatment options. In vivo models have been indispensable in understanding CDI pathophysiology and establishing treatment protocols and continue to be essential in pre-clinal testing. More importantly, in vivo models offer the opportunity to probe the complex systemic host response to the microbe, which is impossible to recapitulate in vitro. Nonetheless, constraints related to the availability of animal models, cost, ethical considerations, and regulatory control limit their accessibility for basic research. Furthermore, physiological and habitual divergences between animal models and humans often result in poor translatability to human patients. In addition to being more accessible, in vitro CDI models offer more control over experimental parameters and allow dynamic analysis of early infection. In vitro fermentation offers models for probing microbe-microbe and microbe-microbiome interactions, while continuous multi-stage platforms allow opportunities to study C. difficile pathophysiology and treatment in context with human-derived microbiota. However, these platforms are not suitable for probing the host-pathogen interface, leaving the challenge of modeling early CDI unanswered. As a result, alternative in vitro co-culture platforms are being developed. This review evaluates the strengths and weaknesses of each approach, as well as future directions for C. difficile research.}, }
@article {pmid39912642, year = {2025}, author = {Masarweh, C and Maldonado-Gomez, M and Paviani, B and Bhattacharya, M and Weng, C-Y and Suarez, C and Ehlers-Cheang, S and Stacy, A and Castillo, J and Krishnakumar, N and Kalanetra, KA and Barile, D and German, JB and Lebrilla, CB and Mills, DA}, title = {Generation of novel prebiotic oligosaccharide pools from fiber drives biological insight in bacterial glycan metabolism.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0207724}, doi = {10.1128/aem.02077-24}, pmid = {39912642}, issn = {1098-5336}, abstract = {Prebiotic oligosaccharides are dietary supplements that modulate the intestinal gut microbiome by selectively nourishing subsets of the microbial community with a goal to enhance host health. To date, the diversity of polysaccharide compositions in the fiber consumed by humans is not well represented by the limited scope of oligosaccharide compositions present in current commercial prebiotics. Recently, our UC Davis group developed a novel method to generate oligosaccharides from any polysaccharide fiber, termed Fenton's Initiation Toward Defined Oligosaccharide Groups (FITDOG). Using this method, sugar beet pulp (SBP) was transformed into sugar beet oligosaccharides (SBOs) composed of arabinose- and galactose-containing oligosaccharides. Fecal fermentations of SBO and SBP produced similar shifts in donor-specific bacterial communities and acid metabolite profiles with a general enrichment of Bacteroides and Bifidobacterium. However, in vitro tests revealed more Bifidobacterium strains could consume SBO than sugar beet arabinan, and specific strains showed differential consumption of arabinofuranooligosaccharides or galactooligosaccharide (GOS) portions of the SBO pool. Genomic and glycomic comparisons suggest that previously characterized, arabinan-specific, extracellular arabinofuranosidases from Bifidobacterium are not necessary to metabolize the arabino-oligosaccharides within SBO. Synbiotic application of SBO with an SBO-consuming strain Bifidobacterium longum subsp. longum SC596 in serial fecal enrichments resulted in enhanced persistence among 9 of 10 donor feces. This work demonstrates a novel workflow whereby FITDOG creates novel oligosaccharide pools that can provide insight into how compositional differences in fiber drive differential gut fermentation behaviors as well as their downstream health impacts. Moreover, these oligosaccharides may be useful in new prebiotic and synbiotic applications.IMPORTANCEPrebiotics seek to selectively alter the host microbiome composition or function, resulting in a concurrent health benefit to the host. However, commercial prebiotics represent a small fraction of the diversity of food polysaccharide compositions. In this work a novel method, Fenton's Initiation Toward Defined Oligosaccharide Groups (FITDOG) was used to generate an oligosaccharide pool from sugar beet pulp (SBP). Sugar beet oligosaccharides (SBOs) resulted in similar changes to SBP in fecal enrichments; however, SBO could be consumed by more beneficial bifidobacterial strains than the cognate polysaccharide. These results demonstrate how the details of glycan structure have a profound influence on how gut bacteria metabolize food carbohydrates. The implications of this work are relevant to understanding how different dietary sources influence the human microbiome and extend to developing novel oligosaccharide pools for prebiotic applications.}, }
@article {pmid39912537, year = {2025}, author = {Otake, T and Washio, J and Ezoe, K and Sato, S and Abiko, Y and Igarashi, K and Takahashi, N}, title = {The Effect of Environmental Factors on the Nitrate and Nitrite Metabolism of Oral Actinomyces and Schaalia Species.}, journal = {Molecular oral microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/omi.12492}, pmid = {39912537}, issn = {2041-1014}, support = {21H03151//Grants-in-Aid for Scientific Research B/ ; 20K10241//Grants-in-Aid for Scientific Research C/ ; //Japan Society for the Promotion of Science/ ; }, abstract = {Actinomyces naeslundii and Schaalia odontolytica belong to the most predominant nitrite-producing bacteria in the oral microbiome. Nitrite has antibacterial and vasodilatory effects that may contribute to maintaining oral and systemic health. We have previously elucidated the metabolic characteristics of the nitrite-producing activity of oral Veillonella species and the effects of oral environmental factors. However, this is still unknown for Actinomyces and Schaalia species. Furthermore, these bacteria are thought to degrade nitrite. Therefore, this study aimed to comprehensively elucidate the effects of environmental factors (pH, oxygen concentration, glucose, lactate, and the presence of nitrate/nitrite during growth) on nitrate and nitrite metabolism of these bacterial species using the type strains. Nitrite was quantified by Griess reagent, and final metabolites were analyzed by high-performance liquid chromatography (HPLC). The nitrite-producing activity of A. naeslundii and S. odontolytica was affected variously by environmental factors. Especially in A. naeslundii, under anaerobic conditions, the activity increased in a concentration-dependent manner with the addition of glucose or lactate and was higher at lower pH when lactate was added. The nitrite-degrading activity of both bacteria was lower than the nitrite-producing activity and was less affected by environmental factors. Metabolites from glucose by A. naeslundii were different with and without nitrate, suggesting that nitrate altered metabolic pathways. The growth was inhibited under anaerobic conditions but promoted under aerobic conditions. These results indicate that the nitrite-producing capacity of the oral microflora must take into account not only the composition and abundance of bacteria but also the variation in metabolic activity due to various environmental factors.}, }
@article {pmid39912125, year = {2025}, author = {Xu, X and Fu, H and Quan, H and Li, Y and Chen, Q and Qu, D and Pi, X}, title = {Effects of fructooligosaccharides and Lactobacillus reuteri on the composition and metabolism of gut microbiota in students.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4fo03763d}, pmid = {39912125}, issn = {2042-650X}, abstract = {Fructooligosaccharides (FOSs) and Lactobacillus reuteri have shown great potential in treating gastrointestinal diseases by regulating gut microbiota and metabolites. However, the synergistic effect between these two remains unclear. In this study, an in vitro fermentation model was constructed to investigate the regulatory effects of FOSs and L. reuteri on the gut microbiota of healthy student populations. After 24 hours of fecal fermentation, the results indicated that the experimental group added with FOSs had increased relative abundances of Bifidobacterium and Lactobacillus, while it exhibited lower relative abundances of Escherichia-Shigella and Bacteroides. Conversely, the groups added with L. reuteri had higher relative abundances of Bacillus and unclassified_c_Bacilli. The results of microbial metabolism revealed that the addition of FOSs produced a large amount of acetic acid, but reduced the contents of propionic acid, butyric acid, isobutyric acid, and isovaleric acid, along with reducing the production of H2, H2S and NH3. In contrast, the addition of L. reuteri had no significant effect on metabolism. Compared to the single additions, the combination of FOSs and L. reuteri had its advantages and had a more balanced microbial structure and metabolic regulation similar to the addition of FOSs alone. Additionally, correlation analysis revealed a negative correlation between gas production and Bifidobacterium, Lactobacillus, and Bacillus, and a positive correlation with Escherichia-Shigella and Bacteroides. Moreover, the formation of acetic acid was positively correlated with Bifidobacterium and negatively correlated with Escherichia-Shigella. These findings demonstrated that the combination of FOSs and L. reuteri can effectively synergistically regulate the fecal microbiome of students. This study can provide a theoretical reference for the precise development of functional foods. However, the regulatory mechanisms need further in-depth investigation.}, }
@article {pmid39912062, year = {2025}, author = {Kumar, A and Bisht, A and SammraMaqsood,  and SaiqaAmjad,  and Baghel, S and Jaiswal, SG and Wei, S}, title = {The role of Micro-biome engineering in enhancing Food safety and quality.}, journal = {Biotechnology notes (Amsterdam, Netherlands)}, volume = {6}, number = {}, pages = {67-78}, pmid = {39912062}, issn = {2665-9069}, abstract = {Microbiome engineering has emerged as a transformative approach to enhancing food safety and quality by strategically modulating microbial communities. This review critically examines state-of-the-art techniques, including synthetic biology, artificial intelligence (AI), and systems biology, that are revolutionizing our ability to improve nutritional profiles, extend shelf life, and optimize food production processes. The review further explores complex social, ethical, and regulatory considerations, emphasizing the importance of robust public engagement and the establishment of standardized frameworks to ensure safe and effective implementation. While microbiome engineering holds significant promise for revolutionizing food safety and quality control, further research is needed to address critical challenges, including understanding microbial dynamics in complex food systems and developing harmonized regulatory frameworks. By bridging interdisciplinary gaps, this paper underscores the necessity of collaborative efforts to unlock the full potential of microbiome-driven innovations for a more resilient and sustainable food industry.}, }
@article {pmid39912061, year = {2024}, author = {Shi, L and Li, Z and Ma, X and Wang, J and Wu, Y and Zhu, Y and Wang, Y and Yang, Y and Luo, M and Li, J and Sun, X and He, S}, title = {Effects of ultra-processed foods on the liver: insights from gut microbiome and metabolomics studies in rats.}, journal = {Frontiers in nutrition}, volume = {11}, number = {}, pages = {1503879}, pmid = {39912061}, issn = {2296-861X}, abstract = {PURPOSE: High consumption of Ultra-processed foods (UPF) have been identified as a potential risk factor for Non-alcoholic fatty liver disease (NAFLD). Nevertheless, there is limited empirical evidence regarding the impact of UPF, which are typical combination of processed foods, on liver health through alterations in gut microbiota and metabolic processes. We aim to examine the potential impact of UPF on liver health and to explore the role of gut microbiota and metabolites.<br><br>METHODS: This study used Sprague-Dawley rats to mimic modern UPF diets for 90&#x202f;days. Some serum biochemical indices, inflammatory factors, oxidative stress markers, hematoxylin-eosin (HE) staining of the liver, 16S ribosomal RNA (rRNA) and Liquid chromatography-mass spectrometry (LC-MS) of rat feces were detected.<br><br>RESULTS: The UPF diet-induced simple steatosis of the liver in rats without affecting the levels of IL-6, GSH, MDA, and SOD. Additionally, it modified the gut microbiota, increasing potentially harmful bacteria, such as norank_f__Desulfovibrionaceae and Staphylococcus, while also elevating the relative abundance of potentially beneficial bacteria, including Dubosiella and Allobaculum. Furthermore, the consumption of UPF led to a metabolomic disorder characterized by disruptions in the sphingolipid signaling pathway, sulfur relay system, and arachidonic acid metabolism.<br><br>CONCLUSION: In conclusion, the findings of this study indicate that the consumption of UPF influences the development of simple hepatic steatosis, potentially through alterations in gut microbiota and metabolomics.}, }
@article {pmid39911984, year = {2025}, author = {Pyle, HJ and Dyson, T and Gadre, A and Harris-Tryon, TA and Aguh, C}, title = {A Pilot Study Characterization of the Scalp Microbiome in Central Centrifugal Cicatricial Alopecia Shows Shift in Corynebacterium.}, journal = {Skin appendage disorders}, volume = {11}, number = {1}, pages = {19-26}, pmid = {39911984}, issn = {2296-9195}, abstract = {INTRODUCTION: Aberrant fibrosis in central centrifugal cicatricial alopecia (CCCA) is thought to be driven by persistent low-grade inflammation, but the source of inflammation is unclear. Alterations in the scalp microbiota may contribute to inflammation and thus provide a target for therapeutic intervention. We sought to compare the bacterial and fungal cutaneous scalp microbiota in patients with CCCA versus controls.<br><br>METHODS: Six patients with CCCA and seven controls were sampled at the vertex scalp. 16S rRNA sequencing of V3-V4 region and internal transcribed spacer amplicon sequencing was used to compare bacterial and fungal microbiomes.<br><br>RESULTS: A significantly higher relative abundance of Corynebacterium was noted in patients with CCCA versus controls. No significant difference in scalp fungal or bacterial microbiota composition was observed.<br><br>LIMITATIONS: V3-V4 sequencing can be limited in detection of major skin bacterial species.<br><br>CONCLUSION: CCCA is characterized by a distinct bacterial microbiome community and high relative abundances of Corynebacterium. Future studies should characterize the relationship between Corynebacterium and scalp inflammation and the role it may play in the progression of CCCA.}, }
@article {pmid39911715, year = {2024}, author = {Przymus, P and Rykaczewski, K and Martín-Segura, A and Truu, J and Carrillo De Santa Pau, E and Kolev, M and Naskinova, I and Gruca, A and Sampri, A and Frohme, M and Nechyporenko, A}, title = {Deep learning in microbiome analysis: a comprehensive review of neural network models.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1516667}, pmid = {39911715}, issn = {1664-302X}, abstract = {Microbiome research, the study of microbial communities in diverse environments, has seen significant advances due to the integration of deep learning (DL) methods. These computational techniques have become essential for addressing the inherent complexity and high-dimensionality of microbiome data, which consist of different types of omics datasets. Deep learning algorithms have shown remarkable capabilities in pattern recognition, feature extraction, and predictive modeling, enabling researchers to uncover hidden relationships within microbial ecosystems. By automating the detection of functional genes, microbial interactions, and host-microbiome dynamics, DL methods offer unprecedented precision in understanding microbiome composition and its impact on health, disease, and the environment. However, despite their potential, deep learning approaches face significant challenges in microbiome research. Additionally, the biological variability in microbiome datasets requires tailored approaches to ensure robust and generalizable outcomes. As microbiome research continues to generate vast and complex datasets, addressing these challenges will be crucial for advancing microbiological insights and translating them into practical applications with DL. This review provides an overview of different deep learning models in microbiome research, discussing their strengths, practical uses, and implications for future studies. We examine how these models are being applied to solve key problems and highlight potential pathways to overcome current limitations, emphasizing the transformative impact DL could have on the field moving forward.}, }
@article {pmid39911711, year = {2024}, author = {Kimeklis, AK and Gladkov, GV and Orlova, OV and Lisina, TO and Afonin, AM and Aksenova, TS and Kichko, AA and Lapidus, AL and Abakumov, EV and Andronov, EE}, title = {Metagenomic insights into the development of microbial communities of straw and leaf composts.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1485353}, pmid = {39911711}, issn = {1664-302X}, abstract = {INTRODUCTION: Soil microbiome is a major source of physiologically active microorganisms, which can be potentially mobilized by adding various nutrients. To study this process, a long-term experiment was conducted on the decomposition of oat straw and leaf litter using soil as a microbial inoculum.<br><br>METHODS: Combined analyses of enzymatic activity and NGS data for 16S rRNA gene amplicon and full metagenome sequencing were applied to study taxonomic, carbohydrate-active enzyme (CAZy), and polysaccharide utilization loci (PULs) composition of microbial communities at different stages of decomposition between substrates.<br><br>RESULTS: In straw degradation, the microbial community demonstrated higher amylase, protease, catalase, and cellulase activities, while peroxidase, invertase, and polyphenol oxidase were more active in leaf litter. Consistent with this, the metagenome analysis showed that the microbiome of straw compost was enriched in genes for metabolic pathways of simpler compounds. At the same time, there were more genes for aromatic compound degradation pathways in leaf litter compost. We identified nine metagenome-assembled genomes (MAGs) as the most promising prokaryotic decomposers due to their abnormally high quantity of PULs for their genome sizes, which were confirmed by 16S rRNA gene amplicon sequencing to constitute the bulk of the community at all stages of substrate degradation. MAGs from Bacteroidota (Chitinophaga and Ohtaekwangia) and Actinomycetota (Streptomyces) were found in both composts, while those from Bacillota (Pristimantibacillus) were specific for leaf litter. The most frequently identified PULs were specialized on xylans and pectins, but not cellulose, suggesting that PUL databases may be underrepresented in clusters for complex substrates.<br><br>DISCUSSION: Our study explores microbial communities from natural ecosystems, such as soil and lignocellulosic waste, which are capable of decomposing lignocellulosic substrates. Using a comprehensive approach with chemical analyses of the substrates, amplicon, and full metagenome sequencing data, we have shown that such communities may be a source of identifying the highly effective decomposing species with novel PULs.}, }
@article {pmid39911706, year = {2024}, author = {Leon-Gomez, P and Romero, VI}, title = {Human papillomavirus, vaginal microbiota and metagenomics: the interplay between development and progression of cervical cancer.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1515258}, pmid = {39911706}, issn = {1664-302X}, abstract = {Persistent infection with oncogenic human papillomavirus (HPV) types, such as HPV 16 or 18, is a major factor in cervical cancer development. However, only a small percentage of infected women develop cancer, indicating that other factors are involved. Emerging evidence links vaginal microbiota with HPV persistence and cancer progression. Alterations in microbial composition, function, and metabolic pathways may contribute to this process. Despite the potential of metagenomics to explore these interactions, studies on the vaginal microbiota's role in cervical cancer are limited. This review systematically examines the relationship between cervical microbiota, HPV, and cervical cancer by analyzing studies from PubMed, EBSCO, and Scopus. We highlight how microbial diversity influences HPV persistence and cancer progression, noting that healthy women typically have lower microbiota diversity and higher Lactobacillus abundance compared to HPV-infected women, who exhibit increased Gardenella, Prevotella, Sneathia, Megasphaera, Streptococcus, and Fusobacterium spp., associated with dysbiosis. We discuss how microbial diversity is associated with HPV persistence and cancer progression, noting that studies suggest healthy women typically have lower microbiota diversity and higher Lactobacillus abundance, while HPV-infected women exhibit increased Gardnerella, Prevotella, Sneathia, Megasphaera, Streptococcus, and Fusobacterium spp., indicative of dysbiosis. Potential markers such as Gardnerella and Prevotella have been identified as potential microbiome biomarkers associated with HPV infection and cervical cancer progression. The review also discusses microbiome-related gene expression changes in cervical cancer patients. However, further research is needed to validate these findings and explore additional microbiome alterations in cancer progression.}, }
@article {pmid39911698, year = {2025}, author = {Shi, Y and Li, J and Xie, J and Yang, T and Ma, Q and Chen, H and Guo, W}, title = {Comparison of the lower genital tract microbiome composition in patients with benign gynecological disease.}, journal = {Frontiers in global women's health}, volume = {6}, number = {}, pages = {1507907}, pmid = {39911698}, issn = {2673-5059}, abstract = {OBJECTIVE: Lower genital tract microbiome dysbiosis has been associated with several gynecological diseases. However, the differences in microbiome composition among patients with several gynecological diseases, such as endometrial polyps and uterine myoma, are poorly understood. Studying the lower genital tract microbiome composition in patients with benign gynecological diseases could provide new insights for interpreting the complex interplay between the microbiome and pathogenesis and finding new targets for preventive measures.<br><br>METHODS: A total of 16 patients with endometrial polyps (EPs), 11 patients with uterine myoma (UM), 6 patients with ovarian cysts (OC) and 36 healthy women (HWs) were recruited for this study. Samples were obtained from vaginal secretions. The DNA was isolated from the samples, and the V3-V4 regions were amplified. The sequencing libraries were generated and sequenced on an Illumina NovaSeq 6000 platform.<br><br>RESULTS: Firmicutes, Actinobacteria and Bacteroidota were the most common phyla in all four groups, whereas OC presented the highest abundance of Firmicutes and the lowest abundance of Bacteroidota. At the genus level, Lactobacillus in the OC group was significantly greater than that in the HW group, and Atopobium in the UM group was significantly lower than that in the HW group. The abundance of Gardnerella was greater in the UM group than in the EP group, and the abundance of Streptococcus was greater in the EP group. The richness and evenness of the microbiome were generally consistent among the HW, EP, UM, and OC groups. Principal component analysis (PCA), principal coordinate analysis (PCoA) and nonmetric multidimensional scaling (NMDS) revealed no distinct separation trends among the four groups. According to ANOSIM, there was no significant difference in community structure among the four groups.<br><br>CONCLUSIONS: A nonsignificant result was obtained from the microbiome diversity comparison among the different groups. However, we demonstrated that the OC group had a greater abundance of Lactobacillus and that the UM group had a lower abundance of Atopobium, which might contribute to the occurrence of diseases, providing new clues for preventive measures.}, }
@article {pmid39911696, year = {2025}, author = {Beli, E and Yan, Y and Moldovan, L and Lydic, TA and Krishman, P and Tersey, SA and Duan, Y and Salazar, TE and Dominguez, JM and Nguyen, DV and Cox, A and Calzi, SL and Beam, C and Mirmira, RG and Evans-Molina, C and Busik, JV and Grant, MB}, title = {Reshaping lipid metabolism with long-term alternate day feeding in type 2 diabetes mice.}, journal = {npj metabolic health and disease}, volume = {3}, number = {1}, pages = {3}, pmid = {39911696}, issn = {2948-2828}, abstract = {Strategies to improve metabolic health include calorie restriction, time restricted eating and fasting several days per week or month. These approaches have demonstrated benefits for individuals experiencing obesity, metabolic syndrome, and prediabetes. However, their impact on established diabetes remains incompletely studied. The chronicity of type 2 diabetes (T2D) requires that interventions must be undertaken for extended periods of time, typically the entire lifetime of the individual. In this study, we examined the impact of intermittent fasting (IF), with an every-other-day protocol for a duration of 6 months in a murine model of T2D, the db/db (D) mouse on metabolism and liver steatosis. We compared D-IF mice with diabetic ad-libitum (AL; D-AL), control-IF (C-IF) and control-AL (C-AL) cohorts. We demonstrated using lipidomic, microbiome, metabolomic and liver transcriptomic studies that chronic IF improved carbohydrate utilization and glucose homeostasis without weight loss and reduced white adipose tissue inflammation and significantly impacted lipid metabolism in the liver. Microbiome studies and predicted functional analysis of gut microbiota showed that IF increased beneficial bacteria involved in sphingolipid (SL) metabolism. The metabolomic studies showed that oxidation of lipid species and ceramide levels were reduced in D-IF compared to D-AL. The liver lipidomic analysis and liver microarray confirmed a reduction in overall lipid content in D-IF mice compared to D-AL mice, especially in the feeding state as well as an overall reduction in oxidized lipids and ceramides. These studies support that long-term IF can improve glucose homeostasis and dramatically altered lipid metabolism in the absence of weight loss.}, }
@article {pmid39911488, year = {2024}, author = {Vaselek, S and Alten, B}, title = {Microbial ecology of sandflies-the correlation between nutrition, Phlebotomus papatasi sandfly development and microbiome.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1522917}, pmid = {39911488}, issn = {2297-1769}, abstract = {The role and the impact of the microbial component on the biology, ecology, and development of sandflies is largely unknown. We evaluated the impact of larval nutrition on laboratory-reared sandflies in correlation to the abundance of food, light starvation, and food with/without live microbiome, by monitoring the survival and development of immature stages, and the longevity of adult sandflies. Within this study we examined 360 larvae, 116 pupae, and 120 adult flies of Phlebotomus papatasi for the microbial gut content. The data showed that the presence of a live and diverse microbiome plays a role in the development and survival of larvae. The mortality rate of the larvae was higher, and larval development was longer for sandflies maintained on microbiome-depleted medium, in comparison to the larvae fed with medium containing alive and complex microbiome. Actively feeding larvae reduce microbial abundance and diversity of the medium. The microbial content of the larval gut depends on the composition of the rearing medium, indicating a potential attraction to certain bacteria. The microbial content of the pupa gut was severely diminished, with overall survival of two bacterial species in adult insects - Ochrobactrum intermedium (found in 95% of dissected adults) and Bacillus subtilis (16%). Further microbial studies may aid in developing biological control methods for sandfly larval or adult stages.}, }
@article {pmid39911483, year = {2024}, author = {Bharani, KK and Devarasetti, AK and Bobbili, R and Khurana, A and Veera Hanuman, DD and Gudepu, R and Guda, S}, title = {The role of Ashwagandha in modulating gut parameters in dogs-a randomized double-blind placebo-controlled trial.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1491989}, pmid = {39911483}, issn = {2297-1769}, abstract = {INTRODUCTION: This study explored the role of Withania somnifera/Ashwagandha root extract (ARE) on important gut-microbiome parameters in healthy geriatric dogs. We hypothesized that ARE might promote a healthy gut by its adaptogenic and anti-inflammatory effects and improve vital parameters for healthy ageing.<br><br>METHODS: A randomized, double-blind, placebo-controlled trial was conducted in Telangana, India. Twelve healthy geriatric Beagle dogs aged 12-15 years were enrolled. The dogs were divided into two groups to receive ARE (15 mg/kg, once daily, orally, for 2 months) or a placebo control. Various parameters were assessed, including serum haematology, biochemical markers, stool parameters, and gut-microbiome parameters.<br><br>RESULTS: The erythrocyte counts and haemoglobin levels were significantly increased with ARE (p < 0.01 and p < 0.001). Moreover, a significant decrease in important serum liver biomarkers (alanine transaminase [ALT], aspartate transaminase [AST]; p < 0.01 and p < 0.001 at day 60) was observed in the ARE-treated dogs compared to that in the placebo control group. In addition, the levels of L-citrulline were significantly modulated by ARE intervention, whereas the intervention did not affect intestinal-type alkaline phosphatase (I-ALP), lactate, and carbamoyl-phosphate synthase (CPS). Interestingly, the faecal score reduced significantly with ARE (p < 0.001), while the faecal pH remained unaltered. Compared to the baseline, ARE significantly decreased two microbial metabolites, propionic acid, and total short chain fatty acids (SCFAs) levels after 60 days of intervention, whereas butyrate and acetic acid levels remained unchanged in the faecal samples.<br><br>CONCLUSION: In summary, these findings suggest that ARE has gut health promoting benefits in healthy geriatric dogs by improving haematological and biochemical profiles; the levels of L-citrulline; propionic acid; and SCFA; thus, reducing age-related changes by modulating the microbiome and the associated metabolites.}, }
@article {pmid39911482, year = {2024}, author = {Graham, D and Petrone-Garcia, VM and Hernandez-Velasco, X and Coles, ME and Juarez-Estrada, MA and Latorre, JD and Chai, J and Shouse, S and Zhao, J and Forga, AJ and Senas-Cuesta, R and Laverty, L and Martin, K and Trujillo-Peralta, C and Loeza, I and Gray, LS and Hargis, BM and Tellez-Isaias, G}, title = {Corrigendum: Assessing the effects of a mixed Eimeria spp. challenge on performance, intestinal integrity, and the gut microbiome of broiler chickens.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1548502}, doi = {10.3389/fvets.2024.1548502}, pmid = {39911482}, issn = {2297-1769}, abstract = {[This corrects the article DOI: 10.3389/fvets.2023.1224647.].}, }
@article {pmid39911400, year = {2025}, author = {Zhang, R and Ding, N and Feng, X and Liao, W}, title = {The gut microbiome, immune modulation, and cognitive decline: insights on the gut-brain axis.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1529958}, pmid = {39911400}, issn = {1664-3224}, mesh = {*Gastrointestinal Microbiome/immunology ; Humans ; *Brain-Gut Axis/immunology ; *Cognitive Dysfunction/immunology/microbiology/etiology ; Animals ; Dysbiosis/immunology ; Brain/immunology/metabolism ; Immunomodulation ; Fatty Acids, Volatile/metabolism/immunology ; Immunity, Mucosal ; }, abstract = {The gut microbiome has emerged as a pivotal area of research due to its significant influence on the immune system and cognitive functions. Cognitive disorders, including dementia and Parkinson's disease, represent substantial global health challenges. This review explores the relationship between gut microbiota, immune modulation, and cognitive decline, with a particular focus on the gut-brain axis. Research indicates that gut bacteria produce metabolites, including short-chain fatty acids (SCFAs), which affect mucosal immunity, antigen presentation, and immune responses, thereby influencing cognitive functions. A noteworthy correlation has been identified between imbalances in the gut microbiome and cognitive impairments, suggesting novel pathways for the treatment of cognitive disorders. Additionally, factors such as diet, environment, and pharmaceuticals play a role in shaping the composition of the gut microbiome, subsequently impacting both immune and cognitive health. This article aims to clarify the complex interactions among gut microbiota, immune regulation, and cognitive disorders, evaluating their potential as therapeutic targets. The goal is to promote microbiome-based treatments and lay the groundwork for future research in this field.}, }
@article {pmid39911351, year = {2025}, author = {Wang, P and Shen, Y and Yan, K and Wang, S and Jiao, J and Chi, H and Zhong, J and Sun, Q and Dong, Y and Li, J}, title = {CKD patients comorbid with hypertension are associated with imbalanced gut microbiome.}, journal = {iScience}, volume = {28}, number = {2}, pages = {111766}, pmid = {39911351}, issn = {2589-0042}, abstract = {Intestinal flora has been linked to chronic kidney disease (CKD) and hypertension, respectively. This study aimed to investigate the microbial community among 54 individuals without CKD, 46 hypertensive CKD patients (CKD_HTN), and 48 non-hypertensive CKD patients. Variations in microbial diversity were detected in CKD. The Prevotella-dominated type progressively increased from CKD to CKD_HTN. Based on the variation patterns, we identified six distinct clusters. Klebsiella, Turicibacter, and Enterobacter were enriched in CKD, whereas Escherichia and Mogibacterium were elevated, and Blautia and Clostridium were reduced in CKD_HTN. Enhanced phenylalanine metabolism and siderophore group nonribosomal peptides biosynthesis from non-CKD to CKD were observed, particularly in CKD with hypertension. The connections between genera and KEGG pathways suggest an impact of microbial dysbiosis on metabolism. Our findings demonstrate that imbalances in gut microorganisms and functions are associated with increased susceptibility to hypertension in CKD patients and could be targeted for improving kidney function in CKD.}, }
@article {pmid39911241, year = {2024}, author = {Lu, CM and Hsu, YH and Lin, IH and Kuo, KL and Liao, JF and Huang, HF and Lu, PH}, title = {Conventional and complementary alternative medicine therapies for renal anemia: a literature review.}, journal = {Frontiers in endocrinology}, volume = {15}, number = {}, pages = {1342873}, pmid = {39911241}, issn = {1664-2392}, mesh = {Humans ; *Anemia/therapy ; *Complementary Therapies/methods ; Renal Insufficiency, Chronic/therapy ; }, abstract = {Renal anemia stems mainly from chronic inflammation with elevated hepcidin levels, iron deficiency, and reduced red blood cell lifespan. Inadequate erythropoietin (EPO) production, worsened kidney function, leads to symptoms such as low energy, fatigue, and impaired physical function, significantly affecting patients' quality of life. We conducted a comprehensive search across electronic databases including PubMed, Embase, Cochrane Library, Chinese National Knowledge Infrastructure, Airiti library, and Wanfang, to compile recent clinical trials and pilot studies on conventional and complementary alternative medicine approaches for renal anemia. This discussion focuses on the hypoxia-inducible factor prolyl hydroxylase domain (HIF-PHD) axis theory, from lab research to clinical applications. It explores non-extracorporeal treatments for renal anemia, including pharmaceutical interventions, dietary strategies, and complementary and alternative medicine (CAM). The article details the effects of Roxadustat, Ferumoxytol, and Epodion. Clinical studies show that modulating the gut microbiome can reduce inflammation and improve renal anemia. Clinical trials suggest that CAM therapy can improve renal anemia through mechanisms such as enhanced iron metabolism, anti-inflammatory effects, reduced hepcidin levels, and increased EPO and HIF expressions. By synthesizing this information, the review aims to furnish valuable insights and treatment recommendations aimed at ameliorating renal anemia in individuals grappling with chronic kidney disease.}, }
@article {pmid39910939, year = {2025}, author = {Mohamed, KT and Shabayek, S and Fahmy Mahmoud, N and Tawfick, MM and Hanora, AMS}, title = {Investigation of bacterial gut microbiome in diverse Egyptian populations "pilot study".}, journal = {Cellular and molecular biology (Noisy-le-Grand, France)}, volume = {71}, number = {1}, pages = {75-87}, doi = {10.14715/cmb/2025.70.1.8}, pmid = {39910939}, issn = {1165-158X}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Egypt ; Adult ; Middle Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; *Feces/microbiology ; Pilot Projects ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The gut microbiota plays a huge role in human health regarding immunity, metabolism, and nutrient absorption. In this work, the gut microbiota, with its bacterial community structure, is studied using whole genome shotgun (WGS) sequencing for populations from two different geographical regions in Egypt: Cairo (urban) and Ismailia (rural). Fecal samples were obtained from six healthy individuals, three from Cairo and three from Ismailia, of ages ranging from 43 to 52 years. Alpha diversity, measured as Shannon, inverse Simpson, and OTUs, showed no significant differences between the two cities. However, beta diversity analysis by Principal Coordinate Analysis (PCoA) revealed diverse microbial compositions. Thus, only the Ismailia samples contained higher levels of butyrate-producing bacteria involved in maintaining intestinal health, such as Faecalibacterium prausnitzii and Akkermansia muciniphila. On the other hand, there was a higher prevalence in Cairo of bacteria associated with protein and fat metabolism, like Bacteroides thetaiotaomicron. Such findings explain the influence of environmental factors in shaping gut microbiota and show that to get a comprehensive understanding of regional differences, many wider-ranging studies need to be conducted.}, }
@article {pmid39910460, year = {2025}, author = {Cui, S and Liu, X and Han, F and Zhang, L and Bu, J and Wu, S and Wang, J}, title = {Helicobacter pylori CagA+ strains modulate colorectal pathology by regulating intestinal flora.}, journal = {BMC gastroenterology}, volume = {25}, number = {1}, pages = {54}, pmid = {39910460}, issn = {1471-230X}, support = {LCYJZR202116//Project of Binzhou People's Hospital/ ; }, mesh = {Animals ; *Antigens, Bacterial/metabolism ; *Helicobacter pylori ; *Gastrointestinal Microbiome ; *Mice, Inbred C57BL ; *Helicobacter Infections/microbiology/pathology ; *Bacterial Proteins/metabolism ; Mice ; *Colon/microbiology/pathology ; Intestinal Mucosa/microbiology/pathology/metabolism ; Gastric Mucosa/microbiology/pathology ; Rectum/microbiology/pathology ; Male ; Cytokines/metabolism ; }, abstract = {AIM: This article aims to investigate the role of Helicobacter Pylori (HP) CagA+ strains affected colorectal lesion via gut microbiota.<br><br>METHOD: 6-week C57BL/6J mice were divided into: (a) HP CagA+&#x2009;group undergoing HP CagA+&#x2009;strains administration by gavage at 0.2 mL for 10 days; (b) HP CagA- group undergoing HP CagA- strains administration by gavage at 0.2 mL for 10 days; (c) control group intragastrically given 0.2 mL of brian heart infusion (BHI) medium for 10 days. Gastric mucosa was collected for Giemsa staining, and colorectal mucosa was for hematoxylin and eosin (H&amp;E) staining, 16&#xa0;S ribosomal RNA (rRNA) sequencing and immunohistochemistry for Major Histocompatibility Complex (MHC). Colon tissues and serum from caudal vein was collected for quantification of interleukin (IL)-6, IL-8, IL10 and tumor necrosis factor (TNF-&#x3b1;).<br><br>RESULTS: Mice with HP CagA+&#x2009;infection developed loss of some resident cells and inflammation infiltration in colorectal mucosa, and increased Giemsa-positive cells in gastric tissue. Also, MHC II-positive cells were increased in colorectal tissue in HP CagA+&#x2009;strains infection. HP CagA+&#x2009;infection cause increase of TNF-&#x3b1;, IL-6, IL-8 and IL-10 in the serum. Meanwhile, HP CagA+&#x2009;stainis evoked gut microbiota dysbiosis which was characterized by altered microbiome distribution, reduction in Front-to-Back (F/B ratio), decreased &#x3b1;-diversity metric (Chao1 and Shannon). In &#x3b2;-diversity, gut microbiota in control and HP CagA+&#x2009;groups showed the significant distance based on UniFrac distance. Cag group was enriched a higher abundance of Staphylococcus and Corynebacterium, while control subjects were enriched in Marinifilaceae and Odoribacter.<br><br>CONCLUSION: HP CagA+&#x2009;strains are capable of causing gut microbiota dysbiosis to develop destruction of intestinal barrier, and it may affect the development of colorectal cancer by increasing colonization of Staphylococcus and Corynebacterium.}, }
@article {pmid39910446, year = {2025}, author = {Ajayi, O and Mahalingam, R}, title = {Seed endophytes of malting barley from different locations are shaped differently and are associated with malt quality traits.}, journal = {BMC plant biology}, volume = {25}, number = {1}, pages = {151}, pmid = {39910446}, issn = {1471-2229}, mesh = {*Hordeum/microbiology/genetics ; *Endophytes/physiology ; *Seeds/microbiology ; Microbiota ; Genotype ; Ascomycota/physiology ; Bacteria/genetics/classification/isolation &amp; purification ; Edible Grain/microbiology/genetics ; }, abstract = {Maximizing microbial functions for improving crop performance requires better understanding of the important drivers of plant-associated microbiomes. However, it remains unclear the forces that shapes microbial structure and assembly, and how plant seed-microbiome interactions impact grain quality. In this work, we characterized the seed endophytic microbial communities of malting barley from different geographical locations and investigated associations between microbial (bacterial and fungal) species diversity and malt quality traits. Host genotype, location, and interactions (genotype x location) significantly impacted the seed endophytic microbial communities. Taxonomic composition analysis identified the most abundant genera for bacterial and fungal communities to be Bacillus (belonging to phylum Firmicutes) and Blumeria (belonging to phylum Ascomycota), respectively. We observed that a greater proportion of bacterial amplicon sequence variants (bacterial ASVs) were shared across genotypes and across locations while the greater proportion of the fungal ASVs were unique to each genotype and location. Association analysis showed a significant negative correlation between bacterial alpha diversity indices (Faith PD and Shannon indices) and malt quality traits for barley protein (BP), free amino nitrogen (FAN), diastatic power (DP) and alpha amylase (AA), while fungal alpha diversity (Shannon and Simpson) showed significant negative relationship with β-D-glucan content. In addition, some bacterial and fungal genera were significantly associated with malt extract (ME) -a key trait for maltsters and brewers. We conclude that barley genotype, location, and their interactions shape the seed endophytic microbiome and is key to microbiome manipulation and management during barley production and/or malting.}, }
@article {pmid39910204, year = {2025}, author = {Bijnens, K and Thijs, S and Alfano, R and McAmmond, B and Van Hamme, J and Artois, T and Plusquin, M and Vangronsveld, J and Smeets, K}, title = {Impact of host physiology and external stressors on the bacterial community of Schmidtea mediterranea.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {4398}, pmid = {39910204}, issn = {2045-2322}, support = {GOH3817N//European Marine Biological Resource Centre Belgium/ ; 08M03VGRJ//Hasselt University Methusalem Project/ ; G.0B83.17N//Fonds Wetenschappelijk Onderzoek/ ; BOF16NI03//Bijzonder Onderzoeksfonds UHasselt, Belgium/ ; }, mesh = {Animals ; *Planarians/physiology/microbiology ; *Microbiota ; *Stress, Physiological ; Bacteria/classification/genetics ; Host Microbial Interactions/physiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {To fully comprehend host-microorganism interactions, it is crucial to understand the composition and diversity of the microbiome, as well as the factors that shape these characteristics. We investigated microbiome variation using the freshwater planarian Schmidtea mediterranea, an invertebrate model in regeneration biology and (eco-)toxicology, by exposing the organisms to various controlled conditions. The microbiome composition exhibited high variability, with most of the bacteria belonging to the Betaproteobacteria. Among the diverse microbial communities, a few genera, such as Curvibacter, were consistently present, but exhibited significant alterations in response to changing conditions. The relative abundance of Curvibacter fluctuated during the regeneration process, initially increasing before returning to a composition similar to the beginning situation. After applying external stress, the relative abundance of Curvibacter and other genera decreased. Variation over time, between different origin laboratories and between individuals, showed that additional, yet to-be-identified, factors of variation are present. Taking all results together, our study provides a solid basis for future research focusing on bacterial functionality in planarians and other invertebrates.}, }
@article {pmid39909847, year = {2025}, author = {Schmid, M and Haas, VP and Sarpong, N and Rodehutscord, M and Seifert, J and Camarinha-Silva, A and Bennewitz, J}, title = {Fecal Microbiota-based Investigations of Nitrogen Utilization Efficiency and related Traits in a Landrace x Piétrain crossbred Population.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skaf028}, pmid = {39909847}, issn = {1525-3163}, abstract = {Improving protein efficiency in pork production is a desired goal regarding resource conservation and climate protection, whereby animal breeding has great potential for sustainable improvements. Nitrogen utilization efficiency (NUE) is an important trait but laborious to measure. As blood urea nitrogen (BUN) can be used to predict NUE, it is often used as indicator trait. Both NUE and BUN were found to be heritable, however, microbial studies have not yet been carried out. The present study aimed to investigate the role of the gastrointestinal microbiota in the context of N efficiency in different fattening phases. The dataset consisted of 450 Landrace x Piétrain pigs fattened in a two-phase feeding regime. All pigs were fecal sampled and phenotyped in two fattening phases, referred to as sampling period (SP) 1 and SP2 in week 13 and week 16 post natum, respectively. Microbial communities in feces were compared across SPs and significant differences were observed. Mixed linear models were applied to quantify the microbial variance and microbiability for NUE, BUN, and related traits within each of the SPs. Except for NUE in SP1, all microbiabilities were significant and ranged from 0.079 to 0.471. Microbiome-wide association studies revealed a polymicrobial trait architecture, characterized by the contribution of many genera, with each genus having a relatively small effect on the traits. In total, four and eleven microbial genera were significantly associated with NUE and BUN, respectively. Microbial correlations were estimated between traits within SPs via bivariate analyses. Blood urea nitrogen was significantly correlated with N intake and retention in SP1 but not in SP2. Fecal microbiota composition differed significantly between SPs and the use of microbiota data across SPs resulted in a remarkable drop in microbiability for nearly all traits. This implies that microbiota data should be representative of the time point of phenotyping to fully capture microbial contribution to trait expression. The results suggest that jointly using genomic and fecal microbial data might be expedient to improve protein efficiency in fattening pigs.}, }
@article {pmid39909191, year = {2025}, author = {Weitzman, CL and Brown, GP and Day, K and Shilton, CM and Gibb, K and Christian, K}, title = {Protection against anuran lungworm infection may be mediated by innate defenses rather than their microbiome.}, journal = {International journal for parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijpara.2025.01.010}, pmid = {39909191}, issn = {1879-0135}, abstract = {Host-associated microbiomes provide protection against disease in diverse systems, through both direct and indirect interactions with invaders, although these interactions are less understood in the context of non-gut helminth infections in wildlife. Here, we used a widespread, invasive host-parasite system to better understand helminth-amphibian-microbiome dynamics. We focus on cane toads and their lungworm parasites, which invade the host through the skin, to study the interactions between lungworm infection abundance and skin and gut (colon) bacterial microbiomes. Through two experiments, first reducing skin bacterial loads, and second reducing bacterial diversity, we found no evidence of protection by skin bacteria against infection. We also did not find divergent gut communities dependent on lungworm infection, signifying little to no immune modulation from infection causing changes to gut communities, at least in the first month after initial parasite exposure. In light of previous work in the system, these results underscore the contribution of toads' innate susceptibility (including possible protection provided by skin secretions) rather than skin microbes in determining the chance of infection by these macroparasites.}, }
@article {pmid39909132, year = {2025}, author = {Benitez, AJ and Margolis, KG}, title = {A Microbiome-directed therapy for malnutrition that performs better than standard nutritional interventions.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2025.01.231}, pmid = {39909132}, issn = {1528-0012}, }
@article {pmid39909118, year = {2025}, author = {Li, Y and Zhang, J and Lei, Y and Chang, M and Xu, J and Tang, S}, title = {Multi-omics approaches reveal the therapeutic mechanism of Naoxintong Capsule against ischemic stroke.}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {119435}, doi = {10.1016/j.jep.2025.119435}, pmid = {39909118}, issn = {1872-7573}, abstract = {Ischemic stroke (IS) is a leading cause of long-term disability and mortality worldwide. The Chinese Pharmacopeia 2020 lists Naoxintong Capsule (NXT), a traditional Chinese medicine prescription, as having demonstrated substantial therapeutic efficacy for IS.<br><br>AIM OF THE STUDY: Our study aimed to evaluate the mechanism by which NXT treats IS by integrating the microbiome, transcriptome, and metabolomics.<br><br>MATERIALS AND METHODS: In a middle cerebral artery occlusion (MCAO) mouse model, the infarction rate, neurological scores, lipopolysaccharide (LPS) levels, inflammatory factor levels (IL-1&#x3b2;, IL-17A, and IL-6), and intestinal permeability proteins (ZO-1, MUC2, and MUC4) were measured to confirm the effect of NXT on the brain and colon. 16S rRNA sequencing, transcriptomics analysis, and targeted amino acid (AA) metabolism were employed to evaluate the mechanism by which NXT treats IS. Furthermore, the neuroprotective effects of specific AAs, identified through targeted AA metabolism, were assessed in PC12 cells following oxygen-glucose deprivation (OGD) injury. In addition, the TLR4/NF-&#x3ba;B pathway was evaluated by western blot (WB).<br><br>RESULTS: NXT administration substantially alleviated brain damage and colon injury by decreasing the infarction rate, neurological scores, LPS levels, and inflammatory factors, and increasing the expression of intestinal permeability protein. Transcriptomic analysis revealed that NXT regulated "inflammatory response," "Toll-like receptor signaling pathway,", and "NF-&#x3ba;B signaling pathway." Furthermore, WB confirmed that NXT inhibited the brain TLR4/NF-&#x3ba;B pathway. 16S rRNA sequencing indicated that NXT adjusted the intestinal microbiota composition and decreased the abundance of pathogenic bacteria, including Parasutterella_massiliensis and Ihubacter_excrementihominis. Targeted AA metabolism analysis demonstrated that NXT regulated the serum levels of serine, lysine, and proline in MCAO mice. Furthermore, serine, lysine, and proline inhibited the TLR4/NF-&#x3ba;B pathway to protect against OGD injury in PC12 cells.<br><br>CONCLUSION: Our study indicates that NXT reduces the abundance of Parasutterella_massiliensis and Ihubacter_excrementihominis, while increasing the levels of serine, lysine, and proline. These changes are significantly associated with neuroinflammation. Furthermore, NXT alleviates IS-induced neuroinflammation by inhibiting the TLR4/NF-&#x3ba;B pathway. Importantly, our study provides novel insights into the mechanisms underlying NXT's therapeutic effects on IS.}, }
@article {pmid39909037, year = {2025}, author = {Lim, B and Xu, J and Wierzbicki, IH and Gonzalez, CG and Chen, Z and Gonzalez, DJ and Gao, X and Goodman, AL}, title = {A human gut bacterium antagonizes neighboring bacteria by altering their protein-folding ability.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2025.01.008}, pmid = {39909037}, issn = {1934-6069}, abstract = {Antagonistic interactions play a key role in determining microbial community dynamics. Here, we report that one of the most widespread contact-dependent effectors in human gut microbiomes, Bte1, directly targets the PpiD-YfgM periplasmic chaperone complex in related microbes. Structural, biochemical, and genetic characterization of this interaction reveals that Bte1 reverses the activity of the chaperone complex, promoting substrate aggregation and toxicity. Using Bacteroides, we show that Bte1 is active in the mammalian gut, conferring a fitness advantage to expressing strains. Recipient cells targeted by Bte1 exhibit sensitivity to membrane-compromising conditions, and human gut microbes can use this effector to exploit pathogen-induced inflammation in the gut. Further, Bte1 allelic variation in gut metagenomes provides evidence for an arms race between Bte1-encoding and immunity-encoding strains in humans. Together, these studies demonstrate that human gut microbes alter the protein-folding capacity of neighboring cells and suggest strategies for manipulating community dynamics.}, }
@article {pmid39909032, year = {2025}, author = {Zhu, X and Hu, M and Huang, X and Li, L and Lin, X and Shao, X and Li, J and Du, X and Zhang, X and Sun, R and Tong, T and Ma, Y and Ning, L and Jiang, Y and Zhang, Y and Shao, Y and Wang, Z and Zhou, Y and Ding, J and Zhao, Y and Xuan, B and Zhang, H and Zhang, Y and Hong, J and Fang, JY and Xiao, X and Shen, B and He, S and Chen, H}, title = {Interplay between gut microbial communities and metabolites modulates pan-cancer immunotherapy responses.}, journal = {Cell metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmet.2024.12.013}, pmid = {39909032}, issn = {1932-7420}, abstract = {Immune checkpoint blockade (ICB) therapy has revolutionized cancer treatment but remains effective in only a subset of patients. Emerging evidence suggests that the gut microbiome and its metabolites critically influence ICB efficacy. In this study, we performed a multi-omics analysis of fecal microbiomes and metabolomes from 165 patients undergoing anti-programmed cell death protein 1 (PD-1)/programmed death ligand 1 (PD-L1) therapy, identifying microbial and metabolic entities associated with treatment response. Integration of data from four public metagenomic datasets (n = 568) uncovered cross-cohort microbial and metabolic signatures, validated in an independent cohort (n = 138). An integrated predictive model incorporating these features demonstrated robust performance. Notably, we characterized five response-associated enterotypes, each linked to specific bacterial taxa and metabolites. Among these, the metabolite phenylacetylglutamine (PAGln) was negatively correlated with response and shown to attenuate anti-PD-1 efficacy in vivo. This study sheds light on the interplay among the gut microbiome, the gut metabolome, and immunotherapy response, identifying potential biomarkers to improve treatment outcomes.}, }
@article {pmid39908950, year = {2025}, author = {Alonso-Vásquez, T and Fagorzi, C and Mengoni, A and Oliva, M and Cavalieri, D and Pretti, C and Cangioli, L and Bacci, G and Ugolini, A}, title = {Metagenomic surveys show a widespread diffusion of antibiotic resistance genes in a transect from urbanized to marine protected area.}, journal = {Marine pollution bulletin}, volume = {213}, number = {}, pages = {117640}, doi = {10.1016/j.marpolbul.2025.117640}, pmid = {39908950}, issn = {1879-3363}, abstract = {Ports are hot spots of pollution; they receive pollution from land-based sources, marine traffic and port infrastructures. Marine ecosystems of nearby areas can be strongly affected by pollution from port-related activities. Here, we investigated the microbiomes present in sea floor sediments along a transect from the harbour of Livorno (Central Italy) to a nearby marine protected area. Results of 16S rRNA amplicon sequencing and metagenome assembled genomes (MAGs) analyses indicated the presence of different trends of specific bacterial groups (e.g. phyla NB1-j, Acidobacteriota and Desulfobulbales) along the transect, correlating with the measured pollution levels. Human pathogenic bacteria and antibiotic resistance genes (ARGs) were also found. These results demonstrate a pervasive impact of human port activities and highlight the importance of microbiological surveillance of marine sediments, which may constitute a reservoir of ARGs and pathogenic bacteria.}, }
@article {pmid39908935, year = {2025}, author = {Lu, T and Li, J and Xiao, E and Zhong, H and Deng, J and Ma, L and Ning, Z and Xiao, T}, title = {Assemblage of root-associated microbiome contributes to disparate performance of two rice genotypes under aluminum stress.}, journal = {Plant physiology and biochemistry : PPB}, volume = {220}, number = {}, pages = {109539}, doi = {10.1016/j.plaphy.2025.109539}, pmid = {39908935}, issn = {1873-2690}, abstract = {Aluminum (Al) toxicity severely inhibits rice growth under acidic soils, posing a significant threat to food security. The assemblies of root-associated microbiomes throughout the lifecycle of rice are hypothesized to furnish a resilient reservoir of ecological functions for rice growth performance under Al stresses. However, the mechanisms that drive the assembly of root-associated microbiomes of rice are largely unknown. In this study, we chose two rice genotypes (including aluminum-tolerant (Al-T) and aluminum-sensitive (Al-S)) as model plants to investigate the microbial assemblage of root-associated microbiome and their potential roles on the plant growth performance under Al stress. The microbial community diversity (Shannon) and evenness (Chao1) in the endosphere of the Al-T genotype gradually decreased, converging towards levels observed in the Al-S genotype. In addition, the rhizosphere and endosphere microbiomes of Al-T genotype are primarily influenced by deterministic processes, while those of Al-S genotype are more influenced by stochastic processes. Compared to Al-S genotype, Al-T genotype exhibited higher complexity and stability in its rhizosphere and endosphere microbiomes, while the rhizoplane microbiome showed the opposite trend. In the rhizosphere microbiome of the Al-T genotype, we identified Gallionellales, Rhodobacterales, and Rhizobiales as keystone taxa. Their abundance was closely associated with microbial functions, including indole-3-acetic acid (IAA) synthesis, phosphorus solubilization, glutathione (GSH) metabolism, and 1-aminocyclopropane-1-carboxylate (ACC) metabolism. In the Al-S genotype, the keystone taxa included Actinomycetales and Burkholderiales. This study offers new insights into plant adaptation to abiotic stress and underscores the significance of the assemblage of root-associated microbiome in this process.}, }
@article {pmid39908601, year = {2025}, author = {Jin, X and Wang, J and Du, Y and Lu, Z and Wang, Y and Wu, H and Huang, R and Li, K and Wang, Y and Li, B}, title = {Potential effects of indoor microbiome characteristics on health: A systematic review.}, journal = {Public health}, volume = {240}, number = {}, pages = {137-147}, doi = {10.1016/j.puhe.2025.01.030}, pmid = {39908601}, issn = {1476-5616}, abstract = {OBJECTIVES: This systematic review aims to assess the potential effects of exposure to microbial agents in the indoor environment on health outcomes.<br><br>STUDY DESIGN: Systematic review.<br><br>METHODS: A systematic literature search was conducted on Embase, PubMed, and Web of Science through January 2024, and reference lists of relevant articles were reviewed. Studies that investigated the relationship between indoor microbial agents and human symptoms and diseases were eligible for inclusion.<br><br>RESULTS: In total, 20 articles were considered eligible for inclusion and reported consistency and variability in the health effects of indoor microorganisms. In microbial diversity analyses, studies showed an increasing trend in microbial &#x3b1;-diversity in patients with allergic and inflammatory diseases and a decreasing trend in fungal &#x3b1;-diversity in patients with behavioral and cognitive disorders. In microbial composition analyses, phylum Cyanobacteria, genus Izhakiella, genus Rhodomicrobiu, species Aeromonas enteropelogenes, and species Brasilonema bromeliae showed a decreasing trend in allergic and inflammatory diseases, while phylum Actinomycetota, phylum Bacillota, phylum Bacteriodota, class Gammaproteobacteria and species Deinococcus gobiensis showed an increasing trend. There were fewer consistent results for respiratory infectious diseases and behavioral and cognitive disorders.<br><br>CONCLUSION: To our knowledge, this is the first systematic review of the association between indoor microbial exposure and human health risk. In this systematic review, we explored the potential impact of microbiota characterization of indoor environments on different diseases or symptoms from the perspective of microbial taxonomic levels through a comprehensive review of differential analysis of indoor microbiota diversity and composition, which provided potential intervention strategies for the management of the indoor microbiome.}, }
@article {pmid39908270, year = {2025}, author = {Owens, F and Souchak, J and Nazaire, V and Akkaoui, J and Shil, R and Carbajal, C and Panda, K and Delgado, DC and Claassen, I and Moreno, S and Yi, S and Dong, Y and Adrita, N and Lau, LS and El-Hage, N}, title = {A Connection Between the Gut Microbiome and Epigenetic Modification in Age-Related Cancer: A Narrative Review.}, journal = {Aging and disease}, volume = {}, number = {}, pages = {}, doi = {10.14336/AD.2024.1618}, pmid = {39908270}, issn = {2152-5250}, abstract = {As individuals age, physiological changes influence the composition and function of the gut microbiome, significantly impacting the onset and progression of various illnesses, including cancer. Notably, the gut microbiome affects epigenetic modifications such as DNA methylation and histone alterations. Furthermore, it contributes to the age-related decline in immune system efficiency, increasing susceptibility to infections and cancers. This dual role of the gut microbiome-both a protective factor and a risk factor-is a key aspect of its importance in maintaining long-term health, making it a significant topic of discussion in this review. Moreover, a challenge faced by the elderly is the concurrent use of multiple medications. Polypharmacy can interact with the gut microbiome, potentially altering its efficacy, leading to adverse drug reactions, and affecting vital microbiome diversity. The effects of these interactions on cancer therapies and the overall health of elderly patients are becoming increasingly important. Understanding the complex relationship between aging, the gut microbiome, cancer, and polypharmacy is crucial for developing more effective therapeutic strategies and improving patient outcomes. Here, we discuss recent advances in understanding age-related physiological changes in the microbiome and their significance in cancer development and therapy. Specifically, we will explor how epigenetic changes acquired during aging, along with ongoing prescriptions of multiple medications and the decline of immune function, contribute to the intricate relationship between aging and cancer.}, }
@article {pmid39908139, year = {2025}, author = {Zhang, Z and Guo, Q and Yang, Z and Sun, Y and Jiang, S and He, Y and Li, J and Zhang, J}, title = {Bifidobacterium adolescentis-derived nicotinic acid improves host skeletal muscle mitochondrial function to ameliorate sarcopenia.}, journal = {Cell reports}, volume = {44}, number = {2}, pages = {115265}, doi = {10.1016/j.celrep.2025.115265}, pmid = {39908139}, issn = {2211-1247}, abstract = {Sarcopenia significantly diminishes quality of life and increases mortality risk in older adults. While the connection between the gut microbiome and muscle health is recognized, the underlying mechanisms are poorly understood. In this study, shotgun metagenomics revealed that Bifidobacterium adolescentis is notably depleted in individuals with sarcopenia, correlating with reduced muscle mass and function. This finding was validated in aged mice. Metabolomics analysis identified nicotinic acid as a key metabolite produced by B. adolescentis, linked to improvements in muscle mass and functionality in individuals with sarcopenia. Mechanistically, nicotinic acid restores nicotinamide adenine dinucleotide (NAD+) levels in muscle, inhibits the FoxO3/Atrogin-1/Murf-1 axis, and promotes satellite cell proliferation, reducing muscle atrophy. Additionally, NAD+ activation enhances the silent-information-regulator 1 (SIRT1)/peroxisome-proliferator-activated-receptor-γ-coactivator 1-alpha (PGC-1α) axis, stimulating mitochondrial biogenesis and promoting oxidative metabolism in slow-twitch fibers, ultimately improving muscle function. Our findings suggest that B. adolescentis-derived nicotinic acid could be a promising therapeutic strategy for individuals with sarcopenia.}, }
@article {pmid39907694, year = {2025}, author = {Song, N and Gao, H and Li, J and Liu, Y and Wang, M and Ma, Z and Zhang, N and Zhang, W}, title = {Microbiota from young mice counteracts susceptibility to age-related gout through modulating butyric acid levels in aged mice.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, doi = {10.7554/eLife.98714}, pmid = {39907694}, issn = {2050-084X}, support = {3220889//National Natural Science Foundation of China - State Grid Corporation Joint Fund for Smart Grid/ ; 31972749//National Natural Science Foundation of China - State Grid Corporation Joint Fund for Smart Grid/ ; 2022010304JC//Natural Science Foundation of Jilin Province/ ; }, mesh = {Animals ; *Gout/metabolism/microbiology ; *Gastrointestinal Microbiome ; Mice ; *Butyric Acid/metabolism ; *Uric Acid/blood/metabolism ; Aging ; Disease Susceptibility ; Mice, Inbred C57BL ; Male ; Inflammasomes/metabolism ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism/genetics ; }, abstract = {Gout is a prevalent form of inflammatory arthritis that occurs due to high levels of uric acid in the blood leading to the formation of urate crystals in and around the joints, particularly affecting the elderly. Recent research has provided evidence of distinct differences in the gut microbiota of patients with gout and hyperuricemia compared to healthy individuals. However, the link between gut microbiota and age-related gout remained underexplored. Our study found that gut microbiota plays a crucial role in determining susceptibility to age-related gout. Specifically, we observed that age-related gut microbiota regulated the activation of the NLRP3 inflammasome pathway and modulated uric acid metabolism. More scrutiny highlighted the positive impact of 'younger' microbiota on the gut microbiota structure of old or aged mice, enhancing butanoate metabolism and butyric acid content. Experimentation with butyrate supplementation indicated that butyric acid exerts a dual effect, inhibiting inflammation in acute gout and reducing serum uric acid levels. These insights emphasize the potential of gut microbiome rejuvenation in mitigating senile gout, unraveling the intricate dynamics between microbiota, aging, and gout. It potentially serves as a therapeutic target for senile gout-related conditions.}, }
@article {pmid39907513, year = {2025}, author = {Mwape, RK and Barday, MA and van der Zalm, MM and Verhagen, LM}, title = {Overview of mucosal immunity and respiratory infections in children: a focus on Africa.}, journal = {Current opinion in pediatrics}, volume = {}, number = {}, pages = {}, doi = {10.1097/MOP.0000000000001438}, pmid = {39907513}, issn = {1531-698X}, abstract = {PURPOSE OF REVIEW: Given the substantial burden of respiratory tract infections (RTIs) on global paediatric health, enhancing our understanding of mucosal immunity can help us advance mucosal biomarkers for diagnosis, prognosis and possible interventions in order to improve health outcomes. This review highlights the critical role of mucosal immunity in paediatric RTIs and recent advances in mucosal interventions, which offer promising strategies to improve outcomes.<br><br>RECENT FINDINGS: The significant burden of paediatric RTIs and growing interest in mucosal immunity advanced our understanding of the role of the respiratory mucosal immune system in protective immunity against RTIs. Studies show that sub-Saharan Africa is disproportionately affected by paediatric RTIs with poverty-associated factors such as human immunodeficiency virus (HIV) and malnutrition as risk factors. Emerging evidence highlights the important role of the respiratory microbiome and mucosal innate and adaptive immune responses in protective immunity against RTIs.<br><br>SUMMARY: The growing interest in mucosal immunity in RTIs has not only advanced our understanding of the overall immune responses in RTIs but also created opportunities to improve RTI care through translation of knowledge from these studies into diagnostics, therapeutics, and vaccines.}, }
@article {pmid39907444, year = {2025}, author = {Kontoyiannis, DP and Casadevall, A}, title = {Would global warming bring an increase of invertebrate-associated cutaneous invasive fungal infections?.}, journal = {mBio}, volume = {}, number = {}, pages = {e0344724}, doi = {10.1128/mbio.03447-24}, pmid = {39907444}, issn = {2150-7511}, abstract = {Invasive mold-associated cutaneous disease is a rare but potentially catastrophic consequence of trauma. However, invertebrate bites are not well recognized as a mechanism for the inoculation of fungi into subcutaneous tissue that can also result in severe infections. Invertebrates often carry fungi with human pathogenic potential as part of their microbiome, and bites break the skin, providing a conduit for them to penetrate subcutaneous tissues where the establishment of infection can produce serious skin and soft tissue fungal diseases. In this essay, we review the existing data for invertebrate bite-associated cutaneous invasive fungal infections (IBA-cIFIs) and consider the potential consequences of global warming on their epidemiology. Climate changes will be associated with changes in the range of invertebrates and adaptation of their associated microbes to warmer temperatures. Fungal adaptation to higher temperatures can defeat the mammalian protective barrier and be associated with both more and different IBA-cIFIs.}, }
@article {pmid39907436, year = {2025}, author = {Guo, J and Han, J and Li, F and Ma, Q and He, J and You, F and Ren, Y and Fu, X}, title = {16S rRNA sequencing reveals relationships among enrichment of oral microbiota in the lower respiratory tract and pulmonary nodules malignant progression.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0128424}, doi = {10.1128/spectrum.01284-24}, pmid = {39907436}, issn = {2165-0497}, abstract = {UNLABELLED: Micro-aspiration of oral microorganisms results in considerable enrichment within the lower respiratory tract (LRT), constituting an early event in lung cancer pathogenesis. To explore the correlation between malignant risk of pulmonary nodules (PNs) and oral commensals enrichment in LRT, oral saliva and bronchial alveolar lavage fluid samples from 22 low-risk PN patients, 17 intermediate-risk PN patients, and 11 high-risk PN patients were analyzed using 16S rRNA gene sequencing. Alpha and beta diversity analyses reveal minimal variation in oral microbial diversity and abundance among patients with different risks of PN. In contrast, a significant reduction in the diversity of LRT microbiota is observed in patients at high risk of PN. Based on multigroup comparative analysis of species differences and the linear discriminant analysis effect size method, Synergistes and Tannerella were identified as the dominant bacterial genera in the oral and LRT of high-risk PN patients, respectively. The study found that the LRT microbiota of PN patients seemed to originate from the oral, and the high enrichment of oral microbiota in the lower respiratory tract was most common in high-risk PN patients. The predominant bacterial genera present in the oral cavity and LRT of patients with PN were identified through abundance variance analysis. Eight key microbial genera were found in both the oral cavity and LRT: Streptococcus, Granulicatella, Porphyromonas, Bacillus, Neisseria, Alloprevotella, Prevotella, and Leptotrichia. Notably, receiver operating characteristic analysis identified Streptococcus, Granulicatella, and Leptotrichia as reliable biomarkers to differentiate high-risk PN. Spearman correlation analysis confirmed that the accumulation of oral microorganisms in the LRT played an important role in the process of PN cancerization. The co-occurrence network showed that the coexistence of Veillonella and Streptococcus in the oral and LRT may be involved in the occurrence of PN, while the LRT cluster of Rothia occurred in high-risk PN patients. Correlation analysis among species identified microbial communities predominantly composed of Veillonella, which may facilitate pulmonary carcinogenesis.<br><br>IMPORTANCE: This study is the first to elucidate the composition and interrelationships of oral and lower respiratory tract (LRT) microbiota in patients with pulmonary nodule (PN) across varying malignancy risk levels. We conducted an analysis to investigate the correlation between the malignant potential of PNs and the enrichment of oral microbiota within the LRT. Additionally, we explored the feasibility of utilizing oral-lower respiratory commensal microbiota as biomarkers to assess the benign and malignant nature of pulmonary nodules. This study aims to provide evidence supporting early diagnosis and intervention strategies for lung cancer.}, }
@article {pmid39907412, year = {2025}, author = {Kavitha, L and Kuzhalmozhi, M and Vijayashree Priyadharsini, J and Arun Kumar, A and Umadevi, KMR and Ranganathan, K}, title = {Microbial signatures in head and neck squamous cell carcinoma: an in silico study.}, journal = {Journal of applied oral science : revista FOB}, volume = {33}, number = {}, pages = {e20240392}, doi = {10.1590/1678-7757-2024-0392}, pmid = {39907412}, issn = {1678-7765}, mesh = {Humans ; *Head and Neck Neoplasms/microbiology ; *Squamous Cell Carcinoma of Head and Neck/microbiology ; Gastrointestinal Microbiome/physiology ; Dysbiosis/microbiology ; Proteomics ; Computer Simulation ; Microbiota/physiology ; Gastrointestinal Neoplasms/microbiology ; Mouth/microbiology ; Transcriptome ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {OBJECTIVES: The oral cavity harbors a plethora of bacterial species. Dysbiosis of oral and gut microbiota is associated with several oral and systemic pathologies, such as cancer, obesity, diabetes, atherosclerosis and gastrointestinal diseases. Imbalance in the oral-gut microbial axis has been associated with head and neck squamous cell carcinoma (HNSCC). This study aims to analyze the bacterial profile of HNSCC across various taxonomic units, investigate molecular patterns associated with prevalent bacterial phylum in HNSCC, and compare the bacterial profile in HNSCC and gastrointestinal (GI) carcinoma using computational analysis.<br><br>METHODOLOGY: The microbe-host transcriptomic, proteomic, and epigenetic analyses of HNSCC and GI carcinomas were performed using The Cancer Microbiome Atlas (TCMA) database. The differential expression of the host's mRNA transcripts and proteins associated with tumor microbiome were analyzed using The University of Alabama at Birmingham Cancer data analysis (UALCAN) and Clinical Proteomic Tumor Analysis Consortium (CPTAC) websites.<br><br>RESULTS: A decrease in Actinobacteria and an enrichment of Flavobacteria at the class level, Neisseriales, Pasteurellales, and Campylobacterales at the order level, Pasteurellaceae, Flavobacteriaceae, Campylobacteraceae, and Peptoniphilaceae at the family level, and Hemophilus, Porphyromonas, and Leptotrichia at the genus level were observed in HNSCC compared to the normal mucosa. RICTOR protein, mRNA transcripts (HIST1H2BB, SCARNA11, TBC1D21 gene), and hsa-miR-200a-5p miRNA were significantly correlated with prevalent bacterial species in HNSCC. A major increase in Actinobacteria, Fusobacteria, and Spirochaetes was observed in HNSCC compared to GI carcinoma.<br><br>CONCLUSION: The oral-gut microbial dysbiosis, as reflected by the differential abundance of bacterial species in oral and GI carcinomas, suggests the implication of tumor microbiome and their genomic interactions with the host in carcinogenesis.}, }
@article {pmid39907302, year = {2025}, author = {Talat, A and Khan, AU}, title = {From supplements to superbugs: how probiotic patent gaps drive antimicrobial resistance and the CRISPR-Cas solutions.}, journal = {Pharmaceutical patent analyst}, volume = {}, number = {}, pages = {1-3}, doi = {10.1080/20468954.2025.2459592}, pmid = {39907302}, issn = {2046-8962}, }
@article {pmid39907181, year = {2025}, author = {Doghish, AS and Elazazy, O and Mohamed, HH and Mansour, RM and Ghanem, A and Faraag, AHI and Elballal, MS and Elrebehy, MA and Elesawy, AE and Abdel Mageed, SS and Saber, S and Nassar, YA and Abulsoud, AI and Abdel-Reheim, MA and Elawady, AS and Ali, MA and Basiouny, MS and Hemdan, M and Lutfy, RH and Awad, FA and El-Sayed, SA and Ashour, MM and El-Sayyad, GS and Mohammed, OA}, title = {A Review on miRNAs in Enteric Bacteria-mediated Host Pathophysiology: Mechanisms and Implications.}, journal = {Journal of biochemical and molecular toxicology}, volume = {39}, number = {2}, pages = {e70160}, doi = {10.1002/jbt.70160}, pmid = {39907181}, issn = {1099-0461}, support = {//This study was supported by WHO./ ; }, mesh = {Humans ; *MicroRNAs/genetics/metabolism ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Animals ; }, abstract = {Recently, many studies focused on the billions of native bacteria found inside and all over the human body, commonly known as the microbiota, and its interactions with the eukaryotic host. One of the niches for such microbiota is the gastrointestinal tract (GIT), which harbors hundreds to thousands of bacterial species commonly known as enteric bacteria. Changes in the enteric bacterial populations were linked to various pathologies such as irritable bowel syndrome and obesity. The gut microbiome could affect the health status of individuals. MicroRNAs (miRNAs) are one of the extensively studied small-sized noncoding RNAs (ncRNAs) over the past decade to explore their multiple roles in health and disease. It was proven that miRNAs circulate in almost all body fluids and tissues, showing signature patterns of dysregulation associated with pathologies. Both cellular and circulating miRNAs participate in the posttranscriptional regulation of genes and are considered the potential key regulators of genes and participate in cellular communication. This manuscript explores the unique interplay between miRNAs and enteric bacteria in the gastrointestinal tract, emphasizing their dual role in shaping host-microbiota dynamics. It delves into the molecular mechanisms by which miRNAs influence bacterial colonization and host immune responses, linking these findings to gut-related diseases. The review highlights innovative therapeutic and diagnostic opportunities, offering insights for targeted treatments of dysbiosis-associated pathologies.}, }
@article {pmid39906849, year = {2025}, author = {Vinogradova, E and Jarmukhanov, Z and Nurgaziyev, M and Kossumov, A and Nurgozhina, A and Mukhanbetzhanov, N and Sergazy, S and Chulenabyeva, L and Issilbayeva, A and Askarova, S and Kaiyrlykyzy, A and Rakhimova, S and Kozhamkulov, U and Kairov, U and Khassenbekova, Z and Tarzhanova, D and Akilzhanova, A and Lee, JH and Terwilliger, J and Sailybayeva, A and Bekbossynova, M and Zhumadilov, Z and Kozhakhmetov, S and Kushugulova, A}, title = {Enterococcus dysbiosis as a mediator of vitamin D deficiency-associated memory impairments.}, journal = {Heliyon}, volume = {11}, number = {2}, pages = {e41969}, pmid = {39906849}, issn = {2405-8440}, abstract = {Low vitamin D status is linked to disturbance in cognitive performance. This study explored possible ways how composition and functional capacity of the gut microbiome affects vitamin D metabolism, directing serum vitamin D (VitD) levels and memory impairmets. It was found that gut microbiome composition, characterized by an increase in the relative abundance of Enterococcus and correlated with vitamin D deficiency and, as consequence, with memory impairments. A key mechanism identified in the study was the differential utilization of short-chain fatty acids (SCFAs) produced by gut bacteria as substrates for synthesizing vitamin D3 precursor in the skin. This finding confirms a complex interplay between the gut microbiome, host metabolism, and cognitive health, highlighting the potential significance of targeting Enterococcus dysbiosis in future preventive and therapeutic strategies to address VitD deficiency-related memory impairments. These results underscore the importance of understanding and modulating gut microbiome composition to optimize VitD status and cognitive function.}, }
@article {pmid39906741, year = {2024}, author = {Zhang, X and Li, B and Lan, T and Chiari, C and Ye, X and Wang, K and Chen, J}, title = {The role of interleukin-17 in inflammation-related cancers.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1479505}, pmid = {39906741}, issn = {1664-3224}, mesh = {Humans ; *Interleukin-17/metabolism/immunology ; *Neoplasms/immunology/etiology/metabolism ; *Inflammation/immunology ; Animals ; Signal Transduction ; Receptors, Interleukin-17/metabolism/immunology ; Tumor Microenvironment/immunology ; Microbiota/immunology ; }, abstract = {Emerging evidence indicates a correlation between inflammation and the development and progression of cancer. Among the various inflammatory signals, interleukin-17 (IL-17) family cytokines serve as a critical link between inflammation and cancer. IL-17 is a highly versatile pro-inflammatory cytokine that plays a pivotal role in host defense, tissue repair, the pathogenesis of inflammatory diseases, and cancer progression. During the early stages of tumorigenesis, IL-17 signaling directly promotes the proliferation of tumor cells. Conversely, IL-17 has been shown to exhibit antitumor immunity in several models of grafted subcutaneous tumors. Additionally, dynamic changes in the microbiome can influence the secretion of IL-17, thereby affecting tumor development. The specific role of IL-17 is contingent upon its functional classification, spatiotemporal characteristics, and the stage of tumor development. In this review, we introduce the fundamental biology of IL-17 and the expression profile of its receptors in cancer, while also reviewing and discussing recent advancements regarding the pleiotropic effects and mechanisms of IL-17 in inflammation-related cancers. Furthermore, we supplement our discussion with insights into the mechanisms by which IL-17 impacts cancer progression through interactions with the microbiota, and we explore the implications of IL-17 in cancer therapy. This comprehensive analysis aims to enhance our understanding of IL-17 and its potential role in cancer treatment.}, }
@article {pmid39906737, year = {2024}, author = {Żak-Bochenek, A and Żebrowska-Różańska, P and Bajzert, J and Łaczmański, &#x141; and Szponar, B and Siwińska, N and Gładysz, K and Sikorska, K and Chełmońska-Soyta, A}, title = {Investigating the potential immunomodulatory effects of commercial oral probiotic supplements on equine gastrointestinal tract barrier function.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1487664}, pmid = {39906737}, issn = {1664-3224}, mesh = {Animals ; *Probiotics/administration &amp; dosage/pharmacology ; Horses/immunology/microbiology ; *Gastrointestinal Microbiome/drug effects/immunology ; *Feces/microbiology ; Dietary Supplements ; Male ; Administration, Oral ; Female ; RNA, Ribosomal, 16S/genetics ; Gastrointestinal Tract/immunology/microbiology ; Immunoglobulin A, Secretory ; Immunity, Mucosal/drug effects ; }, abstract = {BACKGROUND: Oral probiotic dietary supplements are widely used in veterinary medicine, including in horses. It is hypothesized that the presence of probiotic strains can both modulate the intestinal microbiota and affect mucosal immunity parameters. Such a study has not yet been conducted in horses.<br><br>METHODS: This study involved 12 healthy horses, which were randomly divided into a control group and a group that received a commercial oral probiotic formula containing Lactobacillus rhamnosus, Pedioccus acidilactici or Enterococcus faecium for 84 days. Fecal samples were collected from all horses on day 0 (D0), 28 days after starting the probiotic (D28), 56 days (D56), 84 days (D84) and 28 days after stopping the probiotic (DX) treatment. The samples were subjected to microbiome analysis via next-generation sequencing of hypervariable regions V3-V4 and V7-V9 of the 16S rRNA gene for analysis of short-chain fatty acids via HPLC analysis and fecal secretory immunoglobulin A (SIgA) quantification via ELISA.<br><br>RESULTS: Microbiome analysis revealed no significant differences in either alpha or beta diversity parameters between the groups. No probiotic strains were detected in the samples. Significant changes were detected in three taxa: the family Bacteroidales RF16 group, the genus Erysipelotrichaceae UCG-004, and the genus Fibrobacter during the study in both groups. In all the cases, there was a gradual decrease in relative abundance over time. The concentrations of SCFAs, specifically acetic and propionic acids, significantly increased over time in both groups according to the generalized linear mixed effects (GLME) model. There were no significant differences in fecal SIgA secretion.<br><br>CONCLUSION: The present study revealed no effect of the use of a commercial probiotic dietary supplement on either mucosal immunity or the composition of the intestinal microbiota.}, }
@article {pmid39906673, year = {2025}, author = {Zhu, J and He, M and Li, S and Lei, Y and Xiang, X and Guo, Z and Wang, Q}, title = {Shaping oral and intestinal microbiota and the immune system during the first 1,000 days of life.}, journal = {Frontiers in pediatrics}, volume = {13}, number = {}, pages = {1471743}, pmid = {39906673}, issn = {2296-2360}, abstract = {The first 1, 000 days of life, from the fetal stage of a woman's pregnancy to 2 years of age after the baby is born, is a critical period for microbial colonization of the body and development of the immune system. The immune system and microbiota exhibit great plasticity at this stage and play a crucial role in subsequent development and future health. Two-way communication and interaction between immune system and microbiota is helpful to maintain human microecological balance and immune homeostasis. Currently, there is a growing interest in the important role of the microbiota in the newborn, and it is believed that the absence or dysbiosis of human commensal microbiota early in life can have lasting health consequences. Thus, this paper summarizes research advances in the establishment of the oral and intestinal microbiome and immune system in early life, emphasizing the substantial impact of microbiota diversity in the prenatal and early postnatal periods, and summarizes that maternal microbes, mode of delivery, feeding practices, antibiotics, probiotics, and the environment shape the oral and intestinal microbiota of infants in the first 1, 000 days of life and their association with the immune system.}, }
@article {pmid39906620, year = {2025}, author = {Wawrety, W and Kedziora, A}, title = {Role of bacteria in cancers and their therapeutic potential: Review of current knowledge.}, journal = {Iranian journal of basic medical sciences}, volume = {28}, number = {3}, pages = {273-282}, pmid = {39906620}, issn = {2008-3866}, abstract = {Cancers are extremely dynamic diseases that can actively cause refractorines to be gained from applied therapies, which is why they are at the forefront of deaths worldwide. In this literature review, we covered the most recent and important discoveries regarding the influence of human microbiota, including tumor bacteriome, on the development and treatment of cancer. Advances in research on microbial communities have enabled us to discover the role of the human microbiome in the development and course of this disease, helping us understand neoplasms better and design new potential therapies. As we show through our findings, by immunomodulation and the secretion of certain chemical substances, the correct bacteriome of the intestinal tract, respiratory system, or skin can protect humans against cancer development and help during the treatment process. Bacteria also reside inside tumors, forming part of the tumor microenvironment (TME), where they interact with immunological and cancer cells in many complex ways. Some bacteria, such as Pseudomonas aeruginosa or Akkermansia muciniphila, can stimulate anticancer cell-mediated immune responses or even directly lead to cancer cell death. We also present the clinical possibilities of using some live, usually modified bacteria to develop bacteriotherapies. Modifying the gut microbiome to stimulate standard treatment is also important. Research on the microbiome and cancer remains a challenging topic in microbiology, having a great potential for advancements in cancer therapy in the future, and is continuously becoming a more and more popular field of research, as shown by our statistical analysis of PubMed data.}, }
@article {pmid39906593, year = {2025}, author = {Herisson, FM and Cluzel, GL and Llopis-Grimalt, MA and O'Donovan, AN and Koc, F and Karnik, K and Laurie, I and Canene-Adams, K and Ross, RP and Stanton, C and Caplice, NM}, title = {Targeting the Gut-Heart Axis Improves Cardiac Remodeling in a Clinical Scale Model of Cardiometabolic Syndrome.}, journal = {JACC. Basic to translational science}, volume = {10}, number = {1}, pages = {1-15}, pmid = {39906593}, issn = {2452-302X}, abstract = {Poor diet, gut dysbiosis, and systemic inflammation constitute a gut-heart axis (GHA) that may affect heart failure with preserved ejection fraction. Clinical scale models to interrogate this axis are limited. Here, we show the full extent of the GHA-gut barrier function loss, systemic and microvascular inflammation, and its colocalization with apoptosis (left atrium) and hypertrophy (left ventricle). Gut barrier function primacy in regulating the GHA is supported by a synbiotic intervention that shuts down gut epithelial permeability, markedly decreasing systemic inflammation and, remarkably, cardiac structural changes in left heart chambers. These data support a new paradigm for targeting heart failure with preserved ejection fraction via the GHA.}, }
@article {pmid39906166, year = {2025}, author = {Shi, WX and Guo, JJ and Yu, XX and Li, ZX and Weng, BY and Wang, DX and Su, SH and Sun, YF and Tan, JF and Xie, RH}, title = {Diversity and interactions of rhizobacteria determine multinutrient traits in tomato host plants under nitrogen and water disturbances.}, journal = {Horticulture research}, volume = {12}, number = {2}, pages = {uhae290}, pmid = {39906166}, issn = {2662-6810}, abstract = {Coevolution within the plant holobiont extends the capacity of host plants for nutrient acquisition and stress resistance. However, the role of the rhizospheric microbiota in maintaining multinutrient utilization (i.e. multinutrient traits) in the host remains to be elucidated. Multinutrient cycling index (MNC), analogous to the widely used multifunctionality index, provides a straightforward and interpretable measure of the multinutrient traits in host plants. Using tomato as a model plant, we characterized MNC (based on multiple aboveground nutrient contents) in host plants under different nitrogen and water supply regimes and explored the associations between rhizospheric bacterial community assemblages and host plant multinutrient profiles. Rhizosphere bacterial community diversity, quantitative abundance, predicted function, and key topological features of the co-occurrence network were more sensitive to water supply than to nitrogen supply. A core bacteriome comprising 61 genera, such as Candidatus Koribacter and Streptomyces, persisted across different habitats and served as a key predictor of host plant nutrient uptake. The MNC index increased with greater diversity and higher core taxon abundance in the rhizobacterial community, while decreasing with higher average degree and graph density of rhizobacterial co-occurrence network. Multinutrient absorption by host plants was primarily regulated by community diversity and rhizobacterial network complexity under the interaction of nitrogen and water. The high biodiversity and complex species interactions of the rhizospheric bacteriome play crucial roles in host plant performance. This study supports the development of rhizosphere microbiome engineering, facilitating effective manipulation of the microbiome for enhanced plant benefits, which supports sustainable agricultural practices and plant health.}, }
@article {pmid39906157, year = {2025}, author = {Bilal, H and Khan, MN and Khan, S and Shafiq, M and Fang, W and Khan, RU and Rahman, MU and Li, X and Lv, QL and Xu, B}, title = {The role of artificial intelligence and machine learning in predicting and combating antimicrobial resistance.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {423-439}, pmid = {39906157}, issn = {2001-0370}, abstract = {Antimicrobial resistance (AMR) is a major threat to global public health. The current review synthesizes to address the possible role of Artificial Intelligence and Machine Learning (AI/ML) in mitigating AMR. Supervised learning, unsupervised learning, deep learning, reinforcement learning, and natural language processing are some of the main tools used in this domain. AI/ML models can use various data sources, such as clinical information, genomic sequences, microbiome insights, and epidemiological data for predicting AMR outbreaks. Although AI/ML are relatively new fields, numerous case studies offer substantial evidence of their successful application in predicting AMR outbreaks with greater accuracy. These models can provide insights into the discovery of novel antimicrobials, the repurposing of existing drugs, and combination therapy through the analysis of their molecular structures. In addition, AI-based clinical decision support systems in real-time guide healthcare professionals to improve prescribing of antibiotics. The review also outlines how can AI improve AMR surveillance, analyze resistance trends, and enable early outbreak identification. Challenges, such as ethical considerations, data privacy, and model biases exist, however, the continuous development of novel methodologies enables AI/ML to play a significant role in combating AMR.}, }
@article {pmid39906131, year = {2025}, author = {Babalola, OO and Enagbonma, BJ}, title = {Dataset of shotgun metagenomic evaluation of Sorghum bicolor rhizosphere microbiome in soils preceded by Glycine max.}, journal = {Data in brief}, volume = {58}, number = {}, pages = {111270}, pmid = {39906131}, issn = {2352-3409}, abstract = {The dataset presents the microbial diversity, community structure, and functional potential of the rhizosphere microbiome associated with Sorghum bicolor in response to crop rotation involving a Glycine max precursor. Soil samples were collected from the rhizospheres of two Sorghum bicolor cultivars, Avenger and NS55, cultivated in soils previously used for Glycine max and cultivated in soils that have not previously been used for Glycine max cultivation, as follows: i) Sorghum bicolor Avenger (SA1, SA2, and SA3) cultivated in soils previously used for Glycine max, ii) Sorghum bicolor NS55 (SN1, SN2, and SN3) grown in soils that had been cultivated with Glycine max, iii) Sorghum bicolor Avenger (RA1, RA2, and RA3) cultivated in soils not previously used for Glycine max, iv) Sorghum bicolor NS55 (RN1, RN2, and RN3) grown in soils not previously cultivated with Glycine max. Thereafter, the shotgun sequencing was done to assess the microbial composition and functional genes from the extracted DNA. The effective metagenome after QC of the twelve samples include SA1 (99.72%), SA2 (99.50%), SA3 (99.68%), SN1 (99.75%), SN2 (99.76%), SN3 (99.70%), RA1 (99.72%), RA2 (99.77%), RN3 (99.72%), RN1 (99.67%), RN2 (99.68%), and RN3 (99.54%). Information from the metagenome sequences is accessible under the bioproject numbers PRJNA1166458 (SA1, SA2, and SA3), PRJNA1166463 (SN1, SN2, and SN3), PRJNA1166623 (RA1, RA2, and RA3), PRJNA1166627 (RN1, RN2 and RN3). Actinomycetota and Function unknown dominated the microbiomes across all cropping systems. The insights gained from this dataset hold promise for advancing sustainable agricultural practices, particularly through optimizing crop rotations, developing microbial bioinoculants, and enhancing soil health. Furthermore, the functional data and the function unknown from this dataset could enrich our understanding of microbial roles in nutrient cycling, plant growth promotion, and stress mitigation, which are critical for addressing challenges in food security and environmental sustainability.}, }
@article {pmid39906083, year = {2025}, author = {Mohamadkhani, A and Ghanbari, R and Shakeri, R and Mohammadkhani, MA and Pourshams, A}, title = {Causal Exposures in Pancreatic Cancer Incidence: Insights From Mendelian Randomization Studies.}, journal = {JGH open : an open access journal of gastroenterology and hepatology}, volume = {9}, number = {2}, pages = {e70105}, pmid = {39906083}, issn = {2397-9070}, abstract = {AIM: Pancreatic cancer, marked by its high lethality and poor 5-year survival rate, requires a thorough understanding of its risk factors and etiological mechanisms. In this review, we collected the latest findings from Mendelian randomization (MR) studies to identify potential causal factors for pancreatic cancer.<br><br>METHOD AND RESULTS: The present analysis encompasses MR studies on the gut and oral microbiomes, non-malignant phenotypes, blood metabolites, immune cells, and chronic inflammation. Specific gut and oral microbiome species have been identified as potential causal factors for pancreatic cancer, some with protective effects, and others increasing the risk. The review also highlights causal associations between obesity, type 2 diabetes, and pancreatic cancer, as well as the impact of blood metabolites and immune cell phenotypes on disease risk. Additionally, it investigates the causal effects of inflammatory bowel disease, showing a significant risk increase associated with Crohn's disease.<br><br>CONCLUSION: These insights emphasize the need for interdisciplinary research and personalized medicine to enhance prevention and treatment strategies for pancreatic cancer.}, }
@article {pmid39905904, year = {2025}, author = {Järvinen, KM}, title = {Effect of Feeding Human Milk on Development of the Infant Immune System and Allergic Outcomes-An Area of Research Challenge and Need.}, journal = {Breastfeeding medicine : the official journal of the Academy of Breastfeeding Medicine}, volume = {}, number = {}, pages = {}, doi = {10.1089/bfm.2024.0302}, pmid = {39905904}, issn = {1556-8342}, abstract = {Surprisingly little is known about the effect of breastfeeding on the infant's immune system development. Systematic reviews have suggested the role of breastfeeding in the prevention against asthma, autoimmune diseases, inflammatory bowel disease, and childhood leukemia. However, studies on atopic disease suffer from reverse causation, small size, and those assessing food allergy (FA) have often relied on parent-reported outcomes. Randomized controlled trials (RCTs) are not possible for ethical reasons. In addition, epidemiological studies have not considered that there is a large interindividual variation in human milk (HM) composition and feeding at the breast versus pumped HM potentially impacting the effect of breastfeeding between mothers. While prevention strategies such as early introduction of highly allergenic food are impactful in preventing peanut and egg allergies, implementation of early introduction guidelines has been slow, and many infants are already sensitized by 4-6 months of age. To be more effective, primary prevention strategies must commence much earlier, during breastfeeding. There are studies that imply a definitive effect of breastfeeding on the gut microbiome and regulatory T cells (Tregs) as well as a higher rate of FA in populations with historically low rates of breastfeeding. These provide a strong rationale for assessing the effect of feeding HM in the context of HM composition and mode of feeding on immune development. The lack of well-conducted, large studies assessing the role of breastfeeding and HM composition in the development of immune system development is a significant gap when designing prevention strategies.}, }
@article {pmid39905557, year = {2025}, author = {Agudelo, C and Kateete, DP and Nasinghe, E and Kamulegeya, R and Lubega, C and Mbabazi, M and Baker, N and Lin, KY and Liu, CC and Kasambula, AS and Kigozi, E and Komakech, K and Mukisa, J and Mulumba, K and Mwachan, P and Nakalanda, BS and Nalubega, GP and Nsubuga, J and Sitenda, D and Ssenfuka, H and Cirolia, GT and Gustafson, JT and Wang, R and Nsubuga, ML and Yiga, F and Stanley, SA and Bagaya, BS and Elliott, A and Joloba, M and Wolf, AR}, title = {Enterococcus and Eggerthella species are enriched in the gut microbiomes of COVID-19 cases in Uganda.}, journal = {Gut pathogens}, volume = {17}, number = {1}, pages = {9}, pmid = {39905557}, issn = {1757-4749}, abstract = {BACKGROUND: Infection with the COVID-19-causing pathogen SARS-CoV-2 is associated with disruption in the human gut microbiome. The gut microbiome enables protection against diverse pathogens and exhibits dysbiosis during infectious and autoimmune disease. Studies based in the United States and China have found that severe COVID-19 cases have altered gut microbiome composition when compared to mild COVID-19 cases. We present the first study to investigate the gut microbiome composition of COVID-19 cases in a population from Sub-Saharan Africa. Given the impact of geography and cultural traditions on microbiome composition, it is important to investigate the microbiome globally and not draw broad conclusions from homogenous populations.<br><br>RESULTS: We used stool samples in a Ugandan biobank collected from COVID-19 cases during 2020-2022. We profiled the gut microbiomes of 83 symptomatic individuals who tested positive for SARS-CoV-2 along with 43 household contacts who did not present any symptoms of COVID-19. The inclusion of healthy controls enables us to generate hypotheses about bacterial strains potentially related to susceptibility to COVID-19 disease, which is highly heterogeneous. Comparison of the COVID-19 patients and their household contacts revealed decreased alpha diversity and blooms of Enterococcus and Eggerthella in COVID-19 cases.<br><br>CONCLUSIONS: Our study finds that the microbiome of COVID-19 individuals is more likely to be disrupted, as indicated by decreased diversity and increased pathobiont levels. This is either a consequence of the disease or may indicate that certain microbiome states increase susceptibility to COVID-19 disease. Our findings enable comparison with cohorts previously published in the Global North, as well as support new hypotheses about the interaction between the gut microbiome and SARS-CoV-2 infection.}, }
@article {pmid39905530, year = {2025}, author = {Rauer, L and De Tomassi, A and Müller, CL and Hülpüsch, C and Traidl-Hoffmann, C and Reiger, M and Neumann, AU}, title = {De-biasing microbiome sequencing data: bacterial morphology-based correction of extraction bias and correlates of chimera formation.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {38}, pmid = {39905530}, issn = {2049-2618}, mesh = {*Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Humans ; *DNA, Bacterial/genetics ; *Sequence Analysis, DNA/methods ; Skin/microbiology ; Bias ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {INTRODUCTION: Microbiome amplicon sequencing data are distorted by multiple protocol-dependent biases from bacterial DNA extraction, contamination, sequence errors, and chimeras, hindering clinical microbiome applications. In particular, extraction bias is a major confounder in sequencing-based microbiome analyses, with no correction method available to date. Here, we suggest using mock community controls to computationally correct extraction bias based on bacterial morphological properties.<br><br>METHODS: We compared dilution series of 3 cell mock communities with an even or staggered composition. DNA of these mock, and additional skin microbiome samples, was extracted with 8 different extraction protocols (2 buffers, 2 extraction kits, 2 lysis conditions). Extracted DNA was sequenced (V1-V3 16S rRNA gene) together with corresponding DNA mocks.<br><br>RESULTS: Microbiome composition was significantly different between extraction kits and lysis conditions, but not between buffers. Independent of the extraction protocol, chimera formation increased with higher input cell numbers. Contaminants originated mostly from buffers, and considerable cross-contamination was observed in low-input samples. Comparing the microbiome composition of the cell mocks to corresponding DNA mocks revealed taxon-specific protocol-dependent extraction bias. Strikingly, this extraction bias per species was predictable by bacterial cell morphology. Morphology-based computational correction of extraction bias significantly improved resulting microbial&#xa0;compositions when applied to different mock samples, even with different taxa. Equivalent correction of the skin samples showed a substantial impact on microbiome compositions.<br><br>CONCLUSIONS: Our results indicate that higher DNA density increases chimera formation during PCR amplification. Furthermore, we show that computational correction of extraction bias based on bacterial cell morphology would be feasible using appropriate positive controls, thus constituting an important step toward overcoming protocol biases in microbiome analysis. Video Abstract.}, }
@article {pmid39905490, year = {2025}, author = {Molina-Pardines, C and Haro-Moreno, JM and Rodriguez-Valera, F and López-Pérez, M}, title = {Extensive paralogism in the environmental pangenome: a key factor in the ecological success of natural SAR11 populations.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {41}, pmid = {39905490}, issn = {2049-2618}, support = {PRE2021-098122//Ministerio de Econom&#xed;a y Competitividad/ ; PID2020-118052GB-I00//Ministerio de Econom&#xed;a y Competitividad/ ; 2021/PER/00020//Ministerio de Universidades/ ; }, mesh = {*Metagenomics/methods ; Mediterranean Sea ; *Genetic Variation ; Microbiota/genetics ; Genome, Bacterial ; Metagenome ; Phylogeny ; Seawater/microbiology ; }, abstract = {BACKGROUND: The oceanic microbiome is dominated by members of the SAR11 clade. Despite their abundance, challenges in recovering the full genetic diversity of natural populations have hindered our understanding of the eco-evolutionary mechanisms driving intra-species variation. In this study, we employed a combination of single-amplified genomes and long-read metagenomics to recover the genomic diversity of natural populations within the SAR11 genomospecies Ia.3/VII, the dominant group in the Mediterranean Sea.<br><br>RESULTS: The reconstruction of the first complete genome within this genomospecies revealed that the core genome represents a significant proportion of the genome (~&#x2009;81%), with highly divergent areas that allow for greater strain-dependent metabolic flexibility. The flexible genome was concentrated in small regions, typically containing a single gene, and was&#xa0;located in equivalent regions within the genomospecies. Each variable region was associated with a specific set of genes that, despite exhibiting some divergence, maintained equivalent biological functionality within the population. The environmental pangenome is large and enriched in genes involved in nutrient transport, as well as cell wall synthesis and modification, showing an extremely high degree of functional redundancy in the flexible genome (i.e. paralogisms).<br><br>CONCLUSIONS: This genomic architecture promotes polyclonality, preserving genetic variation within the population. This, in turn,&#xa0;mitigates intraspecific competition and enables the population to thrive under variable environmental conditions and selective pressures. Furthermore, this study demonstrates the power of long-read metagenomics in capturing the full genetic diversity of environmental SAR11 populations, overcoming the limitations of second-generation sequencing technologies in genome assembly. Video Abstract.}, }
@article {pmid39905469, year = {2025}, author = {Li, S and Zhan, Y and Wang, Y and Li, W and Wang, X and Wang, H and Sun, W and Cao, X and Li, Z and Ye, F}, title = {One-step diagnosis of infection and lung cancer using metagenomic sequencing.}, journal = {Respiratory research}, volume = {26}, number = {1}, pages = {48}, pmid = {39905469}, issn = {1465-993X}, support = {No. 2021YFC2301101//National Key Research and Development Program/ ; No. 82100118//Youth fund of National Natural Science Foundation of China/ ; 92048203//National Natural Science Foundation of China/ ; No. 2022SKLID308//the Science Foundation for the State Key Laboratory for Infectious Disease Prevention and Control of China/ ; }, mesh = {Humans ; *Lung Neoplasms/genetics/diagnosis/microbiology ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Aged ; Respiratory Tract Infections/diagnosis/microbiology/genetics ; Adult ; }, abstract = {BACKGROUND: Traditional detection methods face challenges in meeting the diverse clinical needs for diagnosing both lung cancer and infections within a single test. Onco-mNGS has emerged as a promising solution capable of accurately identifying infectious pathogens and tumors simultaneously. However, critical evidence is still lacking regarding its diagnostic performance in distinguishing between pulmonary infections, tumors, and non-infectious, non-tumor conditions in real clinical settings.<br><br>METHODS: In this study, data were gathered from 223 participants presenting symptoms of lung infection or tumor who underwent Onco-mNGS testing. Patients were categorized into four groups based on clinical diagnoses: infection, tumor, tumor with infection, and non-infection-non-tumor. Comparisons were made across different groups, subtypes, and stages of lung cancer regarding copy number variation (CNV) patterns, microbiome compositions, and clinical detection indices.<br><br>RESULTS: Compared to conventional infection testing methods, Onco-mNGS demonstrates superior infection detection performance, boasting a sensitivity of 81.82%, specificity of 72.55%, and an overall accuracy of 77.58%. In lung cancer diagnosis, Onco-mNGS showcases excellent diagnostic capabilities with sensitivity, specificity, accuracy, positive predictive value, and negative predictive value reaching 88.46%, 100%, 91.41%, 100%, and 90.98%, respectively. In bronchoalveolar lavage fluid (BALF) samples, these values stand at 87.5%, 100%, 94.74%, 100%, and 91.67%, respectively. Notably, more abundant CNV mutation types and higher mutation rates were observed in adenocarcinoma (ADC) compared to squamous cell carcinoma (SCC). Concurrently, onco-mNGS data revealed specific enrichment of Capnocytophaga sputigeria in the ADC group and Candida parapsilosis in the SCC group. These species exhibited significant correlations with C reaction protein (CRP) and CA153 values. Furthermore, Haemophilus influenzae was enriched in the early-stage SCC group and significantly associated with CRP values.<br><br>CONCLUSIONS: Onco-mNGS has exhibited exceptional efficiencies in the detection and differentiation of infection and lung cancer. This study provides a novel technological option for achieving single-step precise and swift detection of lung cancer.}, }
@article {pmid39905243, year = {2025}, author = {Donohue, ME and Lamb, A and Absangba, AE and Noromalala, E and Weisenbeck, DR and Stumpf, RM and Wright, PC}, title = {Why Didn't the Sifaka Cross the Road? Divergence of Propithecus edwardsi Gut Microbiomes Across Geographic Barriers in Ranomafana National Park, Madagascar.}, journal = {American journal of primatology}, volume = {87}, number = {2}, pages = {e23732}, doi = {10.1002/ajp.23732}, pmid = {39905243}, issn = {1098-2345}, support = {//This study was supported by the RW Primate Fund, the Lichtenstein Foundation, the Directorate for Biological Sciences, and NSF BCS 0935347 (RMS)./ ; }, mesh = {Animals ; Madagascar ; *Gastrointestinal Microbiome ; *RNA, Ribosomal, 16S/analysis/genetics ; *Ecosystem ; *Parks, Recreational ; Strepsirhini/microbiology/physiology ; Endangered Species ; }, abstract = {This study uses a biogeographic framework to identify patterns of gut microbiome divergence in an endangered lemur species endemic to Madagascar's southeastern rainforests, the Milne-Edwards's sifaka (Propithecus edwardsi). Specifically, we tested the effects of (1) geographic barriers, (2) habitat disturbance, and (3) geographic distance on gut microbiome alpha and beta diversity. We selected 10 social groups from 4 sites in Ranomafana National Park with varied histories of selective logging. Sites were spaced between 4 and 17 km apart falling on either side of two parallel barriers to animal movement: the Namorona River and the RN25 highway. Using 16S rRNA metabarcoding, we found the greatest beta diversity differentiation to occur between social groups, with significant divisions on opposite sides of geographic barriers (road/river). Habitat disturbance had the most significant effect on alpha diversity, though, contrary to many other studies, disturbance was associated with higher microbial species richness. Without biomedical context, it is unclear whether microbiome differences observed herein are neutral, adaptive, or maladaptive. However, microbiome divergence associated with the road/river may be a symptom of reduced host gene flow, warranting further investigation and perhaps conservation action (e.g., construction of wildlife bridges). Finally, this work demonstrates that significant microbiome variation can accrue over small sampling areas, lending new insight into host-microbe-environmental interactions.}, }
@article {pmid39905218, year = {2025}, author = {Coolahan, M and Whalen, KE}, title = {A review of quorum-sensing and its role in mediating interkingdom interactions in the ocean.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {179}, pmid = {39905218}, issn = {2399-3642}, support = {IOS 2041748//National Science Foundation (NSF)/ ; Beckman Scholar Fellowship to M.C.//Arnold and Mabel Beckman Foundation/ ; }, mesh = {*Quorum Sensing ; *Oceans and Seas ; Ecosystem ; Aquatic Organisms/physiology ; Bacteria/metabolism/genetics ; Bacterial Physiological Phenomena ; Seawater/microbiology ; Microbiota ; }, abstract = {Quorum sensing, first described in marine systems five decades ago, is a well-characterized chemical communication system used to coordinate bacterial gene expression and behavior; however, the impact of quorum sensing on interkingdom interactions has been vastly understudied. In this review, we examine how these molecules mediate communication between bacteria and marine eukaryotes; influencing processes such as development, disease pathogenesis, and microbiome regulation within marine ecosystems. We describe the varied mechanisms eukaryotes have evolved to interfere with bacterial quorum sensing signaling, the crucial role these signals play in host-virus interactions, and how their exchange may be governed by outer membrane vesicles, prevalent in marine systems. Here, we present a dynamic portrayal of the impact of quorum sensing signals beyond bacterial communication, laying the groundwork for future investigations on their roles in shaping marine ecosystem structure and function.}, }
@article {pmid39905205, year = {2025}, author = {Almosuli, M and Kirtava, A and Chkhotua, A and Tsveniashvili, L and Chanishvili, N and Irfan, SS and Ng, E and McIntyre, H and Hockenberry, AJ and Araujo, RP and Zhou, W and Vuong, N and Birkaya, B and Liotta, L and Luchini, A}, title = {Urinary bacteriophage cooperation with bacterial pathogens during human urinary tract infections supports lysogenic phage therapy.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {175}, pmid = {39905205}, issn = {2399-3642}, mesh = {Humans ; *Urinary Tract Infections/microbiology/therapy/virology ; *Lysogeny ; *Phage Therapy/methods ; *Bacteriophages/physiology/genetics ; Female ; }, abstract = {Despite much promise in overcoming drug-resistant infections, clinical studies of bacteriophage antibacterial therapy have failed to show durable effectiveness. Although lysogeny plays an important role in bacterial physiology, its significance in diverse microbiomes remains unclear. Here, we tested the following hypotheses: 1) urinary microbiome phage populations switch to a higher relative proportion of temperate phages, and 2) the activity of the phage recombination machinery (integration/excision/transposition) is higher during human urinary tract infections (UTIs) than in non-infected urinary tracts. Using human urine, model organisms, mass spectrometry, gene expression analysis, and the phage phenotype prediction model BACPHLIP, the results corroborated our hypotheses at the functional protein and gene levels. From a human health perspective, these data suggest that temperate phages may facilitate bacterial infections rather than function as protective agents. These findings support the use of lysogenic phages as therapeutic Trojan Horses.}, }
@article {pmid39905173, year = {2025}, author = {Turroni, S}, title = {Is precision microbiome medicine just around the corner?.}, journal = {Nature reviews. Gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, pmid = {39905173}, issn = {1759-5053}, }
@article {pmid39905170, year = {2025}, author = {}, title = {Ensuring rigour of low-biomass microbiome research.}, journal = {Nature microbiology}, volume = {10}, number = {2}, pages = {261-262}, pmid = {39905170}, issn = {2058-5276}, }
@article {pmid39905038, year = {2025}, author = {Qu, Q and Dou, Q and Xiang, Z and Yu, B and Chen, L and Fan, Z and Zhao, X and Yang, S and Zeng, P}, title = {Population-level gut microbiome and its associations with environmental factors and metabolic disorders in Southwest China.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {24}, pmid = {39905038}, issn = {2055-5008}, mesh = {*Gastrointestinal Microbiome ; Humans ; China ; *Metabolic Diseases/microbiology/etiology ; *Feces/microbiology ; *Metagenomics/methods ; Female ; Male ; Middle Aged ; Diet ; Adult ; Bacteria/classification/genetics/isolation &amp; purification ; Life Style ; Socioeconomic Factors ; }, abstract = {Gut microbiota affects host health and disease. Large-scale cohorts have explored the interactions between the microbiota, host, and environment to reveal the disease-associated microbiota variation. A population-level gut metagenomic cohort is still rare in China. Here, we performed metagenomic sequencing on fecal samples from the CMEC Microbiome Project in Southwest China. In this study, we identified host socioeconomics, diet, lifestyle, and medical measurements that were significantly associated with microbiome function and composition. We revealed extensive novel associations between the host microbiome and common metabolic disorders. Our results provide new insight into associations of gut microbiota with metabolic disorders so as to support the translation of gut microbiome findings into potential clinical practice.}, }
@article {pmid39904968, year = {2025}, author = {Ashiqueali, SA and Hayslip, N and Chaudhari, DS and Schneider, A and Zhu, X and Rubis, B and Seavey, CE and Alam, MT and Hussein, R and Noureddine, SA and Golusinska-Kardach, E and Pazdrowski, P and Yadav, H and Masternak, MM}, title = {Fecal microbiota transplant from long-living Ames dwarf mice alters the microbial composition and biomarkers of liver health in normal mice.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {39904968}, issn = {2509-2723}, support = {R56AG074499/NH/NIH HHS/United States ; R56AG069676/NH/NIH HHS/United States ; R56AG064075/NH/NIH HHS/United States ; RF1AG071762/NH/NIH HHS/United States ; R21AG072379/NH/NIH HHS/United States ; U01AG076928/NH/NIH HHS/United States ; W81XWH-18-PRARP AZ180098//U.S. Department of Defense/ ; 22A17//Florida Department of Health/ ; 22A17//Florida Department of Health/ ; HORIZON 2020-MSCA-RISE//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; HORIZON 2020-MSCA-RISE//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; }, abstract = {Aging is associated with intestinal dysbiosis, a condition characterized by diminished microbial biodiversity and inflammation. This leads to increased vulnerability to extraintestinal manifestations such as autoimmune, metabolic, and neurodegenerative conditions thereby accelerating mortality. As such, modulation of the gut microbiome is a promising way to extend healthspan. In this study, we explore the effects of fecal microbiota transplant (FMT) from long-living Ames dwarf donors to their normal littermates, and vice versa, on the recipient gut microbiota and liver transcriptome. Importantly, our previous studies highlight differences between the microbiome of Ames dwarf mice relative to their normal siblings, potentially contributing to their extended lifespan and remarkable healthspan. Our findings demonstrate that FMT from Ames dwarf mice to normal mice significantly alters the recipient's gut microbiota, potentially reprogramming bacterial functions related to healthy aging, and changes the liver transcriptome, indicating improved metabolic health. Particularly, the microbiome of Ames dwarf mice, characterized by a higher abundance of beneficial bacterial families such as Peptococcaceae, Oscillospiraceae, and Lachnospiraceae, appears to play a crucial role in modulating these effects. Alongside, our mRNA sequencing and RT-PCR validation reveals that FMT may contribute to the significant downregulation of p21, Elovl3, and Insig2, genes involved with cellular senescence and liver metabolic pathways. Our data suggest a regulatory axis exists between the gut and liver, highlighting the potential of microbiome-targeted therapies in promoting healthy aging. Future research should focus on functional validation of altered microbial communities and explore the underlying biomolecular pathways that confer geroprotection.}, }
@article {pmid39904699, year = {2025}, author = {Bukavina, L and Abbosh, P}, title = {Unlocking the Potential of the Genitourinary Microbiome.}, journal = {European urology focus}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.euf.2025.01.005}, pmid = {39904699}, issn = {2405-4569}, }
@article {pmid39904479, year = {2025}, author = {Amin, M and Rahardjo, KKE and Panosa, AE and Satyantini, WH and Mukti, AT and Ali, M and Musdalifah, L and Akhyar, H and Yanuhar, U and Azmai, MNA and Arai, T}, title = {Gut Microbiota and Functional Metabolic Predictions in White Feces Disease-Infected Pacific White Shrimp, Penaeus vannamei, from Indonesian Farms.}, journal = {Fish &amp; shellfish immunology}, volume = {}, number = {}, pages = {110171}, doi = {10.1016/j.fsi.2025.110171}, pmid = {39904479}, issn = {1095-9947}, abstract = {The etiological agent of white feces disease (WFD) infecting Pacific white shrimp Penaeus vannamei in Indonesia farms remains obscure. The present study aimed to identify possible causative agents of WFD infection in Pacific white shrimps cultured in Indonesian farms. WFD-infected and healthy samples (shrimp gut and rearing water) were collected from 8 commercial shrimp farms in East Java, Indonesia followed by bacterial community profiling using HiSeq sequencing of 16S rRNA gene amplicons. The results showed that the microbiota composition in the guts of WFD-infected shrimps was significantly different (p < 0.05) from the guts of healthy shrimps in term of genus and bacterial species. The intestinal bacterial communities of WFS-infected shrimps were overrepresented by Vibrio coralliilyticus, whereas Paracoccus was underrepresented. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States functional predictions indicated that relative abundances of 12 genes associated with the pathogenicity of bacteria including amino acid metabolisms, carbohydrate metabolisms, glycan biosynthesis, and xenobiotic biodegradation and metabolism were significantly (p < 0.05) higher in the gut microbiota of WFD-infected shrimps. These findings provide insights into the microbiome domination and their metabolic activities in the digestive tract of WFD-infected shrimps and suggest that V. coralliilyticus is a possible causative agent of WFD in cultured Indonesia Pacific white shrimp.}, }
@article {pmid39904217, year = {2025}, author = {Ren, P and Sun, A and Jiao, X and Chen, QL and Hu, HW}, title = {The relationship between protist consumers and soil functional genes under long-term fertilization.}, journal = {The Science of the total environment}, volume = {966}, number = {}, pages = {178658}, doi = {10.1016/j.scitotenv.2025.178658}, pmid = {39904217}, issn = {1879-1026}, abstract = {Protists play a crucial role in terrestrial ecosystems by participating in biogeochemical cycles and contributing to ecological balance and stability. However, much remains to be understood about the intricate interactions between soil protists and biogeochemical processes. Here, we collected rhizosphere soil samples from seven distinct fertilization treatments to investigate the responses of bacteria, protists and functional genes to these varying fertilization practices during sorghum's maturity season. The community composition of both protists and bacteria were significantly affected by different fertilization treatments, with organic fertilization increasing protist diversity but not affecting bacterial diversity. There were noticeable variations in the compositions of functional genes across different fertilization treatments, with organic fertilization enhancing the relative abundance of carbon and phosphorus cycling genes. While fertilization generally increased the relative abundance of protistan consumers, it was observed that organic fertilizers decreased the relative abundance of phototrophs. A substantial number of bacterial taxa, including Acidibacter, Steroidobacter, Lysobacter and Agromyces, which correlated positively with functional genes, were found to be prey for protistan consumers, indicating their crucial role in predicting soil functional genes. Altogether, this study highlights the significant impact of fertilization treatments, especially organic fertilization, on the diversity and functional dynamics of protist and bacterial communities, emphasizing the key role of protistan consumers in regulating the soil microbial community and modulating soil biogeochemical cycles.}, }
@article {pmid39904096, year = {2025}, author = {Huang, C and Wang, L and Wu, WM and Capowiez, Y and Qiao, Y and Hou, D}, title = {When plastisphere and drilosphere meet: Earthworms facilitate microbiome and nutrient turnover to accelerate biodegradation of agricultural plastic films.}, journal = {Environment international}, volume = {196}, number = {}, pages = {109309}, doi = {10.1016/j.envint.2025.109309}, pmid = {39904096}, issn = {1873-6750}, abstract = {Agricultural plastic mulching films have been an environmental concern for decades. The effects of the interactions between the anthropogenic plastisphere and other soil biospheres, particularly that of earthworms, on the fate of plastics remain poorly understood. Here, we investigated the decomposition of buried nonbiodegradable low-density polyethylene (LDPE) versus biodegradable PBTA/PLA copolymers in the presence of earthworms (Amynthas cortices) in dynamic microcosms. Earthworms significantly enhanced the biodegradation of plastic films in situ, as confirmed by mass reduction, surface modification, and changes in the molecular weights of films. Notably, the PBTA/PLA films exhibited a 1.41-fold increase in mass loss and a 5.69% reduction in the number-average molecular weight when incubated with earthworms. Earthworms influenced the microbial assembly within the plastisphere by increasing both bacterial and fungal biodiversity, as well as their network complexity. The time-decay patterns in the abundance of keystone degrader taxa, including the genera Noviherbaspirillum, Rhizobacter, and Mortierella, were mitigated by earthworms over the 60-day period. Additionally, earthworms preferentially consumed recalcitrant dissolved organic matter in LDPE and PBAT/PLA plastisphere soils, thereby increasing the bioavailability of components that serve as nutrient supplies for plastisphere microbiomes. Our findings demonstrate that earthworms enhance the decomposition of plastics in soils via cross-species interplay within the plastisphere and drilosphere, contributing not only to soil conditioning and biodiversity but also to plastic biodegradation in natural agroecosystems.}, }
@article {pmid39904001, year = {2025}, author = {Zhang, M and Hu, J and Zhang, Y and Cao, Y and Rensing, C and Dong, Q and Hou, F and Zhang, J}, title = {Roles of the soil microbiome in sustaining grassland ecosystem health on the Qinghai-Tibet Plateau.}, journal = {Microbiological research}, volume = {293}, number = {}, pages = {128078}, doi = {10.1016/j.micres.2025.128078}, pmid = {39904001}, issn = {1618-0623}, abstract = {Soil microbes, as intermediaries in plant-soil interactions, are closely linked to plant health in grassland ecosystems. In recent years, varying degrees of degradation have been observed in the alpine grasslands of the Qinghai-Tibet Plateau (QTP). Addressing grassland degradation, particularly under the influence of climate change, poses a global challenge. Understanding the factors driving grassland degradation on the QTP and developing appropriate mitigation measures is essential for the future sustainability of this fragile ecosystem. In this review, we discuss the environmental and anthropogenic factors affecting grassland degradation and the corresponding impacts on soil microbe community structure. We summarize the current research on the microbiome of the QTP, in particular the effect of vegetation, climate change, grazing, and land use, respectively on the alpine grassland microbiome. The results of these studies indicate that microbially mediated soil bioprocesses are important drivers of grassland ecosystem functional recovery. Therefore, a thorough understanding of the spatial distribution characteristics of the soil microbiome in alpine grasslands is required, and this necessitates an integrated approach in which the interactions among climatic factors, vegetation characteristics, and human activities are evaluated. Additionally, we assess and summarise current technological developments and prospects for applying soil microbiome technologies in sustainable agriculture, including: (i) single-strain inoculation, and (ii) inoculation of synthetic microbial communities, (iii) microbial community transplantation. Grassland restoration projects should be carried out with the understanding that each restoration measure has a unique effect on the soil microbial activity. We propose that the sustainable development of alpine grassland ecosystems can be achieved by adopting advanced microbiome technologies and integrating microbe-based sustainable agricultural practices to maximise grassland biomass, increase soil carbon, and optimise soil nutrient cycling.}, }
@article {pmid39903999, year = {2025}, author = {Mondal, A and Parvez, SS and Majumder, A and Sharma, K and Das, B and Bakshi, U and Alam, M and Banik, A}, title = {Co-inoculation of Trichoderma and tea root-associated bacteria enhance flavonoid production and abundance of mycorrhizal colonization in tea (Camellia sinensis).}, journal = {Microbiological research}, volume = {293}, number = {}, pages = {128084}, doi = {10.1016/j.micres.2025.128084}, pmid = {39903999}, issn = {1618-0623}, abstract = {Tea is one of the most popular nonalcoholic beverages, that contains several medicinally important flavonoids. Due to seasonal variation and various environmental stresses, the overall consistency of tea flavonoids affects the tea quality. To combat stress, plants stimulate symbiotic relationships with root-associated beneficial microbiomes that sustain nutrient allocation. Therefore, a study has been designed to understand the role of the tea root microbiome in sustaining tea leaf flavonoid production. To enumerate the microbiome, tea root and rhizoplane soil were collected from 3 years of healthy plants from Jalpaiguri district, West Bengal, India. A culture-independent approach was adopted to identify root and rhizosphere microbial diversity (BioSample: SAMN31404869; SRA: SRS15503027 [rhizosphere soil metagenome] BioSample: SAMN31404868;SRA:SRS15503030 [root metagenome]. In addition to diverse microbes, four mycorrhiza fungi, i.e., Glomus intraradices, Glomus irregulare, Paraglomus occultum and Scutellospora heterogama were predominant in collected root samples. A culture-dependent approach was also adopted to isolate several plant growth-promoting bacteria [Bacillus sp. D56, Bacillus sp. D42, Bacillus sp. DR15, Rhizobium sp. DR23 (NCBI Accession: OR821747-OR821750)] and one fungal [Trichoderma sp. AM6 (NCBI Accession:OM915414)] strain. A pot experiment was designed to assess the impact of that isolated microbiome on tea seedlings. After six months of microbiome inoculation, tea plants' physicochemical and transcriptional parameters were evaluated. The results confer that the microbiome-treated treatments [(T1-without any microbial inoculation; NCBI Accession: SAMN33591153), Trichoderma sp. AM6 (T2; NCBI Accession: SAMN33591155) and Trichoderma sp. AM6 +VAM containing tea root+synthetic microbial consortia (T5; NCBI Accession: SAMN33591154)] could enhance the total flavonoid content in tea seedlings by upregulating certain transcripts associated with the flavonoid biosynthesis pathway of tea.}, }
@article {pmid39903927, year = {2025}, author = {Luntamo, M and Hallamaa, L and Kulmala, T and Maleta, K and Ashorn, P}, title = {Effect of Antenatal Monthly Sulfadoxine-Pyrimethamine, Alone or with Azithromycin, on Gestational Weight Gain and Anemia during Pregnancy and One Month Postpartum in Malawi: A Randomized Controlled Trial Secondary Analysis.}, journal = {The American journal of tropical medicine and hygiene}, volume = {}, number = {}, pages = {}, doi = {10.4269/ajtmh.23-0829}, pmid = {39903927}, issn = {1476-1645}, abstract = {Low gestational weight gain (GWG) and prenatal anemia are associated with adverse pregnancy, maternal and infant health outcomes. In a secondary analysis of a single-center, randomized, partially placebo-controlled, outcome assessor-blinded, controlled trial conducted in Malawi from 2003 to 2006, when antiretroviral treatment (ART) for HIV was not widely available, we studied whether GWG can be increased and the prevalence of maternal anemia decreased during pregnancy and at 1 month postpartum through the intermittent preventive treatment in pregnancy (IPTp) of maternal malaria and reproductive tract infections. The participants (≥15-year-old women with uncomplicated second trimester single pregnancies) received either sulfadoxine (1,500 mg) and pyrimethamine (75 mg; SP) twice (control group, n = 433), monthly SP (n = 439), or monthly SP and azithromycin (1,000 mg) twice (AZI-SP, n = 441) during pregnancy. The mean weekly GWG in the sample was 256 g/week. The participants in the monthly SP group gained, on average (95% CI), 4 g (-13 to 20; P = 0.671), and those in the AZI-SP group gained 25 g (8-41; P = 0.003) more weight per week than control group participants. Among HIV-positive participants (12%), the differences were larger and also significant between the monthly SP group and control group. Mean hemoglobin and anemia prevalence did not differ between the groups during pregnancy or postnatally. The data support a hypothesis that IPTp with monthly SP and two doses of azithromycin can increase GWG, especially among HIV-positive women who are not on ART, possibly through the reduction of infections, inflammation, and effects on the maternal gut microbiome.}, }
@article {pmid39903702, year = {2025}, author = {Suolang, Q and Basang, Z and Silang, W and Nima, C and Yang, Q and Da, W}, title = {Study on intestinal microbial communities of three different cattle populations on Qinghai-Tibet Plateau.}, journal = {PloS one}, volume = {20}, number = {2}, pages = {e0312314}, doi = {10.1371/journal.pone.0312314}, pmid = {39903702}, issn = {1932-6203}, mesh = {Animals ; Cattle/microbiology ; *Gastrointestinal Microbiome ; Tibet ; Bacteria/classification/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The Tibetan cattle, indispensable·animals on the Qinghai-Tibet Plateau, have become a focal point for the region's economic development. As such, the hybridization of these cattle has been recognized as a pivotal strategy to enhance the local cattle industry. However, research on the gut microbiota of Tibetan hybrid cattle remains scarce. Based on this, we conducted a comparative analysis of the gut microbiota and its functional implications across three distinct cattle populations: two the hybrid cattle populations (Tibetan local cattle × Holstein cattle, TH and Tibetan local cattle × Jersey cattle, TJ) and one the Tibetan locoal cattle population (BL). Bacteroidetes and Firmicutes dominate the gut microbiota across all populations at the phylum level. In addition, the predominant phyla in BL cattle were found to be Cyanobacteria, Verrucomicrobiota, and Actinobacteria, which may be one of the important reasons for the adaptability of Tibetan local cattle to the high-altitude environment of the Qinghai-Tibet Plateau. Further analysis identified specific biomarkers associated with the immune systems of BL cattle, including Bacteroidales_RF16, Coriobacterium, and Muribaculaceae. In contrast, TH cattle are primarily dominated by Oscillospiraceae and Clostridia_UCG_014, and TJ cattle are mainly dominated by Christensenellaceae and Gammaproteobacteria. KEGG enrichment analysis revealed that BL and TH cattle showed significant enrichment in the immune system, energy metabolism, and amino acid metabolism-related pathways compared with TJ cattle. Overall, these results suggest that BL and TH cattle demonstrate enhanced adaptability compared to TJ cattle, and indicate that intestinal microbiota of cattle at different altitudes and breeds have diverse structures and functions. Our study presents a new perspective on the role of the microbiome in the hybridization and enhancement of Tibetan cattle.}, }
@article {pmid39903534, year = {2025}, author = {Tortelli, BA and Contreras, J and Markovina, S and Ding, L and Wylie, KM and Schwarz, JK}, title = {Characterization of the vaginal microbiome of postmenopausal patients receiving chemoradiation for locally advanced cervical cancer.}, journal = {JCI insight}, volume = {}, number = {}, pages = {}, doi = {10.1172/jci.insight.176839}, pmid = {39903534}, issn = {2379-3708}, abstract = {The standard-of-care treatment of locally advanced cervical cancer includes pelvic radiation therapy with concurrent cisplatin-based chemotherapy and is associated with a 30-50% failure rate. New prognostic and therapeutic targets are needed to improve clinical outcomes. The vaginal microbiome has been linked to the pathogenesis of cervical cancer, but little is known about the vaginal microbiome in locally advanced cervical cancer as it relates to chemoradiation. In this pilot study we utilized 16S rRNA gene community profiling to characterize the vaginal microbiomes of 26 postmenopausal women with locally advanced cervical cancer receiving chemoradiation. Our analysis revealed diverse anaerobe-dominated communities whose taxonomic composition, diversity or bacterial abundance did not change with treatment. We hypothesized that characteristics of the microbiome might correlate with treatment response. Pretreatment microbial diversity and bacterial abundance were not associated with disease recurrence. We observed a greater relative abundance of Fusobacterium in patients that later had cancer recurrence, suggesting that Fusobacterium could play a role in modifying treatment response. Taken together, this hypothesis generating pilot study provides insight into the composition and dynamics of the vaginal microbiome, offering proof-of-concept for future study of the microbiome and its relationship with treatment outcomes in locally advanced cervical cancer.}, }
@article {pmid39903521, year = {2025}, author = {Johnson, SD and Pino, M and Acharya, A and Clain, JA and Bose, D and Nguyen, K and Harper, J and Villinger, F and Paiardini, M and Byrareddy, SN}, title = {Interleukin-21 and anti-α4β7 dual therapy during ART promotes immunological and microbiome responses in SIV-infected macaques.}, journal = {JCI insight}, volume = {}, number = {}, pages = {}, doi = {10.1172/jci.insight.184491}, pmid = {39903521}, issn = {2379-3708}, abstract = {Despite combination antiretroviral therapy (ART), HIV causes persistent gut barrier dysfunction, immune depletion, and dysbiosis. Further, ART interruption results in reservoir reactivation and rebound viremia. Both IL-21 and anti-α4β7 improve gut barrier functions, and we hypothesized combining them would synergize as a dual therapy to improve immunological outcomes in SIV-infected rhesus macaques (RMs). We found no significant differences in CD4+ T-cell reservoir size by intact proviral DNA assay. SIV rebounded in both dual-treated and control RMs following analytical therapy interruption (ATI), with time to rebound and initial rebound viremia comparable between groups; however, dual-treated RMs showed slightly better control of viral replication at the latest time points post-ATI. Additionally, following post-ATI, dual-treated RMs showed immunological benefits, including T-cell preservation and lower PD-1+ central memory T-cell (TCM) frequency. Notably, PD-1+ TCMs were associated with reservoir size, which predicted viral loads (VLs) post-ATI. Finally, 16S rRNA sequencing revealed better recovery from dysbiosis in treated animals, and the butyrate-producing Firmicute Roseburia predicted PD-1-expressing TCMs and VLs after ATI. PD-1+ TCMs and gut dysbiosis represent mechanisms of HIV persistence and pathogenesis, respectively. Therefore, combining IL-21 and anti-α4β7 may be an effective therapeutic strategy to improve immunological outcomes for people with HIV.}, }
@article {pmid39903340, year = {2025}, author = {Yan, Z and Zheng, Z and Cao, L and Zhu, Z and Zhou, C and Sun, Q and Tang, B and Zhao, G}, title = {Altered gut microbiome and serum metabolome profiles associated with essential tremor.}, journal = {Metabolic brain disease}, volume = {40}, number = {2}, pages = {118}, pmid = {39903340}, issn = {1573-7365}, support = {U20A20355//National Natural Science Foundation of China/ ; WKJ-ZJ-ZZ08//Major Health Science and Technology Program of Zhejiang Province/ ; LZ23H090004//Key Projects of Zhejiang Provincial Natural Science Fund/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Metabolome ; *Essential Tremor/blood/microbiology ; Male ; Female ; Middle Aged ; Aged ; Dysbiosis/blood ; Lipid Metabolism/physiology ; }, abstract = {The genetic predisposition and environmental factors both trigger the complex neurological dyskinesia of essential tremor (ET). Gut dysbiosis may facilitate the occurrence and development of neurological diseases. Therefore, it is worth exploring the inner connections between gut microbiota and ET. First, the gut microbiota of 19 ET patients and 21 healthy controls (HCs) were analysed with metagenomics approach. Second, the potential linkages between gut microbiome and serum metabolome profiles were explored by integrative analysis. The gut microbiota disorders were present in ET patients. The LEfSe method showed a significant decrease in Bacteroides. The functional analysis revealed that there were differences in gut microbial apoptosis, retinol metabolism, and steroid hormone biosynthesis pathways. The levels of various lipids and lipid-like molecules alter in serum of ET patients, which correlated with altered gut microbial abundance, indicating the alterations in lipid metabolism involved in apoptosis pathway in ET. All of these data point to the gut dysbiosis in ET, and some changed gut microbial species were linked to abnormalities in blood lipid metabolism, which open up new avenues for investigation into the pathophysiology of ET.}, }
@article {pmid39903098, year = {2025}, author = {Medrano-Ruiz, LG and Molina-Domínguez, CC and Rascón-Valenzuela, LA and Dórame-Miranda, RF and Osorio-Díaz, P and Medina-Juárez, L&#xc1; and Ovando-Martínez, M}, title = {Bioaccessibility of bioactive compounds and associated compounds to the indigestible fraction after in vitro digestion of three dry Capsicum annuum varieties.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4fo04168b}, pmid = {39903098}, issn = {2042-650X}, abstract = {Mexico has a wide variety of dry chilies used in Mexican food preparation because they are spicy, a property related to the bioactive compound named capsaicin. Apart from capsaicin, dry chilies have compounds such as phenolic compounds and tocopherols. Except for phenolic compounds, capsaicin and tocopherol have not been totally assessed to measure their release from the food matrix (bioaccessibility) after in vitro digestion. Therefore, this study is aimed at analyzing the bioaccessibility of phenolic compounds, tocopherols and capsaicinoids after in vitro digestion process of three dry chilies, namely, chiltepin, Colorado, and de Arbol, as well as the bioactive compounds associated with the indigestible fraction (IF). Results indicated that the bioaccessibility values of capsaicinoids were above 80% for all the three chili varieties without showing significant differences. Although these chilies showed high capsaicinoid bioaccessibility values, there were still compounds associated with the IF that could reach the colon and exhibit bioactivity. Regarding phenolic compounds, no differences in the bioaccessibility values were observed; however, there was a major concentration of flavonoids in the IF of the Colorado and de Arbol chilies, which could have a regulatory effect on the colonic microbiome. Regarding the bioaccessibility of α-tocopherol, there was a significant difference between de Arbol and the other two varieties (above 60%). The IF of Colorado chili was a source of α-tocopherol in the colon because it had the lowest bioaccessibility percentage. The overall results demonstrate that dry chilies are a source of bioactive compounds with bioaccessibility values favorable to human health.}, }
@article {pmid39903016, year = {2025}, author = {Hou, Q and Zhang, J and Su, Z and Wang, X and Fang, H and Qian, S and Shi, H and Wang, Q and Li, Y and Lin, J and Wang, X and Wang, Z and Liao, L}, title = {Clinical Trial of Ozonated Water Enema for the Treatment of Fibromyalgia: A Randomized, Double-Blind Trial.}, journal = {Pain physician}, volume = {28}, number = {1}, pages = {E13-E22}, pmid = {39903016}, issn = {2150-1149}, mesh = {Humans ; Double-Blind Method ; *Fibromyalgia/drug therapy/therapy ; Female ; Middle Aged ; *Water ; Adult ; *Enema/methods ; *Ozone/therapeutic use/administration &amp; dosage ; Male ; }, abstract = {BACKGROUND: The pathogenesis of fibromyalgia (FM) is currently unknown. Many patients with this condition are not effectively treated, and disorders of the intestinal dysbiosis have been identified in patients with FM. This trial aimed to investigate whether ozonated water enema could alleviate the symptoms of FM by improving intestinal dysbiosis in these patients.<br><br>OBJECTIVE: This trial aims to evaluate the therapeutic advantages of ozonated water enema therapy for patients suffering from FM.<br><br>STUDY DESIGN: A single-center, double-blind, randomized controlled trial.<br><br>SETTING: Department of Pain Management, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China.<br><br>METHODS: This is a randomized, double-blind trial conducted on FM patients (n = 66). The selected patients were randomly categorized into the O3 and control groups. The patients in the O3 and control groups received an ozonated and deionized water enema, respectively, at the same dose and frequency. After the treatment, the scores on the numerical rating scale (NRS), widespread pain index (WPI), Hamilton anxiety scale (HAMA), and the Pittsburgh sleep quality index (PSQI) were compared between the 2 groups, as were the doses of duloxetine, to evaluate the treatment effect. Furthermore, the effectiveness of the treatment was assessed by comparing fecal samples from the O3 group collected before and after treatment with 25 healthy individuals from the physical examination department of Shanghai East Hospital.<br><br>RESULTS: The patients in the O3 group indicated significant relief in pain and reduced NRS, HAMA, PSQI, and WPI scores at each follow-up time point (P < 0.001) when compared to the control group. In addition, the patients in the O3 group used lower doses of duloxetine than did those the control group (P < 0.001). Moreover, FM patients treated with ozonated water indicated improvements to their gut microbiome.<br><br>LIMITATIONS: The trial's findings might be affected by confounding factors, including medicines, diet, and environmental circumstances. Also, this trial was limited by its sample size, and the symptom severity scores (SSS) of the patients at 3 months after treatment at the given follow-up period were not assessed.<br><br>CONCLUSION: This trial confirmed that the symptoms of pain, anxiety, and sleep disorders in FM patients were effectively relieved after treatment with an ozonated water enema. Furthermore, the ozonated water enema was associated with a significant reduction in duloxetine dosage and improved gut microbiome disorder, suggesting that the enema could target disorders related to the gut microbiome and therefore serve as a therapeutic intervention for FM.}, }
@article {pmid39902954, year = {2025}, author = {Tran, L and Lansing, L and Cunningham, M and Ho, J and Deckers, T and Newman, T and Wu, L and Gregoris, AS and Zorz, J and Muntz, L and Lee, K and Trépanier-Leroux, D and Conflitti, IM and Pepinelli, M and Walsh, EM and Morfin, N and Powell, JE and Moran, N and Hoover, SE and Pernal, SF and Currie, RW and Giovenazzo, P and Guzman-Novoa, E and Jabbari, H and Foster, LJ and Zayed, A and Ortega Polo, R and Guarna, MM}, title = {Gut microbiome metagenomic sequences of honey bees (Apis mellifera) exposed to crops.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0073124}, doi = {10.1128/mra.00731-24}, pmid = {39902954}, issn = {2576-098X}, abstract = {The gut microbiome of the European honey bee (Apis mellifera) is vital to its health, yet large-scale studies are scarce. We present metagenomic sequencing data from 180 samples collected near and far from eight crops across Canada over 2 years. These data sets will help address various biological and environmental questions.}, }
@article {pmid39902951, year = {2025}, author = {Chen, H( and Yi, B and Ma, Z(}, title = {Resilience of human gut microbiomes in autism spectrum disorder: measured using stiffness network analysis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0107824}, doi = {10.1128/spectrum.01078-24}, pmid = {39902951}, issn = {2165-0497}, abstract = {Autism spectrum disorder (ASD) affects an estimated 1%-2% of children worldwide, but its specific etiology remains unclear. In recent years, the gut microbiome's role in ASD pathogenesis has garnered increasing attention. However, the exact relationship between microbiota and ASD-such as which microbial species significantly impact disease onset and progression-remains unresolved, and effective methods to measure microbial interactions are still lacking. In this study, we introduce an innovative stiffness network analysis (SNA) method to quantify changes in microbial network structure and identify disease-specific microbial bacteria theoretically. The SNA method was applied to reanalyze eight ASD gut microbiome data sets, encompassing 898 ASD samples and 467 healthy control (HC) samples from 16S-rRNA sequencing data. Key findings include the following: (i) an "allies" biomarker subgroup consisting of Bacteroides plebeius, Sutterella, Lachnospira, and Prevotella copri was identified; (ii) a profile monitoring score of 0.72 for the biomarker subgroup, indicating significant relationship changes between HC and ASD states, and (iii) a P/N ratio of biomarker subgroup in ASD-associated gut bacteria that was three times higher than that of HC microbiomes. Additionally, we discuss the non-monotonic relationship alterations within microbial sub-communities in the ASD gut microbiome.IMPORTANCEIt is crucial to assess alterations in network structure in different biological states in order to promote health. The stiffness network allows for the exploration of species interactions and the measurement of resilience in complex microbial networks. The objective of this study was to develop a stiffness network analysis (SNA) method for evaluating the contribution of microbial bacteria in differentiating disease samples from healthy control samples by examining changes in network stiffness parameters. Furthermore, the SNA method was employed on both simulated and real autism spectrum disorder gut microbiome data sets to identify potential microbial biomarker subgroups, with a particular focus on the relationship alterations within microbial networks.}, }
@article {pmid39902937, year = {2025}, author = {Tian, C and Zhang, T and Zhuang, D and Luo, Y and Li, T and Zhao, F and Sang, J and Tang, Z and Jiang, P and Zhang, T and Liu, P and Zhu, L and Zhang, Z}, title = {Industrialization drives the gut microbiome and resistome of the Chinese populations.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0137224}, doi = {10.1128/msystems.01372-24}, pmid = {39902937}, issn = {2379-5077}, abstract = {UNLABELLED: Industrialization has driven lifestyle changes in eastern and western Chinese populations, yet we have a poor understanding of the dynamic changes in their gut microbiome and resistome under industrialization, which is essential for the scientific management of public health. Here, this study employed metagenomics to analyze the gut microbiota of 1,382 healthy individuals from China, including 415 individuals from the eastern region of advanced industrialization and 967 individuals from the western region of developing industrialization. Compared with western populations, eastern populations show a significant increase in interindividual dissimilarity of microbial species composition and metabolic pathways but a significant decrease in intraindividual species and functional diversity. Furthermore, our results found significantly less abundance and richness of antibiotic resistance genes (ARGs) in the gut microbiota of eastern populations, alongside a lower prevalence of unique core ARG subtypes. For the 12 core ARG types shared between eastern and western populations, the mean relative abundance of two types was notably higher in the eastern populations, while eight core ARG types had significantly higher mean relative abundance in the western populations. Based on the reconstruction of metagenomic assembled genomes, we found that Escherichia coli genomes from western populations carried more virulence factor genes (VFGs) and mobile genetic elements (MGEs) compared to those from eastern populations. This large-scale study for the first time revealed industrialization potentially led to unexpected alterations of the gut microbiome and resistome between eastern and western populations that provide a vital implication for Chinese public health and may aid in the development of region-specific strategies for managing pathogenic infections.<br><br>IMPORTANCE: As China experiences rapid but uneven industrialization, understanding its effect on people's gut bacteria is critical for public health. This study reveals how industrialization may reshape the health risks related to gut bacteria and antibiotic resistance. This work provides crucial information to help create customized public health policies for different regions.}, }
@article {pmid39902917, year = {2025}, author = {Gelbard, A and Shilts, MH and Hoke, A and Strickland, B and Motz, K and Tsai, HW and Boone, H and Drake, WP and Wanjalla, C and Smith, PM and Brown, H and Powell, J and Ramirez-Solano, M and Atkinson, JB and Simpson, J and V Rajagopala, S and Mallal, S and Sheng, Q and Hillel, AT and Das, SR}, title = {Idiopathic Subglottic Stenosis and the Epithelial Interface of Host and Environment.}, journal = {Journal of the American College of Surgeons}, volume = {}, number = {}, pages = {}, doi = {10.1097/XCS.0000000000001340}, pmid = {39902917}, issn = {1879-1190}, abstract = {BACKGROUND: Idiopathic subglottic stenosis (iSGS) is a rare fibrotic disease of the proximal airway affecting adult Caucasian women nearly exclusively. Life-threatening ventilatory obstruction occurs secondary to pernicious subglottic mucosal scar. Disease rarity and wide geographic patient distribution has previously limited substantive mechanistic investigation into iSGS pathogenesis.<br><br>STUDY DESIGN: Harnessing pathogenic mucosa from an international iSGS patient cohort and single cell RNA sequencing we provide an unbiased characterization of the cell subsets present in the proximal airway scar and detail their molecular phenotypes.<br><br>RESULTS: Airway epithelium in iSGS patients is depleted of basal progenitor cells and the residual epithelial cells acquire a mesenchymal phenotype. Observed displacement of bacteria beneath the lamina propria provides functional support for the molecular evidence of epithelial dysfunction. Matched superficial and deep tissue microbiomes support displacement of the native microbiome into the lamina propria of iSGS patients rather than disrupted bacterial community structure. However, animal models confirm bacteria are necessary for pathologic proximal airway fibrosis and suggest an equally essential role for host adaptive immunity. Human samples from iSGS airway scar demonstrate adaptive immune activation in response to the proximal airway microbiome of both matched iSGS patients and healthy controls. Clinical outcome data from iSGS patients suggests surgical extirpation of airway scar and reconstitution with unaffected tracheal mucosa halts the progressive fibrosis.<br><br>CONCLUSION: Our novel data support an iSGS disease model where epithelial alterations facilitate microbiome displacement, dysregulated immune activation, and localized fibrosis. Overall, these results refine our understanding of iSGS and implicate shared pathogenic mechanisms with distal airway fibrotic diseases.}, }
@article {pmid39902908, year = {2025}, author = {Kelley, K and Dogru, D and Huang, Q and Yang, Y and Palm, NW and Altindis, E and Ludvigsson, J}, title = {Children who develop celiac disease are predicted to exhibit distinct metabolic pathways among their gut microbiota years before diagnosis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0146824}, doi = {10.1128/spectrum.01468-24}, pmid = {39902908}, issn = {2165-0497}, abstract = {UNLABELLED: Celiac disease (CD) is an autoimmune disease caused by a loss of gluten tolerance in genetically predisposed individuals. While 30%-40% of people possess the predisposing alleles, only 1%-2% are diagnosed with CD, suggesting that environmental factors are involved in disease pathogenesis. To determine an association between pediatric CD and the gut microbiome, we analyzed fecal samples from a prospective cohort study (ABIS). These samples were collected from children who later developed CD (CD progressors) and age-matched healthy children (at ages 1, 2.5, and 5) with similar HLA genotypes, breastfeeding durations, and gluten exposure times. We previously reported gut microbiome differences at ages 2.5 and 5 in this cohort; here, we present findings from samples collected at age 1 (n = 5). We identified 14 ASVs differing significantly between CD progressors and controls, including taxa linked to CD pathogenesis. CD progressors had increased Firmicutes and higher alpha diversity in IgA- bacteria. Using PICRUSt, we analyzed metabolic pathways enriched in CD progressors compared to controls at ages 1, 2.5, and 5 (n = 5-16), revealing enriched inflammatory and pathogenic pathways potentially contributing to CD-related immune dysregulation. While results are based on the primary EdgeR analysis, we also applied a non-parametric method of statistical analysis, reporting those results with supplementary figures. In conclusion, our findings suggest distinct metabolic pathways enriched in the gut microbiome of CD progressors years before diagnosis, which could inform targeted therapeutics for CD. As discussed in the limitations section, this small pilot study should be replicated with larger sample sizes for broader generalization.<br><br>IMPORTANCE: We analyzed gut microbiome data from children who later developed celiac disease (CD progressors) compared to healthy children in the first 5 years of life. Using fecal samples corresponding to the three phases of gut microbiome development, we uncovered enriched functional microbial pathways in CD progressors at age 1. Some of these pathways, implicated in bacterial pathogenesis, microbiota modulation, and inflammation, have been correlated with CD. We also identified taxa in CD progressors at age 1 including Lachnospiraceae, Alistipes, and Bifidobacterium dentium that were previously associated with CD. These findings suggest a potential role for these taxa and enriched pathways in pediatric CD onset years before diagnosis, highlighting potential for early interventions. While the findings of this exploratory study should be validated with larger sample sizes, our study suggests microbial metabolic pathways related to CD onset, enhancing our understanding of CD pathogenesis and the role of gut microbiome-mediated early alterations.}, }
@article {pmid39902755, year = {2025}, author = {Ebersole, JL and Novak, MJ and Cappelli, D and Dawson, DR and Gonzalez, OA}, title = {Use of Nonhuman Primates in Periodontal Disease Research: Contribution of the Caribbean Primate Research Center and Cayo Santiago Rhesus Colony.}, journal = {American journal of primatology}, volume = {87}, number = {2}, pages = {e23724}, doi = {10.1002/ajp.23724}, pmid = {39902755}, issn = {1098-2345}, support = {//This study was supported by National Institute on Minority Health and Health Disparities (MD007600), National Institute of Dental and Craniofacial Research (DE05599, DE07267, DE07457), National Center for Research Resources (RR003051, RR020145, RR03640), National Institute of General Medical Sciences (GM103538), Office of Research Infrastructure Programs (OD012217, OD021458), and National Institute on Aging (AG021406)./ ; }, mesh = {Animals ; *Periodontal Diseases/veterinary/microbiology ; *Disease Models, Animal ; *Primates ; Macaca mulatta ; Puerto Rico ; Periodontitis/microbiology/veterinary ; Microbiota ; Humans ; }, abstract = {This review article provides a historical summary regarding the use, value, and validity of the nonhuman primate model of periodontal disease. The information provided cites results regarding the features of naturally occurring periodontitis in various nonhuman primate species, as well as the implementation of a model of experimental periodontitis. Clinical similarities to human disease are discussed, as well as the use of these models to document physiological and pathophysiological tissue changes in the periodontium related to the initiation and progression of the disease. Additionally, the use of these analytics in examination of the tissue characteristics of the disease, and the utility of nonhuman primates in testing and describing various therapeutic modalities are described. As periodontitis represents a disease of an oral microbiome dysbiosis, features of the altered microbiome in the disease in nonhuman primates are related to similar findings in the human condition. The review then provides a summary of the features of local and systemic host responses to a periodontal infection in an array of nonhuman primate species. This includes attributes of innate immunity, acute and chronic inflammation, and adaptive immune responses. Finally, extensive information is presented regarding the role of Macaca mulatta derived from the Cayo Santiago community in evaluating critical biologic details of disease initiation, progression, and resolution. This unique resource afforded the capacity to relate risk and expression of disease and traits of the responses to age, sex, and matriline derivation (e.g., heritability) of the animals. The Cayo Santiago colony continues to provide a critical preclinical model for assessment of molecular aspects of the disease process that can lead to both new targets for therapeutics and consideration of vaccine approaches to preventing and/or treating this global disease.}, }
@article {pmid39902230, year = {2024}, author = {Ronan, V}, title = {An open window: the crucial role of the gut-brain axis in neurodevelopmental outcomes post-neurocritical illness.}, journal = {Frontiers in pediatrics}, volume = {12}, number = {}, pages = {1499330}, pmid = {39902230}, issn = {2296-2360}, abstract = {Among patients admitted to the pediatric intensive care unit, approximately 10% are discharged with a new functional morbidity. For those who were admitted with a neurocritical illness, the number can be as high as 60%. The most common diagnoses for a neurocritical illness admission include traumatic brain injury, status epilepticus, post-cardiac arrest, hypoxic ischemic encephalopathy, meningo/encephalitis, and stroke. The gut-brain axis is crucial to childhood development, particularly neurodevelopment. Alterations on either side of the bidirectional communication of the gut-brain axis have been shown to alter typical development and have been associated with autism spectrum disorder, anxiety, sleep disturbances, and learning disabilities, among others. For those patients who have experienced a direct neurologic insult, subsequent interventions may contribute to dysbiosis, which could compound injury to the brain. Increasing data suggests the existence of a critical window for both gut microbiome plasticity and neurodevelopment in which interventions could help or could harm and warrant further investigation.}, }
@article {pmid39902218, year = {2025}, author = {Lucchese, A and Marcolina, M and Mancini, N and Ferrarese, R and Acconciaioco, S and Gherlone, E and Bonini, C and Manuelli, M and Polimeni, A}, title = {A comparison of the alterations of oral microbiome with fixed orthodontic therapy and clear aligners: a systematic review.}, journal = {Journal of oral microbiology}, volume = {17}, number = {1}, pages = {2372751}, pmid = {39902218}, issn = {2000-2297}, abstract = {AIM: The oral microbiome plays a fundamental role in maintaining homeostasis of the oral cavity. In the last decade there has been an increasing use of clear aligners, which guarantee aesthetics and comfort for the patient. The aim of this work is to conduct a systematic review regarding the alterations in bacterial flora and oral health with aligner and fixed orthodontic therapy.<br><br>DESIGN: A systematic review was conducted following the PRISMA Statement. Using the search strategy "(clear aligners OR Invisalign) AND (fixed therapy OR fixed orthodont * therapy) NOT (thermoplastic retainers) AND (oral microbiome OR oral microbiota * OR oral microbiology * OR oral health)", in the main scientific databases. Two scales were applied to assess the quality of scientific evidence: ROBINS-I and RoB 2.<br><br>RESULTS: A total of 484 articles emerged of which 9 met our inclusion/exclusion criteria. Afterwards the application of the rating scales, 1 article was found to be at low risk of bias, 6 at moderate and 2 at serious risk of bias.<br><br>CONCLUSION: Both therapies cause an alteration of the oral microbiome, but the changes induced by the aligners seem to be compatible with a better oral health compared to fixed appliances.}, }
@article {pmid39902217, year = {2025}, author = {Al-Maweri, SA and Al-Mashraqi, AA and Al-Qadhi, G and Al-Hebshi, N and Ba-Hattab, R}, title = {The association between the oral microbiome and hypertension: a systematic review.}, journal = {Journal of oral microbiology}, volume = {17}, number = {1}, pages = {2459919}, pmid = {39902217}, issn = {2000-2297}, abstract = {BACKGROUND: This study systematically reviewed the available evidence regarding the potential association between oral microbiota and hypertension.<br><br>METHODS: A comprehensive search of online databases was conducted by two independent investigators for all relevant articles. All observational studies that assessed the association between oral microbiota and hypertension were included. Quality appraisal was conducted using the NOS tool.<br><br>RESULTS: A total of 17 studies comprising 6007 subjects were included. The studies varied with respect to sample type and microbial analysis method. All studies, except one, found significant differences in microbial composition between hypertensive and normotensive subjects. However, there were substantial inconsistencies regarding the specific differences identified. Still, a few taxa were repeatedly found enriched in hypertension including Aggregatibacter, Kingella, Lautropia, and Leptotrachia besides the red complex periodontal pathogens. When considering only studies that controlled for false discovery rates and confounders, Atopobium, Prevotella, and Veillonella were identified as consistently associated with hypertension.<br><br>CONCLUSION: There are significant differences in the oral microbiome between hypertensive and normotensive subjects. Despite the heterogeneity between the included studies, a subset of microbial taxa seems to be consistently enriched in hypertension. Further studies are highly recommended to explore this association.<br><br>REGISTRATION: PROSPERO database (ID: CRD42023495005).}, }
@article {pmid39902181, year = {2024}, author = {Veerapandian, R and Paudyal, A and Schneider, SM and Lee, STM and Vediyappan, G}, title = {A mouse model of immunosuppression facilitates oral Candida albicans biofilms, bacterial dysbiosis and dissemination of infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1467896}, pmid = {39902181}, issn = {2235-2988}, mesh = {Animals ; *Biofilms/growth &amp; development/drug effects ; *Disease Models, Animal ; *Candida albicans/physiology ; *Dysbiosis/microbiology ; Mice ; *Candidiasis, Oral/microbiology ; *Tongue/microbiology ; Enterococcus faecalis/physiology ; Mouth/microbiology ; Liver/microbiology ; Immunosuppression Therapy ; }, abstract = {Opportunistic pathogens are a major threat to people, especially those with impaired immune systems. Two of the most important microbes in this category are the fungus Candida albicans and Gram-positive bacteria of the genus Enterococcus, which share overlapping niches in the oral cavity, gastrointestinal and urogenital tracts. The clinical importance of oral C. albicans biofilm and its interaction with the host under immunosuppressive conditions remains largely understudied. Here, we used a mouse model of oropharyngeal candidiasis (OPC) with cortisone acetate injection on alternate days and a continuous supply of C. albicans in drinking water for three days, resulting in immunosuppression. Results showed abundant growth of resident oral bacteria and a strong C. albicans biofilm on the tongue consisting of hyphae which damaged papillae, the epidermal layer, and invaded tongue tissue with the accumulation of inflammatory cells as demonstrated by Grocott's methenamine silver and hematoxylin and eosin staining, respectively. The dispersed microbes from the oral biofilm colonized the gastrointestinal (GI) tract and damaged its integrity, disseminating microbes to other organs. Although no visible damage was observed in the kidney and liver, except increased lipid vacuoles in the liver cells, C. albicans was found in the liver homogenate. Intriguingly, we found co-occurrence of Enterococcus faecalis in the tongue, liver, and stool of immunosuppressed control and C. albicans infected organs. Targeted 16S rRNA and ITS2 amplicon sequencing of microbes from the fecal samples of mice confirmed the above results in the stool samples and revealed an inverse correlation of beneficial microbes in the dysbiosis condition. Our study shows that mucosal-oral infection of C. albicans under immunosuppressed conditions causes tissue damage and invasion in local and distant organs; the invasion may be aided by the overgrowth of the resident endogenous Enterobacteriaceae and other members, including the opportunistic pathogen Enterococcus faecalis.}, }
@article {pmid39901928, year = {2025}, author = {Demirci, M and Çubuk, C and Dasdemir, F and Saribas, AS and Balcıoglu, EB and Ozbey, D and Yorulmaz, D and Olmez Hanci, T and Basa, S and Kocazeybek, BS}, title = {Comparative microbial metagenomic analysis of drinking water plants and wastewater treatment plants in Istanbul.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1488268}, pmid = {39901928}, issn = {1664-302X}, abstract = {INTRODUCTION: Wastewater treatment plants (WWTPs) and drinking-water treatment plants (DWTPs) are critical for public health due to the potential risks posed by microorganisms that may persist after treatment. The aim of this study was to detect the microbiome profiles of waters from both DWTPs and WWTPs under the Istanbul Water and Sewerage Administration (ISKI), identify the antimicrobial resistance profiles in all these facilities, and observe the differences in the microbiome between the inlet and outlet of different WWTPs.<br><br>METHODS: A total of 52 samples were examined, comprising 18 samples from DWTPs and 34 samples from WWTPs. All water samples underwent pre-isolation filtration. DNA isolation was conducted using filter material, followed by sequencing on a NovaSeq 6000 instrument. Kraken2 tools and R scripts were used for statistical analysis and data visualization.<br><br>RESULTS: The microbial metagenomic analysis identified 71 phyla, 113 classes, 217 orders, 480 families, and 1,282 genera across all samples. There were unclassified microbes (53.14% vs. 58.75%), Eukaryota (3.64% vs. 3.5%), Archaea (0.08% vs. 0.03%), bacteria (42% vs. 36.25%), and viruses (0.02% vs. 0.04%) in the raw water and ozonation unit outlet of DWTPs. The inlet and outlet of WWTPs showed unclassified microbes (52.68% vs. 59.62%), Eukaryota (0.6% vs. 1.72%), Archaea (0.26% vs. 0.15%), bacteria (46.43% vs. 38.43%), and viruses (0.05% vs. 0.04%). No statistically significant results were found in the analysis of raw waters collected from DWTPs and samples taken from the ozonation unit outlet-from the phylum level to the genus level (p&#x202f;>&#x202f;0.05). The inlet and outlet points of WWTPs showed no statistically significant results from the phylum to species levels (p&#x202f;>&#x202f;0.05). The most detected genera were Desulfobacter (4.82%) in preliminary WWTPs, Thauera (1.93%) in biological WWTPs, Pseudomonas (1.44%) in advanced biological WWTPs, Acidovorax (1.85%) in biological package WWTPs, and Pseudomonas (11.55%) in plant-based WWTPs. No antimicrobial resistance gene markers were detected in water samples from raw water inlets and ozonation unit outlets from DWTPs, membrane wastewater recovery plants, or ultraviolet (UV) recycling facilities. The ANT(3&#x2033;), Erm, and Sul resistance gene markers were detected in all raw WWTPs samples.<br><br>DISCUSSION: There were no significant microbial risk differentiation between biological WWTPs and advanced biological WWTPs. The data could serve as preliminary information for future research. More extensive studies are needed, with multiple sample tracking in these facilities and their feeding basins.}, }
@article {pmid39901817, year = {2025}, author = {Galvin, S and Honari, B and Anishchuk, S and Healy, CM and Moran, GP}, title = {Oral Leukoplakia Microbiome Predicts the Degree of Dysplasia and is Shaped by Smoking and Tooth Loss.}, journal = {Oral diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/odi.15272}, pmid = {39901817}, issn = {1601-0825}, support = {/HRBI_/Health Research Board/Ireland ; }, abstract = {OBJECTIVE: This study aimed to determine if the oral potentially malignant disorder, oral leukoplakia (OLK), exhibited microbiome changes that predict the degree of dysplasia and the risk of malignant progression.<br><br>RESULTS: We examined the microbiome in 216 swabs of OLK from 177 patients. Compared to healthy controls (n&#x2009;=&#x2009;120 swabs from 61 patients), who were less likely to smoke and had better oral health, OLK patients exhibited an increased abundance of Rothia mucilaginosa, Streptococcus parasanguinis and S. salivarius, resembling acetaldehyde generating communities described previously. Compared to the patients' healthy contralateral normal (CLN) mucosa (n&#x2009;=&#x2009;202), which acts as a matched control for oral health parameters, OLK exhibited increased S. infantis, Leptotrichia spp., Bergeyella spp., Porphyromonas spp. and F. nucleatum. Machine learning with clinical and microbiome data could discriminate high-risk dysplasia (moderate to severe) from low-risk dysplasia (none or mild) (sensitivity 87.4%; specificity 76.5%). Follow-up swabs were recovered from 58 patients, eight of whom progressed to a higher grade of dysplasia or OSCC and these eight patients exhibited a higher abundance of Fusobacterium species at their initial presentation.<br><br>CONCLUSIONS: Our study suggests that the OLK microbiome has potential to be an aid to the prediction of dysplasia grade and the risk of malignant transformation.}, }
@article {pmid39901675, year = {2025}, author = {Sultana, A and Hussain, MS and Maqbool, M and Agrawal, M and Bisht, AS and Khurrana, N and Singh, G and Kumar, R}, title = {The Gut Connection: A Narrative Review on the In-depth Analysis of Gut Microbiota and Metabolites in Depression.}, journal = {Current reviews in clinical and experimental pharmacology}, volume = {}, number = {}, pages = {}, doi = {10.2174/0127724328332998250118182255}, pmid = {39901675}, issn = {2772-4336}, abstract = {Depression is a prevalent mood disorder with significant public health implications. Despite extensive research, its precise causes remain inadequately understood. Recently, interest has surged in the role of the gut microbiome and its metabolites in the pathophysiology of depression. This review aims to provide a comprehensive overview of the relationship between gut microbiota, its metabolites, and depression while exploring potential mechanisms influencing the efficacy of antidepressant medications. A narrative review methodology was employed, synthesizing recent studies utilizing a multi-omics approach. We examined alterations in gut microbiome composition and metabolite production in individuals diagnosed with depression, discussing the technical tools and methods commonly applied in this research area. The findings indicate that individuals with depression show significant alterations in gut microbiome composition, notably an imbalance in Firmicutes, Bacteroidetes, and Actinobacteria. Changes in metabolite production, including short-chain fatty acids, tryptophan, and bile acids, were also observed. Moreover, the review highlights that antidepressant medications may exert their therapeutic effects by modulating gut microbiota and its metabolites. This review emphasizes the intricate interplay between gut microbiota, its metabolites, and depression, revealing critical insights into the mechanisms underlying antidepressant efficacy. We recommend that future research focus on elucidating these interactions to develop innovative therapeutic strategies, potentially transforming the management of depression through microbiota-targeted approaches.}, }
@article {pmid39901379, year = {2025}, author = {Zhou, LS and Yang, Y and Mou, L and Xia, X and Liu, M and Xu, LJ and Liu, R and Liu, JP and Zhang, HY and Ao, XJ and Liu, CJ and Xiao, Q and Liu, SX}, title = {Melatonin Ameliorates Age-Related Sarcopenia via the Gut-Muscle Axis Mediated by Serum Lipopolysaccharide and Metabolites.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {16}, number = {1}, pages = {e13722}, doi = {10.1002/jcsm.13722}, pmid = {39901379}, issn = {2190-6009}, support = {21JR7RA372//Natural Science Foundation Project of Gansu Province, China/ ; CSTB2022NSCQ-MSX1666//Natural Science Foundation Project of Chongqing, China/ ; }, mesh = {Animals ; *Melatonin/pharmacology/therapeutic use ; *Sarcopenia/metabolism ; Mice ; *Lipopolysaccharides ; Male ; *Muscle, Skeletal/drug effects/metabolism ; Gastrointestinal Microbiome/drug effects ; Aging ; Disease Models, Animal ; Apoptosis/drug effects ; }, abstract = {BACKGROUND: Sarcopenia affects the quality of life and increases adverse outcomes in the elderly. However, as a potential safe and effective remedy to many age-related disorders, little is known about the protective effect of melatonin against sarcopenia, especially the underlying mechanisms of pathophysiology related to the gut-muscle axis.<br><br>METHODS: The young (4&#x2009;months) and old-aged (24&#x2009;months) wild-type C57BL/6J male mice were included in this study, of which the old-aged mice in the experimental group were treated with 10&#x2009;mg/kg/day of melatonin for 16&#x2009;weeks. After that, muscle strength, muscle mass and the cross-sectional area (CSA) of the gastrocnemius muscle fibres were measured. Then, the putative pathways, based on the data obtained from 16S rDNA sequencing of the gut microbiota, RNA sequencing of gastrocnemius muscle and serum untargeted metabolomics, were screened out by the integrated multiomics analysis and validated using immunohistochemistry, ELISA and TUNEL staining. C2C12 myoblasts were treated with LPS. Flow cytometric analysis and western blotting were applied to detect cell apoptosis and protein expressions of Tnfrsf12a and caspase8, respectively. In addition, the mediation analysis was carried out to infer the causal role of the microbiome in contributing to the skeletal muscle through metabolites.<br><br>RESULTS: Melatonin treatment ameliorated age-related declines in muscle strength (p&#x2009;<&#x2009;0.05), muscle mass (p&#x2009;<&#x2009;0.01) and CSA of the gastrocnemius muscle fibres (p&#x2009;<&#x2009;0.01), as well as changed the gut microbial composition (beta-diversity analysis; R&#x2009;=&#x2009;0.513, p&#x2009;=&#x2009;0.005). The integrated multiomics analysis implied two main mechanisms about the impact of melatonin-related modifications in the gut microbiota on sarcopenia. First, a lower serum lipopolysaccharide (LPS) level associated with the altered gut microbiota was observed in melatonin-treated mice (p&#x2009;<&#x2009;0.001) and was most relevant to the transcription level of Tnfrsf12a in skeletal muscle (R&#x2009;=&#x2009;0.926, p&#x2009;<&#x2009;0.001). Further bioinformatics analyses and in&#xa0;vitro experiments showed that LPS could contribute to skeletal muscle apoptosis by regulating the Tnfrsf12a/caspase-8 signalling pathway. Second, melatonin significantly altered serum metabolites (variable importance on projection (VIP)&#x2009;>&#x2009;1.5, p&#x2009;<&#x2009;0.05). Mediation models showed that changes in the gut microbiome also influenced skeletal muscle through these metabolites (27 linkages; BH-adjusted p&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: Our study revealed functional insights and a putative causality for the role of the gut-muscle axis in the mechanism of melatonin ameliorating age-related sarcopenia, namely, inhibition of the LPS-induced Tnfrsf12a/caspase-8 signalling pathway or serum metabolites as intermediates in the gut-muscle axis.}, }
@article {pmid39901297, year = {2025}, author = {Azouggagh, L and Ibáñez-Escriche, N and Martínez-Álvaro, M and Varona, L and Casellas, J and Negro, S and Casto-Rebollo, C}, title = {Characterization of microbiota signatures in Iberian pig strains using machine learning algorithms.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {13}, pmid = {39901297}, issn = {2524-4671}, support = {PID2020-114705RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-114705RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-114705RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-114705RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-114705RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-114705RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-114705RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, abstract = {BACKGROUND: There is a growing interest in uncovering the factors that shape microbiome composition due to its association with complex phenotypic traits in livestock. Host genetic variation is increasingly recognized as a major factor influencing the microbiome. The Iberian pig breed, known for its high-quality meat products, includes various strains with recognized genetic and phenotypic variability. However, despite the microbiome's known impact on pigs' productive phenotypes such as meat quality traits, comparative analyses of gut microbial composition across Iberian pig strains are lacking. This study aims to explore the gut microbiota of two Iberian pig strains, Entrepelado (n = 74) and Retinto (n = 63), and their reciprocal crosses (n = 100), using machine learning (ML) models to identify key microbial taxa relevant for distinguishing their genetic backgrounds, which holds potential application in the pig industry. Nine ML algorithms, including tree-based, kernel-based, probabilistic, and linear algorithms, were used.<br><br>RESULTS: Beta diversity analysis on 16&#xa0;S rRNA microbiome data revealed compositional divergence among genetic, age and batch groups. ML models exploring maternal, paternal and heterosis effects showed varying levels of classification performance, with the paternal effect scenario being the best, achieving a mean Area Under the ROC curve (AUROC) of 0.74 using the Catboost (CB) algorithm. However, the most genetically distant animals, the purebreds, were more easily discriminated using the ML models. The classification of the two Iberian strains reached the highest mean AUROC of 0.83 using Support Vector Machine (SVM) model. The most relevant genera in this classification performance were Acetitomaculum, Butyricicoccus and Limosilactobacillus. All of which exhibited a relevant differential abundance between purebred animals using a Bayesian linear model.<br><br>CONCLUSIONS: The study confirms variations in gut microbiota among Iberian pig strains and their crosses, influenced by genetic and non-genetic factors. ML models, particularly CB and RF, as well as SVM in certain scenarios, combined with a feature selection process, effectively classified genetic groups based on microbiome data and identified key microbial taxa. These taxa were linked to short-chain fatty acids production and lipid metabolism, suggesting microbial composition differences may contribute to variations in fat-related traits among Iberian genetic groups.}, }
@article {pmid39901227, year = {2025}, author = {Maestro-Gaitán, I and Redondo-Nieto, M and González-Bodí, S and Rodríguez-Casillas, L and Matías, J and Bolaños, L and Reguera, M}, title = {Insights into quinoa endophytes: core bacterial communities reveal high stability to water stress and genotypic variation.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {16}, pmid = {39901227}, issn = {2524-6372}, support = {CONSOLIDACI&#xd3;N 2022 (CNS2022-135167)//Agencia Estatal de Investigaci&#xf3;n/ ; CEX2020-000999-S-20-4//Agencia Estatal de Investigaci&#xf3;n/ ; PID2019-105748RA-I00 AEI/10.13039/501100011033//Agencia Estatal de Investigaci&#xf3;n/ ; }, abstract = {BACKGROUND: Plant endophytes, comprising non-pathogenic bacteria, fungi, and archaea, inhabit various plant parts, including roots, stems, leaves, and seeds. These microorganisms play a crucial role in plant development by enhancing germination, growth, and stress resilience. Seed endophytes, in particular, represent the most adapted and conserved segment of plant microbiota, significantly influencing the initial stages of plant growth and microbial community establishment. This study investigates the impact of environmental and genotypic factors on the endophytic communities of Chenopodium quinoa Willd. (quinoa), a crop notable for its adaptability and nutritional value.<br><br>RESULTS: We aimed to characterize the core endophytic communities in quinoa seeds and roots from two distinct genotypes under well-watered (WW) and water-deficit (WD) conditions, utilizing various soil infusions as inoculants to explore potential changes in these endophytes. Our findings reveal distinct changes with quinoa seeds exhibiting a high degree of conservation in their endophytic microbiome, even between maternal and offspring seeds, with specific bacterial taxa showing only minor differences. Tissue specificity emerged as a key factor, with seeds maintaining a stable microbial community, while roots exhibited more pronounced shifts, highlighting the tissue-dependent patterns of microbial enrichment.<br><br>CONCLUSIONS: The results highlight the stability and conservation of endophytic communities in quinoa seeds, even under varying water conditions and across different genotypes, emphasizing the role of tissue specificity in shaping microbial associations. These findings suggest that quinoa-associated endophytes, particularly those conserved in seeds, may play a crucial role in enhancing drought resilience. Understanding the dynamics of plant-microbe interactions in quinoa is vital for developing stress-resilient crop varieties, supporting sustainable agricultural practices, and ensuring food security in the face of climate change and environmental challenges.}, }
@article {pmid39901058, year = {2025}, author = {Richardson, M and Zhao, S and Lin, L and Sheth, RU and Qu, Y and Lee, J and Moody, T and Ricaurte, D and Huang, Y and Velez-Cortes, F and Urtecho, G and Wang, HH}, title = {SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.}, journal = {Nature microbiology}, volume = {10}, number = {2}, pages = {527-540}, pmid = {39901058}, issn = {2058-5276}, support = {MCB-2025515//National Science Foundation (NSF)/ ; DGE-1644869//National Science Foundation (NSF)/ ; DGE-1644869//National Science Foundation (NSF)/ ; DGE-1644869//National Science Foundation (NSF)/ ; 2R01AI132403, 1R01DK118044, 1R01EB031935, 1R21AI146817//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; N00014-18-1-2237//United States Department of Defense | United States Navy | ONR | Office of Naval Research Global (ONR Global)/ ; 1016691//Burroughs Wellcome Fund (BWF)/ ; HR0011-23-2-0001//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; W911NF-22-2-0210//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; High-Throughput Nucleotide Sequencing/methods ; Feces/microbiology ; Inulin/metabolism ; RNA, Ribosomal, 16S/genetics ; Metagenome ; }, abstract = {The local arrangement of microbes can profoundly impact community assembly, function and stability. However, our understanding of the spatial organization of the human gut microbiome at the micron scale is limited. Here we describe a high-throughput and streamlined method called Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) to capture spatial co-localization in a complex microbial consortium. The method obtains microbial composition of micron-scale subcommunities through split-and-pool barcoding. SAMPL-seq analysis of the healthy human gut microbiome identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These co-localized microbes organize into spatially distinct groups or 'spatial hubs' dominated by Bacteroidaceae, Ruminococcaceae and Lachnospiraceae families. Using inulin as a dietary perturbation, we observed reversible spatial rearrangement of the gut microbiome where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock insights into microbiomes at the micron scale.}, }
@article {pmid39900806, year = {2025}, author = {Stanton, C and Koc, F and Kelleher, S and Ross, P and Magnier, C and McMahon, CJ}, title = {Rebuttal to Gut Microbiome in Children with Congenital Heart Disease After Cardiopulmonary Bypass Surgery (GuMiBear Study).}, journal = {Pediatric cardiology}, volume = {}, number = {}, pages = {}, pmid = {39900806}, issn = {1432-1971}, }
@article {pmid39900569, year = {2025}, author = {Priest, T and Oldenburg, E and Popa, O and Dede, B and Metfies, K and von Appen, WJ and Torres-Valdés, S and Bienhold, C and Fuchs, BM and Amann, R and Boetius, A and Wietz, M}, title = {Seasonal recurrence and modular assembly of an Arctic pelagic marine microbiome.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1326}, pmid = {39900569}, issn = {2041-1723}, mesh = {Arctic Regions ; *Seasons ; *Microbiota/genetics ; *Seawater/microbiology ; *Oceans and Seas ; Metagenomics/methods ; Bacteria/genetics/classification/metabolism ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; DNA Barcoding, Taxonomic ; Metagenome ; Phylogeny ; }, abstract = {Deciphering how microbial communities are shaped by environmental variability is fundamental for understanding the structure and function of ocean ecosystems. While seasonal environmental gradients have been shown to structure the taxonomic dynamics of microbiomes over time, little is known about their impact on functional dynamics and the coupling between taxonomy and function. Here, we demonstrate annually recurrent, seasonal structuring of taxonomic and functional dynamics in a pelagic Arctic Ocean microbiome by combining autonomous samplers and in situ sensors with long-read metagenomics and SSU ribosomal metabarcoding. Specifically, we identified five temporal microbiome modules whose succession within each annual cycle represents a transition across different ecological states. For instance, Cand. Nitrosopumilus, Syndiniales, and the machinery to oxidise ammonia and reduce nitrite are signatures of early polar night, while late summer is characterised by Amylibacter and sulfur compound metabolism. Leveraging metatranscriptomes from Tara Oceans, we also demonstrate the consistency in functional dynamics across the wider Arctic Ocean during similar temporal periods. Furthermore, the structuring of genetic diversity within functions over time indicates that environmental selection pressure acts heterogeneously on microbiomes across seasons. By integrating taxonomic, functional and environmental information, our study provides fundamental insights into how microbiomes are structured under pronounced seasonal changes in understudied, yet rapidly changing polar marine ecosystems.}, }
@article {pmid39900290, year = {2025}, author = {Ward, CP and Perelman, D and Durand, LR and Robinson, JL and Cunanan, KM and Sudakaran, S and Sabetan, R and Madrigal-Moeller, MJ and Dant, C and Sonnenburg, ED and Sonnenburg, JL and Gardner, CD}, title = {Effects of fermented and fiber-rich foods on maternal &amp; offspring microbiome study (FeFiFo-MOMS) - Study design and methods.}, journal = {Contemporary clinical trials}, volume = {}, number = {}, pages = {107834}, doi = {10.1016/j.cct.2025.107834}, pmid = {39900290}, issn = {1559-2030}, abstract = {BACKGROUND: Recent research underscores the crucial role of the gut microbiota in human health, particularly during states of altered homeostasis, including pregnancy. Additionally, it is not well understood how dietary changes during pregnancy affect the development of microbiomes of both mother and child.<br><br>METHODS: Here, we describe the study design and methods for our randomized controlled trial, the fermented and fiber-rich foods on maternal and offspring microbiome study (FeFiFo-MOMS). We enrolled 135 women during early pregnancy, randomizing them to one of four diet arms: increased fiber, increased fermented foods, increase in both, and no dietary intervention as a comparator arm. Samples were collected across pregnancy continuing to 18&#x202f;months post-birth for clinical, microbiome, and immune marker analysis.<br><br>RESULTS: Our trial design intended to investigate the effects of dietary interventions-specifically, increased intake of high-fiber and fermented foods-on maternal gut microbiota diversity and its subsequent transmission to infants.<br><br>CONCLUSION: The FeFiFo-MOMS trial was designed to provide valuable insights into the modifiable dietary factors that could influence maternal and infant health through microbiota-mediated mechanisms and examine the broader implications of diet on pregnant mothers' and infants' health and disease.<br><br>CLINICALTRIALS: govID:NCT05123612.}, }
@article {pmid39406381, year = {2025}, author = {Sharma, SP and Suk, KT}, title = {Correspondence to editorial on: "Gut microbiome and metabolome signatures in liver cirrhosis-related complications".}, journal = {Clinical and molecular hepatology}, volume = {31}, number = {1}, pages = {e74-e77}, doi = {10.3350/cmh.2024.0872}, pmid = {39406381}, issn = {2287-285X}, }
@article {pmid39900146, year = {2025}, author = {Antoine, D and Tao, J and Singh, S and Singh, PK and Marin, BG and Roy, S}, title = {Neonatal exposure to morphine results in prolonged pain hypersensitivity during adolescence, driven by gut microbial dysbiosis and gut-brain axis-mediated inflammation.}, journal = {Brain, behavior, and immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.bbi.2025.01.021}, pmid = {39900146}, issn = {1090-2139}, abstract = {Opioids, such as morphine, are used in the Neonatal Intensive Care Unit (NICU) for pain relief in neonates. However, the available evidence concerning the benefits and harms of opioid therapy in neonates remains limited. While previous studies have reported that neonatal morphine exposure (NME) results in long-term heightened pain sensitivity, the underlying mechanisms are not well understood. This study proposes that dysbiosis of the gut microbiome contributes to pain hypersensitivity following NME. Using an adolescent female murine model, pain sensitivity was evaluated using tail flick and hot plate assays for thermal pain and the Von Frey assay for mechanical pain. Gut microbiome composition was assessed using 16 s rRNA sequencing, while transcriptomic changes in midbrain samples were investigated using bulk RNA-sequencing. NME induced prolonged hypersensitivity to thermal and mechanical pain in adolescence, accompanied by persistent gut microbial dysbiosis and sustained systemic inflammation, characterized by elevated circulating cytokine levels (e.g., IL-1α, IL-12p70, IFN-γ, IL-10). Transplantation of the microbiome from NME adolescents recapitulated pain hypersensitivity in naïve adolescent mice, while neonatal probiotic intervention with Bifidobacterium infantis (B. infantis) reversed the hypersensitivity by preventing gut dysbiosis and associated systemic inflammation. Furthermore, transcriptomic analysis of the midbrain tissues revealed that NME upregulated several genes and key signaling pathways, including those related to immune activation and excitatory signaling, which were notably mitigated by neonatal B. infantis administration. Together, these findings highlight the critical role of the gut-brain axis in modulating pain sensitivity and suggest that targeting the gut microbiome offers a promising therapeutic strategy for managing neurobiological disorders following early opioid exposure.}, }
@article {pmid39900089, year = {2025}, author = {Fretheim, H and Barua, I and Bakland, G and Dhainaut, A and Halse, AK and Carstens, MN and Didriksen, H and Midtvedt, &#xd8; and Lundin, KEA and Aabakken, L and Sarna, VK and Zaré, HK and Khanna, D and Distler, O and Midtvedt, T and Bækkevold, ES and Olsen, IC and Domanska, D and Pesonen, ME and Molberg, &#xd8; and Hoffmann-Vold, AM}, title = {Faecal microbiota transplantation in patients with systemic sclerosis and lower gastrointestinal tract symptoms in Norway (ReSScue): a phase 2, randomised, double-blind, placebo-controlled trial.}, journal = {The Lancet. Rheumatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2665-9913(24)00334-5}, pmid = {39900089}, issn = {2665-9913}, abstract = {BACKGROUND: Gastrointestinal tract involvement is highly prevalent in systemic sclerosis, with few treatment options. We assessed the efficacy and safety of faecal microbiota transplantation using standardised anaerobic cultivated human intestinal microbiome (ACHIM) as a novel treatment option for patients with systemic sclerosis and symptomatic lower gastrointestinal tract involvement.<br><br>METHODS: In this phase 2, randomised, double-blind, placebo-controlled trial done at four university hospitals in Norway, we enrolled adults aged 18-85 years with systemic sclerosis and moderate-to-severe lower gastrointestinal tract symptoms (bloating or diarrhoea). Participants were randomly assigned 1:1 to intestinal infusions of placebo or ACHIM at weeks 0 and 2, stratified by worst symptom (bloating or diarrhoea). The primary endpoint was change in worst lower gastrointestinal tract symptom (bloating or diarrhoea) from week 0 to week 12, measured using the University of California Los Angeles Scleroderma Clinical Trial Consortium Gastrointestinal Tract 2.0 scoring system in the intention-to-treat population. Safety was assessed at weeks 0, 2, 4, 6, and 12 in all participants who received at least one infusion. A person with lived experience of systemic sclerosis was involved in the study planning and conduct. This trial was registered at ClinicalTrials.gov, NCT04300426.<br><br>FINDINGS: Between Sept 24, 2020, and Jan 14, 2022, 67 participants were enrolled and randomly allocated to placebo (n=34) or ACHIM (n=33). Mean age was 58&#xb7;91 years (SD 11&#xb7;59). 62 (93%) of 67 participants were women, five (7%) were men, and 50 (75%) were anti-centromere antibody positive. Change in worst lower gastrointestinal tract symptom from week 0 to week 12 did not differ between participants who received ACHIM (-0&#xb7;13, 95% CI -0&#xb7;37 to 0&#xb7;11) and participants who received placebo (-0&#xb7;33, -0&#xb7;57 to -0&#xb7;09; average marginal effect 0&#xb7;20, 95% CI -0&#xb7;12 to 0&#xb7;52; p=0&#xb7;22). Adverse events, mostly mild and short-lived gastrointestinal tract symptoms, were reported by 16 (48%) of 33 participants in the ACHIM group and 19 (56%) of 34 in the placebo group. During gastroscopy, one participant had a duodenal perforation.<br><br>INTERPRETATION: Faecal microbiota transplantation with ACHIM was well tolerated in participants with systemic sclerosis but did not result in an improvement in lower gastrointestinal tract symptoms.<br><br>FUNDING: KLINBEFORSK.<br><br>TRANSLATION: For the Norwegian translation of the abstract see Supplementary Materials section.}, }
@article {pmid39900010, year = {2025}, author = {Faust, KB and Lupatsii, M and Römer, F and Graspeuntner, S and Waschina, S and Zimmermann, S and Humberg, A and Fortmann, MI and Hanke, K and Böckenholt, K and Dirks, J and Silwedel, C and Rupp, J and Herting, E and Göpel, W and Härtel, C}, title = {Use of Macrogol to accelerate feeding advancement in extremely preterm infants.}, journal = {Neonatology}, volume = {}, number = {}, pages = {1-19}, doi = {10.1159/000543050}, pmid = {39900010}, issn = {1661-7819}, abstract = {Introduction Delayed enteral nutrition is associated with a higher risk for adverse outcomes in extremely preterm infants. Limited evidence exists on therapeutic options to support meconium evacuation and increase gastrointestinal motility. The aim of this study was to determine the effect of macrogol on feeding tolerance and microbiome establishment in preterm infants < 27 weeks of gestation. Methods We investigated the impact of early macrogol administration in two observational cohort studies: the multi-center German-Neonatal-Network (GNN) study comparing extremely preterm infants born in Neonatal intensive care units (NICUs) using macrogol in the first week of life in >30% of their infants as compared to the remaining units, and the single center Immunoregulation-of-the-Newborn (IRoN) study including gut microbiome assessment of infants born before and after implementation of macrogol use in this NICU. Results In the GNN study cohort including 4290 infants, advancement to full enteral feedings was significantly faster in macrogol-using NICUs compared to the remaining NICUs (median/SD: 14/16.5 vs. 16/16.7days, p=0.001). Risk for short-term outcomes such as sepsis or abdominal complications was not elevated in units with regular use of macrogol. In the IRoN cohort (n=68), macrogol treated infants had a shorter time to reach full enteral feeding (median/SD: Macrogol 12/4.8, Control 16/6.6days, p=0.004). Higher Bifidobacterium longum abundance in the gut microbiome correlated with acceleration to full enteral nutrition. Conclusion Our observational data suggests that early off-label use of macrogol may support feeding advancement in highly vulnerable babies. These data provide a basis for a randomized controlled trial.}, }
@article {pmid39899987, year = {2024}, author = {Tluway, F and Agongo, G and Baloyi, V and Boua, PR and Kisiangani, I and Lingani, M and Mashaba, RG and Mohamed, SF and Nonterah, EA and Ntimana, CB and Rouamba, T and Mathema, T and Madala, S and Maghini, DG and Choudhury, A and Crowther, NJ and Hazelhurst, S and Sengupta, D and Ansah, P and Choma, SSR and Debpuur, C and Gómez-Olivé, FX and Kahn, K and Micklesfield, LK and Norris, SA and Oduro, AR and Sorgho, H and Tindana, P and Tinto, H and Tollman, S and Wade, A and Ramsay, M and , }, title = {Cohort Profile: Africa Wits-INDEPTH partnership for Genomic studies (AWI-Gen) in four sub-Saharan African countries.}, journal = {International journal of epidemiology}, volume = {54}, number = {1}, pages = {}, doi = {10.1093/ije/dyae173}, pmid = {39899987}, issn = {1464-3685}, support = {/HG/NHGRI NIH HHS/United States ; }, }
@article {pmid39899882, year = {2025}, author = {Mansoori Moghadam, Z and Zhao, B and Raynaud, C and Strohmeier, V and Neuber, J and Lösslein, AK and Qureshi, S and Gres, V and Ziegelbauer, T and Baasch, S and Schell, C and Warnatz, K and Inohara, N and Nunez, G and Clavel, T and Rosshart, SP and Kolter, J and Henneke, P}, title = {Reactive oxygen species regulate early development of the intestinal macrophage-microbiome interface.}, journal = {Blood}, volume = {}, number = {}, pages = {}, doi = {10.1182/blood.2024025240}, pmid = {39899882}, issn = {1528-0020}, abstract = {Controlled development of cellular intestinal immunity in the face of dynamic microbiota emergence constitutes a major challenge in very early life, and a bottleneck for sustained growth and well-being. Early-onset inflammatory bowel disease (IBD) represents an extreme disturbance of intestinal immunity. It is a hallmark, and often the first manifestation of chronic granulomatous disease (CGD), caused by inborn defects in the NADPH oxidase NOX2 and thus the failure to produce reactive oxygen species (ROS) in phagocytes. However, in contrast to the known role of ROS in antimicrobial defense, the mechanisms underlying intestinal immunopathology in CGD remain enigmatic. This is partly due to the incomplete recapitulation of the CGD-IBD phenotype in established mouse models. We found that mice deficient in the NOX2 subunits p47phox or gp91phox showed similar baseline disturbances in lamina-propria macrophage differentiation, but they responded differently to chemically-induced colitis. Although p47phox and gp91phox-deficient mice differed markedly in microbiota composition, cross-fostering failed to equalize discrepant IBD phenotypes and microbiota, pointing at extremely early and functionally important microbiota fixation under specific pathogen-free housing conditions. In contrast, neonatal acquisition of a complex wild-mouse-microbiota triggered spontaneous IBD, granuloma formation and secondary sepsis with intestinal pathogens in both NOX2-deficient mouse lines, which was in part dependent on NOX2 in intestinal macrophages. Thus, in experimental CGD, the aberrant development of tissue immunity and the microbiota are closely intertwined immediately after birth.}, }
@article {pmid39899646, year = {2025}, author = {de Oliveira, DA and Oliveira, R and Braga, BV and Straker, LC and Rodrigues, LS and Bueno, LL and Fujiwara, RT and Lopes-Torres, EJ}, title = {Experimental trichuriasis: Changes in the immune response and bacterial translocation during acute phase development illustrated with 3D model animation.}, journal = {PLoS neglected tropical diseases}, volume = {19}, number = {2}, pages = {e0012841}, doi = {10.1371/journal.pntd.0012841}, pmid = {39899646}, issn = {1935-2735}, abstract = {Trichuriasis, a well-known type of soil-transmitted helminthiasis, is a neglected gastrointestinal nematode disease predominantly affecting children in tropical regions and is caused by Trichuris trichiura. The potential zoonotic transmission of this disease is indicated by its presence in nonhuman primates. Chronic infection leads to mucosal damage, bacterial translocation, and intense inflammatory infiltration; however, the progression of these processes remains poorly understood. This study tracks the acute phase of experimental trichuriasis, providing detailed insights into nematode tissue migration stages, inflammatory infiltration, cytokine production, and 2D/3D imaging of the bacterial translocation process. We showed a mixed immune response (Th1, Th2, and Th17) initiated by larval-induced lesions in the intestine tissue and modulated by L4 larvae and adult worms in the cecum, with systemic changes observed in the mesenteric lymph nodes, peritoneal macrophages, and spleen. Despite the disruption of the intestinal mucosa within the first 10 days post-infection (d.p.i.), bacterial invasion becomes evident only after the development of the nematode into the L3 larval stage (17 d.p.i.), intensifying with lesions caused by the L4 larvae (22 d.p.i.) and adult worms (35 d.p.i.). Our multidimensional approach, which incorporates microscopy tools, micro-CT, physiological evaluations, tissue/organ assessments, and immunological parameters, demonstrates the ability of larvae to breach the intestinal mucosa, further indicating the timing of extensive bacterial infiltration. Additionally, a 3D animation illustrates how adult worm attachment mechanisms may facilitate bacterial translocation. This study provides significant insights into the immunological and pathological mechanisms of trichuriasis progression, highlighting the complex interplay among host immune responses, the gut microbiome, and parasite survival strategies, all of which are crucial aspects for future therapeutic development.}, }
@article {pmid39899616, year = {2025}, author = {Oyono, MG and Kenmoe, S and Ebogo Belobo, JT and Mbah Ntepe, LJ and Kameni, M and Kamguia, LM and Mpotje, T and Nono, JK}, title = {Diagnostic, prognostic, and therapeutic potentials of gut microbiome profiling in human schistosomiasis: A comprehensive systematic review.}, journal = {PLoS neglected tropical diseases}, volume = {19}, number = {2}, pages = {e0012844}, doi = {10.1371/journal.pntd.0012844}, pmid = {39899616}, issn = {1935-2735}, abstract = {BACKGROUND: Several studies have highlighted alteration in the gut microbiome associated with the onset and progression of diseases. Recognizing the potential of gut microbiota as biomarkers, this systematic review seeks to synthesize current data on the intricate relationship between the host gut microbiome profiles and their usefulness for the development of diagnostic, prognostic and therapeutic approaches to control human schistosomiasis.<br><br>METHODS: A systematic literature review was carried out by searching for relevant studies published until date, that is May 2024, using Medline, Embase, Global Health, Web of Science, and Global Index Medicus databases. The keywords used to select articles were "Gut microbiome", "Gut Microbiota", "Schistosomiasis", "Bilharziasis ", and "Human". Extracted data were analysed qualitatively from the selected articles.<br><br>RESULTS: Of the 885 articles retrieved and screened, only 13 (1.47%) met the inclusion criteria and were included in this review. Of the included studies, 6 (46.2%) explored alterations of gut microbiome in schistosome-infected patients, 4 (30.7%) in patients with liver pathologies, and 3 (23.1%) in patients treated with praziquantel. Bacteria from the genera Bacteroides, Faecalibacterium, Blautia and Megasphaera were associated with S. japonicum and S. haematobium infection in school-aged children, whereas infection with S. mansoni rather associated with Klebsiella and Enterobacter. The gut microbiota signature in patient with schistosomiasis-induced liver pathology was reported only for S. japonicum, and the genus Prevotella appeared as a non-invasive biomarker of S. japonicum-associated liver fibrosis. For S. mansoni-infected school-aged children, it further appeared that the treatment outcome following praziquantel administration associated with the abundance in the gut microbiome of bacteria from the classes Fusobacteriales, Rickettsiales and Neisseriales.<br><br>CONCLUSION: The host gut microbiome appears to be a valuable, non-invasive, but still poorly utilized, source of host biomarkers potentially informative for better diagnosing, prognosing and treating schistosomiasis. Further studies are therefore needed to comprehensively define such gut microbial biomarkers of human schistosomiasis and catalyse the informed development of gut microbiome-based tools of schistosomiasis control.}, }
@article {pmid39898934, year = {2025}, author = {Chen, J and Guo, S and Shi, S}, title = {Effects of water acidifiers on the growth performance, intestinal function and gut microflora in broilers.}, journal = {British poultry science}, volume = {}, number = {}, pages = {1-8}, doi = {10.1080/00071668.2025.2454958}, pmid = {39898934}, issn = {1466-1799}, abstract = {1. This study evaluated the effect of acidified drinking water on the gastrointestinal function and intestinal health of broilers.2. A total of 630 one-day-old male broilers (Arbor Acre) were randomly assigned to one of three treatment groups: drinking water treatment (CON), drinking water + 0.5 ml Selko pH®/L (Selko pH), or + 0.85 ml Forticoat®/L (Forticoat) treated groups. Performance data, gut and digesta samples were collected from the broilers at the age of 21 and 42 d.3. The results showed that acidifying drinking water had no significant effect on body weight or average daily gain (ADG). However, addition of Forticoat significantly increased (p < 0.05) feed conversion ratio (FCR) throughout the experimental period and significantly increased (p < 0.05) pepsin activity on d 21. The Selko pH supplemented drinking water significantly increased (p < 0.05) the relative length of the duodenum and jejunum on d 21. The relative length of the jejunum and caecum on d 42 compared to birds receiving CON. The addition of the Forticoat to drinking water significantly increased (p < 0.05) the relative length of the jejunum and caecum on d 42 than for samples from birds in the CON group. In the caecal chyme, abundance of Blautia, Bifidobasterium, Faecalibacterium, Limosilactobacillus and Akkermania spp. on d 21 were significantly higher (p < 0.05) in the caecum of birds receiving Selko pH than those in CON group and the number of Escherichia Shigella in Selko pH and Forticoat group were significantly lower (p < 0.05).4. Overall, adding Seiko pH and Forticoat to drinking water improved pepsin activity, reduced the number of caecal pathogens, increased the number of beneficial bacteria and improved intestinal health in broilers.}, }
@article {pmid39898899, year = {2025}, author = {Yu, J and Wang, Y and Wei, W and Wang, X}, title = {A review on lipid inclusion in preterm formula: Characteristics, nutritional support, challenges, and future perspectives.}, journal = {Comprehensive reviews in food science and food safety}, volume = {24}, number = {2}, pages = {e70099}, doi = {10.1111/1541-4337.70099}, pmid = {39898899}, issn = {1541-4337}, support = {2021YFD2100700//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Infant Formula/chemistry ; *Infant, Premature/growth &amp; development ; Infant, Newborn ; *Lipids/chemistry ; *Milk, Human/chemistry ; Infant Nutritional Physiological Phenomena ; Nutritional Support/methods ; }, abstract = {The lack of nutrient accumulation during the last trimester and the physiological immaturity at birth make nutrition for preterm infants a significant challenge. Lipids are essential for preterm infant growth, neurodevelopment, immune function, and intestinal health. However, the inclusion of novel lipids in preterm formulas has rarely been discussed. This study discusses specific lipid recommendations for preterm infants according to authoritative legislation based on their physiological characteristics. The gaps in lipid composition, such as fatty acids, triacylglycerols, and complex lipids, between preterm formulas and human milk have been summarized. The focus of this study is mainly on the vital roles of lipids in nutritional support, including long-chain polyunsaturated fatty acids, structural lipids, milk fat global membrane ingredients, and other minor components. These lipids have potential applications in preterm formulas for improving lipid absorption, regulating lipid metabolism, and protecting against intestinal inflammation. The lipidome and microbiome can be used to provide adequately powered evidence of the effects of lipids. This study proposes nutritional strategies for preterm infants and suggests approaches to enhance their lipid quality in preterm formula.}, }
@article {pmid39898649, year = {2025}, author = {Taylor, BC and Weldon, KC and Ellis, RJ and Franklin, D and Groth, T and Gentry, EC and Tripathi, A and McDonald, D and Humphrey, G and Bryant, M and Toronczak, J and Schwartz, T and Oliveira, MF and Heaton, R and Grant, I and Gianella, S and Letendre, S and Swafford, A and Dorrestein, PC and Knight, R}, title = {Correction for Taylor et al., "Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome".}, journal = {mSystems}, volume = {}, number = {}, pages = {e0130524}, doi = {10.1128/msystems.01305-24}, pmid = {39898649}, issn = {2379-5077}, }
@article {pmid39898646, year = {2025}, author = {Zhao, Y and Ferri, JT and White, JR and Schollenberger, MD and Peloza, K and Sears, CL and Lipson, EJ and Shaikh, FY}, title = {Gut microbiome features associate with immune checkpoint inhibitor response in individuals with non-melanoma skin cancers: an exploratory study.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0255924}, doi = {10.1128/spectrum.02559-24}, pmid = {39898646}, issn = {2165-0497}, abstract = {Immune checkpoint inhibitor (ICI) therapy has yielded revolutionary outcomes among some individuals with skin cancer, but a large percentage of individuals do not benefit from these treatments. The gut microbiota is hypothesized to impact ICI therapy outcomes. However, data on ICI therapy, gut microbiota, and non-melanoma skin cancers are limited. To examine the association of gut microbiota structure and function with non-melanoma skin cancer ICI outcomes, we performed 16S rRNA V1-V2 gene amplicon sequencing of 68 fecal samples collected longitudinally from individuals with basal cell carcinoma (n = 5), Merkel cell carcinoma (n = 5), or cutaneous squamous cell carcinoma (CSCC, n = 11), followed by tumor-dependent differential analyses of bacterial composition and fecal sample analysis by untargeted metabolomics. Across all tumor types, we identified 10 differential bacterial genera between responders (R) or non-responders (NR) to ICI therapy. Among individuals with CSCC, we identified 10 genera and 20 species that differentiated between R and NR and yielded 8 pathways enriched in NR and 12 pathways enriched in R by predicted functional pathway analyses. Untargeted fecal metabolomics to examine putative gut microbiota metabolites associated with CSCC ICI R/NR identified nine KEGG pathways associated with ICI efficacy. In summary, this exploratory study suggests gut microbiota features that are associated with ICI efficacy in individuals with non-melanoma skin cancers and highlights the need for larger studies to validate the results.IMPORTANCEPrior studies examining associations between ICI efficacy and the gut microbiome have focused primarily on individuals with melanoma, for whom ICI therapy was first approved. Meanwhile, data regarding microbiome features associated with ICI responses in individuals with non-melanoma skin cancers (NMSCs) have remained limited. This initial fecal microbiota examination of individuals with NMSCs suggests that larger-scale studies to extend and validate our findings may yield predictive or prognostic biomarkers for individuals with NMSC receiving ICI with potential to provide insight to complementary, effective therapeutic interventions through microbiota modification.}, }
@article {pmid39898356, year = {2025}, author = {Duan, C and Sheng, J and Ma, X}, title = {Innovative approaches in colorectal cancer screening: advances in detection methods and the role of artificial intelligence.}, journal = {Therapeutic advances in gastroenterology}, volume = {18}, number = {}, pages = {17562848251314829}, pmid = {39898356}, issn = {1756-283X}, abstract = {Colorectal cancer (CRC) is the third most prevalent cancer globally and poses a significant health threat, making early detection crucial. This review paper explored emerging detection methods for early screening of CRC, including gut microbiota, metabolites, genetic markers, and artificial intelligence (AI)-based technologies. Current screening methods have their respective advantages and limitations, particularly in detecting precursors. First, the importance of the gut microbiome in CRC progression is discussed, highlighting how specific microbial alterations can serve as biomarkers for early detection, potentially enhancing diagnostic accuracy when combined with traditional screening methods. Next, research on metabolic reprogramming illustrates the relationship between metabolic changes and CRC, with studies developing metabolite-based detection models that show good sensitivity for early diagnosis. In terms of genetic markers, methylated DNA markers like SEPTIN9 have demonstrated high sensitivity, although further validation across diverse populations is necessary. Lastly, AI technology has shown immense potential in improving adenoma detection rates, significantly enhancing the quality of colonoscopic examinations through image recognition techniques. This review aims to provide a comprehensive perspective on new strategies for CRC screening, emphasizing the potential of noninvasive detection technologies and the prospects of AI and genomics in clinical applications. Despite several challenges, this review advocates for future large-scale prospective studies to validate the effectiveness and cost-effectiveness of these new screening methods while promoting the implementation of screening protocols tailored to individual characteristics.}, }
@article {pmid39898328, year = {2025}, author = {Thomsen, AR and Monroy Ordonez, EB and Henke, M and Luka, B and Sahlmann, J and Schäfer, H and Verma, V and Schlueter, N and Grosu, AL and Sprave, T}, title = {Evaluating the radiosensitivity of the oral microbiome to predict radiation-induced mucositis in head and neck cancer patients: A prospective trial.}, journal = {Clinical and translational radiation oncology}, volume = {51}, number = {}, pages = {100915}, pmid = {39898328}, issn = {2405-6308}, abstract = {BACKGROUND: Predicting the occurrence and/or severity of oral mucositis (OM) before commencing radiotherapy (RT) remains very difficult. The aim of this prospective trial was to investigate whether the ex-vivo radiation sensitivity of oral keratinocytes from head and neck (H&amp;N) cancer patients correlates with severe OM.<br><br>METHODS: Oral microbiopsies of healthy gingival mucosa were collected from 63H&amp;N cancer patients undergoing (chemo)RT, of which 58 samples were useable. Keratinocytes from these microbiopsies underwent ex-vivo proliferation, irradiation, and subsequently the cell spreading assay. Tubes with the cell suspension were placed within the irradiation chamber of a [137]Cs Gammacell 40 Exactor (Best Theratronics, Canada) and exposed to 0, 2, 4, 6, or 8&#xa0;Gy at a dose rate of 0.63&#xa0;Gy min[-1]. Cell suspension was then immediately pipetted into custom-made polydimethylsiloxane (PDMS) rings.The effect of demographic and clinical parameters on the cell spreading assay were also analyzed. Systematic clinical recording of OM was conducted twice a week by a specially trained examiner.<br><br>RESULTS: Most patients had node-positive disease and cancer of the oropharynx or oral cavity. The vast majority of patients received adjuvant RT and concurrent chemotherapy. Overall, 34 (58.6&#xa0;%) participants developed grade 3 OM after a median dose of 32&#xa0;Gy. No patient experienced a grade&#xa0;&#x2265;&#xa0;4 event. There was a correlation between the cell spreading assay area and grade 3 OM (p&#xa0;<&#xa0;0.05), equivalent to approximately 0.5&#xa0;Gy dose. Demographic and clinical parameters had no significant impact on the cell spreading assay (p&#xa0;>&#xa0;0.05 for all).<br><br>CONCLUSIONS: It is necessary to establish reliable predictors of severe OM before treatment in H&amp;N cancer to allow early management of treatment-related sequelae. This prospective trial illustrates that the intrinsic ex-vivo radiosensitivity of oral keratinocytes could be correlated with RT-induced OM in patients with H&amp;N cancer. This novel predictor requires validation in larger prospective cohorts.}, }
@article {pmid39898315, year = {2025}, author = {Walker, JR and Bente, DA and Burch, MT and Cerqueira, FM and Ren, P and Labonté, JM}, title = {Molecular assessment of oyster microbiomes and viromes reveals their potential as pathogen and ecological sentinels.}, journal = {One health (Amsterdam, Netherlands)}, volume = {20}, number = {}, pages = {100973}, pmid = {39898315}, issn = {2352-7714}, abstract = {Oyster aquaculture world-wide is a booming industry that can provide many benefits to coastal habitats, including economic, ecosystem-level, and cultural benefits. Oysters present several risks for human consumption, including transmission of parasites, and bacterial and viral pathogens. Oyster microbiomes are well-defined, but their connection to the incidence of pathogens, humans or others, is unclear. Furthermore, viruses associated with oysters are largely unknown, and their connection to humans, animals, and ecosystem health has not been explored. Here, we employed a One Health framework and modern molecular techniques, including 16S rRNA amplicon and metagenomic sequencing, to identify links between changes in the microbial and viral communities associated with oysters and the incidence of pathogens detected in oyster tissues and their surrounding environments. In addition, we adapted the BioFire® FilmArray®, commonly used in hospitals, to determine the presence of human pathogens within the sampled oysters. We detected known human pathogens in 50 % of the oysters tested. Within the genomic datasets, we noted that pathogens of humans, animals, and plants in oysters were shared with the nearby water and sediments, suggesting a sink-source dynamic between the oysters and their surroundings. 16S rRNA gene analysis revealed that while oysters share common microbial constituents with their surrounding environments, they enrich for certain bacteria such as Mycoplasmatales, Fusobacteriales, and Spirochaetales. On the contrary, we found that oyster viromes harbored the same viruses in near equal relative abundances as their surrounding environments. Our results show how oysters could be used not only to determine the risk of human pathogens within coastal estuaries but also how oyster viruses could be used as ecosystem-level sentinels.}, }
@article {pmid39897886, year = {2025}, author = {Qayyum, H and Talib, MS and Ali, A and Kayani, MUR}, title = {Evaluating the potential of assembler-binner combinations in recovering low-abundance and strain-resolved genomes from human metagenomes.}, journal = {Heliyon}, volume = {11}, number = {2}, pages = {e41938}, pmid = {39897886}, issn = {2405-8440}, abstract = {Human-associated microbial communities are a complex mixture of bacterial species and diverse strains prevalent at varying abundances. Due to the inherent limitations of metagenomic assemblers and genome binning tools in recovering low-abundance species (<1 %) and strains, we lack comprehensive insight into these communities. Although many bioinformatics approaches are available for recovering metagenome-assembled genomes, their effectiveness in recovering low-abundance species and strains is often questioned. Moreover, each tool has its trade-offs, making selecting the right tools challenging. In this study, we investigated the combinatory effect of various assemblers and binning tools on the recovery of low-abundance species and strain-resolved genomes from real and simulated human metagenomes. We evaluated the performance of nine combinations of metagenome assemblers and genome binning tools for their potential to recover genomes of useable quality. Our results revealed that the metaSPAdes-MetaBAT2 combination is highly effective in recovering low-abundance species, while MEGAHIT-MetaBAT2 excels in recovering strain-resolved genomes. These findings highlight the significant variation in the performance of different combinations, even when aiming for the same objective. This suggests the profound impact of selecting the right assembler-binner combination for metagenome analyses. We believe this study will be a cornerstone for the scientific community, guiding the choice of tools by highlighting their complementary effects. Furthermore, it underscores the potential of existing tools to address the current challenges in the field improving the recovery of information from metagenomes.}, }
@article {pmid39897812, year = {2025}, author = {Yang, Y and Lu, Y and Gao, C and Nie, Y and Wang, H and Huang, Y and Dong, H and Sun, Q}, title = {Effects of housing conditions on health and gut microbiome of female cynomolgus monkeys and improvement of welfare by checking menstruation under socially housed condition.}, journal = {Heliyon}, volume = {11}, number = {2}, pages = {e41912}, pmid = {39897812}, issn = {2405-8440}, abstract = {Laboratory non-human primates (NHPs) are commonly subjected to social deprivation in various scientific researches. However, the impact of social deprivation on gut microbiome remains largely unknown. We examined the health status and gut microbiota of female cynomolgus monkeys housed in isolation or social conditions and found that social deprivation brought adverse effects to monkeys by inhibiting their growth, remodeling the immune status, and decreasing the level of beneficial biochemical parameters. 16S rRNA gene sequencing revealed that the gut microbial composition and function differed between grouped and isolated monkeys. Specifically, grouping the single-caged young monkeys to socially housed condition could decrease the relative abundance of Firmicutes and increase the relative abundance of Bacteroidetes, while separating the socially housed middle-aged monkeys into single cages showed the opposite trend. Besides, training female monkeys to detect menstruation under socially-housed condition could increase their body weight change and adjusting their immune status, thus attenuating the adverse effects of separating them to single cages. Our results verified the significant role of grouping in mitigating adverse health and microbiota alterations caused by isolation in female cynomolgus monkeys and emphasized the importance of training NHPs to cooperate with experimental procedures under socially housed condition, which could not only improve the welfare of cynomolgus monkeys but also enhance the accuracy and reliability of scientific results.}, }
@article {pmid39897789, year = {2025}, author = {Schmidt, JE and Lewis, CA and Firl, AJ and Umaharan, P}, title = {Microbial bioindicators associated with cadmium uptake in sixteen genotypes of Theobroma cacao.}, journal = {Heliyon}, volume = {11}, number = {2}, pages = {e41890}, pmid = {39897789}, issn = {2405-8440}, abstract = {Recent regulatory limits on concentrations of cadmium (Cd), an element of concern for human health, have made Cd reduction a key issue in the global chocolate industry. Research into Cd minimization has investigated soil management, cacao genetic variation, and postharvest processing, but has overlooked the cacao-associated microbiome despite promising evidence in other crops that root-associated microorganisms could help reduce Cd uptake. A novel approach combining both amplicon and metagenomic sequencing identified microbial bioindicators associated with leaf and stem Cd accumulation in sixteen field-grown genotypes of Theobroma cacao. Sequencing highlighted over 200 amplicon sequence variants (ASVs) whose relative abundance was related to cacao leaf and stem Cd content or concentration. The two highest-accumulating genotypes, PA 32 and TRD 94, showed enrichment of four ASVs belonging to the genus Haliangium, the family Gemmataceae, and the order Polyporales. ASVs whose relative abundance was most negatively associated with plant Cd were identified as Paenibacillus sp. (β = -2.21), Candidatus Koribacter (β = -2.17), and Candidatus Solibacter (β = -2.03) for prokaryotes, and Eurotiomycetes (β = -4.58) and two unidentified ASVs (β = -4.32, β = -3.43) for fungi. Only two ASVs were associated with both leaf and stem Cd, both belonging to the Ktedonobacterales. Of 5543 C d-associated gene families, 478 could be assigned to GO terms, including 68 genes related to binding and transport of divalent heavy metals. Screening for Cd-related bioindicators prior to planting or developing microbial bioamendments could complement existing strategies to minimize the presence of Cd in the global cacao supply.}, }
@article {pmid39897714, year = {2025}, author = {Morshead, ML and Tanguay, RL}, title = {Advancements in the Developmental Zebrafish Model for Predictive Human Toxicology.}, journal = {Current opinion in toxicology}, volume = {41}, number = {}, pages = {}, pmid = {39897714}, issn = {2468-2934}, abstract = {The rapid assessment of chemical hazards to human health, with reduced reliance on mammalian testing, is essential in the 21st century. Early life stage zebrafish have emerged as a leading model in the field due to their amenability to high throughput developmental toxicity testing while retaining the benefits of using a whole vertebrate organism with high homology with humans. Zebrafish are particularly well suited for a variety of study areas that are more challenging in other vertebrate model systems including microbiome work, transgenerational studies, gene-environment interactions, molecular responses, and mechanisms of action. The high volume of data generated from zebrafish screening studies is highly valuable for QSAR modeling and dose modeling for use in predictive hazard assessment. Recent advancements and challenges in using early life stage zebrafish for predictive human toxicology are reviewed.}, }
@article {pmid39897551, year = {2025}, author = {Yu, C and Sun, R and Yang, W and Gu, T and Ying, X and Ye, L and Zheng, Y and Fan, S and Zeng, X and Yao, S}, title = {Exercise ameliorates osteopenia in mice via intestinal microbial-mediated bile acid metabolism pathway.}, journal = {Theranostics}, volume = {15}, number = {5}, pages = {1741-1759}, pmid = {39897551}, issn = {1838-7640}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Fecal Microbiota Transplantation/methods ; *Bone Diseases, Metabolic/metabolism/therapy ; *Bile Acids and Salts/metabolism ; Female ; *Physical Conditioning, Animal/physiology ; Ovariectomy ; Mice, Inbred C57BL ; Disease Models, Animal ; Osteoporosis/metabolism/therapy ; RNA, Ribosomal, 16S/genetics ; Bone and Bones/metabolism ; Metabolomics/methods ; }, abstract = {Rationale: Physical exercise is essential for skeletal integrity and bone health. The gut microbiome, as a pivotal modulator of overall physiologic states, is closely associated with skeletal homeostasis and bone metabolism. However, the potential role of intestinal microbiota in the exercise-mediated bone gain remains unclear. Methods: We conducted microbiota depletion and fecal microbiota transplantation (FMT) in ovariectomy (OVX) mice and aged mice to investigate whether the transfer of gut ecological traits could confer the exercise-induced bone protective effects. The study analyzed the gut microbiota and metabolic profiles via 16S rRNA gene sequencing and LC-MS untargeted metabolomics to identify key microbial communities and metabolites responsible for bone protection. Transcriptome sequencing and RNA interference were employed to explore the molecular mechanisms. Results: We found that gut microbiota depletion hindered the osteogenic benefits of exercise, and FMT from exercised osteoporotic mice effectively mitigated osteopenia. Comprehensive profiling of the microbiome and metabolome revealed that the exercise-matched FMT reshaped intestinal microecology and metabolic landscape. Notably, alterations in bile acid metabolism, specifically the enrichment of taurine and ursodeoxycholic acid, mediated the protective effects on bone mass. Mechanistically, FMT from exercised mice activated the apelin signaling pathway and restored the bone-fat balance in recipient MSCs. Conclusion: Our study underscored the important role of the microbiota-metabolic axis in the exercise-mediated bone gain, heralding a potential breakthrough in the treatment of osteoporosis.}, }
@article {pmid39897492, year = {2025}, author = {Keleher, JG and Strope, TA and Estrada, NE and Griggs Mathis, AM and Easson, CG and Fiore, C}, title = {Freshwater sponges in the southeastern U.S. harbor unique microbiomes that are influenced by host and environmental factors.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18807}, pmid = {39897492}, issn = {2167-8359}, mesh = {*Porifera/microbiology ; *Microbiota ; Animals ; *Fresh Water/microbiology ; North Carolina ; *Symbiosis ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Marine, and more recently, freshwater sponges are known to harbor unique microbial symbiotic communities relative to the surrounding water; however, our understanding of the microbial ecology and diversity of freshwater sponges is vastly limited compared to those of marine sponges. Here we analyzed the microbiomes of three freshwater sponge species: Radiospongilla crateriformis, Eunapius fragilis, and Trochospongilla horrida, across four sites in western North Carolina, U.S.A. Our results support recent work indicating that freshwater sponges indeed harbor a distinct microbiome composition compared to the surrounding water and that these varied across sampling site indicating both environmental and host factors in shaping this distinct community. We also sampled sponges at one site over 3 months and observed that divergence in the microbial community between sponge and water occurs at least several weeks after sponges emerge for the growing season and that sponges maintain a distinct community from the water as the sponge tissue degrades. Bacterial taxa within the Gammproteobacteria, Alphproteobacteria, Bacteroidota (Flavobacteriia in particular), and Verrucomicrobia, were notable as enriched in the sponge relative to the surrounding water across sponge individuals with diverging microbial communities from the water. These results add novel information on the assembly and maintenance of microbial communities in an ancient metazoan host and is one of few published studies on freshwater sponge microbial symbiont communities.}, }
@article {pmid39897478, year = {2024}, author = {Li, Y and Wu, X}, title = {Vaginal microbiome distinction in women with HPV+, cervical intraepithelial neoplasia, and cervical cancer, a retrospective study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1483544}, pmid = {39897478}, issn = {2235-2988}, mesh = {Humans ; Female ; *Vagina/microbiology/virology ; *Microbiota ; *Uterine Cervical Dysplasia/microbiology/virology ; *Uterine Cervical Neoplasms/virology/microbiology ; *Papillomavirus Infections/virology/microbiology ; Adult ; Retrospective Studies ; Middle Aged ; *Genotype ; Papillomaviridae/genetics/isolation &amp; purification/classification ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/isolation &amp; purification/genetics ; Lactobacillus/isolation &amp; purification/genetics ; Young Adult ; Gardnerella/isolation &amp; purification/genetics ; }, abstract = {INTRODUCTION: The vaginal microbiota is a complex and dynamic micro-ecosystem that plays a pivotal role in protecting the host from various pathogens. Previous studies have investigated the diversity of the vaginal microbiome and its association with health outcomes, particularly the development of HPV-related disorders. This study aimed to investigate the correlation between the vaginal microbiota, HPV infection, cervical intraepithelial neoplasias (CINs), and cervical cancers in 69 women.<br><br>METHODS: DNA was extracted from vaginal samples, followed by HPV genotyping through PCR and sequenced of the16S rRNA gene.<br><br>RESULTS: Our results revealed that Lactobacillus was the predominant bacterium across all groups, with prevalence rates of 60.2% in women with HPV+, 63.9% in CINI, 97.7% in CINII, 52.0% in CINIII, 36.9% in cervical cancer, and 70.9% in NILM (normal cytology). Additionally, an elevated proportion of Gardnerella was identified as a high-risk bacterium associated with HPV infection, potentially contributing to the progression of cervical lesions. High-risk HPV genotypes, particularly HPV16, 52, and 33, were found to be more prevalent among women with HPV+, CIN, and cervical cancer. We also observed significantly higher alpha diversity in the vaginal microbiome of women with HPV+ and CIN, as indicated by increased Sobs, Shannon, Ace, and Chao indices, compared to the NILM group.<br><br>CONCLUSION: These findings suggest that HPV infection and its associated pathological conditions are closely linked to alterations in the vaginal microbiome. This underscores the need for further research to unravel the intricate relationship between HPV genotype infections and vaginal microbiota, which could pave the way for new diagnostic and therapeutic approaches.}, }
@article {pmid39897450, year = {2025}, author = {Knudsen, B and Narain, S and Moore, BB and Corr, PG and Frame, LA}, title = {Information About the Gut Microbiome's Connection to Health and Disease can Impact Knowledge: Feasibility of an Education-Based Intervention in a General Internal Medicine Clinic.}, journal = {American journal of lifestyle medicine}, volume = {}, number = {}, pages = {15598276251317129}, pmid = {39897450}, issn = {1559-8284}, abstract = {The gut microbiome (gMicrobiome)-a dynamic ecosystem of microorganisms-is emerging as a correlate of healthy lifestyle. Patients may not be aware of this. General Internal Medicine patients completed surveys evaluating gMicrobiome knowledge, lifestyle knowledge, dietary intake, physical activity, sleep, and stress. Surveys were given pre-/post-education (n = 112) and at 1 month follow-up (n = 60). The educational-module comprised a video and handout describing how lifestyle enhances gMicrobiome and health outcomes. Post-educational-module, 9 of 19 (47%) statements showed favorable change in knowledge (P < 0.05). Two statements reached statistical significance at 1-month follow-up: "Exercise influences the types of bacteria present in the digestive system" [7 (12%) to 24 (41%), P = 0.004] and "An inactive lifestyle promotes the growth of healthy types of digestive system bacteria" [12 (20%) to 24 (41%), P = 0.035]. We observed a small but favorable change in knowledge but not behavior. Large lifestyle changes are challenging to adopt, and education alone is necessary but insufficient for change. Our results confirm that education is a viable first step to establish the importance of pursuing lifestyle changes, perhaps moving from pre-contemplation to contemplation. Baseline knowledge in our participants was higher than anticipated, indicating that this intervention may have been too introductory. Future interventions should investigate baseline knowledge.}, }
@article {pmid39897390, year = {2025}, author = {Gubler, S and Zaugg, A and Yi, R and Sherren, E and Milner, E and Conyer, W and May, T and Jack, T and Heaton, T and Christopherson, J and Higbee, P and Powers, E and Takara, M and Linder, A and Boyack, B and Pauga, F and Salmon, M and Thomas, M and Shiraki, M and Deng, S and Savage, PB}, title = {Design, synthesis, antimicrobial activity, stability, and mechanism of action of bioresorbable ceragenins.}, journal = {RSC medicinal chemistry}, volume = {}, number = {}, pages = {}, pmid = {39897390}, issn = {2632-8682}, abstract = {Device-related infections (DRIs) from bacterial/fungal biofilms that form on surfaces are a major cause of death in first-world countries. DRIs and the increasing prevalence of antibiotic resistant strains require development of new antimicrobials for improved antimicrobial prophylaxis. New antimicrobial prophylaxis practices necessitate novel agents to combat a broad spectrum of both fungi and bacteria, to be less toxic to patients, and to be locally administrable to prevent perturbations to a patient's microbiome. A class of antimicrobials that we have previously developed to fit these criteria is ceragenins. Here we describe the design, synthesis, and characterization of a new series of ceragenins that is composed of and degrades into endogenous compounds: cholic acid, B alanine, and glycerides. From this series we identify an optimized bioresorbable ceragenin that has comparable antimicrobial activities to other ceragenins, degrades rapidly through the action of lipase and at pH 7.2, and has a similar mechanism of action to previously developed ceragenins.}, }
@article {pmid39896799, year = {2024}, author = {Dong, Y and Han, M and Qi, Y and Wu, Y and Zhou, Z and Jiang, D and Gai, Z}, title = {Enhancement of host defense against Helicobacter pylori infection through modulation of the gastrointestinal microenvironment by Lactiplantibacillus plantarum Lp05.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1469885}, pmid = {39896799}, issn = {1664-3224}, mesh = {Animals ; *Helicobacter Infections/immunology/microbiology ; *Helicobacter pylori ; Mice ; *Probiotics/therapeutic use/administration &amp; dosage ; *Gastrointestinal Microbiome ; *Mice, Inbred C57BL ; Gastric Mucosa/microbiology/immunology/metabolism/pathology ; Disease Models, Animal ; Male ; Oxidative Stress ; }, abstract = {OBJECTIVE: This study aimed to assess the impact of Lactiplantibacillus plantarum Lp05 (Lp05) on the gastrointestinal microbiome and pathophysiological status of mice infected with Helicobacter pylori (H. pylori), exploring its potential as a probiotic treatment for H. pylori infections.<br><br>METHODS: In vitro, the interaction between Lp05 and H. pylori was analyzed using laser confocal and scanning electron microscopy. In vivo, C57BL/6 mice infected with H. pylori were treated with Lp05 and divided into six groups: control, model, quadruple therapy, and three dosage levels of Lp05 (2&#xd7;10[7], 2&#xd7;10[8], 2&#xd7;10[9] CFU/mouse/day). Over six weeks, the impact of Lp05 on the gastrointestinal microbiome and physiological markers was assessed. Measurements included digestive enzymes (&#x3b1;-amylase, pepsin, cellulase), inflammatory markers (interleukin-17A, interleukin-23, interleukin-10, interferon-&#x3b2;, interferon-&#x3b3;, FoxP3, endothelin, IP-10, TGF-&#x3b2;1), oxidative stress markers (catalase, malondialdehyde, superoxide dismutase, myeloperoxidase), and tissue pathology (via modified Warthin-Starry silver and H&amp;E staining). Microbial community structure in the stomach and intestines was evaluated through 16S rRNA gene sequencing.<br><br>RESULTS: In vitro studies showed Lp05 and H. pylori formed co-aggregates, with Lp05 potentially disrupting H. pylori cell structure, reducing its stomach colonization. In vivo, Lp05 significantly lowered gastric mucosal urease activity and serum H. pylori-IgG antibody levels in infected mice (p < 0.01). It also mitigated pathological changes in the stomach and duodenum, decreased inflammatory responses (ET, IL-17A, IL-23, TGF-beta1, and IP-10, p < 0.01 for all), and enhanced antioxidant enzyme activities (CAT and SOD, p < 0.01) while reducing MDA and MPO levels (p < 0.01), combating oxidative stress from H. pylori infection. Lp05 treatment significantly modified the intestinal and gastric microbiota, increasing beneficial bacteria like Lactobacillus and Ligilactobacillus, and decreasing harmful bacteria such as Olsenella, linked to pathological conditions.<br><br>CONCLUSION: Lp05 effectively modulates the gastrointestinal microbiome, reduces inflammation and oxidative stress, and suppresses H. pylori, promising for probiotic therapies with further research needed to refine its clinical use.}, }
@article {pmid39896755, year = {2025}, author = {Zhao, B and Zhou, H and Lin, K and Xu, J and Zhou, B and Xie, D and Ma, J and Yang, L and Su, C and Yang, L}, title = {Antimicrobial peptide DP7 alleviates dextran sulfate sodium (DSS)-induced colitis via modifying gut microbiota and regulating intestinal barrier function.}, journal = {MedComm}, volume = {6}, number = {2}, pages = {e70085}, pmid = {39896755}, issn = {2688-2663}, abstract = {Inflammatory bowel diseases (IBDs), such as Crohn's disease (CD) and ulcerative colitis (UC), represent a growing global health concern. Restoring the balance of the gut microbiota, a crucial factor in intestinal health, offers potential for treating IBD. DP7, a novel antimicrobial peptide with potent antibacterial activity, was investigated for its anti-inflammatory effects in a dextran sulfate sodium (DSS)-induced UC mouse model. DP7 significantly ameliorated key disease parameters, including disease activity index, weight loss, and shortened colon length, while preserving colonic epithelial integrity and reducing inflammatory infiltration. Further analysis revealed potential targets of DP7, highlighting the significant role of Muribaculaceae bacteria during inflammatory states. To further explore the role of the gut microbiota in DP7's efficacy, fecal microbiota transplantation (FMT) was performed using feces from DP7-treated mice. FMT successfully ameliorated colitis in recipient mice, providing further evidence for the crucial role of the gut microbiome in IBD treatment and DP7's ability to modulate the gut microbiota for therapeutic benefit. Moreover, our findings suggest that DP7's modulation of the immune system is intricately linked to the complex microbial environment. Our findings demonstrate that DP7 effectively mitigates inflammation, attenuates barrier dysfunction, and shapes the gut microbiota, suggesting its potential as a therapeutic agent for UC.}, }
@article {pmid39896730, year = {2025}, author = {Trumbo, PR and Ard, J and Bellisle, F and Drewnowski, A and Gilbert, JA and Kleinman, R and Misra, A and Sievenpiper, J and Tahiri, M and Watson, KE and Hill, J}, title = {Perspective: Current Scientific Evidence and Research Strategies in the Role of Almonds in Cardiometabolic Health.}, journal = {Current developments in nutrition}, volume = {9}, number = {1}, pages = {104516}, pmid = {39896730}, issn = {2475-2991}, abstract = {Almonds are consumed by individuals around the world. Because almonds are rich in protein, unsaturated fatty acids, and fiber, a significant amount of research has been conducted on their role in affecting various cardiometabolic endpoints (body weight, blood pressure, blood cholesterol levels, and glycemic response). The most current meta-analyses on almond consumption and various health-related endpoints suggest that almond consumption does not result in weight gain and results in small reductions in LDL cholesterol and diastolic blood pressure, as well as improved glycemic responses in certain populations (i.e. Asian Indians). A number of research gaps on almond consumption and cardiometabolic health were identified that should be addressed to further understand their role in the various cardiometabolic endpoints, including the mechanisms of action interactions with the microbiome with regular consumption and their role as part of a healthy dietary pattern for both individuals and the general population.}, }
@article {pmid39896720, year = {2024}, author = {Coltro, EP and Cafferati Beltrame, L and da Cunha, CR and Zamparette, CP and Feltrin, C and Benetti Filho, V and Vanny, PA and Beduschi Filho, S and Klein, TCR and Scheffer, MC and Palmeiro, JK and Wagner, G and Sincero, TCM and Zárate-Bladés, CR}, title = {Evaluation of the resistome and gut microbiome composition of hospitalized patients in a health unit of southern Brazil coming from a high animal husbandry production region.}, journal = {Frontiers in antibiotics}, volume = {3}, number = {}, pages = {1489356}, pmid = {39896720}, issn = {2813-2467}, abstract = {INTRODUCTION: Antimicrobial resistance (AMR) poses a significant threat to global public health. The One Health approach, which integrates human, animal, and environmental health, highlights the roles of agricultural and hospital settings in the propagation of AMR. This study aimed to analyze the resistome and gut microbiome composition of individuals from a high-intensity animal husbandry area in the western region of Santa Catarina, Southern Brazil, who were subsequently admitted to the University Hospital in the city of Florianopolis, located in the eastern part of the same state.<br><br>METHODS: Rectal swab samples were collected upon admission and discharge. Metagenomic sequencing and resistome analysis were employed to identify antimicrobial resistance genes (ARGs) and their associated bacterial taxa. Additionally, the impact of the hospital environment on the resistome and microbiome profiles of these patients was assessed.<br><br>RESULTS: A total of 247 genetic elements related to AMR were identified, with 66.4% of these elements present in both admission and discharge samples. Aminoglycoside resistance genes were the most prevalent, followed by resistance genes for tetracyclines and lincosamides. Notably, unique resistance genes, including dfrF and mutations in gyrB, were identified at discharge. ARGs were associated with 55 bacterial species, with Lactobacillus fermentum, harboring the ermB gene. (MLSB), detected in both admission and discharge samples. The most prevalent bacterial families included Mycobacteriaceae, Enterobacteriaceae, and Bacteroidaceae. Among these, Mycobacteriaceae was the most abundant, with ARGs primarily associated with mutations in the 16S rRNA gene, RNA polymerase subunits, and gyrases.<br><br>DISCUSSION: The study revealed a high prevalence of genes related to aminoglycoside and tetracycline resistance, with a notable increase in certain resistance determinants at discharge, likely influenced by extended antimicrobial use. The presence of mcr genes, associated with colistin resistance, in both admission and discharge samples from a single patient highlights a concerning trend in AMR, particularly in relation to animal husbandry. These findings underscore the substantial impact of antimicrobial use on resistance development and the complex dynamics of the resistome in hospital settings. They also emphasize the influence of local factors, such as intensive animal production, on resistance patterns and advocate for ongoing surveillance and policy development to manage multidrug-resistant bacteria eVectively.}, }
@article {pmid39896683, year = {2025}, author = {McManus, D and Copsel, SN and Pffeifer, BJ and Wolf, D and Barreras, H and Ma, S and Khodor, A and Komai, S and Burgos da Silva, M and Hazime, H and Gallardo, M and van den Brink, MR and Abreu, MT and Hill, GR and Perez, VL and Levy, RB}, title = {Pretransplant targeting of TNFRSF25 and CD25 stimulates recipient Tregs in target tissues ameliorating GVHD post-HSCT.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.16.633453}, pmid = {39896683}, issn = {2692-8205}, abstract = {The current approach to minimize transplant-associated complications, including graft-versus-host disease (GVHD) includes long-term pharmacological immune suppression frequently accompanied by unwanted side effects. Advances in targeted immunotherapies regulating alloantigen responses in the recipient continue to reduce the need for pan-immunosuppression. Here, in vivo targeting of the TNF superfamily receptor 25 (TNFRSF25) and the high affinity IL-2 receptor with a TL1A-Ig fusion protein and low dose IL-2, respectively, was used to pretreat recipient mice prior to allogeneic-HSCT (aHSCT). Pretreatment induced Treg expansion persisting early post-aHSCT leading to diminished GVHD and improved transplant outcomes. Expansion was accompanied by an increase in frequency of stable and functionally active Tregs as evidenced by in vitro assays using cells from major GVHD target tissues including colon, liver, and eye. Importantly, pretreatment supported epithelial cell function/integrity, a diverse microbiome including reduction of pathologic bacteria overgrowth and promotion of butyrate producing bacteria, while maintaining physiologic levels of obligate/facultative anaerobes. Notably, using a sphingosine 1-phosphate receptor agonist to sequester T cells in lymphoid tissues, we found that the increased tissue Treg frequency included resident CD69 [+] CD103 [+] FoxP3 [+] hepatic Tregs. In contrast to infusion of donor Treg cells, the strategy developed here resulted in the presence of immunosuppressive target tissue environments in the recipient prior to the receipt of donor allo-reactive T cells and successful perseveration of GVL responses. We posit strategies that circumvent the need of producing large numbers of ex-vivo manipulated Tregs, may be accomplished through in vivo recipient Treg expansion, providing translational approaches to improve aHSCT outcomes.}, }
@article {pmid39896561, year = {2025}, author = {Ghaddar, BC and Blaser, MJ and De, S}, title = {Revisiting the cancer microbiome using PRISM.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.21.634087}, pmid = {39896561}, issn = {2692-8205}, abstract = {Recent controversy around the cancer microbiome highlights the need for improved microbial analysis methods for human genomics data. We developed PRISM, a computational approach for precise microorganism identification and decontamination from low-biomass sequencing data. PRISM removes spurious signals and achieves excellent performance when benchmarked on a curated dataset of 62,006 known true- and false-positive taxa. We then use PRISM to detect microbes in 8 cancer types from the CPTAC and TCGA datasets. We identify rich microbiomes in gastrointestinal tract tumors in CPTAC and identify bacteria in a subset of pancreatic tumors that are associated with altered glycoproteomes, more extensive smoking histories, and higher tumor recurrence risk. We find relatively sparse microbes in other cancer types and in TCGA, which we demonstrate may reflect differing sequencing parameters. Overall, PRISM does not replace gold-standard controls, but it enables higher-confidence analyses and reveals tumor-associated microorganisms with potential molecular and clinical significance.}, }
@article {pmid39896492, year = {2025}, author = {Siguenza, N and Bailey, S and Sadegi, M and Gootin, H and Tiu, M and Price, JD and Ramer-Tait, A and Zarrinpar, A}, title = {Gut Competition Dynamics of Live Bacterial Therapeutics Are Shaped by Microbiome Complexity, Diet, and Therapeutic Transgenes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.21.634159}, pmid = {39896492}, issn = {2692-8205}, abstract = {Competitive exclusion is conventionally believed to prevent the establishment of a secondary strain of the same bacterial species in the gut microbiome, raising concerns for the deployment of live bacterial therapeutics (LBTs), especially if the bacterial chassis is a strain native to the gut. In this study, we investigated factors influencing competition dynamics in the murine gut using isogenic native Escherichia coli strains. We found that competition outcomes are context-dependent, modulated by microbiome complexity, LBT transgene expression, intestinal inflammation, and host diet. Furthermore, we demonstrated that native LBTs can establish long-term engraftment in the gut alongside a parental strain, with transgene-associated fitness effects influencing competition. We identified various interventions, including strategic dosing and dietary modulation, that significantly enhanced LBT colonization levels by 2 to 3 orders of magnitude. These insights provide a framework for optimizing LBT engraftment and efficacy, supporting their potential translation for human therapeutic applications.}, }
@article {pmid39896159, year = {2025}, author = {Kapoor, MP and Abe, A and Morishima, S and Nakajima, A and Ozeki, M and Sato, N}, title = {Dietary intervention of prebiotic partially hydrolyzed guar gum improves skin viscoelasticity, stratum corneum hydration, and reduction of trans-epidermal water loss: a randomized, double-blind, and placebo-controlled clinical study in healthy humans.}, journal = {Journal of clinical biochemistry and nutrition}, volume = {76}, number = {1}, pages = {96-115}, pmid = {39896159}, issn = {0912-0009}, abstract = {Dietary fiber-rich diets are gaining popularity as an alternative therapy for skin health. Plant-based prebiotic partially hydrolyzed guar gum (PHGG) dietary fiber promotes gastrointestinal health, which is imperative for skin health through the gut microbiome. In this randomized, double-blind, and placebo-controlled study, the purpose was to assess the therapeutic effects of PHGG on skin hydration, trans-epidermal water loss (TEWL), and skin viscoelastic properties during the winter season. Healthy male and female subjects (n = 70; 9 male and 61 female; mean age: 45.5 ± 8.1 years) were recruited. They received either the 5 ‍g PHGG dietary fiber (n = 35) or a 5 ‍g placebo (n = 35) for twelve weeks. Skin moisture, TEWL, skin elasticity and skin color parameters, and related features were assessed at baseline, after 6 and 12 weeks, and questionnaires to evaluate the study outcomes. The results confirmed the improvement in skin conditions throughout the winter season by restoring skin hydration, reducing TEWL, and improving skin elasticity parameters. After 6 weeks of PHGG intake, there was a substantial decrease in TEWL and improvement in viscoelasticity metrics when compared to placebo. Subject satisfaction with efficacy reflected these encouraging findings, and PHGG was well tolerated, with no adverse events occurring during the study period.}, }
@article {pmid39896100, year = {2025}, author = {Gutzeit, O and Gulati, A and Izadifar, Z and Stejskalova, A and Rhbiny, H and Cotton, J and Budnik, B and Shahriar, S and Goyal, G and Junaid, A and Ingber, DE}, title = {Cervical mucus in linked human Cervix and Vagina Chips modulates vaginal dysbiosis.}, journal = {npj women's health}, volume = {3}, number = {1}, pages = {5}, pmid = {39896100}, issn = {2948-1716}, abstract = {This study explores the protective role of cervicovaginal mucus in maintaining vaginal health, particularly in relation to bacterial vaginosis (BV), using organ chip technology. By integrating human Cervix and Vagina Chips, we demonstrated that cervical mucus significantly reduces inflammation and epithelial damage caused by a dysbiotic microbiome commonly associated with BV. Proteomic analysis of the Vagina Chip, following exposure to mucus from the Cervix Chip, revealed differentially abundant proteins, suggesting potential biomarkers and therapeutic targets for BV management. Our findings highlight the essential function of cervical mucus in preserving vaginal health and underscore the value of organ chip models for studying complex interactions within the female reproductive tract. This research provides new insights into the mechanisms underlying vaginal dysbiosis and opens avenues for developing targeted therapies and diagnostic tools to enhance women's reproductive health.}, }
@article {pmid39896099, year = {2025}, author = {Iwami, N and Komiya, S and Asada, Y and Tatsumi, K and Habara, T and Kuramoto, T and Seki, M and Yoshida, H and Takeuchi, K and Shiotani, M and Mukaida, T and Odawara, Y and Mio, Y and Kamiya, H}, title = {"Shortening time to pregnancy in infertile women by personalizing treatment of microbial imbalance through Emma &amp; Alice: A multicenter prospective study".}, journal = {Reproductive medicine and biology}, volume = {24}, number = {1}, pages = {e12634}, pmid = {39896099}, issn = {1445-5781}, abstract = {PURPOSE: To evaluate the impact of Endometrial Microbiome Metagenomic Analysis and Analysis of Infectious Chronic Endometritis (EMMA &amp; ALICE) on pregnancy outcomes following recommended treatments in women with recurrent implantation failure (RIF) or recurrent pregnancy loss (RPL).<br><br>METHODS: This prospective, multicenter cohort study included 527 women under 42&#x2009;years old with RIF or RPL across 14 IVF centers in Japan. Endometrial samples were analyzed using EMMA &amp; ALICE, and patients received antibiotics, probiotics, or no treatment based on test results. Pregnancy outcomes were assessed using Kaplan-Meier survival analysis and multivariate generalized linear models.<br><br>RESULTS: Amongst participants, 43.4% had a normal Lactobacillus-dominated microbiota, 20.9% had dysbiosis, and 35.7% had mild dysbiosis or ultralow biomass. Kaplan-Meier analysis revealed significantly higher ongoing pregnancy rates in the dysbiosis group treated with antibiotics and probiotics compared to other groups (p&#x2009;=&#x2009;0.031). Post-treatment, ongoing pregnancy rates in the dysbiosis and mild dysbiosis groups were comparable to the normal group.<br><br>CONCLUSIONS: EMMA &amp; ALICE-guided antimicrobial and probiotic treatments improved pregnancy outcomes, enabling the dysbiosis group to achieve pregnancy earlier than the normal group. Addressing uterine dysbiosis may reduce the time to pregnancy in patients with RIF and RPL.<br><br>TRIAL REGISTRATION: University Hospital Medical Information Network (UMIN), UMIN000036917.}, }
@article {pmid39895839, year = {2025}, author = {Zhang, Z and Bi, C and Wu, R and Qu, M}, title = {Association of the newly proposed dietary index for gut microbiota and constipation: a cross-sectional study from NHANES.}, journal = {Frontiers in nutrition}, volume = {12}, number = {}, pages = {1529373}, pmid = {39895839}, issn = {2296-861X}, abstract = {OBJECTIVE: The dietary index for gut microbiota. DI-GM is an innovative metric designed to capture the diversity of the gut microbiome, yet its association with constipation remains unstudied.<br><br>METHODS: In this cross-sectional study, 11,405 adults aged 20 and older were selected from the National Health and Nutrition Examination Survey 2005-2010 for the sample. Constipation was defined as fewer than three defecation frequencies per week using bowel health questionnaire (BHQ). Fewer than three bowel movements per week were considered as constipation by Bowel Health Questionnaire (BHQ). DI-GM was derived from dietary recall data, including avocado, broccoli, chickpeas, coffee, cranberries, fermented dairy, fiber, green tea, soybean and whole grains as beneficial elements, red meat, processed meat, refined grains, and high fat as detrimental components. Multivariable weighted logistic was employed to investigate the association of DI-GM with constipation. Secondary analyses included subgroup analyses, restricted cubic spline (RCS), and multiple imputation.<br><br>RESULTS: A higher DI-GM and beneficial gut microbiota score were associated with a lower prevalence of constipation (DI-GM: OR = 0.82, 95% CI = 0.75, 0.90; beneficial gut microbiota score: OR = 0.77, 95% CI = 0.67, 0.89). After grouping DI-GM, in the fully adjusted model, participants with DI-GM &#x2265; 6 were significantly negatively correlated with both the prevalence of constipation (OR = 0.48, 95% CI = 0.33, 0.71). RCS indicated a non-linear relationship between DI-GM and constipation. Subgroup analyses by age, sex and common complications showed no statistically significant interactions (p > 0.05).<br><br>CONCLUSION: The newly proposed DI-GM was inversely related with the prevalence of constipation. When treating patients with constipation, it is necessary for clinicians to provide timely and effective dietary interventions incorporating the DI-GM for patients with constipation to avoid further deterioration of the condition.}, }
@article {pmid39895797, year = {2025}, author = {Gao, Y and Zheng, H and Ye, M and Zhou, G and Chen, J and Qiang, X and Bai, J and Lu, X and Tang, Q}, title = {Characteristics and function of the gut microbiota in patients with rectal neuroendocrine tumors.}, journal = {Journal of Cancer}, volume = {16}, number = {4}, pages = {1040-1050}, pmid = {39895797}, issn = {1837-9664}, abstract = {The gut microbiota plays a significant role in the initiation and progression of tumors, but its role in rectal neuroendocrine tumors (rNETs) remains unclear. Fecal samples were collected from 19 healthy individuals and 21 rNET patients,with the rNET cohort further divided into metastatic (rNETs-M) and non-metastatic (rNETs-nM) groups. Using metagenomic high-throughput sequencing, we analyzed the diversity, species composition, and functional characteristics of the gut microbiota. We applied a random forest model to identify potential microbial biomarkers for predicting rNET and specifically distinguishing rNETs-M cases. Alpha diversity analysis revealed that species diversity was lower in the rNETs group than in the control group. In contrast, the rNETs-M group exhibited higher species diversity than the rNETs-nM group. Beta diversity analysis demonstrated significant differences in community structure between the rNETs and control groups between the rNET-M and rNETs-nM groups. Notably, in the rNETs group, the abundance of potential pathogens such as Escherichia coli and Shigella was elevated.Furthermore, the rNETs-M group exhibited an increased abundance of potential pathogens such as Alistipes. KEGG enrichment analysis indicated that these distinct microbiota play a significant role in environmental information processing, genetic information processing, and metabolic pathways. Random forest analysis and ROC curve results identified Lachnospira pectinoschiza (AUC=0.885), Parasutterella muris (AUC=0.862), Sodaliphilus pleomorphus(AUC=0.956), Methylobacterium iners (AUC=0.971) as biomarkers with significant discriminatory value.}, }
@article {pmid39895695, year = {2025}, author = {Cumbo, F and Joshi, J and Thurnher, D and Maniakas, A}, title = {Editorial: The role of the microbiome in head and neck cancer.}, journal = {Frontiers in oncology}, volume = {15}, number = {}, pages = {1545067}, doi = {10.3389/fonc.2025.1545067}, pmid = {39895695}, issn = {2234-943X}, }
@article {pmid39895632, year = {2025}, author = {Gazzaniga, FS and Kasper, DL}, title = {The gut microbiome and cancer response to immune checkpoint inhibitors.}, journal = {The Journal of clinical investigation}, volume = {135}, number = {3}, pages = {}, doi = {10.1172/JCI184321}, pmid = {39895632}, issn = {1558-8238}, mesh = {*Gastrointestinal Microbiome/drug effects/immunology ; Humans ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Animals ; *Neoplasms/immunology/drug therapy/microbiology/therapy ; Mice ; *Fecal Microbiota Transplantation ; Immunotherapy ; }, abstract = {Immune checkpoint inhibitors (ICIs) are widely used for cancer immunotherapy, yet only a fraction of patients respond. Remarkably, gut bacteria impact the efficacy of ICIs in fighting tumors outside of the gut. Certain strains of commensal gut bacteria promote antitumor responses to ICIs in a variety of preclinical mouse tumor models. Patients with cancer who respond to ICIs have a different microbiome compared with that of patients who don't respond. Fecal microbiota transplants (FMTs) from patients into mice phenocopy the patient tumor responses: FMTs from responders promote response to ICIs, whereas FMTs from nonresponders do not promote a response. In patients, FMTs from patients who have had a complete response to ICIs can overcome resistance in patients who progress on treatment. However, the responses to FMTs are variable. Though emerging studies indicate that gut bacteria can promote antitumor immunity in the absence of ICIs, this Review will focus on studies that demonstrate relationships between the gut microbiome and response to ICIs. We will explore studies investigating which bacteria promote response to ICIs in preclinical models, which bacteria are associated with response in patients with cancer receiving ICIs, the mechanisms by which gut bacteria promote antitumor immunity, and how microbiome-based therapies can be translated to the clinic.}, }
@article {pmid39895627, year = {2025}, author = {Scharschmidt, TC and Segre, JA}, title = {Skin microbiome and dermatologic disorders.}, journal = {The Journal of clinical investigation}, volume = {135}, number = {3}, pages = {}, doi = {10.1172/JCI184315}, pmid = {39895627}, issn = {1558-8238}, mesh = {Humans ; *Microbiota/immunology ; *Skin/microbiology/immunology/pathology ; *Dermatitis, Atopic/microbiology/immunology/pathology ; *Skin Diseases/microbiology/immunology ; Animals ; }, abstract = {Human skin acts as a physical barrier to prevent the entry of pathogenic microbes while simultaneously providing a home for commensal bacteria and fungi. Microbiome sequencing studies have demonstrated the unappreciated diversity and selectivity of these microbes. Functional studies have demonstrated the impact of specific strains to tune the immune system, sculpt the microbial community, provide colonization resistance, and promote epidermal barrier integrity. Recent studies have integrated the microbiome, immunity, and tissue integrity to understand their interplay in common disorders such as atopic dermatitis. In this Review, we explore microbiome shifts associated with cutaneous disorders with an eye toward how the microbiome can be mined to identify new therapeutic opportunities.}, }
@article {pmid39895623, year = {2025}, author = {Bordelon, RC and Herath, M and Speer, AL}, title = {Innervation of Human Intestinal Organoids.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {215}, pages = {}, doi = {10.3791/67702}, pmid = {39895623}, issn = {1940-087X}, mesh = {*Organoids/cytology ; Humans ; Animals ; Mice ; *Pluripotent Stem Cells/cytology ; *Intestine, Small/cytology ; Enteric Nervous System/cytology ; Neural Crest/cytology ; Cell Differentiation/physiology ; }, abstract = {The complexity of intestinal cytoarchitecture and function poses significant challenges for the creation of the bioengineered small intestine. Techniques for generating human intestinal organoids (HIOs) resembling human small intestine have been previously reported. HIOs contain epithelium and mesenchyme but lack other critical components of functional intestine such as the enteric nervous system (ENS), immune cells, vasculature, and microbiome. Two independent research groups have published distinct methods to innervate HIOs with an ENS. Here we discuss a unique method of incorporating the ENS into an HIO-derived bioengineered small intestine, which utilizes components of these prior reports to optimize progenitor cell identity as well as developmental timing. Human pluripotent stem cells (hPSCs) are differentiated to independently generate HIOs and enteric neural crest cells (ENCCs) by temporal regulation of differentiation markers over a period of several days per published protocols. Once HIOs reach the mid-hindgut spheroid stage (approximately day 8), day 15-21 ENCC spheroids are dissociated, co-cultured with HIOs, and suspended within clear three-dimensional (3D) basement membrane matrix droplets. HIO + ENCC co-cultures are maintained in vitro for 28-40 days before transplantation into >9-week-old immunodeficient mice for further development and maturation. Transplanted HIOs (tHIOs) with ENS can be harvested 4-20 weeks later. This method integrates elements from two previously published techniques by utilizing ENCCs generated from hPSCs and co-culturing them with HIOs at an early stage of development to maximize exposure to early developmental cues that likely contribute to the formation of a more mature intestinal morphology.}, }
@article {pmid39895585, year = {2025}, author = {Li, Y and Mai, Y and Jiao, Y and Yuan, Y and Qu, Y and Zhang, Y and Wang, M and Zhang, W and Lu, X and Lin, Z and Liang, C and Li, J and Mao, T and Xie, C}, title = {Alterations in the Tongue Coating Microbiome in Patients With Diarrhea-Predominant Irritable Bowel Syndrome: A Cross-Sectional Study.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {133}, number = {2}, pages = {e70001}, doi = {10.1111/apm.70001}, pmid = {39895585}, issn = {1600-0463}, support = {2022-1-4201//Capital's Funds for Health Improvement and Research/ ; 7242232//Beijing Natural Science Foundation Proposed Program/ ; JCYJ20240813153504007//Shenzhen Science and Technology Program/ ; CACM-2022-QNRC2-A02//China Association of Chinese Medicine Young Talent Support Project/ ; CYJH2024057//Young Talents Program for Traditional Chinese Medicine Clinical Practice under the Eagle Plan of China Association of Chinese Medicine/ ; K2023A01//Qihuang Excellent Youth Science and Technology Talent Cultivation Plan of Beijing University of Chinese Medicine/ ; DFRCZY-2024GJRC010//National High Level Chinese Medicine Hospital Clinical Research Funding/ ; }, mesh = {Humans ; *Irritable Bowel Syndrome/microbiology ; Adult ; Male ; Female ; *Tongue/microbiology ; Cross-Sectional Studies ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; *Diarrhea/microbiology ; Microbiota/genetics ; Dysbiosis/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Young Adult ; High-Throughput Nucleotide Sequencing ; DNA, Bacterial/genetics ; Gastrointestinal Microbiome/genetics ; Sequence Analysis, DNA ; }, abstract = {The gut microbiota plays a critical role in the occurrence and development of IBS-D, however, IBS-D-associated tongue coating microbiome dysbiosis has not yet been clearly defined. To address this, we analyzed the structure and composition of the tongue coating microbiome in 23 IBS-D patients and 12 healthy controls using 16S rRNA high-throughput sequencing analysis. The 16S rRNA sequencing results revealed that the overall observed OTUs of tongue coating microbiome in IBS-D patients exhibited a significant decrease compared with the healthy controls. Alpha diversity analysis showed that the diversity and community richness were significantly reduced in IBS-D patients, and PCoA revealed a distinct clustering of tongue coating microbiome between the IBS-D patients and healthy controls. Microbial comparisons at the genus level showed that the abundance of Veillonella, Prevotella in IBS-D patients was higher than those in healthy controls, while Streptococcus, Haemophilus, Granulicatella, and Rothia were significantly reduced compared with the healthy volunteers. Functional analysis results showed significant differences in 88 functional metabolic pathways between the IBS-D patients and the healthy controls, including fatty acid biosynthesis. These findings identified the structure, composition, functionality of tongue coating microbiome in IBS-D patients, and hold promise the potential for therapeutic targets during IBS-D management.}, }
@article {pmid39895304, year = {2025}, author = {Markley, JD and Bajaj, JS}, title = {Rethinking Antibiotic Prophylaxis for Spontaneous Bacterial Peritonitis in Patients with Cirrhosis: First, Do No Harm.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciaf047}, pmid = {39895304}, issn = {1537-6591}, abstract = {Antibiotic prophylaxis for spontaneous bacterial peritonitis (SBPPr) in patients with cirrhosis has been considered standard of care since the 1990s and is currently recommended by several major gastroenterological societies. However, the evidence supporting this practice is weak and there is no clear mortality benefit. The unintended consequences of this strategy are not insignificant, both at the patient and population level. Recent evidence suggests that SBPPr may even cause harm. Since the widespread implementation of SBPPr three decades ago, our overall approach to antibiotic use has shifted. We now recognize the growing threat of antimicrobial resistance (AMR), the potential harms of antibiotics, and the vital role of antimicrobial stewardship. In light recent developments and evidence, there is an urgent need for infectious disease, antimicrobial stewardship, and hepatology leaders to collaborate to develop an updated and cohesive approach to SBPPr.}, }
@article {pmid39895284, year = {2025}, author = {Costa de Almeida, T and Sabino, YNV and Brasiel, PGA and Rocha, BMO and de Cássia Ávila Alpino, G and Rocha, VN and Dias, VC and Diniz, CG and Paiva, AD and Silva, VLD and Dutra Medeiros, J and Potente Dutra Luquetti, SC and Barbosa Ferreira Machado, A}, title = {Maternal kefir intake during lactation impacts the breast milk and gut microbiota of the Wistar rat's offspring.}, journal = {International journal of food sciences and nutrition}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/09637486.2025.2461142}, pmid = {39895284}, issn = {1465-3478}, abstract = {Environmental factors can play fundamental role in health in childhood and adulthood during critical developmental periods like lactation. The maternal intake of probiotics like kefir during lactation could benefit newborns' intestinal health. This study aimed to evaluate the effects of maternal kefir intake during lactation on bacterial breast milk composition and the gut microbiota of offspring Wistar male rats at weaning. Lactating Wistar rats and their pups were divided into four groups based on litter size and maternal kefir intake. Sequencing of the 16S rRNA gene in breast milk revealed the predominance of the Proteobacteria, Firmicutes, and Actinobacteriota phyla. Offspring gut microbiota exhibited clustering tendencies in kefir groups with varying genus abundance. Additionally, maternal kefir intake led to increased levels of butyrate acid in offspring faeces (> +30%, p > 0.05). These findings show that the lactation period could be a window of opportunity to program intestinal health through microbiota modulation.}, }
@article {pmid39895076, year = {2025}, author = {Jung, S}, title = {Advances in functional analysis of the microbiome: Integrating metabolic modeling, metabolite prediction, and pathway inference with Next-Generation Sequencing data.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {63}, number = {1}, pages = {e.2411006}, doi = {10.71150/jm.2411006}, pmid = {39895076}, issn = {1976-3794}, support = {2022R1A2C1007345//National Research Foundation of Korea/ ; //Ministry of Science and ICT/ ; }, mesh = {*Microbiota/genetics ; Humans ; *High-Throughput Nucleotide Sequencing ; *Metabolic Networks and Pathways/genetics ; Bacteria/genetics/metabolism/classification ; Computational Biology/methods ; Models, Biological ; }, abstract = {This review explores current advancements in microbiome functional analysis enabled by next-generation sequencing technologies, which have transformed our understanding of microbial communities from mere taxonomic composition to their functional potential. We examine approaches that move beyond species identification to characterize microbial activities, interactions, and their roles in host health and disease. Genome-scale metabolic models allow for in-depth simulations of metabolic networks, enabling researchers to predict microbial metabolism, growth, and interspecies interactions in diverse environments. Additionally, computational methods for predicting metabolite profiles offer indirect insights into microbial metabolic outputs, which is crucial for identifying biomarkers and potential therapeutic targets. Functional pathway analysis tools further reveal microbial contributions to metabolic pathways, highlighting alterations in response to environmental changes and disease states. Together, these methods offer a powerful framework for understanding the complex metabolic interactions within microbial communities and their impact on host physiology. While significant progress has been made, challenges remain in the accuracy of predictive models and the completeness of reference databases, which limit the applicability of these methods in under-characterized ecosystems. The integration of these computational tools with multi-omic data holds promise for personalized approaches in precision medicine, allowing for targeted interventions that modulate the microbiome to improve health outcomes. This review highlights recent advances in microbiome functional analysis, providing a roadmap for future research and translational applications in human health and environmental microbiology.}, }
@article {pmid39895074, year = {2025}, author = {Lee, KA and Ul-Haq, A and Seo, H and Jo, S and Kim, S and Song, HY and Kim, HS}, title = {Characteristics of skin microbiome associated with disease severity in systemic sclerosis.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {63}, number = {1}, pages = {e.2409018}, doi = {10.71150/jm.2409018}, pmid = {39895074}, issn = {1976-3794}, support = {//Korea Health Industry Development Institute/ ; HI21C1888//Ministry of Health and Welfare/ ; //National Research Foundation of Korea/ ; RS-2023-00219563//Ministry of Science and ICT/ ; //Soonchunhyang University Research Fund/ ; }, mesh = {Humans ; *Scleroderma, Systemic/microbiology ; *Skin/microbiology/pathology ; *Microbiota ; Female ; Middle Aged ; Male ; *RNA, Ribosomal, 16S/genetics ; Adult ; *Bacteria/classification/genetics/isolation &amp; purification ; Severity of Illness Index ; Aged ; Biomarkers ; Metagenomics ; }, abstract = {Systemic sclerosis (SSc) is a chronic autoimmune disorder characterised by skin fibrosis and internal organ involvement. Disruptions in the microbial communities on the skin may contribute to the onset of autoimmune diseases that affect the skin. However, current research on the skin microbiome in SSc is lacking. This study aimed to investigate skin microbiome associated with disease severity in SSc. Skin swabs were collected from the upper limbs of 46 healthy controls (HCs) and 36 patients with SSc. Metagenomic analysis based on the 16S rRNA gene was conducted and stratified by cutaneous subtype and modified Rodnan skin score (mRSS) severity. Significant differences in skin bacterial communities were observed between the HCs and patients with SSc, with further significant variations based on subtype and mRSS severity. The identified biomarkers were Bacteroides and Faecalibacterium for patients with diffuse cutaneous SSc with high mRSS (≥ 10) and Mycobacterium and Parabacteroides for those with low mRSS (< 10). Gardnerella, Abies, Lactobacillus, and Roseburia were the biomarkers in patients with limited cutaneous SSc (lcSS) and high mRSS, whereas Coprococcus predominated in patients with lcSS and low mRSS. Cutaneous subtype analysis identified Pediococcus as a biomarker in the HCs, whereas mRSS analysis revealed the presence of Pseudomonas in conjunction with Pediococcus. In conclusion, patients with SSc exhibit distinct skin microbiota compared with healthy controls. Bacterial composition varies by systemic sclerosis cutaneous subtype and skin thickness.}, }
@article {pmid39895049, year = {2025}, author = {Lu, ZJ and Shi, WJ and Qiao, LK and Ma, DD and Zhang, JG and Yao, CR and Li, SY and Long, XB and Ying, GG}, title = {Benzimidazole Fungicide Carbendazim Induces Gut Inflammation through the TLR5/NF-κB Pathway in Grass Carp.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c12695}, pmid = {39895049}, issn = {1520-5851}, abstract = {Fungicides have been increasingly used across various sectors, including agriculture and textiles. The biocidal properties of fungicides may negatively impact the stability of intestinal microbiota, thereby posing a threat to intestinal health. In this study, we investigated the mechanisms of intestinal damage and functional abnormalities in grass carp following a 42-day exposure to the widely used fungicide carbendazim at environmentally relevant concentrations (0.2 to 20 μg/L). Histopathological observations, mRNA and protein expression analyses, biochemical analysis, quantification of short-chain fatty acids (SCFAs), cytokines, lipopolysaccharide (LPS), and 16S ribosomal ribonucleic acid (rRNA), as well as internal transcribed spacer (ITS) sequencing, were performed. At environmentally relevant concentrations, carbendazim strongly induced intestinal inflammation, leading to increased transcriptional and translational levels of genes involved in the toll-like receptor five (TLR5)/nuclear factor kappa B (NF-κB) pathway, including TLR5, NF-κB, interleukin-1 beta (IL-1β), and tumor necrosis factor-alpha (TNFα). Additionally, carbendazim damaged intestinal barriers and reduced the expression of tight junction proteins (e.g., occludin and zonula occludens-1/2), goblet cells, and immunoglobulin M levels, while also disrupting the gut microbiome, leading to intestinal metabolic disorders, particularly decreases in SCFAs and increases in LPS. Treatment with the TLR5 antagonist TH1020 mitigated intestinal inflammation caused by carbendazim, subsequently improving mechanical barrier function. Overall, our findings provide new insights into the toxicological mechanisms underlying intestinal damage caused by carbendazim in grass carp, indicating that carbendazim poses a significant threat to nontarget organisms. Given its widespread detection in the environment, these results underscore the substantial ecological risks to the gut health of fish living in carbendazim-contaminated water bodies.}, }
@article {pmid39895020, year = {2025}, author = {Mazurel, D and Brandt, BW and Boomsma, M and Crielaard, W and Lagerweij, M and Exterkate, RAM and Deng, DM}, title = {Streptococcus mutans and Caries: A Systematic Review and Meta-Analysis.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {220345241303880}, doi = {10.1177/00220345241303880}, pmid = {39895020}, issn = {1544-0591}, abstract = {It has been questioned whether Streptococcus mutans can still be considered the major etiological agent for caries. The main argument is that most evidence has been based on single-species identification. The composition of the oral microbiome was not analyzed. This systemic review aims to assess the prevalence and abundance of S. mutans in caries-active (CA) and caries-free (CF) subjects based on clinical studies in which the microbiome was investigated. Three databases (PubMed, Cochrane, Embase) were searched until May 22, 2023, for eligible publications that included CA and CF subjects and reported the detection of both S. mutans and the oral microbial community, using DNA-based methods. The clinical and microbial outcomes were summarized and further analyzed using a random-effects model. Of 22 eligible studies, 3 were excluded due to the high risk of bias. In the remaining 19 studies, 16 reported the prevalence of S. mutans, 11 reported its relative abundance, and 8 reported both parameters. The prevalence of S. mutans in CA was either similar to (n = 4) or higher than (n = 12) the CF group. The reported relative abundance in CA was higher than CF in all 11 studies, although the values varied from 0.001% to 5%. Meta-analysis confirmed the significance of these findings. The summary of microbial community data did not reveal other caries-associated bacterial genera/species than S. mutans. In conclusion, the collected evidence based on microbiome studies suggests a strong association between the prevalence and abundance of S. mutans and caries experience. While the cariogenic role of S. mutans in the oral ecosystem should be recognized, its actual function warrants further exploration.}, }
@article {pmid39894829, year = {2025}, author = {Li, Z and Azad, MAK and Meng, C and Kong, X and Gui, J and Lin, W and Cui, Y and Lan, W and He, Q}, title = {Metabolomics, network pharmacology, and microbiome analyses uncover the mechanisms of the Chinese herbal formula for the improvement of meat quality in spent hens.}, journal = {Journal of animal science and biotechnology}, volume = {16}, number = {1}, pages = {17}, pmid = {39894829}, issn = {1674-9782}, support = {2022YFC3400700//National Key Research and Development Project/ ; SXHZ2020007//City-School Cooperation Project of the Fuyang Science and Technology Special Fund/ ; JCYJ20200109114242138//Basic Research Program of Shenzhen Municipal Government/ ; KTP20210345//Special Commissioner for Rural Science and Technology of Guangdong Province/ ; }, abstract = {BACKGROUND: Meat originating from the spent hen is an important source of poultry meat production; however, multiple factors cause the decline in the meat quality of spent hens. Chinese herbs have been widely used as medicine for a long time to prevent diseases and as nutrient supplements to improve the product quality. This experiment explored the effects of adding 1.0% Chinese herbal formula (CHF, including 0.30% Leonurus japonicus Houtt., 0.20% Salvia miltiorrhiza Bge., 0.25% Ligustrum lucidum Ait., and 0.25% Taraxacum mongolicum Hand.-Mazz.) for 120 d to the spent hens' diet through metabolomics, network pharmacology, and microbiome strategies.<br><br>RESULTS: The results indicated that CHF supplementation improved the meat quality by reducing drip loss (P&#x2009;<&#x2009;0.05), b* value (P&#x2009;=&#x2009;0.058), and shear force (P&#x2009;=&#x2009;0.099) and increasing cooked meat percentage (P&#x2009;=&#x2009;0.054) and dry matter (P&#x2009;<&#x2009;0.05) of breast muscle. The addition of CHF improved the nutritional value of breast muscle by increasing (P&#x2009;<&#x2009;0.05) the content of C18:2n-6, n-6/n-3 polyunsaturated fatty acids (PUFA), total PUFA, PUFA-to-saturated fatty acids (SFA) ratio, and hypocholesterolemic-to-hypercholesterolemic ratio, and tending to increase serine content (P&#x2009;=&#x2009;0.069). The targeted metabolomics analysis revealed that the biosynthesis of SFA, linoleic acid metabolism, fatty acid degradation, fatty acid elongation, and fatty acid biosynthesis pathways were enriched by CHF supplementation. Furthermore, the network pharmacology analysis indicated that CHF was closely associated with oxidative stress and lipid metabolism. The CHF supplementation increased the glutathione peroxidase level (P&#x2009;<&#x2009;0.05) and upregulated gene expression related to the Nrf2 pathway (including HO-1, P&#x2009;<&#x2009;0.05; Nrf2, P&#x2009;=&#x2009;0.098; CAT, P&#x2009;=&#x2009;0.060; GPX1, P&#x2009;=&#x2009;0.063; and SOD2, P&#x2009;=&#x2009;0.052) and lipid metabolism (including PPAR&#x3b3;, P&#x2009;<&#x2009;0.05; SREBP1, P&#x2009;=&#x2009;0.059; and CPT1A, P&#x2009;=&#x2009;0.058). Additionally, CHF supplementation increased Firmicutes and decreased Bacteroidetes, Spirochaetes, and Synergistetes abundances (P&#x2009;<&#x2009;0.05), which may contribute to better meat quality.<br><br>CONCLUSIONS: Our results suggest that CHF supplementation improved the quality and nutritional value of meat, which will provide a theoretical basis for the utilization of CHF as a feed additive in spent hens' diets.}, }
@article {pmid39894814, year = {2025}, author = {El Leithy, AA and Youssef, ASE and Nassar, A and Aziz, RK and Khaled, NM and Mahrous, MT and Farahat, GN and Mohamed, AH and Bakr, YM}, title = {Long-read 16S rRNA amplicon sequencing reveals microbial characteristics in patients with colorectal adenomas and carcinoma lesions in Egypt.}, journal = {Gut pathogens}, volume = {17}, number = {1}, pages = {8}, doi = {10.1186/s13099-025-00681-9}, pmid = {39894814}, issn = {1757-4749}, abstract = {BACKGROUND: Colorectal cancer (CRC) is among the five leading causes of cancer incidence and mortality. During the past decade, the role of the gut microbiota and its dysbiosis in colorectal tumorigenesis has been emphasized. Metagenomics and amplicon-based microbiome profiling provided insights into the potential role of microbial dysbiosis in the development of CRC.<br><br>AIM: To address the scarcity of information on differential microbiome composition of tumor tissue in comparison to adenomas and the lack of such data from Egyptian patients with CRC.<br><br>MATERIALS AND METHODS: Long-read nanopore sequencing of 16S rRNA amplicons was used to profile the colonic microbiota from fresh colonoscopic biopsy samples of Egyptian patients with CRC and patients with colonic polyps.<br><br>RESULTS: Species richness of CRC lesions was significantly higher than that in colonic polyps (p-value&#x2009;=&#x2009;0.0078), while evenness of the CRC group was significantly lower than the colonic polyps group (p-value&#x2009;=&#x2009;0.0055). Both species richness and Shannon diversity index of the late onset CRC samples were significantly higher than those of the early onset ones. The Firmicutes-to-Bacteroidetes (F/B) ratio was significantly higher in the CRC group than in the colonic polyps group (p-value&#x2009;=&#x2009;0.0054), and significantly higher in samples from early-onset CRC. The Enterococcus spp. were significantly overabundant in patients with rectal cancer and early-onset CRC, while Staphylococcus spp. were significantly higher in patients with sigmoid cancer and late-onset CRC. In addition, the relative abundance of Fusobacterium nucleatum was significantly higher in CRC patients.<br><br>CONCLUSION: Differentiating trends were identified at phylum, genus, and species levels, despite the inter-individual differences. In summary, this study addressed the microbial dysbiosis associated with CRC and colonic polyps groups, paving the way for a better understanding of the pathogenesis of early and late-onset CRC in Egyptian patients.}, }
@article {pmid39894796, year = {2025}, author = {Palrasu, M and Kakar, K and Marudamuthu, A and Hamida, H and Thada, S and Zhong, Y and Staley, S and Busbee, PB and Li, J and Garcia-Buitrago, M and Nagarkatti, M and Nagarkatti, P}, title = {AhR Activation Transcriptionally Induces Anti-Microbial Peptide Alpha-Defensin 1 Leading to Reversal of Gut Microbiota Dysbiosis and Colitis.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2460538}, doi = {10.1080/19490976.2025.2460538}, pmid = {39894796}, issn = {1949-0984}, mesh = {Animals ; *alpha-Defensins/metabolism/genetics ; *Receptors, Aryl Hydrocarbon/metabolism/genetics ; *Dysbiosis/microbiology ; *Colitis/microbiology/chemically induced/metabolism ; *Gastrointestinal Microbiome ; Mice ; Humans ; Mice, Inbred C57BL ; Crohn Disease/microbiology/metabolism/drug therapy ; Epithelial Cells/metabolism/microbiology ; Intestinal Mucosa/metabolism/microbiology ; Disease Models, Animal ; Male ; Female ; Basic Helix-Loop-Helix Transcription Factors/metabolism/genetics ; }, abstract = {Alpha-defensin 1 is a small antimicrobial peptide that acts as the first line of defense against pathogens. It is induced following microbial cues and inflammatory signals in neutrophils and Paneth cells in the small intestine, which suggests that it plays a role in microbial homeostasis in the gut. The gut microbial products also serve as ligands for the aryl hydrocarbon receptor (AhR), an environmental sensor. In the current study, we investigated if there is any crosstalk between AhR and alpha-defensin 1. Interestingly, we found a positive correlation between AhR and alpha-defensin 1 protein levels in ileal tissues from active Crohn's' (CD) patients and epithelial cells (IECs) from multiple models of murine colitis. In vitro downregulation of AhR led to inhibition of α-defensin 1, while activation of AhR induced α-defensin 1 in IECs. AhR directly targeted the dioxin response element 3 (DRE3) region on the α-defensin 1 promoter in IECs. AhR-mediated induction of α-defensin 1 in colitis mice reversed the gut microbial dysbiosis and alleviated colitis. Our data identify a novel signaling pathway in which AhR acts as a transcription factor for α-defensin 1, leading to regulation of homeostasis between gut microbiota, intestinal mucosa, and mucosal immunity.}, }
@article {pmid39894735, year = {2025}, author = {Dizman, N and Roberts, M and McQuade, J}, title = {Beyond the Microbiome: The Role of the Metabolome and Diet in Antitumor Immunity.}, journal = {European urology focus}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.euf.2025.01.010}, pmid = {39894735}, issn = {2405-4569}, abstract = {Microbiome-derived or -modulated metabolites (short-chain fatty acids, bile acids, and amino acids) could mediate antitumor immunity. Diet offers an actionable route for manipulating both the microbiome and the metabolome. Diet- and microbiome-directed trials with robust translational correlates are eagerly awaited.}, }
@article {pmid39894724, year = {2025}, author = {Kleebayoon, A and Wiwanitkit, V}, title = {Effects of Electronic Cigarettes on Oral Microbiome and Metabolome in 3D Tissue-Engineered Models: Comment.}, journal = {International dental journal}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.identj.2025.01.004}, pmid = {39894724}, issn = {1875-595X}, }
@article {pmid39894593, year = {2025}, author = {Pack, A}, title = {Developing a Personalized Approach to Obstructive Sleep Apnea.}, journal = {Sleep medicine clinics}, volume = {20}, number = {1}, pages = {127-134}, doi = {10.1016/j.jsmc.2024.10.008}, pmid = {39894593}, issn = {1556-4088}, mesh = {Humans ; *Precision Medicine/methods ; *Sleep Apnea, Obstructive/therapy/diagnosis ; }, abstract = {All areas of medicine are focused on developing a personalized approach to diagnosis and treatment of specific conditions. This is based on the fundamental concept that all subjects with apparently the same disorder are different. There are multiple reasons for these differences. These include differences in the sequence of DNA, differences in the environment, differences in epigenetics, some of which may be driven by environmental differences and differences in the microbiome. These different factors will result in variations in multiple aspects of the phenotype. This includes different pathways to disease, different symptoms, different pattern of comorbidities and risk for adverse outcomes, and different physiological changes during sleep as a result of breathing episodes.}, }
@article {pmid38228101, year = {2025}, author = {Tan, Z and Mao, M and Jiang, Z and Hu, H and He, C and Zhai, C and Qian, G}, title = {Causal Relationship between Gut Microbiota and Aneurysm: A Mendelian Randomization Study.}, journal = {Cerebrovascular diseases (Basel, Switzerland)}, volume = {54}, number = {1}, pages = {59-69}, doi = {10.1159/000536177}, pmid = {38228101}, issn = {1421-9786}, mesh = {*Mendelian Randomization Analysis ; Humans ; *Gastrointestinal Microbiome ; *Genome-Wide Association Study ; Risk Factors ; Risk Assessment ; Bacteria/genetics/isolation &amp; purification/classification ; Phenotype ; Aortic Aneurysm/microbiology/diagnostic imaging/genetics ; Aortic Aneurysm, Abdominal/microbiology/diagnostic imaging ; Intracranial Aneurysm/microbiology/genetics ; }, abstract = {INTRODUCTION: Observational studies have suggested a possible relationship between gut microbiota (GM) and aneurysm development. However, the nature of this association remains unclear due to the inherent limitations of observational research, such as reverse causation and confounding factors. To address this knowledge deficit, this study aimed to investigate and establish a causal link between GM and aneurysm development.<br><br>METHODS: Summary statistics regarding GM and aneurysms were collected from relevant genome-wide association studies. Two samples were used in mendelian randomization (MR). The principal MR technique utilized was inverse-variance weighting, a technique renowned for producing reliable causal effect estimations. Additional MR methods, including weighted median (WM), MR-Egger, MR-PRESSO, and simple mode methods, were employed to ensure the robustness of the aforementioned association and investigate potential biases. Sensitivity analyses were performed to determine the consistency of the MR findings.<br><br>RESULTS: Varying associations were observed between specific microbial taxa and the different aneurysms analyzed. A negative correlation was observed between aortic aneurysm (AA) and Lentisphaerae, Lentisphaeria, and Victivallales. Conversely, the genus FamilyXIIIUCG001 exhibited an increased risk association. Regarding abdominal AA, Victivallaceae showed a reduced risk, and Bilophila and Catenibacterium were associated with an increased risk. For thoracic AA, negative and positive correlations were observed with Lentisphaerae and Turicibacter, respectively. Lastly, in the case of cerebral aneurysm (CA), Firmicutes and Haemophilus were associated with a decreased risk, and Lachnoclostridium demonstrated an increased risk of association.<br><br>CONCLUSION: Our research has established causal relationships between specific GM components and various aneurysms. The obtained knowledge may aid in the development of microbiome-based interventions and the identification of novel biomarkers for targeted prevention strategies.}, }
@article {pmid39897133, year = {2024}, author = {Longtine, AG and Greenberg, NT and Gonzalez, A and Lindquist, A and VanDongen, NS and Mahoney, SA and Rahman, G and Clayton, ZS and Ziemba, BP and Ludwig, KR and Widlansky, ME and Knight, R and Seals, DR and Brunt, VE}, title = {Oral Supplementation with the Short-Chain Fatty Acid Acetate Ameliorates Age-Related Arterial Dysfunction in Mice.}, journal = {Aging biology}, volume = {2}, number = {}, pages = {}, pmid = {39897133}, issn = {2994-2578}, abstract = {Adverse changes in the gut microbiome with aging are an emerging mediator of arterial dysfunction, which contributes to cardiovascular disease (CVD) development. We investigated the therapeutic potential of enhancing the bioavailability of gut-derived short-chain fatty acids (SCFAs; produced from dietary fiber) for improving age-related arterial dysfunction. We performed gut microbial whole-genome sequencing in young (3 months) versus old (24 months) male C57BL/6N mice to explore changes in bacterial taxonomic abundance and functional pathways with aging and relations to arterial function. We then supplemented young and old mice with the SCFA acetate in drinking water versus controls and versus a high-fiber diet for 8-10 weeks to test the effects of these interventions on vascular function and explore potential mechanisms. Of the various differences in the gut microbiomes of old mice, lower SCFA-producing capacity (taxonomic abundance and functional pathways) stood out as a key feature related to worse arterial function after adjusting for age. Acetate supplementation and a high-fiber diet reversed ~30% of the age-related increase in aortic pulse wave velocity (stiffness) and fully restored carotid artery endothelium-dependent dilation (endothelial function) to young levels. Acetate and a high-fiber diet reduced age-related increases in systemic inflammation. We also found that improvements in endothelial function were likely mediated by suppressed early growth response-1 signaling using innovative siRNA-based knockdown in isolated arteries. There were no effects of the interventions in young mice. Acetate supplementation was comparably effective for ameliorating arterial dysfunction with aging as a high-fiber diet and thus shows promise for reducing CVD risk in older adults.}, }
@article {pmid39894225, year = {2025}, author = {Kim, SY and Woo, SY and Kim, HL and Chang, YS and Ryu, S and Kim, HN}, title = {A shotgun metagenomic study identified short-chain fatty acid-producing species and their functions in the gut microbiome of adults with depressive symptoms: Large-scale shotgun sequencing data of the gut microbiota using a cross-sectional design.}, journal = {Journal of affective disorders}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jad.2025.01.149}, pmid = {39894225}, issn = {1573-2517}, abstract = {BACKGROUND: The gut-brain axis is emerging as a novel mechanism to explain depressive disorders.<br><br>METHODS: We performed shotgun metagenomic sequencing of stool samples obtained from 133 individuals with depression and 532 without depression. This study examined the taxonomy, functional pathways, and predicted metabolites profiles associated with depressive symptoms, using generalized linear models. To explore links between the taxonomic and functional pathway results, we compared the relative abundance of specific species contributing to pathways significantly associated with depressive symptoms.<br><br>RESULTS: Taxonomic composition suggested a disruption in short-chain fatty acid (SCFA)-producing capacity of the gut microbiome in the depressed group. Pathways related to SCFA biosynthesis were also depleted in this group. Faecalibacterium prausnitzii, a well-known SCFA-producing bacterium, was significantly decreased in the depressed group and was identified as a major contributor to the depleted pathways. When inferring the metabolites related to depression from metagenomic data, higher levels of docosapentaenoic acid, stearoyl ethanolamide, putrescine, and bilirubin were more likely to be found in the depressed group.<br><br>CONCLUSION: The present findings highlight the altered gut microbiota and associated SCFA-related pathways in individuals with depression. The depletion of F. prausnitzii and its contribution to SCFA production suggest that it is a potential therapeutic target for depression.}, }
@article {pmid39894030, year = {2025}, author = {The Lancet Microbe, }, title = {Brain microbiome: is it all in our heads?.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101075}, doi = {10.1016/j.lanmic.2025.101075}, pmid = {39894030}, issn = {2666-5247}, }
@article {pmid39893935, year = {2025}, author = {Luo, Y and Gao, J and Su, X and Li, H and Li, Y and Qi, W and Han, X and Han, J and Zhao, Y and Zhang, A and Zheng, Y and Qian, F and He, H}, title = {Unraveling the immunological landscape and gut microbiome in sepsis: a comprehensive approach to diagnosis and prognosis.}, journal = {EBioMedicine}, volume = {113}, number = {}, pages = {105586}, doi = {10.1016/j.ebiom.2025.105586}, pmid = {39893935}, issn = {2352-3964}, abstract = {BACKGROUND: Comprehensive and in-depth research on the immunophenotype of septic patients remains limited, and effective biomarkers for the diagnosis and treatment of sepsis are urgently needed in clinical practice.<br><br>METHODS: Blood samples from 31 septic patients in the Intensive Care Unit (ICU), 25 non-septic ICU patients, and 18&#xa0;healthy controls were analyzed using flow cytometry for deep immunophenotyping. Metagenomic sequencing was performed in 41 fecal samples, including 13 septic patients, 10 non-septic ICU patients, and 18 healthy controls. Immunophenotype shifts were evaluated using differential expression sliding window analysis, and random forest models were developed for sepsis diagnosis or prognosis prediction.<br><br>FINDINGS: Septic patients exhibited decreased proportions of natural killer (NK) cells and plasmacytoid dendritic cells (pDCs) in CD45[+] leukocytes compared with non-septic ICU patients and healthy controls. These changes statistically mediated the association of Bacteroides salyersiae with sepsis, suggesting a potential underlying mechanism. A&#xa0;combined diagnostic model incorporating B.salyersia, NK cells in CD45[+] leukocytes, and C-reactive protein (CRP) demonstrated high accuracy in distinguishing sepsis from non-sepsis (area under the receiver operating characteristic curve, AUC&#xa0;=&#xa0;0.950, 95% CI: 0.811-1.000). Immunophenotyping and disease severity analysis identified an Acute Physiology and Chronic Health Evaluation (APACHE) II score threshold of 21, effectively distinguishing mild (n&#xa0;=&#xa0;19) from severe (n&#xa0;=&#xa0;12) sepsis. A prognostic model based on the proportion of total lymphocytes, Helper T (Th) 17&#xa0;cells, CD4[+] effector memory T (TEM) cells, and Th1 cells in CD45[+] leukocytes achieved robust outcome prediction (AUC&#xa0;=&#xa0;0.906, 95% CI: 0.732-1.000), with further accuracy improvement when combined with clinical scores (AUC&#xa0;=&#xa0;0.938, 95% CI: 0.796-1.000).<br><br>INTERPRETATION: NK cell subsets within innate immunity exhibit significant diagnostic value for sepsis, particularly when combined with B.&#xa0;salyersiae and CRP. In addition, T cell phenotypes within adaptive immunity are correlated with sepsis severity and may serve as reliable prognostic markers.<br><br>FUNDING: This project was supported by the National Key R&amp;D Program of China (2023YFC2307600, 2021YFA1301000), Shanghai Municipal Science and Technology Major Project (2023SHZDZX02, 2017SHZDZX01), Shanghai Municipal Technology Standards Project (23DZ2202600).}, }
@article {pmid39893882, year = {2025}, author = {Xia, F and Fan, T and Wang, M and Yang, L and Ding, D and Wei, J and Zhou, Y and Jiang, D and Deng, S}, title = {Biodegradation of CAHs and BTEX in groundwater at a multi-polluted pesticide site undergoing natural attenuation: Insights from identifying key bioindicators using machine learning methods based on microbiome data.}, journal = {Ecotoxicology and environmental safety}, volume = {291}, number = {}, pages = {117609}, doi = {10.1016/j.ecoenv.2024.117609}, pmid = {39893882}, issn = {1090-2414}, abstract = {Groundwater pollution, particularly in retired pesticide sites, is a significant environmental concern due to the presence of chlorinated aliphatic hydrocarbons (CAHs) and benzene, toluene, ethylbenzene, and xylene (BTEX). These contaminants pose serious risks to ecosystems and human health. Natural attenuation (NA) has emerged as a sustainable solution, with microorganisms playing a crucial role in pollutant biodegradation. However, the interpretation of the diverse microbial communities in relation to complex pollutants is still challenging, and there is limited research in multi-polluted groundwater. Advanced machine learning (ML) algorithms help identify key microbial indicators for different pollution types (CAHs, BTEX plumes, and mixed plumes). The accuracy and Area Under the Curve (AUC) achieved by Support Vector Machines (SVM) were impressive, with values of 0.87 and 0.99, respectively. With the assistance of model explanation methods, we identified key bioindicators for different pollution types which were then analyzed using co-occurrence network analysis to better understand their potential roles in pollution degradation. The identified key genera indicate that oxidation and co-metabolism predominantly drive dechlorination processes within the CAHs group. In the BTEX group, the primary mechanism for BTEX degradation was observed to be anaerobic degradation under sulfate-reducing conditions. However, in the CAHs&amp;BTEX groups, the indicative genera suggested that BTEX degradation occurred under iron-reducing conditions and reductive dechlorination existed. Overall, this study establishes a framework for harnessing the power of ML alongside co-occurrence network analysis based on microbiome data to enhance understanding and provide a robust assessment of the natural attenuation degradation process at multi-polluted sites.}, }
@article {pmid39893588, year = {2025}, author = {Ha, S and Kim, J and Seo, HW and Kim, L and Yi, YS and Seo, SE and Kim, KH and Kim, S and An, JE and Kim, GJ and Ko, KC and Jun, S and Ryu, CM and Kwon, OS}, title = {Siderophore-Functionalized Nanodrug for Treating Antibiotic-Resistant Bacteria.}, journal = {ACS nano}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsnano.4c06501}, pmid = {39893588}, issn = {1936-086X}, abstract = {The development of nanodrugs targeting multidrug-resistant bacteria, while sparing the beneficial constituents of the microbiome, has emerged as a promising approach to combat disease and curb the rise of antimicrobial resistance. In this investigation, we devised a siderophore-functionalized nanodrug based on a gold nanoparticle construct (AuNP-NSC; Gold nanoparticle_N-heterocyclic_Siderophore_Cyanine7), offering an innovative treatment modality against drug-resistant bacterial pathogens. As a proof of concept, the efficacy of this nanodrug delivery and antimicrobial therapy was evaluated against the notoriously resistant bacterium P. aeruginosa. N-Heterocyclic carbenes (NHCs) exhibit a strong affinity for transition metals, forming highly stable complexes resistant to ligand displacement. The entry of siderophore-conjugated nanodrugs into bacteria is facilitated through specific receptors on the outer membrane. In our study, AuNP-NSC was specifically targeted and imported into resistant Gram-negative P. aeruginosa via binding with ferric iron. Treatment with the developed nanodrug significantly inhibited the proliferation of antibiotic-resistant P. aeruginosa, reducing bacterial counts by more than 95% and mitigating drug resistance. Furthermore, AuNP-NSC markedly diminished P. aeruginosa-induced skin lesions and forestalled systemic organ failure triggered by secondary sepsis in mouse models. These findings underscore the potential of nanodrugs as specialized therapeutic agents for the management of antibiotic-resistant bacterial infections.}, }
@article {pmid39893498, year = {2025}, author = {Zhao, H and Zhou, X and Song, Y and Zhao, W and Sun, Z and Zhu, J and Yu, Y}, title = {Multi-omics analyses identify gut microbiota-fecal metabolites-brain-cognition pathways in the Alzheimer's disease continuum.}, journal = {Alzheimer's research &amp; therapy}, volume = {17}, number = {1}, pages = {36}, pmid = {39893498}, issn = {1758-9193}, support = {YJS20230012//Postgraduate Innovation Research and Practice Program of Anhui Medical University/ ; 82471952//National Natural Science Foundation of China/ ; 82371928//National Natural Science Foundation of China/ ; 2308085MH277//Anhui Provincial Natural Science Foundation/ ; 2022AH051135//Scientific Research Key Project of Anhui Province Universities/ ; 2022xkj143//Scientific Research Foundation of Anhui Medical University/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Alzheimer Disease/metabolism/microbiology/diagnostic imaging/pathology ; Male ; Aged ; Female ; *Cognitive Dysfunction/metabolism/microbiology/diagnostic imaging ; *Feces/microbiology ; *Magnetic Resonance Imaging/methods ; Brain/metabolism/diagnostic imaging/pathology ; Cognition/physiology ; Dysbiosis/metabolism ; Metabolomics/methods ; Aged, 80 and over ; Middle Aged ; Metabolome ; Multiomics ; }, abstract = {BACKGROUND: Gut microbiota dysbiosis is linked to Alzheimer's disease (AD), but our understanding of the molecular and neuropathological bases underlying such association remains fragmentary.<br><br>METHODS: Using 16S rDNA amplicon sequencing, untargeted metabolomics, and multi-modal magnetic resonance imaging, we examined group differences in gut microbiome, fecal metabolome, neuroimaging measures, and cognitive variables across 30 patients with AD, 75 individuals with mild cognitive impairment (MCI), and 61 healthy controls (HC). Furthermore, we assessed the associations between these multi-omics changes using correlation and mediation analyses.<br><br>RESULTS: There were significant group differences in gut microbial composition, which were driven by 8 microbial taxa (e.g., Staphylococcus and Bacillus) exhibiting a progressive increase in relative abundance from HC to MCI to AD, and 2 taxa (e.g., Anaerostipes) showing a gradual decrease. 26 fecal metabolites (e.g., Arachidonic, Adrenic, and Lithocholic acids) exhibited a progressive increase from HC to MCI to AD. We also observed progressive gray matter atrophy in broadly distributed gray matter regions and gradual micro-structural integrity damage in widespread white matter tracts along the AD continuum. Integration of these multi-omics changes revealed significant associations between microbiota, metabolites, neuroimaging, and cognition. More importantly, we identified two potential mediation pathways: (1) microbiota &#x2192; metabolites &#x2192; neuroimaging &#x2192; cognition, and (2) microbiota &#x2192; metabolites &#x2192; cognition.<br><br>CONCLUSION: Aside from elucidating the underlying mechanism whereby gut microbiota dysbiosis is linked to AD, our findings may contribute to groundwork for future interventions targeting the microbiota-metabolites-brain-cognition pathways as a therapeutic strategy in the AD continuum.}, }
@article {pmid39893452, year = {2025}, author = {Pilmer, L and Woolley, L and Lymbery, A and Dam, C and Elizur, A and Foysal, MJ and Partridge, G}, title = {Exploring single cell microbial protein as a sustainable fishmeal alternative in yellowtail kingfish (Seriola lalandi) diets: impacts on health and gut microbiome.}, journal = {Journal of animal science and biotechnology}, volume = {16}, number = {1}, pages = {16}, pmid = {39893452}, issn = {1674-9782}, support = {2017-030//Fisheries Research and Development Corporation/ ; }, abstract = {BACKGROUND: With the global expansion of aquaculture and the increasing demand for fish meal, identifying appropriate and sustainable alternative protein sources for aquafeeds has become essential. Single-cell protein (SCP), derived from methanotrophic bacteria, presents a promising alternative by converting methane into protein, potentially addressing both the need for alternative protein sources and reducing industrial greenhouse gas emissions. This study aimed to evaluate the effects of different levels of SCP inclusion (0%, 25%, 50%, and 75% fish meal replacement) on the health, gene expression, and gut microbiome of yellowtail kingfish (YTK, Seriola lalandi) following a 35-day growth trial.<br><br>RESULTS: The study found that SCP inclusion at the highest level of fishmeal replacement (75%) induced a mild inflammatory response in the hindgut of the fish. However, micromorphological assessments of the hindgut, serum biochemistry, and gene expression analyses revealed no significant detrimental effects from SCP replacement. Notably, there were indications of improved lipid digestibility with SCP. Furthermore, SCP inclusion significantly enhanced microbial richness and altered the composition of the gut microbiome, introducing beneficial bacterial taxa that may contribute to improved gut health and resilience.<br><br>CONCLUSIONS: This study highlights SCP as a viable and sustainable alternative to fish meal in YTK diets. The findings suggest that SCP can be included in YTK diets without adverse health effects at moderate levels and may even offer benefits in terms of lipid digestibility and gut microbiome diversity. These results contribute to the advancement of more sustainable aquaculture practices.}, }
@article {pmid39893273, year = {2025}, author = {Coelho, C and Martins, LO and Tiago, I}, title = {Isolation of lignocellulosic biomass-degrading bacteria from Porcellio dilatatus gut-enriched cultures.}, journal = {Applied microbiology and biotechnology}, volume = {109}, number = {1}, pages = {35}, pmid = {39893273}, issn = {1432-0614}, support = {SFRH/BD/148270/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; IF/01061/2014/CP1223/CT0004//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {*Lignin/metabolism ; Animals ; *Bacteria/metabolism/classification/isolation &amp; purification/genetics ; *Gastrointestinal Microbiome ; *Biomass ; Biodegradation, Environmental ; Isopoda/microbiology/metabolism ; Chitin/metabolism ; Microbial Consortia ; }, abstract = {The lignocellulosic biomass (LCB) is an attractive, sustainable, and environmentally friendly alternative to fossil sources to produce biofuel, biomaterials, and biochemicals. However, its recalcitrant and heterogenous structure challenges its biodegradation and valorization. The gut microbiome of soil invertebrate species has emerged as a rich source of LCB-degrading bacteria and enzymes in terrestrial ecosystems. The primary objective of this investigation was to identify the bacterial communities within the Porcellio dilatatus gut (Crustacea: Isopods), to obtain enriched cultures, and to identify bacterial isolates with LCB-degrading activity. A total of 112 enriched cultures were screened, all exhibiting xylanolytic activity. Among them, 94 displayed cellulolytic activity, 30 showed chitinolytic activity, and 21 demonstrated ligninolytic activity. Four enriched cultures were selected, and 128 bacteria with cellulolytic, xylanolytic, chitinolytic, or ligninolytic activity were isolated and taxonomically classified. The obtained results reinforce the potential of bacterial communities within the digestive tract of soil invertebrates as a valuable source of lignocellulose-degrading microorganisms. Thirty-one isolates underwent in-depth enzymatic characterization, and five were selected and functionally evaluated. An artificial bacterial consortium was constructed to assess the potential benefits of using consortia to achieve enhanced LCB degradation. The positive results of this proof-of-concept artificial consortium (PdG-AC) can be used in future applications and is a valuable tool for enzymatic and microbial consortia engineering by, e.g., changing growth conditions for enhanced LCB-degrading abilities. KEY POINTS: • The gut microbiome of Porcellio dilatatus was characterized. • Porcellio dilatatus gut hosts many lignocellulose-degrading bacteria. • Developed an artificial bacterial consortium for lignocellulose degradation.}, }
@article {pmid39893166, year = {2025}, author = {Bourquin, M and Peter, H and Michoud, G and Busi, SB and Kohler, TJ and Robison, AL and Styllas, M and Ezzat, L and Geers, AU and Huss, M and Fodelianakis, S and ,  and Battin, TJ}, title = {Predicting climate-change impacts on the global glacier-fed stream microbiome.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1264}, pmid = {39893166}, issn = {2041-1723}, mesh = {*Microbiota/genetics ; *Ice Cover/microbiology ; *Climate Change ; *Phylogeny ; *Bacteria/genetics/classification ; *Rivers/microbiology ; Metagenome ; Biodiversity ; Ecosystem ; }, abstract = {The shrinkage of glaciers and the vanishing of glacier-fed streams (GFSs) are emblematic of climate change. However, forecasts of how GFS microbiome structure and function will change under projected climate change scenarios are lacking. Combining 2,333 prokaryotic metagenome-assembled genomes with climatic, glaciological, and environmental data collected by the Vanishing Glaciers project from 164 GFSs draining Earth's major mountain ranges, we here predict the future of the GFS microbiome until the end of the century under various climate change scenarios. Our model framework is rooted in a space-for-time substitution design and leverages statistical learning approaches. We predict that declining environmental selection promotes primary production in GFSs, stimulating both bacterial biomass and biodiversity. Concomitantly, predictions suggest that the phylogenetic structure of the GFS microbiome will change and entire bacterial clades are at risk. Furthermore, genomic projections reveal that microbiome functions will shift, with intensified solar energy acquisition pathways, heterotrophy and algal-bacterial interactions. Altogether, we project a 'greener' future of the world's GFSs accompanied by a loss of clades that have adapted to environmental harshness, with consequences for ecosystem functioning.}, }
@article {pmid39893159, year = {2025}, author = {Sampson, TR and Wallen, ZD and Won, WJ and Standaert, DG and Payami, H and Harms, AS}, title = {Alpha synuclein overexpression can drive microbiome dysbiosis in mice.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {4014}, pmid = {39893159}, issn = {2045-2322}, support = {ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-000375//Aligning Science Across Parkinson's/ ; }, mesh = {Animals ; *alpha-Synuclein/metabolism/genetics ; *Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Mice ; *Mice, Transgenic ; *Parkinson Disease/microbiology/metabolism/genetics ; Disease Models, Animal ; Humans ; Aging ; Male ; }, abstract = {Growing evidence indicates that persons with Parkinson disease (PD), have a unique composition of indigenous gut microbes. Given the long prodromal or pre-diagnosed period, longitudinal studies of the human and rodent gut microbiome before symptomatic onset and for the duration of the disease are currently lacking. PD is partially characterized by the accumulation of the protein α-synuclein (α-syn) into insoluble aggregates, in both the central and enteric nervous systems. As such, several experimental rodent and non-human primate models of α-syn overexpression recapitulate some of the hallmark pathophysiologies of PD. These animal models provide an opportunity to assess how the gut microbiome changes with age under disease-relevant conditions. Here, we used a transgenic mouse strain, which overexpress wild-type human α-syn to test how the gut microbiome composition responds in this model of PD pathology during aging. Using shotgun metagenomics, we find significant, age and genotype-dependent bacterial taxa whose abundance becomes altered with age. We reveal that α-syn overexpression can drive alterations to the gut microbiome composition and suggest that it limits diversity through age. Taxa that were most affected by genotype-age interaction were Lactobacillus and Bifidobacteria. In a mouse model, we showed direct link between alpha synuclein geneotype (hallmark of PD), a dysbiotic and low-diversity gut microbiome, and dysbiotic levels of Bifidobacteria and Lactobacillus (most robust features of PD microbiome). Given emerging data on the potential contributions of the gut microbiome to PD pathologies, our data provide an experimental foundation to understand how the PD-associated microbiome may arise as a trigger or co-pathology to disease.}, }
@article {pmid39892949, year = {2025}, author = {McGann, C and Phyu, R and Bittinger, K and Mukhopadhyay, S}, title = {Role of the Microbiome in Neonatal Infection: Pathogenesis and Implications for Management.}, journal = {Clinics in perinatology}, volume = {52}, number = {1}, pages = {147-166}, doi = {10.1016/j.clp.2024.10.010}, pmid = {39892949}, issn = {1557-9840}, mesh = {Humans ; Infant, Newborn ; *Probiotics/therapeutic use ; *Gastrointestinal Microbiome ; *Anti-Bacterial Agents/therapeutic use ; *Fecal Microbiota Transplantation/methods ; Neonatal Sepsis/microbiology/therapy ; Microbiota ; }, abstract = {The human microbiome refers to the collective genome of microorganisms, including bacteria, fungi, and viruses residing on human body surfaces that are in contact with the environment. Together these communities protect against invasive infections. Conversely, when disrupted, the microbiome can be the source of pathogens causing invasive infection. Interventions to manipulate it via probiotics, antibiotics, and fecal transplantation are available. The risk benefit of these interventions remains unclear. In this review, the authors discuss evidence linking the gut microbiome to neonatal sepsis and also discuss the challenges for translating this knowledge into better clinical care.}, }
@article {pmid39892863, year = {2025}, author = {Toffoli, M and Campisciano, G and Santin, A and Pegoraro, S and Zito, G and Spedicati, B and Balduit, A and Romano, F and Di Lorenzo, G and Mangogna, A and Tesolin, P and Nardone, GG and Zanotta, N and Sanna, S and Corbu, F and Kishore, U and Ricci, G and Bulla, R and Girotto, G and Agostinis, C}, title = {A possible association between low MBL/lectin pathway functionality and microbiota dysbiosis in endometriosis patients.}, journal = {Life sciences}, volume = {}, number = {}, pages = {123427}, doi = {10.1016/j.lfs.2025.123427}, pmid = {39892863}, issn = {1879-0631}, abstract = {AIMS: Endometriosis (EM) is a chronic inflammatory disorder with multifactorial etiologies (i.e., genetics and environmental factors, hormonal and immunological changes, and microbiome alterations). The complement system is one of the most frequently dysregulated pathways in EM. Mannose-binding lectin (MBL), a carbohydrate pattern recognition molecule, is the first described recognition subcomponent of the complement lectin pathway (LP). Here, we unveiled the interplay among MBL polymorphisms, plasma levels, LP functionality, and microbiota as potential contributors to EM pathogenesis.<br><br>MATERIALS AND METHODS: A cohort of 38 EM patients and 20 healthy controls was enrolled and the levels and functionality of the lectin pathway were assessed via ELISA assays. MBL genetic variants and the endometrial and vaginal microbiome were investigated and correlated.<br><br>KEY FINDINGS: High MBL levels were related to the disease severity, although not accountable to the MBL2 genotype. MBL and MASP-2 were present in the uterine mucosa but appeared to have no function at the endometriotic lesion. EM patients with LP functional deficit displayed pathogenic bacterial species more frequently in the endometrial microbiome. Moreover, women affected by EM showed a higher frequency of rare gene variants in the estrogen pathway genes, potentially affecting MBL plasma levels.<br><br>SIGNIFICANCE: A lower functionality of LP in the uterine mucosa may contribute to an unbalanced bacterial environment that could activate endometrial cells. Not only the genotype and the inflammatory condition, but also the estrogen pathway can cause altered MBL levels, thus contributing to changes in the LP functionality.}, }
@article {pmid39892390, year = {2025}, author = {Zhang, Y and Luo, K and Peters, BA and Mossavar-Rahmani, Y and Moon, JY and Wang, Y and Daviglus, ML and Van Horn, L and McClain, AC and Cordero, C and Floyd, JS and Yu, B and Walker, RW and Burk, RD and Kaplan, RC and Qi, Q}, title = {Sugar-sweetened beverage intake, gut microbiota, circulating metabolites, and diabetes risk in Hispanic Community Health Study/Study of Latinos.}, journal = {Cell metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmet.2024.12.004}, pmid = {39892390}, issn = {1932-7420}, abstract = {No population-based studies examined gut microbiota and related metabolites associated with sugar-sweetened beverage (SSB) intake among US adults. In this cohort of US Hispanic/Latino adults, higher SSB intake was associated with nine gut bacterial species, including lower abundances of several short-chain-fatty-acid producers, previously shown to be altered by fructose and glucose in animal studies, and higher abundances of fructose- and glucose-utilizing Clostridium bolteae and Anaerostipes caccae. Fifty-six serum metabolites were correlated with SSB intake and a gut microbiota score based on these SSB-related species in consistent directions. These metabolites were clustered into several modules, including a glycerophospholipid module, two modules comprising branched-chain amino acid (BCAA) and aromatic amino acid (AAA) derivatives from microbial metabolism, etc. Higher glycerophospholipid and BCAA derivative levels and lower AAA derivative levels were associated with higher incident diabetes risk during follow-up. These findings suggest a potential role of gut microbiota in the association between SSB intake and diabetes.}, }
@article {pmid39892258, year = {2025}, author = {Contos, P and Gibb, H and Murphy, NP and Jellinek, S and Wood, JL}, title = {Rebuilding microbiomes: Facilitating animal-microbe interactions through ecological restoration and rewilding.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124344}, doi = {10.1016/j.jenvman.2025.124344}, pmid = {39892258}, issn = {1095-8630}, abstract = {Restoring degraded ecosystems is a complex process that involves rebuilding myriad species interactions that make a functioning ecological community. Microorganisms are key to robust ecological restoration - their mutualisms with above-ground communities drive community assembly and increase host fitness. However, microbes are largely ignored during restoration and there is a significant knowledge gap regarding how to restore their interactions with above-ground communities. Here, we tested whether we could enhance interactions between microbes and their invertebrate hosts by reintroducing, or 'rewilding', leaf litter and soil from remnant sites containing species-rich microbial communities, into species poor and geographically isolated revegetated farmland sites. We sequenced both the soil microbiome and the gut microbiome of two dominant invertebrates: native Ecnolagria grandis beetles and introduced Ommatoiulus moreleti millipedes. We sampled 35 months after the initial reintroduction event in remnant (conservation area and source of litter and soil transplant), rewilding transplant (revegetation site with transplant), and control sites (revegetation with no transplant). We found that even ∼20 years after revegetation, restoration sites had distinct microbial communities compared to remnant areas. Although litter and soil transplants failed to increase soil microbial community similarity towards remnant sites, we found marked increases in the diversity and richness of E. grandis microbiomes and a greater degree of overlap with soil microbiomes within rewilding transplant sites relative to control sites. In contrast, there were few changes in O. moreleti microbiomes. Overall, our results suggest rewilding can recover some species interactions during restoration but may not influence all host-microbe systems.}, }
@article {pmid39892243, year = {2025}, author = {Mootapally, C and Sharma, P and Dash, S and Kumar, M and Sharma, S and Kothari, R and Nathani, N}, title = {Microbial drivers of biogeochemical cycles in deep sediments of the Kathiawar Peninsula Gulfs of India.}, journal = {The Science of the total environment}, volume = {965}, number = {}, pages = {178609}, doi = {10.1016/j.scitotenv.2025.178609}, pmid = {39892243}, issn = {1879-1026}, abstract = {Deep marine sediments are rich in microbial diversity, which holds metabolic repertoire to modulate biogeochemical cycles on a global scale. We undertook the environmental microbiome inhabiting the Gulf of Kathiawar Peninsula as a model system to understand the potential involvement of the deep marine sediment microbial community and as a cohort in the carbon, nitrogen, and sulfur biogeochemical cycles. These gulfs are characterized by dynamic tidal variations, diverse sediment textures, and nutrient-rich waters, driven by coastal processes and the interaction between natural coastal dynamics and anthropogenic inputs that shape its microbial community diversity. Our findings suggest that carbon fixation was carried out by Gamma-proteobacteria with CBB cycle-related genes or by microbial participants with Wood-Ljungdahl pathway-related genes. Microbial communities involved in nitrogen metabolism were observed to be rich and diverse, and most microbial communities potentially contribute to the nitrogen cycle via processing nitrogen oxides. Bacteria belonging to the KSB1 phylum were also found to fix nitrogen. The sulfur cycle was spread throughout, with Verrucomicrobiota phylum being a major contributor. The varying napAB genes, significantly lower in the Gulf of Kutch compared to the Gulf of Cambay and the Arabian Sea, mediated nitrate reduction. Dynamics between these pathways were mutually exclusive, and organic carbon oxidation was widespread across the microbial community. Finally, the proteobacteria phylum was highly versatile and conceivably contributed to biogeochemical flux with exceptionally high abundance and the ability to form metabolic networks to survive. The work highlights the importance of critical zones and microbial diversity therein, which needs further exploration.}, }
@article {pmid39892234, year = {2025}, author = {Nguyen, TBH and Henri-Sanvoisin, A and Le Floch, G and Picot, A}, title = {Delving into the soil and phytomicrobiome for disease suppression: A case study for the control of Fusarium Head Blight of cereals.}, journal = {The Science of the total environment}, volume = {965}, number = {}, pages = {178655}, doi = {10.1016/j.scitotenv.2025.178655}, pmid = {39892234}, issn = {1879-1026}, abstract = {Fusarium Head Blight is one of the most devastating fungal diseases of cereals worldwide, causing significant yield losses and affecting grain quality. The predominant role of the interactions within the Fusarium communities as well as with members of the phytomicrobiome in disease onset and development has gained increasing attention. Understanding the diversity and dynamics of bacterial and fungal communities across different substrates colonized by Fusarium spp. in wheat fields can provide valuable insights into disease ecology and lead to the discovery of native microorganisms with biocontrol potential. In this study, the bacterial and fungal communities associated with soil, maize residues, and wheat grains, were studied based on metabarcoding sequencing of 16S rRNA and ITS2 regions in six wheat fields over two years and characterized by different levels of FHB disease pressure and mycotoxin contamination. Overall, the diversity and composition of microbial communities were primarily influenced by substrate type followed by geographic origins of fields and sampling time, notably for grains and residues while the soil microbiome was less impacted by environmental fluctuations. Notably, our findings suggest that crop residues function as a transient substrate between soil and wheat microbiomes. In addition, we found several taxa either strongly negatively correlated to Fusarium spp. and/or to levels of Fusarium DNA or mycotoxins in grains or residues, including Cladosporium, Epicoccum, Paenibacillus, Curtobacterium, Pseudomonas, Pantoea, and Sphingomonas, which could be potential antagonistic agents against Fusarium spp. Altogether, these findings provide novel insights into the field microbiome functioning and their complex interactions with the Fusarium communities.}, }
@article {pmid39892168, year = {2025}, author = {Zha, H and Li, S and Zhuge, A and Shen, J and Yao, Y and Chang, K and Li, L}, title = {Hazard assessment of airborne and foodborne biodegradable polyhydroxyalkanoates microplastics and non-biodegradable polypropylene microplastics.}, journal = {Environment international}, volume = {196}, number = {}, pages = {109311}, doi = {10.1016/j.envint.2025.109311}, pmid = {39892168}, issn = {1873-6750}, abstract = {Microplastics (MP) are ubiquitous in the environment, and are toxic to various living organisms. Proper application of biodegradable plastics may alleviate the hazards of conventional non-biodegradable plastics. In the current study, multi-omics analyses were performed to compare the biodegradable polyhydroxyalkanoates (PHA) and non-biodegradable polypropylene (PP) MP for their toxicity on mouse liver and lung. Airborne PHA MP induced nasal microbiome dysbiosis, pulmonary microbiome alteration, pulmonary and serum metabolome disruption, and hepatic transcriptome disturbances, resulting in mild pulmonary toxicity. By contrast, airborne PP MP caused greater alterations in nasal and pulmonary microbiome, pulmonary and serum metabolome, and hepatic transcriptome, resulting in pulmonary and hepatic toxicity. Both foodborne PHA and PP MP caused intestinal microbiome dysbiosis, while foodborne PHA MP caused slighter intestinal and serum metabolome disruption, hepatic transcriptome disturbances and hepatotoxicity (e.g., lower serum aspartate aminotransferase and alanine aminotransferase) compared to foodborne PP MP. Some potential differential biomarkers were determined between PP and PHA MP exposures, i.e., nasal Allobaculum and pulmonary Alloprevotella for airborne PHA; nasal Lactobacillus and pulmonary Acinetobacter for airborne PP; intestinal Faecalibacterium for foodborne PHA; and intestinal unclassified_Erysipelatoclostridiaceae for foodborne PP. The results show that PHA MP can induce less pulmonary and hepatic toxicity compared to PP MP, suggesting PHA is a potential substitution for PP. The findings can benefit the hazard assessment of airborne and foodborne PHA and PP MP.}, }
@article {pmid39892121, year = {2025}, author = {Scairati, R and Auriemma, RS and Del Vecchio, G and Di Meglio, S and Pirchio, R and Graziadio, C and Pivonello, R and Colao, A}, title = {Diabetes mellitus, vaginal microbiome and sexual function: Outcomes in postmenopausal women.}, journal = {Maturitas}, volume = {194}, number = {}, pages = {108210}, doi = {10.1016/j.maturitas.2025.108210}, pmid = {39892121}, issn = {1873-4111}, abstract = {Diabetes mellitus is a chronic disease and a public health challenge worldwide, associated with numerous complications, including genitourinary infections and sexual dysfunction in women, particularly in menopause. The vaginal microbiome, which comprises beneficial and pathogenic bacteria, their genomes, and the surrounding environment, plays a crucial role in maintaining genitourinary health. Chronic hyperglycemia disrupts immune functions, exacerbates oxidative stress, and alters the vaginal microbiome, increasing the risk of genitourinary infections. Recent advances in microbial analysis, including 16S rRNA sequencing, have provided insights into the complex composition of the vaginal microbiome and its dysbiosis in diabetes mellitus. Some glucose-lowering drugs, such as sodium-glucose cotransporter 2 inhibitors, may increase the risk of genitourinary infections. Additionally, psychological distress, hormonal imbalances, and diabetes-related genitourinary symptoms contribute to sexual dysfunction in diabetic women. Healthcare for diabetic women requires a multidisciplinary approach, including not only glycemic control but also vaginal and sexual health assessment. A holistic approach is essential to advance personalized strategies, including medications and psychological support.}, }
@article {pmid39892071, year = {2025}, author = {Amirbekov, A and Vrchovecká, S and Říha, J and Wacławek, S and Ševců, A and Hrabák, P}, title = {Synergistic effect of Alnus glutinosa saplings and rhizosphere microorganisms on organochlorine pesticides remediation in contaminated soil.}, journal = {Chemosphere}, volume = {373}, number = {}, pages = {144174}, doi = {10.1016/j.chemosphere.2025.144174}, pmid = {39892071}, issn = {1879-1298}, abstract = {The widespread use of hexachlorocyclohexanes (HCH) as pesticides has raised environmental concerns due to their persistence and toxicity. Addressing the pressing need for effective bioremediation strategies, this study explores the effects of α-, β-, δ-, and ε-HCH isomers on the growth, hormonal changes, physiological parameters and bioaccumulation in Alnus glutinosa saplings (1-year-old and 2-year-old) and bacterial communities in polluted soil. A. glutinosa saplings not only withstanded HCH exposure but also enhanced the remediation efficiency by 6.8-24.4%, suggesting an acceleration of pollutant breakdown likely mediated by root exudates positively affecting the soil microbiome. Interestingly, 1-year-old saplings demonstrated greater remediation efficiency post-pruning than unpruned 2-year-old saplings, despite the latter having a larger root biomass. The hormonal analysis indicated that HCH presence led to a reduction in abscisic acid (ABA) and an increase in jasmonic acid (JA), with the magnitude of changes being age-dependent. Salicylic acid (SA) levels increased 1-year-old and decreased in 2-year-old saplings under HCH stress. Moreover, a higher presence of lin-degrading genes in the rhizosphere of treated saplings compared to controls confirmed ongoing biodegradation processes. The outcomes help to better understand the processes involved in degradation of persistent pesticides in soil. The mechanism of in-plant isomerization and the identification of metabolites should be the focus of future research.}, }
@article {pmid39891374, year = {2025}, author = {Mohamed-Ahmed, R and Robinson, D}, title = {Up-and-coming pharmacotherapeutic options for treating patients with refractory overactive bladder.}, journal = {Expert opinion on pharmacotherapy}, volume = {}, number = {}, pages = {}, doi = {10.1080/14656566.2025.2458577}, pmid = {39891374}, issn = {1744-7666}, abstract = {INTRODUCTION: Overactive bladder (OAB) is a prevalent disorder with a significant impact on quality of life. The pathophysiology of OAB is multifactorial and the majority of patients will require treatment with multiple therapies across the course of their disease. First line treatments include bladder retraining, fluid advice and pelvic floor muscle training. Following this, patients may be offered treatment with anticholinergic and β3 agonist medications. Anticholinergics are known to have high rates of discontinuation due to side effects and there are concerns regarding anticholinergic load and its impact on cognitive function in older adults.<br><br>AREAS COVERED: This paper aims to discuss the current and emerging treatment options available for patients who suffer from OAB.<br><br>EXPERT OPINION: The management of OAB in the clinical setting remains challenging. The goal of newer pharmacotherapies in OAB would be treatment that provides long term symptomatic relief with minimal side effects and an improved quality of life. The future of OAB research is promising and should consider the implications of the gut-bladder axis, regenerative medicine, biomarkers and the role of digital health.}, }
@article {pmid39891234, year = {2025}, author = {Noble, AS and Abbaszadeh, J and Lee, CK}, title = {Host selection is not a universal driver of phyllosphere community assembly among ecologically similar native New Zealand plant species.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {35}, pmid = {39891234}, issn = {2049-2618}, mesh = {New Zealand ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Plant Leaves/microbiology ; RNA, Ribosomal, 16S/genetics ; Plants/microbiology/classification ; Phylogeny ; }, abstract = {BACKGROUND: A growing body of evidence demonstrates that host-associated microbial communities of plant leaf surfaces (i.e. the phyllosphere) can influence host functional traits. However, it remains unclear whether host selection is a universal driver of phyllosphere community assembly. We targeted mānuka (Leptospermum scoparium) and three neighbouring non-mānuka plant species along an 1800-m transect in a New Zealand native bush to conduct a hypothesis-driven investigation of the relative influence of host species identity and stochastic dispersal on the composition of natural phyllosphere bacterial communities.<br><br>RESULTS: We detected significant correlations between host species identity and m&#x101;nuka phyllosphere communities that are consistent with a dominant role of host selection in the assembly of the m&#x101;nuka phyllosphere microbiome. In contrast, the phyllosphere community compositions of neighbouring, ecologically similar native plants were highly variable, suggesting that stochastic processes, such as dispersal, had a stronger influence on the phyllosphere microbiomes of those non-m&#x101;nuka plants compared to the phyllosphere microbiome of m&#x101;nuka. Furthermore, the distribution of phyllosphere taxa among plant species was congruent with a scenario in which microorganisms had dispersed from m&#x101;nuka to non-m&#x101;nuka phyllosphere microbiomes.<br><br>CONCLUSIONS: We conclude that host selection of phyllosphere communities is not and should not be presumed to be a universal trait across plant species. The specificity of the m&#x101;nuka phyllosphere microbiome suggests the presence of functionally significant bacteria that are under direct, possibly chemically mediated, selection by the host. Furthermore, we propose that phyllosphere microbiomes under strong host selection, such as that of m&#x101;nuka, may act as a source of microorganisms for the phyllosphere microbiomes of neighbouring plants. Video Abstract.}, }
@article {pmid39891232, year = {2025}, author = {Wulczynski, M and Brooks, SPJ and Green, J and Matias, F and Kalmokoff, M and Green-Johnson, JM and Clarke, ST}, title = {Environmental enrichment with nylon gnaw sticks introduces variation in Sprague Dawley rat immune and lower gastrointestinal parameters with differences between sexes.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {12}, pmid = {39891232}, issn = {2524-4671}, support = {SPJB//A-base funding at Health Canada/ ; RGPIN-2017-05237//Natural Sciences and Engineering Research Council of Canada Grant/ ; }, abstract = {BACKGROUND: Environmental enrichment (EE) is commonly included as an important component of animal housing to promote well being of laboratory animals; however, much remains to be learned about the impact of chewable forms of EE on experimental outcomes in the context of nutritional and microbiome-related studies, and whether outcomes differ between sexes. In the present study, nylon chew bones (gnaw sticks, GS) were evaluated for their effects on fermentation profiles, microbial community structure, and cytokine profiles of gastrointestinal and systemic tissues in pair-housed female and male Sprague Dawley (SD) rats.<br><br>RESULTS: Food consumption and weight gain were not significantly altered by access to GS. Cecal short-chain fatty acid and branched-chain fatty acid profiles significantly differed between sexes in rats with access to GS, and alpha diversity of the microbiome decreased in females provided GS. Sex-related tissue cytokine profiles also significantly differed between rats with and without access to GS.<br><br>CONCLUSIONS: These findings indicate that including GS can influence microbiota and immune-related parameters, in a sex dependent manner. This shows that environmental enrichment strategies need to be clearly reported in publications to properly evaluate and compare experimental results, especially with respect to the use of chewable EE in the context of studies examining diet, microbiome and immune parameters.}, }
@article {pmid39891205, year = {2025}, author = {Huang, D and Liao, J and Balcazar, JL and Ye, M and Wu, R and Wang, D and Alvarez, PJJ and Yu, P}, title = {Adaptive modification of antiviral defense systems in microbial community under Cr-induced stress.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {34}, pmid = {39891205}, issn = {2049-2618}, support = {42177113//National Natural Science Foundation of China/ ; 42277418//National Natural Science Foundation of China/ ; Y2022084//the Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; 2022YFC3704700//National Key Research and Development Program of China/ ; }, mesh = {*Chromium/pharmacology ; *Soil Microbiology ; *Stress, Physiological ; *Bacteria/genetics/classification/drug effects ; *Microbiota/drug effects ; Soil Pollutants ; Metagenomics/methods ; Viruses/genetics/drug effects/classification ; Soil/chemistry ; }, abstract = {BACKGROUND: The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence and significance of prokaryotic antiviral defense systems, their responses to abiotic stress and ecological consequences remain poorly understood in soil ecosystems. We established microcosm systems with varying concentrations of hexavalent chromium (Cr(VI)) to investigate the adaptive modifications of prokaryotic antiviral defense systems under abiotic stress.<br><br>RESULTS: Utilizing hybrid metagenomic assembly with long-read and short-read sequencing, we discovered that antiviral defense systems were more diverse and prevalent in heavily polluted soils, which was corroborated by meta-analyses of public datasets from various heavy metal-contaminated sites. As the Cr(VI) concentration increased, prokaryotes with defense systems favoring prokaryote-virus mutualism gradually supplanted those with defense systems incurring high adaptive costs. Additionally, as Cr(VI) concentrations increased, enriched antiviral defense systems exhibited synchronization with microbial heavy metal resistance genes. Furthermore, the proportion of antiviral defense systems carried by mobile genetic elements (MGEs), including plasmids and viruses, increased by approximately 43% and 39%, respectively, with rising Cr concentrations. This trend is conducive to strengthening the dissemination and sharing of defense resources within microbial communities.<br><br>CONCLUSIONS: Overall, our study reveals the adaptive modification of prokaryotic antiviral defense systems in soil ecosystems under abiotic stress, as well as their positive contributions to establishing prokaryote-virus mutualism and the evolution of microbial heavy metal resistance. These findings advance our understanding of microbial adaptation in stressful environments and may inspire novel approaches for microbiome manipulation and bioremediation. Video Abstract.}, }
@article {pmid39891202, year = {2025}, author = {Ma, S and Chen, Q and Zheng, Y and Ren, T and He, R and Cheng, L and Zou, P and Jing, C and Zhang, C and Li, Y}, title = {A tale for two roles: Root-secreted methyl ferulate inhibits P. nicotianae and enriches the rhizosphere Bacillus against black shank disease in tobacco.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {33}, pmid = {39891202}, issn = {2049-2618}, mesh = {*Plant Diseases/microbiology/prevention &amp; control ; *Rhizosphere ; *Plant Roots/microbiology ; *Nicotiana/microbiology ; *Bacillus/metabolism/genetics ; Soil Microbiology ; Disease Resistance ; }, abstract = {BACKGROUND: Root exudates serve as chemical signaling molecules that regulate rhizosphere interactions and control soil-borne diseases. The interactions between plants and the soil microbiome play dynamic and crucial roles in regulating the resistance of plants to biotic stress. However, the specific roles of many root exudates in plant pathogens remain unclear. The root exudate methyl ferulate, a naturally occurring and relatively non-toxic antifungal agent, has been applied to control postharvest pathogens and preserve foodstuffs and has not been used in plant disease control.<br><br>RESULTS: This study investigated the role of the root exudate methyl ferulate in controlling tobacco black shank disease. We observed that methyl ferulate was secreted in greater quantities in the tobacco resistant cultivar Gexin 3 following inoculation with P. nicotianae than in the susceptible cultivar Xiaohuangjin 1025. Our findings also revealed that methyl ferulate strongly inhibited P. nicotianae (EC50&#x2009;=&#x2009;67.51 &#xb5;g/mL), effectively controlling tobacco black shank disease by impairing NADH dehydrogenase function (the activity decreased by 50%). Furthermore, methyl ferulate recruited disease-suppressive rhizosphere microbes, such as Bacillus (the relative abundance of these microbes increases from 4.69% to 13.79%), thereby increasing disease resistance. The overexpression of caffeic acid O-methyltransferase NtCOMT10 resulted in increased methyl ferulate secretion (increased to 221.09% compared with that of the wild-type), concomitant improvement in the disease suppression of tobacco black shank disease (disease index decreased from 20% to less than 10%) and enrichment of beneficial microbes. In addition, methyl ferulate exerted antagonistic effects on other phytopathogens, such as B. cinerea, P. aphanidermatum, P. sojae, C. lagenarium and F. oxysporum.<br><br>CONCLUSIONS: Our findings indicated that methyl ferulate, a component of root exudates regulated by NtCOMT10, can inhibit phytopathogens and enrich rhizosphere Bacillus against plant disease. The great dual effect of methyl ferulate on the control of phytopathogens and its low cost enable a novel potential avenue for controlling soil-borne fungal diseases. This study provides ingenious insights into controlling soil-borne diseases through beneficial root exudates. Video Abstract.}, }
@article {pmid39891198, year = {2025}, author = {Berdeja, MP and Reynolds, NK and Pawlowska, T and Heuvel, JEV}, title = {Commercial bioinoculants improve colonization but do not alter the arbuscular mycorrhizal fungal community of greenhouse-grown grapevine roots.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {15}, pmid = {39891198}, issn = {2524-6372}, abstract = {BACKGROUND: Arbuscular mycorrhizal fungi (AMF) are beneficial root symbionts contributing to improved plant growth and development and resistance to abiotic and biotic stresses. Commercial bioinoculants containing AMF are widely considered as an alternative to agrochemicals in vineyards. However, their effects on grapevine plants grown in soil containing native communities of AMF are still poorly understood. In a greenhouse experiment, we evaluated the influence of five different bioinoculants on the composition of native AMF communities of young Cabernet Sauvignon vines grown in a non-sterile soil. Root colonization, leaf nitrogen concentration, plant biomass and root morphology were assessed, and AMF communities of inoculated and non-inoculated grapevine roots were profiled using high-throughput sequencing.<br><br>RESULTS: Contrary to our predictions, no differences in the microbiome of plants exposed to native AMF communities versus commercial AMF bioinoculants&#x2009;+&#x2009;native AMF communities were detected in roots. However, inoculation induced positive changes in root traits as well as increased AMF colonization, plant biomass, and leaf nitrogen. Most of these desirable functional traits were positively correlated with the relative abundance of operational taxonomic units identified as Glomus, Rhizophagus and Claroideoglomus genera.<br><br>CONCLUSION: These results suggest synergistic interactions between commercial AMF bioinoculants and native AMF communities of roots to promote grapevine growth. Long-term studies with further genomics, metabolomics and physiological research are needed to provide a deeper understanding of the symbiotic interaction among grapevine roots, bioinoculants and natural AMF communities and their role to promote plant adaptation to current environmental concerns.}, }
@article {pmid39891167, year = {2025}, author = {Marangon, E and Rädecker, N and Li, JYQ and Terzin, M and Buerger, P and Webster, NS and Bourne, DG and Laffy, PW}, title = {Destabilization of mutualistic interactions shapes the early heat stress response of the coral holobiont.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {31}, pmid = {39891167}, issn = {2049-2618}, mesh = {*Anthozoa/microbiology/physiology ; *Symbiosis ; Animals ; *Heat-Shock Response/physiology ; *Dinoflagellida/physiology/genetics ; RNA, Ribosomal, 16S/genetics ; Coral Reefs ; Microbiota/physiology ; Hot Temperature ; Bacteria/classification/genetics/metabolism ; }, abstract = {BACKGROUND: The stability of the symbiotic relationship between coral and their dinoflagellate algae (Symbiodiniaceae) is disrupted by ocean warming. Although the coral thermal response depends on the complex interactions between host, Symbiodiniaceae and prokaryotes, the mechanisms underlying the initial destabilization of these symbioses are poorly understood.<br><br>RESULTS: In a 2-month manipulative experiment, we exposed the coral Porites lutea to gradually increasing temperatures corresponding to 0-8 degree heating weeks (DHW) and assessed the response of the coral holobiont using coral and Symbiodiniaceae transcriptomics, microbial 16S rRNA gene sequencing and physiological measurements. From early stages of heat stress (<&#x2009;1 DHW), the increase in metabolic turnover shifted the holobiont to a net heterotrophic state in which algal-derived nutrients were insufficient to meet host energy demands, resulting in reduced holobiont performance at 1 DHW. We postulate the altered nutrient cycling also affected the coral-associated microbial community, with the relative abundance of Endozoicomonas bacteria declining under increasing heat stress. Integration of holobiont stress responses correlated this decline to an increase in expression of a host ADP-ribosylation factor, suggesting that Symbiodiniaceae and Endozoicomonas may underlie similar endosymbiotic regulatory processes.<br><br>CONCLUSIONS: The thermotolerance of coral holobionts therefore is influenced by the nutritional status of its members and their interactions, and this identified metabolic interdependency highlights the importance of applying an integrative approach to guide coral reef conservation efforts. Video Abstract.}, }
@article {pmid39891011, year = {2025}, author = {Bakshani, CR and Ojuri, TO and Pilgaard, B and Holck, J and McInnes, R and Kozak, RP and Zakhour, M and Çakaj, S and Kerouedan, M and Newton, E and Bolam, DN and Crouch, LI}, title = {Carbohydrate-active enzymes from Akkermansia muciniphila break down mucin O-glycans to completion.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {39891011}, issn = {2058-5276}, support = {224240/Z/21/Z//Wellcome Trust (Wellcome)/ ; 224240/Z/21/Z//Wellcome Trust (Wellcome)/ ; SBF0061175/AMS_/Academy of Medical Sciences/United Kingdom ; BB/M029018/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, abstract = {Akkermansia muciniphila is a human microbial symbiont residing in the mucosal layer of the large intestine. Its main carbon source is the highly heterogeneous mucin glycoprotein, and it uses an array of carbohydrate-active enzymes and sulfatases to access this complex energy source. Here we describe the biochemical characterization of 54 glycoside hydrolases, 11 sulfatases and 1 polysaccharide lyase from A. muciniphila to provide a holistic understanding of their carbohydrate-degrading activities. This was achieved using a variety of liquid chromatography techniques, mass spectrometry, enzyme kinetics and thin-layer chromatography. These results are supported with A. muciniphila growth and whole-cell assays. We find that these enzymes can act synergistically to degrade the O-glycans on the mucin polypeptide to completion, down to the core N-acetylgalactosaime. In addition, these enzymes can break down human breast milk oligosaccharide, ganglioside and globoside glycan structures, showing their capacity to target a variety of host glycans. These data provide a resource to understand the full degradative capability of the gut microbiome member A. muciniphila.}, }
@article {pmid39890997, year = {2025}, author = {Marter, P and Freese, HM and Ringel, V and Brinkmann, H and Pradella, S and Rohde, M and Jarek, M and Spröer, C and Wagner-Döbler, I and Overmann, J and Bunk, B and Petersen, J}, title = {Superior Resolution Profiling of the Coleofasciculus Microbiome by Amplicon Sequencing of the Complete 16S rRNA Gene and ITS Region.}, journal = {Environmental microbiology reports}, volume = {17}, number = {1}, pages = {e70066}, doi = {10.1111/1758-2229.70066}, pmid = {39890997}, issn = {1758-2229}, support = {34509606-TRR 51//Deutsche Forschungsgemeinschaft/ ; //Collaborative Research Center Roseobacter (TRR51)/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Cyanobacteria/genetics/classification/isolation &amp; purification ; Sequence Analysis, DNA ; Phylogeny ; DNA, Ribosomal Spacer/genetics ; DNA, Bacterial/genetics ; Bacteria/genetics/classification/isolation &amp; purification ; Metagenomics ; }, abstract = {The filamentous cyanobacterium Coleofasciculus chthonoplastes is the key primary producer of marine microbial mats. We elucidated the microbiomes of 32 non-axenic Coleofasciculus isolates using PacBio-based amplicon sequencing of the complete 16S rRNA gene and the internally transcribed spacer (16S-ITS). The length of authentic amplicon sequence variants (ASVs) ranged from 1827 to 3044 nucleotides (median: 2267 nt). The results, which were complemented by metagenome analyses and cultivation approaches, revealed the presence of more than 70 associated heterotrophs in the culture of Coleofasciculus sp. WW12. The great bacterial diversity in the cyanosphere is dominated by Pseudomonadota (59%) and Bacteroidota (23%). Allelic ribosomal operon variants were detected in 18 Coleofasciculus strains and our analyses proposed the presence of at least four different species. A comparative analysis of cyanobacterial microbiomes documented complementary advantages of amplicon sequencing versus metagenomics with an individual strength of the 16S-ITS approach in terms of (i) ribosomal target sequence quality, (ii) contaminant detection and (iii) identification of rare bacteria. The characterisation of the Coleofasciculus microbiome showed that long-read amplicon sequencing of the 16S-ITS region is the method of choice for rapid profiling of non-axenic cyanobacteria. Its superior resolution allows a reliable differentiation of even very closely related strains.}, }
@article {pmid39890778, year = {2025}, author = {Zhu, B and Bai, Y and Yeo, YY and Lu, X and Rovira-Clavé, X and Chen, H and Yeung, J and Nkosi, D and Glickman, J and Delgado-Gonzalez, A and Gerber, GK and Angelo, M and Shalek, AK and Nolan, GP and Jiang, S}, title = {A multi-omics spatial framework for host-microbiome dissection within the intestinal tissue microenvironment.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1230}, pmid = {39890778}, issn = {2041-1723}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Colitis/microbiology ; Mice ; *Proteomics ; *Mice, Inbred C57BL ; Intestinal Mucosa/microbiology/metabolism ; Glycomics/methods ; Disease Models, Animal ; Cellular Microenvironment ; Intestines/microbiology ; Transcriptome ; Host Microbial Interactions/immunology ; Multiomics ; }, abstract = {The intricate interactions between the host immune system and its microbiome constituents undergo dynamic shifts in response to perturbations to the intestinal tissue environment. Our ability to study these events on the systems level is significantly limited by in situ approaches capable of generating simultaneous insights from both host and microbial communities. Here, we introduce Microbiome Cartography (MicroCart), a framework for simultaneous in situ probing of host and microbiome across multiple spatial modalities. We demonstrate MicroCart by investigating gut host and microbiome changes in a murine colitis model, using spatial proteomics, transcriptomics, and glycomics. Our findings reveal a global but systematic transformation in tissue immune responses, encompassing tissue-level remodeling in response to host immune and epithelial cell state perturbations, bacterial population shifts, localized inflammatory responses, and metabolic process alterations during colitis. MicroCart enables a deep investigation of the intricate interplay between the host tissue and its microbiome with spatial multi-omics.}, }
@article {pmid39890664, year = {2025}, author = {Zhou, Y and Jiang, P and Ding, Y and Zhang, Y and Yang, S and Liu, X and Cao, C and Luo, G and Ou, L}, title = {Deciphering the Distinct Associations of Rhizospheric and Endospheric Microbiomes with Capsicum Plant Pathological Status.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {1}, pmid = {39890664}, issn = {1432-184X}, support = {2023YFD1201502//National Key Research and Development Program of China/ ; 42107262//National Natural Science Foundation of China/ ; CARS-24-A05//China Agriculture Research System of MOF and MARA/ ; }, mesh = {*Capsicum/microbiology/growth &amp; development ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Endophytes/isolation &amp; purification/classification/physiology/genetics ; Plant Diseases/microbiology ; Plant Roots/microbiology ; Fungi/classification/genetics/isolation &amp; purification/physiology ; }, abstract = {Exploring endospheric and rhizospheric microbiomes and their associations can help us to understand the pathological status of capsicum (Capsicum annuum L.) for implementing appropriate management strategies. To elucidate the differences among plants with distinct pathological status in the communities and functions of the endospheric and rhizospheric microbiomes, the samples of healthy and diseased capsicum plants, along with their rhizosphere soils, were collected from a long-term cultivation field. The results indicated a higher bacterial richness in the healthy rhizosphere than in the diseased rhizosphere (P < 0.05), with rhizospheric bacterial diversity surpassing endospheric bacterial diversity. The community assemblies of both the endospheric and rhizospheric microbiomes were driven by a combination of stochastic and deterministic processes, with the stochastic processes playing a primary role. The majority of co-enriched taxa in the healthy endophyte and rhizosphere mainly belonged to bacterial Proteobacteria, Actinobacteria, and Firmicutes, as well as fungal Ascomycota. Most of the bacterial indicators, primarily Alphaproteobacteria and Actinobacteria, were enriched in the healthy rhizosphere, but not in the diseased rhizosphere. In addition, most of the fungal indicators were enriched in both the healthy and diseased endosphere. The diseased endophyte constituted a less complex and stable microbial community than the healthy endophyte, and meanwhile, the diseased rhizosphere exhibited a higher complexity but lower stability than the healthy rhizosphere. Notably, only a microbial function, namely biosynthesis of other secondary metabolites, was higher in the healthy endophytes than in the diseased endophyte. These findings indicated the distinct responses of rhizospheric and endospheric microbiomes to capsicum pathological status, and in particular, provided a new insight into leveraging soil and plant microbial resources to enhance agriculture production.}, }
@article {pmid39890521, year = {2025}, author = {Rafie, E and Zugman, M and Pal, SK and Routy, B and Elkrief, A}, title = {What Is the Role of Fecal Microbiota Transplantation in Immunotherapy Trials? Current Perspectives and Future Directions.}, journal = {European urology focus}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.euf.2024.12.009}, pmid = {39890521}, issn = {2405-4569}, abstract = {Immune checkpoint inhibitors (ICIs) are rapidly transforming the treatment landscape of genitourinary and other immunogenic malignancies. Despite these advances, biomarkers for the prediction of ICI response remain to be established. The gut microbiome has been identified as a modulator of immune regulation and a potential regulator of response to ICIs. Fecal microbiota transplantation (FMT) has emerged as a potential novel therapeutic tool to enhance ICI response, as demonstrated in several trials, spanning across genitourinary malignancies as well as others. While safety and clinical potential of FMT have been demonstrated, FMT parameters including optimal treatment regimens, bowel preparation protocols, patient selection, and donor-host compatibility need to be defined. Furthermore, targeted interventions including probiotic supplementation represent promising therapeutic avenues meriting further study.}, }
@article {pmid39890294, year = {2025}, author = {Baker, JM and Dickson, RP}, title = {The Microbiome and Pulmonary Immune Function.}, journal = {Clinics in chest medicine}, volume = {46}, number = {1}, pages = {77-91}, doi = {10.1016/j.ccm.2024.10.006}, pmid = {39890294}, issn = {1557-8216}, mesh = {Humans ; *Microbiota/immunology/physiology ; *Lung/microbiology/immunology ; Lung Diseases/immunology/microbiology ; }, abstract = {In the last decade, the lung microbiome field has matured into a promising area of translational and clinical research due to emerging evidence indicating a role for respiratory microbiota in lung immunity and pathogenesis. Here, we review recent insights pertaining to the lung microbiome's relationship with pulmonary immune function. We discuss areas of future investigation that will be essential to the development of immunomodulatory therapies targeting the respiratory microbiome.}, }
@article {pmid39890144, year = {2025}, author = {Pogreba Brown, K and Austhof, E and McFadden, CM and Scranton, C and Sun, X and Vujkovic-Cviji, I and Rodriguez, D and Falk, L and Heslin, KM and Arani, G and Obergh, V and Bessey, K and Cooper, K}, title = {Determining the incidence, risk factors and biological drivers of irritable bowel syndrome (IBS) as part of the constellation of postacute sequelae of SARS-CoV-2 infection (PASC) outcomes in the Arizona CoVHORT-GI: a longitudinal cohort study.}, journal = {BMJ open}, volume = {15}, number = {1}, pages = {e095093}, doi = {10.1136/bmjopen-2024-095093}, pmid = {39890144}, issn = {2044-6055}, mesh = {Humans ; *COVID-19/epidemiology ; *Irritable Bowel Syndrome/epidemiology ; Longitudinal Studies ; Arizona/epidemiology ; *Post-Acute COVID-19 Syndrome ; Incidence ; Risk Factors ; *SARS-CoV-2 ; Male ; Female ; Biomarkers/blood ; Adult ; Middle Aged ; Gastrointestinal Microbiome ; }, abstract = {INTRODUCTION: Postacute sequelae of SARS-CoV-2 infection (PASC) are extensive. Also known as long COVID, primary outcomes reported are neurologic, cardiac and respiratory in nature. However, several studies have also reported an increase in gastrointestinal (GI) symptoms and syndromes following COVID-19. This study of PASC will include extensive analyses of GI symptoms, determine if people with pre-existing irritable bowel syndrome (IBS) are at higher risk of developing PASC generally or PASC-GI, and which biomarkers are impacted and to what degree. This R01 study is being funded by the National Institute of Diabetes and Digestive and Kidney Diseases (1R01DK135483-01) from 2023 to 2028.<br><br>METHODS AND ANALYSES: This study combines a longitudinal epidemiologic cohort study and in-depth, novel biologic analyses. In collaboration with a pre-existing study, the Arizona CoVID-19 Cohort (CoVHORT)-GI will recruit participants based on the history of COVID infection(s), new or ongoing GI symptoms 3-6 months postinfection, and pre-existing or incident IBS diagnosis to represent five study groups for comparison and analyses. A subset (n=1000) of those recruited will submit both stool and blood samples. Both samples will undergo a novel method to quantitate humoral and mucosal immune responses to host-derived faecal communities in conjunction with magnetic bead-based separation and high-depth shotgun microbial sequencing. Stool samples will also undergo traditional microbiome analyses (diversity and abundance) and faecal calprotectin assays. Additional serum analyses will aim to determine if a proteomics-based signature exists that differentiates a unique biomarker compositional signature discriminating PASC-GI versus no PASC. All laboratory data will be linked with in-depth epidemiologic data on demographics, symptoms and chronic conditions.<br><br>ETHICS AND DISSEMINATION: This study involves human participants and was approved by the University of Arizona Institutional Review Board (IRB (#00002332) and has been deemed minimal risk. Participants gave informed consent to participate in the study before taking part. All publications from the study will be shared back to participants along with alternative lay summaries and webinars to communicate key findings. The data management plan has been published and is publicly available online, including protocols for data requests.}, }
@article {pmid39890137, year = {2025}, author = {Kennedy, EC and Ross, FC and O'Shea, CA and Lavelle, A and Ross, P and Dempsey, E and Stanton, C and Hawkes, CP}, title = {Observational study protocol: the faecal microbiome in the acute stage of new-onset paediatric type 1 diabetes in an Irish cohort.}, journal = {BMJ open}, volume = {15}, number = {1}, pages = {e089206}, doi = {10.1136/bmjopen-2024-089206}, pmid = {39890137}, issn = {2044-6055}, mesh = {Humans ; *Diabetes Mellitus, Type 1/microbiology ; *Feces/microbiology ; Child ; *Gastrointestinal Microbiome ; Male ; Female ; Prospective Studies ; Ireland ; Child, Preschool ; Adolescent ; Metabolome ; }, abstract = {INTRODUCTION: Type 1 diabetes (T1D) is an autoimmune-mediated disorder caused by the destruction of pancreatic beta cells. Although there is an underlying genetic predisposition to developing T1D, the trigger is multifactorial and likely includes environmental factors. The intestinal microbiome has been identified as one such factor. Previous studies have illustrated differences in the microbiota of people with T1D compared with healthy controls. This study aims to describe the evolution of the microbiome and metabolome during the first year of clinical T1D, or stage 3 T1D diagnosis, and investigate whether there are differences in the microbiome and metabolome of children who present with and without diabetic ketoacidosis. The study will also explore possible associations between the microbiome, metabolome, glycaemic control and beta cell reserve.<br><br>METHODS AND ANALYSIS: This prospective cohort study will include children with newly diagnosed T1D and sibling controls (n=100, males and females) and their faecal microbiome will be characterised using shotgun metagenomic sequencing at multiple time points during the first year of diagnosis. We will develop a microbial culture biobank based on culturomic studies of stool samples from the healthy controls that will support future investigation. Metabolomic analysis will aim to identify additional biomarkers which may be involved in disease presentation and progression. Through this initial exploratory study, we aim to identify specific microbial biomarkers which may be used as future interventional targets throughout the various stages of T1D progression.<br><br>ETHICS AND DISSEMINATION: This study has been approved by the Clinical Research Ethics Committee of the Cork Teaching Hospitals. Study results will be available to patients with T1D and their families, carers, support networks and microbiome societies and other researchers.<br><br>TRIAL REGISTRATION NUMBER: The clinicaltrials.gov registration number for this trial is NCT06157736.}, }
@article {pmid39890135, year = {2025}, author = {George, S and Lucero, Y and Cabrera, C and Zabala Torres, B and Fernández, L and Mamani, N and Lagomarcino, A and Aguilera, X and O'Ryan, M}, title = {Protocol for a randomised 'screen-and-treat' Helicobacter pylori eradication trial in 14-18-years-old adolescents residing in three regions of Chile: effectiveness and microbiological host implications.}, journal = {BMJ open}, volume = {15}, number = {1}, pages = {e084984}, doi = {10.1136/bmjopen-2024-084984}, pmid = {39890135}, issn = {2044-6055}, mesh = {Humans ; *Helicobacter Infections/drug therapy ; Adolescent ; *Helicobacter pylori ; Chile ; *Anti-Bacterial Agents/therapeutic use ; Male ; Female ; Breath Tests ; Randomized Controlled Trials as Topic ; Mass Screening/methods ; }, abstract = {INTRODUCTION: Gastric cancer is a major global health concern, being the final stage of a long-term process, primarily associated with Helicobacter pylori (H. pylori) infection. Early childhood acquisition of H. pylori with low spontaneous eradication rates underscores the need for preventive measures. Our previous pilot treatment study revealed high eradication rates, favourable tolerance profile and a decline in serum biomarkers indicative of gastric damage in asymptomatic school-aged children. The purpose of this study is to determine the potential benefit of a 'screen-and-treat' strategy targeting persistently infected, asymptomatic adolescents. Specific aims are to assess eradication efficacy, its clinical and molecular outcomes and potential clinical and microbiological side effects.<br><br>METHODS AND ANALYSIS: The screening phase will involve testing 500-1000 asymptomatic adolescents aged 14-18 from three cities in Chile using the urea breath test (UBT) to identify 210 participants with persistent infection. They will proceed to a randomised, non-blinded, controlled trial, receiving either a sequential eradication scheme for H. pylori or no treatment. Follow-up will span up to 24 months post-treatment, involving UBT, gastroenterological assessments and blood and stool sample collections. Concurrently, a subset of 60 uninfected adolescents will undergo matched follow-up. Enzyme-linked immunosorbent assay (ELISA) commercial kits will evaluate gastric damage biomarkers in serum (pepsinogen I and II, gastrin-17, VCAM-1, CXCL13). Stool samples will be employed for Escherichia coli and Enterococcus spp-culture, assessing AMR via the disk diffusion method. H. pylori clarithromycin resistance will be determined by molecular method from stool samples. The gut microbiome will be characterised by amplifying and sequencing the 16S rRNA gene from stool samples, followed by bioinformatics analysis.<br><br>ETHICS AND DISSEMINATION: Approved by the Human Research Ethics Committee at the Faculty of Medicine, University of Chile (073-2022). Findings will be disseminated in peer-reviewed journals and scientific meetings to guide future practices.<br><br>TRIAL REGISTRATION NUMBER: NCT05926804.}, }
@article {pmid39890073, year = {2025}, author = {Waters, SM and Roskam, E and Smith, PE and Kenny, DA and Popova, M and Eugène, M and Morgavi, DP}, title = {The role of rumen microbiome in the development of methane mitigation strategies for ruminant livestock.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2024-25778}, pmid = {39890073}, issn = {1525-3198}, abstract = {Ruminants play an important role in global food security and nutrition. The rumen microbial community provides ruminants with a unique ability to convert human indigestible plant matter, into high quality edible protein. However, enteric CH4 produced in the rumen is both a potent GHG and a metabolizable energy loss for ruminants. As the rumen microbiome constitutes 15-40% of the inter-animal variation in enteric CH4 emissions, understanding the microbiological mechanisms underpinning ruminal methanogenesis and its interaction with the host animal, is crucial for developing CH4 mitigation strategies. Variation in the relative abundance of different microbial species has been observed in cattle with contrasting residual CH4 emission and CH4 yield with up to 20% of the variation in inter-animal CH4 emissions attributable to the presence of a small number of microbial species. The demonstration of ruminotypes associated with high or low CH4 emissions suggests that interactions within complex microbial consortia and with their host are a major source of variation in CH4 emissions. Consequently, microbiome-assisted genomic approaches are being developed to select low CH4 emitting cattle, with breeding values for enteric CH4 being included as part of national breeding programmes. Generating rumen microbiome data for use in selection programs is expensive, therefore, identifying microbial biomarkers in milk or plasma to develop predictive models which include microbial predictors in equations based on animal related data, is required. A better understanding of the rumen microbiome has also aided the development and refinements of anti-methanogenic feed additives. However, these strategies, which increase the amount of reducing equivalents in the rumen ecosystem, do not generally result in an enrichment of propionate or an improvement in animal performance. Current research aims to provide alternative sinks to reducing equivalents and to stimulate activity of commensal microbes or the supplementation of direct fed microbials to capture lost energy. Furthering our knowledge of the rumen microbiome and its interaction with the host, will aid in the development of CH4 mitigation strategies for ruminant livestock.}, }
@article {pmid39890034, year = {2025}, author = {Huchzermeier, R and Vorst, EPCV}, title = {Aryl hydrocarbon receptor (AHR) and nuclear factor erythroid-derived 2-like 2 (NRF2): An important crosstalk in the gut-liver axis.}, journal = {Biochemical pharmacology}, volume = {}, number = {}, pages = {116785}, doi = {10.1016/j.bcp.2025.116785}, pmid = {39890034}, issn = {1873-2968}, abstract = {The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor, mainly involved in detoxification. However, in the intestine, metabolites derived from the diet, which are converted by a wide range of bacteria can also activate the AHR. This intestinal AHR activation plays a key role in maintaining the gut barrier by, for example, upregulating antimicrobial peptides and anti-inflammatory cytokines. Since the gut barrier influences the gut-liver axis by regulating the leaking of metabolites, bacteria, and endotoxins into circulation and particularly into the liver, the AHR is a key factor in the gut-liver axis. Vice versa, certain liver pathologies also influence the gut microbiome, thereby altering bacteria-derived activation of the AHR. Additionally, bile acids can impact the gut via the liver and thereby also affect the AHR. The aryl hydrocarbon receptor (AHR) interacts with several molecular factors, one of which is the nuclear factor erythroid-derived 2-like 2 (NRF2), a transcription factor primarily associated with regulating antioxidant stress responses. The interplay between AHR and NRF2 has been investigated in the context of various diseases; this review highlights the significance of this interaction within the framework of the gut-liver axis.}, }
@article {pmid39890009, year = {2025}, author = {Alverdy, JC}, title = {Invited Commentary: Human effluvia, microbiome-based biomarkers and cancer screening.}, journal = {Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract}, volume = {}, number = {}, pages = {101976}, doi = {10.1016/j.gassur.2025.101976}, pmid = {39890009}, issn = {1873-4626}, }
@article {pmid39889605, year = {2025}, author = {Gong, X and Peng, Q and Jiang, R and Yang, N and Xing, C and Wang, R}, title = {Mn-oxidizing microalgae and woodchip-denitrifying bioreactor system for recovering manganese and removing nitrogen from electrolytic manganese metal industrial tailwater.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137383}, doi = {10.1016/j.jhazmat.2025.137383}, pmid = {39889605}, issn = {1873-3336}, abstract = {Excess manganese (Mn) and NH4[+]-N emissions from electrolytic manganese metal industrial tailwater may harm the environment. However, previous studies have not combined Mn-oxidizing microalgae to reclaim Mn with woodchip substrates for nitrogen removal from tailwater. Here, a two-stage bioreactor system was constructed to recover Mn by microalgal-mediated bio-oxidation in an algae reactor (AR) and remove nitrogen by denitrification in a woodchip reactor (WR). The results showed that up to 100 % of Mn[2+] in the tailwater was removed after a 3-day incubation period. The maximum amount of biogenerated Mn oxide nanoparticles reached 13.34 mg/L with Mn[4+] as the main Mn valence. Mn recovery reached 65.69 % through precipitate collection, and the NH4[+]-N removal efficiency reached 97 % in the AR. Mn oxidation by algae might promote oxidative removal of NH4[+]-N. NO3[-]-N and total nitrogen removal efficiencies in the WR reached 82-90 % and 65-87 %, respectively, which was attributed to denitrification. The predominance of the denitrification gene narG in the WR may have driven the efficient nitrate removal. Flavobacterium, Acidovora, Massilia, Arcticibacter, and Acinetobacter were the most abundant genera in the WR and represented dominant denitrifying bacteria in the woodchip microbiome, indicating their important contribution to denitrification. Overall, the combined application of Mn-oxidizing algae and woodchip-denitrifying bioreactors may represent an efficient treatment technology for electrolytic manganese wastewater remediation.}, }
@article {pmid39889197, year = {2025}, author = {Fu, Y and Yang, Y and Mu, K and Zhou, Y and Chai, H}, title = {Efficacy of toothpaste containing OPTIMEALTH® OR in inhibiting dental plaque and gingivitis: A randomized controlled trial.}, journal = {Medicine}, volume = {104}, number = {5}, pages = {e41225}, doi = {10.1097/MD.0000000000041225}, pmid = {39889197}, issn = {1536-5964}, mesh = {Humans ; *Gingivitis/prevention &amp; control/microbiology/drug therapy ; *Toothpastes/therapeutic use ; *Dental Plaque/microbiology/prevention &amp; control/drug therapy ; Double-Blind Method ; Female ; Male ; Adult ; Young Adult ; Dental Plaque Index ; Phosphates ; Periodontal Index ; Fluorides/therapeutic use/administration &amp; dosage ; Microbiota/drug effects ; Treatment Outcome ; Middle Aged ; }, abstract = {BACKGROUND: This randomized double-blind, placebo-controlled clinical trial evaluated the effects of 2% OPTIMEALTH® OR toothpaste in regulating dental plaque microbiota and alleviating gingivitis.<br><br>METHODS: Subjects were randomly assigned to the placebo group and test group. They were instructed to brush their teeth with placebo toothpaste (placebo group) or OPTIMEALTH&#xae; OR toothpaste (test group) for a continuous 4 weeks. Clinical indices of plaque index, gingival index, and bleeding on probe (%) were examined, and images of dental plaque staining were captured at baseline and after 2 and 4 weeks. The plaque microbiome was analyzed by 16s rDNA amplicon sequencing at baseline and after 4 weeks.<br><br>RESULTS: Thirty-two participants with similar characteristics were recruited. After using OPTIMEALTH&#xae; OR toothpaste for 4 weeks, a decrease of 27.05% (P&#x2005;<&#x2005;.01), 8.29% (P&#x2005;>&#x2005;.05), and 47.44% (P&#x2005;<&#x2005;.05) in plaque index, gingival index, and bleeding on probe (%) scores was observed compared to the baseline, respectively. The extent of decline in these indices is greater than that in the placebo group. A decrease in dental plaque could be observed after 2 and 4 weeks in the test group. The 16s rDNA sequencing results showed that the observed species index and Chao index, but not the Shannon index and beta diversity, were reduced significantly after using OPTIMEALTH&#xae; OR toothpaste for 4 weeks. In addition, compared with the placebo group, using OPTIMEALTH&#xae; OR toothpaste reduced the abundance of bacterial species such as Veillonella parvula and Prevotella denticola.<br><br>CONCLUSION: Brushing teeth with 2% OPTIMEALTH&#xae; OR-fortified toothpaste could effectively reduce dental plaque and regulate plaque microbiota.}, }
@article {pmid39888908, year = {2025}, author = {Graells, T and Lin, YT and Ahmad, S and Fall, T and Ärnlöv, J}, title = {The urinary microbiome in association with diabetes and diabetic kidney disease: A systematic review.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0317960}, pmid = {39888908}, issn = {1932-6203}, mesh = {Humans ; *Diabetic Nephropathies/microbiology/urine ; *Microbiota ; *Diabetes Mellitus, Type 2/microbiology/complications/urine ; Male ; Female ; Cross-Sectional Studies ; }, abstract = {BACKGROUND: The urinary microbiome, or urobiome, is a novel area of research that has been gaining attention recently, as urine was thought to be sterile for years. There is limited information about the composition of the urobiome in health and disease. The urobiome may be affected by several factors and diseases such as diabetes, a disease that often leads to kidney damage. Thus, we need to understand the role of the urobiome to assess and monitor kidney disease related to diabetes over time.<br><br>METHODS: We conducted a systematic review to summarize knowledge about the urobiome in association with diabetes mellitus and diabetic kidney disease. The search was conducted in several electronic databases until November 2024.<br><br>RESULTS: Eighteen studies were selected including cross-sectional case-control studies, cross-sectional surveys and one prospective longitudinal study. In total, the urobiome of 1,571 people was sequenced, of which 662 people had diabetes, and of these 36 had confirmed diabetic kidney disease; 609 were healthy individuals, 179 had prediabetes or were at risk of type 2 diabetes mellitus and 121 did not have diabetes but had other comorbidities. Eight studies analysed data from females, one was focused on male data, and the other nine had mixed female-male data. Most of the studies had a small sample size, used voided midstream urine, and used 16S rRNA sequencing.<br><br>CONCLUSION: This systematic review summarizes trends seen throughout published data available to have a first baseline knowledge of the urinary microbiome, and its microbiota, in association with diabetes including the decreased richness and &#x3b1;-diversity in urinary microbiota in individuals with diabetes compared to healthy controls and the decreased &#x3b1;-diversity with the evolution of kidney disease independently of the cause.}, }
@article {pmid39888507, year = {2025}, author = {Schaub, J and Tang, SC}, title = {Beyond checkpoint inhibitors: the three generations of immunotherapy.}, journal = {Clinical and experimental medicine}, volume = {25}, number = {1}, pages = {43}, pmid = {39888507}, issn = {1591-9528}, mesh = {Humans ; *Immunotherapy/methods ; *Immune Checkpoint Inhibitors/therapeutic use ; *CTLA-4 Antigen/antagonists &amp; inhibitors ; Neoplasms/therapy/drug therapy/immunology ; Programmed Cell Death 1 Receptor/antagonists &amp; inhibitors ; B7-H1 Antigen/antagonists &amp; inhibitors ; }, abstract = {Anti-tumor immunotherapy was rediscovered and rejuvenated in the last two decades with the discovery of CTLA-4, PD-1 and PD-L1 and the roles in inhibiting immune function and tumor evasion of anti-tumor immune response. Following the approval of the first checkpoint inhibitor ipilimumab against CTLA-4 in melanoma in 2011, there has been a rapid development of tumor immunotherapy. Furthermore, additional positive and negative molecules among the T-cell regulatory systems have been identified that that function to fine tune the stimulatory or inhibitory immune cells and modulate their functions (checkpoint modulators). Many strategies are being explored to target macrophages, NK-cells, cytotoxic T-cells, fibroblasts, endothelial cells, cytokines and molecules involved in tumor tolerance and microbiome. Similar to agents that target checkpoint modulators, these newer targets have the potential to synergize with other classes of immunotherapeutic agents and importantly may overcome the resistance to other immunotherapies. In order to better understand the mechanism of action of all major classes of immunotherapy, design clinical trials taking advantage of different types of immunotherapeutic agents and use them rationally in clinical practice either in combination or in sequence, we propose the group all immunotherapies into three generations: with CTLA-4, PD-1 and PD-L1 inhibitors as the first generation, agents that target the checkpoint modulators as the second generation, while those that target TME as the third generation. This review discusses all three generations of immunotherapy in oncology, their mechanism of actions, major clinical trial results and indication, strategies for future clinical trial designs and rational clinical applications.}, }
@article {pmid39887959, year = {2025}, author = {Emadi, R and Saki, S and Yousefi, P and Tabibzadeh, A}, title = {A Perspective on Lung Cancer and Lung Microbiome: Insight on Immunity.}, journal = {Immunity, inflammation and disease}, volume = {13}, number = {2}, pages = {e70145}, pmid = {39887959}, issn = {2050-4527}, mesh = {Humans ; *Lung Neoplasms/microbiology/immunology ; *Microbiota/immunology ; Animals ; *Dysbiosis/microbiology/immunology ; Lung/microbiology/immunology ; Immunity ; }, abstract = {BACKGROUND: Although the carcinogenic potential of microbes has long been recognized, their significance may have been underestimated. Currently, the connection between microbiota and cancer is under extensive research. The lung microbiota may serve as a proxy for the state of lung health based on its crucial role in preserving lung hemostasis.<br><br>OBJECTIVES: This review tried to outline the state of our understanding of the contribution of lung microbiome and lung cancer.<br><br>METHODS: A literature search was performed using PubMed, Google Scholar, and Scopus databases for recent research focusing on the development and possible pathogenesis of lung microbiome and lung cancer.<br><br>RESULTS: Early research on lung cancer indicated that dysbiosis significantly impacted the development and spread of the tumor. As a result of these findings, the study of the lung microbiota as a possible therapeutic target and diagnostic marker has accelerated. Early-stage disease diagnostic biomarkers could be represented as microbiota profiles. Additionally, the microbiome is involved in anticancer therapy. There are limited studies on lung microbiota, and most microbiome studies commonly concentrate on the gut microbiota. A proper understanding of lung microbiota can have several potential therapeutic approaches. Therefore, more studies in this field may initiate remarkable advancements in microbiome-dependent treatment.<br><br>CONCLUSION: Convincing data from studies on both humans and animals indicates that the microbiota might play a role in cancer initiation, influenced by internal and environmental factors of the host. Notably, the lung harbors its microbiome, as do lung cancers. In general view, it seems microbiome diversity in lung cancer patients is reduced. Meanwhile, some genera were increased in lung cancer patients in comparison with a noncancerous population (such as Streptococcus genus), and some of them were decreased (Granulicatella adiacens, G. adiacens). Furthermore, research on the microbiome-carcinogenesis relationship is still in its infancy, and much remains to be fully understood.}, }
@article {pmid39887906, year = {2025}, author = {Baquiran, JIP and Quijano, JB and van Oppen, MJH and Cabaitan, PC and Harrison, PL and Conaco, C}, title = {Microbiome Stability Is Linked to Acropora Coral Thermotolerance in Northwestern Philippines.}, journal = {Environmental microbiology}, volume = {27}, number = {2}, pages = {e70041}, doi = {10.1111/1462-2920.70041}, pmid = {39887906}, issn = {1462-2920}, support = {FIS/2019/123//Australian Centre for International Agricultural Research/ ; QMSR- MRRD-MEC-295-1449//Philippine Council for Agriculture, Aquatic and Natural Resources Research and Development/ ; }, mesh = {*Anthozoa/microbiology/physiology ; Animals ; *Thermotolerance ; *Microbiota/physiology ; Philippines ; *RNA, Ribosomal, 16S/genetics ; Symbiosis ; Bacteria/classification/genetics ; Hot Temperature ; }, abstract = {Corals associate with a diverse community of prokaryotic symbionts that provide nutrition, antioxidants and other protective compounds to their host. However, the influence of microbes on coral thermotolerance remains understudied. Here, we examined the prokaryotic microbial communities associated with colonies of Acropora cf. tenuis that exhibit high or low thermotolerance upon exposure to 33°C (heated) relative to 29°C (control). Using 16S rRNA sequencing, we show that the microbial community structure of all A. cf. tenuis colonies was similar to each other at control temperature. Thermotolerant colonies, however, had relatively greater abundance of Endozoicomonas, Arcobacter, Bifidobacterium and Lactobacillus. At elevated temperature, only thermosensitive colonies showed a distinct shift in their microbiome, with an increase in Flavobacteriales, Rhodobacteraceae and Vibrio, accompanying a marked bleaching response. Functional prediction indicated that prokaryotic communities associated with thermotolerant corals were enriched for genes related to metabolism, while microbiomes of thermosensitive colonies were enriched for cell motility and antibiotic compound synthesis. These differences may contribute to the variable performance of thermotolerant and thermosensitive corals under thermal stress. Identification of microbial taxa correlated with thermotolerance provides insights into beneficial bacterial groups that could be used for microbiome engineering to support reef health in a changing climate.}, }
@article {pmid39887792, year = {2025}, author = {Zhang, L and Chun, Y and Grishina, G and Lo, T and Reed, K and Wang, J and Sicherer, S and Berin, MC and Bunyavanich, S}, title = {Oral and Gut Microbial Hubs Associated With Reaction Threshold Interact With Circulating Immune Factors in Peanut Allergy.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.16481}, pmid = {39887792}, issn = {1398-9995}, support = {U19 AI136053/NH/NIH HHS/United States ; R01 AI147028/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Among peanut-allergic individuals, there is high variability in the amount of peanut that triggers reactions (i.e., reaction threshold) that is not predictable or well-understood. We conducted this study to characterize relationships between the oral and gut microbiomes and systemic processes associated with reaction threshold in peanut allergy (PA).<br><br>METHODS: In a cohort of 120 children with suspected PA who underwent double-blind, placebo-controlled food challenges, we generated and analyzed parallel profiles of the oral microbiome, gut microbiome, peripheral blood transcriptome, peripheral blood cytometry, and serum antibody levels to identify threshold-associated markers and their inter-relationships.<br><br>RESULTS: The 120 participants included 23 children with no PA, 74 with high-threshold PA (reacting to &#x2265;&#x2009;443&#x2009;mg cumulative peanut protein), and 23 with low-threshold PA (reacting to <&#x2009;443&#x2009;mg cumulative peanut protein). Ten hub microbes were each identified in saliva and stool microbiome networks that were constructed, including the hub microbes Rothia aeria in saliva and Bacteroides sp. in stool that were associated with reaction threshold. These hub microbes were also associated with peripheral blood transcript levels for threshold-associated key drivers of Fc&#x3b3;R-mediated phagocytosis and TLR signaling. Correlation network construction with additional data on threshold-associated peripheral blood neutrophil abundance and peanut-specific serum IgE and Ara h 2 antibody levels revealed central roles for saliva Rothia aeria and stool Bacteroides sp. in local-systemic networks for IgE- and IgG-mediated peanut allergy.<br><br>CONCLUSIONS: This integrated study of oral and stool microbiomes, blood transcriptome, cellular profiles, and peanut-specific serum antibodies revealed new relationships between local microbiota and systemic measures associated with reaction threshold in peanut allergy.}, }
@article {pmid39887373, year = {2025}, author = {Byrd, DA and Damerell, V and Gomez Morales, MF and Hogue, SR and Lin, T and Ose, J and Himbert, C and Ilozumba, MN and Kahlert, C and Shibata, D and Toriola, AT and Li, CI and Figueiredo, J and Stephens, WZ and Warby, CA and Hardikar, S and Siegel, EM and Round, J and Ulrich, CM and Gigic, B}, title = {The gut microbiome is associated with disease-free survival in stage I-III colorectal cancer patients.}, journal = {International journal of cancer}, volume = {}, number = {}, pages = {}, doi = {10.1002/ijc.35342}, pmid = {39887373}, issn = {1097-0215}, support = {//ERA-NET on Translational Cancer Research (TRANSCAN)/ ; //Heidelberger Stiftung Chirurgie, Heidelberg University Hospital/ ; //Medizinische Fakult&#xe4;t Heidelberg, Universit&#xe4;t Heidelberg/ ; //Matthias-Lackas Foundations/ ; //Stiftung LebensBlicke/ ; R01 CA189184/NH/NIH HHS/United States ; U01 CA206110/NH/NIH HHS/United States ; //Rahel Goitein-Straus-Program/ ; 01KD2101D//German Federal Ministry of Education and Research/ ; 01KT1503//German Federal Ministry of Education and Research/ ; }, abstract = {Colorectal cancer (CRC) is the second overall leading cause of cancer death in the United States, with recurrence being a frequent cause of mortality. Approaches to improve disease-free survival (DFS) are urgently needed. The gut microbiome, reflected in fecal samples, is likely mechanistically linked to CRC progression and may serve as a non-invasive biomarker. Accordingly, we leveraged baseline fecal samples from N = 166 stage I-III CRC patients in the ColoCare Study, a prospective cohort of newly diagnosed CRC patients. We sequenced the V3 and V4 regions of the 16S rRNA gene to characterize fecal bacteria. We calculated estimates of alpha diversity, beta diversity, and a priori- and exploratory-selected bacterial presence/absence and relative abundance. Associations of microbial metrics with DFS were estimated using multivariable Cox proportional hazards models. We found that alpha diversity was strongly associated with improved DFS, most strongly among rectal cancer patients (Shannon HRrectum = 0.40 95% CI = 0.19, 0.87; p = .02). Overall microbiome composition differences (beta diversity), as characterized by principal coordinate axes, were statistically significantly associated with DFS. Peptostreptococcus was statistically significantly associated with worse DFS (HR = 1.62, 95% CI = 1.13, 2.31; p = .01 per 1-SD) and Order Clostridiales was associated with improved DFS (HR = 0.62, 95% CI = 0.43-0.88; p = .01 per 1-SD). In exploratory analyses, Coprococcus and Roseburia were strongly associated with improved DFS. Overall, higher bacterial diversity and multiple bacteria were strongly associated with DFS. Metagenomic sequencing to elucidate species, gene, and functional level details among larger, diverse patient populations are critically needed to support the microbiome as a biomarker of CRC outcomes.}, }
@article {pmid39887250, year = {2025}, author = {Tang, X and Zeng, T and Deng, W and Zhao, W and Liu, Y and Huang, Q and Deng, Y and Xie, W and Huang, W}, title = {Gut microbe-derived betulinic acid alleviates sepsis-induced acute liver injury by inhibiting macrophage NLRP3 inflammasome in mice.}, journal = {mBio}, volume = {}, number = {}, pages = {e0302024}, doi = {10.1128/mbio.03020-24}, pmid = {39887250}, issn = {2150-7511}, abstract = {UNLABELLED: Sepsis-induced acute liver injury (SALI) is a prevalent and life-threatening complication associated with sepsis. The gut microbiota plays a crucial role in the maintenance of health and the development of diseases. The impact of physical exercise on gut microbiota modulation has been well-documented. However, the potential impact of gut microbiome on exercise training-induced protection against SALI remains uncertain. Here, we discovered exercise training ameliorated SALI and systemic inflammation in septic mice. Notably, gut microbiota pre-depletion abolished the protective effects of exercise training in SALI mice. Fecal microbiota transplantation treatment revealed that exercise training-associated gut microbiota contributed to the beneficial effect of exercise training on SALI. Exercise training modulated the metabolism of Ligilactobacillus and enriched betulinic acid (BA) levels in mice. Functionally, BA treatment conferred protection against SALI by inhibiting the hepatic inflammatory response in mice. BA bound and inactivated hnRNPA2B1, thus suppressing NLRP3 inflammasome activation in macrophages. Collectively, this study reveals gut microbiota is involved in the protective effects of exercise training against SALI, and gut microbiota-derived BA inhibits the hepatic inflammatory response via the hnRNPA2B1-NLRP3 axis, providing a potential therapeutic strategy for SALI.<br><br>IMPORTANCE: Sepsis is characterized by a dysregulated immune response to an infection that leads to multiple organ dysfunction. The occurrence of acute liver injury is frequently observed during the initial stage of sepsis and is directly linked to mortality in the intensive care unit. The preventive effect of physical exercise on SALI is well recognized, yet the underlying mechanism remains poorly elucidated. Exercise training alters the gut microbiome in mice, increasing the abundance of Ligilactobacillus and promoting the generation of BA. Additionally, BA supplementation can suppress the NLRP3 inflammasome activation in macrophages by directly binding to hnRNPA2B1, thereby mitigating SALI. These results highlight the beneficial role of gut microbiota-derived BA in inhibiting the hepatic inflammatory response, which represents a crucial stride toward implementing microbiome-based therapeutic strategies for the clinical management of sepsis.}, }
@article {pmid39887099, year = {2025}, author = {Mazel, F}, title = {[Did humans co-evolve with the gut microbiota?].}, journal = {Medecine sciences : M/S}, volume = {41}, number = {1}, pages = {53-61}, doi = {10.1051/medsci/2024190}, pmid = {39887099}, issn = {1958-5381}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Biological Evolution ; Animals ; Diet ; Bacteria/genetics/classification ; }, abstract = {The gut microbiome plays an important role in animal physiology and development. While the molecular, cellular and ecological mechanisms that determine its diversity and impact on animal health are beginning to unfold, we still know relatively little about its evolutionary history. Fundamental questions such as "Is the microbiota evolving and at what race?", "What are its origins?", "What are the consequences of microbiota evolution for human health?" or "Did we co-evolve with our gut bacteria?" are only beginning to be explored. In the short term (from a few days to a few years, or microevolution), gut microbes can evolve and adapt very rapidly within an individual in responses to environmental changes, such as diet shifts, which can affect human health. On the longer term (ten to millions of years, or macroevolution), evolution within individuals is counterbalanced by the transfer of microbes from other people, so that human evolution is decoupled from the evolution of most gut microbes over many generations. This suggests that, while gut microbes have probably evolved rapidly within humans, most of them have a history of exchange between host populations over millennia. Whether the evolution of the microbiota over the last hundreds of thousands of years has facilitated human adaptations remains an open question and an exciting avenue for future research.}, }
@article {pmid39887086, year = {2025}, author = {Breton, J and Tu, V and Tanes, C and Wilson, N and Quinn, R and Kachelries, K and Friedman, ES and Bittinger, K and Baldassano, RN and Compher, C and Albenberg, L}, title = {A pro-inflammatory diet is associated with growth and virulence of Escherichia coli in pediatric Crohn's disease.}, journal = {Journal of Crohn's &amp; colitis}, volume = {}, number = {}, pages = {}, doi = {10.1093/ecco-jcc/jjaf018}, pmid = {39887086}, issn = {1876-4479}, abstract = {BACKGROUND &amp; AIMS: Epidemiological studies have suggested an association between the inflammatory potential of dietary patterns and Crohn's disease (CD). However, relationships of these inflammatory dietary determinants with the microbiome remain largely unknown. In this cross-sectional study, we evaluate the association between the inflammatory potential of habitual diet, as assessed by the modified Children-Dietary Inflammatory Index (mC-DII), and the fecal microbiome and metabolome of children with CD in comparison to healthy children.<br><br>METHODS: A cross-sectional study including 51 children with CD between 6 and 18 years of age and 50 healthy controls was conducted. Dietary inflammatory potential was measured using the modified Children-Dietary Inflammatory Index (mC-DII) and diet quality assessed by the Healthy Eating Index (HEI)-2015 and alternate Mediterranean eating index (aMed). Microbiome was analysed using shotgun metagenomic sequencing and untargeted metabolomic analysis.<br><br>RESULTS: A poor-quality, pro-inflammatory diet with similar mC-DII, HEI-2015 and aMed scores was found across healthy children and children with CD. In children with active disease, a pro-inflammatory diet was associated with decreased diversity, increased virulence potential and expansion of the Proteobacteria phylum dominated by Escherichia coli (E. coli) spp. Positive correlation between E. coli relative abundance and mC-DII was associated with a low intake of a cluster composed of fibers, vitamins and minerals with anti-inflammatory potential. A negative association between metabolites of fatty acid metabolism and HEI was found.<br><br>CONCLUSIONS: In total, our results suggest that a pro-inflammatory diet may potentiate hallmarks of the inflammation-associated dysbiosis in CD and highlight the need for microbiome-targeted dietary interventions optimizing the anti-inflammatory potential of habitual diet in the management of pediatric CD.}, }
@article {pmid39887051, year = {2025}, author = {Yu, X and Zhang, L and Srinivasan, A and Xie, MG and Xue, L}, title = {A unified combination framework for dependent tests with applications to microbiome association studies.}, journal = {Biometrics}, volume = {81}, number = {1}, pages = {}, doi = {10.1093/biomtc/ujaf001}, pmid = {39887051}, issn = {1541-0420}, support = {1R01GM152812/NH/NIH HHS/United States ; DMS-1811552//National Science Foundation/ ; }, mesh = {*Microbiota ; Humans ; Models, Statistical ; Computer Simulation ; Meta-Analysis as Topic ; }, abstract = {We introduce a novel meta-analysis framework to combine dependent tests under a general setting, and utilize it to synthesize various microbiome association tests that are calculated from the same dataset. Our development builds upon the classical meta-analysis methods of aggregating P-values and also a more recent general method of combining confidence distributions, but makes generalizations to handle dependent tests. The proposed framework ensures rigorous statistical guarantees, and we provide a comprehensive study and compare it with various existing dependent combination methods. Notably, we demonstrate that the widely used Cauchy combination method for dependent tests, referred to as the vanilla Cauchy combination in this article, can be viewed as a special case within our framework. Moreover, the proposed framework provides a way to address the problem when the distributional assumptions underlying the vanilla Cauchy combination are violated. Our numerical results demonstrate that ignoring the dependence among the to-be-combined components may lead to a severe size distortion phenomenon. Compared to the existing P-value combination methods, including the vanilla Cauchy combination method and other methods, the proposed combination framework is flexible and can be adapted to handle the dependence accurately and utilizes the information efficiently to construct tests with accurate size and enhanced power. The development is applied to the microbiome association studies, where we aggregate information from multiple existing tests using the same dataset. The combined tests harness the strengths of each individual test across a wide range of alternative spaces, enabling more efficient and meaningful discoveries of vital microbiome associations.}, }
@article {pmid39887002, year = {2025}, author = {Jones, SJ and Bell, DJ and McFarlane, JS}, title = {Structure of Clostridium leptum carboxyspermidine decarboxylase and comparison to homologs prevalent within the human gut microbiome.}, journal = {Acta crystallographica. Section F, Structural biology communications}, volume = {}, number = {}, pages = {}, doi = {10.1107/S2053230X25000482}, pmid = {39887002}, issn = {2053-230X}, support = {R16GM146714//National Institutes of Health, National Institute of General Medical Sciences/ ; RL5GM118990//National Institutes of Health, National Institute of General Medical Sciences/ ; T34GM14090//National Institutes of Health, National Institute of General Medical Sciences/ ; }, abstract = {Polyamines are key signalling and substrate molecules that are made by all organisms. The polyamine known as spermidine is typically made by spermidine synthase, but in many bacterial species, including 70% of human gut microbes, carboxyspermidine decarboxylase (CASDC) performs the terminal step in the production of spermidine. An X-ray crystal structure of CASDC from the human gut microbe Clostridium leptum has been solved by molecular replacement at a resolution of 1.41 Å. CASDC is a homodimer, with each monomer composed of two domains: a β/α-barrel pyridoxal 5'-phosphate-binding domain that forms most of the active site and a β-barrel domain that extends the dimeric interface and contributes to the active site of the opposing monomer. We performed a structural comparison of CASDC enzymes for 15 common genera within the human gut flora. This analysis reveals structural differences occurring in the β6/β7 loop that acts as a `flap' covering the active site and in the α9/β12 loop that is connected to the α9 helix which is thought to select substrates by their chain length. This structural analysis extends our understanding of a key enzyme in spermidine biosynthesis in many bacterial species.}, }
@article {pmid39886920, year = {2025}, author = {Letchumanan, G and Marlini, M and Baharom, N and Lawley, B and Syed Mohideen, FB and Jogulu, SR and Addnan, FH and Nur Fariha, MM and Omar, MR and Pathmanathan, SG}, title = {Ethnicity-matched case-control study reveals significant gut microbiota differences in Malaysian adults with type 2 diabetes.}, journal = {Journal of medical microbiology}, volume = {74}, number = {1}, pages = {}, doi = {10.1099/jmm.0.001963}, pmid = {39886920}, issn = {1473-5644}, mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology ; Malaysia/epidemiology ; Case-Control Studies ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *RNA, Ribosomal, 16S/genetics ; Adult ; *Feces/microbiology ; Ethnicity ; Bacteria/classification/genetics/isolation &amp; purification ; Aged ; }, abstract = {Introduction. Type 2 diabetes mellitus (T2DM) is a major global health issue projected to exceed 700 million cases by 2045. In Malaysia, T2DM prevalence has risen, with notable ethnic disparities.Gap statement. The gut microbiota's role in T2DM pathogenesis is well recognized, yet its composition in Malaysia's ethnically diverse population remains underexplored.Aim. This study aimed to characterize gut microbiota composition among T2DM and ethnicity-matched adults without diabetes (nonDM) in Malaysia.Methodology. A case-control study was conducted with 45 T2DM and 45 nonDM participants matched by ethnicity from a primary care clinic in Klang Valley, Malaysia. Faecal DNA was subjected to 16S rRNA sequencing to identify microbiota diversity and composition differences and compare predicted functional capabilities. Correlations between bacterial taxa, clinical characteristics and dietary intake were analysed.Results. T2DM participants showed decreased alpha diversity (observed, P-value=0.002, r=0.69; Shannon, P-value<0.001, r=0.73) and significant differences in beta diversity (permutational multivariate ANOVA, R[2]=0.036, P-value=0.001). Linear discriminant analysis effect size and multiple regression analysis, adjusted for covariates age, gender, BMI and intakes of protein, fat, carbohydrate and fibre, identified the phylum Proteobacteria and genera Escherichia-Shigella to be increased, while the genera Anaerostipes and Romboutsia decreased in T2DM. These bacteria were associated with various clinical characteristics and dietary intake. However, these 'potential biomarkers' were not uniformly present across all participants, suggesting that individual bacterial taxa may not serve as universal biomarkers.Conclusion. Significant gut microbiota differences exist between T2DM and nonDM individuals in Malaysia, indicating a dysbiosis characterized by increased pro-inflammatory bacteria and reduced short-chain fatty acid-producing bacteria in T2DM. While these findings highlight the potential functional relevance of gut microbiota in T2DM pathogenesis, addressing limitations such as participant matching for confounding factors in future studies could uncover additional significant differences in microbiota composition. Furthermore, the variability in taxa prevalence across individuals suggests that targeting microbial metabolic products may offer more promising strategies to inform microbiota-targeted interventions than relying solely on specific bacterial taxa as biomarkers.}, }
@article {pmid39886918, year = {2025}, author = {Yin, Y and Yang, T and Tian, Z and Shi, C and Yan, C and Li, H and Du, Y and Li, G}, title = {Progress in the investigation of the Firmicutes/Bacteroidetes ratio as a potential pathogenic factor in ulcerative colitis.}, journal = {Journal of medical microbiology}, volume = {74}, number = {1}, pages = {}, doi = {10.1099/jmm.0.001966}, pmid = {39886918}, issn = {1473-5644}, mesh = {*Colitis, Ulcerative/microbiology ; Humans ; *Gastrointestinal Microbiome ; *Firmicutes/isolation &amp; purification ; *Bacteroidetes/isolation &amp; purification ; }, abstract = {Ulcerative colitis (UC) is a chronic inflammatory bowel disease (IBD) that presents significant challenges in terms of treatment owing to a pronounced likelihood of recurrence and an elevated risk of cancer development, thereby imposing substantial risks on affected individuals. The gut microbiota of Firmicutes and Bacteroidetes (F/B) can affect diseases associated with IBD, which is also a risk factor for breast cancer. This review discusses the hazards associated with UC, highlights the existing disparities in UC-associated gut microbiome research, explores the concept of the F/B ratio and scrutinizes its correlation with UC. Moreover, the differences in the F/B ratios between healthy individuals and those with UC were thoroughly examined. These findings suggest that an elevated F/B ratio may promote the occurrence and progression of UC. Consequently, the F/B ratio may play a significant role in UC by influencing gut microbiota composition and inflammatory responses, suggesting that future research should focus on this ratio as a potential biomarker for disease progression and therapeutic targets in managing UC.}, }
@article {pmid39886876, year = {2025}, author = {Kintner, J and Callaghan, M and Bulawa, L and Chu, A and Ma, Z and Williams, DL and Schoborg, RV and Kruppa, MD and Hall, JV}, title = {Dectin-1 stimulating β-glucans inhibit Chlamydia infections both in vitro and in vivo.}, journal = {Pathogens and disease}, volume = {}, number = {}, pages = {}, doi = {10.1093/femspd/ftaf002}, pmid = {39886876}, issn = {2049-632X}, abstract = {Chlamydia trachomatis and Candida albicans are common inhabitants of the female genital tract. C. albicans can impact viability and pathogenesis of some bacteria. Previously, we investigated physical interactions between C. trachomatis elementary bodies (EB) and C. albicans. This work indicated that EB bind to C. albicans and become noninfectious by 24 hours post binding. Here, we continue our investigation of these interkingdom, polymicrobial interactions. C. albicans adheres to bacteria or host surfaces via agglutinin-like sequence (Als) or heat shock 70 (Ssa) proteins. C. trachomatis EB did not bind C. albicans Ssa2 deficient strains as efficiently as wild type or complemented strains, indicating a role for this protein in chlamydial adherence to Candida. Additionally, C. albicans β-glucans inhibit chlamydial infection when exposure occurs during EB adsorption onto cervical cells. Laminarin (Lam), a β-glucan agonist of the C-type lectin receptor Dectin-1, inhibited chlamydial infection both cervical epithelial cells and mice when exposure occurred prior to, during, or immediately following EB inoculation. Conversely, a Dectin-1 antagonist laminarin (Lam-Ant) did not inhibit infection in vitro, suggesting β-glucan inhibition of C. trachomatis requires CTLR signaling. Overall, our data demonstrate that β-glucans from multiple species, including Candida albicans, inhibits Chlamydia via stimulation of host signaling pathways.}, }
@article {pmid39886210, year = {2024}, author = {Shehata, HR and Pane, M and Buys, EM and Koshy, B and Vegge, CS and Schoeni, JL}, title = {Editorial: Emerging technologies for viability enumeration of live microorganisms.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1546438}, pmid = {39886210}, issn = {1664-302X}, }
@article {pmid39886072, year = {2024}, author = {Li, W and Qing, Y and Yu, Q and Zhang, H and Rang, Z and Li, S and Cui, F}, title = {Alterations of the Intestinal Mucosal Barrier and Gut Fungal Microbiome in Asymptomatic HIV-Infected Patients.}, journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2024}, number = {}, pages = {6995192}, pmid = {39886072}, issn = {1712-9532}, abstract = {Damage to the intestinal mucosal barrier and dysbiosis of the gut microbiota are critical factors in HIV progression, reciprocally influencing each other. Besides bacteria, the fungal microbiota, a significant component of the gut, plays a pivotal role in this dysregulation. This study aims to investigate changes in the gut mucosal barrier and mycobiota during the initial stages of HIV infection, focusing on the involvement of intestinal fungi and their secretions in mucosal damage. Peripheral blood, intestinal mucosa, and fecal samples were collected from 13 asymptomatic HIV-infected individuals at the non-AIDS stage and 13 healthy controls. Assessments included colonoscopy, immune function analysis, and measurement of mucosal damage markers (LPS, I-FABP, and D-LA) and inflammatory cytokines (IL-6 and IL-18). Additionally, Claudin-1 levels in mucosal samples and fungal profiles in fecal samples were evaluated. The study found that colonic abnormalities were significantly more prevalent in the HIV group compared to healthy controls (p < 0.001) and Claudin-1 levels were notably lower in the HIV group (p < 0.001). Candida albicans (p=0.0084), its secretion SAP1 (p=0.023), and the levels of IL-18 (p=0.0016) and IL-6 (p < 0.001) were all significantly higher in the HIV group. CD4+ T-cell counts were positively correlated with Claudin-1 expression (p=0.034, r = 0.417). Candida albicans showed negative correlations with several virulence factors, while other fungi exhibited varied correlations. Additionally, Claudin-1 levels were significantly negatively correlated with Candida albicans (p=0.013, r = -0.668), SAP1 (p=0.027, r = -0.609), IL-18 (p < 0.001, r = -0.922), and IL-6 (p < 0.001, r = -0.920). Overall, these findings suggest that asymptomatic HIV-infected individuals have already exhibited intestinal mucosal damage in the early stage and highlight the critical role of Candida albicans and its secretions in early-stage intestinal mucosal barrier damage.}, }
@article {pmid39885963, year = {2024}, author = {Saadaoui, M and Djekidel, MN and Murugesan, S and Kumar, M and Elhag, D and Singh, P and Kabeer, BSA and Marr, AK and Kino, T and Brummaier, T and McGready, R and Nosten, F and Chaussabel, D and Terranegra, A and Al Khodor, S}, title = {Exploring the composition of placental microbiome and its potential origin in preterm birth.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1486409}, pmid = {39885963}, issn = {2235-2988}, mesh = {Humans ; Female ; Pregnancy ; *Placenta/microbiology ; *Microbiota/genetics ; *Premature Birth/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Vagina/microbiology ; Adult ; *Bacteria/classification/genetics/isolation &amp; purification ; Mouth/microbiology ; DNA, Bacterial/genetics ; Infant, Newborn ; }, abstract = {INTRODUCTION: For years, the placenta was believed to be sterile, but recent studies reveal it hosts a unique microbiome. Despite these findings, significant questions remain about the origins of the placental microbiome and its effects on pregnancy and fetal health. Some studies suggest it may originate from the vaginal tract, while others indicate that oral bacteria can enter the maternal bloodstream and seed the placenta. However, research analyzing the vaginal, oral, and placental microbiomes within the same cohort is lacking. Additionally, it's unclear whether the placental microbiome differs between healthy pregnancies and those with complications like preterm birth (PTB), which remains a leading cause of neonatal morbidity and mortality worldwide.<br><br>METHODS: In this study, we performed 16S rRNA gene sequencing to investigate the composition of the oral and placental microbiome in samples collected from 18 women who experienced PTB and 36 matched controls who delivered at term (TB), all of whom were part of the Molecular Signature in Pregnancy (MSP) study. We leveraged on the multisite microbiome sampling from the MSP participants and on our previously published vaginal microbiome data to investigate the potential origins of the placental microbiome and assess whether its composition varies between healthy and complicated pregnancies.<br><br>RESULTS AND DISCUSSION: Our analysis revealed distinct profiles in the oral microbiome of PTB subjects compared to those who delivered at term. Specifically, we observed an increased abundance of Treponema maltophilum, Bacteroides sp, Mollicutes, Prevotella buccae, Leptotrichia, Prevotella_sp_Alloprevotella, in the PTB group. Importantly, Treponema maltophilum species showed higher abundance in the PTB group during the second trimester, suggesting its potential use as biomarkers. When we assessed the placenta microbiome composition, we found that Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were the most dominant phyla. Interestingly, microorganisms such as Ureaplasma urealyticum were more abundant in PTB placenta samples. Our findings suggest that the placenta microbiome could originate from the oral or vaginal cavities, with a notable increase in the crosstalk between the vaginal and placental sites in cases of PTB. Specifically, our data revealed that in PTB cases, the placental microbiome exhibited a closer resemblance to the vaginal microbiome, whereas in term pregnancies, the placental microbiome was similar to the oral microbiome.}, }
@article {pmid39885953, year = {2025}, author = {Pagalilauan, A and Pavloudi, C and Ospina, SM and Smith, A and Saw, JH}, title = {Interaction with refuse piles is associated with co-occurrence of core gut microbiota in workers of the ant Aphaenogaster picea.}, journal = {Access microbiology}, volume = {7}, number = {1}, pages = {}, pmid = {39885953}, issn = {2516-8290}, abstract = {Comparing the diversity of gut microbiota between and within social insect colonies can illustrate interactions between bacterial community composition and host behaviour. In many eusocial insect species, different workers exhibit different task behaviours. Evidence of compositional differences between core microbiota in different worker types could suggest a microbial association with the division of labour among workers. Here, we present the core microbiota of Aphaenogaster picea ant workers with different task behaviours. The genus Aphaenogaster is abundant worldwide, yet the associated microbiota of this group is unstudied. Bacterial communities from Aphaenogaster picea gut samples in this study consist of 19 phyla, dominated by Proteobacteria, Cyanobacteria and Firmicutes. Analysis of 16S rRNA gene sequences reveals distinct similarity clustering of Aphaenogaster picea gut bacterial communities in workers that have more interactions with the refuse piles. Though gut bacterial communities of nurse and foraging ants are similar in overall composition and structure, the worker groups differ in relative abundances of dominant taxa. Gut bacterial communities from ants that have more interactions with refuse piles are dominated by amplicon sequence variants associated with Entomoplasmataceae. Interaction with faecal matter via refuse piles seems to have the greatest impact on microbial taxa distribution, and this effect appears to be independent of worker type. This is the first report surveying the gut microbiome community composition of Aphaenogaster ants.}, }
@article {pmid39885562, year = {2025}, author = {Grieves, LA and Gloor, GB}, title = {Uropygial gland microbiota of nearctic-neotropical migrants vary with season and migration distance.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {11}, pmid = {39885562}, issn = {2524-4671}, abstract = {Symbiotic microbiota are important drivers of host behaviour, health, and fitness. While most studies focus on humans, model organisms, and domestic or economically important species, research investigating the role of host microbiota in wild populations is rapidly accumulating. Most studies focus on the gut microbiota; however, skin and other glandular microbiota also play an important role in shaping traits that may impact host fitness. The uropygial gland is an important source of chemical cues and harbours diverse microbes that could mediate chemical communication in birds, so determining the factors most important in shaping host microbiota should improve our understanding of microbially-mediated chemical communication. Hypothesizing that temporal, geographic, and taxonomic effects influence host microbiota, we evaluated the effects of season, migration distance, and taxonomy on the uropygial gland microbiota of 18 passerine species from 11 families. By sampling 473 birds at a single stopover location during spring and fall migration and using 16S rRNA sequencing, we demonstrate that season, followed by migration distance, had the strongest influence on uropygial gland microbial community composition. While statistically significant, taxonomic family and species had only weak effects on gland microbiota. Given that temporal effects on gland microbiota were nearly ubiquitous among the species we tested, determining the consequences of and mechanisms driving this seasonal variation are important next steps.}, }
@article {pmid39885558, year = {2025}, author = {Sampson, TR and Tansey, MG and West, AB and Liddle, RA}, title = {Lewy body diseases and the gut.}, journal = {Molecular neurodegeneration}, volume = {20}, number = {1}, pages = {14}, pmid = {39885558}, issn = {1750-1326}, support = {ASAP-020527//Aligning Science Across Parkinson's/ ; PF-JFA-830658/PDF/Parkinson's Disease Foundation/United States ; R01 ES032440/NH/NIH HHS/United States ; RF1NS128800/NH/NIH HHS/United States ; U01NS113851/NH/NIH HHS/United States ; R01 NS064934/NH/NIH HHS/United States ; I01 BX002230/BX/BLRD VA/United States ; }, mesh = {Humans ; *Lewy Body Disease/pathology/metabolism ; *Gastrointestinal Microbiome/physiology ; Animals ; Gastrointestinal Tract ; alpha-Synuclein/metabolism ; Gastrointestinal Diseases ; }, abstract = {Gastrointestinal (GI) involvement in Lewy body diseases (LBDs) has been observed since the initial descriptions of patients by James Parkinson. Recent experimental and human observational studies raise the possibility that pathogenic alpha-synuclein (⍺-syn) might develop in the GI tract and subsequently spread to susceptible brain regions. The cellular and mechanistic origins of ⍺-syn propagation in disease are under intense investigation. Experimental LBD models have implicated important contributions from the intrinsic gut microbiome, the intestinal immune system, and environmental toxicants, acting as triggers and modifiers to GI pathologies. Here, we review the primary clinical observations that link GI dysfunctions to LBDs. We first provide an overview of GI anatomy and the cellular repertoire relevant for disease, with a focus on luminal-sensing cells of the intestinal epithelium including enteroendocrine cells that express ⍺-syn and make direct contact with nerves. We describe interactions within the GI tract with resident microbes and exogenous toxicants, and how these may directly contribute to ⍺-syn pathology along with related metabolic and immunological responses. Finally, critical knowledge gaps in the field are highlighted, focusing on pivotal questions that remain some 200 years after the first descriptions of GI tract dysfunction in LBDs. We predict that a better understanding of how pathophysiologies in the gut influence disease risk and progression will accelerate discoveries that will lead to a deeper overall mechanistic understanding of disease and potential therapeutic strategies targeting the gut-brain axis to delay, arrest, or prevent disease progression.}, }
@article {pmid39885552, year = {2025}, author = {Koh, H and Kim, J and Jang, H}, title = {MiCML: a causal machine learning cloud platform for the analysis of treatment effects using microbiome profiles.}, journal = {BioData mining}, volume = {18}, number = {1}, pages = {10}, pmid = {39885552}, issn = {1756-0381}, support = {2021R1C1C1013861//National Research Foundation of Korea/ ; }, abstract = {BACKGROUND: The treatment effects are heterogenous across patients due to the differences in their microbiomes, which in turn implies that we can enhance the treatment effect by manipulating the patient's microbiome profile. Then, the coadministration of microbiome-based dietary supplements/therapeutics along with the primary treatment has been the subject of intensive investigation. However, for this, we first need to comprehend which microbes help (or prevent) the treatment to cure the patient's disease.<br><br>RESULTS: In this paper, we introduce a cloud platform, named microbiome causal machine learning (MiCML), for the analysis of treatment effects using microbiome profiles on user-friendly web environments. MiCML is in particular unique with the up-to-date features of (i) batch effect correction to mitigate systematic variation in collective large-scale microbiome data due to the differences in their underlying batches, and (ii) causal machine learning to estimate treatment effects with consistency and then discern microbial taxa that enhance (or lower) the efficacy of the primary treatment. We also stress that MiCML can handle the data from either randomized controlled trials or observational studies.<br><br>CONCLUSION: We describe MiCML as a useful analytic tool for microbiome-based personalized medicine. MiCML is freely available on our web server (http://micml.micloud.kr). MiCML can also be implemented locally on the user's computer through our GitHub repository (https://github.com/hk1785/micml).}, }
@article {pmid39885499, year = {2025}, author = {Zhang, Z and Zheng, K and Zhang, Z and Cao, L and Lin, L and Sun, W and Qiu, F}, title = {Lactobacillus gasseri LGV03-derived indole-3-lactic acid ameliorates immune response by activating aryl hydrocarbon receptor.}, journal = {Microbial cell factories}, volume = {24}, number = {1}, pages = {34}, pmid = {39885499}, issn = {1475-2859}, support = {2023A1515011439//Natural Science Foundation of Guangdong Province/ ; 2021A1515220025//Basic and Applied Basic Research Foundation of Guangdong Province/ ; }, mesh = {*Receptors, Aryl Hydrocarbon/metabolism/genetics ; *Zebrafish ; Animals ; *Indoles/pharmacology ; *Lactobacillus gasseri/metabolism ; Macrophages/immunology/drug effects/metabolism ; Female ; Neutropenia ; Humans ; }, abstract = {Previous studies showed that the female genital tract microbiome plays a crucial role in regulating the host's immune defense mechanisms. Our previous research has shown that Lactobacillus gasseri LGV03 (L. gasseri LGV03) isolated from cervico-vagina of HPV-cleared women contributes to clearance of HPV infection and beneficially regulate immune response. However, the mechanisms behind the regulation of L. gasseri LGV03 in immune response remain unclear. To better understand the interaction between female genital tract microbiome and immune function, the immunomodulatory activities of L. gasseri LGV03 were investigated in zebrafish models of neutropenia, macrophage and T cells deficiency. L. gasseri LGV03 showed higher potent activities in ameliorating vinorelbine-induced neutropenia, macrophage and T cells deficiency, and significantly enhanced mRNA expressions of cytokines TNF-α, TNF-β and IFN-α. Moreover, the transcriptome sequencing results indicated L. gasseri LGV03 might alleviate vinorelbine-induced immunosuppression in zebrafish. Non-targeted detection and analysis revealed that indole derivatives including phenylacetaldehyde, 3-phenyllactic acid, N-acetylserotonin and indole-3-lactic acid were significantly increased in the lysate and supernatant of L. gasseri LGV03. Meanwhile, L. gasseri LGV03 supernatant and indole-3-lactic acid ameliorated the vinorelbine-induced reduction in abundance of macrophages, neutrophils and T cells. However, the alleviating effects of L. gasseri LGV03 supernatant or indole-3-lactic acid were eliminated by aryl hydrocarbon receptor (AHR) antagonist CH-223,191. Furthermore, L. gasseri LGV03 supernatant and indole-3-lactic acid significantly increased the secretion of IFN-α, IFN-β and chemokines (MIP-1α, MIP-1β) in Ect1/E6E7 cells, meanwhile, these benefits were eliminated by CH-223,191 treatment. In summary, L. gasseri LGV03-derived indole-3-lactic acid can activate AHR-mediated immune response.}, }
@article {pmid39885466, year = {2025}, author = {Gopalakrishnan, V and Sparklin, B and Kim, JH and Bouquet, J and Kehl, M and Kenny, T and Morehouse, C and Caceres, C and Warrener, P and Hristova, VA and Wilson, S and Shandilya, H and Barnes, A and Ruzin, A and Wang, J and Oberg, L and Angermann, B and McCrae, C and Platt, A and Muthas, D and Hess, S and Tkaczyk, C and Sellman, BR and Ostridge, K and Belvisi, MG and Wilkinson, TMA and Staples, KJ and DiGiandomenico, A and , }, title = {NTHi killing activity is reduced in COPD patients and is associated with a differential microbiome.}, journal = {Respiratory research}, volume = {26}, number = {1}, pages = {45}, pmid = {39885466}, issn = {1465-993X}, abstract = {Chronic obstructive pulmonary disease (COPD) is a chronic lung disease characterized by airway obstruction and inflammation. Non-typeable Haemophilus influenzae (NTHi) lung infections are common in COPD, promoting frequent exacerbations and accelerated lung function decline. The relationship with immune responses and NTHi are poorly understood. Herein, we comprehensively characterized the respiratory microbiome and mycobiome of patients while investigating microbial dynamics and host immune changes attributable to NTHi killing activity. Mild-to-moderate COPD patients encompassing frequent and infrequent exacerbators and healthy volunteers (HV) were enrolled. Microbial composition, proteomics and NTHi killing activity was analyzed using bronchoalveolar lavage fluid (BALF). In addition, antigen-antibody titers in sera to COPD pathogens were determined using a multiplex assay. Differential abundance analysis revealed an enrichment of Actinobacteria and Bacteroidetes in the BALF of COPD and HV subjects respectively. Significant differences in the IgA titer response were observed against NTHi antigens in COPD vs. HV. Notably, there was also significantly greater killing activity against NTHi in BALF from COPD vs. HV subjects (OR = 5.64; 95% CI = 1.75-20.20; p = 0.001). Stratification of COPD patients by NTHi killing activity identified unique microbial and protein signatures wherein Firmicutes, Actinobacteria and haptoglobin were enriched in patients with killing activity. We report that differences in host immune responses and NTHi-killing activity are associated with microbiome changes in mild-to-moderate COPD. This is suggestive of a potential link between the respiratory microbiome and immune activity against NTHi in the context of COPD pathogenesis even at this disease stage.}, }
@article {pmid39885408, year = {2025}, author = {Tischler-Strasser, V and Burdiladze, I and Cabral, G and Ekizoglu, E and Grodzka, O and Pardo, K and Sochan, P and Zaunandra, L and MaassenVanDenBrink, A and Lampl, C and , }, title = {Effects of proton pump inhibitor (PPI) use on migraine - a critical review.}, journal = {The journal of headache and pain}, volume = {26}, number = {1}, pages = {20}, pmid = {39885408}, issn = {1129-2377}, abstract = {BACKGROUND: Proton pump inhibitor (PPI) drugs are widely used and are among the most significant achievements of modern pharmacology. Their primary purpose is treating and preventing gastric acid-related disorders. Migraine and PPI intake are prevalent, and many people are affected by both. In the last few years, a potential link between PPI intake and the development of headaches-especially migraine-has come to increased attention. In this review, we critically examine the scientific data concerning the co-occurrence of these two entities.<br><br>FINDINGS: There seems to be a possible link between the use of PPIs and the occurrence of headache, especially migraine, suggesting a pathophysiological connection on several levels. Moreover, PPI use is only partially without side effects, even if these may not occur immediately. Whether the relation is causative or merely co-existential is currently not yet clear. The influence of genetics, environment, gut microbiome, medication intake and evolution of headache is multidirectional.<br><br>CONCLUSION: A relation between the prevalence of migraine and the use of PPIs on a population and personal level seems likely. Although PPIs have many advantages, they should be prescribed with caution, especially in patients who suffer from headaches and migraine. In this narrative review, we aim to critically evaluate existing data and offer a potential approach to accurately identify any connections and interactions, leading to a better understanding of how these conditions may influence each other.}, }
@article {pmid39885060, year = {2025}, author = {Song, JH and Lim, KM and Yoo, SH and Kim, GD and Shin, HS and Park, S and Lim, MY and Lee, SY}, title = {Effects of Limosilactobacillus fermentum KBL375 on Immune Enhancement and Gut Microbiota Composition in Cyclophosphamide-Induced Immunosuppressed Mice.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {39885060}, issn = {1867-1314}, support = {E0210202-04//Korea Food Research Institute/ ; E0210202-04//Korea Food Research Institute/ ; E0210202-04//Korea Food Research Institute/ ; E0210202-04//Korea Food Research Institute/ ; E0210202-04//Korea Food Research Institute/ ; E0210202-04//Korea Food Research Institute/ ; E0210202-04//Korea Food Research Institute/ ; I0230701//weBiom/ ; I0230701//weBiom/ ; I0230701//weBiom/ ; I0230701//weBiom/ ; I0230701//weBiom/ ; }, abstract = {This study evaluated the immune-enhancing efficacy of Limosilactobacillus fermentum KBL375 isolated from the feces of healthy Koreans. KBL375-treated splenocytes showed enhancement of cytotoxicity against YAC-1 cells, the target of natural killer (NK) cells, with an increase in CD335, granzyme B, perforin, and interferon-gamma (IFN-γ). Oral administration of KBL375 in mice with cyclophosphamide (CP)-induced immunosuppression improved body weight and immune functions, including immune organ indices, lymphocyte proliferations, and immunoglobulin (Ig) A levels. Notably, KBL375 increased NK cell cytotoxicity and proportion in immunosuppressed mice. Perforin/IFN-γ expression levels, which indicated NK cell activation, were also increased in KBL375-treated mice. Furthermore, KBL375 led to an increase in beneficial microbes, such as Bifidobacterium, in the gut microbiome of immunosuppressed mice, fostering a favorable intestinal microbial environment. These comprehensive results suggest that KBL375 exhibits potent immune regulatory functions and positively influences the gut microbiota, implying its potential as a probiotic agent for immune enhancement.}, }
@article {pmid39884483, year = {2025}, author = {Lin, B and Bai, G and Zhang, Y and Wang, Y and Chen, S}, title = {Betulinic acid from Inonotus obliquus ameliorates T2DM by modulating short-chain fatty acids producing bacteria and amino acids metabolism in db/db mice.}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {119417}, doi = {10.1016/j.jep.2025.119417}, pmid = {39884483}, issn = {1872-7573}, abstract = {Inonotus obliquus has also been used as a traditional folk medicine in Europe and Northeastern China to treat metabolic diseases. Betulinic acid (BA) is a major ingredient with anti-diabetic property derived from I. obliquus, however, its bioavailability is limited. Whether the beneficial effects of BA on type 2 diabetic mellitus (T2DM) referring to modulation of gut microbiota and associated metabolites remain unclear.<br><br>AIM OF THE STUDY: This work aims to investigate the alleviating effect of BA on T2DM in db/db mice and elucidate the mechanism from perspective of network pharmacology, gut microbiome and fecal metabolome.<br><br>MATERIALS AND METHODS: BA was orally administered to db/db mice for 45 days, and the related biochemical parameters were evaluated. The associated mechanism was explored using network pharmacology analysis, 16S rRNA sequencing and UHPLC-MS metabolomics comprehensively. Additionally, Spearman analysis was performed to assess the correlation between gut microbes, metabolites, and T2DM-related biochemical parameters.<br><br>RESULTS: BA ameliorated T2DM symptoms by reducing body weight gain, regulating serum glucose and lipid levels, and mitigating T2DM-associated liver injury in db/db mice. Network pharmacology analysis indicated the ameliorative effect was via targeting at PPAR activity. BA intervention increased the relative abundance of short-chain fatty acids (SCFAs) producing bacteria including Lactobacillus and Eubacterium_xylanophilum group, and enhanced the production of SCFAs. Moreover, BA primarily regulates arginine and proline metabolism, D-glutamine and D-glutamate metabolism, and alanine, aspartate and glutamate metabolism. Spearman analysis indicated a negative correlation between SCFAs-producing bacteria and amino acids, as well as serum glucose and lipid levels.<br><br>CONCLUSION: Apart from PPAR signaling pathway, BA modulated gut microbiota composition and associated metabolites in db/db mice. This study provided novel insights into the therapeutic potential of BA for alleviating T2DM symptoms.}, }
@article {pmid39884375, year = {2025}, author = {Marino, Y and Inferrera, F and Genovese, T and Cuzzocrea, S and Fusco, R and Di Paola, R}, title = {Mitochondrial dynamics: molecular mechanism and implications in endometriosis.}, journal = {Biochimie}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.biochi.2025.01.012}, pmid = {39884375}, issn = {1638-6183}, abstract = {Endometriosis affects about 10% of women of reproductive age, leading to a disabling gynecologic condition. Chronic pain, inflammation, and oxidative stress have been identified as the molecular pathways involved in the progression of this disease, although its precise etiology remains uncertain. Although mitochondria are considered crucial organelles for cellular activity, their dysfunction has been linked to the development of this disease. The purpose of this review is to examine the functioning of the mitochondrion in endometriosis: in particular, we focused on the mitochondrial dynamics of biogenesis, fusion, and fission. Since excessive mitochondrial activity is reported to affect cell proliferation, we also considered mitophagy as a mechanism involved in limiting disease development. To better understand mitochondrial activity, we also considered alterations in circadian rhythms, the gut microbiome, and estrogen receptors: indeed, these mechanisms are also involved in the development of endometriosis. In addition, we focused on recent research about the impact of numerous substances on mitochondrial activity; some of them may offer a future breakthrough in endometriosis treatment by acting on mitochondria and inhibiting cell proliferation.}, }
@article {pmid39884252, year = {2025}, author = {Lima, FDS and Santos, MQD and Makiyama, EN and Hoffmann, C and Fock, RA}, title = {The essential role of magnesium in immunity and gut health: Impacts of dietary magnesium restriction on peritoneal cells and intestinal microbiome.}, journal = {Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS)}, volume = {88}, number = {}, pages = {127604}, doi = {10.1016/j.jtemb.2025.127604}, pmid = {39884252}, issn = {1878-3252}, abstract = {Magnesium (Mg[2+]) is essential for life, and low levels impair immune function, promote chronic inflammation, and influence the intestinal microbiome, with the peritoneal cavity serving as a site for direct interaction between the cavity and intestinal contents, including the microbiota. This study investigates the effects of a Mg[2+]-restricted diet on peritoneal immune cells and its interplay with the intestinal microbiome. Male C57BL/6NTaq mice were divided into three groups: control, restricted, and restored. The control group received a diet containing 500 mg Mg[2+]/kg, the restricted group received a diet with 50 mg Mg[2+]/kg for four weeks, and the restored group first received the restricted diet for four weeks, followed by the control diet supplemented with 0.5 g MgCl2 per liter of water for an additional four weeks. Results showed Mg[2+] restriction did not affect body weight, food intake, or water consumption but induced hypomagnesemia, reversible upon dietary restoration. Mg[2+] deficiency increased in neutrophils numbers in the blood and peritoneal cavity, indicating an inflammatory response. Gene expression analysis in peritoneal mononuclear cells revealed elevated levels of Nfkb, Stat1 and Stat3, suggesting heightened inflammatory signaling. Additionally, cytokine expression analysis showed increased levels of Tnfa, Il1b and Il10, but not Il6, in Mg[2+]-restricted group. The intestinal microbiome of Mg[2+]-restricted mice exhibited increased alpha diversity, with changes in taxa abundance, including an increase in Romboutsia ilealis and a decrease in the Oscillospiraceae and Lachnospiraceae. Mg[2+] deficiency significantly affects some immune functions and gut microbiota, highlighting the importance of Mg[2][+] in maintaining the gut health.}, }
@article {pmid39884207, year = {2025}, author = {Yesankar, PJ and Qureshi, A}, title = {Insights into the functionality of biofilm-forming bacterial consortia as bioavailability enhancers towards biodegradation of pyrene in hydrocarbon-contaminated soil.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124295}, doi = {10.1016/j.jenvman.2025.124295}, pmid = {39884207}, issn = {1095-8630}, abstract = {Hydrophobic organic compounds (HOCs), such as pyrene, pose significant challenges for microbial-based remediation in soil due to limited substrate availability and the sustainability of augmented microbes. Research targets are to investigate the potential of biofilm-forming bacterial cells to enhance pyrene bioavailability and biodegradation in two different hydrocarbon-contaminated soil microcosms, employing microbiological, molecular, and chemical analysis validated through statistical tools. The microcosm augmented with strong biofilm bacterial consortia (A) significantly enhanced pyrene availability by 1-1.5% compared to the weak biofilm consortia (B) and mixed consortia (AB). Analysis of 16 S rDNA amplicons revealed notable differences in bacterial community composition between consortia A and B augmented soil, with Proteobacteria as the dominant phylum. Taxonomic composition of soil microbiome predicted enhanced xenobiotic biodegradative potential of strong biofilm consortia (A) up to 20 days, exhibiting a higher abundance of functional genes related to upstream degradative pathway of PAHs, such as naphthalene dioxygenase (nahAa), PAH dioxygenase subunit genes (nidA, nidB), extradiol dioxygenase (phdF) and aldehyde dehydrogenase (nidD). Our study highlights the significant role of biofilm-forming bacteria as "bioavailability enhancers," for high molecular weight PAHs like pyrene, in contaminated soils with their implications for designing future sustainable bioremediation programs.}, }
@article {pmid39884152, year = {2025}, author = {Maphosa, S and Steyn, M and Lebre, PH and Gokul, JK and Convey, P and Marais, E and Maggs-Kölling, G and Cowan, DA}, title = {Rhizosphere bacterial communities of Namib Desert plant species: Evidence of specialised plant-microbe associations.}, journal = {Microbiological research}, volume = {293}, number = {}, pages = {128076}, doi = {10.1016/j.micres.2025.128076}, pmid = {39884152}, issn = {1618-0623}, abstract = {Rhizosphere microbial communities are intimately associated with plant root surfaces. The rhizosphere microbiome is recruited from the surrounding soil and is known to impact positively on the plant host via enhanced resistance to pathogens, increased nutrient availability, growth stimulation and increased resistance to desiccation. Desert ecosystems harbour a diversity of perennial and annual plant species, generally exhibiting considerable physiological adaptation to the low-water environment. In this study, we explored the rhizosphere bacterial microbiomes associated with selected desert plant species. The rhizosphere bacterial communities of 11 plant species from the central Namib Desert were assessed using 16S rRNA gene-dependent phylogenetic analyses. The rhizosphere microbial community of each host plant species was compared with control soils collected from their immediate vicinity, and with those of all other host plants. Rhizosphere and control soil bacterial communities differed significantly and were influenced by both location and plant species. Rhizosphere-associated genera included 67 known plant growth-promoting taxa, including Rhizobium, Bacillus, Microvirga, Kocuria and Paenibacillus. Other than Kocuria, these genera constituted the 'core' rhizosphere bacterial microbiome, defined as being present in > 90 % of the rhizosphere communities. Nine of the 11 desert plant species harboured varying numbers and proportions of species-specific microbial taxa. Predictive analyses of functional pathways linked to rhizosphere microbial taxa showed that these were significantly enriched in the biosynthesis or degradation of a variety of substances such as sugars, secondary metabolites, phenolic compounds and antimicrobials. Overall, our data suggest that plant species in the Namib Desert recruit unique taxa to their rhizosphere bacterial microbiomes that may contribute to their resilience in this extreme environment.}, }
@article {pmid39883994, year = {2025}, author = {Li, J and Xie, Z and Yang, L and Guo, K and Zhou, Z}, title = {The impact of gut microbiome on immune and metabolic homeostasis in type 1 diabetes: Clinical insights for prevention and treatment strategies.}, journal = {Journal of autoimmunity}, volume = {151}, number = {}, pages = {103371}, doi = {10.1016/j.jaut.2025.103371}, pmid = {39883994}, issn = {1095-9157}, abstract = {Type 1 diabetes (T1D) is a complex disease triggered by a combination of genetic and environmental factors, where abnormal autoimmune responses lead to progressive damage of the pancreatic β cells and severe glucose metabolism disorder. Recent studies have increasingly highlighted the close link between gut microbiota dysbiosis and the development of T1D. This review delves into existing population studies to explore the intricate interactions between the gut microbiota and the immune and metabolic homeostasis in T1D. It summarizes how changes in the structure and function of the gut microbiota are closely associated with the onset and progression of T1D across its natural course and clinical stages. More importantly, based on evidence accumulated from clinical observations and trials, we pioneer the discussion on gut microbiota-based T1D prevention and treatment strategies, this not only enriches our understanding of the complex pathological mechanisms of T1D but also provides potential directions for developing novel prevention and treatment strategies.}, }
@article {pmid39883349, year = {2024}, author = {Li, P and Tian, Y and Yang, K and Tian, M and Zhu, Y and Chen, X and Hu, R and Qin, T and Liu, Y and Peng, S and Yi, Z and Liu, Z and Ao, H and Li, J}, title = {Mechanism of microbial action of the inoculated nitrogen-fixing bacterium for growth promotion and yield enhancement in rice (Oryza sativa L.).}, journal = {Advanced biotechnology}, volume = {2}, number = {4}, pages = {32}, pmid = {39883349}, issn = {2948-2801}, abstract = {The use of nitrogen-fixing bacteria in agriculture is increasingly recognized as a sustainable method to boost crop yields, reduce chemical fertilizer use, and improve soil health. However, the microbial mechanisms by which inoculation with nitrogen-fixing bacteria enhance rice production remain unclear. In this study, rice seedlings were inoculated with the nitrogen-fixing bacterium R3 (Herbaspirillum) at the rhizosphere during the seedling stage in a pot experiment using paddy soil. We investigated the effects of such inoculation on nutrient content in the rhizosphere soil, plant growth, and the nitrogen-fixing microbial communities within the rhizosphere and endorhizosphere. The findings showed that inoculation with the R3 strain considerably increased the amounts of nitrate nitrogen, ammonium nitrogen, and available phosphorus in the rhizosphere by 14.77%, 27.83%, and 22.67%, respectively, in comparison to the control (CK). Additionally, the theoretical yield of rice was enhanced by 8.81% due to this inoculation, primarily through a 10.24% increase in the effective number of rice panicles and a 4.14% increase in the seed setting rate. Further analysis revealed that the structure of the native nitrogen-fixing microbial communities within the rhizosphere and endorhizosphere were altered by inoculation with the R3 strain, significantly increasing the α-diversity of the communities. The relative abundance of key nitrogen-fixing genera such as Ralstonia, Azotobacter, Geobacter, Streptomyces, and Pseudomonas were increased, enhancing the quantity and community stability of the nitrogen-fixing community. Consequently, the nitrogen-fixing capacity and sustained activity of the microbial community in the rhizosphere soil were strengthened. Additionally, the expression levels of the nitrogen absorption and transport-related genes OsNRT1 and OsPTR9 in rice roots were upregulated by inoculation with the R3 strain, potentially contributing to the increased rice yield. Our study has revealed the potential microbial mechanisms through which inoculation with nitrogen-fixing bacteria enhances rice yield. This finding provides a scientific basis for subsequent agricultural practices and is of critical importance for increasing rice production and enhancing the ecosystem services of rice fields.}, }
@article {pmid39882875, year = {2025}, author = {Cross, K and Beckman, N and Jahnes, B and Sabree, ZL}, title = {Microbiome metabolic capacity is buffered against phylotype losses by functional redundancy.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0236824}, doi = {10.1128/aem.02368-24}, pmid = {39882875}, issn = {1098-5336}, abstract = {UNLABELLED: Many animals contain a species-rich and diverse gut microbiota that likely contributes to several host-supportive services that include diet processing and nutrient provisioning. Loss of microbiome taxa and their associated metabolic functions as result of perturbations may result in loss of microbiome-level services and reduction of metabolic capacity. If metabolic functions are shared by multiple taxa (i.e., functional redundancy), including deeply divergent lineages, then the impact of taxon/function losses may be dampened. We examined to what degree alterations in phylotype diversity impact microbiome-level metabolic capacity. Feeding two nutritionally imbalanced diets to omnivorous Periplaneta americana over 8 weeks reduced the diversity of their phylotype-rich gut microbiomes by ~25% based on 16S rRNA gene amplicon sequencing, yet PICRUSt2-inferred metabolic pathway richness was largely unaffected due to their being polyphyletic. We concluded that the nonlinearity between taxon and metabolic functional losses is due to microbiome members sharing many well-characterized metabolic functions, with lineages remaining after perturbation potentially being capable of preventing microbiome "service outages" due to functional redundancy.<br><br>IMPORTANCE: Diet can affect gut microbiome taxonomic composition and diversity, but its impacts on community-level functional capabilities are less clear. Host health and fitness are increasingly being linked to microbiome composition and further modeling of the relationship between microbiome taxonomic and metabolic functional capability is needed to inform these linkages. Invertebrate animal models like the omnivorous American cockroach are ideal for this inquiry because they are amenable to various diets and provide high replicates per treatment at low costs and thus enabling rigorous statistical analyses and hypothesis testing. Microbiome taxonomic composition is diet-labile and diversity was reduced after feeding on unbalanced diets (i.e., post-treatment), but the predicted functional capacities of the post-treatment microbiomes were less affected likely due to the resilience of several abundant taxa surviving the perturbation as well as many metabolic functions being shared by several taxa. These results suggest that both taxonomic and functional profiles should be considered when attempting to infer how perturbations are altering gut microbiome services and possible host outcomes.}, }
@article {pmid39882867, year = {2025}, author = {Asmus, AE and Gaire, TN and Schweisthal, KJ and Staben, SM and Noyes, NR}, title = {Microbiome characterization of two fresh pork cuts during production in a pork fabrication facility.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0220924}, doi = {10.1128/spectrum.02209-24}, pmid = {39882867}, issn = {2165-0497}, abstract = {The goal of this study was to characterize the microbial profile of two different fresh pork cuts, bootjack (BJ) trim and tenderloin (TL), through a 16S rRNA sequencing workflow developed specifically for investigating low-biomass fresh meat within a commercial production schedule. Additionally, this study aimed to determine a baseline Salmonella prevalence and enumeration profile across these two fresh pork cuts. Results showed that microbiome diversity was different between the BJ and TL, and also differed significantly by processing date. The relative abundance of key bacterial genera associated with food safety and spoilage was also different between the two meat types. However, over the course of the production shift, changes in the meat microbiome were limited in both the BJ and TL. The crude prevalence and enumerated burden of Salmonella were lower than what has been previously reported in similar fresh pork cuts, and all of the Salmonella-positive samples occurred on just two processing windows of 1-2 days each. Taken together, the results of this study suggest that the microbial profile of two fresh pork cuts is significantly different even within the same plant at the same time points, and that day-to-day variability within the production process likely influences both the fresh pork microbiome and Salmonella profile of these two meat types.IMPORTANCEModern pork processing involves a series of processes that begin with the handling and transport of the live animals, proceed through harvest and fabrication, and end with the packaging and distribution of fresh pork to the consumer. Each step in this process can alter the microbial community of fresh pork and influence the meat's safety and shelf life. However, little is known about the microbial ecology of individual, unprocessed pork cuts and if the diversity of the meat microbiome remains consistent throughout a production schedule. Additionally, the crude prevalence and enumeration of Salmonella have not been well established for individual fresh pork cuts throughout a production schedule. A more thorough understanding of the microbial profile at different stages of pork production will help processors determine processing steps that impact the microbial characteristics of fresh pork. This insight will help processors implement targeted intervention strategies to enhance food safety and quality.}, }
@article {pmid39882861, year = {2025}, author = {Johnson, G and Westcott, SL and Schloss, PD}, title = {clustur: an R package for clustering features using sparse distance matrices.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0123824}, doi = {10.1128/mra.01238-24}, pmid = {39882861}, issn = {2576-098X}, abstract = {The clustur R package implements the de novo clustering algorithms found in the mothur software package for assigning 16S rRNA gene sequences to operational taxonomic units (OTUs). Making these algorithms accessible through the R ecosystem will foster their further development, broader application, and integration within other R packages.}, }
@article {pmid39882793, year = {2025}, author = {}, title = {Discussion of Survival Disparity and the Unique Genomic and Microbiome Profiles of Colon Cancer in Appalachian Kentucky.}, journal = {Journal of the American College of Surgeons}, volume = {}, number = {}, pages = {}, doi = {10.1097/XCS.0000000000001331}, pmid = {39882793}, issn = {1879-1190}, }
@article {pmid39882755, year = {2025}, author = {Huey, SL and Mehta, NH and Steinhouse, RS and Jin, Y and Kibbee, M and Kuriyan, R and Finkelstein, JL and Mehta, S}, title = {Precision nutrition-based interventions for the management of obesity in children and adolescents up to the age of 19 years.}, journal = {The Cochrane database of systematic reviews}, volume = {1}, number = {}, pages = {CD015877}, pmid = {39882755}, issn = {1469-493X}, mesh = {Humans ; Adolescent ; Child ; *Randomized Controlled Trials as Topic ; *Pediatric Obesity/therapy/diet therapy ; *Precision Medicine/methods ; Bias ; Female ; Weight Loss ; Male ; Child, Preschool ; Young Adult ; Feeding Behavior ; Body Mass Index ; Quality of Life ; Exercise ; Diet ; Overweight/therapy/diet therapy ; Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: Precision nutrition-based methods develop tailored interventions and/or recommendations accounting for determinants of intra- and inter-individual variation in response to the same diet, compared to current 'one-size-fits-all' population-level approaches. Determinants may include genetics, current dietary habits and eating patterns, circadian rhythms, health status, gut microbiome, socioeconomic and psychosocial characteristics, and physical activity. In this systematic review, we examined the evidence base for the effect of interventions based on precision nutrition approaches on overweight and obesity in children and adolescents to help inform future research and global guidelines.<br><br>OBJECTIVES: To examine the impact of precision nutrition-based interventions for the management of obesity in children and adolescents in all their diversity.<br><br>SEARCH METHODS: We searched CENTRAL, MEDLINE, CINAHL, Web of Science Core Collection, BIOSIS Previews, Global Index Medicus (all regions), IBECS, SciELO, PAHO, PAHO IRIS, WHO IRIS, WHOLIS, Bibliomap, and TRoPHI, as well as the WHO ICTRP and ClinicalTrials.gov. We last searched the databases on 23 July 2024. We did not apply any language restrictions.<br><br>SELECTION CRITERIA: We included randomised or quasi-randomised controlled trials that evaluated precision nutrition-based interventions (accounting for 'omics' such as phenotyping, genotyping, gut microbiome; clinical data, baseline dietary intake, postprandial glucose response, etc., and/or including artificial intelligence such as machine learning methods) compared to general or one-size-fits-all interventions or no intervention in children and adolescents aged 0 to 9 years or 10 to 19 years with overweight or obesity.<br><br>DATA COLLECTION AND ANALYSIS: Two review authors independently conducted study screening, data extraction, and risk of bias and GRADE assessments. We used fixed-effect analyses. Our outcomes of interest were physical and mental well-being, physical activity, health-related quality of life, obesity-associated disability, and adverse events associated with the interventions as defined or measured by trialists, and weight change (reduction, stabilisation or maintenance).<br><br>MAIN RESULTS: Two studies (3 references, 105 participants) conducted in Ukraine and Greece met our eligibility criteria. One study reported nonprofit funding sources, whilst the other did not report funding, and the certainty of evidence ranged from very low to low across outcomes (all measured at endpoint). Only one trial (65 participants) contributed data on our primary outcomes of interest. Precision nutrition-based intervention versus one-size-fits-all intervention or standard of care In children 0 to 9 years of age, evidence is very uncertain about the effect of a precision nutrition-based intervention (a computerised Decision Support Tool (DST) that incorporates a variety of participant data and provides personalised diet recommendations based on decision-tree algorithms) on body mass index (BMI) (mean difference (MD) -1.40 kg/m[2], 95% confidence interval (CI) -3.48 to 0.68; 1 study, 35 participants; very low-certainty evidence) and on weight (MD -2.60 kg, 95% CI -8.42 to 3.22; 1 study, 35 participants; very low-certainty evidence) compared with a one-size-fits-all control intervention. In children and adolescents 10 to 19 years of age, evidence is very uncertain about the effect of a precision nutrition-based intervention (computerised DST) on BMI (MD 3.00 kg/m[2], 95% CI -0.26 to 6.26; 1 study, 30 participants; very low-certainty evidence) and on weight (MD 11.40 kg, 95% CI -0.47 to 23.27; 1 study, 30 participants; very low-certainty evidence) compared with a one-size-fits-all control intervention.<br><br>AUTHORS' CONCLUSIONS: Based on data from two small studies with a total of 105 participants, the evidence is very uncertain about the effect of precision nutrition-based interventions on body weight or BMI. This review was limited by the number of available randomised controlled trials in this relatively nascent field. Given these limitations, the two studies do not provide sufficient evidence to adequately inform practice. Future research should report participant outcome data, including outcomes related to mental, emotional, and functional well-being, in addition to biochemical and physical measures, stratified by World Health Organization-defined age groups (children (0 to 9 years), and children and adolescents (10 to 19 years)). Future studies should also report methods related to randomisation, blinding, and compliance, as well as include prespecified analysis plans.}, }
@article {pmid39882630, year = {2025}, author = {Boulund, U and Thorsen, J and Trivedi, U and Tranæs, K and Jiang, J and Shah, SA and Stokholm, J}, title = {The role of the early-life gut microbiome in childhood asthma.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2457489}, doi = {10.1080/19490976.2025.2457489}, pmid = {39882630}, issn = {1949-0984}, mesh = {*Asthma/microbiology ; Humans ; *Gastrointestinal Microbiome ; Child ; Animals ; Risk Factors ; Bacteria/classification/genetics/isolation &amp; purification ; Female ; Anti-Bacterial Agents/therapeutic use ; Breast Feeding ; }, abstract = {Asthma is a chronic disease affecting millions of children worldwide, and in severe cases requires hospitalization. The etiology of asthma is multifactorial, caused by both genetic and environmental factors. In recent years, the role of the early-life gut microbiome in relation to asthma has become apparent, supported by an increasing number of population studies, in vivo research, and intervention trials. Numerous early-life factors, which for decades have been associated with the risk of developing childhood asthma, are now being linked to the disease through alterations of the gut microbiome. These factors include cesarean birth, antibiotic use, breastfeeding, and having siblings or pets, among others. Association studies have highlighted several specific microbes that are altered in children developing asthma, but these can vary between studies and disease phenotype. This demonstrates the importance of the gut microbial ecosystem in asthma, and the necessity of well-designed studies to validate the underlying mechanisms and guide future clinical applications. In this review, we examine the current literature on the role of the gut microbiome in childhood asthma and identify research gaps to allow for future microbial-focused therapeutic applications in asthma.}, }
@article {pmid39882401, year = {2025}, author = {Gónzalez Arceo, IJ and Robles Rojo, GA}, title = {Abscess in the posterior region of the uterus due to Streptococcus thoraltensis in 38‑year‑old female: A case report.}, journal = {Medicine international}, volume = {5}, number = {2}, pages = {16}, pmid = {39882401}, issn = {2754-1304}, abstract = {Streptococcus thoraltensis (S. thoraltensis) is a bacterium usually present in the gut microbiome of quadruped mammals. S. thoraltensis is not considered pathogenic for humans; however, several reports have identified it as the etiological agent in cases of chorioamnionitis, postpartum pneumonia and fever of unknown origin. Furthermore, it has been isolated in samples from patients with endocarditis both with and without heart valve replacement. The present study describes the case of a 38-year-old healthy female patient who experienced acute abdominal pain accompanied by dysuria, vesical tenesmus and constipation. A computed tomography scan revealed a retro-uterine cystic mass due to a bacterial abscess. Following surgical drainage, microbiological culture identified S. thoraltensis as the etiological agent. The patient was thus treated with doxycycline and metronidazole, and exhibited a successful response to treatment. The increasing occurrence of S. thoraltensis in human infections suggests potential changes in the epidemiological profile of this bacterium. It is possible that human activity contributes directly or indirectly to the emergence of new pathogens.}, }
@article {pmid39882346, year = {2024}, author = {Parvez, R and Vijayakumar, S and Vins, A and Ramaiah, S and Anbarasu, A and Biswas, L and Beniwal, N and Kaur, H and Muruganandam, N}, title = {Understanding the vaginal microbiome among women with different genotypes of human papillomavirus infection in remote Andaman islands.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1486166}, pmid = {39882346}, issn = {2235-2988}, mesh = {Humans ; Female ; *Vagina/microbiology/virology ; *Microbiota ; *Papillomavirus Infections/virology/microbiology ; Adult ; *Genotype ; *Papillomaviridae/genetics/isolation &amp; purification/classification ; Young Adult ; Middle Aged ; Bacteria/classification/isolation &amp; purification/genetics ; India ; Adolescent ; DNA, Bacterial/genetics ; }, abstract = {BACKGROUND: Human papillomavirus (HPV) is a viral infection, and its acquisition and persistence are significantly influenced by the vaginal microbiota. Understanding and comparing the vaginal microbiome of HPV infected women in Andaman and Nicobar Islands is crucial.<br><br>METHODS: The study involved collecting vaginal swabs and extracting DNA using the QIAamp DNA Minikit. The DNA was then subjected to PCR amplification to confirm HPV infection. illumina NovaSeq 6000 platform was utilized to perform sequencing utilizing 2 x 250 paired end chemistry. Taxonomic analysis was performed and Bacterial abundance plots were generated and samples were grouped based on demographic parameters, pap test diagnosis, and genotypes. To assess diversity, samples were rarefied to 49,000 sequence reads per sample, and alpha and beta diversity metrics were calculated.<br><br>RESULTS: The study analyzed the presence of 21 assigned phyla, with Firmicutes, Actinobacteria, Bacteriodetes, and Proteobacteria emerging as the predominant taxa. At the genus level, Lactobacillus and Gardnerella dominated across all samples. Gardnerella was significantly more abundant in HPV-positive (22.40%) compared to HPV-negative samples (10.04%). Symptomatic group of HPV-positive samples had Gardnerella, and unclassified Coriobacteriaceae being dominant. In terms of bacterial diversity, the study found statistically significant association when comprising individuals aged 21 to 30 years to those aged 31 to 40 years.<br><br>CONCLUSION: Most research concluded that exposure to HPV can boost bacterial diversity in vagina compared to healthy women, increasing the risk of cervical cancer development. Current study highlights the importance of vaginal microbiome associated with high and low risk HPV, various age group as well as the symptomatic and asymptomatic cases of HPV infected women in South Andaman.}, }
@article {pmid39882279, year = {2024}, author = {Tsoukalas, D and Sarandi, E and Fragoulakis, V and Xenidis, S and Mhliopoulou, M and Charta, M and Paramera, E and Papakonstantinou, E and Tsatsakis, A}, title = {Metabolomics-based treatment for chronic diseases: results from a multidisciplinary clinical study.}, journal = {BMJ nutrition, prevention &amp; health}, volume = {7}, number = {2}, pages = {e000883}, pmid = {39882279}, issn = {2516-5542}, abstract = {BACKGROUND: Non-communicable diseases (NCDs), known as chronic diseases, significantly impact patients' quality of life (QoL) and increase medical expenses. The majority of risk factors are modifiable, and metabolomics has been suggested as a promising strategy for their evaluation, though real-world data are scarce. This study evaluated the QoL improvement and cost-effectiveness of a metabolomics-based treatment for NCDs, aiming to restore metabolic dysfunctions and nutritional deficiencies.<br><br>METHODS: We performed a pre-post intervention analysis using clinical, metabolomics, QoL and economic data obtained from the electronic health records of 765 patients visiting a private practice. The intervention consisted of personalised treatment to restore metabolic dysfunctions and nutritional deficiencies identified by metabolomics alongside the standard treatment for their condition. The mean intervention duration was 401 days.<br><br>RESULTS: Significant improvement was identified in energy levels, sleep quality, gastrointestinal function and physical activity (p<0.001). 67.9% of participants reported significant improvement in the overall QoL, and the average quality-adjusted life-years (QALYs) increased by 0.064 (95% uncertainty interval 0.050 to 0.078) post-treatment. The incremental cost-effectiveness ratio was estimated at &#x20ac;49.774/QALY (95% CI &#x20ac;40.110 to &#x20ac;61.433). Metabolic profiling demonstrated that 16/35 organic acids and 11/24 total fatty acids were significantly changed post-treatment (p<0.001), participating in key pathways such as energy metabolism, microbiome and neurotransmitter turnover. Vitamin D and 5-methyltetrahydrofolate insufficiency was significantly restored (p=0.036).<br><br>CONCLUSION: This is the first study providing evidence that the integration of metabolomics in clinical practice can have a clinical benefit for patients' QoL and may be a cost-effective method.}, }
@article {pmid39882224, year = {2025}, author = {Takamaru, H and Tsay, C and Shiba, S and Yachida, S and Saito, Y}, title = {Microbiome and Colorectal Cancer in Humans: A Review of Recent Studies.}, journal = {Journal of the anus, rectum and colon}, volume = {9}, number = {1}, pages = {20-24}, pmid = {39882224}, issn = {2432-3853}, abstract = {The tumor microenvironment has recently been well-studied in various gastrointestinal cancers, including colorectal cancer (CRC). The gut microbiota, a collection of microorganisms in the human gastrointestinal tract, is one of the microenvironments associated with colon carcinogenesis. It has been challenging to elucidate the mechanisms by which gut microbiota contributes to carcinogenesis and cancer progression due to complex interactions with the host, including its metabolites and immune and inflammatory responses. Various studies described the influence of diet on reported changes in the composition and microbiota of gut bacteria and its association with CRC. In recent years, metagenomic techniques such as shotgun sequencing and genome-wide association studies focused on understanding the role of the microbiota and the metabolome on early CRCs and colon carcinogenesis to determine if there are modifiable or intervenable targets for CRC. In this review, we will attempt to provide an overview of gut microbiota related to CRC, with particular attention to the findings of recent studies.}, }
@article {pmid39881993, year = {2024}, author = {Enea, M and Beauregard, J and De Bellis, T and Faticov, M and Laforest-Lapointe, I}, title = {The temperate forest phyllosphere and rhizosphere microbiome: a case study of sugar maple.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1504444}, pmid = {39881993}, issn = {1664-302X}, abstract = {The interactions between sugar maple (Acer saccharum, Marshall) and its microbial communities are important for tree fitness, growth, and establishment. Despite recent progress in our understanding of the rhizosphere and phyllosphere microbial communities of sugar maple, many outstanding knowledge gaps remain. This review delves into the relationships between sugar maple and its microbes, as climate change alters plant species distributions. It highlights the multifaceted roles of key microbes, such as arbuscular mycorrhizal (AM) fungi and pathogens, in affecting the distribution and establishment of sugar maple in novel habitats. Furthermore, this review examines how microbial communities in different compartments contribute to tree fitness. Finally, it explores how microbial dispersal and altered species interactions under changing environmental conditions can affect sugar maple's ability to migrate beyond its current range, emphasizing the different scenarios associated with such shifts. In the rhizosphere, AM fungi are known for their roles in nutrient acquisition and improving stress tolerance. Yet, key questions remain about how these fungi interact with other microbes, how soil chemistry and climate change alter these interactions, and how the presence of beneficial microbes influences sugar maple's establishment. Additionally, the role of dark septate endophytes (DSE) in sugar maple's fitness remains underexplored, emphasizing the need for more research on their diversity and functions. In the phyllosphere, microbial communities are subject to shifts due to rising global change, with potential impacts on sugar maple's fitness. These changes may influence the tree's resistance to pathogens, tolerance to environmental stress, and overall health. Yet, our understanding of these interactions relies mostly on short-read sequencing methods targeting marker genes (e.g., 16S, ITS, 18S), which often fail to identify microbes at the species level. Limitations in molecular techniques and poor microbial reference databases hinder our ability to fully characterize tree-associated microbial diversity and functions. Future research should thus prioritize advanced molecular tools such as shotgun, hybrid, or long-read sequencing. Controlled experiments are also needed to establish causal links between sugar maple fitness and microbial communities, and to study whether microbial communities change throughout the tree's lifespan.}, }
@article {pmid39881988, year = {2024}, author = {Dong, Y and Gong, J and Yang, L and Jiang, Q and Wen, C and Zhang, J and Yang, R and Wang, Y and Dai, Y and Gao, G and Li, S and Cao, Y and Ding, W}, title = {Superiority of native seed core microbiomes in the suppression of bacterial wilt disease.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1506059}, pmid = {39881988}, issn = {1664-302X}, abstract = {INTRODUCTION: Native endophytic microorganisms in tobacco seeds are closely related to their resistance to Ralstonia solanacearum (R. solanacearum) infections. However, the role of the native seed core microbiome in the suppression of bacterial wilt disease (BWD) remains underexplored.<br><br>METHODS: The characteristics of endophytic bacterial communities in both resistant and susceptible tobacco varieties were characterized using high-throughput sequencing technology.<br><br>RESULTS: This study found Paenibacillus as a potential microbial antagonist against BWD based on its significantly greater presence in BWD-resistant tobacco varieties, with a relative abundance that was 83.10% greater in the seeds of resistant tobacco than in those of susceptible varieties. Furthermore, a Paenibacillus strain identified as Paenibacillus odorifer 6036-R2A-26 (P. odorifer 26) was isolated from the seeds of the resistant variety. Following irrigation treatment with P. odorifer 26, the BWD index was reduced by 51.08%. Additionally, this strain exhibited significant growth-promoting effects on tobacco. It significantly increased the fresh weight of the tobacco plants by 30.26% in terms of aboveground weight, 37.75% in terms of underground weight, and 33.97% in terms of aboveground dry weight. This study highlights the critical role of Paenibacillus in tobacco seeds in the suppression of BWD, which may result from its antagonistic and growth-promoting properties.<br><br>DISCUSSION: The results of this study revealed differences in the structural characteristics of endophytic bacterial communities between resistant and susceptible tobacco varieties, with groups such as Paenibacillus potentially playing significant roles in resisting BWD. These findings highlight the superiority of seed endophytic microorganisms. In the context of declining plant disease resistance and the spread of bacterial wilt, core endophytic microorganisms in seeds may emerge as a viable option for enhancing the productivity of agricultural ecosystems.}, }
@article {pmid39881984, year = {2024}, author = {Li, J and Tang, G and Liu, H and Luo, X and Wang, J}, title = {Characterizing the microbiome recruited by the endangered plant Firmiana danxiaensis in phosphorus-deficient acidic soil.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1439446}, pmid = {39881984}, issn = {1664-302X}, abstract = {Phosphorus (P)-deficient soils serve as crucial habitats for endangered plant species. Microbiomes play pivotal roles in soil element cycling and in determining a plant's adaptability to the environment. However, the relationship between the endangered plant, microbiome, and soil stoichiometric traits, and how it affects plant adaption to P-deficient habitats remain largely unexplored. In this study, we investigated the microbiome (bacteria and fungi) in the rhizosphere of Firmiana danxiaensis, an endangered plant species growing exclusively in P-deficient acidic soils on Mt. Danxia, South China; the non-endangered coexisting tree species Pinus massoniana was used as a reference. Our results showed that soil traits in the rhizosphere of F. danxiaensis differed significantly from that of P. massoniana, including higher soil pH, lower C:N, and higher N:P. The rhizosphere of F. danxiaensis harbors higher microbial diversity and different microbial communities from P. massoniana. Using the machine learning approach, we characterized 76 bacterial and 20 fungal phylotypes dominated in F. danxiaensis rhizosphere, most of which had strong impacts on microbial ecological network structure (they accounted for only 0.33% node numbers but linked 21.2% of the nodes in the network); specifically, Udaeobacter spp., a highly abundant (constituting 4.07% of the total bacterial community) member of Verrucomicrobiota exclusively accumulated in the rhizosphere of F. danxiaensis but not P. massoniana, demonstrated a pronounced ecological prefers toward F. danxiaensis rhizosphere habitat (high pH, low C:N and high N:P) and potential antagonistic indication. In contrast, P. massoniana rhizosphere harbored more Subgroup2 of Acidobacteria and Gammaproteobacterial N-fixer. Taken together, this study provided novel evidence that endangered plants recruited a unique microbiome characterized by Udaeobacter spp. favoring high N habitat. It contributes not only to our understanding of microbiome recruitment by plants in P-deficient acidic soils, but also underscores the importance of microbiome in the conservation and population restoration of endangered plants.}, }
@article {pmid39881980, year = {2024}, author = {Renk, H and Schoppmeier, U and Müller, J and Kuger, V and Neunhoeffer, F and Gille, C and Peter, S}, title = {Oxygenation and intestinal perfusion and its association with perturbations of the early life gut microbiota composition of children with congenital heart disease.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1468842}, pmid = {39881980}, issn = {1664-302X}, abstract = {BACKGROUND: Early life gut microbiota is known to shape the immune system and has a crucial role in immune homeostasis. Only little is known about composition and dynamics of the intestinal microbiota in infants with congenital heart disease (CHD) and potential influencing factors.<br><br>METHODS: We evaluated the intestinal microbial composition of neonates with CHD (n&#x202f;=&#x202f;13) compared to healthy controls (HC, n&#x202f;=&#x202f;30). Fecal samples were analyzed by shotgun metagenomics. Different approaches of statistical modeling were applied to assess the impact of influencing factors on variation in species composition. Unsupervised hierarchical clustering of the microbial composition of neonates with CHD was used to detect associations of distinct clusters with intestinal tissue oxygenation and perfusion parameters, obtained by the "oxygen to see" (O2C) method.<br><br>RESULTS: Overall, neonates with CHD showed an intestinal core microbiota dominated by the genera Enterococcus (27%) and Staphylococcus (20%). Furthermore, a lower abundance of the genera Bacteroides (8% vs. 14%), Parabacteroides (1% vs. 3%), Bifidobacterium (4% vs. 12%), and Escherichia (8% vs. 23%) was observed in CHD compared to HCs. CHD patients that were born by vaginal delivery showed a lower fraction of the genera Bacteroides (15% vs. 21%) and Bifidobacterium (7% vs. 22%) compared to HCs and in those born by cesarean section, these genera were not found at all. In infants with CHD, we found a significant impact of oxygen saturation (SpO2) on relative abundances of the intestinal core microbiota by multivariate analysis of variance (F[8,2]&#x202f;=&#x202f;24.9, p&#x202f;=&#x202f;0.04). Statistical modeling suggested a large proportional shift from a microbiota dominated by the genus Streptococcus (50%) in conditions with low SpO2 towards the genus Enterococcus (61%) in conditions with high SpO2. We identified three distinct compositional microbial clusters, corresponding neonates differed significantly in intestinal blood flow and global gut perfusion.<br><br>CONCLUSION: Early life differences in gut microbiota of CHD neonates versus HCs are possibly linked to oxygen levels. Delivery method may affect microbiota stability. However, further studies are needed to assess the effect of potential interventions including probiotics or fecal transplants on early life microbiota perturbations in neonates with CHD.}, }
@article {pmid39881948, year = {2025}, author = {Said, SS and Ibrahim, WN}, title = {Gut Microbiota-Tumor Microenvironment Interactions: Mechanisms and Clinical Implications for Immune Checkpoint Inhibitor Efficacy in Cancer.}, journal = {Cancer management and research}, volume = {17}, number = {}, pages = {171-192}, pmid = {39881948}, issn = {1179-1322}, abstract = {Cancer immunotherapy has transformed cancer treatment in recent years, with immune checkpoint inhibitors (ICIs) emerging as a key therapeutic approach. ICIs work by inhibiting the mechanisms that allow tumors to evade immune detection. Although ICIs have shown promising results, especially in solid tumors, patient responses vary widely due to multiple intrinsic and extrinsic factors within the tumor microenvironment. Emerging evidence suggests that the gut microbiota plays a pivotal role in modulating immune responses at the tumor site and may even influence treatment outcomes in cancer patients receiving ICIs. This review explores the complex interactions between the gut microbiota and the tumor microenvironment, examining how these interactions could impact the effectiveness of ICI therapy. Furthermore, we discuss how dysbiosis, an imbalance in gut microbiota composition, may contribute to resistance to ICIs, and highlight microbiota-targeted strategies to potentially overcome this challenge. Additionally, we review recent studies investigating the diagnostic potential of microbiota profiles in cancer patients, considering how microbial markers might aid in early detection and stratification of patient responses to ICIs. By integrating insights from recent preclinical and clinical studies, we aim to shed light on the potential of microbiome modulation as an adjunct to cancer immunotherapy and as a diagnostic tool, paving the way for personalized therapeutic approaches that optimize patient outcomes.}, }
@article {pmid39881872, year = {2024}, author = {Xu, L and Hu, B and He, J and Fu, X and Liu, N}, title = {Intratumor microbiome-derived butyrate promotes chemo-resistance in colorectal cancer.}, journal = {Frontiers in pharmacology}, volume = {15}, number = {}, pages = {1510851}, pmid = {39881872}, issn = {1663-9812}, abstract = {INTRODUCTION: Colorectal cancer (CRC) is a leading cause of cancer-related mortality globally. Although tumor immunotherapy is widely recognized for treating unresectable CRC, challenges such as ineffective immunotherapy and drug resistance remain prevalent. While intratumor microbiome-derived butyrate has been implicated in promoting lung cancer metastasis, its role in CRC chemoresistance is not well understood. This study aimed to explore the relationship between intratumor butyrate and chemoresistance in CRC.<br><br>METHODS: We performed a comprehensive analysis of the microbiome composition in CRC patients with varying resistance-free survival (RFS) durations, utilizing 16S rRNA sequencing. Furthermore, we assessed the prognostic significance of circulating microbiome DNA (cmDNA) and examined the effects of exogenous butyrate supplementation on the chemosensitivity of CRC cell lines.<br><br>RESULTS: Our 16S sequencing analysis revealed a reduction in microbial diversity within tumor samples of patients with resistance, as indicated by metrics such as observed taxonomic units, Shannon, and Simpson indices. Notably, Roseburia and Fusobacteria emerged as prominent biomarkers for the resistance group, whereas Bifidobacterium, Helicobacter, and Akkermansia were identified as biomarkers for the non-resistant group. Utilizing a Lasso regression model, we identified six genera-Roseburia, Helicobacter, Gardnerella, Flavonifractor, Coprococcus, and Anaerostipes-that significantly correlated with recurrence-free survival. Furthermore, both the intratumor microbiome signature and circulating microbiome DNA were effective in accurately predicting CRC resistance. Experimental assays, including CCK8 and wound-healing, demonstrated that intratumor microbiome-derived butyrate enhances the proliferation and migration of HCT15 cells in a time- and concentration-dependent manner. Cell survival analysis further indicated that butyrate treatment significantly increased the IC50 value, suggesting heightened drug resistance in HCT15 cells. Mechanistically, this resistance was attributed to butyrate's activation of the PI3K-AKT signaling pathway.<br><br>CONCLUSION: Our results suggest that intratumor microbiome-derived butyrate contributes to chemoresistance in colorectal cancer, highlighting the potential prognostic and therapeutic significance of the intratumor microbiome.}, }
@article {pmid39881818, year = {2024}, author = {Esfand, SM and Querdasi, FR and Gancz, NN and Savoca, PW and Nussbaum, S and Somers, JA and Ditzer, J and Figueroa, MB and Chu, K and Towner, E and Callaghan, BL}, title = {The mind, brain, and body study: A protocol for examining the effects of the gut-brain-immune axis on internalizing symptoms in youth exposed to caregiving-related early adversity.}, journal = {Brain, behavior, &amp; immunity - health}, volume = {42}, number = {}, pages = {100880}, pmid = {39881818}, issn = {2666-3546}, abstract = {Experiences of caregiving-related adversity are common and one of the strongest predictors of internalizing psychopathology (i.e., anxiety and depression). Specifically, individuals who have been exposed to such early adversities have altered affective neurodevelopment, impaired memory systems, increased risk of developing internalizing disorders, greater inflammation, and differences in gastrointestinal (gut) microbiome composition. Crucially, the gut microbiome undergoes a sensitive period of development that precedes neural and immune sensitive periods, thus making it a potentially fruitful target for intervention. Though previous work has assessed neural, immune, and gut microbiome systems in individuals exposed to early adversity, studies have primarily looked at these biological systems independently. The Mind, Brain, and Body study (MBB) implements multimodal and longitudinal design to assess how changes in the gut microbiome following caregiving-related adversity may underlie altered affective neurodevelopment, memory, and immune functioning in youth and contribute to internalizing symptoms. Across three waves, spread approximately 12-18 months apart, youth with and without previous experiences of caregiving-related adversity completed self-report measures of mental and physical health, provided stool, saliva, hair, and blood samples, and completed an MRI scan. Results of this study will expand our knowledge on how the gut microbiome shapes several biological and cognitive systems and motivate future work investigating the gut microbiome as potential target for intervention.}, }
@article {pmid39881467, year = {2025}, author = {Herath Mudiyanselage, H and Ali, A and Mohmoud, ME and Farooq, M and Isham, IM and Ghaffar, A and Jovel, J and Gomis, SM and Niu, D and Abdul-Careem, MF}, title = {Delmarva (DMV1639) infectious bronchitis virus infection alters the microbiome of gastrointestinal and respiratory tracts of broiler chickens.}, journal = {Virology}, volume = {604}, number = {}, pages = {110428}, doi = {10.1016/j.virol.2025.110428}, pmid = {39881467}, issn = {1096-0341}, abstract = {Infectious bronchitis virus (IBV) is known to cause significant alterations in tracheal microbial flora in broiler chickens 5 days post-infection (dpi) and our focus is to understand the changes in both respiratory and gastrointestinal microbiome in broilers over a period of time following IBV infection. A study was conducted to characterize the tracheal and cecal microbiome in IBV infected and control broiler chickens at 6, 9 and 15 dpi. IBV genome in trachea, lung and cecal tonsils could be observed in the infected group at all the time points. Immune response parameters and histopathological lesion scores were significantly higher in IBV infected trachea and cecal tonsils at 6, 9 and 15 dpi compared to the controls. We observed that cecal microbial diversity (alpha diversity) was increased in the IBV infected group at 6 and 15 dpi. On the other hand, diversity (alpha diversity) of tracheal microbiome was elevated only at 9 dpi in the IBV infected group. Moreover, significant shift of microbial communities (beta diversity), in both cecum and trachea was observed following IBV infection. Enzyme and metabolic pathway analyses of cecum indicated an upregulation of DNA replication and cell wall synthesis pathways and a downregulation of pathways related to short chain fatty acid (SCFA) production in the IBV infected group compared to the controls. Analysis of tracheal metabolic pathways suggested initial adaptation to the infection stress and gradually shifting to enhanced microbial growth and stability. The study outcome adds to the understanding of microbiome changes secondary to histological changes and immune response following IBV infection in broiler chickens.}, }
@article {pmid39881417, year = {2025}, author = {Ye, GC and Peng, H and Xiang, JC and Miao, LT and Liu, CZ and Wang, SG and Xia, QD}, title = {Comprehensive analysis of the interaction microbiome and prostate cancer: an initial exploration from multi-cohort metagenome and GWAS studies.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {130}, pmid = {39881417}, issn = {1479-5876}, mesh = {Humans ; Male ; *Prostatic Neoplasms/microbiology/genetics/pathology ; *Metagenome/genetics ; *Genome-Wide Association Study ; *Gastrointestinal Microbiome/genetics ; Cohort Studies ; Neoplasm Metastasis ; Mendelian Randomization Analysis ; }, abstract = {INTRODUCTION: Prostate cancer is one of the most common cancers in the United States with a high mortality rate. In recent years, the traditional opinion about prostate microbiome was challenged. Although there still are some arguments, an escalating number of researchers are shifting their focus toward the microbiome within the prostate tumor environment.<br><br>METHODS: We mined the data of the microbiome extracted from the metagenome, and it offers a broader taxonomic coverage and accurate functional profiling. We used Kraken2, a mapping tool, to mine the gut microbiota of prostate cancer patients. A two-sample Mendelian Randomization was conducted to reflect the association between gut microbiome and cancer.<br><br>RESULTS: In the study, we found the consistency of the special intratumor microbiome of both non-metastatic tumors and metastatic tumors. And we dig the gut microbiome in patients with different treatments. We found that some microbiotas may be associated with prostate cancer progression and a special microbiome in metastatic prostate cancer may exist. The anti-androgen therapy can significantly change both the intratumor and gut microbiome.<br><br>CONCLUSION: With the progression and metastasis of prostate cancer, some intratumor microbiome changes. And anti-androgen influences both the intratumor and gut microbiome. Our discovery may help researchers further understand the progression, metastasis, and resistance of prostate cancer from the perspective of microbiome level.}, }
@article {pmid39881387, year = {2025}, author = {Pangga, GM and Star-Shirko, B and Psifidi, A and Xia, D and Corcionivoschi, N and Kelly, C and Hughes, C and Lavery, U and Richmond, A and Ijaz, UZ and Gundogdu, O}, title = {Impact of commercial gut health interventions on caecal metagenome and broiler performance.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {30}, pmid = {39881387}, issn = {2049-2618}, support = {BB/T008709/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; EP/V030515/1//Engineering and Physical Sciences Research Council/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome ; *Cecum/microbiology ; *Metagenome ; *Probiotics/administration &amp; dosage ; Prebiotics ; Bacteria/classification/genetics/isolation &amp; purification ; Animal Feed/microbiology ; Vaccination/veterinary ; Dietary Supplements ; }, abstract = {BACKGROUND: Maintaining gut health is a persistent and unresolved challenge in the poultry industry. Given the critical role of gut health in chicken performance and welfare, there is a pressing need to identify effective gut health intervention (GHI) strategies to ensure optimal outcomes in poultry farming. In this study, across three broiler production cycles, we compared the metagenomes and performance of broilers provided with ionophores (as the control group) against birds subjected to five different GHI combinations involving vaccination, probiotics, prebiotics, essential oils, and reduction of ionophore use.<br><br>RESULTS: Using a binning strategy, 84 (&#x2265;&#x2009;75% completeness,&#x2009;&#x2264;&#x2009;5% contamination) metagenome-assembled genomes (MAGs) from 118 caecal samples were recovered and annotated for their metabolic potential. The majority of these (n&#x2009;=&#x2009;52, 61%) had a differential response across all cohorts and are associated with the performance parameter - European poultry efficiency factor (EPEF). The control group exhibited the highest EPEF, followed closely by the cohort where probiotics are used in conjunction with vaccination. The use of probiotics B, a commercial Bacillus strain-based formulation, was determined to contribute to the superior performance of birds. GHI supplementation generally affected the abundance of microbial enzymes relating to carbohydrate and protein digestion and metabolic pathways relating to energy, nucleotide synthesis, short-chain fatty acid synthesis, and drug-transport systems. These shifts are hypothesised to differentiate performance among groups and cycles, highlighting the beneficial role of several bacteria, including Rikenella microfusus and UBA7160 species.<br><br>CONCLUSIONS: All GHIs are shown to be effective methods for gut microbial modulation, with varying influences on MAG diversity, composition, and microbial functions. These metagenomic insights greatly enhance our understanding of microbiota-related metabolic pathways, enabling us to devise strategies against enteric pathogens related to poultry products and presenting new opportunities to improve overall poultry performance and health. Video Abstract.}, }
@article {pmid39881368, year = {2025}, author = {Liu, R and Galiwango, RM and Park, D and Huibner, S and Aziz, M and Anok, A and Nnamutete, J and Isbirye, Y and Wasswa, JB and Male, D and Kigozi, G and Tobian, AAR and Prodger, JL and Liu, C and Coburn, B and Kaul, R}, title = {Gardnerella vaginalis-binding IgA in the urethra of sexually experienced males.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {29}, pmid = {39881368}, issn = {2049-2618}, mesh = {Humans ; *Gardnerella vaginalis/immunology ; Male ; *Urethra/microbiology ; *Immunoglobulin A/immunology/metabolism ; Adult ; Cross-Sectional Studies ; Antibodies, Bacterial/immunology ; Streptococcus mitis/immunology ; Sexual Behavior ; Immunoglobulin G/immunology ; Young Adult ; Vagina/microbiology/immunology ; Uganda ; Female ; HIV Infections/microbiology/immunology ; }, abstract = {BACKGROUND: Genital inflammation increases HIV susceptibility and is associated with the density of pro-inflammatory anaerobes in the vagina and coronal sulcus. The penile urethra is a critical site of HIV acquisition, although correlates of urethral HIV acquisition are largely unknown. While Streptococcus mitis is a consistent component of the urethral flora, the presence of Gardnerella vaginalis has been linked with prior penile-vaginal sex and urethral inflammation. Here, we use a flow cytometry-based bacterial assay to quantify urethral IgA and IgG that bind G. vaginalis and S. mitis in a cross-sectional cohort of 45 uncircumcised Ugandan men and to evaluate their association with the urethral microbiome and local soluble immune factors.<br><br>RESULTS: Urethral antibodies binding both bacterial species were readily detectable, with G. vaginalis predominantly bound by IgA, and S. mitis equivalently by IgA and IgG. Gardnerella vaginalis-binding IgA was elevated in participants with detectable urethral Gardnerella, with the latter only present in participants who reported prior penile-vaginal sex. In contrast, detectable urethral S. mitis was not associated with sexual history or levels of S. mitis-binding IgA/IgG. The time from the last penile-vaginal sex was inversely correlated with the urethral concentrations of total IgA, G. vaginalis-binding IgA, and chemokines IL-8 and MIP-1&#x3b2;; these inflammatory chemokines were independently associated with higher total IgA concentration, but not with G. vaginalis-binding IgA.<br><br>CONCLUSIONS: This first description of microbe-binding antibodies in the penile urethra suggests that urethral colonization by Gardnerella after penile-vaginal sex specifically induces a G. vaginalis-binding IgA response. Prospective studies of the host-microbe relationship in the urethra may have implications for the development of vaccines&#xa0;against sexually-transmitted bacteria. Video Abstract.}, }
@article {pmid39881353, year = {2025}, author = {Feizi, H and Kafil, HS and Plotnikov, A and Kataev, V and Balkin, A and Filonchikova, E and Rezaee, MA and Ghotaslou, R and Sadrkabir, M and Kadkhoda, H and Kamounah, FS and Nikitin, S}, title = {Polyp and tumor microenvironment reprogramming in colorectal cancer: insights from mucosal bacteriome and metabolite crosstalk.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {24}, number = {1}, pages = {9}, pmid = {39881353}, issn = {1476-0711}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism/pathology ; *Tumor Microenvironment ; Male ; *Bacteria/metabolism/classification/genetics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Female ; Gastrointestinal Microbiome ; Aged ; Adenomatous Polyps/microbiology/metabolism/pathology ; Acetoacetates/metabolism ; }, abstract = {BACKGROUND: Highly frequent colorectal cancer (CRC) is predicted to have 3.2 million novel cases by 2040. Tumor microenvironment (TME) bacteriome and metabolites are proposed to be involved in CRC development. In this regard, we aimed to investigate the bacteriome and metabolites of healthy, adenomatous polyp, and CRC tissues.<br><br>METHODS: Sixty samples including healthy (H), adenomatous polyps (AP), adenomatous polyps-adjacent (APA), cancer tumor (CT), and cancer tumor-adjacent (CA) tissues were collected and analyzed by 16&#xa0;S rRNA sequencing and [1]H NMR spectroscopy.<br><br>RESULTS: Our results revealed that the bacteriome and metabolites of the H, AP, and CT groups were significantly different. We observed that the Lachnospiraceae family depleted concomitant with acetoacetate and beta-hydroxybutyric acid (BHB) accumulations in the AP tissues. In addition, some bacterial species including Gemella morbillorum, and Morganella morganii were enriched in the AP compared to the H group. Furthermore, fumarate was accumulated concomitant to Aeromonas enteropelogenes, Aeromonas veronii, and Fusobacterium nucleatum subsp. animalis increased abundance in the CT compared to the H group.<br><br>CONCLUSION: These results proposed that beneficial bacteria including the Lachnospiraceae family depletion cross-talk with acetoacetate and BHB accumulations followed by an increased abundance of driver bacteria including G. morbillorum, and M. morganii may reprogram polyp microenvironment leading to tumor initiation. Consequently, passenger bacteria accumulation like A. enteropelogenes, A.veronii, and F. nucleatum subsp. animalis cross-talking fumarate in the TME may aggravate cancer development. So, knowledge of TME bacteriome and metabolites might help in cancer prevention, early diagnosis, and a good prognosis.}, }
@article {pmid38967078, year = {2025}, author = {Dhanawat, M and Malik, G and Wilson, K and Gupta, S and Gupta, N and Sardana, S}, title = {The Gut Microbiota-Brain Axis: A New Frontier in Alzheimer's Disease Pathology.}, journal = {CNS &amp; neurological disorders drug targets}, volume = {24}, number = {1}, pages = {7-20}, pmid = {38967078}, issn = {1996-3181}, mesh = {Humans ; *Alzheimer Disease/metabolism/microbiology ; *Gastrointestinal Microbiome/physiology ; *Brain-Gut Axis/physiology ; *Brain/metabolism ; Animals ; }, abstract = {Dr. Aloysius Alzheimer, a German neuropathologist and psychiatrist, recognized the primary instance of Alzheimer's disease (AD) for a millennium, and this ailment, along with its related dementias, remains a severe overall community issue related to health. Nearly fifty million individuals worldwide suffer from dementia, with Alzheimer's illness contributing to between 60 and 70% of the instances, estimated through the World Health Organization. In addition, 82 million individuals are anticipated to be affected by the global dementia epidemic by 2030 and 152 million by 2050. Furthermore, age, environmental circumstances, and inherited variables all increase the likelihood of acquiring neurodegenerative illnesses. Most recent pharmacological treatments are found in original hypotheses of disease, which include cholinergic (drugs that show affective cholinergic system availability) as well as amyloid-accumulation (a single drug is an antagonist receptor of Nmethyl D-aspartate). In 2020, the FDA provided approval on anti-amyloid drugs. According to mounting scientific data, this gut microbiota affects healthy physiological homeostasis and has a role in the etiology of conditions that range between obesity and neurodegenerative disorders like Alzheimer's. The microbiota-gut-brain axis might facilitate interconnection among gut microbes as well as the central nervous system (CNS). Interaction among the microbiota-gut system as well as the brain occurs through the "two-way" microbiota-gut-brain axis. Along this axis, the stomach as well as the brain develop physiologically and take on their final forms. This contact is constant and is mediated by numerous microbiota-derived products. The gut microbiota, for instance, can act as non-genetic markers to set a threshold for maintaining homeostasis or getting ill. The scientific community has conducted research and found that bowel dysbiosis and gastrointestinal tract dysregulation frequently occur in Alzheimer's disease (AD) patients. In this review, the effects of the microbiota- gut-brain axis on AD pathogenesis will be discussed.}, }
@article {pmid39881025, year = {2025}, author = {Haider, K and Sufian, M and Abbas, D and Kabir, K and Ali, MS and Kausar, Y and Ghafar, MA}, title = {The Role of Gut Microbiota in Shaping Immune Responses in Tephritidae Fruit Fly and Prospective Implications for Management.}, journal = {Neotropical entomology}, volume = {54}, number = {1}, pages = {34}, pmid = {39881025}, issn = {1678-8052}, mesh = {*Tephritidae/immunology/microbiology ; Animals ; *Gastrointestinal Microbiome ; Symbiosis ; Pest Control, Biological ; }, abstract = {The interaction of microbial communities with host immunity has become one of the most explored research areas with significant implications for pest control strategies. It has been found that the gut microbiota plays substantial roles in immune response regulation and host-gut microbiome symbiosis, as well as in pathogen resistance and overall fitness in Tephritidae fruit flies that are major pests of agricultural importance. In this review, we discuss the modulation of immune responses of Tephritidae fruit flies by the gut microbiota with particular emphasis on the general interactions between microbiota and the immune system. These interactions help to unravel new horizons of pest management. Regulating gut microbiota modifies the performance of biological control agents and SIT and allows the creation of microbial therapies that affect the vital physiological functions of fruit flies. Besides, deploying microbes that can modulate the immune response and using microbial-derived signals provide an eco-friendly and more sustainable way of eradicating chemical pesticides and making farming systems less susceptible to climatic variability. This paper reviews various aspects of the possibility of using gut microbiota for changing the approach to Integrated Pest Management (IPM) programs that would improve methods of controlling Tephritidae fruit fly populations more ecologically.}, }
@article {pmid39880965, year = {2025}, author = {Contreras-Negrete, G and Valiente-Banuet, A and Molina-Freaner, F and Partida-Martínez, LP and Hernández-López, A}, title = {Agricultural Practices and Environmental Factors Drive Microbial Communities in the Mezcal-Producing Agave angustifolia Haw.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {181}, pmid = {39880965}, issn = {1432-184X}, support = {CV549242//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 319061//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 319061//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; 319061//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; }, mesh = {*Agave/microbiology ; *Soil Microbiology ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification ; *Fungi/genetics/classification/isolation &amp; purification ; *Agriculture ; *RNA, Ribosomal, 16S/genetics ; Mexico ; Alcoholic Beverages/microbiology ; Biodiversity ; Rhizosphere ; }, abstract = {Mezcal, a traditional Mexican alcoholic beverage, has been a vital source of livelihood for indigenous and rural communities for centuries. However, increasing international demand is exerting pressure on natural resources and encouraging intensive agricultural practices. This study investigates the impact of management practices (wild, traditional, and conventional) and environmental factors on the microbial communities associated with Agave angustifolia, a key species in mezcal production. High-throughput sequencing of the 16S rRNA and ITS2 gene regions revealed distinct prokaryotic and fungal community structures across different plant compartments (endosphere, episphere, and soil), identifying 8214 prokaryotic and 7459 fungal ASVs. Core microbial communities were dominated by Proteobacteria, Actinobacteria, Ascomycota, and Basidiomycota. Alpha diversity analyses showed significant increases in prokaryotic diversity from the endosphere to soil, while fungal diversity remained stable. Notably, conventional management practices were associated with reductions in beneficial microbial taxa. Environmental factors such as precipitation and temperature significantly influenced microbial diversity and composition, especially in the rhizosphere. Beta diversity patterns underscored the strong impact of plant compartment, with management practices and aridity further shaping microbial communities. These results reveal the intricate interactions between management practices, environmental conditions, and microbial diversity, providing valuable insights for the sustainable cultivation of A. angustifolia.}, }
@article {pmid39880958, year = {2025}, author = {Maghini, DG and Oduaran, OH and Olubayo, LAI and Cook, JA and Smyth, N and Mathema, T and Belger, CW and Agongo, G and Boua, PR and Choma, SSR and Gómez-Olivé, FX and Kisiangani, I and Mashaba, GR and Micklesfield, L and Mohamed, SF and Nonterah, EA and Norris, S and Sorgho, H and Tollman, S and Wafawanaka, F and Tluway, F and Ramsay, M and Wirbel, J and ,  and Bhatt, AS and Hazelhurst, S}, title = {Expanding the human gut microbiome atlas of Africa.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {39880958}, issn = {1476-4687}, abstract = {Population studies provide insights into the interplay between the gut microbiome and geographical, lifestyle, genetic and environmental factors. However, low- and middle-income countries, in which approximately 84% of the world's population lives[1], are not equitably represented in large-scale gut microbiome research[2-4]. Here we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,801 women from Burkina Faso, Ghana, Kenya and South Africa. By engaging with communities that range from rural and horticultural to post-industrial and urban informal settlements, we capture a far greater breadth of the world's population diversity. Using shotgun metagenomic sequencing, we identify taxa with geographic and lifestyle associations, including Treponema and Cryptobacteroides species loss and Bifidobacterium species gain in urban populations. We uncover 1,005 bacterial metagenome-assembled genomes, and we identify antibiotic susceptibility as a factor that might drive Treponema succinifaciens absence in urban populations. Finally, we find an HIV infection signature defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals so far, and paired with extensive clinical biomarkers and demographic data, provides extensive opportunity for microbiome-related discovery.}, }
@article {pmid39880761, year = {2025}, author = {Nandwana, D and Zhang, Y and Feng, N}, title = {Contribution of the Microbiome to Interstitial Cystitis/Bladder Pain Syndrome: A Mini Review.}, journal = {European urology focus}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.euf.2025.01.008}, pmid = {39880761}, issn = {2405-4569}, abstract = {Interstitial cystitis/bladder pain syndrome (IC/BPS) is a chronic and debilitating condition characterized by pelvic pain and urinary urgency and frequency with an unclear etiology. Emerging evidence implicates microbiome dysbiosis-disruptions in the microbial communities inhabiting the body-in IC/BPS pathophysiology. This review synthesizes the literature on microbial alterations in IC/BPS, including urinary, vaginal, and gastrointestinal microbiota, and their interactions with host inflammatory and metabolic pathways. PATIENT SUMMARY: We reviewed studies from the past 10 years on microbial communities in the body for patients with interstitial cystitis/bladder pain syndrome (IC/BPS). Studies have revealed significant changes in microbial species for these patients, especially in urine. However, research on whether IC/BPS can be treated with interventions to modify microbial communities in the body is still needed.}, }
@article {pmid39880365, year = {2025}, author = {Liu, T and Xu, X and Wang, T and Xu, P}, title = {CRAmed: a conditional randomization test for high-dimensional mediation analysis in sparse microbiome data.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf038}, pmid = {39880365}, issn = {1367-4811}, abstract = {MOTIVATION: Numerous microbiome studies have revealed significant associations between the microbiome and human health and disease. These findings have motivated researchers to explore the causal role of the microbiome in human complex traits and diseases. However, the complexities of microbiome data pose challenges for statistical analysis and interpretation of causal effects.<br><br>RESULTS: We introduced a novel statistical framework, CRAmed, for inferring the mediating role of the microbiome between treatment and outcome. CRAmed improved the interpretability of the mediation analysis by decomposing the natural indirect effect into two parts, corresponding to the presence-absence and abundance of a microbe, respectively. Comprehensive simulations demonstrated the superior performance of CRAmed in Recall, precision, and F1 score, with a notable level of robustness, compared to existing mediation analysis methods. Furthermore, two real data applications illustrated the effectiveness and interpretability of CRAmed. Our research revealed that CRAmed holds promise for uncovering the mediating role of the microbiome and understanding of the factors influencing host health.<br><br>The R package CRAmed implementing the proposed methods is available online at https://github.com/liudoubletian/CRAmed.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid39880356, year = {2025}, author = {Wang, S and Yan, K and Dong, Y and Chen, Y and Song, J and Chen, Y and Liu, X and Qi, R and Zhou, X and Zhong, J and Li, J}, title = {The influence of microplastics on hypertension-associated cardiovascular injury via the modulation of gut microbiota.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {125760}, doi = {10.1016/j.envpol.2025.125760}, pmid = {39880356}, issn = {1873-6424}, abstract = {Microplastics (MPs) have been found to interfere with the gut microbiota and compromise the integrity of the gut barrier. Excessive exposure to MPs markedly elevates the risk of cardiovascular disease, yet their influence on hypertension remains elusive, calling for investigation into their potential impacts on blood pressure (BP) regulation. In the present study, an increase in the concentration of MPs was observed in the fecal samples of individuals suffering from hypertension, as compared to the controls. Oral administration of MPs led to obvious increases in systolic, diastolic and mean BP levels in mice. MPs were associated with promoting myocardial hypertrophy, fibrosis, and cardiac remodeling through alterations in gut microbial composition, such as Prevotella and Coprobacillus, or fecal metabolites Betaine and Glycyrrhetinic acid. The hypertensive damage mediated by MPs was significantly mitigated by the high-fiber diet or antibiotics that targeted the gut microbiota. Notablely, fecal microbiota transplantation from mice treated with MPs led to an increase in systolic BP levels and the development of cardiac dysfunction. Our findings offer valuable insights into the complex interplay between MPs and the gut microbiome in the context of hypertension, and suggest potential strategies for reducing the vascular and cardiac injury caused by MPs.}, }
@article {pmid39880121, year = {2025}, author = {Almeida-Santos, AC and Novais, C and Peixe, L and Freitas, AR}, title = {Vancomycin-Resistant Enterococcus faecium: A current perspective on resilience, adaptation, and the urgent need for novel strategies.}, journal = {Journal of global antimicrobial resistance}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgar.2025.01.016}, pmid = {39880121}, issn = {2213-7173}, abstract = {Vancomycin-resistant Enterococcus faecium (VREfm) has become a critical opportunistic pathogen, urgently requiring new antimicrobial strategies due to its rising prevalence and significant impact on patient safety and healthcare costs. VREfm continues to evolve through mutations and the acquisition of new genes via horizontal gene transfer, contributing to resistance against several last-resort antibiotics. Although primarily hospital-associated, VREfm is also detected in the community, food chain, livestock, and environmental sources like wastewater, indicating diverse transmission pathways and the need for a One Health approach. Advances in genomics have shed light on VREfm's persistence in hospital settings, particularly its adaptation to the gastrointestinal tract of hospitalized patients, recent clonal shifts, and the dominance of specific clonal lineages. Despite extensive research, significant gaps remain in understanding the molecular mechanisms behind VREfm's unique adaptation to clinical environments. In this review, we aim to present an overview of VREfm current prevalence, mechanisms of resistance, and unveil the adaptive traits that have facilitated VREfm's rise and global success. A particular focus is given to key plasmids, namely linear plasmids, virulence factors, and bacteriocins as potential drivers in the global emergence of the ST78 clonal lineage. We also address diagnostic challenges and the limited treatment options available for VREfm, as well as emerging antibiotic alternatives aimed at restoring gut microbiota balance and curbing VREfm proliferation. A multifaceted approach combining research, clinical practices, and public health policies is crucial to mitigate the impact of this superbug and preserve antimicrobial effectiveness for future generations.}, }
@article {pmid39880115, year = {2025}, author = {Sun, K and Yang, R and Liu, J and Zhao, W and Li, X and Wang, Y and Song, S}, title = {Precipitation changes reshape desert soil microbial community assembly and potential functions.}, journal = {Environmental research}, volume = {}, number = {}, pages = {120958}, doi = {10.1016/j.envres.2025.120958}, pmid = {39880115}, issn = {1096-0953}, abstract = {Understanding the responses of desert microbial communities to escalating precipitation changes is a significant knowledge gap in predicting future soil health and ecological function. Through a five-year precipitation manipulation experiment, we investigated the contrasting eco-evolutionary processes of desert bacteria and fungi that manifested in changes to the assembly and potential functions of the soil microbiome. Elevated precipitation increased the alpha diversity and network complexity of bacteria and fungi, proportion of non-dominant phyla, and abundance of carbon- and nitrogen-fixing bacteria and saprophytic, symbiotic, and pathogenic fungi. Conversely, decreased precipitation reduced the alpha diversity and network complexity of bacteria and fungi while increasing the proportion of non-dominant phyla, stability of the network, and abundance of functional genes related to carbon and nitrogen degradation, nitrification, and ammonification. This suggests that soil microbes may attenuate the negative effects of reduced precipitation by streamlining communities, enhancing carbon and nitrogen acquisition, and promoting nitrogen cycling. Furthermore, we revealed that soil properties and vegetation attributes explained approximately 27.86%-37.75% and 17.76%-22.84% of the variation in bacterial and fungal communities, respectively. Finally, we demonstrated that precipitation-driven soil nutrient content and vegetation attributes are the potentially critical factors in shaping the soil microbial assembly and functions. These findings provide a foundation for understanding the response of desert soil microbes to escalating climate change.}, }
@article {pmid39879970, year = {2025}, author = {Stallmach, A}, title = {[The gastrointestinal microbiome - vision and mission].}, journal = {Deutsche medizinische Wochenschrift (1946)}, volume = {150}, number = {4}, pages = {157-162}, doi = {10.1055/a-2303-3368}, pmid = {39879970}, issn = {1439-4413}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Fecal Microbiota Transplantation ; Germany ; Dysbiosis ; Clostridium Infections/therapy ; }, abstract = {The gastrointestinal microbiome influences physiological functions and is altered in a variety of diseases. The causality of "dysbiosis" in the pathogenesis is not always proven; association studies are often involved. Patients with IBD, bacteria, fungi, bacteriophages, and archaea show disease-typical patterns associated with metabolome disturbances. Fecal microbiome transfer (FMT) for treating various diseases is the subject of numerous clinical studies. Currently, recurrent Clostridioides difficile infection (rCDI) is the only confirmed indication recommended in medical guidelines. In Germany, the FMT is subject to the Medicines Act and may only be carried out as part of individual healing attempts or clinical studies. For patient safety, repeated donor screening, ideally with the construction of a chair bench, is necessary. This significantly limits the nationwide availability of the FMT in Germany. Microbiota-based therapeutics prepared from the stool of tested donors have recently been approved by the US Food and Drug Administration (FDA) for the prevention of rCDI. More microbiome-based medicines can be expected in the future.}, }
@article {pmid39879949, year = {2025}, author = {Manzoor, M and Guan, DX and Ma, LQ}, title = {Plant-microbiome interactions for enhanced crop production under cadmium stress: A review.}, journal = {The Science of the total environment}, volume = {965}, number = {}, pages = {178538}, doi = {10.1016/j.scitotenv.2025.178538}, pmid = {39879949}, issn = {1879-1026}, abstract = {Cadmium (Cd) is a toxic heavy metal that has detrimental effects on agriculture crops and human health. Both natural and anthropogenic processes release Cd into the environment, elevating its contents in soils. Under Cd stress, strong plant-microbiome interactions are important in improving crop production, but a systematic review is still missing. This review demonstrates the importance of microbiomes and their interactions with plants in mitigating Cd toxicity and promoting crop growth. Endogenous and exogenous microbiomes play a role to enhance plant's ability to respond to Cd stress. Specifically, the rhizosphere microbiome, which includes plant growth-promoting rhizobacteria and arbuscular mycorrhizal fungi, endosphere microbiome, and phyllosphere microbiome, are involved in Cd accumulation, immobilization, and translocation, and Cd-induced stress management. The mechanisms underlying these plant-microbiome interactions vary depending on the species and varieties of crops, composition and diversity of the microbiome, and level of Cd stress. Among the microbiome-mediated approaches, biosorption, bioprecipitation, and bioaccumulation are promising for Cd remediation in soil. Additionally, the endosphere microbiome, particularly Cd resistant endophytes, reduces Cd toxicity, increases the expression of Cd efflux genes, and enhances crop growth through regulating crops' antioxidant machinery and endogenous hormones. Furthermore, improved agricultural practices modulate the soil and plant microbiomes, thereby reducing Cd stress and increasing crop productivity.}, }
@article {pmid39879257, year = {2025}, author = {Mulenga, M and Rajamanikam, A and Kumar, S and Muhammad, SB and Bhassu, S and Samudid, C and Sabri, AQM and Seera, M and Eke, CI}, title = {Revolutionizing colorectal cancer detection: A breakthrough in microbiome data analysis.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0316493}, doi = {10.1371/journal.pone.0316493}, pmid = {39879257}, issn = {1932-6203}, mesh = {*Colorectal Neoplasms/microbiology/diagnosis ; Humans ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/methods ; Algorithms ; Deep Learning ; Data Analysis ; Area Under Curve ; Neural Networks, Computer ; Microbiota ; }, abstract = {The emergence of Next Generation Sequencing (NGS) technology has catalyzed a paradigm shift in clinical diagnostics and personalized medicine, enabling unprecedented access to high-throughput microbiome data. However, the inherent high dimensionality, noise, and variability of microbiome data present substantial obstacles to conventional statistical methods and machine learning techniques. Even the promising deep learning (DL) methods are not immune to these challenges. This paper introduces a novel feature engineering method that circumvents these limitations by amalgamating two feature sets derived from input data to generate a new dataset, which is then subjected to feature selection. This innovative approach markedly enhances the Area Under the Curve (AUC) performance of the Deep Neural Network (DNN) algorithm in colorectal cancer (CRC) detection using gut microbiome data, elevating it from 0.800 to 0.923. The proposed method constitutes a significant advancement in the field, providing a robust solution to the intricacies of microbiome data analysis and amplifying the potential of DL methods in disease detection.}, }
@article {pmid39879247, year = {2025}, author = {Huang, S and Xing, M and Wang, H}, title = {Comparative analysis of antibiotic resistance genes between fresh pig manure and composted pig manure in winter, China.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0317827}, doi = {10.1371/journal.pone.0317827}, pmid = {39879247}, issn = {1932-6203}, mesh = {Animals ; *Manure/microbiology ; China ; Swine ; *Drug Resistance, Microbial/genetics ; RNA, Ribosomal, 16S/genetics ; Seasons ; Composting ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Feces/microbiology ; }, abstract = {Antibiotic resistance is a critical global public health issue. The gut microbiome acts as a reservoir for numerous antibiotic resistance genes (ARGs), which influence both existing and future microbial populations within a community or ecosystem. However, the differences in ARG expression between fresh and composted feces remain poorly understood. In this study, we collected eight samples from a farm in Kaifeng City, China, comprising both fresh and composted pig manure. Using a high-throughput quantitative PCR array, we analyzed differences in ARG expression between these two types of manure. Our findings revealed significant differences in ARG profiles, as demonstrated by principal coordinate analysis (PCoA). Further analysis identified 39 ARGs (log2FC > 1, p < 0.05) in composted pig manure, with 25 genes downregulated and 14 upregulated. Notably, tetB-01, blaOCH, and blaOXY were the most abundant in composted pig manure compared to fresh manure. Additionally, 16S rRNA species profiling revealed that the composting process significantly altered the microbial community structure, with an increased abundance of Firmicutes and a decreased abundance of Bacteroidetes in composted pig manure. In summary, composting substantially transforms both the microbial community structure and the ARG profile in pig manure, underscoring its potential role in modulating the dynamics of ARGs in agricultural environments.}, }
@article {pmid39879083, year = {2025}, author = {Carroll, A and Bell, MJ and Bleach, ECL and Turner, D and Williams, LK}, title = {Impact of dairy calf management practices on the intestinal tract microbiome pre-weaning.}, journal = {Journal of medical microbiology}, volume = {74}, number = {1}, pages = {}, doi = {10.1099/jmm.0.001957}, pmid = {39879083}, issn = {1473-5644}, mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome/physiology ; *Weaning ; *Animal Husbandry/methods ; Dairying ; }, abstract = {Introduction. Microbiota in the gastrointestinal tract (GIT) consisting of the rumen and hindgut (the small intestine, cecum and colon) in dairy calves play a vital role in their growth and development. This review discusses the development of dairy calf intestinal microbiomes with an emphasis on the impact that husbandry and rearing management have on microbiome development, health and growth of pre-weaned dairy calves.Discussion. The diversity and composition of the microbes that colonize the lower GIT (small and large intestine) can have a significant impact on the growth and development of the calf, through influence on nutrient metabolism, immune modulation, resistance or susceptibility to infection, production outputs and behaviour modification in adult life. The colonization of the calf intestinal microbiome dynamically changes from birth, increasing microbial richness and diversity until weaning, where further dynamic and drastic microbiome change occurs. In dairy calves, neonatal microbiome development prior to weaning is influenced by direct and indirect factors, some of which could be considered stressors, such as maternal interaction, environment, diet, husbandry and weaning practices. The specific impact of these can dictate intestinal microbial colonization, with potential lifelong consequences.Conclusion. Evidence suggests the potential detrimental effect that sudden changes and stress may have on calf health and growth due to management and husbandry practices, and the importance of establishing a stable yet diverse intestinal microbiome population at an early age is essential for calf success. The possibility of improving the health of calves through intestinal microbiome modulation and using alternative strategies including probiotic use, faecal microbiota transplantation and novel approaches of microbiome tracking should be considered to support animal health and sustainability of dairy production systems.}, }
@article {pmid39878936, year = {2025}, author = {Gauthier, LK and Foster, A and Wagner, BD and Kirby, CW}, title = {Isolation of Soil Microorganisms Using iChip Technology.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {215}, pages = {}, doi = {10.3791/67426}, pmid = {39878936}, issn = {1940-087X}, mesh = {*Soil Microbiology ; Bacteriological Techniques/methods/instrumentation ; Microbiological Techniques/methods/instrumentation ; }, abstract = {The iChip isolation technique uses an in-situ isolation device that increases the cultivability of previously unculturable microorganisms. Microorganisms are an important source of novel chemistries and potentially bioactive molecules. However, only 1% of environmental microorganisms can be cultured using conventional laboratory methods. With the rise in antimicrobial resistance, finding new drugs to combat infections and diseases is of foremost importance, and a critical method to finding new molecules is the discovery of new microorganisms. By incubating colonies of soil microorganisms in the wells of a 96-well plate, sealed with a semipermeable membrane and incubated on top of soil, the microbes are in contact with water and growth factors from the soil, allowing for the isolation of novel microbes in a laboratory setting. After a period of domestication in an iChip, microorganisms can potentially be subcultured onto conventional media and used for further study. This device is valuable to bioactive molecule discovery and soil microbiome research and has been used previously in both applications.}, }
@article {pmid39878828, year = {2025}, author = {Das, P and Kashyap, S and Sharma, I and Ray, SK and Agarwala, N}, title = {Exploration of endophytic and rhizospheric bacteria of invasive plant Xanthium strumarium L. reveals their potential in plant growth promotion and bacterial wilt suppression.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {39878828}, issn = {1678-4405}, support = {F.30- 386/2017//University Grants Commission/ ; }, abstract = {Plant-associated microbiome plays important role in maintaining overall health of the host plant. Xanthium strumarium displaying resilience to various environmental fluctuations may harbor some bacterial isolates which can help this plant to grow worldwide. The present study aims to isolate endophytic and rhizospheric bacteria from X. strumarium and assess their plant growth-promoting and Ralstonia solanacearum antagonism activity. From a total of 148 isolated bacteria, 7 endophytic and 2 rhizospheric bacterial isolates were found to endow with significant in vitro plant growth promotion activities. The 16S rRNA gene sequence similarity of the 7 endophytic isolates has revealed these bacteria belonging to 5 genera viz. Curtobacterium, Pantoea, Pseudomonas, Microbacterium and Paracoccus whereas, the two rhizospheric isolates were identified as species of Ralstonia pickettii and Priestia megaterium. Maximum growth promotion was observed using the strains Pseudomonas fluorescens XSS6 and Microbacterium hydrothermale XSS20 in the assay conducted on tomato plants. In the in planta inhibition assay of R. solanacearum carried out in tomato seedlings using root bacterization method, Pseudomonas fluorescens XSS6 and Panotea vagans XSS3 showed antagonistic activity with biocontrol efficacy of 94.83% and 83.96%, respectively. GC-MS analysis detected several known antimicrobial compounds in the extract of the culture supernatant of Pseudomonas fluorescens XSS6 and Panotea vagans XSS3 strains, which may contribute to the inhibition of R. solanacearum by these strains. The results of our study indicated that the bacteria associated with X. strumarium exhibit multiple plant-beneficial effects. These bacteria have the potential to be developed as effective biofertilizers and biological control agents, promoting sustainable agriculture practices.}, }
@article {pmid39878529, year = {2025}, author = {Guo, M and Wu, G and Tan, Y and Li, Y and Jin, X and Qi, W and Guo, X and Zhang, C and Zhu, Z and Zhao, L}, title = {Erratum for Guo et al., "Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis".}, journal = {mBio}, volume = {}, number = {}, pages = {e0014925}, doi = {10.1128/mbio.00149-25}, pmid = {39878529}, issn = {2150-7511}, }
@article {pmid39878514, year = {2025}, author = {Kim, D and Trang, K and Pees, B and Karimzadegan, S and Bodkhe, R and Hammond, S and Shapira, M}, title = {Identification of intestinal mediators of Caenorhabditis elegans DBL-1/BMP immune signaling shaping gut microbiome composition.}, journal = {mBio}, volume = {}, number = {}, pages = {e0370324}, doi = {10.1128/mbio.03703-24}, pmid = {39878514}, issn = {2150-7511}, abstract = {The composition of the gut microbiome is determined by a complex interplay of diet, host genetics, microbe-microbe interactions, abiotic factors, and stochasticity. Previous studies have demonstrated the importance of host genetics in community assembly of the Caenorhabditis elegans gut microbiome and identified a central role for DBL-1/BMP immune signaling in determining the abundance of gut Enterobacteriaceae. However, the effects of DBL-1 signaling on gut bacteria were found to depend on its activation in extra-intestinal tissues, highlighting a gap in our understanding of the proximal factors that determine microbiome composition. In the present study, we used RNA-seq gene expression analysis of wildtype, dbl-1 and sma-3 mutants, and dbl-1 over-expressors to identify candidate DBL-1/BMP targets that may mediate the pathway's effects on gut commensals. Bacterial colonization experiments in mutants, or following RNAi-mediated knock-down of candidate genes specifically in the intestine, demonstrated their local contribution to intestinal control of Enterobacteriaceae abundance. Furthermore, epistasis analysis suggested that these contributions were downstream of the DBL-1 pathway, together suggesting that examined candidates were intestinal effectors and mediators of DBL-1 signaling, contributing to the shaping of gut microbiome composition.IMPORTANCECompared to the roles of diet, environmental availability, or lifestyle in determining gut microbiome composition, that of genetic factors is the least understood and often underestimated. The identification of intestinal effectors of distinct molecular functions that control enteric bacteria offers a glimpse into the genetic logic of microbiome control as well as a list of targets for future exploration of this logic.}, }
@article {pmid39878512, year = {2025}, author = {Flanagan, K and Gassner, K and Lang, M and Ozelyte, J and Hausmann, B and Crepaz, D and Pjevac, P and Gasche, C and Berry, D and Vesely, C and Pereira, FC}, title = {Human-derived microRNA 21 regulates indole and L-tryptophan biosynthesis transcripts in the gut commensal Bacteroides thetaiotaomicron.}, journal = {mBio}, volume = {}, number = {}, pages = {e0392824}, doi = {10.1128/mbio.03928-24}, pmid = {39878512}, issn = {2150-7511}, abstract = {UNLABELLED: In the gut, microRNAs (miRNAs) produced by intestinal epithelial cells are secreted into the lumen and can shape the composition and function of the gut microbiome. Crosstalk between gut microbes and the host plays a key role in irritable bowel syndrome (IBS) and inflammatory bowel diseases, yet little is known about how the miRNA-gut microbiome axis contributes to the pathogenesis of these conditions. Here, we investigate the ability of miR-21, a miRNA that we found decreased in fecal samples from IBS patients, to associate with and regulate gut microbiome function. When incubated with the human fecal microbiota, miR-21 revealed a rapid internalization or binding to microbial cells, which varied in extent across different donor samples. Fluorescence-activated cell sorting and sequencing of microbial cells incubated with fluorescently labeled miR-21 identified organisms belonging to the genera Bacteroides, Limosilactobacillus, Ruminococcus, or Coprococcus, which predominantly interacted with miR-21. Surprisingly, these and other genera also interacted with a miRNA scramble control, suggesting that physical interaction and/or uptake of these miRNAs by gut microbiota is not sequence-dependent. Nevertheless, transcriptomic analysis of the gut commensal Bacteroides thetaiotaomicron revealed a miRNA sequence-specific effect on bacterial transcript levels. Supplementation of miR-21, but not of small RNA controls, resulted in significantly altered levels of many cellular transcripts and increased transcription of a biosynthetic operon for indole and L-tryptophan, metabolites known to regulate host inflammation and colonic motility. Our study identifies a novel putative miR-21-dependent pathway of regulation of intestinal function through the gut microbiome with implications for gastrointestinal conditions.<br><br>IMPORTANCE: The mammalian gut represents one of the largest and most dynamic host-microbe interfaces. Host-derived microRNAs (miRNAs), released from the gut epithelium into the lumen, have emerged as important contributors to host-microbe crosstalk. Levels of several miRNAs are altered in the stool of patients with irritable bowel syndrome or inflammatory bowel disease. Understanding how miRNAs interact with and shape gut microbiota function is crucial as it may enable the development of new targeted treatments for intestinal diseases. This study provides evidence that the miRNA miR-21 can rapidly associate with diverse microbial cells form the gut and increase levels of transcripts involved in tryptophan synthesis in a ubiquitous gut microbe. Tryptophan catabolites regulate key functions, such as gut immune response or permeability. Therefore, this mechanism represents an unexpected host-microbe interaction and suggests that host-derived miR-21 may help regulate gut function via the gut microbiota.}, }
@article {pmid39877991, year = {2025}, author = {Zhong, H and Yu, Y and Abdullah,  and Zhang, H and Du, J and Sun, J and Chen, L and Feng, F and Guan, R}, title = {Lactiplantibacillus plantarum N1 derived lipoteichoic acid alleviates insulin resistance in association with modulation of the gut microbiota and amino acid metabolism.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4fo06100d}, pmid = {39877991}, issn = {2042-650X}, abstract = {This study aimed to investigate the effects of heat-killed Lactiplantibacillus plantarum N1 (HK-N1) and lipoteichoic acid (LTA) derived from it on alleviating insulin resistance by modulating the gut microbiota and amino acid metabolism. High-fat diet (HFD)-fed mice were administered live bacteria or HK-N1, and the results demonstrated that HK-N1 significantly reduced epididymal adipocyte size and serum low density lipoprotein-cholesterol, and improved insulin resistance by increasing the YY peptide and glucagon-like peptide levels. HK-N1 also modulated the gut microbiome composition, enhancing microbiota uniformity and reducing the abundance of Ruminococcus, Oscillospira and norank_f_Mogibacteriaceae. Three main active substances obtained from HK-N1 (membrane protein, peptidoglycan, and lipoteichoic acid) were also used to investigate their potential effects in hyperglycemic zebrafish. Only LTA reduced blood sugar and altered the gut microbiome, particularly reducing Aeromonas, which is positively related to hyperglycemia. Untargeted metabolomics revealed that LTA improved vitamin and amino acid metabolism, thereby alleviating metabolic disorders in zebrafish. Collectively, our findings indicate that HK-N1, primarily through LTA, modulated insulin sensitivity by regulating the gut microbiota and amino acid metabolism, offering a potential therapeutic strategy for insulin resistance and type 2 diabetes mellitus.}, }
@article {pmid39877906, year = {2025}, author = {Jameson, KG and Kazmi, SA and Ohara, TE and Son, C and Yu, KB and Mazdeyasnan, D and Leshan, E and Vuong, HE and Paramo, J and Lopez-Romero, A and Yang, L and Schweizer, FE and Hsiao, EY}, title = {Select microbial metabolites in the small intestinal lumen regulates vagal activity via receptor-mediated signaling.}, journal = {iScience}, volume = {28}, number = {2}, pages = {111699}, pmid = {39877906}, issn = {2589-0042}, abstract = {The vagus nerve is proposed to enable communication between the gut microbiome and the brain, but activity-based evidence is lacking. We find that mice reared germ-free exhibit decreased vagal tone relative to colonized controls, which is reversed via microbiota restoration. Perfusing antibiotics into the small intestines of conventional mice, but not germ-free mice, acutely decreases vagal activity which is restored upon re-perfusion with intestinal filtrates from conventional, but not germ-free, mice. Microbiome-dependent short-chain fatty acids, bile acids, and 3-indoxyl sulfate indirectly stimulate vagal activity in a receptor-dependent manner. Serial perfusion of each metabolite class activates both shared and distinct neuronal subsets with varied response kinetics. Metabolite-induced and receptor-dependent increases in vagal activity correspond with the activation of brainstem neurons. Results from this study reveal that the gut microbiome regulates select metabolites in the intestinal lumen that differentially activate vagal afferent neurons, thereby enabling the microbial modulation of chemosensory signals for gut-brain communication.}, }
@article {pmid39877797, year = {2025}, author = {Li, W and Tu, J and Zheng, J and Das, A and Yan, Q and Jiang, X and Ding, W and Bai, X and Lai, K and Yang, S and Yang, C and Zou, J and Diwan, AD and Zheng, Z}, title = {Gut Microbiome and Metabolome Changes in Chronic Low Back Pain Patients With Vertebral Bone Marrow Lesions.}, journal = {JOR spine}, volume = {8}, number = {1}, pages = {e70042}, pmid = {39877797}, issn = {2572-1143}, abstract = {BACKGROUND: Chronic low back pain (LBP) is a significant global health concern, often linked to vertebral bone marrow lesions (BML), particularly fatty replacement (FR). This study aims to explore the relationship between the gut microbiome, serum metabolome, and FR in chronic LBP patients.<br><br>METHODS: Serum metabolomic profiling and gut microbiome analysis were conducted in chronic LBP patients with and without FR (LBP&#x2009;+&#x2009;FR, n&#x2009;=&#x2009;40; LBP, n&#x2009;=&#x2009;40) and Healthy Controls (HC, n&#x2009;=&#x2009;31). The study investigates alterations in branched-chain amino acids (BCAAs) levels and identifies key microbial species associated with BCAA metabolism. In&#xa0;vitro experiments elucidate the role of BCAAs in adipogenesis of bone marrow mesenchymal stem cells (BM-MSCs) via the SIRT4 pathway.<br><br>RESULTS: Chronic LBP patients with FR exhibit depleted BCAA levels in their serum metabolome, along with alterations in the gut microbiome. Specific microbial species, including Ruminococcus gnavus, Roseburia hominis, and Lachnospiraceae bacterium 8 1 57FAA, are identified as influential in BCAA metabolism and BM-MSCs metabolism. In&#xa0;vitro experiments demonstrate the ability of BCAAs to induce BM-MSCs adipogenesis through SIRT4 pathway activation.<br><br>CONCLUSION: This study sheds light on the intricate relationship between the disturbed gut ecosystem, serum metabolites, and FR in chronic LBP. Dysbiosis in the gut microbiome may contribute to altered BCAA degradation, subsequently promoting BM-MSCs adipogenesis and FR. Understanding these interactions provides insights for targeted therapeutic strategies to mitigate chronic LBP associated with FR by restoring gut microbial balance and modulating serum metabolite profiles.}, }
@article {pmid39877757, year = {2024}, author = {Zhao, Q and Sen, B and Smyth, DS and Cônsoli, FL}, title = {Editorial: Insights in systems microbiology: 2022/2023.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1538030}, doi = {10.3389/fmicb.2024.1538030}, pmid = {39877757}, issn = {1664-302X}, }
@article {pmid39877755, year = {2024}, author = {Xu, X and Wang, Z and Jian, Y and Zhang, L and Zhou, C and Liu, L and Liu, H}, title = {Establishment and maturation of gut microbiota in White King pigeon squabs: role of pigeon milk.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1481529}, pmid = {39877755}, issn = {1664-302X}, abstract = {BACKGROUND: Pigeons are significant economic animals in China; however, research regarding the establishment and influencing factors of gut microbiota in squabs remains limited. Understanding how the gut microbiota develops in pigeons, particularly in relation to pigeon milk, is importance in pigeon production. This study aims to elucidate the establishment characteristics of the gut microbiota in White King pigeon squabs and explore the role of pigeon milk in this process.<br><br>METHODS: This study employed 16S rRNA sequencing technology to investigate the dynamics of microbial composition in feces and pigeon milk at various growth stages of White King pigeon. Functional prediction analysis was performed to assess the metabolic pathways involved, and correlation analysis was used to explore the relationships between microbial communities in different sample types.<br><br>RESULTS: The findings revealed a diverse microbiome present in the meconium of newborn pigeons, with a microbial composition that significantly differed from that of other feces groups. In contrast, the microbial composition of feces (FN) from pigeons aged 7 to 21 days exhibited less variability. At the phylum level, the predominant microbial taxa identified in the feces of FN were Firmicutes, Actinobacteriota, and Proteobacteria. At the genus level, the main dominant bacterial groups included Lactobacillus, Limosilactobacillus, and Turicibacter. Functional prediction analysis indicated that the gut microbiota of pigeons primarily participate in metabolic pathways related to carbohydrates, amino acids, lipids, cofactors, and vitamins. Furthermore, the dominant bacteria found in pigeon milk (MN) were identified as probiotics, including Limosilactobacillus, Ligilactobacillus, Lactobacillus, Bifidobacterium, and Aeriscardovia, which collectively accounted for over 90% of the total abundance. Correlation analysis of the abundance of shared microbes revealed that the association between meconium and feces at the other stages was extremely low. In contrast, the correlation between colostrum and feces at the post-feeding stage were found to be the highest.<br><br>CONCLUSION: This study indicates that prenatal colonization occurs in White King pigeons. Notably, within the first week after birth, the gut microbial composition of young pigeons becomes stable. Furthermore, the colostrum serves as the most significant driver for the establishment of intestinal microbiota in squab post-birth. The findings of this study suggest that microorganisms can be added to artificial pigeon milk based on the predominant microbial composition of colostrum. This approach could facilitate the establishment of gut microbiota in young pigeons, thereby promoting their growth and development and providing production benefits.}, }
@article {pmid39877709, year = {2025}, author = {Cortés-Martín, A and Plaza-Diaz, J}, title = {Exploring the therapeutic potential of glucagon-like peptide 1 agonists in metabolic disorders.}, journal = {World journal of gastroenterology}, volume = {31}, number = {4}, pages = {101436}, pmid = {39877709}, issn = {2219-2840}, mesh = {Humans ; *Glucagon-Like Peptide-1 Receptor ; Treatment Outcome ; Liver/drug effects/metabolism/pathology ; Glucagon-Like Peptide 1/agonists/metabolism ; Metabolic Diseases/drug therapy ; Liver Cirrhosis/drug therapy ; Non-alcoholic Fatty Liver Disease/drug therapy ; Life Style ; Fatty Liver/drug therapy ; Hypoglycemic Agents/therapeutic use/pharmacology ; }, abstract = {This article comments on the work by Soresi and Giannitrapani. The authors have stated that one of the most novel and promising treatments for metabolic dysfunction-associated steatotic liver disease (MASLD) is the use of glucagon-like peptide 1 receptor agonists, especially when used in combination therapy. However, despite their notable efficacy, these drugs were not initially designed to target MASLD directly. In a groundbreaking development, the Food and Drug Administration has recently approved resmetirom, the first treatment specifically aimed at reducing liver fibrosis in metabolic-associated steatohepatitis. Resmetirom, an orally administered, liver-directed thyroid hormone beta-selective agonist, acts directly on intrahepatic pathways, enhancing its therapeutic potential and marking the beginning of a new era in the treatment of MASLD. Furthermore, the integration of lifestyle modifications into liver disease management is an essential component that should be considered and reinforced. By incorporating dietary changes and regular physical exercise into treatment, patients may achieve improved outcomes, reducing the need for pharmacological interventions and/or improving treatment efficacy. As a complement to medical therapies, lifestyle factors should not be overlooked in the broader strategy for managing MASLD.}, }
@article {pmid39877539, year = {2024}, author = {Du, M and Liu, X and Ji, X and Wang, Y and Liu, X and Zhao, C and Jin, E and Gu, Y and Wang, H and Zhang, F}, title = {Berberine alleviates enterotoxigenic Escherichia coli-induced intestinal mucosal barrier function damage in a piglet model by modulation of the intestinal microbiome.}, journal = {Frontiers in nutrition}, volume = {11}, number = {}, pages = {1494348}, pmid = {39877539}, issn = {2296-861X}, abstract = {INTRODUCTION: Enterotoxic Escherichia coli (ETEC) is the main pathogen that causes diarrhea, especially in young children. This disease can lead to substantial morbidity and mortality and is a major global health concern. Managing ETEC infections is challenging owing to the increasing prevalence of antibiotic resistance. Berberine, categorized as a substance with similarities in "medicine and food," has been used in China for hundreds of years to treat gastrointestinal disorders and bacteria-induced diarrhea. This study investigated the preventive effect of dietary berberine on the intestinal mucosal barrier induced by ETEC and the microbial community within the intestines of weaned piglets.<br><br>METHODS: Twenty-four piglets were randomly divided into four groups. Piglets were administered either a standard diet or a standard diet supplemented with berberine at concentrations of 0.05 and 0.1%. and orally administered ETEC or saline.<br><br>RESULTS: Dietary supplementation with berberine reduced diamine oxidase, d-lactate, and endotoxin levels in piglets infected with ETEC (P < 0.05). Berberine increased jejunal villus height, villus/crypt ratio, mucosal thickness (P < 0.05), and goblet cell numbers in the villi and crypts (P < 0.05). Furthermore, berberine increased the optical density of mucin 2 and the mucin 2, P-glycoprotein, and CYP3A4 mRNA expression levels (P < 0.05). Berberine increased the expressions of zonula occludins-1 (ZO-1), zonula occludins-2 (ZO-2), Claudin-1, Occludin, and E-cadherin in the ileum (P < 0.05). Moreover, berberine increased the expression of BCL2, reduced intestinal epithelial cell apoptosis (P < 0.05) and decreased the expression of BAX and BAK in the duodenum and jejunum, as well as that of CASP3 and CASP9 in the duodenum and ileum (P < 0.05). Berberine decreased the expression of IL-1&#x3b2;, IL-6, IL-8, TNF-&#x3b1;, and IFN-&#x3b3; (P < 0.05) and elevated total volatile fatty acids, acetic acid, propionic acid, valeric acid, and isovaleric acid concentrations (P < 0.05). Notably, berberine enhanced the abundance of beneficial bacteria including Enterococcus, Holdemanella, Weissella, Pediococcus, Muribaculum, Colidextribacter, Agathobacter, Roseburia, Clostridium, Fusicatenibacter, and Bifidobacterium. Simultaneously, the relative abundance of harmful and pathogenic bacteria, such as Prevotella, Paraprevotella, Corynebacterium, Catenisphaera, Streptococcus, Enterobacter, and Collinsella, decreased (P < 0.05).<br><br>DISCUSSION: Berberine alleviated ETEC-induced intestinal mucosal barrier damage in weaned piglets models. This is associated with enhancement of the physical, chemical, and immune barrier functions of piglets by enhancing intestinal microbiota homeostasis.}, }
@article {pmid39877362, year = {2024}, author = {Slater, AS and Hickey, RM and Davey, GP}, title = {Interactions of human milk oligosaccharides with the immune system.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1523829}, pmid = {39877362}, issn = {1664-3224}, mesh = {*Milk, Human/immunology/chemistry/metabolism ; Humans ; *Oligosaccharides/immunology ; *Immune System/metabolism/immunology ; Gastrointestinal Microbiome/immunology ; Animals ; Immunomodulation ; Infant, Newborn ; }, abstract = {Human milk oligosaccharides (HMOs) are abundant, diverse and complex sugars present in human breast milk. HMOs are well-characterized barriers to microbial infection and by modulating the human microbiome they are also thought to be nutritionally beneficial to the infant. The structural variety of over 200 HMOs, including neutral, fucosylated and sialylated forms, allows them to interact with the immune system in various ways. Clinically, HMOs impact allergic diseases, reducing autoimmune and inflammatory responses, and offer beneficial support to the preterm infant immune health. This review examines the HMO composition and associated immunomodulatory effects, including interactions with immune cell receptors and gut-associated immune responses. These immunomodulatory properties highlight the potential for HMO use in early stage immune development and for use as novel immunotherapeutics. HMO research is rapidly evolving and promises innovative treatments for immune-related conditions and improved health outcomes.}, }
@article {pmid39877321, year = {2025}, author = {Ito, E and Ohki, T and Toya, N and Emoto, T and Yamashita, T and Sugiyama, T and Yamada, T and Mori, H and Toyoda, A and Hirata, KI}, title = {Metagenomic Analysis of Gut Microbiota for Abdominal Aortic Aneurysm.}, journal = {Annals of vascular diseases}, volume = {18}, number = {1}, pages = {}, pmid = {39877321}, issn = {1881-641X}, abstract = {Objectives: The pathophysiological mechanism of abdominal aortic aneurysm (AAA) remains unclear. We previously reported that Bifidobacterium adolescentis levels were reduced in the feces of patients with AAA by 16S ribosomal ribonucleic acid (RNA) gene sequencing. In this study, we increased the number of cases and conducted metagenomic analyses to examine bacterial genes associated with the pathophysiology of AAA. Methods: For gut microbiota data, feces from 55 patients with AAA and 52 patients with no history of AAA, lower extremity artery disease, or coronary artery disease (control group) were collected. Metagenomic analysis was performed by collecting raw stool samples from patients. For intestinal microbiota analysis, metagenomic analysis of the fecal samples was performed. Results: Oral bacteria, including Actinomyces oris (p <0.0001), Streptococcus salivarius (p <0.001), Lactobacillus salivarius (p <0.001), and Streptococcus sp. (p <0.001), were increased in the feces of patients with AAA. In addition, bacterial genes related to alpha lipoic acid (ALA) biosynthesis (M00882, M00883, and M00884, p <0.0001) were decreased in patients with AAA. Conclusions: In the feces of patients with AAA, there was an increase in oral bacteria, and the expression of bacterial genes related to ALA biosynthesis was reduced. The results suggest the possibility of developing gut microbial drug treatments for AAA.}, }
@article {pmid39877175, year = {2025}, author = {Pathak, N and Guan, H and Fan, P and Sultana, H and Arriola, K and Oyebade, A and Nino de Guzman, C and Malekkhahi, M and Jeong, KC and Vyas, D}, title = {Comparing rumen fluid collection methods on fermentation profile and microbial population in lactating dairy cows.}, journal = {JDS communications}, volume = {6}, number = {1}, pages = {34-38}, pmid = {39877175}, issn = {2666-9102}, abstract = {The objective of this study was to compare fermentation profile and microbial diversity from rumen samples collected using a rumen cannula (RC) or stomach tube (ST) in lactating dairy cows. Three ruminally cannulated lactating dairy cows were used in a 3 × 3 Latin square design. The experimental period was 28 d and rumen fluid was collected 4 h after feeding on d 22 and 26 of each experimental period. Treatments were rumen fluid collected from the ST or RC. The pH of rumen contents was measured immediately after fluid collection and samples were analyzed for VFA, ammonia-N (NH3-N) concentration, and microbiome composition. Rumen pH was greater for ST compared with RC (6.88 vs. 6.25). However, NH3-N (15.2 vs. 10.6 mg/dL) and total VFA (121.8 vs. 95.5 mM) were greater for RC compared with ST. The rumen fluid collection methods had no effects on the molar proportion of acetate and propionate; however, the acetate-to-propionate ratio tended to increase with ST compared with RC. The majority of sequences obtained with microbiome analysis belonged to Bacteroidetes, Firmicutes, and Cyanobacteria, regardless of the rumen fluid collection method. However, the abundance of Bacteroidetes was greater and the abundance of Firmicutes was lower for ST compared with RC. No effects were observed on the abundance of phylum Cyanobacteria. The rumen fluid collection methods had no effects on Chao1 and Shannon index. In conclusion, the molar proportion of individual VFA, Chao1, and Shannon index were similar, whereas rumen pH, NH3-N, and total VFA were affected by the rumen fluid collection method.}, }
@article {pmid39877152, year = {2025}, author = {Plewka, J and Alibrandi, A and Bornemann, TLV and Esser, SP and Stach, TL and Sures, K and Becker, J and Moraru, C and Soares, A and di Primio, R and Kallmeyer, J and Probst, AJ}, title = {Metagenomic analysis of pristine oil sheds new light on the global distribution of microbial genetic repertoire in hydrocarbon-associated ecosystems.}, journal = {microLife}, volume = {6}, number = {}, pages = {uqae027}, pmid = {39877152}, issn = {2633-6693}, abstract = {Oil reservoirs are society's primary source of hydrocarbons. While microbial communities in industrially exploited oil reservoirs have been investigated in the past, pristine microbial communities in untapped oil reservoirs are little explored, as are distribution patterns of respective genetic signatures. Here, we show that a pristine oil sample contains a complex community consisting of bacteria and fungi for the degradation of hydrocarbons. We identified microorganisms and their pathways for the degradation of methane, n-alkanes, mono-aromatic, and polycyclic aromatic compounds in a metagenome retrieved from biodegraded petroleum encountered in a subsurface reservoir in the Barents Sea. Capitalizing on marker genes from metagenomes and public data mining, we compared the prokaryotes, putative viruses, and putative plasmids of the sampled site to those from 10 other hydrocarbon-associated sites, revealing a shared network of species and genetic elements across the globe. To test for the potential dispersal of the microbes and predicted elements via seawater, we compared our findings to the Tara Ocean dataset, resulting in a broad distribution of prokaryotic and viral signatures. Although frequently shared between hydrocarbon-associated sites, putative plasmids, however, showed little coverage in the Tara Oceans dataset, suggesting an undiscovered mode of transfer between hydrocarbon-affected ecosystems. Based on our analyses, genetic information is globally shared between oil reservoirs and hydrocarbon-associated sites, and we propose that currents and other physical occurrences within the ocean along with deep aquifers are major distributors of prokaryotes and viruses into these subsurface ecosystems.}, }
@article {pmid39877080, year = {2025}, author = {Fehringer, M and Vogl, T}, title = {Molecular mimicry in the pathogenesis of autoimmune rheumatic diseases.}, journal = {Journal of translational autoimmunity}, volume = {10}, number = {}, pages = {100269}, pmid = {39877080}, issn = {2589-9090}, abstract = {Autoimmune rheumatic diseases (ARDs) are a heterogeneous group of conditions characterized by excessive and misdirected immune responses against the body's own musculoskeletal tissues. Their exact aetiology remains unclear, with genetic, demographic, behavioural and environmental factors implicated in disease onset. One prominent hypothesis for the initial breach of immune tolerance (leading to autoimmunity) is molecular mimicry, which describes structural or sequence similarities between human and microbial proteins (mimotopes). This similarity can lead to cross-reactive antibodies and T-cell receptors, resulting in an immune response against autoantigens. Both commensal microbes in the human microbiome and pathogens can trigger molecular mimicry, thereby potentially contributing to the onset of ARDs. In this review, we focus on the role of molecular mimicry in the onset of rheumatoid arthritis and systemic lupus erythematosus. Moreover, implications of molecular mimicry are also briefly discussed for ankylosing spondylitis, systemic sclerosis and myositis.}, }
@article {pmid39877012, year = {2024}, author = {Baranova, MN and Soboleva, EA and Kornienko, MA and Malakhova, MV and Mokrushina, YA and Gabibov, AG and Terekhov, SS and Smirnov, IV}, title = {Bacteriocin from the Raccoon Dog Oral Microbiota Inhibits the Growth of Pathogenic Methicillin-Resistant Staphylococcus aureus.}, journal = {Acta naturae}, volume = {16}, number = {4}, pages = {105-108}, pmid = {39877012}, issn = {2075-8251}, abstract = {The growing incidence of infections caused by antibiotic-resistant strains of pathogens is one of the key challenges of the 21[st] century. The development of novel technological platforms based on single-cell analysis of antibacterial activity at the whole-microbiome level enables the transition to massive screening of antimicrobial agents with various mechanisms of action. The microbiome of wild animals remains largely underinvestigated. It can be considered a natural reservoir of biodiversity for antibiotic discovery. Here, the Staphylococcus pseudintermedius E18 strain was isolated from the oral microbiome of a raccoon dog (Nyctereutes procyonoides) using a microfluidic ultrahigh-throughput screening platform. S. pseudintermedius E18 efficiently inhibited the growth of pathogenic methicillin-resistant Staphylococcus aureus (MRSA). It was established that the main active substance of the S. pseudintermedius E18 strain was a bacteriocin with a molecular weight of 27 kDa. The identified bacteriocin had a high positive charge and an extremely narrow spectrum of activity. Bacteriocin S. pseudintermedius E18 was inactivated by elevated temperature, proteinase K, and EDTA. Further investigation on the structure of the bacteriocin produced by S. pseudintermedius E18 will provide a comprehensive understanding of its mechanism of action, which will open up prospects for developing novel DNA-encoded antimicrobials.}, }
@article {pmid39876877, year = {2025}, author = {L'Heureux, JE and Corbett, A and Ballard, C and Vauzour, D and Creese, B and Winyard, PG and Jones, AM and Vanhatalo, A}, title = {Oral microbiome and nitric oxide biomarkers in older people with mild cognitive impairment and APOE4 genotype.}, journal = {PNAS nexus}, volume = {4}, number = {1}, pages = {pgae543}, pmid = {39876877}, issn = {2752-6542}, abstract = {Apolipoprotein E4 (APOE4) genotype and nitric oxide (NO) deficiency are risk factors for age-associated cognitive decline. The oral microbiome plays a critical role in maintaining NO bioavailability during aging. The aim of this study was to assess interactions between the oral microbiome, NO biomarkers, and cognitive function in 60 participants with mild cognitive impairment (MCI) and 60 healthy controls using weighted gene co-occurrence network analysis and to compare the oral microbiomes between APOE4 carriers and noncarriers in a subgroup of 35 MCI participants. Within the MCI group, a high relative abundance of Neisseria was associated with better indices of cognition relating to executive function (Switching Stroop, rs = 0.33, P = 0.03) and visual attention (Trail Making, rs = -0.30, P = 0.05), and in the healthy group, Neisseria correlated with working memory (Digit Span, rs = 0.26, P = 0.04). High abundances of Haemophilus (rs = 0.38, P = 0.01) and Haemophilus parainfluenzae (rs = 0.32, P = 0.03), that co-occurred with Neisseria correlated with better scores on executive function (Switching Stroop) in the MCI group. There were no differences in oral nitrate (P = 0.48) or nitrite concentrations (P = 0.84) between the MCI and healthy groups. Linear discriminant analysis Effect Size identified Porphyromonas as a predictor for MCI and Prevotella intermedia as a predictor of APOE4-carrier status. The principal findings of this study were that a greater prevalence of oral P. intermedia is linked to elevated genetic risk for dementia (APOE4 genotype) in individuals with MCI prior to dementia diagnosis and that interventions that promote the oral Neisseria-Haemophilus and suppress Prevotella-dominated modules have potential for delaying cognitive decline.}, }
@article {pmid39876648, year = {2025}, author = {O'Connor, G and Cleghorn, S and Salam, M and Watson, K}, title = {Exploring Dietitians' Experience of Blended Tube Feed in Paediatric Inpatient Settings: National Cross-Sectional Survey, United Kingdom.}, journal = {Journal of human nutrition and dietetics : the official journal of the British Dietetic Association}, volume = {38}, number = {1}, pages = {e70016}, doi = {10.1111/jhn.70016}, pmid = {39876648}, issn = {1365-277X}, support = {//The authors received no specific funding for this work./ ; }, mesh = {Humans ; Cross-Sectional Studies ; *Enteral Nutrition/methods ; United Kingdom ; *Nutritionists ; Child ; Prospective Studies ; Hospitals, Pediatric ; Surveys and Questionnaires ; Inpatients/statistics &amp; numerical data ; Male ; Female ; Dietetics/methods ; Child, Preschool ; Pediatrics/methods ; }, abstract = {BACKGROUND: Enteral tube feeding is used for children who are unable to meet their nutritional requirements orally. Gastrointestinal symptoms are some complications that can occur in enteral tube-fed patients. Blended tube feeds (BTFs) for children who are gastrotomy tube-fed have significantly increased in the last decade. BTF refers to homemade food that has been liquidised for enteral tube feeds. An increasing amount of evidence suggests that children on BTF have improved feed tolerance. It is unknown whether children admitted to a hospital established on a BTF can continue a BTF due to the potential barriers such as catering processes, staffing hours (limited to syringe bolus feeding) and food safety concerns. This national cross-sectional survey aimed to explore the use of BTF in a paediatric hospital setting.<br><br>METHODS: This was a prospective, cross-sectional, practice-based survey of registered paediatric dietitians who work in an inpatient care setting to explore the use of BTF. The final survey consisted of 13 questions and took dietitians approximately 15&#x2009;min to complete. The questions focused on the dietitian's experience, knowledge and confidence in children on a BTF.<br><br>RESULTS: Across the United Kingdom, 51 hospitals completed the survey. Of these, 16 of 19 were specialist children's hospitals (79% response rate) and 35 of 89 were general paediatric hospitals (39% response rate). All responders were paediatric dietitians. 49 of 51 (96%) dietitians knew of the British Dietetic Association (BDA) Practice Toolkit for Blended diets. Dietitians were asked to estimate on average per month how many children were admitted on a BTF; 41% (21 of 51) of dietitians reported that on average there are one to five children admitted on a BTF. There was no significant difference in the number of children admitted on a BTF between a specialist and a general children's hospital (&#x3c7;[2] statistic&#x2009;=&#x2009;4.96, p&#x2009;value&#x2009;<&#x2009;0.08). The number of dietitians who had clinical guidelines to support children admitted on a BTF was 49% (25 of 51). Specialist children's hospitals were more likely to have a clinical guideline compared with a general hospital (&#x3c7;[2] statistic&#x2009;=&#x2009;6.348, p&#x2009;value&#x2009;=&#x2009;0.01). However, only 18 of 51 (35%) dietitians reported being confident or very confident to review a child on a BTF. The most common perceived benefit was that parents/carers could incorporate family foods into their child's diet. 26% reported that a varied diet was beneficial in relation to the gut microbiome. If a BTF was contraindicated for children admitted to a hospital (immunocompromised, post-pyloric feeding or intensive care), 49 of 51 (96%) dietitians reported they would use an enteral formula with food-derived ingredients (Compleat paediatric-Nestle Health Science) as an alternative to a BTF.<br><br>CONCLUSION: BTF continues to grow in popularity. Our survey reported that children on BTF are frequently admitted to the hospital. There is growing evidence to support BTF in relation to family psychosocial health and feed tolerance. Dietitians must keep abreast of this fast-evolving area practice to ensure that they are the experts in BTF. When a BTF is contraindicated, an enteral formula with food-derived ingredients is a suitable alternative. Issues such as microbial contamination, nutritional composition, and adequacy of diluted BTF need further exploration.}, }
@article {pmid39876557, year = {2025}, author = {Morsink, MC and van Schaik, EN and Bossers, K and Duijker, DA and Speksnijder, AGCL}, title = {Metagenomics education in a modular CURE format positively affects students' scientific discovery perception and data analytical skills.}, journal = {Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology}, volume = {}, number = {}, pages = {}, doi = {10.1002/bmb.21888}, pmid = {39876557}, issn = {1539-3429}, abstract = {Targeted metagenomics is a rapidly expanding technology to analyze complex biological samples and genetic monitoring of environmental samples. In this research field, data analytical aspects play a crucial role. In order to teach targeted metagenomics data analysis, we developed a 4-week inquiry-driven modular course-based undergraduate research experience (mCURE) using publicly available Australian coral microbiome DNA sequencing data and associated metadata. Since an enormous amount of metadata was provided alongside the DNA sequencing data, groups of students were able to develop their own authentic research questions. Throughout the course, the student groups worked on these research questions and were supported with bioinformatics and statistics lessons. Additionally, practical aspects of data collection and analysis were addressed during hands-on field work on a nearby Dutch beach. Evaluation of the course indicated that the majority of students (1) achieved the intended metagenomics-based learning outcomes and (2) experienced scientific discovery while working on their research projects. In conclusion, the huge amount of data and metadata available in the coral microbiome data set facilitated the development of a strongly inquiry-driven course. Different groups of students were able to develop and conduct their own distinct microbiome research projects and our current mCURE format positively affected students' metagenomics data analytical skills and scientific discovery perception.}, }
@article {pmid39876091, year = {2025}, author = {Tocarruncho, OI and Neuta, Y and Lesmes, Y and Castillo, DM and Leal, S and Chambrone, L and Lafaurie, GI}, title = {Submucosal Microbiome Profiles in Paired and Unpaired Samples From Healthy and Peri-Implantitis Dental Implants.}, journal = {Clinical implant dentistry and related research}, volume = {27}, number = {1}, pages = {e13423}, doi = {10.1111/cid.13423}, pmid = {39876091}, issn = {1708-8208}, support = {490-21//Research Vice Rectory of Universidad El Bosque/ ; }, mesh = {Humans ; *Peri-Implantitis/microbiology ; *Microbiota ; Cross-Sectional Studies ; Female ; Male ; *Dental Implants/microbiology/adverse effects ; Middle Aged ; RNA, Ribosomal, 16S/analysis ; Adult ; Aged ; }, abstract = {BACKGROUND: This cross-sectional study aimed to compare the composition of the submucosal microbiome of peri-implantitis with paired and unpaired healthy implant samples.<br><br>METHODS: We evaluated submucosal plaque samples obtained in 39 cases, including 13 cases of peri-implantitis, 13 cases involving healthy implants from the same patient (paired samples), and 13 cases involving healthy implants from different individuals (unpaired samples). The patients were evaluated using next-generation genomic sequencing (Illumina) based on 16S rRNA gene amplification. The sequences were grouped according to the amplicon sequence variant (ASV) to define the taxonomic categories. Alpha diversity was analyzed using Shannon's and Simpson's indices, while beta diversity was evaluated using principal coordinate analysis, analysis of similarities, and permutational multivariate variance analysis. Additionally, UniFrac distances were evaluated using Quantitative Insights into Microbial Ecology 2. Finally, we evaluated between-group differences in the taxonomic components.<br><br>RESULTS: There were no significant between-group differences in alpha diversity. The average bacterial ratios of Filifactor alocis, Porphyromona endodontalis, Tannerella forsythia, Treponema denticola, Peptostreptococcaceae [Eubacterium nodatum], Desulfobulbus sp. HTM 041, and Mogibacterium timidum significantly differed between peri-implantitis samples and unpaired samples from the healthy implants (p&#x2009;<&#x2009;0.05). However, there were few differences in the microbiota between peri-implantitis samples and those paired with healthy implants in the same patient.<br><br>CONCLUSIONS: Future studies comparing the microbiome compositions using sequencing techniques between healthy implants and implants with peri-implantitis should focus on retrieving samples from the same patient, especially in individuals with a history of periodontitis.}, }
@article {pmid39876003, year = {2025}, author = {Li, Q and Huo, J and Ni, G and Zhang, F and Zhang, S and Zhang, X and Wang, R and Jiao, J and Yu, Z and Pu, X and Yue, Y and Ungerfeld, EM and Zhang, X and Wu, J and Tan, Z and Greening, C and Wang, M}, title = {Reductive acetogenesis is a dominant process in the ruminant hindgut.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {28}, pmid = {39876003}, issn = {2049-2618}, mesh = {Animals ; *Rumen/microbiology ; *Goats/microbiology ; *Cecum/microbiology ; *Hydrogen/metabolism ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; *Fermentation ; *Acetates/metabolism ; *Fatty Acids, Volatile/metabolism ; Archaea/classification/metabolism/genetics ; Ruminants/microbiology ; Methane/metabolism ; }, abstract = {BACKGROUND: The microbes residing in ruminant gastrointestinal tracts play a crucial role in converting plant biomass to volatile fatty acids, which serve as the primary energy source for ruminants. This gastrointestinal tract comprises a foregut (rumen) and hindgut (cecum and colon), which differ in structures and functions, particularly with respect to feed digestion and fermentation. While the rumen microbiome has been extensively studied, the cecal microbiome remains much less investigated and understood, especially concerning the assembling microbial communities and overriding pathways of hydrogen metabolism.<br><br>RESULTS: To address this gap, we comparatively investigated the composition, capabilities, and activities of the rumen and the cecum microbiome using goats as an experimental ruminant model. In situ measurements showed significantly higher levels of dissolved hydrogen and acetate in the cecum than in the rumen. Increased dissolved hydrogen indicated distinct processes and reduced coupling between fermentative H2 production and utilization, whereas higher levels of acetate could be caused by slower VFA absorption through cecal papillae than through the rumen papillae. Microbial profiling indicated that the cecum harbors a greater abundance of mucin-degrading microbes and fermentative hydrogen producers, whereas the rumen contains a higher abundance of fibrolytic fermentative bacteria, hydrogenotrophic respiratory bacteria, and methanogenic archaea. Most strikingly, reductive acetogenic bacteria were 12-fold more abundant in the cecum. Genome-resolved metagenomic analysis unveiled that the cecum acetogens are both phylogenetically and functionally distinct from those found in the rumen. Further supporting these findings, two in vitro experiments demonstrated a marked difference in hydrogen metabolism pathways between the cecum and the rumen, with increased acetate production and reduced methanogenesis in the cecum. Moreover, comparative analysis across multiple ruminant species confirmed a strong enrichment of reductive acetogens in the hindguts, suggesting a conserved functional role.<br><br>CONCLUSIONS: These findings highlight an enrichment of acetogenesis in a key region of the gastrointestinal tract and reshape our understanding of ruminant hydrogen metabolism and how the H2 can be managed in accord to livestock methane mitigation efforts. Video Abstract.}, }
@article {pmid39875992, year = {2025}, author = {Hussain, U and Downie, J and Ellison, A and Denman, S and McDonald, J and Cambon, MC}, title = {Peptide nucleic acid (PNA) clamps reduce amplification of host chloroplast and mitochondria rRNA gene sequences and increase detected diversity in 16S rRNA gene profiling analysis of oak-associated microbiota.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {14}, pmid = {39875992}, issn = {2524-6372}, support = {BB/T010886/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T01069X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T010886/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T010886/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T010886/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {BACKGROUND: Acquiring representative bacterial 16S rRNA gene community profiles in plant microbiome studies can be challenging due to the excessive co-amplification of host chloroplast and mitochondrial rRNA gene sequences that reduce counts of plant-associated bacterial sequences. Peptide Nucleic Acid (PNA) clamps prevent this by blocking PCR primer binding or binding within the amplified region of non-target DNA to stop the function of DNA polymerase. Here, we applied a universal chloroplast (p)PNA clamp and a newly designed mitochondria (m)PNA clamp to minimise host chloroplast and mitochondria amplification in 16S rRNA gene amplicon profiles of leaf, bark and root tissue of two oak species (Quercus robur and Q. petraea).<br><br>RESULTS: Adding PNA clamps to PCR led to an overall reduction of host chloroplast and mitochondrial 16S rRNA gene sequences of 79%, 46% and 99% in leaf, bark and root tissues, respectively. This resulted in an average increase in bacterial sequencing reads of 72%, 35%, and 17% in leaf, bark, and root tissue, respectively. Moreover, the bacterial diversity in the leaf and bark increased, with the number of ASVs rising by 105 in the leaf samples and 218 in the bark samples, respectively. In root tissues, where host oak chloroplast and mitochondria contamination were low, alpha and beta diversity did not change, suggesting the PNA clamps did not bias the bacterial community.<br><br>CONCLUSION: In conclusion, this study shows that PNA clamps can effectively reduce host chloroplast and mitochondria PCR amplification and improve assessment of the detected bacterial diversity in Quercus petraea and Quercus robur bacterial 16S rRNA gene sequencing studies.}, }
@article {pmid39875977, year = {2025}, author = {Horvath, M and Yang, R and Castaneda, DC and Callender, M and Aiken, ES and Voigt, AY and Caldwell, R and Fachi, J and Di Luccia, B and Scholar, Z and Yu, P and Salner, A and Colonna, M and Palucka, K and Oh, J}, title = {Species- and strain-specific microbial modulation of interferon, innate immunity, and epithelial barrier in 2D air-liquid interface respiratory epithelial cultures.}, journal = {BMC biology}, volume = {23}, number = {1}, pages = {28}, pmid = {39875977}, issn = {1741-7007}, support = {T32HG010463/NH/NIH HHS/United States ; U19AI142733/NH/NIH HHS/United States ; U19AI142733/NH/NIH HHS/United States ; U19AI142733/NH/NIH HHS/United States ; U19AI142733/NH/NIH HHS/United States ; U19AI142733/NH/NIH HHS/United States ; U19AI142733/NH/NIH HHS/United States ; U19AI142733/NH/NIH HHS/United States ; U19AI142733/NH/NIH HHS/United States ; U19AI142733/NH/NIH HHS/United States ; U19AI142733/NH/NIH HHS/United States ; U19AI142733/NH/NIH HHS/United States ; U19AI142733/NH/NIH HHS/United States ; U19AI142733/NH/NIH HHS/United States ; }, mesh = {*Immunity, Innate ; Humans ; *Interferons/metabolism ; *Microbiota ; *Respiratory Mucosa/immunology/microbiology ; Epithelial Cells/immunology/microbiology ; Species Specificity ; Cells, Cultured ; }, abstract = {BACKGROUND: The microbiome regulates the respiratory epithelium's immunomodulatory functions. To explore how the microbiome's biodiversity affects microbe-epithelial interactions, we screened 58 phylogenetically diverse microbes for their transcriptomic effect on human primary bronchial air-liquid interface (ALI) cell cultures.<br><br>RESULTS: We found distinct species- and strain-level differences in host innate immunity and epithelial barrier response. Strikingly, we found that host interferon, an antiviral response, was one of the most variable host processes. This variability was not driven by microbial phylogenetic diversity, bioburden, nor by the microbe's ability to stimulate other innate immunity pathways.<br><br>CONCLUSIONS: Microbial colonization differentially stimulates host gene expression with variations observed across phylogenetically diverse microbes and across different strains of the same species. Our study provides a foundation for understanding how the respiratory microbiome's biodiversity affects epithelial, and particularly antiviral, innate immunity.}, }
@article {pmid39875956, year = {2025}, author = {Liu, T and Li, S and Wang, X and Liu, M and Wang, Y and Ying, J and Zhang, S and Lin, Y and Wang, N and Bai, Y and Xie, L and Chen, T and Feng, Q and Xu, X}, title = {Deciphering the therapeutic effects of Xiyanping injection: insights into pulmonary and gut microbiome modulation, SerpinB2/PAI-2 targeting, and alleviation of influenza a virus-induced lung injury.}, journal = {Virology journal}, volume = {22}, number = {1}, pages = {19}, pmid = {39875956}, issn = {1743-422X}, support = {ZYYCXTD-D-202201//National Interdisciplinary Innovation Team of State Administration of Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Lung/microbiology/pathology/virology ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; *Lung Injury/drug therapy ; *Disease Models, Animal ; *Influenza A virus/drug effects ; Orthomyxoviridae Infections/drug therapy/virology ; Cytokines/metabolism ; Molecular Docking Simulation ; Humans ; }, abstract = {Infection with Influenza A virus (IAV) induces severe inflammatory responses and lung injury, contributing significantly to mortality and morbidity rates. Alterations in the microbial composition of the lungs and intestinal tract resulting from infection could influence disease progression and treatment outcomes. Xiyanping (XYP) injection has demonstrated efficacy in clinical treatment across various viral infections. However, its specific effects and mechanisms against IAV remain unclear. In this study, we established an IAV infection mice model, and utilized 16 S rRNA sequencing, RNA sequencing, protein chips, and molecular docking, to investigate the mechanisms of XYP injection on altering pulmonary and gut microbiota, and identifying its target sites. We revealed that XYP injection significantly reduced mortality, weight loss, lung viral titers, and lung pathology in IAV-infected mice. XYP injection down-regulated the activity of malondialdehyde, and the levels of interleukin (IL)-1β, IL-5, IL-6, tumor necrosis factor-α, IL-18, IL-15, granulocyte colony-stimulating factor, IL-9, chemokine (C-C motif) ligand-5, and C-X-C motif chemokine ligand 5, while up-regulated the activities of glutathione peroxidase reactive and superoxide dismutase, and the level of interferon-γ. The diversity of the pulmonary and gut microbiota was altered slightly after XYP injection. The linear discriminant analysis of the gut microbes revealed a higher proportion of potentially beneficial bacteria, including Akkermansia, Parabacteroides goldsteinii, Defluviitaleaceae, Oscillospirales, and Eubacterium_coprostanoligenes_group characterized the XYP group. Peritoneal macrophage RNA sequencing highlighted Serpinb2 as the most significantly regulated gene by XYP injection, along with consistent changes in multiple downstream Th2 structure genes. KEGG pathway analysis indicated significant modifications in genes associated with influenza A, mitogen-activated protein kinase signaling, nuclear factor kappa-B signaling, and apoptosis following XYP injection. Finally, human protein chips and molecular docking were carried out to confirm the binding of the main component of XYP injection, andrographolide, with SERPINB2/PAI-2 protein. Overall, our study provides valuable insights into the therapeutic potential of XYP injection in treating influenza, highlighting its multifaceted effects on host microbiota and immune responses, and pinpointing SerpinB2/PAI-2 as the target for XYP injection in exerting anti-inflammatory and antiviral therapeutic mechanisms.}, }
@article {pmid39870727, year = {2025}, author = {Doenyas, C and Clarke, G and Cserjési, R}, title = {Gut-brain axis and neuropsychiatric health: recent advances.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {3415}, pmid = {39870727}, issn = {2045-2322}, abstract = {The gut–brain axis, a bidirectional communication pathway, permits the central nervous system (CNS) to exert influence over gastrointestinal function in response to stress, while the gut microbiota regulates the CNS via immune, neuroendocrine, and vagal pathways. Current research highlights the importance of the gut microbiota in stress-related disorders and the need for further research into the mechanisms of gut–brain communication, with potential therapeutic implications for a wide range of health conditions. This is a challenge taken on in this Scientific Reports Collection on the Gut-Brain Axis. The gut–brain axis has significant implications for neurodegenerative, psychiatric, and metabolic disorders. Recent studies have underscored the role of the gut microbiome in conditions such as Parkinson’s disease (PD), with evidence indicating that gut dysfunction and pathological features can precede motor symptoms by decades. The use of in vivo animal models has demonstrated that preformed α-synuclein fibrils (PFFs) can travel from the gut to the brain in a dosage-dependent manner, thereby supporting the “gut-first” theory in the context of PD, a theory that is explored in this Collection using in vitro approaches. There is also evidence that the gut–brain axis plays a role in obesity and machine learning algorithms may assist in differentiating between obese and overweight individuals based on their microbiota data. There is also growing interest in the role of the gut at the interface between post-traumatic stress disorder (PTSD), sleep disturbances, and irritable bowel syndrome (IBS). The studies described in this Collection support and expand on the observations from previous preclinical and clinical investigations, while also providing essential novel insights that can drive discovery into previously unexplored avenues of brain-gut-microbiome interactions in health and disease.}, }
@article {pmid39877812, year = {2021}, author = {Zhu, W and Dykstra, K and Zhang, L and Xia, Z}, title = {Gut Microbiome as Potential Therapeutics in Multiple Sclerosis.}, journal = {Current treatment options in neurology}, volume = {23}, number = {11}, pages = {}, pmid = {39877812}, issn = {1092-8480}, abstract = {PURPOSE OF REVIEW: The gut microbiome is an emerging arena to investigate multiple sclerosis (MS) pathogenesis and potential therapeutics. In this review, we summarize the available data and postulate the feasibilities of potential MS therapeutic approaches that modulate the gut microbiome.<br><br>RECENT FINDINGS: Growing evidence indicates dysbiosis in the gut bacterial ecosystem in MS. Diet and other interventions produce biologically significant changes in the gut bacterial communities and functions, can potentially regulate the immune system, and benefit people with MS. While well-conducted investigations of the therapeutic mechanisms for targeting gut microbiome in animal models and humans remain limited, promising connections between various mechanisms of gut microbiome regulation and beneficial effects on MS outcomes are emerging.<br><br>SUMMARY: To date, studies examining the microbiome-based therapies in MS remain limited in number and follow-up duration. There is a clear need to determine the long-term efficacy and safety of these approaches, and to identify their underlying mechanisms of actions.}, }
@article {pmid39875854, year = {2025}, author = {Yu, J and Wu, Y and Zhu, Z and Lu, H}, title = {The impact of dietary patterns on gut microbiota for the primary and secondary prevention of cardiovascular disease: a systematic review.}, journal = {Nutrition journal}, volume = {24}, number = {1}, pages = {17}, pmid = {39875854}, issn = {1475-2891}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Cardiovascular Diseases/prevention &amp; control ; *Diet/methods ; *Primary Prevention/methods ; Secondary Prevention/methods ; Risk Factors ; Feeding Behavior ; Dietary Patterns ; }, abstract = {BACKGROUND: Previous studies found that it is promising to achieve the protective effects of dietary patterns on cardiovascular health through the modulation of gut microbiota. However, conflicting findings have been reported on how dietary patterns impact gut microbiota in individuals either established or at risk of cardiovascular disease (CVD). Our systematic review aimed to explore the effect of dietary patterns on gut microbiota composition and on risk factors for CVD in these populations.<br><br>METHODS: We systematically searched seven databases, including PubMed/MEDLINE, MEDLINE (Ovid), Embase (Ovid), CINHAL (EBSCO), Web of Science, CNKI (Chinese), and Wanfang (Chinese), covering literature from inception to October 2024. Studies were included if they focused on adults aged 18&#xa0;years and older with CVD or at least two CVD risk factors, implemented dietary pattern interventions, and incorporated outcomes related to microbiome analysis. The risk of bias for included studies was assessed using the revised Cochrane risk of bias tool (RoB2) for randomized trials and the Risk Of Bias In Non-randomised Studies of Interventions (ROBINS-I) for non-randomized studies. Changes in the relative abundance of the gut microbiome were summarized at various taxonomic levels, including phylum, class, order, family, genus, and species. Random-effects meta-analysis was conducted to analyze the mean difference in cardiometabolic parameters pre- and post-intervention.<br><br>RESULTS: Nineteen studies were identified, including 17 RCT and two self-controlled trails. Risk of bias across the studies was mixed but mainly identified as low and unclear. The most frequently reported increased taxa were Faecalibacterium (N&#x2009;=&#x2009;8) with plant-rich diets, Bacteroides (N&#x2009;=&#x2009;3) with restrictive diets, and Ruminococcaceae UCG 005 and Alistipes (N&#x2009;=&#x2009;9) with the polyphenol-rich diets. The most frequently reported decreased taxa were Parabacteroides (N&#x2009;=&#x2009;7) with plant-rich diets, Roseburia (N&#x2009;=&#x2009;3) with restrictive diets, and Ruminococcus gauvreauii group (N&#x2009;=&#x2009;6) with the polyphenol-rich diets. Plant-rich diets showed a significant decrease in total cholesterol (TC) with a mean difference of -6.77 (95% CI, -12.36 to -2.58; I[2]&#x2009;=&#x2009;84.7%), while restrictive diets showed a significant decrease in triglycerides (TG) of -22.12 (95% CI, -36.05 to -8.19; I[2]&#x2009;=&#x2009;98.4%).<br><br>CONCLUSIONS: Different dietary patterns showed distinct impacts on gut microbiota composition. Plant-rich diets promoted the proliferation of butyrate-producing bacteria, suggesting promising prospects for modulating gut microbiota and butyrate production through dietary interventions to enhance cardiovascular health. Further research is warranted to investigate the long-term effects of dietary patterns on clinical endpoints, such as CVD events or mortality.<br><br>REVIEW REGISTRATION: Registration number: CRD42024507660.}, }
@article {pmid39875845, year = {2025}, author = {Palmer-Rodríguez, P and Alberich, R and Reyes-Prieto, M and Castro, JA and Llabrés, M}, title = {Metadag: a web tool to generate and analyse metabolic networks.}, journal = {BMC bioinformatics}, volume = {26}, number = {1}, pages = {31}, pmid = {39875845}, issn = {1471-2105}, support = {PID2021-126114NB-C44//MICIU/AEI/ 10.13039/501100011033 and by "ERDF/EU"/ ; PID2021-126114NB-C44//MICIU/AEI/ 10.13039/501100011033 and by "ERDF/EU"/ ; PID2021-126114NB-C44//MICIU/AEI/ 10.13039/501100011033 and by "ERDF/EU"/ ; PID2021-126114NB-C44//MICIU/AEI/ 10.13039/501100011033 and by "ERDF/EU"/ ; }, mesh = {*Metabolic Networks and Pathways ; *Software ; *Internet ; Humans ; }, abstract = {BACKGROUND: MetaDAG is a web-based tool developed to address challenges posed by big data from omics technologies, particularly in metabolic network reconstruction and analysis. The tool is capable of constructing metabolic networks for specific organisms, sets of organisms, reactions, enzymes, or KEGG Orthology (KO) identifiers. By retrieving data from the KEGG database, MetaDAG helps users visualize and analyze complex metabolic interactions efficiently.<br><br>RESULTS: MetaDAG computes two models: a reaction graph and a metabolic directed acyclic graph (m-DAG). The reaction graph represents reactions as nodes and metabolite flow between them as edges. The m-DAG simplifies the reaction graph by collapsing strongly connected components, significantly reducing the number of nodes while maintaining connectivity. MetaDAG can generate metabolic networks from various inputs, including KEGG organisms or custom data (e.g., reactions, enzymes, KOs). The tool displays these models on an interactive web page and provides downloadable files, including network visualizations. MetaDAG was tested using two datasets. In an eukaryotic analysis, it successfully classified organisms from the KEGG database at the kingdom and phylum levels. In a microbiome study, MetaDAG accurately distinguished between Western and Korean diets and categorized individuals by weight loss outcomes based on dietary interventions.<br><br>CONCLUSION: MetaDAG offers an effective and versatile solution for metabolic network reconstruction from diverse data sources, enabling large-scale biological comparisons. Its ability to generate synthetic metabolisms and its broad application, from taxonomy classification to diet analysis, make it a valuable tool for biological research. MetaDAG is available online, with user support provided via a comprehensive guide. MetaDAG: https://bioinfo.uib.es/metadag/ User guide: https://biocom-uib.github.io/MetaDag/.}, }
@article {pmid39875781, year = {2025}, author = {Tiwari, S and Paramanik, V}, title = {Role of Probiotics in Depression: Connecting Dots of Gut-Brain-Axis Through Hypothalamic-Pituitary Adrenal Axis and Tryptophan/Kynurenic Pathway involving Indoleamine-2,3-dioxygenase.}, journal = {Molecular neurobiology}, volume = {}, number = {}, pages = {}, pmid = {39875781}, issn = {1559-1182}, abstract = {Depression is one of the most disabling mental disorders worldwide and characterized by symptoms including worthlessness, anhedonia, sleep, and appetite disturbances. Recently, studies have suggested that tryptophan (Trp) metabolism plays a key role in depressed mood through serotonin and kynurenine pathway involving enzyme tryptophan 5-monooxygenase (TPH) and indoleamine-2,3-dioxygenase (IDO) respectively. Moreover, during neuroinflammation, IDO is activated by proinflammatory cytokines and affects neurogenesis, cognition, disturbed hypothalamic-pituitary-adrenal (HPA) axis, and gut homeostasis by altering the gut bacteria and its metabolites like Trp derivatives. Furthermore, over the decades, researchers have focused on understanding communication between the human microbiome, especially gut microbiota, and mental health, called gut-brain-axis (GBA), particularly through Trp metabolism. Supplementation of probiotics in depression has gained attention from researchers and clinicians. However, there is limited information about probiotics supplementation on depression involving enzyme IDO and kynurenine pathway metabolites. This review discussed the potential role of probiotics in depression through the tryptophan/kynurenine pathway.}, }
@article {pmid39875747, year = {2025}, author = {Kwiatkowski, D and Schuch, LF and Klaus, NM and Martins, MD and Hilgert, JB and Hashizume, LN}, title = {Oral microbiota in head and neck cancer patients during radiotherapy: a systematic review.}, journal = {Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer}, volume = {33}, number = {2}, pages = {127}, pmid = {39875747}, issn = {1433-7339}, mesh = {Humans ; *Head and Neck Neoplasms/radiotherapy/microbiology ; *Microbiota ; *Mouth/microbiology ; Radiotherapy/adverse effects/methods ; }, abstract = {PURPOSE: Radiotherapy (RT) in the head and neck (HN) area causes a series of oral complications and the oral microbiota may play an important role in these complications. The aim of this systematic review was to explore alterations in the oral microbiota among individuals undergoing RT in the HN region.<br><br>METHODS: A comprehensive search across six databases and grey literature was made. No limitations were imposed on language or publication year. Studies meeting the inclusion and exclusion criteria were considered for inclusion.<br><br>RESULTS: Twenty-six articles met the criteria for inclusion in this systematic review. These studies varied in terms of radiation doses administered (ranging from 40&#xa0;Gy to 82.60&#xa0;Gy), microorganisms analyzed, locations within the oral cavity examined, and timing of assessments. Additionally, different methods of analysis were employed by the studies. Regarding oral microbiota changes, post-RT, there was significant increase in Candida species. Bacterial microbiota experienced increases, notably including Streptococcus mutans (S.mutans) and Lactobacillus, with dynamic fluctuations.<br><br>CONCLUSION: RT in the HN region induces significant changes in oral microbiota, including increases in S. mutans, Lactobacillus and Candida species colonization, and decreases in beneficial bacteria such as Neisseria and Fusobacteria. These microbiota changes may contribute to oral complications post-RT, emphasizing the need for preventive measures and targeted therapies to manage oral health in HN cancer patients undergoing RT.}, }
@article {pmid39875606, year = {2025}, author = {Pinto, Y}, title = {Beyond bacteria: Phanta adds flavour to microbiome profiling with a focus on phages.}, journal = {Nature reviews. Immunology}, volume = {}, number = {}, pages = {}, pmid = {39875606}, issn = {1474-1741}, }
@article {pmid39875510, year = {2025}, author = {Foessleitner, P and Cooley Demidkina, B and El-Arar, W and Goldenberg, M and Murthy, M and Bergerat, A and Bar, O and Kwon, DS and Mitchell, CM}, title = {Association between changes in genital immune markers and vaginal microbiome transitions in bacterial vaginosis.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {3536}, pmid = {39875510}, issn = {2045-2322}, mesh = {Humans ; Female ; *Vaginosis, Bacterial/immunology/microbiology ; *Vagina/microbiology/immunology ; Adult ; *Microbiota ; Prospective Studies ; Biomarkers ; Cytokines/metabolism ; Young Adult ; Metronidazole/therapeutic use/pharmacology ; }, abstract = {Bacterial vaginosis (BV), characterized by an imbalance in the vaginal microbiota, is a prevalent condition among women of reproductive age and a risk factor for human immunodeficiency virus, sexually transmitted infections, and preterm birth. BV is generally considered to induce mucosal inflammation, but the specific pathways and cell types involved are not well characterized. This prospective study aimed to assess associations between microbial changes and mucosal immune responses in BV patients. Therefore, samples from 20 premenopausal women with BV and treated with metronidazole were analyzed. Vaginal swabs, menstrual cup, and endocervical cytobrush samples were collected before treatment, weekly for four weeks, and at 2, 4, and 6 months for Nugent scoring, immune cell populations and cytokine analysis. Of 105 study intervals, 27 (25.7%) showed improvement in Nugent category, 61 (58.1%) remained unchanged, and 17 (16.2%) worsened. Improvement correlated with decreased monocytes (p = 0.005), while worsening was linked to increased monocytes (p < 0.001) and dendritic cells (p = 0.02). B cells (p = 0.02) and IFN-γ-induced chemokines - IP-10 (p = 0.007), MIG (p = 0.049), and ITAC (p = 0.005) - were associated with improvement. In conclusion, although the T-cell-associated chemokines IP-10, ITAC, and MIG were strongly associated with improvements in Nugent category, our findings indicate that antigen-presenting cells, particularly monocytes, show the most dynamic response to shifts in the vaginal microbiota in patients with BV.}, }
@article {pmid39875389, year = {2025}, author = {Levy, S and Jiang, AK and Grant, MR and Arp, G and Minabou Ndjite, G and Jiang, X and Hall, B}, title = {Convergent evolution of oxidized sugar metabolism in commensal and pathogenic microbes in the inflamed gut.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1121}, pmid = {39875389}, issn = {2041-1723}, support = {R35-GM155208//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32-AI089621//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; }, mesh = {*Gastrointestinal Microbiome ; *Oxidation-Reduction ; Symbiosis ; Inflammation/metabolism/microbiology ; Humans ; Glucaric Acid/metabolism ; Bacteria/metabolism/genetics ; ATP-Binding Cassette Transporters/metabolism/genetics ; Nitric Oxide/metabolism ; Sugars/metabolism ; Phylogeny ; Carbohydrate Metabolism ; Animals ; Bacterial Proteins/metabolism/genetics ; }, abstract = {Inflammation-associated perturbations of the gut microbiome are well characterized, but poorly understood. Here, we demonstrate that disparate taxa recapitulate the metabolism of the oxidized sugars glucarate and galactarate, utilizing enzymatically divergent, yet functionally equivalent, gud/gar pathways. The divergent pathway in commensals includes a putative 5-KDG aldolase (GudL) and an uncharacterized ABC transporter (GarABC) that recapitulate the function of their non-homologous counterparts in pathogens. A systematic bioinformatic search for the gud/gar pathway in gut microbes identified 887 species putatively capable of metabolizing oxidized sugars. Previous studies showed that inflammation-derived nitrate, formed by nitric oxide reacting with superoxide, promotes pathogen growth. Our findings reveal a parallel phenomenon: oxidized sugars, also produced from reactions with nitric oxide, serve as alternative carbon sources for commensal microbes. Previously considered a pathogen virulence factor, oxidized sugar metabolism is also present in specific commensals and may contribute to their increased relative abundance in gastrointestinal inflammation.}, }
@article {pmid39875095, year = {2025}, author = {Moeller, AH}, title = {Partner fidelity, not geography, drives co-diversification of gut microbiota with hominids.}, journal = {Biology letters}, volume = {21}, number = {1}, pages = {20240454}, doi = {10.1098/rsbl.2024.0454}, pmid = {39875095}, issn = {1744-957X}, support = {/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Phylogeny ; Hominidae/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Genome, Bacterial ; Geography ; }, abstract = {Bacterial strains that inhabit the gastrointestinal tracts of hominids have diversified in parallel (co-diversified) with their host species. The extent to which co-diversification has been mediated by partner fidelity between strains and hosts or by geographical distance between hosts is not clear due to a lack of strain-level data from clades of hosts with unconfounded phylogenetic relationships and geographical distributions. Here, I tested these competing hypotheses through meta-analyses of 7121 gut bacterial genomes assembled from wild-living ape species and subspecies sampled throughout their ranges in equatorial Africa. Across the gut bacterial phylogeny, strain diversification was more strongly associated with host phylogeny than with geography. In total, approximately 14% of the branch length of the gut bacterial phylogeny showed significant evidence of co-diversification independent of geography, whereas only approximately 4% showed significant evidence of diversification associated with geography independent of host phylogeny. Geographically co-occurring heterospecific hosts (Pan and Gorilla) universally maintained distinct co-diversified bacterial strains. Strains whose diversification was associated with geography independent of host phylogeny included clades of Proteobacteria known to adopt free-living lifestyles (e.g. Escherichia). These results show that co-diversification of gut bacterial strains with hominids has been driven primarily by fidelity of strains to host lineages rather than geography.}, }
@article {pmid39875062, year = {2025}, author = {Zhan, M and Li, Z and Chen, J and Zhao, Y and Bai, Z and Lu, B and Chen, H and Liu, Y}, title = {Indoxyl sulfate (IS) mediates pro-inflammatory responses in severe pneumonia in patients with rheumatoid arthritis associated interstitial lung disease.}, journal = {Clinical immunology (Orlando, Fla.)}, volume = {}, number = {}, pages = {110430}, doi = {10.1016/j.clim.2025.110430}, pmid = {39875062}, issn = {1521-7035}, abstract = {OBJECT: Patients with rheumatoid arthritis-associated interstitial lung disease (RA-ILD) have a high risk of serious infection, in particular severe pneumonia. This study aimed to investigate the transcriptional landscape, lower respiratory tract (LRT) microbiome and metabolomic profiles in the lung of RA-ILD patients with pneumonia.<br><br>METHOD: A total of 10 RA-ILD with pneumonia were enrolled in this study. In addition, 11 patients with COVID-19-associated pneumonia and 6 patients with non-autoimmune and non-COVID-19-related ILD with pneumonia were included as controls. Bronchoalveolar lavage fluid (BALF) was collected and prepared for metagenomic next-generation sequencing (mNGS), non-targeted metabolomics and bulk RNA-seq.<br><br>RESULT: Neutrophil-related genes were shared in the BALF cells of RA-ILD patients with pneumonia and patients with COVID-19-associated pneumonia. Carnobacterium, Wujia, Intestinimonas, Apibacter, Anaerotignum and Parvimonas were enriched in the LRT microbiome of RA-ILD, while Wujia, Apibacter, Pseudocitrobacter, and Thermobacillus were enriched in the LRT microbiome of COVID-19. Metabolomics analysis of BALF revealed significant elevation of indoxyl sulfate (IS) in the BALF of RA-ILD patients in comparison to COVID-19. Mechanistically, IS exerts an pro-inflammatory effect on macrophages and bronchial epithelial cells for pro-inflammatory cytokine production and potentiated neutrophils for neutrophil extracellular traps (NETs) formation.<br><br>CONCLUSIONS: Our results demonstrated a significant differences in the LRT microbiome and BALF metabolites between RA-ILD and COVID-19 patients with pneumonia, although they displayed similar local immune responses against lung infection. Alterations of LRT microbiome and related metabolites may be implicated in the pathogenesis of pneumonia in RA-ILD.}, }
@article {pmid39875017, year = {2025}, author = {Qin, L and Fan, B and Zhou, Y and Zheng, J and Diao, R and Wang, F and Liu, J}, title = {Targeted Gut Microbiome Therapy: Applications and Prospects of Probiotics, Fecal Microbiota Transplantation and Natural Products in the Management of Type 2 Diabetes.}, journal = {Pharmacological research}, volume = {}, number = {}, pages = {107625}, doi = {10.1016/j.phrs.2025.107625}, pmid = {39875017}, issn = {1096-1186}, abstract = {Type 2 diabetes mellitus (T2DM) is considered as one of the most pressing public health challenges worldwide. Studies have shown significant differences in the gut microbiota between healthy individuals and T2DM patients, suggesting that gut microorganisms may play a key role in the onset and progression of T2DM. This review systematically summarizes the relationship between gut microbiota and T2DM, and explores the mechanisms through which gut microorganisms may alleviate T2DM. Additionally, it evaluates the potential of probiotics, fecal microbiota transplantation (FMT)/virome transplantation (FVT), and natural products in modulating gut microbiota to treat T2DM. Although existing studies have suggested that these interventions may delay or even halt the progression of T2DM, most research remained limited to animal models and observational clinical studies, with a lack of high-quality clinical data. This has led to an imbalance between theoretical research and clinical application. Although some studies have explored the regulatory role of the gut virome on the gut microbiota, research in this area remains in its early stages. Based on these current studies, future research should be focused on large-scale, long-term clinical studies and further investigation on the potential role of the gut virome in T2DM. In conclusion, this review aims to summarize the current evidence and explore the applications of gut microbiota in T2DM treatment, as well as providing recommendations for further investigation in this field.}, }
@article {pmid39874761, year = {2025}, author = {Wang, R and Chen, J and Chen, H}, title = {Metagenomic insights into efficiency and mechanism of antibiotic resistome reduction by electronic mediators-enhanced microbial electrochemical system.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137350}, doi = {10.1016/j.jhazmat.2025.137350}, pmid = {39874761}, issn = {1873-3336}, abstract = {Electronic mediators are an effective means of enhancing the efficiency of microbial electrochemical electron transfer; however, there are still gaps in understanding the strengthening mechanisms and the efficiency of removing antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). This study systematically elucidates the effects of various electron mediators on bioelectrochemical processes, electron transfer efficiency, and the underlying mechanisms that inhibit ARG propagation within sediment microbial fuel cell systems (SMFCs). The results indicate that the addition of electron mediators significantly increased the output voltage (33.3 %-61.1 %) and maximum power density (14 %-106 %) of SMFCs, while also reducing ARB abundance and transmission risk. The enhancement effect follows the order of biochar, nanoscale zero-valent iron, graphene, and carbon nanotubes, with biochar emerging as the most economical and efficient choice for generating electricity and removing human pathogenic bacteria carrying ARGs. Procrustes analysis revealed that electron mediators facilitated the removal of ARGs by altering the structure of the microbiome, particularly the electricity-generating microorganisms (EGMs). Voltage and mobile genetic elements were the primary drivers of ARGs in the SMFCs. The network analysis results show that multiple carbohydrate-active enzymes, cluster of orthologous groups, and EGMs were negatively correlated with ARGs, indicating that the electron mediator-enhanced SMFCs mainly inhibit the spread of ARGs by promoting cell division, carbohydrate metabolism, and electricity generation. This study provides novel insights into how electron mediators affect ARG removal in microbial electrochemistry, which can inform economically viable strategies for sustainable environmental remediation.}, }
@article {pmid39874446, year = {2025}, author = {Chen, G and Wang, X and Sun, Q and Tang, ZZ}, title = {Multidimensional scaling improves distance-based clustering for microbiome data.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaf042}, pmid = {39874446}, issn = {1367-4811}, abstract = {MOTIVATION: Clustering patients into subgroups based on their microbial compositions can greatly enhance our understanding of the role of microbes in human health and disease etiology. Distance-based clustering methods, such as partitioning around medoids (PAM), are popular due to their computational efficiency and absence of distributional assumptions. However, the performance of these methods can be suboptimal when true cluster memberships are driven by differences in the abundance of only a few microbes, a situation known as the sparse signal scenario.<br><br>RESULTS: We demonstrate that classical multidimensional scaling (MDS), a widely used dimensionality reduction technique, effectively denoises microbiome data and enhances the clustering performance of distance-based methods. We propose a two-step procedure that first applies MDS to project high-dimensional microbiome data into a low-dimensional space, followed by distance-based clustering using the low-dimensional data. Our extensive simulations demonstrate that our procedure offers superior performance compared to directly conducting distance-based clustering under the sparse signal scenario. The advantage of our procedure is further showcased in several real data applications.<br><br>AVAILABILITY: The R package MDSMClust is available at https://github.com/wxy929/MDS-project.<br><br>CONTACT: gchen25@wisc.edu.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid39874355, year = {2025}, author = {Malas, J and Khoury, SC and Tanzillo, M and Fischer, GA and Bogner, JE and Meyer-Dombard, DR}, title = {Impact of antibiotics, iron oxide, and sodium sulfate on microbial community composition in laboratory-built municipal solid waste microcosms.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0318351}, doi = {10.1371/journal.pone.0318351}, pmid = {39874355}, issn = {1932-6203}, mesh = {*Sulfates/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Solid Waste ; *Microbiota/drug effects ; *RNA, Ribosomal, 16S/genetics ; *Ferric Compounds/pharmacology ; Refuse Disposal ; Bacteria/drug effects/genetics/classification ; Waste Disposal Facilities ; }, abstract = {Municipal solid waste (MSW) landfills represent underexplored microbial ecosystems. Landfills contain variable amounts of antibiotic and construction and demolition (C&amp;D) wastes, which have the potential to alter microbial metabolism due to biocidal or redox active components, and these effects are largely underexplored. To circumvent the challenge of MSW heterogeneity, we conducted a 65-day time series study on simulated MSW microcosms to assess microbiome changes using 16S rRNA sequencing in response to 1) Fe(OH)3 and 2) Na2SO4 to represent redox active components of C&amp;D waste as well as 3) antibiotics. The addition of Fe(OH)3 altered the overall community composition and increased Shannon diversity and Chao1 richness. The addition of a mixture of seven antibiotics (1000 ng/L each) altered the community composition without affecting diversity metrics. Sulfate addition had little effect on microbial community composition or diversity. These results suggest that the microbial community composition in fresh MSW may be significantly impacted by influxes of iron waste and a single application of antibiotics.}, }
@article {pmid39874304, year = {2025}, author = {Sabo, MC and Mustafa, S and Saha, A and Oyaro, B and Fiedler, TL and Krueger, M and Fuchs, E and Mureithi, M and Mandaliya, K and Jaoko, W and Richardson, BA and Gharib, SA and Fredricks, DN and Shah, JA and McClelland, RS}, title = {Bacterial vaginosis is associated with transcriptomic changes but not higher concentrations of cervical leukocytes in a study of women at high risk for HIV acquisition.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiaf049}, pmid = {39874304}, issn = {1537-6613}, abstract = {BACKGROUND: The association between bacterial vaginosis (BV) and increased HIV acquisition risk may be related to concentrations of HIV-susceptible immune cells in the cervix.<br><br>METHODS: Participants (31 with BV and 30 with normal microbiota) underwent cervical biopsy at a single visit. Immune cells were quantified and sorted using flow cytometry (N=55), localization assessed by immunofluorescence (N=16), and function determined by bulk RNA sequencing (RNA-seq) of live CD45+ cells (N=21).<br><br>RESULTS: Linear regression analyses demonstrated no differences in mean log2 [cells/mg tissue] between women with BV vs normal microbiota for antigen presenting cell (APC) subtypes linked to HIV risk (including CD1a+HLA-DR+ Langerhans cells, CD11c+CD14+ dendritic cells [DCs], and CD11c+HLA-DR+ DCs) and CD4+ T cells. Women with BV had a higher median proportion of CD11c+HLA-DR+ APCs (out of total cells) in cervical epithelium (0.1% vs 0.0%; p=0.03 using Mann-Whitney testing). RNA-seq identified 1,032 differentially expressed genes (adjusted p-value <0.05) in CD45+ cells between women with BV vs normal microbiota. Women with BV demonstrated downregulation of pathways linked to translation, metabolism, cell stress, and immune signaling.<br><br>CONCLUSIONS: BV alters immune cell localization and function; future studies are needed to address how these changes may mediate HIV acquisition risk.}, }
@article {pmid39874239, year = {2025}, author = {Zhou, H and Balint, D and Shi, Q and Vartanian, T and Kriegel, MA and Brito, I}, title = {Lupus and inflammatory bowel disease share a common set of microbiome features distinct from other autoimmune disorders.}, journal = {Annals of the rheumatic diseases}, volume = {84}, number = {1}, pages = {93-105}, doi = {10.1136/ard-2024-225829}, pmid = {39874239}, issn = {1468-2060}, mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/immunology ; *Lupus Erythematosus, Systemic/microbiology/immunology ; *Gastrointestinal Microbiome/genetics ; *Autoimmune Diseases/microbiology/immunology ; Biomarkers ; Female ; Metagenomics/methods ; Metagenome ; Male ; Receptors, Glucocorticoid/genetics ; }, abstract = {OBJECTIVES: This study aims to elucidate the microbial signatures associated with autoimmune diseases, particularly systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD), compared with colorectal cancer (CRC), to identify unique biomarkers and shared microbial mechanisms that could inform specific treatment protocols.<br><br>METHODS: We analysed metagenomic datasets from patient cohorts with six autoimmune conditions-SLE, IBD, multiple sclerosis, myasthenia gravis, Graves' disease and ankylosing spondylitis-contrasting these with CRC metagenomes to delineate disease-specific microbial profiles. The study focused on identifying predictive biomarkers from species profiles and functional genes, integrating protein-protein interaction analyses to explore effector-like proteins and their targets in key signalling pathways.<br><br>RESULTS: Distinct microbial signatures were identified across autoimmune disorders, with notable overlaps between SLE and IBD, suggesting shared microbial underpinnings. Significant predictive biomarkers highlighted the diverse microbial influences across these conditions. Protein-protein interaction analyses revealed interactions targeting glucocorticoid signalling, antigen presentation and interleukin-12 signalling pathways, offering insights into possible common disease mechanisms. Experimental validation confirmed interactions between the host protein glucocorticoid receptor (NR3C1) and specific gut bacteria-derived proteins, which may have therapeutic implications for inflammatory disorders like SLE and IBD.<br><br>CONCLUSIONS: Our findings underscore the gut microbiome's critical role in autoimmune diseases, offering insights into shared and distinct microbial signatures. The study highlights the potential importance of microbial biomarkers in understanding disease mechanisms and guiding treatment strategies, paving the way for novel therapeutic approaches based on microbial profiles.<br><br>TRIAL REGISTRATION NUMBER: NCT02394964.}, }
@article {pmid39874238, year = {2025}, author = {Scher, JU and Nayak, R and Clemente, JC}, title = {Microbiome research in autoimmune and immune-mediated inflammatory diseases: lessons, advances and unmet needs.}, journal = {Annals of the rheumatic diseases}, volume = {84}, number = {1}, pages = {9-13}, doi = {10.1136/ard-2024-225735}, pmid = {39874238}, issn = {1468-2060}, mesh = {Humans ; *Autoimmune Diseases/immunology/microbiology/therapy ; *Gastrointestinal Microbiome/immunology/physiology ; *Dysbiosis/immunology ; Fecal Microbiota Transplantation ; Microbiota/immunology ; Arthritis, Rheumatoid/immunology/microbiology ; Lupus Erythematosus, Systemic/immunology/microbiology ; Immune System Diseases/immunology/microbiology ; }, abstract = {The increasing prevalence of autoimmune and immune-mediated diseases (AIMDs) underscores the need to understand environmental factors that contribute to their pathogenesis, with the microbiome emerging as a key player. Despite significant advancements in understanding how the microbiome influences physiological and inflammatory responses, translating these findings into clinical practice remains challenging. This viewpoint reviews the progress and obstacles in microbiome research related to AIMDs, examining molecular techniques that enhance our understanding of microbial contributions to disease. We discuss significant discoveries linking specific taxa and metabolites to diseases such as rheumatoid arthritis, systemic lupus erythematosus and spondyloarthritis, highlighting the role of gut dysbiosis and host-microbiome interactions. Furthermore, we explore the potential of microbiome-based therapeutics, including faecal microbiota transplantation and pharmacomicrobiomics, while addressing the challenges of identifying robust microbial targets. We advocate for integrative, transdisease studies and emphasise the need for diverse cohort research to generalise findings across populations. Understanding the microbiome's role in AIMDs will pave the way for personalised medicine and innovative therapeutic strategies.}, }
@article {pmid39874025, year = {2025}, author = {Christen, CH and Elliott, SM and Kiesling, RL and VanDenBoom, A and Kohno, S and Givens, CE and Schoenfuss, HL}, title = {A comprehensive assessment of membrane bioreactor contaminant removal efficacy through analytical chemistry, fish exposures, and microbiome characterization.}, journal = {Environmental toxicology and chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/etojnl/vgaf027}, pmid = {39874025}, issn = {1552-8618}, abstract = {Treated municipal wastewater effluent is an important pathway for Contaminants of Emerging Concern (CEC) to enter aquatic ecosystems. As the aging wastewater infrastructure in many industrialized countries requires upgrades or replacement, assessing new treatment technologies in the context of CEC effects may provide additional support for science-based resource management. Here, we used three lines of evidence, analytical chemistry, fish exposure experiments, and fish and water microbiome analysis, to assess the effectiveness of membrane bioreactor treatment (MBR) to replace traditional activated sludge treatment. To do this, we sampled a municipal wastewater treatment plant with a split wastewater stream, a portion of which was treated with an MBR and another via an oxidation ditch (OXI). The OXI and MBR treatments substantially reduced most measured CECs compared to the primary effluent (PRI). Only pesticides and some pharmaceuticals were recalcitrant to both secondary treatment methods. While ammonia toxicity of PRI prevented its inclusion in fish exposure experiments, exposure of fish with waters from the OXI or MBR treated wastewater produced only subtle biological differences with no adverse apical outcomes. These findings were consistent with low chemically derived exposure: activity ratios (EARs) for OXI and MBR. Microbiome analysis of fish and wastewater highlighted the significant reduction of microbial abundance and diversity in the MBR treatment compared to all other treatments. The comparable removal efficacy of CECs in MBR makes it an attractive alternative to traditional OXI, especially when MBR may eliminate the need for tertiary treatment for wastewater disinfection.}, }
@article {pmid39873814, year = {2025}, author = {Liang, M and Dong, Q and Wu, W and Fan, J}, title = {Short-Chain Fatty Acids: Promising Therapeutic Targets for Respiratory Syncytial Virus Infection.}, journal = {Clinical reviews in allergy &amp; immunology}, volume = {68}, number = {1}, pages = {8}, pmid = {39873814}, issn = {1559-0267}, mesh = {Humans ; *Respiratory Syncytial Virus Infections/immunology/metabolism/therapy ; *Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome/immunology ; Animals ; Respiratory Syncytial Virus, Human/physiology ; Respiratory Syncytial Viruses/physiology/immunology ; }, abstract = {The intestinal microbiota is a complex community of organisms present in the human gastrointestinal tract, some of which can produce short-chain fatty acids (SCFAs) through the fermentation of dietary fiber. SCFAs play a major role in mediating the intestinal microbiota's regulation of host immunity and intestinal homeostasis. Respiratory syncytial virus (RSV) can cause an imbalance between anti-inflammatory and proinflammatory responses in the host. In addition, changes in SCFA levels and the structure of the intestinal microbiota have been observed after RSV infection. Therefore, there may be a link between SCFAs and RSV infection, and SCFAs are expected to be therapeutic targets for RSV infection.}, }
@article {pmid39873757, year = {2025}, author = {Castellano-Hinojosa, A and Gallardo-Altamirano, MJ and Pozo, C and González-Martínez, A and González-López, J}, title = {Inoculum selection and hydraulic retention time impacts in a microbial fuel cell treating saline wastewater.}, journal = {Applied microbiology and biotechnology}, volume = {109}, number = {1}, pages = {29}, pmid = {39873757}, issn = {1432-0614}, support = {101108081//HORIZON EUROPE Marie Sklodowska-Curie Actions/ ; P20-00079//Ministry of University, Research and Innovation of the Junta de Andaluc&#xed;a and by FEDER, A way of Making Europe/ ; PID-2020-112550RB-C22//Spanish Ministry of Science and Innovation/ ; }, mesh = {*Bioelectric Energy Sources/microbiology ; *Wastewater/microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Electricity ; Microbiota ; Sewage/microbiology ; Salinity ; Water Purification/methods ; Electrodes/microbiology ; }, abstract = {Microbial fuel cell (MFC) technology has received increased interest as a suitable approach for treating wastewater while producing electricity. However, there remains a lack of studies investigating the impact of inoculum type and hydraulic retention time (HRT) on the efficiency of MFCs in treating industrial saline wastewater. The effect of three different inocula (activated sludge from a fish-canning industry and two domestic wastewater treatment plants, WWTPs) on electrochemical and physicochemical parameters and the anodic microbiome of a two-chambered continuous-flow MFC was studied. For each inoculum, three different HRTs were tested (1 day, 3 days, and 6 days). The inoculum from the fish canning industry significantly increased voltage production (with a maximum value of 802 mV), power density (with a maximum value of 78 mW m[-2]), coulombic efficiency (with a maximum value of 19.3%), and organic removal rate (ORR) compared to the inocula from domestic WWTPs. This effect was linked to greater absolute and relative abundances of electroactive microorganisms (e.g., Geobacter, Desulfovibrio, and Rhodobacter) and predicted electron transfer genes in the anode microbiome likely due to better adaption to salinity conditions. The ORR and current production were also enhanced at shorter HRTs (1 day vs. 3 and 6 days) across all inocula. This effect was related to a greater abundance and diversity of bacterial communities at HRT of 1 day compared to longer HRTs. Our findings have important bioengineering implications and can help improve the performance of MFCs treating saline effluents such as those from the seafood industry. KEY POINTS: • Inoculum type and HRT impact organic matter removal and current production. • Changes in bioenergy generation were linked to the electroactive anodic microbiome. • Shorter HRT favored increases in the performance of the MFC.}, }
@article {pmid39873731, year = {2025}, author = {Wang, Q and Li, CL and Yu, SY and Dong, HJ and Yang, L and Liu, Y and He, PF and Zhang, SX and Yu, Q}, title = {A predictive model based on the gut microbiota improves the diagnostic effect in patients with rheumatoid arthritis.}, journal = {Rheumatology (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/rheumatology/keae706}, pmid = {39873731}, issn = {1462-0332}, abstract = {OBJECTIVES: Rheumatoid arthritis (RA) is a chronic, destructive autoimmune disorder predominantly targeting the joints, with gut microbiota dysbiosis being intricately associated with its progression. The aim of the present study was to develop of effective early diagnostic methods for early RA based on gut microbiota.<br><br>METHODS: A cohort comprising 262 RA patients and 475 healthy controls (HCs) was recruited. Faecal samples were collected from all participants, and microbial DNA was subsequently extracted. The V3-V4 region of the 16S rRNA gene was amplified via polymerase chain reaction (PCR) and subjected to high-throughput sequencing using the Illumina MiSeq platform. Additionally, a dataset with the accession number PRJNA450340 from the European Nucleotide Archive (ENA) was incorporated into the study. The sequencing data underwent processing and analysis utilizing QIIME2. To construct microbiome-based diagnostic models, Random Forest (RF), Support Vector Machine (SVM), and Generalized Linear Model (GLM) methodologies were employed, with the self-test data functioning as the training set and the PRJNA450340 dataset serving as the validation set.<br><br>RESULT: The results indicated that patients with RA exhibited a significantly reduced gut microbial &#x3b1;-diversity compared with the HCs group. The &#x3b2;-diversity analysis demonstrated notable distinctions in the gut microbiota structure between RA patients and HCs. Variations in the gut microbiome composition between RA patients and HCs were evident at both the phylum and genus levels. LEfSe analysis revealed a substantial number of significantly different microbiota between RA patients and HC, and 7&#x2009;key genera were obtained by intersection of the different flora in the two data sets: Ruminococcus_gnavus_group, Fusicatenibacter, Butyricicoccus, Subdoligranulum, Erysipelotrichaceae_UCG-003, Romboutsia, and Dorea. Utilizing these seven core genera, RA diagnostic models were developed employing RF, SVM, and GLM methodologies. The GLM model exhibited consistent performance, achieving an area under the curve (AUC) of 71.03% in the training set and 74.71% in the validation set.<br><br>CONCLUSION: Notable differences in gut microbiota exist between RA patients and healthy individuals. Diagnostic models based on key microbial genera hold potential for aiding in the early identification of individuals at risk for developing RA, thereby suggesting new avenues for its diagnosis.}, }
@article {pmid39873671, year = {2025}, author = {Kacena, C}, title = {Effects of the Curcuminoid and Non-Curcuminoid Compounds of Turmeric on the Gut Microbiome and Inflammation: Potential Use in the Treatment and Prevention of Disease.}, journal = {Nutrition reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/nutrit/nuae221}, pmid = {39873671}, issn = {1753-4887}, abstract = {The gut microbiome is a complex system that directly interacts with and influences many systems in the body. This delicate balance of microbiota plays an important role in health and disease and is highly influenced by lifestyle factors and the surrounding environment. As further research emerges, understanding the full potential of the gut microbiome and the impact of using nutraceuticals to positively influence its function may open the door to greater therapeutic outcomes in the treatment and prevention of disease. Curcumin, a bioactive compound derived from the turmeric rhizome, has been studied in depth for its influence on human health as a potent anti-inflammatory and antioxidant properties. However, the therapeutic activity of curcumin is limited by its low oral bioavailability. While most available research has primarily focused on the curcuminoid compounds of turmeric, the non-curcuminoid compounds hold promise to offer therapeutic benefits while synergistically enhancing the bioavailability of curcumin and supporting the gut microbiome. This review summarizes current knowledge of the relationship between the gut and the various systems within the body, and how dysbiosis, or disruption in the gut microbial balance, leads to inflammation and increased risk of chronic disease. The review also summarizes recent research that focuses on the bioactivity of both the curcuminoid and non-curcuminoid compounds that comprise the whole turmeric root and their synergistic role in enhancing bioavailability to support a healthy gut microbiome and promising use in the treatment and prevention of disease.}, }
@article {pmid39873522, year = {2025}, author = {Dickey, JR and Mercer, NM and Kuijpers, MCM and Props, R and Jackrel, SL}, title = {Biodiversity within phytoplankton-associated microbiomes regulates host physiology, host community ecology, and nutrient cycling.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0146224}, doi = {10.1128/msystems.01462-24}, pmid = {39873522}, issn = {2379-5077}, abstract = {UNLABELLED: Biological diversity is declining across the tree of life, including among prokaryotes. With the increasing awareness of host-associated microbes as potential regulators of eukaryotic host physiology, behavior, and ecology, it is important to understand the implications of declining diversity within host microbiomes on host fitness, ecology, and ecosystem function. We used phytoplankton and their associated environmental microbiomes as model systems to test the independent and interactive effects of declining microbiome diversity with and without other stressors often caused by human activity-elevated temperature and altered nutrient availability. We found effects of low microbiome diversity on host physiology, phytoplankton community dynamics, and nutrient cycling. Low microbiome diversity caused greater host cellular stress, as indicated by elevated δ[13]C and δ[15]N. Microbiome diversity also significantly affected host cell morphological metrics, likely as a consequence of this effect on cell stress. Despite causing greater host cellular stress, the effects of low microbiome diversity on host community ecology included elevated phytoplankton community diversity and biomass. The diversity of these host-associated microbes also had cascading implications on ecosystem nutrient cycling, where lower microbiome diversity caused a depletion of total dissolved N and P in the environment. The magnitude of these effects, caused by microbiome diversity, was greatest among nutrient-depleted environments and at elevated temperatures. Our results emphasize the widespread implications of declining host-associated microbial diversity from host cellular physiology to ecosystem nutrient cycling. These demonstrated effects of declining microbiome diversity are likely to be amplified in ecosystems experiencing multiple stressors caused by anthropogenic activities.<br><br>IMPORTANCE: As evidence is emerging of the key roles that host-associated microbiomes often play in regulating the physiology, fitness, and ecology of their eukaryotic hosts, human activities are causing declines in biological diversity, including within the microbial world. Here, we use a multifactorial manipulative experiment to test the effects of declining diversity within host microbiomes both alone and in tandem with the effects of emerging global changes, including climate warming and shifts in nutrient bioavailability, which are inflicting increasing abiotic stress on host organisms. Using single-celled eukaryotic phytoplankton that harbor an external microbiome as a model system, we demonstrate that diversity within host-associated microbiomes impacts multiple tiers of biological organization, including host physiology, the host population and community ecology, and ecosystem nutrient cycling. Notably, these microbiome diversity-driven effects became magnified in abiotically stressful environments, suggesting that the importance of microbiome diversity may have increased over time during the Anthropocene.}, }
@article {pmid39873520, year = {2025}, author = {Lehr, K and Oosterlinck, B and Then, CK and Gemmell, MR and Gedgaudas, R and Bornschein, J and Kupcinskas, J and Smet, A and Hold, G and Link, A and , }, title = {Comparison of different microbiome analysis pipelines to validate their reproducibility of gastric mucosal microbiome composition.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0135824}, doi = {10.1128/msystems.01358-24}, pmid = {39873520}, issn = {2379-5077}, abstract = {Microbiome analysis has become a crucial tool for basic and translational research due to its potential for translation into clinical practice. However, there is ongoing controversy regarding the comparability of different bioinformatic analysis platforms and a lack of recognized standards, which might have an impact on the translational potential of results. This study investigates how the performance of different microbiome analysis platforms impacts the final results of mucosal microbiome signatures. Across five independent research groups, we compared three distinct and frequently used microbiome analysis bioinformatic packages (DADA2, MOTHUR, and QIIME2) on the same subset of fastQ files. The source data set encompassed 16S rRNA gene raw sequencing data (V1-V2) from gastric biopsy samples of clinically well-defined gastric cancer (GC) patients (n = 40; with and without Helicobacter pylori [H. pylori] infection) and controls (n = 39, with and without H. pylori infection). Independent of the applied protocol, H. pylori status, microbial diversity and relative bacterial abundance were reproducible across all platforms, although differences in performance were detected. Furthermore, alignment of the filtered sequences to the old and new taxonomic databases (i.e., Ribosomal Database Project, Greengenes, and SILVA) had only a limited impact on the taxonomic assignment and thus on global analytical outcomes. Taken together, our results clearly demonstrate that different microbiome analysis approaches from independent expert groups generate comparable results when applied to the same data set. This is crucial for interpreting respective studies and underscores the broader applicability of microbiome analysis in clinical research, provided that robust pipelines are utilized and thoroughly documented to ensure reproducibility.IMPORTANCEMicrobiome analysis is one of the most important tools for basic and translational research due to its potential for translation into clinical practice. However, there is an ongoing controversy about the comparability of different bioinformatic analysis platforms and a lack of recognized standards. In this study, we investigate how the performance of different microbiome analysis platforms affects the final results of mucosal microbiome signatures. Five independent research groups used three different and commonly used bioinformatics packages for microbiome analysis on the same data set and compared the results. This data set included microbiome sequencing data from gastric biopsy samples of GC patients. Regardless of the protocol used, Helicobacter pylori status, microbial diversity, and relative bacterial abundance were reproducible across all platforms. The results show that different microbiome analysis approaches provide comparable results. This is crucial for the interpretation of corresponding studies and underlines the broader applicability of microbiome analysis.}, }
@article {pmid39873508, year = {2025}, author = {Han, Z and Hu, Y and Lin, X and Cheng, H and Dong, B and Liu, X and Wu, B and Xu, ZZ}, title = {Systematic analyses uncover robust salivary microbial signatures and host-microbiome perturbations in oral squamous cell carcinoma.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0124724}, doi = {10.1128/msystems.01247-24}, pmid = {39873508}, issn = {2379-5077}, abstract = {UNLABELLED: Oral squamous cell carcinoma (OSCC) is a prevalent malignancy in the oral-maxillofacial region with a poor prognosis. Oral microbiomes play a potential role in the pathogenesis of this disease. However, findings from individual studies have been inconsistent, and a comprehensive understanding of OSCC-associated microbiome dysbiosis remains elusive. Here, we conducted a large-scale meta-analysis by integrating 11 publicly available data sets comprising salivary microbiome profiles of OSCC patients and healthy controls. After correcting for batch effects, we observed significantly elevated alpha diversity and distinct beta-diversity patterns in the OSCC salivary microbiome compared to healthy controls. Leveraging random effects models, we identified robust microbial signatures associated with OSCC across data sets, including enrichment of taxa such as Streptococcus, Lactobacillus, Prevotella, Bulleidia moorei, and Haemophilus in OSCC samples. The machine learning models constructed from these microbial markers accurately predicted OSCC status, highlighting their potential as non-invasive diagnostic biomarkers. Intriguingly, our analyses revealed that the age- and gender-associated signatures in normal saliva microbiome were disrupted in the OSCC, suggesting perturbations in the intricate host-microbe interactions. Collectively, our findings uncovered complex alterations in the oral microbiome in OSCC, providing novel insights into disease etiology and paving the way for microbiome-based diagnostic and therapeutic strategies. Given that the salivary microbiome can reflect the overall health status of the host and that saliva sampling is a safe, non-invasive approach, it may be worthwhile to conduct broader screening of the salivary microbiome in high-risk OSCC populations as implications for early detection.<br><br>IMPORTANCE: The oral cavity hosts a diverse microbial community that plays a crucial role in systemic and oral health. Accumulated research has investigated significant differences in the saliva microbiota associated with oral cancer, suggesting that microbiome dysbiosis may contribute to the pathogenesis of oral squamous cell carcinoma (OSCC). However, the specific microbial alterations linked to OSCC remain controversial. This meta-analysis reveals robust salivary microbiome alterations. Machine learning models using differential operational taxonomic units accurately predicted OSCC status, highlighting the potential of the salivary microbiome as a non-invasive diagnostic biomarker. Interestingly, age- and gender-associated signatures in the normal salivary microbiome were disrupted in OSCC, suggesting perturbations in host-microbe interactions.}, }
@article {pmid39873455, year = {2025}, author = {Lan, Y and Song, Y and Zhang, W and Zhao, S and Wang, X and Wang, L and Wang, Y and Yang, X and Wu, H and Liu, X}, title = {Quinoa Ethanol Extract Ameliorates Cognitive Impairments Induced by Hypoxia in Mice: Insights into Antioxidant Defense and Gut Microbiome Modulation.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.4c07530}, pmid = {39873455}, issn = {1520-5118}, abstract = {Quinoa, rich in pharmacologically active ingredients, possesses the potential benefit in preventing cognitive impairments induced by hypoxia. In this study, the efficacy of quinoa ethanol extracts (QEE) consumption (200 and 500 mg/kg/d, respectively) against hypobaric hypoxia (HH)-induced cognitive deficits in mice was investigated. QEE significantly ameliorated hypoxic stress induced by HH, as evidenced by improvements in baseline indices and reductions in hypoxia-inducible factor 1α levels. Furthermore, QEE enhanced antioxidant defense mechanisms, alleviated neuroinflammation in brain regions associated with memory, and improved HH-induced cognitive impairments by modulating the cyclic adenosine monophosphate response element-binding protein/brain-derived neurotrophic factor signaling pathway. Higher doses generally yielded more effective outcomes than lower doses. QEE also significantly reshaped the gut microbiome structure of HH mice, inhibited gut barrier damage, and reduced lipopolysaccharide migration, thereby increasing short-chain fatty acids (SCFAs) levels. Our findings suggest that QEE may be a promising strategy for preventing hypoxia-induced cognitive impairments by maintaining gut microbiome stability and increasing SCFAs levels.}, }
@article {pmid39873427, year = {2025}, author = {Balasubramaniam, A and Srinivasan, S}, title = {Diet-Microbiome-ENS connection: Impact of the Cafeteria Diet.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpgi.00391.2024}, pmid = {39873427}, issn = {1522-1547}, support = {2R01DK080684-13A1//HHS | NIH | NIDDK | Division of Diabetes, Endocrinology, and Metabolic Diseases (DEM)/ ; I01BX000136-08//U.S. Department of Veterans Affairs (VA)/ ; }, abstract = {The interplay between diet-induced obesity and gastrointestinal dysfunction is an evolving area of research with far-reaching implications for understanding the gutbrain axis interactions. In their study, Ramírez-Maldonado et al. employ a cafeteria (CAF) diet model to investigate the effects on gut microbiota, enteric nervous system (ENS) integrity and function, and gastrointestinal motility in mice. Their work provides notable insights while also presenting opportunities for further exploration. The findings highlight early shifts in gut microbiota composition, notably increased Clostridia and Proteobacteria populations, and their association with ENS remodeling and motility impairment. This innovative use of a CAF diet strengthens the relevance of the model to real-world dietary patterns. Future studies will determine the mechanisms linking these microbial changes to neuronal dysfunction, particularly in terms of excitability deficits. The longitudinal approach is a commendable aspect of the study, yet certain dimensions, such as sex-specific responses and long-term outcomes, are underexplored. Further emphasis on these factors could provide a more nuanced understanding of the dietary effects on gastrointestinal health. While inflammation is identified as a mediator, more in-depth analysis of the pathways involved would help substantiate its role in ENS remodeling. Overall, this study makes a valuable contribution to the field, offering a solid foundation for future research. Expanding on the mechanistic insights and addressing the outlined gaps could further the translational relevance of these findings in tackling obesity-related gastrointestinal disorders.}, }
@article {pmid39873130, year = {2025}, author = {Park, SH and Choi, PG and Kim, HS and Lee, E and Lee, DH and Kim, MJ and Kim, D and Seo, HD and Hahm, JH and Jeon, TI and Huh, YH and Ahn, J and Ha, TY and Jung, CH}, title = {A Natural Autophagy Activator Castanea crenata Flower Alleviates Skeletal Muscle Ageing.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {16}, number = {1}, pages = {e13710}, doi = {10.1002/jcsm.13710}, pmid = {39873130}, issn = {2190-6009}, support = {E0210103//Korea Food Research Institute/ ; }, mesh = {Animals ; *Autophagy/drug effects ; Mice ; *Muscle, Skeletal/drug effects/metabolism ; *Plant Extracts/pharmacology ; *Aging/drug effects ; *Flowers ; Male ; Fagaceae/chemistry ; Cell Line ; }, abstract = {BACKGROUND: Sarcopenia, characterized by a gradual decline in skeletal muscle mass and function with age, significantly impacts both quality of life and mortality. Autophagy plays a crucial role in maintaining muscle health. There is growing interest in leveraging autophagy to mitigate muscle ageing effects. The impact of natural autophagy activators on skeletal muscle ageing remains elusive. This study aims to identify natural autophagy activators and assess their effects on skeletal muscle ageing.<br><br>METHODS: To discover novel autophagy activators, we screened 493 natural products and identified Castanea crenata flower extract (CCFE) as a promising candidate. We investigated the effect of CCFE on cellular senescence in C2C12 cells induced by etoposide. In animal experiments, aged mice (18&#x2009;months old) were fed a diet supplemented with 0.1% and 0.2% CCFE for 3&#x2009;months. We assessed exercise capacity, mitochondrial function and autophagic flux to determine the impact of CCFE on skeletal muscle ageing. The components present in CCFE were analysed using LC-MS/MS, and their functional properties were examined.<br><br>RESULTS: CCFE enhanced autophagic flux (LC3II 80% increase, p&#x2009;<&#x2009;0.05) and reduced senescence-associated &#x3b2;-galactosidase activity (32.78% decrease, p&#x2009;<&#x2009;0.001). In aged mice, a 3-month supplementation with CCFE improved muscle weight (18% increase, p&#x2009;<&#x2009;0.05) and function (treadmill performance increased by 60%, p&#x2009;<&#x2009;0.5; grip strength increased by 25%, p&#x2009;<&#x2009;0.05). It alleviated mitochondrial dysfunction (basal oxygen consumption rate increased by 59%, p&#x2009;<&#x2009;0.05) and restored autophagy. CCFE enhanced autophagy by activating AMPK (80% increase, p&#x2009;<&#x2009;0.01) and inhibiting Atg5 protein acetylation (65% decrease, p&#x2009;<&#x2009;0.001), with contributions from ellagic acid and polyamines. CCFE supplementation restored polyamine levels (serum spermidine increased from 0.98&#x2009;&#xb1;&#x2009;0.08 to 2.22&#x2009;&#xb1;&#x2009;0.05&#x2009;&#x3bc;g/mL, p&#x2009;<&#x2009;0.001) and increased urolithin levels (serum urolithin A increased from 0 to 18.79&#x2009;&#xb1;&#x2009;0.062&#x2009;ng/mL, p&#x2009;<&#x2009;0.001), metabolites produced by the gut microbiome from ellagic acid in aged mice.<br><br>CONCLUSIONS: CCFE effectively suppressed skeletal muscle ageing by preventing mitochondrial dysfunction and restoring autophagic flux in aged mice. It achieved this by modulating AMPK and EP300 acetyltransferase activity, with contributions from its constituents, ellagic acid and polyamines. These findings highlight the potential of CCFE as a therapeutic agent for extending healthspan and mitigating sarcopenia, providing a basis for future clinical trials.}, }
@article {pmid39873084, year = {2025}, author = {Ju, HM and Ahn, YW and Ok, SM and Jeong, SH and Na, HS and Chung, J}, title = {Distinctive salivary oral microbiome in patients with burning mouth syndrome depending on pain intensity compared to healthy subjects.}, journal = {Journal of dental sciences}, volume = {20}, number = {1}, pages = {462-469}, pmid = {39873084}, issn = {2213-8862}, abstract = {BACKGROUND/PURPOSE: Burning moouth syndrome (BMS) is a chronic pain condition similar to neuropathic pain. It is characterized by a persistent burning sensation in the oral cavity. Despite the lack of clarity regarding the etiology of BMS, recent studies have reported an association between the gut microbiome and neuropathic pain. However, few studies have investigated the association between the oral microbiome and orofacial pain, such as BMS. This study aimed to compare the oral microbial profiles of healthy controls (HC) and patients with BMS.<br><br>MATERIALS AND METHODS: The BMS group was further divided into BMS_low and BMS_high groups according to pain intensity. A total of 60 patients with BMS (BMS_low, n&#xa0;=&#xa0;16; BMS_high, n&#xa0;=&#xa0;44) and 30 HC provided saliva samples, which were sequenced and analyzed for the V1-V2 region of the 16S rRNA gene.<br><br>RESULTS: The alpha diversity was similar among the three groups. However, a significant difference in the distribution of microbiome composition was observed between BMS_high and HC, as revealed by the Bray-Curtis distance analysis (P&#xa0;<&#xa0;0.01). At the genus level, Prevotella and Alloprevotella were the most abundant genera in the BMS group. Compared to HC, BMS_high exhibited a relatively higher abundance of bacterial species. Some bacteria, including Prevotella spp., exhibit an increasing pattern with subjective pain intensity.<br><br>CONCLUSION: These results suggest the potential involvement of oral microbiota in BMS pathogenesis. Additionally, variations in the microbiome may occur not only in the presence or absence of pain, but also with pain severity.}, }
@article {pmid39873074, year = {2025}, author = {Yang, YH and Yu, JJ and Han, HY and Chang, WM and Wang, CW}, title = {Ex-vivo investigation of human salivary microbial growth with lysogeny broth for translational research-A pilot study.}, journal = {Journal of dental sciences}, volume = {20}, number = {1}, pages = {437-443}, pmid = {39873074}, issn = {2213-8862}, abstract = {BACKGROUND/PURPOSE: Salivary microbiome has become a surrogate indicator of oral disease due to its collective reservoirs and convenience in sampling. However, failed clinical trials often lead to wastes of resources, indicating a need for preclinical models. In this pilot study, we aimed to compare the salivary microbiome by metagenomics analysis before and after lysogeny broth culture for prospective translational studies.<br><br>MATERIALS AND METHODS: The study cohort included seven patients with severe periodontitis (Stage III/IV, Grade C), from whom unstimulated saliva was collected. The salivary microbiome was sequenced over the 16S rRNA gene V3-V4 hypervariable regions at baseline and after 6&#xa0;hours of lysogeny broth culture.<br><br>RESULTS: The results revealed changes in salivary microbiome and reduced bacterial diversity after culture, mainly due to the expansion of genera Neisseria (Median (Mdn) 15.95% to 37.52%, P&#xa0;<&#xa0;0.05), Rothia (Mdn 10.21% to 16.32%, P&#xa0;<&#xa0;0.05), and Haemophilus (Mdn 5.88% to 13.25%, P&#xa0;<&#xa0;0.05). Periodontitis-related pathogens such as phyla Bacteroidetes, Fusobacteria and Spirochaetes were identified, while genera Porphyromonas, Parvimonas, Peptostreptococcus, and Campylobacter showed a decrease after lysogeny broth culture. Caries-related pathogens, including genera Veillonella, Leptotrichia, and species Haemophilus parainfluenzae and Streptococcus salivarius, were also detected.<br><br>CONCLUSION: This pilot study revealed that periodontitis- and caries-related bacteria could be identified in the saliva at baseline and after 6&#xa0;hours ex-vivo culture with lysogeny broth. Our findings also suggested that lysogeny broth favored the growth of specific genera and may serve as a reference to monitor short-term modulation of these bacteria in salivary microbiome.}, }
@article {pmid39872943, year = {2024}, author = {Dong, S and Yao, X and Jiao, J and Lin, B and Yan, F and Wang, X}, title = {Fecal propionate is a signature of insulin resistance in polycystic ovary syndrome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1394873}, pmid = {39872943}, issn = {2235-2988}, mesh = {*Polycystic Ovary Syndrome/metabolism/microbiology ; Humans ; Female ; *Insulin Resistance ; *Propionates/metabolism/analysis ; *Feces/microbiology/chemistry ; Adult ; *Gastrointestinal Microbiome ; *Fatty Acids, Volatile/metabolism/analysis ; Young Adult ; Bacteria/classification/isolation &amp; purification/metabolism ; Biomarkers/metabolism ; ROC Curve ; China ; }, abstract = {OBJECTIVE: To investigate the roles of fecal short-chain fatty acids (SCFAs) in polycystic ovary syndrome (PCOS).<br><br>METHODS: The levels of SCFAs (acetate, propionate, and butyrate) in 83 patients with PCOS and 63 controls were measured, and their relationships with various metabolic parameters were analyzed. Intestinal microbiome analysis was conducted to identify relevant bacteria. The study took place at the Center for Reproductive Medicine at Shengjing Hospital of China Medical University in Shenyang, from 5 February to 23 May 2023. Logistic regression analyses were used to investigate the relationships between SCFAs, PCOS, and PCOS-related insulin resistance (IR). Differences in bacterial populations between women with PCOS-IR and those with PCOS-non-insulin resistance (NIR) were identified using linear discriminant analysis effect Size (LEfSe). The relationships between bacteria and fecal propionate levels were explored through linear regression analyses. The potential of fecal propionate and microbial profiles as biomarkers for insulin resistance in PCOS patients was assessed using receiver operating characteristic (ROC) curve analysis.<br><br>RESULTS: Higher fecal propionate levels were observed in patients with PCOS compared to controls (p = 0.042) and in PCOS-IR compared to PCOS-NIR (p = 0.009). There was no significant difference in fecal propionate levels between the IR and NIR subgroups of women in the control group (p > 0.05). Additionally, higher fecal propionate levels were associated with IR in PCOS (p = 0.039; OR, 1.115; 95% CI, 1.006-1.237). The abundance of Prevotella copri and Megamonas funiformis was higher in PCOS-IR women compared to PCOS-NIR women (LDA score > 3) and correlated with fecal propionate levels (adjusted R&#xb2; = 0.145, p < 0.001). The area under the curve (AUC) for propionate and the combined presence of P. copri and M. funiformis in predicting PCOS was 78.0%, with a sensitivity of 78.5% and a specificity of 72.4%. Pathways related to carbohydrate metabolism were significantly enriched in the microbiota of the PCOS-IR population but not in the control IR group.<br><br>CONCLUSIONS: Higher fecal propionate levels correlate with PCOS-related insulin resistance. P. copri and M. funiformis might be key functional bacteria. Therefore, the combination of propionate levels and the abundance of these two bacteria may serve as a potential biomarker for insulin resistance in PCOS patients. Regulation of the intestinal microbiome might be beneficial for the metabolic health of women with PCOS.}, }
@article {pmid39872928, year = {2024}, author = {Yang, J and Fischer, NG and Ye, Z}, title = {Revolutionising oral organoids with artificial intelligence.}, journal = {Biomaterials translational}, volume = {5}, number = {4}, pages = {372-389}, pmid = {39872928}, issn = {2096-112X}, abstract = {The convergence of organoid technology and artificial intelligence (AI) is poised to revolutionise oral healthcare. Organoids - three-dimensional structures derived from human tissues - offer invaluable insights into the complex biology of diseases, allowing researchers to effectively study disease mechanisms and test therapeutic interventions in environments that closely mimic in vivo conditions. In this review, we first present the historical development of organoids and delve into the current types of oral organoids, focusing on their use in disease models, regeneration and microbiome intervention. We then compare single-source and multi-lineage oral organoids and assess the latest progress in bioprinted, vascularised and neural-integrated organoids. In the next part of the review, we highlight significant advancements in AI, emphasising how AI algorithms may potentially promote organoid development for early disease detection and diagnosis, personalised treatment, disease prediction and drug screening. However, our main finding is the identification of remaining challenges, such as data integration and the critical need for rigorous validation of AI algorithms to ensure their clinical reliability. Our main viewpoint is that current AI-enabled oral organoids are still limited in applications but, as we look to the future, we offer insights into the potential transformation of AI-integrated oral organoids in oral disease diagnosis, oral microbial interactions and drug discoveries. By synthesising these components, this review aims to provide a comprehensive perspective on the current state and future implications of AI-enabled oral organoids, emphasising their role in advancing oral healthcare and improving patient outcomes.}, }
@article {pmid39872848, year = {2024}, author = {Wang, X and He, X and Zhong, B}, title = {Oral microbiota: the overlooked catalyst in cancer initiation and progression.}, journal = {Frontiers in cell and developmental biology}, volume = {12}, number = {}, pages = {1479720}, pmid = {39872848}, issn = {2296-634X}, abstract = {The advancement of high-throughput sequencing technology in recent decades has led to a greater understanding of the components of the oral microbiota, providing a solid foundation for extensive research in this field. The oral microbiota plays an important role in an individual's overall health. It has been shown to be significantly correlated with chronic human diseases, including diabetes, rheumatoid arthritis, cardiovascular disease, periodontal disease, and Alzheimer's disease. Furthermore, tumor occurrence and development are closely related to the oral microbiome. Specific bacteria, such as Fusobacterium nucleatum (F. nucleatum), Porphyromonas gingivalis (P. gingivalis), Streptococcus, Streptomyces, Prevotella, and Fibrophagy gingivalis, play critical roles in cancer development. The oral microbiota has various oncogenic mechanisms, including bacterial inflammation, immunological suppression, tumor growth mediated by bacterial toxins, antiapoptotic activity, and carcinogenic effects. This paper reviews the role of the oral microbiota in the occurrence and progression of cancer and systematically elucidates the molecular mechanisms by which dysbiosis influences tumorigenesis and tumor progression. This information can provide a theoretical basis for exploring cancer treatment strategies and offer new insights for cancer prevention.}, }
@article {pmid39872379, year = {2024}, author = {Taico Oliva, C and Musa, I and Kopulos, D and Ardalani, F and Maskey, A and Wilson, A and Yang, N and Li, XM}, title = {The gut microbiome and cross-reactivity of food allergens: current understanding, insights, and future directions.}, journal = {Frontiers in allergy}, volume = {5}, number = {}, pages = {1503380}, pmid = {39872379}, issn = {2673-6101}, abstract = {This mini-review examines the emerging role of the gut microbiome in influencing food allergen cross-reactivity. It specifically focuses on how microbial diversity, antigens, and metabolites impact IgE-mediated allergic responses. Cross-reactivity occurs when structurally similar food and microbial antigens trigger hypersensitivities, affecting millions of people worldwide. Recent research underscores the significance of microbial diversity in early life for developing immune tolerance. Beneficial strains, such as Lactobacillus and Bifidobacterium, play a crucial role in supporting the functions of T regulatory cells (Tregs) and immunoglobulin A (IgA). Additionally, we discuss microbial metabolites, particularly short-chain fatty acids (SCFAs), which enhance immune tolerance by promoting Treg differentiation and maintaining gut barrier integrity, thereby reducing allergen entry. However, it is important to note that SCFAs can provoke inflammatory responses under certain conditions, highlighting the necessity for targeted research on their dual effects. Dysbiosis-related intestinal permeability, often referred to as "leaky gut," can further worsen cross-reactivity. Microbial antigens like lipopolysaccharides (LPS) are known to influence Th2-dominant responses.}, }
@article {pmid39872288, year = {2025}, author = {Iqbal, H and Kim, Y and Jin, M and Rhee, DK}, title = {Ginseng as a therapeutic target to alleviate gut and brain diseases via microbiome regulation.}, journal = {Journal of ginseng research}, volume = {49}, number = {1}, pages = {12-21}, pmid = {39872288}, issn = {1226-8453}, abstract = {The human gut, which contains a diverse microbiome, plays an important role in maintaining physiological balance and preserving the immune system. The complex interplay between the central nervous system (CNS) and the gut microbiome has gained significant attention due to its profound implications for overall health, particularly for gut and brain disorders. There is emerging evidence that the gut-brain axis (GBA) represents a bidirectional communication system between the CNS and the gastrointestinal tract and plays a pivotal role in regulating many aspects of human health. Ginseng has shown potential to ameliorate conditions associated with dysbiosis, such as gut and CNS disorders by restoring microbial balance and enhancing gut barrier function. This comprehensive review provides valuable insights into the potential of ginseng as a herbal modulator of GBA as a therapeutic intervention for preventing and treating gut and neurological diseases via microbiota regulation to ultimately enhance overall health. Furthermore, we emphasize the therapeutic benefits of ginseng, its ability to enhance beneficial probiotics, such as Firmicutes, Bacteroides, Lactobacillus, Bifidobacterium, and Akkermansia while reducing pathogenic bacteria prevalence, such as Helicobacter, Clostridium, and Proteobacteria. Although the connection between ginseng regulation of microbial communities in response to the gut and neuropsychiatric disorders is lacking, additional investigations are warranted to elucidate the underlying mechanisms, optimize dosages, and explore the clinical relevance of ginseng in promoting GBA balance and ultimately overall health.}, }
@article {pmid39872101, year = {2024}, author = {Kameri, E and Jepsen, VH and Stachura, P and Rüchel, N and Bhave, R and Benitez, L and Crispi, F and Gratacos, E and Dragano, N and Janssen, S and Borkhardt, A and Pandyra, A and Kögler, G and Fischer, U}, title = {A gut instinct for childhood leukemia prevention: microbiome-targeting recommendations aimed at parents and caregivers.}, journal = {Frontiers in public health}, volume = {12}, number = {}, pages = {1445113}, pmid = {39872101}, issn = {2296-2565}, mesh = {Humans ; *Gastrointestinal Microbiome ; Child ; *Parents ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/prevention &amp; control ; *Caregivers ; Risk Factors ; Infant, Newborn ; Child, Preschool ; }, abstract = {Childhood leukemia accounts for 30% of all pediatric cancer cases with acute lymphoblastic leukemia (ALL) being the most common subtype. Involvement of the gut microbiome in ALL development has recently garnered interest due to an increasing recognition of the key contribution the microbiome plays in maintaining the immune system's homeostatic balance. Commensal gut microbiota provide a first line of defense against different pathogens and gut microbiome immaturity has been implicated in ALL pathogenesis. Several environmental factors such as nutrition, mode of delivery, breastfeeding and, early social or livestock contacts are known to alter the composition of the gut microbiota. Variations in these factors influence the risk of childhood leukemia onset. This review aims to elucidate the risk factors influencing microbial composition in the context of childhood ALL. The link between gut microbiome diversity and childhood ALL offers the opportunity to develop risk-reducing strategies that can be communicated to a broad target population of (future) parents and caregivers for childhood leukemia prevention. Here, we summarize evidence on how promoting a diverse gut microbiome in newborns through simple measures such as increasing social contacts early in life may decrease the risk of developing ALL in these children later on.}, }
@article {pmid39871915, year = {2025}, author = {Li, C and Nan, J and Xu, BT}, title = {Helicobacter pylori infection as a contributing factor to metabolic dysfunction-associated steatohepatitis: A population-based insight.}, journal = {World journal of hepatology}, volume = {17}, number = {1}, pages = {103228}, pmid = {39871915}, issn = {1948-5182}, abstract = {This letter discusses the research conducted by Abdel-Razeq et al, highlighting a significant association between Helicobacter pylori (H. pylori) infection and metabolic dysfunction-associated steatohepatitis (MASH) in individuals with a prior history of H. pylori infection. Using a comprehensive patient database, the study establishes an independent correlation between H. pylori and an elevated risk of MASH, even after adjusting for coexisting conditions such as obesity, type 2 diabetes, and dyslipidemia. Notably, the findings suggest that H. pylori may worsen liver pathology through inflammatory pathways, contributing to hepatic insulin resistance and lipid accumulation. Although the study provides strong evidence for this association, limitations related to diagnostic heterogeneity indicate a need for further research to clarify the underlying mechanisms and to explore the potential roles of genetic and microbiome factors in this relationship.}, }
@article {pmid39871903, year = {2025}, author = {Xu, XT and Jiang, MJ and Fu, YL and Xie, F and Li, JJ and Meng, QH}, title = {Gut microbiome composition in patients with liver cirrhosis with and without hepatic encephalopathy: A systematic review and meta-analysis.}, journal = {World journal of hepatology}, volume = {17}, number = {1}, pages = {100377}, pmid = {39871903}, issn = {1948-5182}, abstract = {BACKGROUND: The gut microbiome is associated with hepatic encephalopathy (HE), but research results on the gut microbiome characteristics of patients with liver cirrhosis with and without HE are inconsistent.<br><br>AIM: To study the gut microbiota characteristics of patients with liver cirrhosis with and without HE.<br><br>METHODS: We searched the PubMed, Web of Science, EMBASE, and Cochrane databases using two keywords, HE, and gut microbiome. According to the inclusion and exclusion criteria, suitable literature was screened to extract data on the diversity and composition of the fecal microbiota in patients with liver cirrhosis with and without HE. The data were analyzed using RevMan and STATA.<br><br>RESULTS: Seventeen studies were included: (1) A meta-analysis of 7 studies revealed that the Shannon index in liver cirrhosis patients with HE was significantly lower than that in patients without HE [-0.20, 95% confidence interval (CI): -0.28 to -0.13, I[2] = 20%]; (2) The relative abundances of Lachnospiraceae (-2.73, 95%CI: -4.58 to -0.87, I[2] = 38%) and Ruminococcaceae (-2.93, 95%CI: -4.29 to -1.56, I[2] = 0%) in liver cirrhosis patients with HE was significantly lower than those in patients without HE; (3) In patients with HE, Enterococcus, Proteobacteria, Enterococcaceae, and Enterobacteriaceae proportions increased, but Ruminococcaceae, Lachnospiraceae, Prevotellaceae, and Bacteroidetes proportions decreased; (4) Differences in the fecal metabolome between liver cirrhosis patients with and without HE were detected; and (5) Differential gut microbiomes may serve as diagnostic and prognostic tools.<br><br>CONCLUSION: The gut microbiomes of patients with liver cirrhosis with and without HE differ. Some gut microbiomes may distinguish liver cirrhosis patients with or without HE and determine patient prognosis.}, }
@article {pmid39871894, year = {2024}, author = {Ren, Y and Chen, M and Wang, Z and Han, JJ}, title = {Oral microbiota in aging and diseases.}, journal = {Life medicine}, volume = {3}, number = {3}, pages = {lnae024}, pmid = {39871894}, issn = {2755-1733}, abstract = {Human microbiomes are microbial populations that form a symbiotic relationship with humans. There are up to 1000 species on the surface of human skin and mucosal system, among which gut microbiota attracts the most interest. As the beginning of the digestive tract, oral cavity is also an important microbial habitat in the human body which is the first line of defense against pathogens entering the body. Many studies have revealed that oral microbial dysbiosis could not only contribute to oral diseases but also whole-body systemic diseases and health status. Oral microorganisms can enter the gastrointestinal tract with saliva and food, or enter the blood circulation through mouth breakage, thus causing systemic inflammation and aging-related diseases including some causal links to Alzheimer's disease. A series of changes take place in oral microbial composition during development, with different age stages marked by different dominant microbial species. Despite a lack of comprehensive studies on aging oral microbiota, through systemic inflammation, oral pathogenic microbes are likely to contribute inflammatory aging. As inflammaging is a key signature and one of the causes for accelerated aging, improving the structure of oral microbiome may be not only a new strategy for disease prevention and treatment, but also for aging intervention.}, }
@article {pmid39871788, year = {2025}, author = {Tadimarri, VS and Blanch-Asensio, M and Deshpande, K and Baumann, J and Baumann, C and Müller, R and Trujillo, S and Sankaran, S}, title = {PEARL: Protein Eluting Alginate with Recombinant Lactobacilli.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {}, number = {}, pages = {e2408316}, doi = {10.1002/smll.202408316}, pmid = {39871788}, issn = {1613-6829}, support = {LeibnizScienceCampusLivingTherapeuticMaterials(LifeMat)//Leibniz-Gemeinschaft/ ; SFB1027//Deutsche Forschungsgemeinschaft/ ; 200049484//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Engineered living materials (ELMs) made of bacteria in hydrogels have shown considerable promise for therapeutic applications through controlled and sustained release of complex biopharmaceuticals at low costs and with reduced wastage. While most therapeutic ELMs use E. coli due to its large genetic toolbox, most live biotherapeutic bacteria in development are lactic acid bacteria due to native health benefits they offer. Among these, lactobacilli form the largest family of probiotics with therapeutic potential in almost all sites of the body with a microbiome. A major factor limiting the use of lactobacilli in ELMs is their limited genetic toolbox. This study expands on recent work to expand the genetic programmability of probiotic Lactiplantibacillus plantarum WCFS1 for protein secretion and encapsulate it in a simple, cost-effective, and biocompatible core-shell alginate bead to develop an ELM. The controlled release of recombinant proteins is demonstrated, even up to 14 days from this ELM, thereby terming it PEARL - Protein Eluting Alginate with Recombinant Lactobacilli. Notably, lactobacillus encapsulation offered benefits like bacterial containment, protein release profile stabilization, and metabolite-induced cytotoxicity prevention. These findings demonstrate the mutual benefits of combining recombinant lactobacilli with alginate for the controlled and sustained release of proteins.}, }
@article {pmid39871711, year = {2025}, author = {Baranzini, SE}, title = {Multi-disciplinary research will be the key to stop, restore, and end MS.}, journal = {Multiple sclerosis (Houndmills, Basingstoke, England)}, volume = {}, number = {}, pages = {13524585251314756}, doi = {10.1177/13524585251314756}, pmid = {39871711}, issn = {1477-0970}, abstract = {The past 25 years have brought extraordinary advances in our understanding of MS pathogenesis and the subsequent development of effective therapies. Collaborative genetics efforts have uncovered the association of 236 common DNA variants with disease susceptibility and the first association with disease severity, paving the way to more effective therapies, particularly for progressive forms of the disease. In parallel, and in addition to established environmental disease triggers or modifiers, new collaborative work has revealed new associations with components of the gut microbiome. This research opened a new and exciting prospect for exploring the gut-brain axis, with the potential to also provide new pharmacologic targets and diet-based therapies. Finally, with the availability of massive amounts of information and unprecedented computer power, a new wave of artificial intelligence (AI)-based research is sprawling. These investigations will result in statistically powerful predictive models to identify individuals at risk even years before the disease is clinically apparent. Furthermore, using approaches like semantic representation and causal inference, some of these approaches will be explainable in biomedical terms, thus making them trusted and facilitating their implementation in the clinical setting. The common thread that characterizes all of these advances is multi-disciplinary collaboration among scientists in the form of formal consortia, working groups, or ad hoc partnerships. This may be the "secret sauce" of modern science and the best strategy to stop, restore, and end MS.}, }
@article {pmid39871496, year = {2025}, author = {Ma, Y and Zuohereguli, K and Zhang, L and Kang, Y and Shi, L and Xu, H and Ruan, Y and Wen, T and Mei, X and Dong, C and Xu, Y and Shen, Q}, title = {Soil Microbial Mechanisms to Improve Pear Seedling Growth by Applying Bacillus and Trichoderma-Amended Biofertilizers.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.15395}, pmid = {39871496}, issn = {1365-3040}, support = {//This study was supported by Jiangsu Agricultural Science and Technology Innovation Fund (CX[23]1011), China Agriculture Research System (CARS-28-10) and Natural Science Foundation of China (32272809)./ ; }, abstract = {Bacillus velezensis SQR9 or Trichoderma harzianum NJAU4742-amended bioorganic fertilizers might significantly improve the soil microbial community and crop yields. However, the mechanisms these microorganisms act are far away from distinctness. We combined amplicon sequencing with culturable approaches to investigate the effects of these microorganisms on pear tree growth, rhizosphere nutrients and microbial mechanisms. The SQR9 and T4742 treatments increased the total biomass of pear trees by 68% and 84%, respectively, compared to the conventional organic fertilizer treatment (CK). SQR9 tends to increase soil organic matter and available phosphorus, while T4742 more effectively enhances nitrogen, potassium, iron and zinc levels. These effects were primarily linked to changes in the microbial community. T4742 treatment enriched twice as many differential microbes as SQR9. SQR9 significantly enriched Urebacillus, Streptomyces and Mycobacterium, while T4742 increased the abundance of Pseudomonas, Aspergillus and Penicillium. In vitro experiments revealed that secondary metabolites secreted by B. velezensis SQR9 and T. harzianum NJAU4742 stimulate the growth of key probiotics associated with their respective treatments, enhancing soil fertility and plant biomass. The study revealed the specific roles of these bioorganic fertilizers in agricultural applications, providing new insights for developing effective and targeted bioorganic fertilizer products and promoting sustainable agriculture.}, }
@article {pmid39871424, year = {2025}, author = {Brischetto, C and Rossi, V and Salotti, I and Languasco, L and Fedele, G}, title = {Temperature Requirements Can Affect the Microbial Composition Causing Sour Rot in Grapes.}, journal = {Environmental microbiology reports}, volume = {17}, number = {1}, pages = {e70061}, doi = {10.1111/1758-2229.70061}, pmid = {39871424}, issn = {1758-2229}, mesh = {*Vitis/microbiology ; *Plant Diseases/microbiology ; *Temperature ; *Microbiota ; *Bacteria/classification/isolation &amp; purification/genetics/growth &amp; development ; Italy ; Yeasts/isolation &amp; purification/classification/growth &amp; development/genetics/physiology ; }, abstract = {Sour rot (SR) is a late-season non-Botrytis rot affecting grapevines, resulting from a complex interplay of microorganisms, including non-Saccharomyces yeasts and acetic acid bacteria. Nonmicrobial factors contributing to disease development encompass vectors (e.g., Drosophila spp.), the presence of wounds or microcracks on grape berry surfaces, and environmental conditions during berry ripening. The microbial complexes within SR-affected grapes exhibit variability among different bioclimates and seasons, with certain microorganisms predominating under specific conditions. This study examined the influence of environmental conditions on the microbiome composition associated with SR-affected grape bunches, utilising data from 41 locations across three distinct Italian bioclimates. We selected nine yeast and two bacterial species frequently isolated from sour-rotted grapes for analysis. The growth responses of these microorganisms to temperature were assessed by categorising them into four ecophysiological clusters. Furthermore, we analysed the distribution of these microorganisms and their respective ecophysiological clusters across the three bioclimates. The results indicate that the microbiomes involved in SR can vary according to the bioclimatic conditions of the grape-growing area. Further research is required to comprehend the ecological requirements of these microorganisms, define their ecological niches to understand their geographical distribution and epidemiology, and enhance SR management strategies.}, }
@article {pmid39871397, year = {2025}, author = {Martin, I and Silverberg, M and Abdelgawad, A and Tanaka, K and Halloran, BA and Nicola, T and Myers, ED and Desai, JP and White, CT and Karabayir, I and Akbilgic, O and Tipton, L and Gentle, SJ and Ambalavanan, N and Peters, BM and Vu, LD and Jain, VG and Lal, CV and Cormier, SA and Pierre, JF and Jilling, T and Talati, AJ and Willis, KA}, title = {The fungal microbiota modulate neonatal oxygen-induced lung injury.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {24}, pmid = {39871397}, issn = {2049-2618}, support = {R21 HD100917/HD/NICHD NIH HHS/United States ; R01 HL156275/HL/NHLBI NIH HHS/United States ; KL2 TR3097/HL/NHLBI NIH HHS/United States ; K08 HL141652/HL/NHLBI NIH HHS/United States ; K08 HL151907/HL/NHLBI NIH HHS/United States ; R01 AI134796/AI/NIAID NIH HHS/United States ; R21 AI163503/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Mice ; Infant, Newborn ; Humans ; *Bronchopulmonary Dysplasia/microbiology ; *Gastrointestinal Microbiome ; *Lung Injury/microbiology ; Female ; Mycobiome ; Oxygen/metabolism ; Disease Models, Animal ; Male ; Fungi/classification/genetics ; Lung/microbiology ; Hyperoxia/microbiology/complications ; Infant, Very Low Birth Weight ; Infant, Premature ; Animals, Newborn ; Mice, Inbred C57BL ; Feces/microbiology ; }, abstract = {BACKGROUND: The immature lungs of very preterm infants are exposed to supraphysiologic oxygen, contributing to bronchopulmonary dysplasia (BPD), a chronic lung disease that is the most common morbidity of prematurity. While the microbiota significantly influences neonatal health, the relationship between the intestinal microbiome, particularly micro-eukaryotic members such as fungi and yeast, and lung injury severity in newborns remains unknown.<br><br>RESULTS: Here, we show that the fungal microbiota modulates hyperoxia-induced lung injury severity in very low birth weight premature infants and preclinical pseudohumanized and altered fungal colonization mouse models. Instead of fungal communities dominated by Candida and Saccharomyces, the first stool microbiomes of infants who developed BPD had less interconnected community architectures with a greater diversity of rarer fungi. After using a pseudohumanized model to show that transfer to the neonatal microbiome from infants with BPD increased the severity of lung injury, we used gain and loss of function approaches to demonstrate that modulating the extent of initial neonatal fungal colonization affected the extent of BPD-like lung injury in mice. We also identified alterations in the murine intestinal microbiome and transcriptome associated with augmented lung injury.<br><br>CONCLUSIONS: These findings demonstrate that features of the initial intestinal fungal microbiome are associated with the later development of BPD in premature neonates and exert a microbiome-driven effect that is transferable and modifiable in murine models, which suggests both causality and a potential therapeutic strategy. Video Abstract.}, }
@article {pmid39871363, year = {2025}, author = {Geng, J and Dong, Y and Huang, H and Wen, X and Xu, T and Zhao, Y and Liu, Y}, title = {Role of nasal microbiota in regulating host anti-influenza immunity in dogs.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {27}, pmid = {39871363}, issn = {2049-2618}, mesh = {Animals ; Dogs ; *Orthomyxoviridae Infections/immunology ; *Microbiota ; *Lung/microbiology/immunology ; *Influenza A virus/immunology ; *Nasal Cavity/microbiology/virology/immunology ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology/immunology ; Disease Models, Animal ; Dog Diseases/microbiology/immunology/virology ; }, abstract = {BACKGROUND: Numerous studies have confirmed a close relationship between the pathogenicity of influenza and respiratory microbiota, but the mechanistic basis for this is poorly defined. Also, the majority of these studies have been conducted on murine models, and it remains unclear how far these findings can be extrapolated from murine models to other animals. Considering that influenza A virus is increasingly recognized as an important canine respiratory pathogen, this study investigated the cross-talk between nasal and lung tissues mediated by microbes and its association with influenza susceptibility in a beagle dog model.<br><br>RESULTS: Using 16S rRNA gene sequencing, combined with comparative transcriptomic, anatomical, and histological examinations, we investigated viral presence, gene expression profiles, and microbiota in the nasal cavity and lung after influenza infection in the beagles with antibiotic-induced nasal dysbiosis. Our data showed that dysbiosis of the nasal microbiome exacerbates influenza-induced respiratory disease and the epithelial barrier disruption, and impairs host antiviral responses in the nasal cavity and lung. Moreover, dysregulation of nasal microbiota exacerbates the influenza-induced disturbance in lung microbiota. Further, we also identified a strain of Lactobacillus plantarum isolated from canine nasal cavity with a significant antiviral effect in vitro, and found that its antiviral activity might be associated with the activation of the interferon (IFN) pathway and modulation of the impaired autophagy flux induced by influenza infection.<br><br>CONCLUSIONS: Our investigation reveals that nasal microbiota dysbiosis exerts a prominent impact on host antiviral responses, inflammation thresholds, and mucosal barrier integrity during influenza infection. Lactobacilli, as part of the nasal microbiota, may contribute to host antiviral defenses by modulating the IFN and autophagy pathways. Collectively, this study underscores the importance of nasal microbiota homeostasis in maintaining respiratory health. Video Abstract.}, }
@article {pmid39871306, year = {2025}, author = {Wang, C and Yang, Y and Xu, X and Wang, D and Shi, X and Liu, L and Deng, Y and Li, L and Zhang, T}, title = {The quest for environmental analytical microbiology: absolute quantitative microbiome using cellular internal standards.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {26}, pmid = {39871306}, issn = {2049-2618}, support = {Basic Research for New Staff//University of Hong Kong/ ; T21-705/20-N//Theme-based Research Scheme/ ; }, mesh = {*Microbiota ; *High-Throughput Nucleotide Sequencing/methods ; *Environmental Microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Humans ; }, abstract = {BACKGROUND: High-throughput sequencing has revolutionized environmental microbiome research, providing both quantitative and qualitative insights into nucleic acid targets in the environment. The resulting microbial composition (community structure) data are essential for environmental analytical microbiology, enabling characterization of community dynamics and assessing microbial pollutants for the development of intervention strategies. However, the relative abundances derived from sequencing impede comparisons across samples and studies.<br><br>RESULTS: This review systematically summarizes various absolute quantification (AQ) methods and their applications to obtain the absolute abundance of microbial cells and genetic elements. By critically comparing the strengths and limitations of AQ methods, we advocate the use of cellular internal standard-based high-throughput sequencing as an appropriate AQ approach for studying environmental microbiome originated from samples of complex matrices and high heterogeneity. To minimize ambiguity and facilitate cross-study comparisons, we outline essential reporting elements for technical considerations, and provide a checklist as a reference for environmental microbiome research.<br><br>CONCLUSIONS: In summary, we propose absolute microbiome quantification using cellular internal standards for environmental analytical microbiology, and we anticipate that this approach will greatly benefit future studies. Video Abstract.}, }
@article {pmid39870972, year = {2025}, author = {Atanasova, K and Knödler, LL and Reindl, W and Ebert, MP and Thomann, AK}, title = {Role of the gut microbiome in psychological symptoms associated with inflammatory bowel diseases.}, journal = {Seminars in immunopathology}, volume = {47}, number = {1}, pages = {12}, pmid = {39870972}, issn = {1863-2300}, support = {DFG-TH2341//German Research Foundation/ ; DFG-RE2706//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Inflammatory Bowel Diseases/psychology/immunology/microbiology ; *Brain-Gut Axis ; Probiotics/therapeutic use ; Animals ; Mental Disorders/etiology/microbiology ; Depression/immunology/etiology ; Prebiotics/administration &amp; dosage ; }, abstract = {The brain-gut axis constitutes the basis for the bidirectional communication between the central nervous system and the gastrointestinal tract driven by neural, hormonal, metabolic, immunological, and microbial signals. Alterations in the gut microbiome composition as observed in inflammatory bowel diseases can modulate brain function and emerging empirical evidence has indicated that interactions among the brain-gut microbiome-axis seem to play a significant role in the pathogenesis of both inflammatory bowel diseases and psychiatric disorders and their comorbidity. Yet, the immunological and molecular mechanisms underlying the co-occurrence of inflammatory bowel diseases and psychological symptoms are still poorly understood. The aim of this narrative review is to highlight contemporary empirical findings supporting a pivotal role of the gut microbiome in the pathophysiology of highly prevalent neuropsychiatric symptoms in inflammatory bowel diseases such as fatigue, depression, and anxiety. Finally, we focus on microbiome modulation as potential treatment option for comorbid neuropsychiatric symptoms in immune-mediated diseases and especially in inflammatory bowel diseases. High-quality clinical trials are required to clarify how microbiome modulation through dietary interventions or probiotic, prebiotic or synbiotic treatment can be used clinically to improve mental health and thus quality of life of patients with inflammatory bowel diseases.}, }
@article {pmid39870942, year = {2025}, author = {Lazaro, A and Tiago, I and Mendes, J and Ribeiro, J and Bernardes, A and Oliveira, F and Regateiro, F and Caramelo, F and Silva, H}, title = {Sleeve Gastrectomy and Gastric Bypass Impact in Patient's Metabolic, Gut Microbiome, and Immuno-inflammatory Profiles-A Comparative Study.}, journal = {Obesity surgery}, volume = {}, number = {}, pages = {}, pmid = {39870942}, issn = {1708-0428}, abstract = {BACKGROUND: Bariatric surgery is the most long-term effective treatment option for severe obesity. The role of gut microbiome (GM) in either the development of obesity or in response to obesity management strategies has been a matter of debate. This study aims to compare the impact of two of the most popular procedures, sleeve gastrectomy (SG) and Roux-en-Y gastric bypass (GB), on metabolic syndrome parameters and gut bacterial microbiome and in systemic immuno-inflammatory response.<br><br>METHODS: A prospective observational study enrolled 24 patients with severe obesity, 14 underwent SG and 10&#xa0;GB. Evaluations before (0&#xa0;M) and 6&#xa0;months (6&#xa0;M) after surgical procedures included clinical and biochemical parameters, expression of 17 immuno-inflammatory genes in peripheral blood leukocytes, and assessment of gut microbiome profile using 16&#xa0;s rRNA next-generation sequencing approach. Statistical significance was set to a p value&#x2009;<&#x2009;0.05 with an FDR&#x2009;<&#x2009;0.1.<br><br>RESULTS: A significant and similar decrease in weight-associated parameters and for most metabolic markers was achieved with both surgeries. Considering the gut microbiome in the whole study population, there was an increase in alpha diversity at family-level taxa. Beta diversity between SG and GB at 6&#xa0;M showed near significant differences (p&#x2009;=&#x2009;0.042) at genus levels. Analysis of the relative abundance of individual taxonomic groups highlighted differences between pre- and post-surgical treatment and between both approaches, namely, a higher representation of family Enterobacteriaceae and genera Veillonella and Enterobacteriaceae_unclassified after GB. Increased expression of immune-inflammatory genes was observed mainly for SG patients.<br><br>CONCLUSIONS: We conclude that SG and GB have similar clinical and metabolic outcomes but different impacts in the gut bacterial microbiome. Results also suggest reactivation of immune response after bariatric surgery.}, }
@article {pmid39870904, year = {2025}, author = {Stenger, PL and Tribollet, A and Guilhaumon, F and Cuet, P and Pennober, G and Jourand, P}, title = {A Multimarker Approach to Identify Microbial Bioindicators for Coral Reef Health Monitoring-Case Study in La Réunion Island.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {179}, pmid = {39870904}, issn = {1432-184X}, mesh = {*Coral Reefs ; *Microbiota ; *Anthozoa/microbiology ; Animals ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Reunion ; *Fungi/classification/genetics/isolation &amp; purification/metabolism ; Seawater/microbiology ; Indian Ocean ; Seasons ; Biodiversity ; Environmental Monitoring/methods ; Islands ; Microalgae/classification/metabolism ; Geologic Sediments/microbiology ; }, abstract = {The marine microbiome arouses an increasing interest, aimed at better understanding coral reef biodiversity, coral resilience, and identifying bioindicators of ecosystem health. The present study is a microbiome mining of three environmentally contrasted sites along the Hermitage fringing reef of La Réunion Island (Western Indian Ocean). This mining aims to identify bioindicators of reef health to assist managers in preserving the fringing reefs of La Réunion. The watersheds of the fringing reefs are small, steeply sloped, and are impacted by human activities with significant land use changes and hydrological modifications along the coast and up to mid-altitudes. Sediment, seawater, and coral rubble were sampled in austral summer and winter at each site. For each compartment, bacterial, fungal, microalgal, and protist communities were characterized by high throughput DNA sequencing methodology. Results show that the reef microbiome composition varied greatly with seasons and reef compartments, but variations were different among targeted markers. No significant variation among sites was observed. Relevant bioindicators were highlighted per taxonomic groups such as the Firmicutes:Bacteroidota ratio (8.4%:7.0%), the genera Vibrio (25.2%) and Photobacterium (12.5%) dominating bacteria; the Ascomycota:Basidiomycota ratio (63.1%:36.1%), the genera Aspergillus (40.9%) and Cladosporium (16.2%) dominating fungi; the genus Ostreobium (81.5%) in Chlorophyta taxon for microalgae; and the groups of Dinoflagellata (63.3%) and Diatomea (22.6%) within the protista comprising two dominant genera: Symbiodinium (41.7%) and Pelagodinium (27.8%). This study highlights that the identified bioindicators, mainly in seawater and sediment reef compartments, could be targeted by reef conservation stakeholders to better monitor La Réunion Island's reef state of health and to improve management plans.}, }
@article {pmid39870817, year = {2025}, author = {Kohn, S and Diament, A and Godneva, A and Dhir, R and Weinberger, A and Reisner, Y and Rossman, H and Segal, E}, title = {Phenome-wide associations of sleep characteristics in the Human Phenotype Project.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {39870817}, issn = {1546-170X}, abstract = {Sleep tests commonly diagnose sleep disorders, but the diverse sleep-related biomarkers recorded by such tests can also provide broader health insights. In this study, we leveraged the uniquely comprehensive data from the Human Phenotype Project cohort, which includes 448 sleep characteristics collected from 16,812 nights of home sleep apnea test monitoring in 6,366 adults (3,043 male and 3,323 female participants), to study associations between sleep traits and body characteristics across 16 body systems. In this analysis, which identified thousands of significant associations, visceral adipose tissue (VAT) was the body characteristic that was most strongly correlated with the peripheral apnea-hypopnea index, as adjusted by sex, age and body mass index (BMI). Moreover, using sleep characteristics, we could predict over 15% of body characteristics, spanning 15 of the 16 body systems, in a held-out set of individuals. Notably, sleep characteristics contributed more to the prediction of certain insulin resistance, blood lipids (such as triglycerides) and cardiovascular measurements than to the characteristics of other body systems. This contribution was independent of VAT, as sleep characteristics outperformed age, BMI and VAT as predictors for these measurements in both male and female participants. Gut microbiome-related pathways and diet (especially for female participants) were notably predictive of clinical obstructive sleep apnea symptoms, particularly sleepiness, surpassing the prediction power of age, BMI and VAT on these symptoms. Together, lifestyle factors contributed to the prediction of over 50% of the sleep characteristics. This work lays the groundwork for exploring the associations of sleep traits with body characteristics and developing predictive models based on sleep monitoring.}, }
@article {pmid39870652, year = {2025}, author = {Koizumi, T and Suzuki, K and Mizuki, I and Kumaishi, K and Ichihashi, Y}, title = {A quantitative prediction method utilizing whole omics data for biosensing.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1928}, pmid = {39870652}, issn = {2045-2322}, support = {21J00762//Japan Society for the Promotion of Science/ ; Technologies for Smart Bio-industry and Agriculture//the Cabinet Office, Goverment of Japan/ ; }, mesh = {*Biosensing Techniques/methods ; *Biomarkers ; Transcriptome ; Humans ; Metabolomics/methods ; Gene Regulatory Networks ; Genomics/methods ; Computational Biology/methods ; Metabolome ; Microbiota/genetics ; Gene Expression Profiling/methods ; }, abstract = {Omics data provide a plethora of quantifiable information that can potentially be used to identify biomarkers targeting the physiological processes and ecological phenomena of organisms. However, omics data have not been fully utilized because current prediction methods in biomarker construction are susceptible to data multidimensionality and noise. We developed OmicSense, a quantitative prediction method that uses a mixture of Gaussian distributions as the probability distribution, yielding the most likely objective variable predicted for each biomarker. Our benchmark test using a transcriptome dataset revealed that OmicSense achieves accurate and robust prediction against background noise without overfitting. Weighted gene co-expression network analysis revealed that OmicSense preferentially utilized hub nodes of the network, indicating the interpretability of the method. Application of OmicSense to single-cell transcriptome, metabolome, and microbiome datasets confirmed high prediction performance (r > 0.8), suggesting applicability to diverse scientific fields. Given the recent rapidly expanding availability of omics data, the developed prediction tool OmicSense, can accelerate the use of omics data as a "biosensor" based on an assemblage of potential biomarkers.}, }
@article {pmid39870608, year = {2025}, author = {Kaur, S and Bran, L and Rudakov, G and Wang, J and Verma, MS}, title = {Propidium Monoazide is Unreliable for Quantitative Live-Dead Molecular Assays.}, journal = {Analytical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.analchem.4c05593}, pmid = {39870608}, issn = {1520-6882}, abstract = {Propidium monoazide (PMA) is a dye that distinguishes between live and dead cells in molecular assays like the Polymerase Chain Reaction (PCR). It works by cross-linking to the DNA of cells that have compromised membranes or extracellular DNA upon photoactivation, making the DNA inaccessible for amplification. Currently, PMA is used to detect viable pathogens and alleviate systemic bias in the microbiome analysis of samples using 16S rRNA gene sequencing. In these applications, treated samples consist of different amounts of dead bacteria and a range of bacterial strains, variables that can affect the performance of PMA and lead to inconsistent findings across various research studies. To evaluate the effectiveness of PMA, we used a sensitive qPCR assay and post-treatment sample concentration to determine PMA cross-linkage and activity accurately under varying sample conditions. We report that PMA is unreliable for viability assays when the concentration and composition of the bacterial mixtures are unknown. PMA is suitable only for qualitatively assessing viability in samples containing a known number of dead microbes or extracellular DNA.}, }
@article {pmid39870349, year = {2025}, author = {Vázquez-Cuesta, S and Olmedo, M and Kestler, M and Álvarez-Uría, A and De la Villa, S and Alcalá, L and Marín, M and Rodríguez-Fernández, S and Sánchez-Martínez, C and Muñoz, P and Bouza, E and Reigadas, E}, title = {Prospective analysis of biomarkers associated with successful faecal microbiota transplantation in recurrent Clostridioides difficile Infection.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2025.01.026}, pmid = {39870349}, issn = {1469-0691}, abstract = {OBJECTIVES: Faecal microbiota transplantation (FMT) is an established treatment for recurrent Clostridioides difficile infection (R-CDI). This study aimed to identify calprotectin and microbiome characteristics as potential biomarkers of FMT success.<br><br>METHODS: We conducted a prospective study of patients who underwent oral FMT (single dose of 4-5 capsules) for R-CDI (January 2018 to December 2022). Samples were collected at three time points: at CDI diagnosis, within 24&#xa0;hours prior to FMT administration, and 30&#xa0;days post-FMT. Calprotectin levels were assessed and the V4 region of the 16S rRNA gene was sequenced to analyse the microbiota composition. Sequencing data analysis and statistical analysis were performed using MOTHUR and R.<br><br>RESULTS: Ninety-seven patients underwent FMT (totalling 105 procedures). A total of 221 samples were processed, including 21 donor samples, 24 capsule contents, and 176 patient faecal samples (39 at diagnosis, 63 pre-FMT, and 74 post-FMT). FMT achieved an overall success rate of 85.1% (86/101 cases). The abundance of Bacteroides, Ruminococcus, Megamonas, and certain Prevotella operational taxonomic units (OTUs) was significantly higher in capsules associated with 100% success compared to less effective capsules. FMT engraftment was observed in 95% of patients with favourable outcomes versus 62% of those with recurrences (p = 0.006). Additionally, a negative correlation was found between calprotectin levels and specific microbial genera, suggesting an association with successful outcomes.<br><br>CONCLUSIONS: This study highlights differences in the evolution of faecal microbiota, bacterial engraftment, and inflammation markers (e.g., calprotectin) between patients with varying FMT outcomes. Potential biomarkers for successful FMT were identified, providing valuable insights for optimizing FMT strategies.}, }
@article {pmid39870330, year = {2025}, author = {Ye, Z and Kini, A and Tan, Q and Woltemate, S and Vital, M and Nikolovska, K and Seidler, U}, title = {Oral Tributyrin Treatment affects Short-Chain Fatty Acid Transport, Mucosal Health, and Microbiome in a Mouse Model of Inflammatory Diarrhea.}, journal = {The Journal of nutritional biochemistry}, volume = {}, number = {}, pages = {109847}, doi = {10.1016/j.jnutbio.2025.109847}, pmid = {39870330}, issn = {1873-4847}, abstract = {Butyrate may decrease intestinal inflammation and diarrhea. This study investigates the impact of oral application of sodium butyrate (NaB) and tributyrin (TB) on colonic butyrate concentration, SCFA transporter expression, colonic absorptive function, barrier properties, inflammation, and microbial composition in the colon of slc26a3[-/-] mice, a mouse model for inflammatory diarrhea. In vivo fluid absorption and bicarbonate secretory rates were evaluated in the cecum and mid-colon of slc26a3[+/+] and slc26a3[-/-] mice before and during luminal perfusion of NaB-containing saline and were significantly stimulated in both slc26a3[+/+] and slc26a3[-/-] colon by NaB. Age-matched slc26a3[+/+] and slc26a3[-/-] mice were either fed chow containing 5% NaB or gavaged twice daily with TB for 21 days. Food and water intake, weight, and stool water content were assessed daily. Stool and tissues were collected for further analysis of SCFA production, barrier integrity, mucosal inflammation, and microbiome analysis by 16S rRNA gene sequencing. 5% NaB diet did not exert a significant impact on SCFA levels, mucus barrier, or inflammatory markers, but significantly increased oral water intake. TB gavage treatment increased the expression of SCFA transporters Mct1 and Smct1, mucus content and microbial diversity, and decreased the neutrophil marker Lipocalin 2, Phospholipase A2, and the antimicrobial peptide Reg3b in the slc26a3[-/-] cecum. However, TB treatment also resulted in an increase in inflammatory markers such as TNFα, Il-1β and CD3e in the wildtype mucosa. While there are some benefits with TB ingestion for barrier properties and microbial composition in the diseased cecum, potentially detrimental effects were noted in the healthy colon.}, }
@article {pmid39870258, year = {2025}, author = {Salberg, S and Macowan, M and Doshen, A and Yamakawa, GR and Sgro, M and Marsland, B and Henderson, L and Mychasiuk, R}, title = {A High Fat, High Sugar Diet Exacerbates Persistent Post-Surgical Pain and Modifies the Brain-Microbiota-Gut Axis in Adolescent Rats.}, journal = {NeuroImage}, volume = {}, number = {}, pages = {121057}, doi = {10.1016/j.neuroimage.2025.121057}, pmid = {39870258}, issn = {1095-9572}, abstract = {Persistent post-surgical pain (PPSP) occurs in a proportion of patients following surgical interventions. Research suggests that specific microbiome components are important for brain development and function, with recent studies demonstrating that chronic pain results in changes to the microbiome. Consumption of a high fat, high sugar (HFHS) diet can drastically alter composition of the microbiome and is a modifiable risk factor for many neuroinflammatory conditions. Therefore, we investigated how daily consumption of a HFHS diet modified the development of PPSP, brain structure and function, and the microbiome. In addition, we identified significant correlations between the microbiome and brain in animals with PPSP. Male and female rats were maintained on a control or HFHS diet. Animals were further allocated to a sham or surgery on postnatal day (p) p35. The von Frey task measured mechanical nociceptive sensitivity at a chronic timepoint (p65-67). Between p68-72 rats underwent in-vivo MRI to examine brain volume and diffusivity. At p73 fecal samples were used for downstream 16s rRNA sequencing. Spearman correlation analyses were performed between individual microbial abundance and MRI diffusivity to determine if specific bacterial species were associated with PPSP-induced brain changes. We found that consumption of a HFHS diet exacerbated PPSP in adolescents. The HFHS diet reduced overall brain volume and increased white and grey matter density. The HFHS diet interacted with the surgical intervention to modify diffusivity in numerous brain regions which were associated with specific changes to the microbiome. These findings demonstrate that premorbid characteristics can influence the development of PPSP and advance our understanding of the contribution that the microbiome has on function of the brain-microbiota-gut axis.}, }
@article {pmid39870251, year = {2025}, author = {Oubohssaine, M and Rabeh, K and Hnini, M}, title = {Symbiosis vs Pathogenesis in Plants: Reflections and Perspectives.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {107333}, doi = {10.1016/j.micpath.2025.107333}, pmid = {39870251}, issn = {1096-1208}, abstract = {Plant-microbe partnerships constitute a complex and intricately woven network of connections that have evolved over countless centuries, involving both cooperation and antagonism. In various contexts, plants and microorganisms engage in mutually beneficial partnerships that enhance crop health and maintain balance in ecosystems. However, these associations also render plants susceptible to a range of pathogens. Understanding the fundamental molecular mechanisms governing these associations is crucial, given the notable susceptibility of plants to external environmental influences. Based on quorum sensing signals, phytohormone, and volatile organic carbon (VOC) production and others molecules, microorganisms influence plant growth, health, and defense responses. This review explores the multifaceted relationships between plants and their associated microorganisms, encompassing mutualism, commensalism, and antagonism. The molecular mechanisms of symbiotic and pathogenic interactions share similarities but lead to different outcomes. While symbiosis benefits both parties, pathogenesis harms the host. Genetic adaptations optimize these interactions, involving coevolution driving process. Environmental factors influence outcomes, emphasizing the need for understanding and manipulation of microbial communities for beneficial results. Research directions include employing multi-omics techniques, functional studies, investigating environmental factors, understanding evolutionary trajectories, and harnessing knowledge to engineer synthetic microbial consortia for sustainable agriculture and disease management.}, }
@article {pmid39869650, year = {2025}, author = {Newberger, DR and Deel, HL and Manter, DK and Vivanco, JM}, title = {Effect of intra- and inter-specific plant interactions on the rhizosphere microbiome of a single target plant at different densities.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0316676}, doi = {10.1371/journal.pone.0316676}, pmid = {39869650}, issn = {1932-6203}, mesh = {*Rhizosphere ; *Microbiota ; *Soil Microbiology ; *Plant Roots/microbiology ; Medicago sativa/microbiology ; Bacteria/classification/genetics ; Brassica/microbiology ; }, abstract = {Root and rhizosphere studies often focus on analyzing single-plant microbiomes, with the literature containing minimum empirical information about the shared rhizosphere microbiome of multiple plants. Here, the rhizosphere of individual plants was analyzed in a microcosm study containing different combinations and densities (1-3 plants, 24 plants, and 48 plants) of cover crops: Medicago sativa, Brassica sp., and Fescue sp. Rhizobacterial beta diversity was reduced by increasing plant density for all plant mixtures. Interestingly, plant density had a significant influence over beta diversity while plant diversity was found to be a less important factor since it did not have a significant change. Regardless of plant neighbor identity or density, a low number of rhizobacteria were strongly associated with each target species. Nonetheless, a few bacterial taxa were shown to have conditional associations such as being enriched within only high plant densities, which may alleviate plant competition between these species. Also, we found evidence of bacterial sharing of nitrogen fixers from alfalfa to fescue. Although rhizosphere bacterial networks had overlapping bacterial modules, the modules showing the largest percentage of the network changed depending on plant neighbor. In summary, this study found that for the most part plants maintained their rhizosphere microbiome despite escalating plant-plant competition.}, }
@article {pmid39869087, year = {2025}, author = {Kumar, NR and Khamar, P and Kannan, R and Padmanabhan, A and Shetty, R and D'Souza, S and Vaidya, T and Sethu, S and Ghosh, A}, title = {Distinct Ocular Surface Microbiome in Keratoconus Patients Correlate With Local Immune Dysregulation.}, journal = {Investigative ophthalmology &amp; visual science}, volume = {66}, number = {1}, pages = {60}, doi = {10.1167/iovs.66.1.60}, pmid = {39869087}, issn = {1552-5783}, mesh = {Humans ; *Keratoconus/microbiology/immunology ; Male ; Female ; *Tears/microbiology ; Adult ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Corneal Topography ; Young Adult ; Cornea/microbiology/immunology ; Bacteria/isolation &amp; purification/genetics ; DNA, Bacterial/analysis/genetics ; Middle Aged ; Flow Cytometry ; Enzyme-Linked Immunosorbent Assay ; }, abstract = {PURPOSE: Keratoconus (KC) is characterized by irregular astigmatism along with corneal stromal weakness and is associated with altered immune status. Tissue resident microbiomes are known to influence the immune status in other organs, but such a nexus has not been described in ocular conditions. Therefore, we examined the ocular surface microbiome of patients with KC and correlated it to the immune cell and tear molecular factor profiles.<br><br>METHODS: Sixty-two patients with KC and 21 healthy controls underwent corneal topography analysis and eye examination followed by a collection of Schirmer's strip, ocular surface wash, and ocular surface swabs. Microbiomes were analyzed by extracting DNA from the swabs followed by 16S rRNA gene V3-V4 amplicon sequencing and analyzed using QIIME. Fifty-two molecular factors from Schirmer's strip tear extracts and 11 immune cells from ocular wash were measured using multiplex ELISA and flow cytometry. Alpha diversity, linear discriminant analysis effect size (LEfSe), relative abundance and receiver operating characteristic - area under the curve (ROC-AUC) analysis were performed. Unsupervised clustering at the genus level with clinical parameters, soluble factors, and immune cells was performed.<br><br>RESULTS: Fifty-two phyla/class, 132 order, 283 family, and 718 genera were identified in our cohort. Alpha diversity indices were comparable between patients with KC and the healthy controls. Dominant phyla across groups were Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes. Alphaproteobacteria increased in KC eyes whereas Actinobacteria, Firmicutes_Bacilli reduced compared with the healthy controls. We found a significant positive correlation of Microbacterium, Cutibacterium, and Brevundimonas genera abundance with keratometry and corneal thickness. Levels of IL-21, IL-9, Fractalkine, and VEGF positively correlated with Tetrasphaera (P < 0.05). &#x3b2;2-microglobulin and CD66bhigh cells correlated with Bacteroides (P < 0.05). CD45+ cells correlated with Escherichia_Shigella (P < 0.02).<br><br>CONCLUSIONS: We discovered a unique microbiome signature of KC which correlated to disease grades and secreted molecular factors and immune cells. Therefore, the altered microbiome on the ocular surface may drive immune dysregulation in KC and provide scope for potential interventions in the future.}, }
@article {pmid39869016, year = {2025}, author = {Martin Fuentes, A}, title = {The role of the microbiome in skin cancer development and treatment.}, journal = {Current opinion in oncology}, volume = {}, number = {}, pages = {}, doi = {10.1097/CCO.0000000000001120}, pmid = {39869016}, issn = {1531-703X}, abstract = {PURPOSE OF REVIEW: Recent research underscores the significant influence of the skin and gut microbiota on melanoma and nonmelanoma skin cancer (NMSC) development and treatment outcomes. This review aims to synthesize current findings on how microbiota modulates immune responses, particularly enhancing the efficacy of immunotherapies such as immune checkpoint inhibitors (ICIs).<br><br>RECENT FINDINGS: The microbiota's impact on skin cancer is multifaceted, involving immune modulation, inflammation, and metabolic interactions. Beneficial strains like Bifidobacterium and Lactobacillus have shown potential in supporting anti-PD-1 and anti-CTLA-4 therapies by promoting T-cell activation and immune surveillance. Evidence from preclinical and clinical studies, including fecal microbiota transplantation (FMT), highlights improved response rates in patients with microbiota-rich profiles. Notably, certain bacterial metabolites, such as inosine, contribute to enhanced antitumor activity by stimulating IFN-&#x3b3; in CD8+ T cells.<br><br>SUMMARY: Understanding the interplay between microbiota and skin cancer treatment opens promising avenues for adjunctive therapies. Probiotic and prebiotic interventions, FMT, and microbiota modulation are emerging as complementary strategies to improve immunotherapy outcomes and address treatment resistance in melanoma and NMSC.}, }
@article {pmid39868896, year = {2025}, author = {Yang, CY and Chang, TC and Lee, YT and Shih, TY and Li, CW and Cheng, CM}, title = {Exploring the Interplay Between Cervicovaginal Microbiome, HPV Infection, and Cervical Intraepithelial Neoplasia in Taiwanese Women.}, journal = {Journal of medical virology}, volume = {97}, number = {2}, pages = {e70190}, doi = {10.1002/jmv.70190}, pmid = {39868896}, issn = {1096-9071}, support = {//This research was supported by the Hygeia Touch Inc. (Taipei, Taiwan) and AllBio Life Incorporation (Taichung, Taiwan)./ ; }, mesh = {Humans ; Female ; *Uterine Cervical Dysplasia/virology/microbiology ; *Vagina/microbiology/virology ; *Microbiota ; *Papillomavirus Infections/virology/microbiology/epidemiology ; Adult ; Taiwan/epidemiology ; Middle Aged ; *Uterine Cervical Neoplasms/virology/microbiology ; Bacteria/classification/isolation &amp; purification/genetics ; Cervix Uteri/microbiology/virology ; Papillomaviridae/genetics/classification/isolation &amp; purification ; Young Adult ; Genotype ; Dysbiosis/microbiology ; }, abstract = {This study examined the relationship between the vaginal microbiome, HPV infection, and cervical intraepithelial neoplasia (CIN) in 173 women. Subjects were grouped by HPV status and cervical lesion severity, ranging from HPV-negative to CIN Grade 2 or higher. Using VALENCIA classification, the study identified different community state types (CSTs) of vaginal microbiota, with CST IV subtypes (Staphylococcus dominated) showing high diversity and increased pathogenic bacteria. Results showed a higher microbial diversity in women with CIN compared to HPV-negative women, with specific microbial profiles like Enterococcus faecalis and Staphylococcus aureus correlating with HPV infection severity. LEfSe and STAMP analyses revealed that particular bacterial species, such as Fannyhessea vaginae and Sneathia vaginalis, could serve as biomarkers for HPV and CIN status. Furthermore, Streptococcus and Staphylococcus were associated with HPV genotypes α7 and α9, respectively. These findings highlight how the composition of vaginal microbiota may influence HPV persistence and CIN progression, emphasizing the need for further research into microbial dysbiosis as a potential target for cervical cancer prevention and management.}, }
@article {pmid39868792, year = {2025}, author = {Zhou, Z and Yang, M and Fang, H and Niu, Y and Lu, J and Ma, Y and Zhang, B and Zhu, H and Chen, P}, title = {Interspecies interactions mediated by arginine metabolism enhance the stress tolerance of Fusobacterium nucleatum against Bifidobacterium animalis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0223524}, doi = {10.1128/spectrum.02235-24}, pmid = {39868792}, issn = {2165-0497}, abstract = {Colorectal cancer (CRC) is a common cancer accompanied by microbiome dysbiosis. Exploration of probiotics against oncogenic microorganisms is promising for CRC treatment. Here, differential microorganisms between CRC and healthy control were analyzed. Antibacterial experiments, whole-genome sequencing, and metabolic network reconstruction were combined to reveal the anti-Fusobacterium nucleatum mechanism, which was verified by co-culture assay and mendelian randomization analysis. Sequencing results showed that F. nucleatum was enriched in CRC, yet Bifidobacterium animalis decreased gradually from healthy to CRC. Additionally, F. nucleatum could be inhibited by B. animalis. Whole-genome sequencing of B. animalis showed high phylogenetic similarity with known probiotic strains and highlighted its functions for amino acid and carbohydrate metabolism. Metabolic network reconstruction demonstrated that cross-feeding and specific metabolites (acidic molecules, arginine) had a great influence on the coexistence relationship. Finally, the arginine supplement enhanced the competitive ability of F. nucleatum against B. animalis, and the mendelian randomization and metagenomic sequencing analysis confirmed the positive relationship among F. nucleatum, arginine metabolism, and CRC. Thus, whole-genome sequencing and metabolic network reconstruction are valuable for probiotic mining and patient dietary guidance.IMPORTANCEUsing probiotics to inhibit oncogenic microorganisms (Fusobacterium nucleatum) is promising for colorectal cancer (CRC) treatment. In this study, whole-genome sequencing and metabolic network reconstruction were combined to reveal the anti-F. nucleatum mechanism of Bifidobacterium animalis, which was verified by co-culture assay and mendelian randomization analysis. The result indicated that the arginine supplement enhanced the competitive ability of F. nucleatum, which may be harmful to F. nucleatum-infected CRC patients. B. animalis is a potential probiotic to relieve this dilemma. Thus, using in silico simulation methods based on flux balance analysis, such as genome-scale metabolic reconstruction, provides valuable insights for probiotic mining and dietary guidance for cancer patients.}, }
@article {pmid39868786, year = {2025}, author = {Engelhart, MJ and Brock, OD and Till, JM and Glowacki, RWP and Cantwell, JW and Clarke, DJ and Wesener, DA and Ahern, PP}, title = {BT1549 coordinates the in vitro IL-10 inducing activity of Bacteroides thetaiotaomicron.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0166924}, doi = {10.1128/spectrum.01669-24}, pmid = {39868786}, issn = {2165-0497}, abstract = {UNLABELLED: The intestine is home to a complex immune system that is engaged in mutualistic interactions with the microbiome that maintain intestinal homeostasis. A variety of immune-derived anti-inflammatory mediators have been uncovered and shown to be critical for maintaining these beneficial immune-microbiome relationships. Notably, the gut microbiome actively invokes the induction of anti-inflammatory pathways that limit the development of microbiome-targeted inflammatory immune responses. Despite the importance of this microbiome-driven immunomodulation, detailed knowledge of the microbial factors that promote these responses remains limited. We have previously established that the gut symbiont Bacteroides thetaiotaomicron stimulates the production of the anti-inflammatory cytokine IL-10 via soluble factors in a Toll-like receptor 2 (TLR2)-MyD88-dependent manner. Here, using TLR2 activity reporter cell lines, we show that the capacity of B. thetaiotaomicron to stimulate TLR2 activity was not critically dependent on either of the canonical heterodimeric forms of TLR2, TLR2/TLR1, or TLR2/TLR6, that typically mediate its function. Furthermore, biochemical manipulation of B. thetaiotaomicron-conditioned media suggests that IL-10 induction is mediated by a protease-resistant or non-proteogenic factor. We next uncovered that deletion of gene BT1549, a predicted secreted lipoprotein, significantly impaired the capacity of B. thetaiotaomicron to induce IL-10, while complementation in trans restored IL-10 induction, suggesting a role for BT1549 in the immunomodulatory function of B. thetaiotaomicron. Collectively, these data provide molecular insight into the pathways through which B. thetaiotaomicron operates to promote intestinal immune tolerance and symbiosis.<br><br>IMPORTANCE: Intestinal homeostasis requires the establishment of peaceful interactions between the gut microbiome and the intestinal immune system. Members of the gut microbiome, like the symbiont Bacteroides thetaiotaomicron, actively induce anti-inflammatory immune responses to maintain mutualistic relationships with the host. Despite the importance of such interactions, the specific microbial factors responsible remain largely unknown. Here, we show that B. thetaiotaomicron, which stimulates Toll-like receptor 2 (TLR2) to drive IL-10 production, can stimulate TLR2 independently of TLR1 or TLR6, the two known TLR that can form heterodimers with TLR2 to mediate TLR2-dependent responses. Furthermore, we show that IL-10 induction is likely mediated by a protease-resistant or non-proteogenic factor, and that this requires gene BT1549, a predicted secreted lipoprotein and peptidase. Collectively, our work provides insight into the molecular dialog through which B. thetaiotaomicron coordinates anti-inflammatory immune responses. This knowledge may facilitate future strategies to promote such responses for therapeutic purposes.}, }
@article {pmid39868785, year = {2025}, author = {Ma, L and Hahn, ME and Karchner, SI and Nacci, D and Clark, BW and Apprill, A}, title = {Environmental and population influences on mummichog (Fundulus heteroclitus) gut microbiomes.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0094724}, doi = {10.1128/spectrum.00947-24}, pmid = {39868785}, issn = {2165-0497}, abstract = {UNLABELLED: The mummichog, Fundulus heteroclitus, an abundant estuarine fish broadly distributed along the eastern coast of North America, has repeatedly evolved tolerance to otherwise lethal levels of aromatic hydrocarbon exposure. This tolerance is linked to reduced activation of the aryl hydrocarbon receptor (AHR) signaling pathway. In other animals, the AHR has been shown to influence the gastrointestinal-associated microbial community, particularly when activated by the model toxic pollutant 3,3',4,4',5-pentachlorobiphenyl (PCB-126) and other dioxin-like compounds. To understand host population and PCB-126 exposure effects on mummichog gut microbiota, we sampled two populations of wild fish, one from a PCB-contaminated environment (New Bedford Harbor, MA, USA) and the other from a much less polluted location (Scorton Creek, MA, USA), as well as laboratory-reared F2 generation fish originating from each of these populations. We examined the microbes associated with the gut of these fish using amplicon sequencing of bacterial and archaeal small subunit ribosomal RNA genes. Fish living in the PCB-polluted site had high microbial alpha and beta diversity compared to fish from the low PCB site. These differences between wild fish were not present in laboratory-reared F2 fish that originated from the same populations. Microbial compositional differences existed between wild and lab-reared fish, with the wild fish dominated by Vibrionaceae and the lab-reared fish by Enterococceae. These results suggest that mummichog habitat and/or environmental conditions have a stronger influence on the mummichog gut microbiome compared to population or hereditary-based influences. Mummichog are important eco-evolutionary model organisms; this work reveals their importance for exploring host-environmental-microbiome dynamics.<br><br>IMPORTANCE: The mummichog fish, a common resident of North America's east coast estuaries, has evolved the ability to survive in waters contaminated with toxic chemicals that would typically be deadly. Our study investigates how living in and adapting to these toxic environments may affect their gut microbiomes. We compared mummichogs from a polluted area in Massachusetts with those from a non-polluted site and found significant differences in their gut microbes. Interestingly, when we raised the next generation of these fish in a lab, these differences disappeared, suggesting that the environment plays a more crucial role in shaping the gut microbiome than genetics. Understanding these changes helps shed light on how animals and their associated microbiomes adapt to pollution, which can inform conservation efforts and our broader understanding of environmental impacts on host-microbe dynamics.}, }
@article {pmid39868783, year = {2025}, author = {Zhao, H and Wang, C and Narsing Rao, MP and Rafiq, M and Luo, G and Li, S and Kang, Y-Q}, title = {Effects of vaginal microbiota on in vitro fertilization outcomes in women with different infertility causes.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0125524}, doi = {10.1128/spectrum.01255-24}, pmid = {39868783}, issn = {2165-0497}, abstract = {UNLABELLED: Backed by advancements in technologies like microbial sequencing, many studies indicate that the vaginal microbiome is a key marker of female reproductive health. However, further studies are still needed to investigate the correlation between vaginal microbiota (VMB) and outcomes of assisted reproductive technology (ART). Therefore, this study compared the VMB of two types of infertile women undergoing in vitro fertilization (IVF) with normal control women during the implantation window period and investigated the effects of VMB characteristics on IVF outcomes. Vaginal swabs from IVF patients (n = 85) were collected before embryo transfer (ET), and vaginal swabs from normal control women (n = 37) were collected during the 6-8 days of ovulation detection. Results showed differences in the vaginal community structure between infertile women with polycystic ovary syndrome (PCOS) and with tubal factor infertility (TFI) undergoing IVF treatment. The results revealed a higher relative abundance of Lactobacillus iners in the non-pregnant group compared with the pregnant group. The results also demonstrated the abundance of Pseudomonas spp. in both non-pregnant groups of infertile women. The findings suggested that the VMB composition affects the IVF outcomes and that the pre-ET high abundance of L. iners may potentially indicate an IVF failure. The abundance of Pseudomonas spp. in the vagina may be an adverse factor for ART pregnancy.<br><br>IMPORTANCE: Many studies suggest that vaginal microbiota (VMB) may affect in vitro fertilization-embryo transfer (IVF-ET) outcomes. Assessing VMB before embryo transfer can optimize timing for better assisted reproductive technology (ART) results. This study examined VMB distribution in infertile women undergoing ART using 16S rRNA sequencing. Results revealed that VMB structure impacted ART outcomes in women with polycystic ovary syndrome (PCOS) and tubal factor infertility (TFI) before embryo transfer ([less than or equal to] 24 hours). Lactobacillus iners and Pseudomonas spp. were identified as adverse factors for post-ET pregnancy. The study also showed differences in pre-ET VMB between normal women and women with PCOS and TFI during the ovulatory window. These findings highlight the importance of considering VMB composition to optimize embryo transfer timing and personalize ART treatment based on infertility type, improving the chances of success.}, }
@article {pmid39868782, year = {2025}, author = {Supina, BSI and McCutcheon, JG and Peskett, SR and Stothard, P and Dennis, JJ}, title = {A flagella-dependent Burkholderia jumbo phage controls rice seedling rot and steers Burkholderia glumae toward reduced virulence in rice seedlings.}, journal = {mBio}, volume = {}, number = {}, pages = {e0281424}, doi = {10.1128/mbio.02814-24}, pmid = {39868782}, issn = {2150-7511}, abstract = {Bacteriophages (phages) are being investigated as potential biocontrol agents for the suppression of bacterial diseases in cultivated crops. Jumbo bacteriophages, which possess genomic DNA larger than 200 kbp, generally have a broader host range than other phages and therefore would be useful as biocontrol agents against a wide range of bacterial strains. Thus, the characterization of novel jumbo phages specific for agricultural pathogens would be of importance for the development of phage biocontrol strategies. Herein, we demonstrate that phage S13 requires Burkholderia glumae flagella for its attachment and infection and that loss of B. glumae flagella prevents S13 cellular lysis. As flagella is a known virulence factor, loss of flagella results in a surviving population of B. glumae with reduced virulence. Further experimentation demonstrates that phage S13 can protect rice plants from B. glumae-sponsored destruction in a rice seedling model of infection.IMPORTANCEBacterial plant pathogens threaten many major food crops and inflict large agricultural losses worldwide. B. glumae is a bacterial plant pathogen that causes diseases such as rot, wilt, and blight in several food major crops including rice, tomato, hot pepper, and eggplant. B. glumae infects rice during all developmental stages, causing diseases such as rice seedling rot and bacterial panicle blight (BPB). The B. glumae incidence of rice plant infection is predicted to increase with warming global temperatures, and several different control strategies targeting B. glumae are being explored. These include chemical and antibiotic soil amendment, microbiome manipulation, and the use of partially resistant rice cultivars. However, despite rice growth amelioration, the treatment options for B. glumae plant infections remain limited to cultural practices. Alternatively, phage biocontrol represents a promising new method for eliminating B. glumae from crop soils and improving rice yields.}, }
@article {pmid39868697, year = {2025}, author = {McDonald, HG and Reagan, AM and Faisal, ASM and Goettl, R and Wang, C and Hoyd, R and Spakowicz, D and Evers, BM and Kim, J and Bhakta, AS}, title = {Survival Disparity and the Unique Genomic and Microbiome Profiles of Colon Cancer in Appalachian Kentucky.}, journal = {Journal of the American College of Surgeons}, volume = {}, number = {}, pages = {}, doi = {10.1097/XCS.0000000000001299}, pmid = {39868697}, issn = {1879-1190}, abstract = {BACKGROUND: Colon cancer is a leading cause of mortality in Appalachian Kentucky. Studies suggest that the microbiome may influence cancer outcomes. We investigate differential gene expression, the tumor microbiome, and the association between the two as potential drivers of disparities in colon cancer outcomes.<br><br>STUDY DESIGN: This study analyzed patients diagnosed with colon adenocarcinoma between 2010-2023. Demographic data were extracted from Kentucky Cancer Registry. Somatic mutations and significantly mutated genes were identified using Fischer's exact T-test. RNASeq data was processed for gene expression analysis and Holm-Bonferroni method was used to adjust p-values for multiple comparisons. The STAR aligner, (exotic)v2.1 pipeline, and KrakenUniq database were used to classify microbes in human samples. The R package (exotic) was then used to decontaminate the results.<br><br>RESULTS: The final cohort included 2276 patients, 321 of which had available somatic mutation sequencing data. Demographic differences between Appalachian and non-Appalachian patients included marital status (P = 0.0005), race (P < 0.0001), insurance status, (P = 0.0005), BMI (P = 0.001), type 2 diabetes (P < 0.0001) and Charlson Comorbidity Index (CCI; P = 0.03). There was no difference in gene mutation frequency. There was differential expression of 228 genes. Differential abundance analysis revealed differences in 381 bacterial species. Importantly, 3 microbiota significantly correlated with survival disparities between Appalachian and non-Appalachian patients: C. cadaveris (adjusted P = 0.009), L. salivarius (adjusted P = 0.048), and S. wadsworthensis (adjusted P = 0.009).<br><br>CONCLUSION: This is the first report of the distinct tumor microbiome in Appalachian Kentucky and its impact on survival. Further studies are needed to better characterize the unique tumor and gut microbiome of Appalachian patients with colon cancer.}, }
@article {pmid39868694, year = {2025}, author = {Do, K and Mehta, S and Wagner, R and Griffin, TJ and Jagtap, PD}, title = {A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {215}, pages = {}, doi = {10.3791/67581}, pmid = {39868694}, issn = {1940-087X}, mesh = {Humans ; *Proteomics/methods ; *Microbiota/physiology ; *Workflow ; *Computational Biology/methods ; Mass Spectrometry/methods ; Host Microbial Interactions/physiology ; }, abstract = {Clinical metaproteomics reveals host-microbiome interactions underlying diseases. However, challenges to this approach exist. In particular, the characterization of microbial proteins present in low abundance relative to host proteins is difficult. Other significant challenges are attributed to using very large protein sequence databases, which impedes sensitivity and accuracy during peptide and protein identification from mass spectrometry data in addition to retrieving taxonomy and functional annotations and performing statistical analysis. To address these problems, we present an integrated bioinformatics workflow for mass spectrometry-based metaproteomics that combines custom protein sequence database generation, peptide-spectrum match generation and verification, quantification, taxonomic and functional annotations, and statistical analysis. This workflow also offers characterization of human proteins (while prioritizing microbial proteins), thus offering insights into host-microbe dynamics in disease. The tools and workflow are deployed in the Galaxy ecosystem, enabling the development, optimization, and dissemination of these computational resources. We have applied this workflow for metaproteomic analysis of numerous clinical sample types, such as nasopharyngeal swabs and bronchoalveolar lavage fluid. Here, we demonstrate its utility via the analysis of residual fluid from cervical swabs. The complete workflow and accompanying training resources are accessible on the Galaxy Training Network to equip non-experts and experienced researchers with the necessary knowledge and tools to analyze their data.}, }
@article {pmid39868677, year = {2025}, author = {Pradhan, S and Bhattacharjee, A and Dubey, S and Sharma, S}, title = {Ameliorating salt stress in tomato by a top-down approach of acclimatizing the rhizosphere microbiome.}, journal = {Physiologia plantarum}, volume = {177}, number = {1}, pages = {e70071}, doi = {10.1111/ppl.70071}, pmid = {39868677}, issn = {1399-3054}, support = {//Council of Scientific and Industrial Research, India/ ; CRG/2023/000193//Anusandhan National Research Foundation/ ; }, mesh = {*Rhizosphere ; *Solanum lycopersicum/microbiology/physiology/genetics/growth &amp; development ; *Microbiota ; *Salt Stress ; *Soil Microbiology ; Plant Roots/microbiology/physiology ; Acclimatization ; Gene Expression Regulation, Plant ; }, abstract = {Soil salinization adversely impacts plant and soil health. While amendment with chemicals is not sustainable, the application of bioinoculants suffers from competition with indigenous microbes. Hence, microbiome-based rhizosphere engineering, focussing on acclimatization of rhizosphere microbiome under selection pressure to facilitate plant growth, exhibits promise. This study aimed to acclimatize a salt-susceptible tomato cultivar to high salt concentration through a microbiome-based top-down approach of rhizosphere engineering. Multiple passaging of the rhizosphere microbiome of the cultivar was performed for twelve plant growth cycles in the presence of increasing salt stress. The rhizosphere microbiome of the phenotypically best-grown plant under stress was transferred as inoculum to the next plant growth cycle. Plant growth attributes and stress marker levels were assessed, expression levels of plant salt stress-responsive genes were examined, and the bacterial community composition in the initial and final plant growth cycles was analysed. Rhizosphere microbiome inoculation promoted plant growth under increasing salt concentrations. Stress markers were reduced in plants inoculated with an acclimatized microbiome, while the root architecture was enhanced, indicating salt tolerance. The salt stress-responsive genes were downregulated in salt-treated plants, whereas upregulation of these genes was observed upon microbiome inoculation. The relative abundance of Exiguobacterium, Arthrobacter, and Lysobacter was higher in microbiome-treated plants under salt stress compared to the salt-treated plants without microbiome inoculation. The strategy of acclimatizing the rhizosphere microbiome of a salt-susceptible tomato cultivar was successfully implemented for stress amelioration and plant growth promotion, thereby offering a sustainable means with immense potential for application in other crops.}, }
@article {pmid39868670, year = {2025}, author = {Preidis, GA}, title = {The neonatal gut microbiome in health and disease.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2457499}, doi = {10.1080/19490976.2025.2457499}, pmid = {39868670}, issn = {1949-0984}, }
@article {pmid39868593, year = {2025}, author = {Jia, J and Guo, J and Yan, C and Gu, Y and Xia, X}, title = {Oyster powder supplementation enhances immune function in mice partly through modulating the gut microbiota and arginine metabolism.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4fo06068g}, pmid = {39868593}, issn = {2042-650X}, abstract = {Oysters are well-known for their health benefits such as immuno-modulatory functions. The intestinal microbiome serves as a key mediator between diet and immune regulation. This study aimed to investigate whether oyster consumption could alleviate cyclophosphamide (Cy)-induced immunosuppression by promoting intestinal homeostasis. In mice treated with Cy, a significant decrease in immune cells and cytokines was observed. In contrast, mice supplemented with oyster powder demonstrated elevated numbers of immune cells in the spleen and small intestine, as well as enhanced serum production of IL-1β, IL-2, TNF-α, and IFN-γ. Furthermore, oyster consumption improved the composition of the gut microbiota by promoting beneficial bacteria and inhibiting harmful ones. Metabolomics analysis revealed that oyster powder treatment significantly enhanced the arginine biosynthesis pathway, and further analysis found that the consumption of oysters led to increased arginine levels. Correlation analysis showed a significant positive correlation between L-arginine and immune-related markers. Collectively, these findings suggest that oyster consumption may enhance immunity by modulating the gut microbiota and boosting arginine biosynthesis pathways. Dietary oyster consumption could be an effective strategy to support immune health.}, }
@article {pmid39868555, year = {2025}, author = {Chatterjee, J and Qi, X and Mu, R and Li, X and Eligator, T and Ouyang, M and Bozeman, SL and Rodgers, R and Aggarwal, S and Campbell, DE and Schriefer, LA and Baldridge, MT and Gutmann, DH}, title = {Intestinal Bacteroides drives glioma progression by regulating CD8+ T cell tumor infiltration.}, journal = {Neuro-oncology}, volume = {}, number = {}, pages = {}, doi = {10.1093/neuonc/noaf024}, pmid = {39868555}, issn = {1523-5866}, abstract = {BACKGROUND: The intestinal microbiota regulates normal brain physiology and the pathogenesis of several neurological disorders. While prior studies suggested that this regulation operates through immune cells, the underlying mechanisms remain unclear. Leveraging two well characterized murine models of low-grade glioma (LGG) occurring in the setting of the neurofibromatosis type 1 (NF1) cancer predisposition syndrome, we sought to determine the impact of the gut microbiome on optic glioma progression.<br><br>METHODS: Nf1-mutant mice genetically engineered to develop optic pathway gliomas (Nf1OPG mice) by 3 months of age were reared under germ-free (GF) conditions, treated with specific cocktails of antibiotics, or given fecal matter transplants (FMTs). Intestinal microbial species were identified by 16S genotyping. Neutralizing TGF&#x3b2; antibodies were delivered systemically, while in vitro experiments used isolated murine microglia and T cells. Single cell RNA sequencing analysis was performed using established methods.<br><br>RESULTS: Nf1 OPG mice raised in a GF environment or postnatally treated with vancomycin did not harbor optic gliomas or exhibit OPG-induced retinal nerve fiber layer thinning, which was reversed following conventionally raised mouse FMT or colonization with Bacteroides species. Moreover, this intestinal microbiota-regulated gliomagenesis was mediated by circulating TGF&#x3b2;, such that systemic TGF&#x3b2; neutralization reduced Nf1-OPG growth. TGF&#x3b2; was shown to act on tumor-associated monocytes to induce Ccl3 expression and recruit CD8+ T cells necessary for glioma growth.<br><br>CONCLUSIONS: Taken together, these findings establish, for the first time, a mechanistic relationship between Bacteroides in the intestinal microbiome and NF1-LGG pathobiology, suggesting both future predictive risk assessment strategies and therapeutic opportunities.}, }
@article {pmid39868371, year = {2024}, author = {Heidary, M and Akrami, S and Madanipour, T and Shakib, NH and Mahdizade Ari, M and Beig, M and Khoshnood, S and Ghanavati, R and Bazdar, M}, title = {Effect of Helicobacter pylori-induced gastric cancer on gastrointestinal microbiota: a narrative review.}, journal = {Frontiers in oncology}, volume = {14}, number = {}, pages = {1495596}, pmid = {39868371}, issn = {2234-943X}, abstract = {Helicobacter pylori (H. pylori) infection is a typical microbial agent that interferes with the complex mechanisms of gastric homeostasis by disrupting the balance between the host gastric microbiota and mucosa-related factors, ultimately leading to inflammatory changes, dysbiosis, and gastric cancer (GC). We searched this field on the basis of PubMed, Google Scholar, Web of Science, and Scopus databases. Most studies show that H. pylori inhibits the colonization of other bacteria, resulting in a less variety of bacteria in the gastrointestinal (GI) tract. When comparing the patients with H. pylori-positive and H. pylori-negative GC, the composition of the gastric microbiome changes with increasing abundance of H. pylori (where present) in the gastritis stage, whereas, as the gastric carcinogenesis cascade progresses to GC, oral and intestinal-type pathogenic microbial strains predominate. H. pylori infection induces a premalignant milieu of atrophy and intestinal metaplasia, and the resulting change in gastric microbiota appears to play an important role in gastric carcinogenesis. The effect of H. pylori-induced GC on GI microbiota is discussed in this review.}, }
@article {pmid39868335, year = {2025}, author = {Roos, M and Bunga, S and Tan, A and Maissy, E and Skola, D and Richter, A and Whittaker, DS and Desplats, P and Zarrinpar, A and Conrad, R and Kuersten, S}, title = {Optimizing mouse metatranscriptome profiling by selective removal of redundant nucleic acid sequences.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.15.632452}, pmid = {39868335}, issn = {2692-8205}, abstract = {UNLABELLED: Metatranscriptome (MetaT) sequencing is a critical tool for profiling the dynamic metabolic functions of microbiomes. In addition to taxonomic information, MetaT also provides real-time gene expression data of both host and microbial populations, thus permitting authentic quantification of the functional (enzymatic) output of the microbiome and its host. The main challenge to effective and accurate MetaT analysis is the removal of highly abundant rRNA transcripts from these complex mixtures of microbes, which can number in the thousands of individual species. Regardless of methodology for rRNA depletion, the design of rRNA removal probes based solely upon taxonomic content of the microbiome typically requires very large numbers of individual probes, making this approach complex to commercially manufacture, costly, and frequently technically infeasible. In previous work [1], we designed a set of depletion probes for human stool samples using a design strategy based solely on sequence abundance, completely agnostic of the microbiomal species present. Here, we show that the human-based probes are less effective when used with mouse cecal samples. However, adapting additional rRNA depletion probes specifically to cecal content provides both greater efficiency and consistency for MetaT analysis of mouse samples.<br><br>IMPORTANCE: Sequencing total RNA from microbiome samples is seriously impaired by the overwhelming proportion of rRNA to mRNA content. As much as 99% of sequencing reads can be assigned to the rRNA content, thus removal of these abundant transcripts is critical to MetaT analysis. The use of Ribo Zero Plus rRNA depletion probes designed for human gut microbiomes proved to be less effective and more inconsistent across mouse cecal donor samples, a common experimental system for microbiome studies. In the present work, we have extended and refined a taxonomically-neutral probe design method for mouse cecal content. The additional probes were carefully chosen to limit the number needed for effective depletion to reduce both the cost and risk of introducing bias to MetaT analysis. Our results demonstrate this method as efficient and consistent for rRNA removal in mouse cecal samples, thus providing a significant increase in the number of mRNA-rich sequencing reads for MetaT analysis.}, }
@article {pmid39868296, year = {2025}, author = {Guccione, C and Sfiligoi, I and Gonzalez, A and Shaffer, JP and Kazachkova, M and Weng, Y and McDonald, D and Shah, SC and Minot, SS and Paulson, T and Grady, WM and Alexandrov, LB and Knight, R and Curtius, K}, title = {Community assembly modeling of microbial evolution within Barrett's esophagus and esophageal adenocarcinoma.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.14.633020}, pmid = {39868296}, issn = {2692-8205}, abstract = {Mathematical modeling of somatic evolution, a process impacting both host cells and microbial communities in the human body, can capture important dynamics driving carcinogenesis. Here we considered models for esophageal adenocarcinoma (EAC), a cancer that has dramatically increased in incidence over the past few decades in Western populations, with high case fatality rates due to late-stage diagnoses. Despite advancements in genomic analyses of the precursor Barrett's esophagus (BE), prevention of late-stage EAC remains a significant clinical challenge. Previous microbiome studies in BE and EAC have focused on quantifying static microbial abundance differences rather than evolutionary dynamics. Using whole genome sequencing data from esophageal tissues, we first applied a robust bioinformatics pipeline to extract non-host DNA reads, mapped these putative reads to microbial taxa, and retained those taxa with high genomic coverage. When applying mathematical models of microbial evolution to sequential stages of progression to EAC, we observed evidence of neutral dynamics in community assembly within normal esophageal tissue and BE, but not EAC. In a case-control study of BE patients who progressed to EAC cancer outcomes (CO) versus those who had non-cancer outcomes (NCO) during follow-up (mean=10.5 years), we found that Helicobacter pylori deviated significantly from the neutral expectation in BE NCO, suggesting that factors related to H. pylori or H. pylori infection itself may influence EAC risk. Additionally, simulations incorporating selection recapitulated non-neutral behaviors observed in the datasets. Formally modeling dynamics during progression holds promise in clinical applications by offering a deeper understanding of microbial involvement in cancer development.}, }
@article {pmid39868280, year = {2025}, author = {Coskun, FS and Quick, J and Toprak, E}, title = {A Simple, Low-Cost, and Efficient Protocol for Rapid Isolation of Pathogenic Bacteria from Human Blood.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.14.633023}, pmid = {39868280}, issn = {2692-8205}, abstract = {Bacteremia is a serious clinical condition in which pathogenic bacteria enter the bloodstream, putting patients at risk of septic shock and necessitating antibiotic treatment. Choosing the most effective antibiotic is crucial not only for resolving the infection but also for minimizing side effects, such as dysbiosis in the healthy microbiome and reducing the selection pressure for antibiotic resistance. This requires prompt identification of the pathogen and antibiotic susceptibility testing, yet these processes are inherently slow in standard clinical microbiology labs due to reliance on growth-based assays. Although alternative methods exist, they are rarely adopted in clinical settings because they involve complex protocols and high costs for training and infrastructure. Here, we present an optimized, simple protocol for rapidly and efficiently isolating bacterial pathogens from blood without altering typical laboratory workflows. Our method is cost-effective and compatible with commonly available laboratory instruments, offering the advantage of isolating bacterial cells directly, which bypasses the delays associated with traditional blood culture methods and enables faster diagnostic results. The protocol achieved over 70% efficiency within 30 minutes, remained effective at low bacterial concentrations (1-10 bacteria/0.3 mL blood), and preserved bacterial viability with no notable change in growth lag times. We validated the protocol on several clinically relevant bacterial strains, including Escherichia coli, Klebsiella pneumoniae , and Staphylococcus aureus . These findings highlight our protocol's potential utility in clinical and research settings, facilitating timely cultures and minimizing diagnostic delays.}, }
@article {pmid39868271, year = {2025}, author = {Lucas, LN and Mallikarjun, J and Cattaneo, LE and Gangwar, B and Zhang, Q and Kerby, RL and Stevenson, D and Rey, FE and Amador-Noguez, D}, title = {Investigation of Bile Salt Hydrolase Activity in Human Gut Bacteria Reveals Production of Conjugated Secondary Bile Acids.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.16.633392}, pmid = {39868271}, issn = {2692-8205}, abstract = {Through biochemical transformation of host-derived bile acids (BAs), gut bacteria mediate host-microbe crosstalk and sit at the interface of nutrition, the microbiome, and disease. BAs play a crucial role in human health by facilitating the absorption of dietary lipophilic nutrients, interacting with hormone receptors to regulate host physiology, and shaping gut microbiota composition through antimicrobial activity. Bile acid deconjugation by bacterial bile salt hydrolase (BSH) has long been recognized as the first necessary BA modification required before further transformations can occur. Here, we show that BSH activity is common among human gut bacterial isolates spanning seven major phyla. We observed variation in both the extent and the specificity of deconjugation of BAs among the tested taxa. Unexpectedly, we discovered that certain strains were capable of directly dehydrogenating conjugated BAs via hydroxysteroid dehydrogenases (HSD) to produce conjugated secondary BAs. These results challenge the prevailing notion that deconjugation is a prerequisite for further BA modifications and lay a foundation for new hypotheses regarding how bacteria act individually or in concert to diversify the BA pool and influence host physiology.}, }
@article {pmid39868257, year = {2025}, author = {Ekregbesi, P and Seibert, B and Parish, MA and Flores-Garcia, Y and Creisher, PS and Hoffmann, JP and Liu, J and Brayton, C and Zavala, F and Klein, SL}, title = {Multi-System Dysregulation in Placental Malaria Contributes to Adverse Perinatal Outcomes in Mice.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.15.633265}, pmid = {39868257}, issn = {2692-8205}, abstract = {Sequestration of Plasmodium parasites in the placental vasculature causes increased morbidity and mortality in pregnant compared to non-pregnant patients in malaria- endemic regions. In this study, outbred pregnant CD1 mice with semi allogeneic fetuses were infected with transgenic Plasmodium berghei or mock-inoculated by mosquito bite at either embryonic day (E) 6 (first trimester-equivalent) or 10 (second trimester- equivalent) and compared with non-pregnant females. P. berghei -infected mosquitoes had greater biting avidity for E10 dams than uninfected mosquitoes, which was not apparent for E6 dams nor non-pregnant females. Infected E10 dams had greater numbers of parasites than E6 dams in the uterus and spleen, but not in the blood or liver. While parasites were found in placentas, no parasites were present in fetuses. Maternal infection at E6 caused greater maternal morbidity, with greater rates of fetal reabsorption and stillbirths than at E10. Infection at E10 caused adverse offspring outcomes, including growth restriction. To identify possible mechanisms of adverse offspring outcomes, E10 dams were euthanized during peak parasitemia (8 days post infection), and outcomes were compared with mock-infected dams. P. berghei caused significant systemic maternal immune activation with elevated circulating lymphocytes, eosinophils, and neutrophils and splenic cytokine concentrations. P. berghei infection at E10 increased corticosterone and decreased progesterone concentrations, which could contribute to adverse perinatal outcomes through immunomodulation. There were limited changes in the maternal fecal microbiome after P. berghei infection. Mosquito bite infection of outbred dams with P. berghei causes placental malaria and provides a novel, tractable model to investigate therapeutic treatments.}, }
@article {pmid39868147, year = {2025}, author = {Britton, GJ and Mogno, I and Chen-Liaw, A and Plitt, T and Helmus, D and Bongers, G and Brough, I and Colmenero, P and Lam, LH and Bullers, SJ and Penkava, F and Reyes-Mercedes, P and Braun, J and Jacobs, J and Desch, AN and Gevers, D and Simmons, S and Filer, A and Taylor, PC and Bowness, P and Huttenhower, C and Littman, DR and Dubinsky, MC and Raza, K and Tankou, SK and Faith, JJ}, title = {Inflammatory disease microbiomes share a functional pathogenicity predicted by C-reactive protein.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.14.633015}, pmid = {39868147}, issn = {2692-8205}, abstract = {We examine disease-specific and cross-disease functions of the human gut microbiome by colonizing germ-free mice, at risk for inflammatory arthritis, colitis, or neuroinflammation, with over 100 human fecal microbiomes from subjects with rheumatoid arthritis, ankylosing spondylitis, multiple sclerosis, ulcerative colitis, Crohn's disease, or colorectal cancer. We find common inflammatory phenotypes driven by microbiomes from individuals with intestinal inflammation or inflammatory arthritis, as well as distinct functions specific to microbiomes from multiple sclerosis patients. Inflammatory disease in mice colonized with human microbiomes correlated with systemic inflammation, measured by C-reactive protein, in the human donors. These cross-disease patterns of human microbiome pathogenicity mirror features of the inflammatory diseases, including therapeutic targets and the presence or absence of systemic inflammation, suggesting shared and disease-specific mechanisms by which the microbiome is shaped and drives pathogenic inflammatory responses.}, }
@article {pmid39868118, year = {2025}, author = {Kennedy, EA and Weagley, JS and Kim, AH and Antia, A and DeVeaux, AL and Baldridge, MT}, title = {Microbiota assembly of specific pathogen-free neonatal mice.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.14.633035}, pmid = {39868118}, issn = {2692-8205}, abstract = {BACKGROUND: Neonatal mice are frequently used to model diseases that affect human infants. Microbial community composition has been shown to impact disease progression in these models. Despite this, the maturation of the early-life murine microbiome has not been well-characterized. We address this gap by characterizing the assembly of the bacterial microbiota of C57BL/6 and BALB/c litters from birth to adulthood across multiple independent litters.<br><br>RESULTS: The fecal microbiome of young pups is simple, dominated by only a few pioneering bacterial taxa. These taxa are present at low levels in the microbiota of multiple maternal body sites, precluding a clear identification of maternal source. The pup microbiota begins diversifying after fourteen days, coinciding with the beginning of coprophagy and the consumption of solid foods. Pup stool bacterial community composition and diversity are not significantly different from dams from day 21 onwards. Short-read shotgun sequencing-based metagenomic profiling of young pups enabled the assembly of metagenome-assembled genomes for strain-level analysis of these pioneer Ligilactobacillus, Streptococcus, and Proteus species.<br><br>CONCLUSIONS: Assembly of the murine microbiome occurs over the first weeks of postnatal life and is largely complete by day 21. This detailed view of bacterial community development across multiple commonly employed mouse strains informs experimental design, allowing researchers to better target interventions before, during, or after the maturation of the bacterial microbiota. The source of pioneer bacterial strains appears heterogeneous, as the most abundant taxa identified in young pup stool were found at low levels across multiple maternal body sites, suggesting diverse routes for seeding of the murine microbiome.}, }
@article {pmid39867950, year = {2025}, author = {Liu, C and Yin, Q and Wu, Z and Li, W and Huang, J and Chen, B and Yang, Y and Zheng, X and Zeng, L and Wang, J}, title = {Inflammation and Immune Escape in Ovarian Cancer: Pathways and Therapeutic Opportunities.}, journal = {Journal of inflammation research}, volume = {18}, number = {}, pages = {895-909}, pmid = {39867950}, issn = {1178-7031}, abstract = {Ovarian cancer (OC) remains one of the most lethal gynecological malignancies, largely due to its late-stage diagnosis and high recurrence rates. Chronic inflammation is a critical driver of OC progression, contributing to immune evasion, tumor growth, and metastasis. Inflammatory cytokines, including IL-6, TNF-α, and IL-8, as well as key signaling pathways such as nuclear factor kappa B (NF-kB) and signal transducer and activator of transcription 3 (STAT3), are upregulated in OC, promoting a tumor-promoting environment. The tumor microenvironment (TME) is characterized by immune cells like tumor-associated macrophages (TAMs) and regulatory T cells (Tregs), which suppress anti-tumor immune responses, facilitating immune evasion. Furthermore, OC cells utilize immune checkpoint pathways, including PD-1/PD-L1, to inhibit cytotoxic T cell activity. Targeting these inflammatory and immune evasion mechanisms offers promising therapeutic strategies. COX-2 inhibitors, Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway blockers, and NF-kB inhibitors have shown potential in preclinical studies, while immune checkpoint inhibitors targeting PD-1/PD-L1 and CTLA-4 have been explored with mixed results in OC. Additionally, emerging research on the microbiome and inflammation-related biomarkers, such as microRNAs (miRNAs) and exosomes, points to new opportunities for early detection and precision medicine. Future approaches to OC treatment must focus on personalized strategies that target the inflammatory TME, integrating anti-inflammatory therapies with immunotherapy to enhance patient outcomes. Continued research into the interplay between inflammation and immune evasion in OC is essential for developing effective, long-lasting treatments.}, }
@article {pmid39867867, year = {2025}, author = {Zhang, Q and Liang, D and Zhang, C and Ye, L and Sun, P and Zhu, H and Zhao, Y and Li, Y and Guan, Y and Zhang, H}, title = {Integrated Microbiome and Metabolome Analysis Reveals Correlations Between Gut Microbiota Components and Metabolic Profiles in Mice With Mitoxantrone-Induced Cardiotoxicity.}, journal = {Drug design, development and therapy}, volume = {19}, number = {}, pages = {439-455}, pmid = {39867867}, issn = {1177-8881}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/drug effects ; Male ; *Cardiotoxicity ; *Metabolome/drug effects ; *Mitoxantrone/administration &amp; dosage/pharmacology ; Metabolomics ; Animals, Outbred Strains ; }, abstract = {PURPOSE: Mitoxantrone (MTX) is largely restricted in clinical usage due to its significant cardiotoxicity. Multiple studies have shown that an imbalance in the gut-heart axis plays an important role in the development of cardiovascular disease (CVD). We aim to explore the possible correlations between gut microbiota (GM) compositions and cardiometabolic (CM) disorder in MTX-triggered cardiotoxicity mice.<br><br>METHODS: MTX cumulative dose of 6 mg/kg was administered to healthy Kunming male mice to trigger cardiotoxicity, with 1 mg/kg twice weekly for a duration of 3&#xa0;weeks. Plasma CK-MB and LDH levels were determined, and the heart tissue histopathology was assessed, followed by utilizing an integrated liquid chromatography-mass spectrometry (LC-MS)-based heart metabolomics study alongside the 16S ribosomal RNA (rRNA) sequencing method to assess MTX impact on GM and CM profiles in mice, establishing associations between GM and CM profiles through the Pearson correlation coefficient calculation.<br><br>RESULTS: MTX caused CK-MB and LDH level elevations and cardiotoxicity in our mouse model. MTX primarily affected the processes of protein digestion and absorption, mineral absorption, membrane transport, production of aminoacyl-transfer RNA (tRNA), metabolism of nucleotides, lipids, and amino acids, as well as autophagy. Additionally, MTX increased Romboutsia, Enterococcus, and Turicibacter abundances and lowered norank_f__Muribaculaceae, Alistipes, Odoribacter, norank_f__Lachnospiraceae, norank_f__Ruminococcaceae, norank_f__Oscillospiraceae, unclassified_f__Ruminococcaceae, NK4A214_group, Colidextribacter, norank_f__norank_o__Clostridia_vadinBB60_group, Rikenella, and Anaerotruncus abundances. The correlation analyses showcased variations in the abundance of diverse flora, such as Romboutsia, Enterococcus, Turicibacter, and norank_f__Muribaculaceae, which were related to MTX-induced cardiac injury.<br><br>CONCLUSION: Our study supports the claim that MTX provokes cardiotoxicity by modifying CM and GM profiles. Our results offer new possibilities for controlling MTX-triggered cardiotoxicity.}, }
@article {pmid39867602, year = {2024}, author = {Babu, R and Padmanabhan, S and Ganesan, R and Subbian, E and Van, TTH and Eri, R}, title = {Sustainable, greenhouse gas derived fermented protein in canine diets-a pilot study.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1477182}, pmid = {39867602}, issn = {2297-1769}, abstract = {Sustainability concerns have increased consumer demand for non-animal-derived proteins and the search for novel, alternative protein sources. The nutritional sustainability of the food system without compromising the nutrient quality, composition, digestibility and consumption is pivotal. As with farmed livestock, it is imperative to ensure the well-being and food security of companion animals and to develop sustainable and affordable pet foods. The current pilot study was conducted to determine the effect of greenhouse gas-derived novel, fermented protein ingredient in beagle dogs. The greenhouse gas-derived fermented protein is an alternative protein ingredient with optimal nutritional factors and provides traceability, significantly optimizes the use of land and water, and provides sustainability to the feed value chain of canine diets. Three experimental groups including control, 5 and 10% inclusion of high protein ingredients were included in the study and the results suggest that the fermented protein is palatable and acceptable at 5 and 10% inclusions in the diets of dogs. The present study shows no significant difference in general alertness, clinical symptoms, water consumption and social behavior of dogs between 5 and 10% fermented protein inclusion in canine diets. The diversity of the bacterial community did not change after supplementation with the tested protein source in dogs. Only a few bacterial genera differed significantly in relative abundance between the experimental groups. Feed consumption, faecal scoring and the microbiome data results of this pilot study on the use of novel, methane gas derived, bacterial SCP as a protein ingredient in the canine diets, would pave way for more and more inclusion of such novel alternative protein sources in the pet food industry.}, }
@article {pmid39867434, year = {2024}, author = {Karra Khalil, L and Asthana, A and Gangwar, RS}, title = {Editorial: Key players of the immune system in skin inflammation-allergy and autoimmunity.}, journal = {Frontiers in allergy}, volume = {5}, number = {}, pages = {1536289}, pmid = {39867434}, issn = {2673-6101}, }
@article {pmid39867360, year = {2025}, author = {Gabrilska, RA and Omeir, K and Ancira, J and Miller, C and Tipton, CD and Rumbaugh, KP and Wolcott, J and Noe, A and Subasinghe, K and Rowe, M and Phillips, N and Phillips, CD}, title = {Functionally enriched human polymorphisms associate to species in the chronic wound microbiome.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.15.25320612}, pmid = {39867360}, abstract = {Chronic wounds are a burden to millions of patients and healthcare providers worldwide. With rising incidence and prevalence, there is an urgent need to address non-healing wounds with novel approaches. Impaired wound healing has been shown to be associated with wound microbiota, and multiple bacterial species are known to contribute to delays in closure. Recent evidence suggests human genetics may shape differences in composition of wound microbiomes, and unraveling this relationship has important implications for understanding wound bioburden and tailoring treatment. Here, a two-stage microbiome genome wide association study (mbGWAS; n=509) was used to test effects of human genetics on the relative abundances of bacterial species detected in chronic wounds using bacterial 16S rRNA gene sequencing. Sixteen species were significantly associated to 193 genetic loci distributed across 25 non-overlapping genomic regions. No locus was associated with more than one species, with heritability estimates per species ranging up to 20%. Functional analyses on genomic regions and species resulted in overrepresentation pertaining to pathways relevant to microbial infection and wound healing, suggesting that genetic and species interactions jointly influence the wound microenvironment. Species associated to host genetics in turn exhibited significant co-occurrence relationships with common wound pathogens including Staphylococcus aureus and Finegoldia magna . Moreover, the overall genetic distance among patients was significantly related to differences in their overall wound microbiome composition. Identification of such genetic biomarkers reveals new mechanistic insight into patient-microbiome interactions and provides an avenue to identify predictive risk factors for diagnosis and management of chronic wounds.}, }
@article {pmid39867288, year = {2025}, author = {Zhang, H and Zhang, X and Zheng, Y and Gu, X and Fu, Z and Gai, W and Wang, H}, title = {Impact of Herpesvirus Detection via Metagenomic Next-Generation Sequencing in Patients with Lower Respiratory Tract Infections.}, journal = {Infection and drug resistance}, volume = {18}, number = {}, pages = {377-389}, pmid = {39867288}, issn = {1178-6973}, abstract = {PURPOSE: This study aimed to investigate the impact of herpesvirus detection by metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) on lower respiratory tract infections (LRTIs) patients' lung microbiome composition and prognosis.<br><br>PATIENTS AND METHODS: We initially enrolled 234&#xa0;hospitalized patients with LRTIs who underwent BALF mNGS between February 2022 and May 2023. The study analyzed the clinical manifestations and the pulmonary microbial composition between herpesvirus detection (HD) and non-herpesvirus detection (non-HD) group.<br><br>RESULTS: After exclusions, a total of 201 patients were included, out of which 73 patients had herpesvirus detections (HD). The most frequently detected herpesviruses were Human herpesvirus 7 (HHV-7) (19.4%), Epstein-Barr virus (EBV) (12.4%), and cytomegalovirus (CMV) (10.4%). The HD group had a higher proportion of male patients (78.08% vs 55.04%, P = 0.001) and a greater incidence of hemoptysis and multilobar infiltrates compared non-HD group. Additionally, the HD group tended to have longer hospital stays compared to non-HD group, especially in immunosuppressed patients. Furthermore, in immunocompetent patients, there were significant differences in &#x3b1; diversity and &#x3b2; diversity between the HD group and non-HD group, but such differences were not observed in immunosuppressed patients.<br><br>CONCLUSION: The presence of herpesvirus in patients with non-critical LRTI is associated with longer hospital stays and alterations in the lung's microbial composition. Additionally, the impacts of herpesvirus presence are influenced by the immune status of the patients.}, }
@article {pmid39866837, year = {2025}, author = {Zhao, P and Jiang, Z and Li, X and Ainiwaer, M and Li, L and Wang, D and Fan, L and Chen, F and Liu, J}, title = {Airway stenosis: classification, pathogenesis, and clinical management.}, journal = {MedComm}, volume = {6}, number = {2}, pages = {e70076}, pmid = {39866837}, issn = {2688-2663}, abstract = {Airway stenosis (AS) is a fibroinflammatory disease characterized by abnormal activation of fibroblasts and excessive synthesis of extracellular matrix, which has puzzled many doctors despite its relatively low prevalence. Traditional treatment such as endoscopic surgery, open surgery, and adjuvant therapy have many disadvantages and are limited in the treatment of patients with recurrent AS. Therefore, it is urgent to reveal the pathogenesis of AS and accelerate its clinical transformation. Based on the discovered pathogenesis, including fibrosis, inflammation, epithelial-mesenchymal transition, metabolic reprogramming, microbiome, genetic susceptibility, and other mechanisms, researchers have developed a series of treatments, such as drug therapy, gene therapy, stem cell therapy, growth factor therapy, protein therapy, and photodynamic therapy. This review introduces the classification of AS, explores the existing pathogenesis and preclinical treatments developed based on the pathogenesis, and finally summarizes the current clinical management. In addition, the prospect of exploring the interaction between different types of cells and between microorganisms and cells to identify the intersection of multiple mechanisms based on single-cell RNA sequencing, 16S rRNA gene sequencing and shotgun metagenomic sequencing is worth looking forward to.}, }
@article {pmid39866751, year = {2025}, author = {Ren, Z and Luo, W and Li, H and Ding, H and Zhang, Y}, title = {Decrypting the phylogeny and metabolism of microbial dark matter in green and red Antarctic snow.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf003}, pmid = {39866751}, issn = {2730-6151}, abstract = {Antarctic snow harbors diverse microorganisms, including pigmented algae and bacteria, which create colored snow patches and influence global climate and biogeochemical cycles. However, the genomic diversity and metabolic potential of colored snow remain poorly understood. We conducted a genome-resolved study of microbiomes in colored snow from 13 patches (7 green and 6 red) on the Fildes Peninsula, Antarctica. Using metagenome assembly and binning, we reconstructed 223 metagenome-assembled genomes (MAGs), with 91% representing previously unexplored microbes. Green snow (GS) and red snow (RS) showed distinct MAGs profile, with Polaromonas and Ferruginibacter as the most abundant genera, respectively. GS exhibited higher alpha diversity with more unique and enriched MAGs, while RS showed greater variability with higher beta diversity. All MAGs contained genes encoding auxiliary activities (AAs), carbohydrate esterases (CEs), glycoside hydrolases (GHs), and glycosyl transferases (GTs), indicating microbial degradation of complex carbon substrates. The most abundant enzymes included GT2 (cellulose synthase), GT4 (sucrose synthase), CE1 (acetyl xylan esterase), GT41 (peptide beta-N-acetylglucosaminyltransferase), and CE10 (arylesterase). GS had a higher abundance of GTs, whereas RS was enriched in GHs. Furthermore, 56% of MAGs contained genes for inorganic nitrogen cycling, with 18 gene families involved in assimilatory nitrate reduction, dissimilatory nitrate reduction, and denitrification. Potential coupling of nitrogen cycling and carbohydrate metabolism was observed at both genome and community levels, suggesting close links between these pathways, particularly through nitrate reduction during carbohydrate degradation. This study enhances our understanding of microbial metabolic functions in polar ecosystems and highlights their roles in maintaining Antarctic ecological stability.}, }
@article {pmid39866725, year = {2024}, author = {Kohnert, E and Kreutz, C}, title = {Computational Study Protocol: Leveraging Synthetic Data to Validate a Benchmark Study for Differential Abundance Tests for 16S Microbiome Sequencing Data.}, journal = {F1000Research}, volume = {13}, number = {}, pages = {1180}, pmid = {39866725}, issn = {2046-1402}, mesh = {*Benchmarking ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Computational Biology/methods ; Humans ; }, abstract = {BACKGROUND: Synthetic data's utility in benchmark studies depends on its ability to closely mimic real-world conditions and reproduce results obtained from experimental data. Building on Nearing et al.'s study (1), who assessed 14 differential abundance tests using 38 experimental 16S rRNA datasets in a case-control design, we are generating synthetic datasets that mimic the experimental data to verify their findings. We will employ statistical tests to rigorously assess the similarity between synthetic and experimental data and to validate the conclusions on the performance of these tests drawn by Nearing et al. (1). This protocol adheres to the SPIRIT guidelines, demonstrating how established reporting frameworks can support robust, transparent, and unbiased study planning.<br><br>METHODS: We replicate Nearing et al.'s (1) methodology, incorporating synthetic data simulated using two distinct tools, mirroring the 38 experimental datasets. Equivalence tests will be conducted on a non-redundant subset of 46 data characteristics comparing synthetic and experimental data, complemented by principal component analysis for overall similarity assessment. The 14 differential abundance tests will be applied to synthetic and experimental datasets, evaluating the consistency of significant feature identification and the number of significant features per tool. Correlation analysis and multiple regression will explore how differences between synthetic and experimental data characteristics may affect the results.<br><br>CONCLUSIONS: Synthetic data enables the validation of findings through controlled experiments. We assess how well synthetic data replicates experimental data, try to validate previous findings with the most recent versions of the DA methods and delineate the strengths and limitations of synthetic data in benchmark studies. Moreover, to our knowledge this is the first computational benchmark study to systematically incorporate synthetic data for validating differential abundance methods while strictly adhering to a pre-specified study protocol following SPIRIT guidelines, contributing to transparency, reproducibility, and unbiased research.}, }
@article {pmid39866666, year = {2025}, author = {Manske, F and Durda-Masny, M and Grundmann, N and Mazela, J and Englert-Golon, M and Szymankiewicz-Bręborowicz, M and Ciomborowska-Basheer, J and Makałowska, I and Szwed, A and Makałowski, W}, title = {Development of a new data management system for the study of the gut microbiome of children who are small for their gestational age.}, journal = {Computational and structural biotechnology journal}, volume = {27}, number = {}, pages = {221-232}, pmid = {39866666}, issn = {2001-0370}, abstract = {Microbiome studies aim to answer the following questions: which organisms are in the sample and what is their impact on the patient or the environment? To answer these questions, investigators have to perform comparative analyses on their classified sequences based on the collected metadata, such as treatment, condition of the patient, or the environment. The integrity of sequences, classifications, and metadata is paramount for the success of such studies. Still, the area of data management for the preliminary study results appears to be neglected. Here, we present the development of MetagenomicsDB (http://github.com/IOB-Muenster/MetagenomicsDB; accessed 2024/12/18), a central data management system for the study of the gut microbiome in children who are small for their gestational age (SGA). Our system provided more flexibility to conduct study-specific analyses and to integrate specific external resources than existing and necessarily more generic solutions. It supports short or long read data produced by virtually any sequencing instrument targeting (parts of) popular marker genes, such as the 16S rRNA gene and its variable regions. Classifications of these reads from the MetaG and Kraken 2 software are supported. The main goals of the system are to store the pre-computed study data securely under concurrent load and to make downstream analyses accessible to all researchers, regardless of programming proficiency. Thus, after initial plausibility checks on the input data to reduce human error, data are stored in a relational database and can be continuously updated over the whole life time of the study. We used a modular approach for MetagenomicsDB with comprehensive tests verifying the expected behavior and extensively described the underlying rational which allows users to adapt the system to their needs. We advocate the use of MetagenomicsDB as the backend for a graphical web interface. We showcase the potential of this approach at the example of our study on SGA children (http://www.bioinformatics.uni-muenster.de/tools/metagenomicsDB; accessed 2024/12/02). Without restrictions caused by the level of programming proficiency, our team members could explore the study data and optionally filter them using the graphical interface, before exporting the data in a format directly suitable for external normalization of read counts and statistical analyses. Study results could be conveniently and transparently shared with the public, as demonstrated here. Links to external resources facilitated literature search with regard to the SGA condition and assessments of the potential pathogenicity of taxa. Since different users will have different demands regarding features, data security, and web environments, we provide our implementation of the web interface as a visual example. By providing users with the MetagenomicsDB backend which constitutes the major part of the system, we ensure that custom development can be finished in a reasonable amount of time. We report our endeavors in order to motivate the application of data management systems at the scale of single studies in microbiome research.}, }
@article {pmid39866568, year = {2025}, author = {Pucci, N and Ujčič-Voortman, J and Verhoeff, AP and Mende, DR}, title = {Priority effects, nutrition and milk glycan-metabolic potential drive Bifidobacterium longum subspecies dynamics in the infant gut microbiome.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18602}, pmid = {39866568}, issn = {2167-8359}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Milk, Human/microbiology/chemistry/metabolism ; Infant ; *Bifidobacterium/metabolism/genetics ; *Bifidobacterium longum/metabolism ; Female ; *Polysaccharides/metabolism ; Infant, Newborn ; Feces/microbiology ; Metagenome ; Breast Feeding ; Male ; }, abstract = {BACKGROUND: The initial colonization of the infant gut is a complex process that defines the foundation for a healthy microbiome development. Bifidobacterium longum is one of the first colonizers of newborns' gut, playing a crucial role in the healthy development of both the host and its microbiome. However, B. longum exhibits significant genomic diversity, with subspecies (e.g., Bifidobacterium longum subsp. infantis and subsp. longum) displaying distinct ecological and metabolic strategies including differential capabilities to break down human milk glycans (HMGs). To promote healthy infant microbiome development, a good understanding of the factors governing infant microbiome dynamics is required.<br><br>METHODOLOGY: We analyzed newly sequenced gut microbiome samples of mother-infant pairs from the Amsterdam Infant Microbiome Study (AIMS) and four publicly available datasets to identify important environmental and bifidobacterial features associated with the colonization success and succession outcomes of B. longum subspecies. Metagenome-assembled genomes (MAGs) were generated and assessed to identify characteristics of B. longum subspecies in relation to early-life gut colonization. We further implemented machine learning tools to identify significant features associated with B. longum subspecies abundance.<br><br>RESULTS: B. longum subsp. longum was the most abundant and prevalent gut Bifidobacterium at one month, being replaced by B. longum subsp. infantis at six months of age. By utilizing metagenome-assembled genomes (MAGs), we reveal significant differences between and within B. longum subspecies in their potential to break down HMGs. We further combined strain-tracking, meta-pangenomics and machine learning to understand these abundance dynamics and found an interplay of priority effects, milk-feeding type and HMG-utilization potential to govern them across the first six months of life. We find higher abundances of B. longum subsp. longum in the maternal gut microbiome, vertical transmission, breast milk and a broader range of HMG-utilizing genes to promote its abundance at one month of age. Eventually, we find B. longum subsp. longum to be replaced by B. longum subsp. infantis at six months of age due to a combination of nutritional intake, HMG-utilization potential and a diminishment of priority effects.<br><br>DISCUSSION: Our results establish a strain-level ecological framework explaining early-life abundance dynamics of B. longum subspecies. We highlight the role of priority effects, nutrition and significant variability in HMG-utilization potential in determining the predictable colonization and succession trajectories of B. longum subspecies, with potential implications for promoting infant health and well-being.}, }
@article {pmid39866422, year = {2025}, author = {Memariani, M and Memariani, H}, title = {New horizons in the treatment of psoriasis: Modulation of gut microbiome.}, journal = {Heliyon}, volume = {11}, number = {1}, pages = {e41672}, pmid = {39866422}, issn = {2405-8440}, abstract = {The last decennia have witnessed spectacular advances in our knowledge about the influence of the gut microbiome on the development of a wide swathe of diseases that extend beyond the digestive tract, including skin diseases like psoriasis, atopic dermatitis, acne vulgaris, rosacea, alopecia areata, and hidradenitis suppurativa. The novel concept of the gut-skin axis delves into how skin diseases and the microbiome interact through inflammatory mediators, metabolites, and the intestinal barrier. Elucidating the effects of the gut microbiome on skin health could provide new opportunities for developing innovative treatments for dermatological diseases. Psoriasis is a complex disease with multiple factors contributing to its development, such as diet, lifestyle, genetic predisposition, and the microbiome. This paper has a dual purpose. First, we outline the current knowledge on the unique gut microbiota patterns implicated in the pathogenesis of psoriasis. Second, and of equal importance, we briefly discuss the reciprocal impact of psoriasis treatment and gut microbiome. In addition, this review explores potential therapeutic targets based on microbial interventions, which hold promise for providing new treatment options for psoriasis.}, }
@article {pmid39866415, year = {2025}, author = {Freibauer, A and Pai, N and RamachandranNair, R}, title = {Characterizing the fecal microbiome in patients on the ketogenic diet for drug resistant epilepsy.}, journal = {Heliyon}, volume = {11}, number = {1}, pages = {e41631}, pmid = {39866415}, issn = {2405-8440}, abstract = {BACKGROUND: The ketogenic diet is a dietary therapy with anti-seizure effects. The efficacy of the diet is variable, with initial animal studies suggesting the intestinal microbiome may have a modulating effect. Initial research on the role of the human microbiome in pediatric epilepsy management has been inconclusive.<br><br>METHODS: In this single-center prospective cohort study, stool samples were collected from 4 patients with drug resistant epilepsy on the ketogenic diet and 9 with drug resistant epilepsy as controls. The samples were analyzed by 16S RNA sequencing.<br><br>RESULTS: A trend towards increased alpha diversity was noted among patients on the ketogenic diet compared to the control group. Patients on the ketogenic diet also trended towards a higher relative abundance of Bacteroidaceae, Ruminococcaceae, and Prevotellaceae species. A subset of the control group had a high relative abundance of Bifidobacterium, which may make them a candidate for a trial of the ketogenic diet as a therapeutic option.<br><br>CONCLUSION: These findings add to the growing field of research of how the ketogenic diet modulates the intestinal microbiome in pediatric epilepsy patients. Future emphasis on multi-centre trials, consistent stool collection practices and the establishment of standardized stool biobanking protocols are needed further to validate these novel findings in a pediatric population.}, }
@article {pmid39866149, year = {2025}, author = {Zhao, C and Lei, S and Zhao, H and Li, Z and Miao, Y and Peng, C and Gong, J}, title = {Theabrownin remodels the circadian rhythm disorder of intestinal microbiota induced by a high-fat diet to alleviate obesity in mice.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4fo05947f}, pmid = {39866149}, issn = {2042-650X}, abstract = {The intestinal microbiota undergoes diurnal compositional and functional oscillations within a day, which affect the metabolic homeostasis of the host and exacerbate the occurrence of obesity. TB has the effect of reducing body weight and lipid accumulation, but the mechanism of improving obesity caused by a high-fat diet based on the circadian rhythm of intestinal microorganisms has not been clarified. In this study, we used multi-omics and imaging approaches to investigate the mechanism of TB in alleviating obesity in mice based on the circadian rhythm of gut microbiota. The results showed that TB could significantly regulate the levels and rhythmic expression of serum lipid indicators (TG, TC, LDL) and serum hormones (MT, FT3, LEP, CORT). The number of intestinal microbiota colonizing the colonic epithelium underwent daily fluctuations. TB remodeled the rhythmic oscillation of gut microbes (i.e., Lachnospiraceae_NK4A136_group, Alistipes, etc.), including the number, composition, abundance and rhythmic expression of the biogeographic localization of microbes. TB notably reduced the levels of 16 bile acids (TCA, THDCA, TCDA, GHDCA, T-α-MCA, etc.) and restored the balance of bile acid metabolism. It was found that TB may mitigate high-fat diet-induced obesity in mice by reshaping the circadian rhythm of the gut microbiome and regulating bile acid metabolism.}, }
@article {pmid39865898, year = {2025}, author = {Salvestrini, V and Conti, G and D'Amico, F and Cristiano, G and Candela, M and Cavo, M and Turroni, S and Curti, A}, title = {Gut Microbiome as a Potential Marker of Hematologic Recovery Following Induction Therapy in Acute Myeloid Leukemia Patients.}, journal = {Cancer medicine}, volume = {14}, number = {3}, pages = {e70501}, doi = {10.1002/cam4.70501}, pmid = {39865898}, issn = {2045-7634}, support = {RC-2024-2790087//Ministero della Salute/ ; }, mesh = {Humans ; *Leukemia, Myeloid, Acute/microbiology/drug therapy/therapy ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Adult ; Aged ; *Induction Chemotherapy ; RNA, Ribosomal, 16S/genetics ; Young Adult ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Biomarkers ; }, abstract = {BACKGROUND: The management of acute myeloid leukemia (AML) is hindered by treatment-related toxicities and complications, particularly cytopenia, which remains a leading cause of mortality. Given the pivotal role of the gut microbiota (GM) in hemopoiesis and immune regulation, we investigated its impact on hematologic recovery during AML induction therapy.<br><br>METHODS: We profiled the GM of 27 newly diagnosed adult AML patients using 16S rRNA amplicon sequencing and correlated it with key clinical parameters before and after induction therapy.<br><br>RESULTS: Our investigation revealed intriguing associations between the GM composition and crucial recovery indicators, including platelet, lymphocyte, and neutrophil counts, and identified early GM signatures predictive of improved hematologic recovery. Remarkably, patients demonstrating superior recovery had higher alpha diversity and enrichment in health-associated taxa belonging to the genera Faecalibacterium, Ruminococcus, Blautia, and Butyricimonas at diagnosis.<br><br>CONCLUSIONS: Despite certain study limitations, our findings suggest that evaluating GM features could serve as a potential marker for hematologic recovery. This preliminary work opens avenues for personalized risk assessment and interventions, possibly involving GM modulation tools, to optimize recovery in AML patients undergoing induction therapy and potentially enhancing overall outcomes in individuals with hematologic diseases.}, }
@article {pmid39865827, year = {2025}, author = {Yi, C and Xu, M and Zhang, W and Huang, S and Guo, L and Huang, F and Xia, T and Dai, Y and Yu, B and Li, H}, title = {Traditional Chinese Medicine Treats Obesity by Regulating the Central Nervous System via Short-Chain Fatty Acids.}, journal = {Current pharmaceutical design}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113816128354909241213070313}, pmid = {39865827}, issn = {1873-4286}, abstract = {The increasing global prevalence of obesity (OB) calls for the development of effective treatments. Traditional Chinese Medicine (TCM) offers a promising approach by modulating gut microbiota (GM) to enhance the production of short-chain fatty acids (SCFAs). Research has demonstrated that SCFAs can regulate appetite and energy expenditure via the Central Nervous System (CNS), underscoring the role of the gut-brain axis in maintaining energy balance. A comprehensive review of the literature was conducted using databases, such as ScienceDirect, Google Scholar, and PubMed. The focus was on the impact of TCM on SCFA production and its influence on appetite regulation and energy expenditure through the CNS. This review indicates that TCM enhances the production of SCFAs, which suppress appetite and increase energy expenditure through their interaction with the CNS, particularly the gut-brain axis. TCM demonstrates promise as a therapeutic strategy for obesity by enhancing the production of SCFAs and regulating energy balance. This approach presents a novel avenue for obesity treatment through the modulation of the microbiome.}, }
@article {pmid39865797, year = {2025}, author = {Patel, M and Gill, CM and Chamberland, R and Heflin, T and Mehringer, R}, title = {Impact of adjunct bezlotoxumab for preventing Clostridioides difficile infection recurrence in patients post - hematopoietic stem cell transplantation.}, journal = {Journal of oncology pharmacy practice : official publication of the International Society of Oncology Pharmacy Practitioners}, volume = {}, number = {}, pages = {10781552241310099}, doi = {10.1177/10781552241310099}, pmid = {39865797}, issn = {1477-092X}, abstract = {BACKGROUND: Patients post hematopoietic stem cell transplant (HSCT) are highly susceptible to Clostridioides difficile infection (CDI). Exposure to antibiotic treatment, chemotherapeutic disruption to bacterial microbiome, immunosuppressive therapy, and prolonged hospitalizations synergistically contribute to the risk of CDI and its recurrence. The purpose of this study is to assess if the adjunctive administration of bezlotoxumab decreases the rate of recurrent CDI in patients post-HSCT.<br><br>STUDY DESIGN: This retrospective cohort study included patients post allogeneic or autologous HSCT with CDI who were 18 years of age or older. The first cohort included patients who received standard-of-care (SOC) treatment for CDI. The second cohort included patients who received standard of care treatment for CDI in addition to bezlotoxumab. The primary objective was the proportion of patients with recurrence of CDI within 12 weeks of initial diagnosis after treatment with bezlotoxumab plus SOC compared with controls receiving SOC alone.<br><br>RESULTS: The primary outcome occurred in 2.7% of patients in the bezlotoxumab plus SOC group, and 7.1% of patients in the SOC alone group. Results of the primary outcome were not statistically significant between groups. No difference in CDI recurrence occurred between the two groups (5.4% vs 7.1%) at 6 months. Bezlotoxumab administration was well-tolerated with no documented adverse reactions.<br><br>CONCLUSION: In conclusion, the use of bezlotoxumab did not lead to statistically significant decreases in CDI recurrence in patients post-HSCT. Future studies should be conducted with a larger number of HSCT patients receiving bezlotoxumab to provide supporting evidence of its role in reducing CDI recurrence.}, }
@article {pmid39865640, year = {2025}, author = {Saleh, H and Mirakzehi, MT and Bidokhti, HM and Kazemi, M}, title = {Evaluation of the Effect of Bacteriophages and Organic Acids as a Feed Additive to Reduce Salmonella enteritidis in Challenged Chickens.}, journal = {Journal of animal physiology and animal nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpn.14103}, pmid = {39865640}, issn = {1439-0396}, abstract = {This study aimed to compare the effects of dietary supplementation of bacteriophage (BP) and acidifiers on performance, meat quality, morphology, and intestinal microbiota in chickens challenged and unchallenged with Salmonella enteritidis (SE) and also to investigate the possibility of replacing them in the diet with antibiotics. A total of 1760 male Ross (308) chicks were randomly assigned to 11 dietary treatments (8 pens/with 20 male chickens in each). Dietary treatments were as follows: SE-uninfected (negative control (NC), a basal diet without supplemention; NC+ 500 g/t BP (NBP1); NC+ 1000 g/t BP (NBP2); NC+ 300 mg/kg acidifier A (NAA); NC+ 300 mg/kg acidifier B (NAB)) and SE-infected (positive control (PC), a basal diet without supplemention; PC+ 40 mg/kg Antibiotic enrofloxacin (PA); PC+ 500 g/t BP (PBP1); PC+ 1000 g/t BP (PBP2); PC+ 3000 mg/kg acidifier A (PAA); PC+ 3000 mg/kg acidifier B (PAB)). At 13 D birds in challenged groups were orally gavaged with 1 mL bacterial suspension containing approximately 108 CFU Salmonella enterica. The results indicated that chicks challenged with SE impaired performance so that BWG and FI significantly decreased and FCR increased (p < 0.05). Diets containing a high dose of BP increased BW and improved FCR in challenged and unchallenged chickens. The quality of breast meat showed a decline in oxidation in chickens challenged with SE (p < 0.05). The inclusion of bacteriophage in the diet of chickens (1000 g/t) improved the L*, b*, and oxidation of meat. The use of bacteriophage and acidifier A in the diet significantly increased the Lactobacillus, and LAB count, especially in the challenged groups. The challenge of chickens with SE decreased the villus height and crypt depth in different parts of the small intestine (p < 0.05). The results of the present study suggested that 1000 g/t of BP probably improves chicken performance by increasing beneficial bacteria and decreasing pathogenic bacteria. Also, bacteriophage showed an improvement in the performance reduction of chickens with Salmonella infection. In addition, improved meat quality and beneficial changes in the microbiome and intestinal morphology indicate the effectiveness of BP as an alternative antibiotic growth promoter in broiler diets.}, }
@article {pmid39865360, year = {2025}, author = {Jara-Servin, A and Alcaraz, LD and Juarez-Serrano, SI and Espinosa-Jaime, A and Barajas, I and Morales, L and DeLuna, A and Hernández-López, A and Mancera, E}, title = {Microbial Communities in Agave Fermentations Vary by Local Biogeographic Regions.}, journal = {Environmental microbiology reports}, volume = {17}, number = {1}, pages = {e70057}, pmid = {39865360}, issn = {1758-2229}, support = {755846//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as de M&#xe9;xico (CONAHCYT)/ ; 765278//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as de M&#xe9;xico (CONAHCYT)/ ; CF-2023-G-695//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as de M&#xe9;xico (CONAHCYT)/ ; FORDECYT-PRONACES/103000/2020//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as de M&#xe9;xico (CONAHCYT)/ ; I0200/111/2024//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as de M&#xe9;xico (CONAHCYT)/ ; IN230420//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico, Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; }, mesh = {*Agave/microbiology ; *Fermentation ; Mexico ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Microbiota ; *Fungi/classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Alcoholic Beverages/microbiology ; }, abstract = {The production of traditional agave spirits in Mexico, such as mezcal, involves a process that uses environmental microorganisms to ferment the cooked must from agave plants. By analysing these microorganisms, researchers can understand the dynamics of microbial communities at the interface of natural and human-associated environments. This study involved 16S and ITS amplicon sequencing of 99 fermentation tanks from 42 distilleries across Mexico. The Agave species used, production methods, climatic conditions and biogeographic characteristics varied significantly among sites. However, certain taxa were found in most fermentations, indicating a core group of microorganisms common to these communities. The primary variable consistently associated with the composition of both bacterial and fungal communities was the distillery, suggesting that local production practices and site-specific attributes influence the microbiomes. The fermentation stage, climate and producing region also affected community composition but only for prokaryotes. Analysis of multiple tanks within three distilleries showed taxa enriched in specific fermentation stages or agave species. This research provides a detailed analysis of the microbiome of agave fermentations, offering important knowledge for its management and conservation.}, }
@article {pmid39865249, year = {2025}, author = {Liu, R and Liu, Y and Yi, J and Fang, Y and Guo, Q and Cheng, L and He, J and Li, M}, title = {Imbalance of oral microbiome homeostasis: the relationship between microbiota and the occurrence of dental caries.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {46}, pmid = {39865249}, issn = {1471-2180}, support = {2020YJ0240//Sichuan Science and Technology Program/ ; 2021YFH0188//Sichuan Science and Technology Program/ ; }, mesh = {*Dental Caries/microbiology ; Animals ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Mice ; *Saliva/microbiology ; *Dental Plaque/microbiology ; Mouth/microbiology ; Homeostasis ; Streptococcus mutans/genetics/isolation &amp; purification ; Specific Pathogen-Free Organisms ; Dysbiosis/microbiology ; DNA, Bacterial/genetics ; Male ; }, abstract = {BACKGROUND: Streptococcus mutans is recognized as a key pathogen responsible for the development of dental caries. With the advancement of research on dental caries, the understanding of its pathogenic mechanism has gradually shifted from the theory of a single pathogenic bacterium to the theory of oral microecological imbalance. Acidogenic and aciduric microbial species are also recognized to participate in the initiation and progression of dental caries. This study is designed to elucidate the relationship between oral microbiome dysregulation and the initiation of dental caries.<br><br>RESULTS: 16&#xa0;S rRNA gene sequencing of saliva and dental plaque from the Specific Pathogen Free Control group and the Specific Pathogen Free sucrose diet group revealed that a sucrose diet significantly influenced the composition of the oral microbiome. At the phylum level, the dominant microbial communities in both groups of mice were Firmicutes, Proteobacteria, Unclassified Bacteria, Actinobacteria, and Bacteroidetes. At the genus level, statistical analysis identified significant differences in the abundance of 18 genera between the two groups. The relative abundance of the Gemella genus was significantly increased in the SPF Sucrose group. The SPF Control group and the Germ-free Control group have no differential bacterial genera in the oral microbiome. Micro-CT examination of the mandibles revealed the development of dental caries in both the SPF Sucrose group and the Germ-free Sucrose group.<br><br>CONCLUSIONS: This study indicates that a dysbiotic microbial community can lead to the development of caries. Lays the foundation for further research into the etiology of dental caries.}, }
@article {pmid39656947, year = {2025}, author = {Eix, EF and Nett, JE}, title = {Candida auris: Epidemiology and Antifungal Strategy.}, journal = {Annual review of medicine}, volume = {76}, number = {1}, pages = {57-67}, doi = {10.1146/annurev-med-061523-021233}, pmid = {39656947}, issn = {1545-326X}, mesh = {Humans ; *Antifungal Agents/therapeutic use ; *Candidiasis/drug therapy/epidemiology/transmission ; *Drug Resistance, Fungal ; *Candida auris ; Risk Factors ; Cross Infection/epidemiology/prevention &amp; control/microbiology/drug therapy ; Candida/drug effects ; }, abstract = {Candida auris is a recently emerged fungal pathogen that causes severe infections in healthcare settings around the globe. A feature that distinguishes C. auris from other fungal pathogens is its high capacity to colonize skin, leading to widespread outbreaks in healthcare facilities via patient-to-patient transmission. C. auris can persist on skin or in the surrounding environment for extended periods of time, and it exhibits greater antifungal resistance than other Candida species. These factors pose major obstacles for the prevention and treatment of C. auris infection. Recent reports have identified frequently colonized skin sites, risk factors for developing invasive infection, and patterns of antifungal resistance among C. auris strains, all of which help guide therapeutic options. In this review, we highlight key studies of C. auris epidemiology and antifungal resistance, discussing how these factors influence healthcare-associated transmission and treatment outcomes.}, }
@article {pmid39527719, year = {2025}, author = {Quigley, EMM and Shanahan, F}, title = {Probiotics in Health Care: A Critical Appraisal.}, journal = {Annual review of medicine}, volume = {76}, number = {1}, pages = {129-141}, doi = {10.1146/annurev-med-042423-042315}, pmid = {39527719}, issn = {1545-326X}, mesh = {*Probiotics/therapeutic use ; Humans ; Gastrointestinal Microbiome/physiology ; }, abstract = {Consumption of probiotic products continues to increase, perhaps driven by an interest in gut health. However, the field is filled with controversy, inconsistencies, misuse of terminology, and poor communication. While the probiotic concept is biologically plausible and in some cases mechanistically well established, extrapolation of preclinical results to humans has seldom been proven in well-conducted clinical trials. With noteworthy exceptions, clinical guidance has often been derived not from large, adequately powered clinical trials but rather from comparisons of disparate, small studies with insufficient power to identify the optimal strain. The separation of probiotics from live biotherapeutic products has brought some clarity from a regulatory perspective, but in both cases, consumers should expect scientific rigor and strong supporting evidence for health claims.}, }
@article {pmid39865193, year = {2025}, author = {Chavarria, X and Choi, JH and Oh, S and Kim, M and Kang, D and Lee, IY and Jang, YS and Yi, MH and Yong, TS and Kim, JY}, title = {Metabarcoding for the Monitoring of the Microbiome and Parasitome of Medically Important Mosquito Species in Two Urban and Semi-urban Areas of South Korea.}, journal = {Current microbiology}, volume = {82}, number = {3}, pages = {102}, pmid = {39865193}, issn = {1432-0991}, support = {NRF-2020R1I1A2074562//National Research Foundation of Korea (KR)/ ; 6-2023-0065//Yonsei University College of Medicine/ ; HI23C1527//Ministry of Health and Welfare/ ; }, mesh = {Animals ; Republic of Korea ; *Microbiota ; *DNA Barcoding, Taxonomic ; *Bacteria/classification/genetics/isolation &amp; purification ; *Aedes/microbiology ; Culex/microbiology ; Mosquito Vectors/microbiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; }, abstract = {Interactions between microbial communities and the host can modulate mosquito biology, including vector competence. Therefore, future vector biocontrol measures will utilize these interactions and require extensive monitoring of the mosquito microbiome. Metabarcoding strategies will be useful for conducting vector monitoring on a large scale. We used 16S and 18S rRNA gene metabarcoding through iSeq100 sequencing to characterize the microbiome and eukaryome of Aedes albopictus (Skuse 1894) and Culex pipiens (Linnaeus 1758), two globally important vectors present in South Korea. Mosquitoes were collected from an urban and a semi-urban location in South Korea. Bacterial alpha and beta diversities varied by population. Pseudomonadota dominated the microbiomes of both species. The microbiome composition varied by population and was dominated by different taxa. At the genus level, Wolbachia sp. was the most enriched genus in Cx. pipiens, followed by Aeromonas sp. In Ae. Albopictus, the most abundant group was Enterococcus sp. The gregarine parasite Ascogregarina taiwanensis was highly prevalent in Ae. Albopictus and its absence was marked by the presence of seven bacterial taxa. To our knowledge, this is the first characterization of the microbiome of Ae. albopictus and Cx. pipiens in these regions of South Korea and contributes to the current information on the microbiome of mosquito species, which can be used in further studies to assess pathogen-microbiome and microbiome-microbiome interactions.}, }
@article {pmid39865153, year = {2025}, author = {Wu, Z and Jiang, M and Jia, M and Sang, J and Wang, Q and Xu, Y and Qi, L and Yang, W and Feng, L}, title = {The difference of oropharyngeal microbiome during acute respiratory viral infections in infants and children.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {127}, pmid = {39865153}, issn = {2399-3642}, support = {2022-I2M-CoV19-006//Chinese Academy of Medical Sciences (CAMS)/ ; }, mesh = {Humans ; *Respiratory Tract Infections/microbiology/virology ; Infant ; *Oropharynx/microbiology/virology ; *Microbiota ; Child, Preschool ; Male ; Female ; Child ; Acute Disease ; Virus Diseases/virology/microbiology/epidemiology ; }, abstract = {Acute respiratory infections (ARI) with multiple types of viruses are common in infants and children. This study was conducted to assess the difference of oropharyngeal microbiome during acute respiratory viral infection using whole-genome shotgun metagenomic sequencing. The overall taxonomic alpha diversity did not differ by the types of infected virus. The beta diversity differed by disease severity, disease-related symptoms, and types of infected virus. Nine species had significantly higher abundance in outpatients than in inpatients, with five of them in the genus Achromobacter. Three microbial community types were identified. The prevalence of community type (CT) 1 was higher among patients with influenza virus, enterovirus, and human adenvirus; CT2 was higher among patients with human metapneumovirus; and CT3 was higher among patients with respiratory syncytial virus and human adenvirus infections. Our results suggest that the oropharyngeal microbiome is associated with ARI disease severity, disease-related symptoms, and the types of infected virus.}, }
@article {pmid39865067, year = {2025}, author = {Kordahi, MC and Daniel, N and Gewirtz, AT and Chassaing, B}, title = {Mucus-penetrating microbiota drive chronic low-grade intestinal inflammation and metabolic dysregulation.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2455790}, doi = {10.1080/19490976.2025.2455790}, pmid = {39865067}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Carboxymethylcellulose Sodium/metabolism ; *Mucus/metabolism/microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Inflammation/metabolism/microbiology ; Mice, Inbred C57BL ; Intestinal Mucosa/microbiology/metabolism ; Metabolic Syndrome/microbiology/metabolism ; Feces/microbiology ; Polysorbates ; Male ; Colon/microbiology/pathology/metabolism ; Germ-Free Life ; Humans ; }, abstract = {Metabolic syndrome is, in humans, associated with alterations in the composition and localization of the intestinal microbiota, including encroachment of bacteria within the colon's inner mucus layer. Possible promoters of these events include dietary emulsifiers, such as carboxymethylcellulose (CMC) and polysorbate-80 (P80), which, in mice, result in altered microbiota composition, encroachment, low-grade inflammation and metabolic syndrome. While assessments of gut microbiota composition have largely focused on fecal/luminal samples, we hypothesize an outsized role for changes in mucus microbiota in driving low-grade inflammation and its consequences. In support of this notion, we herein report that both CMC and P80 led to stark changes in the mucus microbiome, markedly distinct from those observed in feces. Moreover, transfer of mucus microbiota from CMC- and P80-fed mice to germfree mice resulted in microbiota encroachment, low-grade inflammation, and various features of metabolic syndrome. Thus, we conclude that mucus-associated bacteria are pivotal determinants of intestinal inflammatory tone and host metabolism.}, }
@article {pmid39865026, year = {2024}, author = {Fayoud, H and Belousov, MV and Antonets, KS and Nizhnikov, AA}, title = {Pathogenesis-Associated Bacterial Amyloids: The Network of Interactions.}, journal = {Biochemistry. Biokhimiia}, volume = {89}, number = {12}, pages = {2107-2132}, doi = {10.1134/S0006297924120022}, pmid = {39865026}, issn = {1608-3040}, mesh = {Humans ; *Amyloid/metabolism ; *Bacterial Proteins/metabolism ; Bacteria/metabolism ; Animals ; Biofilms/growth &amp; development ; Amyloidosis/metabolism ; }, abstract = {Amyloids are protein fibrils with a characteristic cross-β structure that is responsible for the unusual resistance of amyloids to various physical and chemical factors, as well as numerous pathogenic and functional consequences of amyloidogenesis. The greatest diversity of functional amyloids was identified in bacteria. The majority of bacterial amyloids are involved in virulence and pathogenesis either via facilitating formation of biofilms and adaptation of bacteria to colonization of a host organism or through direct regulation of toxicity. Recent studies have shown that, beside their commonly known activity, amyloids may be involved in the spatial regulation of proteome by modulating aggregation of other amyloidogenic proteins with multiple functional or pathological effects. Although the studies on the role of microbiome-produced amyloids in the development of amyloidoses in humans and animals have only been started, it is clear that humans as holobionts contain amyloids encoded not only by the host genome, but also by microorganisms that constitute the microbiome. Amyloids acquired from external sources (e.g., food) can interact with holobiont amyloids and modulate the effects of bacterial and host amyloids, thus adding another level of complexity to the holobiont-associated amyloid network. In this review, we described bacterial amyloids directly or indirectly involved in disease pathogenesis in humans and discussed the significance of bacterial amyloids in the three-component network of holobiont-associated amyloids.}, }
@article {pmid39864907, year = {2025}, author = {Cheng, L and Li, Y and Yan, J}, title = {Space biological and human survival: Investigations into plants, animals, microorganisms and their components and bioregenerative life support systems.}, journal = {Life sciences in space research}, volume = {44}, number = {}, pages = {143-153}, doi = {10.1016/j.lssr.2024.10.007}, pmid = {39864907}, issn = {2214-5532}, mesh = {Humans ; *Life Support Systems ; Animals ; *Space Flight ; Plants/microbiology ; Microbiota ; Extraterrestrial Environment ; Agriculture ; }, abstract = {Space life science has been a frontier discipline in the life sciences, aiming to study the life phenomena of earth organisms and their activity patterns under the special environment of space. This review summarizes studies in various key topics in space life science, namely, how microbiome changes in humans and plants, the development of space agriculture and the use of animal, plant and cell models to study the effect of space environments on physiology. We highlight the new possibilities of using high-quality protein crystals uniquely available when grown under space conditions to aid drug development on earth, and the state-of-the-art Bioregenerative Life Support Systems (BLSS) to achieve long term human survival in space.}, }
@article {pmid39864798, year = {2025}, author = {Nehra, C and Harshini, V and Shukla, N and Chavda, P and Bhure, M and Savaliya, K and Patil, S and Shah, T and Pandit, R and Patil, NV and Patel, AK and Kachhawaha, S and Kumawat, RN and Joshi, M and Joshi, CG}, title = {Ruminal microbial responses to Moringa oleifera feed in lactating goats (Capra hircus): A metagenomic exploration.}, journal = {New biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.nbt.2025.01.006}, pmid = {39864798}, issn = {1876-4347}, abstract = {The purpose of the current study was to explore the effects of Moringa oleifera feed on the taxonomy and function of the rumen microbial community, and further to evaluate its impact on milk yield and body weight in lactating goats. Nineteen goats were divided into moringa leaf diet (ML; n=10) and masoor straw (MS; n=9) groups. For each group fortnight milk yield and body weight was recorded. Rumen solid and liquid fraction samples were processed for metagenomic shotgun sequencing and further analysed. The pairwise comparison between the two groups showed a significant increase (p-value- <0.01) in milk yield of the ML goats after the 4[th] fortnight interval onwards. The metagenomic analysis revealed Bacteroidetes and Firmicutes are the most abundant phyla, with increased Bacteroidetes in response to the moringa diet. The ML group exhibited a reduction in microbial diversity, with an increase in Prevetolla and Bacteroidales populations which are positively associated with carbohydrate, protein, and VFA metabolism, and an increased proportions of Treponema sp., Ruminococcus sp., Ruminobacter amylophilus, and Aeromonas, indicating improved cellulose and nitrogen metabolism. KEGG analysis revealed significant changes in microbial gene pool and metabolic pathways, particularly in carbohydrate metabolism, propanoate metabolism, and fatty acid synthesis genes. These microbial and functional shifts are correlated with improvements in milk yield, growth rates, and potentially reduced methane emissions.This study highlighted the potential benefits of feeding moringa in the animal production system. However, furthermore experimental evidence including genetic and environmental effects is needed for a comprehensive understanding of moringa feed's impact on goat health and productivity.}, }
@article {pmid39864729, year = {2025}, author = {Della-Negra, O and Bastos, MC and Bru-Adan, V and Santa-Catalina, G and Aït-Mouheb, N and Chiron, S and Patureau, D}, title = {Temporal dynamics of the soil resistome and microbiome irrigated with treated wastewater containing clarithromycin.}, journal = {Environmental research}, volume = {}, number = {}, pages = {120954}, doi = {10.1016/j.envres.2025.120954}, pmid = {39864729}, issn = {1096-0953}, abstract = {Clarithromycin, a common antibiotic found in domestic wastewater, persists even after treatment and can transfer to soils when treated wastewater (TWW) is used for irrigation. This residual antibiotic may exert selection pressure, promoting the spread of antibiotic resistance. While Predicted No Effect Concentrations (PNECs) are used in liquid media to predict resistance risks, PNEC values for soils, especially for clarithromycin, are lacking. Thus, this study aimed to assess clarithromycin's fate and its concentration threshold affecting soil microbial communities and macrolide resistance genes. The study used a soil microcosm approach with TWW containing clarithromycin at concentrations of 0, 0.01, 0.1, 0.5, and 1 mg/kgdry soil over a three-month period. Results showed clarithromycin persisted with limited degradation, likely due to strong adsorption to soil particles. Two transformation products were identified: decladinose-CLA (abiotic degradation) and phosphate-CLA (bacterial phosphotransferase activity). Soil bacterial communities were more influenced by TWW than by clarithromycin itself, as its antimicrobial effect was reduced due to adsorption. While clarithromycin did not significantly affect the abundance of resistance genes like intl1, mphA, and ereA, concentrations above 0.01 mg/kg increased the ermB gene abundance during the first week. The mefA gene (macrolide efflux pump) showed a hormetic effect: low doses (<0.1 mg/kg) increased gene abundance, while higher doses (>0.5 mg/kg) inhibited gene transfer or the bacteria carrying it. This study performed under controlled conditions provided insights into antibiotic resistance dynamics in soils exposed to clarithromycin, highlighting key concentration thresholds influencing resistance spread in soils.}, }
@article {pmid39864533, year = {2025}, author = {Chang, Y and Long, M and Shan, H and Liu, L and Zhong, S and Luo, JL}, title = {Combining Gut Microbiota Modulation and Immunotherapy: A Promising Approach for Treating Microsatellite Stable Colorectal Cancer.}, journal = {Critical reviews in oncology/hematology}, volume = {}, number = {}, pages = {104629}, doi = {10.1016/j.critrevonc.2025.104629}, pmid = {39864533}, issn = {1879-0461}, abstract = {Colorectal cancer (CRC) is one of the most prevalent and lethal cancers worldwide, ranking third in incidence and second in mortality. While immunotherapy has shown promise in patients with deficient mismatch repair (dMMR) or high microsatellite instability (MSI-H), its effectiveness in proficient mismatch repair (pMMR) or microsatellite stable (MSS) CRC remains limited. Recent advances highlight the gut microbiota as a potential modulator of anti-tumor immunity. The gut microbiome can significantly influence the efficacy of immune checkpoint inhibitors (ICIs), especially in pMMR/MSS CRC, by modulating immune responses and systemic inflammation. This review explores the role of the gut microbiota in pMMR/MSS CRC, the mechanisms by which it may enhance immunotherapy, and current strategies for microbiota modulation. We discuss the potential benefits of combining microbiota-targeting interventions with immunotherapy to improve treatment outcomes for pMMR/MSS CRC patients.}, }
@article {pmid39864473, year = {2025}, author = {Ramos, CI and de Andrade, LS and Teixeira, RR and Pereira, NBF and da Silva Lima, F and Hoffmann, C and Cuppari, L}, title = {Diet quality components and gut microbiota of patients on peritoneal dialysis.}, journal = {Journal of renal nutrition : the official journal of the Council on Renal Nutrition of the National Kidney Foundation}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.jrn.2025.01.001}, pmid = {39864473}, issn = {1532-8503}, abstract = {OBJECTIVE: To evaluate the associations between the quality of the diet and its components and microbial diversity and composition in peritoneal dialysis (PD) patients.<br><br>DESIGN AND METHODS: This crossectional study included PD patients for at least 3 months, aged 18-75 years and clinically stable. The Diet Quality Index (DQI), validated for the Brazilian population, is based on the energy density of 11 components ("sugar and sweets"; "beef, pork and processed meat"; "refined grains and breads"; "animal fat"; "poultry, fish and eggs"; "whole cereals, tubers and roots"; "fruits"; "non-starch vegetables"; "legumes and nuts"; "milk and dairy products"; "vegetable oil"). A proportional score - based on the adequacy of the intake to Brazilian dietary guidelines - is calculated, and a final score ranged from 0 (worse) to 100 (better) is obtained. Fecal samples were collected at home, in a sterile material, kept refrigerated and delivered to the clinic within 12h. &#x3b1;-diversity indices (Observed OTUs, Chao-1, Shannon', Gini-Simpsons', Pielou eveness and faith phylogenetics) and microbial profile were determined by 16S ribosomal DNA with PCR-amplification and sequenced on an Illumina MiSeq platform.<br><br>RESULTS: Forty-three participants were included (53.5% men, 52.4&#xb1;14.1 years, BMI:25.9&#xb1;4.1 kg/m[2], 30.2% had diabetes mellitus). DQI score was 50.5 (41.9 - 54.9). The lowest energy density was for the components "animal fat" and "whole cereals and breads, tubers, and roots", and the highest were for "refined grains and bread" and "beef, pork and processed meat". Diversity indices and Enterorhabdus genus were directly associated with the energy density of the components "whole cereals and breads, tubers, and roots" and inversely with "refined grains and bread", after adjustments for age and diabetes.<br><br>CONCLUSION: Even low, the intake of whole cereals, tubers and roots has the potential of positively influence the microbiota profile in peritoneal dialysis patients.}, }
@article {pmid39864468, year = {2025}, author = {Kronsten, VT and Paintsil, EK and Rodrigues, S and Seager, MJ and Bernal, W and Shawcross, DL}, title = {Hepatic encephalopathy - when lactulose and rifaximin are not working.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2025.01.010}, pmid = {39864468}, issn = {1528-0012}, }
@article {pmid39864460, year = {2025}, author = {Zhao, YY and Wu, ZJ and Du, Y and Han, QQ and Bai, YY and Liu, B and Li, J}, title = {Gut Microbiome and Serum Metabolites in Neuropathic Pain: The PPARα Perspective.}, journal = {Behavioural brain research}, volume = {}, number = {}, pages = {115442}, doi = {10.1016/j.bbr.2025.115442}, pmid = {39864460}, issn = {1872-7549}, abstract = {Neuropathic pain (NP) is a chronic disease state centred on neuroinflammation with a high prevalence and limited effective treatment options. Peroxisome proliferator-activated receptor α (PPARα) has emerged as a promising target for NP management due to its anti-inflammatory properties. Recent evidence highlights the critical role of the gut microbiome and its metabolites in NP pathogenesis. This study aimed to investigate whether PPARα modulates the development and alleviation of NP by influencing gut microbial communities and serum metabolites. 16S rDNA sequencing and liquid chromatography-mass spectrometry (LC-MS/MS) untargeted metabolomics analyses performed 14 days after the establishment of a chronic constriction injury (CCI) pain model in C57BL/6J mice showed significant changes in gut microbial and metabolite levels in CCI mice. Intraperitoneal injection of the PPARα agonist GW7647 (5mg/kg) significantly attenuated mechanical allodynia and thermal hyperalgesia in CCI mice, whereas injection of the PPARα antagonist GW6471 (20mg/kg) produced the opposite effect. Immunofluorescence analysis revealed that GW7647 effectively suppressed microglial activation. Additionally, PPARα agonist and antagonist treatments markedly altered the composition and abundance of intestinal microbial communities in CCI mice. Further serum LC-MS/MS analysis identified 258 potential serum metabolic biomarkers, many of which correlated with changes in gut microbial composition. These findings demonstrate that PPARα influences serum metabolite profiles by modulating gut microbiota composition, which subsequently affects NP progression. This study provides novel insights into the mechanisms underlying NP and suggests potential therapeutic avenues targeting PPARα and gut microbiota.}, }
@article {pmid39864190, year = {2025}, author = {Choi, NR and Na, HS and Han, H and Chung, J and Kim, YD}, title = {Next-generation sequencing analysis of bacterial species present in the sequestrum of medication-related osteonecrosis of the jaw patients.}, journal = {Archives of oral biology}, volume = {172}, number = {}, pages = {106180}, doi = {10.1016/j.archoralbio.2025.106180}, pmid = {39864190}, issn = {1879-1506}, abstract = {OBJECTIVE: Antiresorptives cases of adverse reactions to highly effective drugs used to treat skeletal-related events that occur during treatment of osteoporosis or malignancy have been reported in the jaw. To date, there is no clear pathophysiology for medication-related osteonecrosis of the jaw (MRONJ), but the role of inflammation or infection has been proposed as one of several possible pathogenesis theories. This study was designed to investigate the role of infection in the pathogenesis of MRONJ by analyzing the microbial communities observed in the bone samples from MRONJ patients.<br><br>DESIGN: Oral microbial samples were collected from 39 MRONJ patients and 45 healthy patients and subjected to next generation sequencing analysis. Alpha diversity, beta diversity, linear discriminant analysis and effect size, and network analysis were applied to compare the microbiome features.<br><br>RESULTS: The 10 predominant microbial strains observed in MRONJ patients were Streptococcus spp. S. constellatus, Tannerella forsythia, Parvimonas micra, Granulicatella adiacens, Bacteroidaceae G-1 bacterium HMT 272, Treponema socranskii, T. maltophilum, Pyramidobacter piscolens, and Fretibacterium fastidiosum. Network analysis revealed a significant correlation between T. forsythia and P. gingivalis. T. socranskii was closely related to T. maltophilum, Fretibacterium fastidiosum, and Peptostreptococcaceae nodatum. G. adiacens was closely related to Streptococcus parasanguinis, S. sanguinis, and Prevotella buccae.<br><br>CONCLUSIONS: In conclusion, this study sheds light on the potential role of infection in the pathogenesis of MRONJ. A distinct microbial profile was identified in MRONJ patients, with notable predominance of S. constellatus, T. forsythia, P. micra and G. adiacens among others. Network analysis further revealed significant correlations between certain microbial strains, suggesting possible synergistic interactions in MRONJ pathogenesis. These findings contribute to a deeper understanding of the complex microbial dynamics underlying MRONJ and may inform future therapeutic strategies aimed at targeting specific bacterial species implicated in this condition.}, }
@article {pmid39864124, year = {2025}, author = {Beghin, M and Ambroise, V and Lambert, J and Garigliany, MM and Cornet, V and Kestemont, P}, title = {Environmental exposure to single and combined ZnO and TiO2 nanoparticles: Implications for rainbow trout gill immune functions and microbiota.}, journal = {Chemosphere}, volume = {373}, number = {}, pages = {144148}, doi = {10.1016/j.chemosphere.2025.144148}, pmid = {39864124}, issn = {1879-1298}, abstract = {ZnO and TiO2 nanoparticles (NPs) are widely employed for their antibacterial properties, but their potential environmental impact is raising concerns. This study aimed to assess their single and combined effects at environmentally relevant concentrations (210 μg L[-1]) on rainbow trout (Oncorhynchus mykiss) gills microbiota and immune functions. 16S rRNA gene sequencing performed after 5 and 28 days of exposure suggests that TiO2 NPs had a more immediate impact on bacterial diversity, while prolonged exposure to the mixture altered community composition. Changes in the relative abundance of potential pathogenic genera such as Candidatus Piscichlamydia and Flavobacterium were observed. Additionally, while the expression of the pro-inflammatory cytokine il1β, and antibacterial compounds (c3) was downregulated by TiO2 NPs and the mixture, ZnO NPs affected immune (mpo) and tight junction proteins (zo1). These results highlight the differences in the toxicity mechanisms existing between the single NPs and their combination, which showed higher toxicity to the gill bacterial community, but not to immune mechanisms. Furthermore, they suggest that exposure to environmental concentrations of NPs could potentially affect fish mucosal immunity and associated microbiota, highlighting the need for further research on the toxicity of NP mixtures.}, }
@article {pmid39863642, year = {2025}, author = {Brombacher, E and Schilling, O and Kreutz, C}, title = {Characterizing the omics landscape based on 10,000+ datasets.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {3189}, pmid = {39863642}, issn = {2045-2322}, mesh = {*Proteomics/methods ; *Metabolomics/methods ; Humans ; Computational Biology/methods ; Genomics/methods ; Lipidomics/methods ; Microbiota/genetics ; Datasets as Topic ; }, abstract = {The characteristics of data produced by omics technologies are pivotal, as they critically influence the feasibility and effectiveness of computational methods applied in downstream analyses, such as data harmonization and differential abundance analyses. Furthermore, variability in these data characteristics across datasets plays a crucial role, leading to diverging outcomes in benchmarking studies, which are essential for guiding the selection of appropriate analysis methods in all omics fields. Additionally, downstream analysis tools are often developed and applied within specific omics communities due to the presumed differences in data characteristics attributed to each omics technology. In this study, we investigate over ten thousand datasets to understand how proteomics, metabolomics, lipidomics, transcriptomics, and microbiome data vary in specific data characteristics. We were able to show patterns of data characteristics specific to the investigated omics types and provide a tool that enables researchers to assess how representative a given omics dataset is for its respective discipline. Moreover, we illustrate how data characteristics can impact analyses at the example of normalization in the presence of sample-dependent proportions of missing values. Given the variability of omics data characteristics, we encourage the systematic inspection of these characteristics in benchmark studies and for downstream analyses to prevent suboptimal method selection and unintended bias.}, }
@article {pmid39863385, year = {2025}, author = {Carrillo-Serradell, L and Borgognone, A and Noguera-Julian, M and Planells-Romeo, V and Aragón-Serrano, L and Parera, M and Català-Moll, F and Casadó-Llombart, S and Velasco-de Andrés, M and Paredes, R and Lozano, F}, title = {Antimicrobial regime for gut microbiota depletion in experimental mice models.}, journal = {Methods in cell biology}, volume = {192}, number = {}, pages = {101-114}, doi = {10.1016/bs.mcb.2024.05.005}, pmid = {39863385}, issn = {0091-679X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Mice, Inbred C57BL ; *Feces/microbiology ; *RNA, Ribosomal, 16S/genetics ; Anti-Bacterial Agents/pharmacology/administration &amp; dosage ; Anti-Infective Agents/pharmacology ; }, abstract = {Mice models serve as a valuable tool to study microbiome-immune system interactions. While the use of germ-free mice may represent the gold-standard method, antibiotic-based microbiome depletion provides a more cost-efficient and feasible system. The protocol here in presented provides a mild antimicrobial regime to deplete basal microbiota in 8-week-old C57BL/6 mice, aiming to ensure reproducibility in microbiota studies. The antibiotic regime combines five different antimicrobial agents delivered either ad libitum or via oral gavage, aiming at depleting core gut microbiota in mice. Various administration timings were explored, concluding there were no differences when the antimicrobial treatment was applied for 3, 5 or 7 consecutive days. By offering a detailed antimicrobial preparation and mouse administration, as well as fecal sample processing and 16s rRNA sequencing, this protocol provides an initial framework to develop mice microbiota studies, with perceptible results in fecal microbiota composition.}, }
@article {pmid39862472, year = {2025}, author = {Peng, S and Meri, AQ and Zhou, M and Yu, Y and Tian, D and Zhu, S}, title = {Human embryo implantation: The complex interplay between endometrial receptivity and the microbiome.}, journal = {Journal of reproductive immunology}, volume = {168}, number = {}, pages = {104440}, doi = {10.1016/j.jri.2025.104440}, pmid = {39862472}, issn = {1872-7603}, abstract = {The endometrial and vaginal microbiota have co-evolved with the reproductive tract and play a key role in both health and disease. However, the difference between endometrial and vaginal microbiota, as well as their association with reproductive outcomes in women undergoing frozen embryo transfer, remains unclear. 120 women who underwent in vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI) and whole embryo freezing were enrolled. The vaginal and uterine microbiome were sequenced during the first frozen thawed embryo transfer. Based on whether or not they were pregnant after embryo transfer, women were assigned into two groups, and the microbiome of their reproductive tract was compared. The V3-V4 regions of the 16S rRNA gene were examined in the samples using the Next Generation Sequencing method. In the vagina, the non-pregnant group had higher bacterial species richness and diversity, with significantly lower Lactobacillus levels (91.66 % &amp; 74.50 %) and higher Gardnerella levels (3.92 % &amp; 12.12 %) than pregnant group (P < 0.05). In the uterine cavity, the diversity of uterine microbiome between pregnant group and non-pregnant group showed no significant differences. However, dramatic decrease in Lactobacillus (37.27 % &amp; 33.45 %) and Pseudomonas (9.80 % &amp; 4.08 %) were observed in the non-pregnant group (P < 0.05). There may be a correlation between the composition of female reproductive tract microbiome and the reproductive outcomes of patients with frozen-thawed embryo transfer. Lactobacillus-dominated microbiome in reproductive tract is more likely to be associated with higher clinical and ongoing pregnancy rate.}, }
@article {pmid39862468, year = {2025}, author = {Amir, S and Kumar, M and Kumar, V and Mohanty, D}, title = {HgutMgene-Miner: In silico genome mining tool for deciphering the drug-metabolizing potential of human gut microbiome.}, journal = {Computers in biology and medicine}, volume = {186}, number = {}, pages = {109679}, doi = {10.1016/j.compbiomed.2025.109679}, pmid = {39862468}, issn = {1879-0534}, abstract = {The biotransformation of drugs by enzymes from the human microbiome can produce active or inactive products, impacting the bioactivity and function of these drugs inside the human host. However, understanding the biotransformation reactions of drug molecules catalyzed by bacterial enzymes in human microbiota is still limited. Hence, to characterize drug utilization capabilities across all the microbial phyla inside the human gut, we have used a knowledge-based approach to develop HgutMgene-Miner software which predicts xenobiotic metabolizing enzymes (XMEs) through genome mining. HgutMgene-Miner derives its predictive power from the MicrobiomeMetDB database, which systematically catalogs all known biotransformation reactions of xenobiotics and primary metabolites mediated by host-associated microbial enzymes. Over 10,000 isolate genomes from 830 different bacterial species found in the Unified Human Gastrointestinal Genome (UHGG) collection have been analyzed by HgutMgene-Miner. This led to the identification of 89,377 xenobiotic metabolizing enzymes (XMEs) across 13 phyla, with the greatest diversity in Bacteroidota, Firmicutes_A, Firmicutes, and Proteobacteria. Bacteroides, Clostridium, and Alitsipes were found to be the richest genera, while Actinomyces were found to encode the fewest XMEs, primarily metabolizing Diclofenac, a nonsteroidal anti-inflammatory drug. Overall, we discovered XMEs in 220 genera, exceeding the number experimentally reported in fewer than 10 genera. Notably, Eggerthella lenta's cgr2 involved in Digoxin inactivation was identified in very distant Holdemania genera, likewise Clostridium leptum's nitroreductase, involved in Nitrazepam metabolism, was found in Fusobacterium. These findings highlight the extensive and diverse distribution of XMEs across microbial taxa.}, }
@article {pmid39863075, year = {2025}, author = {Tirelli, E and Pucci, M and Squillario, M and Bignotti, G and Messali, S and Zini, S and Bugatti, M and Cadei, M and Memo, M and Caruso, A and Fiorentini, S and Villanacci, V and Uberti, D and Abate, G}, title = {Effects of Methylglyoxal on Intestine and Microbiome Composition in Aged Mice.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {}, number = {}, pages = {115276}, doi = {10.1016/j.fct.2025.115276}, pmid = {39863075}, issn = {1873-6351}, abstract = {BACKGROUND: Methylglyoxal (MGO), a highly reactive precursor of advanced glycation end products (AGEs), is endogenously produced and prevalent in various ultra-processed foods. MGO has emerged as a significant precursor implicated in the pathogenesis of type 2 diabetes and neurodegenerative diseases. To date, the effects of dietary MGO on the intestine have been limited explored. Thus, this study investigates the impact of prolonged oral administration of MGOs on gut health in aged mice.<br><br>METHODS: Aged mice received MGO chronically (100 mg/kg/day) for 4 weeks. Intestinal samples were analyzed using RT-PCR and immunohistochemistry for proinflammatory cytokines, permeability markers, and tight junction proteins. 16S rRNA gene-based microbiome analysis was also performed to characterize microbiome composition and its metabolic potential.<br><br>RESULTS: MGO treatment induced notable alterations at the intestinal level, characterized by an increased formation of MGO-glycated proteins with a concurrent induction of a pro-inflammatory status and reduced expression and delocalization of zonulin-1 and occludin, tight junction proteins. Changes in intestinal morphology were also observed, including hyperproliferation of Paneth cells and an augmented thickness of the intestinal mucus layer, as indicated by immunohistochemical data from MGO-treated mice. Investigation into the microbiota composition revealed that MGO is effective in selectively modifying its composition and metabolic pathways. A decreased abundance of bacterial genera associated with the production of acetic and butyric acids (i.e. Harryflintia, Intestinimonas and Ruminococcaceae genera) and a substantial increase in Lachnospiraceae and Akkermansia genera were found in MGO-treated mice.<br><br>CONCLUSION: These findings highlight how dietary MGO can affect intestinal balance, providing valuable insights into the potential links between glycotoxins, gut microbiota, and overall gut functionality.}, }
@article {pmid39863021, year = {2025}, author = {Zheng, Y and Zhang, T and Shao, J and Du, Y and Li, Z and Zhang, L and Gao, J}, title = {Antibiotic-free responsive biomaterials for specific and targeted Helicobacter pylori eradication.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jconrel.2025.01.054}, pmid = {39863021}, issn = {1873-4995}, abstract = {Gastric cancer is highly correlated with Helicobacter pylori (H. pylori) infection. Approximately 50 % of the population worldwide is infected with H. pylori. However, current treatment regimens face severe challenges including drug resistance and gut microbiota disruption. An integrative treatment with slight negative influences on intestinal flora, conforming with concepts of integrative prevention of gastric cancer, is urgently needed. Non-antibiotic responsive biomaterials can respond to different stimuli, including pH, enzymes, light, ultrasound and magnetism, under which biomaterials are specifically activated to perform antibacterial capabilities, while neutral intestinal microenvironments differ from gastric microenvironments or inflammatory sites and have no or minimal irradiation via precisely controlled exogenous stimuli, which may not only overcome antibiotic resistance but also avoid gut microbiota disorders. First, the latest progress in responsive biomaterials against H. pylori without gut microbiome disturbance and their anti-H. pylori performances are profoundly summarized. Second, the mechanisms against planktonic bacteria, biofilms and intracellular bacteria are discussed respectively. Finally, the strategies of specific and targeted H. pylori elimination by responsive biomaterials are introduced. Additionally, the challenges and the focus of future research on translation into clinical application are fully proposed. Antibiotic-free responsive biomaterials for specific and targeted H. pylori eradication represent an innovative approach.}, }
@article {pmid39862070, year = {2025}, author = {Riseh, RS and Fathi, F and Vazvani, MG and Tarkka, MT}, title = {Plant Colonization by Biocontrol Bacteria and Improved Plant Health: A Review.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {30}, number = {1}, pages = {23223}, doi = {10.31083/FBL23223}, pmid = {39862070}, issn = {2768-6698}, mesh = {*Plant Diseases/microbiology/prevention &amp; control ; *Bacteria ; Plant Roots/microbiology ; Biological Control Agents ; Plants/microbiology ; Microbiota/physiology ; Quorum Sensing ; }, abstract = {The use of biological control agents is one of the best strategies available to combat the plant diseases in an ecofriendly manner. Biocontrol bacteria capable of providing beneficial effect in crop plant growth and health, have been developed for several decades. It highlights the need for a deeper understanding of the colonization mechanisms employed by biocontrol bacteria to enhance their efficacy in plant pathogen control. The present review deals with the in-depth understanding of steps involved in host colonization by biocontrol bacteria. The colonization process starts from the root zone, where biocontrol bacteria establish initial interactions with the plant's root system. Moving beyond the roots, biocontrol bacteria migrate and colonize other plant organs, including stems, leaves, and even flowers. Also, the present review attempts to explore the mechanisms facilitating bacterial movement within the plant such as migrating through interconnected spaces such as vessels or in the apoplast, and applying quorum sensing or extracellular enzymes during colonization and what is needed to establish a long-term association within a plant. The impacts on microbial community dynamics, nutrient cycling, and overall plant health are discussed, emphasizing the intricate relationships between biocontrol bacteria and the plant's microbiome and the benefits to the plant's above-ground parts, the biocontrol 40 bacteria confer. By unraveling these mechanisms, researchers can develop targeted strategies for enhancing the colonization efficiency and overall effectiveness of biocontrol bacteria, leading to more sustainability and resilience.}, }
@article {pmid39861468, year = {2025}, author = {Fricker, AD and Sejane, K and Desai, M and Snyder, MW and Duran, L and Mackelprang, R and Bode, L and Ross, MG and Flores, GE}, title = {A Pilot Study Exploring the Relationship Between Milk Composition and Microbial Capacity in Breastfed Infants.}, journal = {Nutrients}, volume = {17}, number = {2}, pages = {}, doi = {10.3390/nu17020338}, pmid = {39861468}, issn = {2072-6643}, support = {SC1GM136546/GM/NIGMS NIH HHS/United States ; R21HD104028/HD/NICHD NIH HHS/United States ; R01HD099813/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; *Milk, Human/chemistry/microbiology ; Pilot Projects ; Female ; *Gastrointestinal Microbiome ; Infant ; *Breast Feeding ; *Oligosaccharides/analysis ; Adult ; *Feces/microbiology/chemistry ; Cross-Sectional Studies ; Male ; Body Mass Index ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Overweight/microbiology ; Infant, Newborn ; Obesity/microbiology ; }, abstract = {BACKGROUND: Maternal obesity may contribute to childhood obesity in a myriad of ways, including through alterations of the infant gut microbiome. For example, maternal obesity may contribute both directly by introducing a dysbiotic microbiome to the infant and indirectly through the altered composition of human milk that fuels the infant gut microbiome. In particular, indigestible human milk oligosaccharides (HMOs) are known to shape the composition of the infant gut microbiome. The goal of this study was to characterize the HMO profiles of normal-weight and overweight mothers and to quantitatively link HMO concentrations to the taxonomic composition and functional potential of the infant gut microbiome.<br><br>METHODS: Normal-weight (BMI = 18.5-24.9; n = 9) and overweight/obese (OW/OB; BMI > 25; n = 11) breastfeeding mothers and their infants were enrolled in this single-center, cross-sectional pilot study. Human milk from the mothers and rectal stool swabs from the infants were collected 7-9 weeks postpartum. The HMO composition, microbiome composition, and microbial functions were assessed using HPLC, 16S rRNA gene sequencing, and metagenomic sequencing, respectively.<br><br>RESULTS: Neither the HMO profiles nor the infant microbiome composition varied according to maternal BMI status. Taxonomically, the gut microbiota of infants were dominated by typical gut lineages including Bifidobacterium. Significant correlations between individual HMOs and bacterial genera were identified, including for Prevotella, a genus of the Bacteroidota phylum that was positively correlated with the concentrations of lacto-N-neotetraose (LNnT) and lacto-N-hexaose (LNH). Using metagenomic assembled genomes, we were also able to identify the broad HMO-degradative capacity across the Bifidobacterium and Prevotella genera.<br><br>CONCLUSIONS: These results suggest that the maternal BMI status does not impact the HMO profiles of human milk. However, select HMOs were correlated with specific bacterial taxa, suggesting that the milk composition influences both the taxonomic composition and the functional capacity of the infant gut microbiome.}, }
@article {pmid39861394, year = {2025}, author = {Meléndez-Oliva, E and Martínez-Pozas, O and Sinatti, P and Martín Carreras-Presas, C and Cuenca-Zaldívar, JN and Turroni, S and Sánchez Romero, EA}, title = {Relationship Between the Gut Microbiome, Tryptophan-Derived Metabolites, and Osteoarthritis-Related Pain: A Systematic Review with Meta-Analysis.}, journal = {Nutrients}, volume = {17}, number = {2}, pages = {}, doi = {10.3390/nu17020264}, pmid = {39861394}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Tryptophan/metabolism ; *Osteoarthritis/microbiology ; Pain ; Female ; Male ; }, abstract = {INTRODUCTION: Osteoarthritis (OA) is the most prevalent form of arthritis and affects over 528 million people worldwide. Degenerative joint disease involves cartilage degradation, subchondral bone remodeling, and synovial inflammation, leading to chronic pain, stiffness, and impaired joint function. Initially regarded as a "wear and tear" condition associated with aging and mechanical stress, OA is now recognized as a multifaceted disease influenced by systemic factors such as metabolic syndrome, obesity, and chronic low-grade inflammation. Recent studies have focused on the gut-joint axis to investigate how the gut microbiome modulates inflammation and pain in OA.<br><br>MATERIALS AND METHODS: A systematic review was conducted following the PRISMA guidelines and was registered with PROSPERO (CRD42024556265). This review included studies involving adults with symptomatic OA and analyzed the relationship between the gut microbiome and OA-related pain. Randomized and non-randomized clinical trials, case reports, editorials, and pilot studies were excluded. Searches were performed in PubMed, Cochrane Library, and Web of Science without publication date restrictions, and filtered for "observational studies". The study selection and data extraction were performed by two independent researchers, and the risk of bias was assessed using appropriate tools.<br><br>RESULTS: Five observational studies were included in the systematic review, and three were included in the meta-analysis. Two studies reported an association between different tryptophan metabolites and pain levels in patients with OA. Two other studies demonstrated a correlation between lipopolysaccharide levels and pain in OA. A fifth study confirmed the relationship between Streptococcus relative abundance of Streptococcus spp. and knee pain. These results were not supported by a meta-analysis, which found no significant association between the presence of pain in OA and the presence of bacilli of the genus Streptococcus or plasma markers of the tryptophan pathway.<br><br>CONCLUSIONS: Current evidence indicates a potential link between gut microbiome dysbiosis and OA-related pain. However, methodological limitations preclude definitive conclusions. Further research using advanced techniques and larger cohorts is needed to validate and extend these findings and elucidate the underlying mechanisms. Targeted manipulation of the gut microbiome may be a valuable strategy for pain management in OA patients.}, }
@article {pmid39861379, year = {2025}, author = {Fang, J and Kang, SG and Huang, K and Tong, T}, title = {Integrating 16S rRNA Gene Sequencing and Metabolomics Analysis to Reveal the Mechanism of L-Proline in Preventing Autism-like Behavior in Mice.}, journal = {Nutrients}, volume = {17}, number = {2}, pages = {}, doi = {10.3390/nu17020247}, pmid = {39861379}, issn = {2072-6643}, support = {7222249//Beijing Natural Science Foundation/ ; }, mesh = {Animals ; *Proline/pharmacology/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Metabolomics ; Mice ; *RNA, Ribosomal, 16S ; *Disease Models, Animal ; Male ; *Valproic Acid/pharmacology ; *Autism Spectrum Disorder/prevention &amp; control ; Behavior, Animal/drug effects ; Dietary Supplements ; Autistic Disorder/prevention &amp; control ; }, abstract = {BACKGROUND/OBJECTIVES: Autism spectrum disorder (ASD) is characterized by impaired social interaction and repetitive stereotyped behavior. Effective interventions for the core autistic symptoms are currently limited.<br><br>METHODS: This study employed a valproic acid (VPA)-induced mouse model of ASD to assess the preventative effects of L-proline supplementation on ASD-like behaviors. The method of 16S rRNA sequencing and untargeted metabolomics analyses were conducted to investigate the modulation of gut microbiota and gut metabolites by L-proline.<br><br>RESULTS: The results indicated that L-proline supplementation significantly prevented ASD-like behavioral disorders, including alleviating social communication deficits and reducing repetitive behavior in the ASD mice. The 16S rRNA sequencing analysis revealed that L-proline regulated the composition and structure of gut microbiota. L-Proline supplementation enhances the abundance of the Verrucomicrobia at the phylum level and the Akkermansia at the genus level, while concurrently reducing the abundance of the Patescibacteria at the phylum level, as well as the Ileibacterium, Candidatus_Saccharimonas, and Lachnospiraceae_UCG-006 at the genus level in the VPA-induced mouse model for ASD. Additionally, the untargeted metabolomics results indicated that L-proline also modified the gut metabolite profiles. Functional analysis of the gut microbiota and KEGG pathway enrichment analysis of differential metabolites between the L-proline-supplemented and VPA groups corroborated that L-proline decreased pathways related to nucleotide metabolism, taurine and hypotaurine metabolism, and pyruvate metabolism, while increasing pathways involved in alpha-linolenic acid metabolism and phenylalanine, tyrosine, and tryptophan biosynthesis. The integrative metabolomic and microbiome analyses showed strong connections between the gut metabolites and gut microbiota affected by L-proline. These findings suggest that the modulatory effects of L-proline on gut microbiota and its metabolites may play a crucial role in preventing autism in mice.<br><br>CONCLUSIONS: These findings suggest that dietary L-proline may represent a viable, effective option for preventing the physiological and behavioral deficits associated with ASD in mice.}, }
@article {pmid39861376, year = {2025}, author = {Plaza-Diaz, J and Brandimonte-Hernández, M and López-Plaza, B and Ruiz-Ojeda, FJ and Álvarez-Mercado, AI and Arcos-Castellanos, L and Feliú-Batlle, J and Hummel, T and Palma-Milla, S and Gil, A}, title = {Effect of a Novel Food Rich in Miraculin on the Intestinal Microbiome of Malnourished Patients with Cancer and Dysgeusia.}, journal = {Nutrients}, volume = {17}, number = {2}, pages = {}, doi = {10.3390/nu17020246}, pmid = {39861376}, issn = {2072-6643}, support = {Cervera Transfer R&amp;D Projects. Ref. IDI-20210622. (Science and Education Ministry, Spain).//Center for Industrial Technological Development (CDTI)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Neoplasms/complications ; Female ; Male ; *Dysgeusia ; Middle Aged ; *Malnutrition ; Aged ; Pilot Projects ; Dietary Supplements ; Feces/microbiology ; Quality of Life ; }, abstract = {BACKGROUND/OBJECTIVES: Dysgeusia contributes to malnutrition and worsens the quality of life of patients with cancer. Despite the different strategies, there is no effective treatment for patients suffering from taste disorders provided by the pharmaceutical industry. Therefore, we developed a novel strategy for reducing side effects in cancer patients by providing a novel food supplement with the taste-modifying glycoprotein miraculin, which is approved by the European Union, as an adjuvant to medical-nutritional therapy.<br><br>METHODS: A pilot randomized, parallel, triple-blind, and placebo-controlled intervention clinical trial was carried out in which 31 malnourished patients with cancer and dysgeusia receiving antineoplastic treatment were randomized into three arms-standard dose of dried miracle berries (DMBs) (150 mg DMB/tablet), high dose of DMBs (300 mg DMB/tablet), or placebo (300 mg freeze-dried strawberry)-for three months. Patients consumed a DMB or placebo tablet before each main meal (breakfast, lunch, and dinner). Using stool samples from patients with cancer, we analyzed the intestinal microbiome via nanopore methodology.<br><br>RESULTS: We detected differences in the relative abundances of genera Phocaeicola and Escherichia depending on the treatment. Nevertheless, only the Solibaculum genus was more abundant in the standard-dose DMB group after 3 months. At the species level, Bacteroides sp. PHL 2737 presented a relatively low abundance in both DMB groups, whereas Vescimonas coprocola presented a relatively high abundance in both treatment groups after 3 months. Furthermore, a standard dose of DMB was positively associated with TNF-&#x3b1; levels and Lachnoclostridium and Mediterraneibacter abundances, and a high dose of DMB was negatively associated with TNF-&#x3b1; levels and the relative abundance of Phocaeicola. Following the administration of a high dose of DMB, a positive correlation was observed between erythrocyte polyunsaturated fatty acids and the presence of Lachnoclostridium and Roseburia. Additionally, a positive association was identified between Phocaeicola and the acetic acid concentration of feces. There was a negative association between the relative abundance of Phocaeicola and taste perception in the high-dose DMB group.<br><br>CONCLUSIONS: The combination of DMB intake with nutritional treatment and individualized dietary guidance results in positive changes in the intestinal microbiome of patients with cancer and dysgeusia. Changes observed in the intestinal microbiome might contribute to maintaining an appropriate immune response in cancer patients. As the current pilot study included a limited number of participants, further clinical trials on a larger group of patients are needed to draw robust findings.}, }
@article {pmid39861331, year = {2025}, author = {Yang, S and Duan, H and Yan, Z and Xue, C and Niu, T and Cheng, W and Zhang, Y and Zhao, X and Hu, J and Zhang, L}, title = {Luteolin Alleviates Ulcerative Colitis in Mice by Modulating Gut Microbiota and Plasma Metabolism.}, journal = {Nutrients}, volume = {17}, number = {2}, pages = {}, doi = {10.3390/nu17020203}, pmid = {39861331}, issn = {2072-6643}, support = {32202873//National Natural Science Foundation of China/ ; Gaufx-05Y07//The Fuxi Young Talents Fund of Gansu Agricultural University/ ; GAU-KYQD-2021-09//Scientific Research Start-up Funds for Openly recruited Doctors of Gansu Agricultural University/ ; }, mesh = {Animals ; *Colitis, Ulcerative/drug therapy/microbiology ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Disease Models, Animal ; *Luteolin/pharmacology ; Male ; *Dextran Sulfate ; Mice, Inbred C57BL ; Anti-Inflammatory Agents/pharmacology ; Dysbiosis ; Colon/drug effects/metabolism/microbiology ; }, abstract = {BACKGROUND/OBJECTIVES: Ulcerative colitis (UC) is a chronic and easily recurrent inflammatory bowel disease. The gut microbiota and plasma metabolites play pivotal roles in the development and progression of UC. Therefore, therapeutic strategies targeting the intestinal flora or plasma metabolites offer promising avenues for the treatment of UC. Luteolin (Lut), originating from a variety of vegetables and fruits, has attracted attention for its potent anti-inflammatory properties and potential to modulate intestinal flora.<br><br>METHODS: The therapeutic efficacy of Lut was evaluated in an established dextran sodium sulfate (DSS)-induced colitis mice model. The clinical symptoms were analyzed, and biological samples were collected for microscopic examination and the evaluation of the epithelial barrier function, microbiome, and metabolomics.<br><br>RESULTS: The findings revealed that Lut administration at a dose of 25 mg/kg significantly ameliorated systemic UC symptoms in mice, effectively reduced the systemic inflammatory response, and significantly repaired colonic barrier function. Furthermore, Lut supplementation mitigated gut microbiota dysbiosis in a UC murine model, increasing the abundance of Muribaculaceae, Rikenella, and Prevotellaceae while decreasing Escherichia_Shigella and Bacteroides levels. These alterations in gut microbiota also influenced plasma metabolism, significantly increasing phosphatidylcholine (PC), 6'-Deamino- 6'-hydroxyneomycin C, and gamma-L-glutamyl-butyrosine B levels and decreasing Motapizone and Arachidoyl-Ethanolamide (AEA) levels.<br><br>CONCLUSIONS: This study reveals that Lut supplementation modulates intestinal inflammation by restoring the gut microbiota community structure, thereby altering the synthesis of inflammation-related metabolites. Lut is a potential nutritional supplement with anti-inflammatory properties and offers a novel alternative for UC intervention and mitigation. In addition, further studies are needed to ascertain whether specific microbial communities or metabolites can mediate the recovery from UC.}, }
@article {pmid39861184, year = {2025}, author = {Lv, L and Maimaitiming, M and Yang, J and Xia, S and Li, X and Wang, P and Liu, Z and Wang, CY}, title = {Quinazolinone Derivative MR2938 Protects DSS-Induced Barrier Dysfunction in Mice Through Regulating Gut Microbiota.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {18}, number = {1}, pages = {}, doi = {10.3390/ph18010123}, pmid = {39861184}, issn = {1424-8247}, support = {42176109//National Natural Science Foundation of China/ ; 202241008//Fundamental Research Funds for the Central Universities of China/ ; 201962002//Fundamental Research Funds for the Central Universities of China/ ; 202212019//Fundamental Research Funds for the Central Universities of China/ ; ZXWH2170101//Shanghai Frontiers Science Center of Drug Target Identification and Delivery/ ; }, abstract = {Background/Objectives: Ulcerative colitis (UC), a chronic inflammatory bowel disease (IBD), is characterized by colorectal immune infiltration and significant microbiota compositional changes. Gut microbiota homeostasis is necessary to maintain the healthy state of humans. MR2938, a quinazolin-4(3H)-one derivative derived from the marine natural product penipanoid C, alleviated DSS-induced colitis in a dose-dependent manner. Herein, we aimed to investigate the impact of MR2938 on the gut microbiota in dextran sodium sulfate (DSS)-induced colitis in mice and to elucidate the role of the gut microbiota in the therapeutic mechanism of MR2938 for alleviating colitis. Methods: Acute colitis was induced with DSS in mice. Mice were administered with 100 mg/kg or 50 mg/kg of MR2938. Cecal content was also preserved in liquid nitrogen and subsequently analyzed following 16S RNA sequencing. Antibiotic cocktail-induced microbiome depletion was performed to further investigate the relationship between MR2938 and gut microbiota. The inflammatory factor levels were performed by quantitative polymerase chain reaction (qPCR) and enzyme-linked immunosorbent assay (ELISA). Alcian blue staining and immunofluorescence were used to estimate the intestinal barrier. Results: The 16S rRNA sequencing revealed microbiota modulation by MR2938. Compared with the model group, the 100 mg/kg MR2938 group was associated with higher abundances of Entercoccus and a lower abundance of Staphylococcus, while the 50 mg/kg MR2938 group was associated with higher abundances of Lactobacillus and a lower abundance of Staphylococcus. The antibiotic-mediated microbiota depletion experiments demonstrated that the gut microbiota primarily contributed to barrier function protection, with little impact on inflammatory factor levels during the MR2938 treatment. Conclusions: These findings suggest that intestinal flora play a crucial role in MR2938's therapeutic mechanism for alleviating colitis.}, }
@article {pmid39861118, year = {2025}, author = {Szymczak-Pajor, I and Drzewoski, J and Kozłowska, M and Krekora, J and Śliwińska, A}, title = {The Gut Microbiota-Related Antihyperglycemic Effect of Metformin.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {18}, number = {1}, pages = {}, doi = {10.3390/ph18010055}, pmid = {39861118}, issn = {1424-8247}, abstract = {It is critical to sustain the diversity of the microbiota to maintain host homeostasis and health. Growing evidence indicates that changes in gut microbial biodiversity may be associated with the development of several pathologies, including type 2 diabetes mellitus (T2DM). Metformin is still the first-line drug for treatment of T2DM unless there are contra-indications. The drug primarily inhibits hepatic gluconeogenesis and increases the sensitivity of target cells (hepatocytes, adipocytes and myocytes) to insulin; however, increasing evidence suggests that it may also influence the gut. As T2DM patients exhibit gut dysbiosis, the intestinal microbiome has gained interest as a key target for metabolic diseases. Interestingly, changes in the gut microbiome were also observed in T2DM patients treated with metformin compared to those who were not. Therefore, the aim of this review is to present the current state of knowledge regarding the association of the gut microbiome with the antihyperglycemic effect of metformin. Numerous studies indicate that the reduction in glucose concentration observed in T2DM patients treated with metformin is due in part to changes in the biodiversity of the gut microbiota. These changes contribute to improved intestinal barrier integrity, increased production of short-chain fatty acids (SCFAs), regulation of bile acid metabolism, and enhanced glucose absorption. Therefore, in addition to the well-recognized reduction of gluconeogenesis, metformin also appears to exert its glucose-lowering effect by influencing gut microbiome biodiversity. However, we are only beginning to understand how metformin acts on specific microorganisms in the intestine, and further research is needed to understand its role in regulating glucose metabolism, including the impact of this remarkable drug on specific microorganisms in the gut.}, }
@article {pmid39861043, year = {2025}, author = {Del Prete, V and Piazzesi, A and Scanu, M and Toto, F and Pane, S and Berrilli, F and Paterno, G and Putignani, L and di Cave, D}, title = {Pneumocystis Pneumonia Severity Is Associated with Taxonomic Shifts in the Respiratory Microbiota.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/pathogens14010082}, pmid = {39861043}, issn = {2076-0817}, support = {Current Research Funds//Italian Ministry of Health/ ; Molecular identification and genetic differentiation of zoonotic and environmental parasites//RSA 2021/ ; }, mesh = {Humans ; *Microbiota ; *Pneumonia, Pneumocystis/microbiology/immunology ; *RNA, Ribosomal, 16S/genetics ; Male ; *Pneumocystis carinii/genetics/isolation &amp; purification ; Middle Aged ; Female ; Severity of Illness Index ; Respiratory System/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Adult ; }, abstract = {Pneumonia caused by Pneumocystis jirovecii infection (PCP) is a potentially life-threatening illness, particularly affecting the immunocompromised. The past two decades have shown an increase in PCP incidence; however, the underlying factors that promote disease severity and fatality have yet to be fully elucidated. Recent evidence suggests that the microbiota of the respiratory tract may play a role in stimulating or repressing pulmonary inflammation, as well as the progression of both bacterial and viral pneumonia. Here, we employed 16S rRNA metataxonomic sequencing to profile the respiratory microbiota of patients with mild-moderate and severe PCP. Our results show that the upper and lower airways of PCP patients have bacterial profiles which have been associated with a pro-inflammatory response. Furthermore, we find that severe PCP is associated with lower bacterial diversity and an increase in Prevotella and a decrease in Neisseria. Functionally, severe PCP was associated with a decrease in metabolic pathways of molecules with anti-inflammatory and antimicrobial properties. To our knowledge, this is the first study showing an association of PCP severity with shifts in the respiratory microbiome and may provide some insight into which patients are more susceptible to the more severe manifestations of the disease.}, }
@article {pmid39861042, year = {2025}, author = {Guo, J and Zhao, Z and Broadwater, C and Tobin, I and Liu, J and Whitmore, M and Zhang, G}, title = {Is Intestinal Microbiota Fully Restored After Chickens Have Recovered from Coccidiosis?.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/pathogens14010081}, pmid = {39861042}, issn = {2076-0817}, support = {2022-67016-37208, 2024-67016-42415, 2024-67011-42944, 2021-67034-35184//USDA-NIFA/ ; }, mesh = {Animals ; *Chickens/microbiology/parasitology ; *Coccidiosis/veterinary/parasitology ; *Gastrointestinal Microbiome/physiology ; *Eimeria/pathogenicity/physiology ; *Poultry Diseases/microbiology/parasitology ; Male ; RNA, Ribosomal, 16S/genetics ; Cecum/microbiology/parasitology ; Feces/microbiology/parasitology ; }, abstract = {The intestinal microbiota is known to be altered by Eimeria-induced coccidiosis, but it remains unclear whether the microbiota is fully restored after recovery. To address this, 110 newly hatched Cobb male broiler chickens were challenged with 2 × 10[4] sporulated oocysts of Eimeria maxima (EM) strain M6 or mock-infected with saline on day 10. Body weight and feed intake were recorded. Additionally, 10 mock- and 12 EM-infected birds were randomly selected to assess the small intestinal lesion, fecal oocyst shedding, and ileal and cecal microbiota compositions using 16S rRNA gene sequencing at 3, 5, 7, 14, and 21 days post-infection (dpi). EM infection significantly decreased (p < 0.001) body weight by 5 dpi, persisting through 21 dpi. The infection also reduced (p < 0.05) weight gain, feed intake, and feed efficiency in the first week; however, these parameters became comparable in the second and third weeks. At 7 dpi, during the peak of infection, major lactic acid bacteria were enriched, while short-chain fatty acid-producing bacteria were mostly suppressed in both the ileum and cecum. Opportunistic pathogens such as Escherichia and Clostridium perfringens transiently bloomed at 7 dpi. By 14 dpi, differential bacterial enrichment subsided, and nearly all commensal bacteria returned to healthy levels by 21 dpi. Coupled with comparable growth performance between healthy and EM-recovered chickens, we conclude that the intestinal microbiota is largely restored to its healthy state after recovery. Understanding the microbiota's responses to coccidiosis may inform probiotic-based mitigation strategies.}, }
@article {pmid39861039, year = {2025}, author = {Zając, V and Bell-Sakyi, L and Wójcik-Fatla, A}, title = {Use of Tick Cell Lines in Co-Infection Studies with a Preliminary Study of Co-Culture of Borrelia burgdorferi and Anaplasma phagocytophilum.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/pathogens14010078}, pmid = {39861039}, issn = {2076-0817}, support = {1750//Instytut Medycyny Wsi im. Witolda Chod&#x17a;ki/ ; 223743/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Anaplasma phagocytophilum/genetics ; *Borrelia burgdorferi ; Animals ; *Coculture Techniques ; *Coinfection/microbiology ; *Ixodes/microbiology ; Cell Line ; *Lyme Disease/microbiology ; Ehrlichiosis/microbiology ; Humans ; }, abstract = {Ixodes ricinus is an important vector of infectious human and livestock diseases in Europe. Co-infections of pathogens in ticks and hosts have been reported. Tick cell lines offer a useful model system for study of co-infections. We present a review of the existing literature on co-infections in tick cell lines. Previous studies have demonstrated the usefulness of tick cell lines in studies on co-infection of different pathogens and their interaction with the tick microbiome. We also carried out a preliminary study to investigate the effects of co-culturing Borrelia burgdorferi and Anaplasma phagocytophilum on their growth and interactions with the Ixodes ricinus cell line IRE/CTVM19 over a 13-day period. Replication of both pathogens was quantified by real-time PCR. The presence of A. phagocytophilum appeared to have a slight inhibitory effect on the multiplication of B. burgdorferi, that were added subsequently. In contrast, the prior presence of B. burgdorferi appeared to have a stimulatory effect on A. phagocytophilum after 6 days in culture. We conclude that the IRE/CTVM19 tick cell line is suitable for simultaneous and continuous cultivation of both bacteria and can be applied in future research.}, }
@article {pmid39860975, year = {2024}, author = {de Mezer, M and Chalama, N and Bratt, C and Kiebalo, M and Dolata, N and Rogaliński, J and Leszczyńska, M}, title = {Changes in the Microbiome During Chronic Rhinosinusitis.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/pathogens14010014}, pmid = {39860975}, issn = {2076-0817}, mesh = {Humans ; *Sinusitis/microbiology/immunology ; *Microbiota ; Chronic Disease ; *Rhinitis/microbiology/immunology ; Paranasal Sinuses/microbiology/immunology ; Rhinosinusitis ; }, abstract = {Chronic rhinosinusitis (CRS) is a common inflammatory disease of the paranasal sinuses with a yet unknown etiology. As studies continue to elucidate the disease's heterogeneity inflammatory profile and presentation, there is a growing interest in the influence of the nasal microbiome on disease pathogenesis and chronicity. The sinus microbiota appear dominated by the Staphylococcus and Corynebacterium genera; known upper airway pathogens, such as Haemophilus influenza, are present in the upper airways of healthy individuals, though at relatively lower abundances than in CRS patients. Viral culprits may induce an unhindered local immune response that contributes to the recurrence and chronicity of inverted papillomas-benign mucosal lesions with the propensity for local destruction and malignant transformation that can be found in patients with a history of nasal infection. The persistence of inverted papillomas warrants investigation into their pathogenesis and how they may contribute to a nasal landscape promoting the chronicity of CRS. Further investigation is needed to uncover the interplay between resident microbiota and viral, fungal, and immunological influence. Discerning between 'healthy' and 'diseased' sinonasal microbiomes and 'keystone' species could shed light on CRS etiology and provide the opportunity for CRS treatment tailored to an individual's microbiome. This review aims to explore the interrelation of microbial residents in the pathogenesis and chronicity of the diseased sinonasal environment.}, }
@article {pmid39860966, year = {2024}, author = {Laryushina, Y and Samoilova-Bedych, N and Turgunova, L and Marchenko, A and Turgunov, Y and Kozhakhmetov, S and Suieubayev, M and Mukhanbetzhanov, N and Kabdulina, N}, title = {Interrelationships of the Intestinal Microbiome, Trimethylamine N-Oxide and Lipopolysaccharide-Binding Protein with Crohn's Disease Activity.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/pathogens14010005}, pmid = {39860966}, issn = {2076-0817}, support = {AP14871959//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, mesh = {Humans ; *Methylamines/metabolism ; *Gastrointestinal Microbiome/physiology ; *Crohn Disease/microbiology/metabolism ; Female ; Male ; Adult ; *Acute-Phase Proteins/metabolism/analysis ; *Feces/microbiology/chemistry ; Middle Aged ; *Membrane Glycoproteins/metabolism ; Carrier Proteins/metabolism ; Young Adult ; Lipopolysaccharides/metabolism ; }, abstract = {UNLABELLED: Crohn's disease (CD) is a multifactorial inflammatory bowel disease whose pathogenetic mechanisms are a field of ongoing study. Changes in the intestinal microbiome in CD may influence metabolite production and reflect the disease's severity. We investigate the relationship between trimethylamine N-oxide (TMAO) and lipopolysaccharide-binding protein (LPS) levels and changes in the gut microbiome in patients with CD of various degrees of activity.<br><br>METHODS: In total, 29 CD patients and 15 healthy individuals were investigated for their levels of TMAO by HPLC-MS, and LPS protein by ELISA and metagenomic 16 s-sequencing of feces was performed.<br><br>RESULTS: We found significant differences in TMAO levels in patients in the remission/mild and moderate/severe groups compared to the control group (p = 0.02 and p = 0.014), changes in alpha diversity with the Shannon index (p = 0. 0151 and p = 0.0018) and in beta diversity (ANOSIM p = 0.009 and PERMANOVA p = 0.005) in both groups compared to controls. Strongly positive correlations in TMAO levels and mixed correlations of LPS with alpha diversity metrics were found, as well as significant correlations with microbiota species.<br><br>CONCLUSIONS: Changes in the level of metabolites may reflect specific disturbances in the composition of the intestinal microbiome at different degrees of severity of CD.}, }
@article {pmid39860963, year = {2024}, author = {D'Antonio, DL and Zenoniani, A and Umme, S and Piattelli, A and Curia, MC}, title = {Intratumoral Fusobacterium nucleatum in Pancreatic Cancer: Current and Future Perspectives.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/pathogens14010002}, pmid = {39860963}, issn = {2076-0817}, mesh = {Humans ; *Fusobacterium nucleatum/pathogenicity ; *Pancreatic Neoplasms/microbiology/pathology/immunology ; Fusobacterium Infections/microbiology ; Prognosis ; Animals ; }, abstract = {The intratumoral microbiome plays a significant role in many cancers, such as lung, pancreatic, and colorectal cancer. Pancreatic cancer (PC) is one of the most lethal malignancies and is often diagnosed at advanced stages. Fusobacterium nucleatum (Fn), an anaerobic Gram-negative bacterium primarily residing in the oral cavity, has garnered significant attention for its emerging role in several extra-oral human diseases and, lately, in pancreatic cancer progression and prognosis. It is now recognized as oncobacterium. Fn engages in pancreatic tumorigenesis and metastasis through multifaceted mechanisms, including immune response modulation, virulence factors, control of cell proliferation, intestinal metabolite interactions, DNA damage, and epithelial-mesenchymal transition. Additionally, compelling research suggests that Fn may exert detrimental effects on cancer treatment outcomes. This paper extends the perspective to pancreatic cancer associated with Fn. The central focus is to unravel the oncogenomic changes driven by Fn in colonization, initiation, and promotion of pancreatic cancer development. The presence of Fusobacterium species can be considered a prognostic marker of PC, and it is also correlated to chemoresistance. Furthermore, this review underscores the clinical research significance of Fn as a potential tumor biomarker and therapeutic target, offering a novel outlook on its applicability in cancer detection and prognostic assessment. It is thought that given the role of Fn in tumor formation and metastasis processes via its FadA, FapA, Fap2, and RadD, new therapies for tumor treatment targeting Fn will be developed.}, }
@article {pmid39860210, year = {2025}, author = {Darlington, DN}, title = {Conjugation of Short-Chain Fatty Acids to Bicyclic-Amines for Analysis by Liquid Chromatography Tandem Mass Spectroscopy.}, journal = {Molecules (Basel, Switzerland)}, volume = {30}, number = {2}, pages = {}, doi = {10.3390/molecules30020341}, pmid = {39860210}, issn = {1420-3049}, support = {none//Material Research Development Command/ ; }, mesh = {*Tandem Mass Spectrometry/methods ; *Fatty Acids, Volatile/analysis/chemistry ; Chromatography, Liquid ; *Amines/chemistry ; Animals ; Humans ; }, abstract = {Conjugation of short-chain fatty acids (SDFAs) to amines containing ring structures allows for better measurement by liquid chromatography tandem mass spectroscopy (LC-MS/MS). However, collision-induced dissociation (CID) results in breaking the conjugate back to the original SCFA and amine. We therefore set out to find an amine that would remain on the SCFA after CID and create a unique daughter for selectivity of measurement. Of twenty-seven amines with ring structures, we found four that contain bicycle-type structures (two rings connected by a carbon) with nitrogen in the second ring. CID removes the second ring at the nitrogen, leaving the first ring on the daughter. Of the four amines, 4-(pyrrolidine-1-ylmethyl) benzylamine (4PyBA) showed the strongest conjugation. Conjugation of 4PyBA to SCFA (C3-C6), their isomers and their phenylated versions (and isomers) resulted in good chromatographic peaks and separation. CID resulted in unique daughters that allowed for selectivity of measurement. Using this method, standard curves were generated that show good linearity (r2 > 0.99) in the nM and μM range with lower limits of detection between 40 and 229 nM for a 10 μL sample. Finally, we used this method to measure SCFA in plasma, liver, platelets, and red blood cells, demonstrating its use in biological systems. Because SCFAs are an index of microbiome diversity in the gastrointestinal track, this method will allow us to study changes in SCFAs and the microbiome in pathologic conditions including trauma, hemorrhage, and sepsis.}, }
@article {pmid39860065, year = {2025}, author = {Bruno, PS and Arshad, A and Gogu, MR and Waterman, N and Flack, R and Dunn, K and Darie, CC and Neagu, AN}, title = {Post-Translational Modifications of Proteins Orchestrate All Hallmarks of Cancer.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {1}, pages = {}, doi = {10.3390/life15010126}, pmid = {39860065}, issn = {2075-1729}, support = {R15CA260126/CA/NCI NIH HHS/United States ; }, abstract = {Post-translational modifications (PTMs) of proteins dynamically build the buffering and adapting interface between oncogenic mutations and environmental stressors, on the one hand, and cancer cell structure, functioning, and behavior. Aberrant PTMs can be considered as enabling characteristics of cancer as long as they orchestrate all malignant modifications and variability in the proteome of cancer cells, cancer-associated cells, and tumor microenvironment (TME). On the other hand, PTMs of proteins can enhance anticancer mechanisms in the tumoral ecosystem or sustain the beneficial effects of oncologic therapies through degradation or inactivation of carcinogenic proteins or/and activation of tumor-suppressor proteins. In this review, we summarized and analyzed a wide spectrum of PTMs of proteins involved in all regulatory mechanisms that drive tumorigenesis, genetic instability, epigenetic reprogramming, all events of the metastatic cascade, cytoskeleton and extracellular matrix (ECM) remodeling, angiogenesis, immune response, tumor-associated microbiome, and metabolism rewiring as the most important hallmarks of cancer. All cancer hallmarks develop due to PTMs of proteins, which modulate gene transcription, intracellular and extracellular signaling, protein size, activity, stability and localization, trafficking, secretion, intracellular protein degradation or half-life, and protein-protein interactions (PPIs). PTMs associated with cancer can be exploited to better understand the underlying molecular mechanisms of this heterogeneous and chameleonic disease, find new biomarkers of cancer progression and prognosis, personalize oncotherapies, and discover new targets for drug development.}, }
@article {pmid39860000, year = {2025}, author = {Hong, S and Lee, DB and Yoon, DW and Yoo, SL and Kim, J}, title = {The Effect of Sleep Disruption on Cardiometabolic Health.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {1}, pages = {}, doi = {10.3390/life15010060}, pmid = {39860000}, issn = {2075-1729}, support = {NRF-2021R1F1A1063264//National Research Foundation of Korea/ ; }, abstract = {Sleep disruption has emerged as a significant public health concern with profound implications for metabolic health. This review synthesizes current evidence demonstrating the intricate relationships between sleep disturbances and cardiometabolic dysfunction. Epidemiological studies have consistently demonstrated that insufficient sleep duration (<7 h) and poor sleep quality are associated with increased risks of obesity, type 2 diabetes, and cardiovascular disease. The underlying mechanisms are multifaceted, involving the disruption of circadian clock genes, alterations in glucose and lipid metabolism, the activation of inflammatory pathways, and the modulation of the gut microbiome. Sleep loss affects key metabolic regulators, including AMPK signaling and disrupts the secretion of metabolic hormones such as leptin and ghrelin. The latest evidence points to the role of sleep-induced changes in the composition and function of gut microbiota, which may contribute to metabolic dysfunction through modifications in the intestinal barrier and inflammatory responses. The NLRP3 inflammasome and NF-κB signaling pathways have been identified as crucial mediators linking sleep disruption to metabolic inflammation. An understanding of these mechanisms has significant implications for public health and clinical practice, suggesting that improving sleep quality could be an effective strategy for preventing and treating cardiometabolic disorders in modern society.}, }
@article {pmid39859943, year = {2024}, author = {Che Mohd Nassir, CMN and Che Ramli, MD and Mohamad Ghazali, M and Jaffer, U and Abdul Hamid, H and Mehat, MZ and Hein, ZM}, title = {The Microbiota-Gut-Brain Axis: Key Mechanisms Driving Glymphopathy and Cerebral Small Vessel Disease.}, journal = {Life (Basel, Switzerland)}, volume = {15}, number = {1}, pages = {}, doi = {10.3390/life15010003}, pmid = {39859943}, issn = {2075-1729}, abstract = {The human microbiota constitute a very complex ecosystem of microorganisms inhabiting both the inside and outside of our bodies, in which health maintenance and disease modification are the main regulatory features. The recent explosion of microbiome research has begun to detail its important role in neurological health, particularly concerning cerebral small vessel disease (CSVD), a disorder associated with cognitive decline and vascular dementia. This narrative review represents state-of-the-art knowledge of the intimate, complex interplay between microbiota and brain health through the gut-brain axis (GBA) and the emerging role of glymphatic system dysfunction (glymphopathy) and circulating cell-derived microparticles (MPs) as mediators of these interactions. We discuss how microbial dysbiosis promotes neuroinflammation, vascular dysfunction, and impaired waste clearance in the brain, which are critical factors in the pathogenesis of CSVD. Further, we discuss lifestyle factors that shape the composition and functionality of the microbiota, focusing on sleep as a modifiable risk factor in neurological disorders. This narrative review presents recent microbiome research from a neuroscientific and vascular perspective to establish future therapeutic avenues in targeting the microbiota to improve brain health and reduce the burden of CSVD.}, }
@article {pmid39859667, year = {2025}, author = {Mašková, Z and Medo, J and Kolesár, E and Tančinová, D and Ivanišová, E and Urminská, D and Hleba, L and Urminská, J and Mrvová, M and Barboráková, Z}, title = {Hermetia illucens in the Process of Kitchen Waste Biodegradation: The Effect of Different Approaches to Waste Storage on the Microbiological Profile and Nutritional Parameters of the Larvae.}, journal = {Insects}, volume = {16}, number = {1}, pages = {}, doi = {10.3390/insects16010087}, pmid = {39859667}, issn = {2075-4450}, support = {VEGA 1/0512/22//The Ministry of Education, Research, Development and Youth of the Slovak Republic/ ; }, abstract = {This study assessed the bioconversion efficiency of Hermetia illucens larvae (BSFL) fed on food waste stored under different conditions, focusing on the nutritional and microbial quality of the resulting larval biomass. Food waste was prepared as a fresh diet (FD) or naturally contaminated and stored at 20-22 °C (OS-T, opened storage-tempered) or under refrigeration, at 5-8 °C (CS-C, closed storage-cooled). Refrigerated, closed storage (CS-C) led to the highest rates of waste reduction (91.0%) and bioconversion efficiency (30.2%), with larvae exhibiting the highest protein content (36.83%) compared to the FD (35.5%) and OS-T (34.71%) groups. Microbiome analysis revealed that the CS-C condition promoted beneficial yeasts like Pichia and Diutia, which correlated positively with improved protein content and microbial safety. In contrast, OS-T storage supported spoilage fungi (Mucor, Rhizopus) and elevated total aerobic counts (7.28 log CFU/g), indicating higher microbial risks. The observed trends in waste reduction and protein content most probably relate to differences in microbial profiles, as controlled cooling affected microbial dynamics, preserving substrate quality and supporting larval growth. These findings emphasize the importance of refrigerated, closed storage to optimize bioconversion, improve larval nutritional value, and minimize microbiological hazards.}, }
@article {pmid39859601, year = {2024}, author = {Wu, H and Ji, C and Wang, R and Gao, L and Luo, W and Liu, J}, title = {Dietary Quercetin Regulates Gut Microbiome Diversity and Abundance in Apis cerana (Hymenoptera Apidae).}, journal = {Insects}, volume = {16}, number = {1}, pages = {}, doi = {10.3390/insects16010020}, pmid = {39859601}, issn = {2075-4450}, support = {CSTB2022NSCQ-MSX0257//Natural Science Foundation of Chongqing, China/ ; 23516C//the Special Financial Fund of Chongqing, China/ ; CARS-44-SYZ12//the Modern Agroindustry Technology Research System/ ; }, abstract = {Honeybee gut microbiota plays a crucial role in maintaining their health and digestive function. Studies have confirmed that quercetin improves honeybee health by enhancing their pesticide tolerance and survival rates. This study aimed to examine the effects of quercetin on the bee gut microbiome by absolute quantification sequencing. We included 1800 bees from the experimental apiary and exposed them to 151.2, 75.6, and 37.8 mg/L of quercetin. Gut samples were collected on the 5th and 9th days, subjected to a polymerase chain reaction and 16S rRNA sequencing, and analyzed. After 5 days of quercetin treatment, the diversity of the honeybee gut microbiota was altered, and total bacterial copies and Lactobacillus abundance significantly decreased at high quercetin concentrations (151.2 and 75.6 mg/L). On day 9, the gut microbial community had recovered from the adverse effects, and Gilliamella abundance increased in response to 37.8 mg/L quercetin treatment. However, quercetin had no noticeable effects on survival rate, food consumption, and gut structure. Our study confirmed the effect of short-term quercetin intake on the gut microbiota of A. cerana, providing valuable insights into how phytochemicals alter the bee gut microbiome, and their repercussions on host physiology.}, }
@article {pmid39859594, year = {2024}, author = {Perveen, N and Cabezas-Cruz, A and Iliashevich, D and Abuin-Denis, L and Sparagano, OA and Willingham, AL}, title = {Microbiome of Hyalomma dromedarii (Ixodida: Ixodidae) Ticks: Variation in Community Structure with Regard to Sex and Host Habitat.}, journal = {Insects}, volume = {16}, number = {1}, pages = {}, doi = {10.3390/insects16010011}, pmid = {39859594}, issn = {2075-4450}, support = {UPAR Grant # G00003709//United Arab Emirates University/ ; }, abstract = {Hyalomma dromedarii ticks are the main hematophagous ectoparasites of camels, harboring a variety of microbes that can affect tick vector competence and pathogen transmission. To better understand the tick microbiome influenced by sex and host habitat, we analyzed the bacterial community of H. dromedarii male and female ticks collected from camel farms, livestock markets, and slaughterhouses, representing the range of major habitats in the UAE, by sequencing the 16S rRNA gene. Tick samples were collected during 2022 and 2023. A total of 40 ticks (male (15), female (15), and nymph (10)) were selected from tick samples collected from camels and processed for genomic DNA and next-generation sequencing using the Illumina MiSeq platform. We obtained 151,168 read counts, and these formed 237 operational taxonomic units representing 11 phyla, 22 classes, 77 families, and 164 genera. The phyla Actinomycetota, Bacillota, Bacteroidota, Pseudomonadota, and Fusobacteriota were the most abundant. The bacterial genus Corynebacterium dominated the microbiomes of farm-collected female H. dromedarii ticks, while Proteus dominated the microbiomes of farm-collected male H. dromedarii ticks. In comparison, the microbiomes of H. dromedarii ticks collected from slaughterhouse samples were dominated by genus Francisella in both males and females. Our results confirm that the bacterial microbiomes of H. dromedarii ticks vary by sex and habitat settings. Furthermore, recent findings could deliver insight into the differences in the ability of camel ticks to acquire, maintain, and transmit pathogens in various habitats that may impact the tick vector competence of medically and agriculturally important species in the Middle East and North Africa (MENA) region and Asia.}, }
@article {pmid39859572, year = {2025}, author = {Kim, P and Joe, S and Kim, H and Jeong, H and Park, S and Song, J and Kim, W and Lee, YG}, title = {Hidden Partner of Immunity: Microbiome as an Innovative Companion in Immunotherapy.}, journal = {International journal of molecular sciences}, volume = {26}, number = {2}, pages = {}, doi = {10.3390/ijms26020856}, pmid = {39859572}, issn = {1422-0067}, support = {RS-2023-00217123//National Research Foundation of Korea/ ; }, mesh = {Humans ; *Immunotherapy/methods ; *Microbiota/immunology ; Neoplasms/therapy/immunology/microbiology ; Animals ; Gastrointestinal Microbiome/immunology ; Immune Checkpoint Inhibitors/therapeutic use ; Mesenchymal Stem Cell Transplantation/methods ; }, abstract = {Recent studies have highlighted that the microbiome is the essential factor that can modulate the clinical activity of immunotherapy. However, the role of the microbiome varies significantly across different immunotherapies, suggesting that it is critical to understand the precise function of the microbiome in each type of immunotherapy. While many previous studies primarily focus on summarizing the role of the microbiome in immune checkpoint inhibitors, we seek to explore a novel aspect of the microbiome in other immunotherapies such as mesenchymal stem cell therapy, chimeric antigen receptor T cell therapy, and antibodies-based therapy (e.g., adalimumab, infliximab, bevacizumab, denosumab, etc.) which are rarely summarized in previous reviews. Moreover, we highlight innovative strategies for utilizing microbiome and microbial metabolites to enhance the clinical response of immunotherapy. Collectively, we believe that our manuscript will provide novel insights and innovative approaches to the researchers, which could drive the development of the next generation of personalized therapeutic interventions using microbiomes.}, }
@article {pmid39859557, year = {2025}, author = {Terracina, S and Caronti, B and Lucarelli, M and Francati, S and Piccioni, MG and Tarani, L and Ceccanti, M and Caserta, M and Verdone, L and Venditti, S and Fiore, M and Ferraguti, G}, title = {Alcohol Consumption and Autoimmune Diseases.}, journal = {International journal of molecular sciences}, volume = {26}, number = {2}, pages = {}, doi = {10.3390/ijms26020845}, pmid = {39859557}, issn = {1422-0067}, mesh = {Humans ; *Autoimmune Diseases/etiology ; *Alcohol Drinking/adverse effects ; Animals ; Gastrointestinal Microbiome ; Alcoholism/metabolism ; }, abstract = {Alcohol is the second-most misused substance after tobacco. It has been identified as a causal factor in more than 200 diseases and 5.3% of all deaths and is associated with significant behavioral, social, and economic difficulties. As alcohol consumption may modulate the immune system's regulatory mechanisms to avoid attacking the body's tissues, it has been proven to play a dichotomic role in autoimmune diseases (ADs) based on the quantity of consumption. In this review, we report updated evidence on the role of alcohol in ADs, with a focus on alcohol addiction and the human biological immune system and the relationship between them, with alcohol as a risk or protective factor. Then, in this narrative review, we report the main evidence on the most studied ADs where alcohol represents a key modulator, including autoimmune thyroiditis, multiple sclerosis, rheumatoid arthritis, systemic lupus erythematosus, diabetes, allergic rhinitis, and primary biliary cholangitis. Alcohol at low-moderate dosages seems mostly to have a protective role in these diseases, while at higher dosages, the collateral risks surpass possible benefits. The specific mechanisms by which low-to-moderate alcohol intake relieves AD symptoms are not yet fully understood; however, emerging studies suggest that alcohol may have a systemic immunomodulatory effect, potentially altering the balance of anti-inflammatory innate and adaptive immune cells, as well as cytokines (via the NF-κB or NLRP3 pathways). It might influence the composition of the gut microbiome (increasing amounts of beneficial gut microbes) and the production of their fatty acid metabolites, such as short-chain fatty acids (SCFAs) and polyunsaturated fatty acids (PUFAs), as well as elevated concentrations of acetate, high-density lipoprotein (HDL), and nitric oxide (NO). Unfortunately, a definite acceptable daily intake (ADI) of ethanol is complicated to establish because of the many mechanisms associated with alcohol consumption such that despite the interesting content of these findings, there is a limit to their applicability and risks should be weighed in cases of alcoholic drinking recommendations. The aim of future studies should be to modulate those beneficial pathways involved in the alcohol-protective role of ADs with various strategies to avoid the risks associated with alcohol intake.}, }
@article {pmid39859492, year = {2025}, author = {Hao, Y and Lee, YJ and Yap, K and Samuel, M and Chow, VT}, title = {Comparison of Respiratory Microbiomes in Influenza Versus Other Respiratory Infections: Systematic Review and Analysis.}, journal = {International journal of molecular sciences}, volume = {26}, number = {2}, pages = {}, doi = {10.3390/ijms26020778}, pmid = {39859492}, issn = {1422-0067}, mesh = {Humans ; *Microbiota ; *Influenza, Human/microbiology/virology ; *Respiratory Tract Infections/microbiology/virology ; Dysbiosis/microbiology ; COVID-19/microbiology/virology ; Respiratory System/microbiology/virology ; Bacteria/classification/isolation &amp; purification/genetics ; }, abstract = {Studies have indicated the potential importance of the human nasal and respiratory microbiomes in health and disease. However, the roles of these microbiomes in the pathogenesis of influenza and its complications are not fully understood. Therefore, the objective of this systematic review and analysis is to identify the patterns of nasal and respiratory microbiome dysbiosis and to define the unique signature bacteria associated with influenza compared with other respiratory tract infections. We compared the respiratory microbiome composition between influenza patients and healthy controls; across different influenza severities; in adult versus pediatric influenza patients; as well as influenza versus other respiratory infections. The desired outcomes include the signature bacteria in each cohort and the Shannon index to reflect the alpha diversity. Of the 2269 articles identified, 31 studies fulfilled the inclusion criteria. These studies investigated the respiratory tract microbiomes of patients with influenza, COVID-19, pneumonia, other respiratory infections, and chronic rhinosinusitis (CRS). Our review revealed that the phylum Firmicutes and Actinobacteria, genus Actinomyces, Streptococcus and Granulicatella, and species Neisseria are more prominent in severe influenza than mild to moderate influenza. Reduced microbiome alpha diversity is noted in influenza patients compared to healthy controls. There are some similarities and differences between the signature bacteria in pediatric and adult influenza patients, e.g., Streptococcus is common in both age groups, whereas Pseudomonas is associated with adults. Intriguingly, there is a common predominance of Streptococcus and Firmicutes among influenza and pneumonia patients. COVID-19 patients exhibit an increased abundance of Firmicutes as well as Pseudomonas. In CRS patients, Proteobacteria and Haemophilus are found in high abundance. This review highlights some similarities and differences in the respiratory microbiomes and their signature organisms in influenza of varying severity and in different age groups compared with other respiratory infections. The dysbiosis of the respiratory microbiomes in these respiratory infections enhances our understanding of their underlying pathogenic mechanisms.}, }
@article {pmid39859442, year = {2025}, author = {Fanijavadi, S and Jensen, LH}, title = {Dysbiosis-NK Cell Crosstalk in Pancreatic Cancer: Toward a Unified Biomarker Signature for Improved Clinical Outcomes.}, journal = {International journal of molecular sciences}, volume = {26}, number = {2}, pages = {}, doi = {10.3390/ijms26020730}, pmid = {39859442}, issn = {1422-0067}, mesh = {Humans ; *Dysbiosis/microbiology ; *Pancreatic Neoplasms/immunology/microbiology/metabolism ; *Killer Cells, Natural/immunology/metabolism ; *Tumor Microenvironment/immunology ; *Biomarkers, Tumor/metabolism ; Carcinoma, Pancreatic Ductal/immunology/microbiology/metabolism/therapy/pathology ; Microbiota ; Animals ; }, abstract = {Pancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with poor prognosis, primarily due to its immunosuppressive tumor microenvironment (TME), which contributes to treatment resistance. Recent research shows that the microbiome, including microbial communities in the oral cavity, gut, bile duct, and intratumoral environments, plays a key role in PDAC development, with microbial imbalances (dysbiosis) promoting inflammation, cancer progression, therapy resistance, and treatment side effects. Microbial metabolites can also affect immune cells, especially natural killer (NK) cells, which are vital for tumor surveillance, therapy response and treatment-related side effects. Dysbiosis can affect NK cell function, leading to resistance and side effects. We propose that a combined biomarker approach, integrating microbiome composition and NK cell profiles, can help predict treatment resistance and side effects, enabling more personalized therapies. This review examines how dysbiosis contributes to NK cell dysfunction in PDAC and discusses strategies (e.g., antibiotics, probiotics, vaccines) to modulate the microbiome and enhance NK cell function. Targeting dysbiosis could modulate NK cell activity, improve the effectiveness of PDAC treatments, and reduce side effects. However, further research is needed to develop unified NK cell-microbiome interaction-based biomarkers for more precise and effective patient outcomes.}, }
@article {pmid39859400, year = {2025}, author = {Przemieniecki, SW and Damszel, M and Kosewska, O}, title = {The Impact of Nanoparticles and Molecular Forms of TiO2 on the Rhizosphere of Plants in the Example of Common Wheat (Triticum aestivum L.)-Shifts in Microbiome Structure and Predicted Microbial Metabolic Functions.}, journal = {International journal of molecular sciences}, volume = {26}, number = {2}, pages = {}, doi = {10.3390/ijms26020685}, pmid = {39859400}, issn = {1422-0067}, support = {30.610.011-110//University of Warmia and Mazury in Olsztyn/ ; }, mesh = {*Titanium/chemistry/pharmacology ; *Triticum/microbiology/metabolism ; *Rhizosphere ; *Microbiota/drug effects ; Soil Microbiology ; Nanoparticles/chemistry ; Plant Roots/microbiology/drug effects/metabolism ; Bacteria/drug effects/metabolism/classification ; Metal Nanoparticles/chemistry ; }, abstract = {This study investigated the effects of various titanium nanoparticles (TiO2NPs) on the structure, function, and trophic levels of the wheat rhizobiome. In contrast to the typically toxic effects of small nanoparticles (~10 nm), this research focused on molecular TiO2 and larger nanoparticles, as follows: medium-sized (68 nm, NPs1) and large (>100 nm, NPs2). The results demonstrated significant yet diverse impacts of different TiO2 forms on the rhizosphere microbiota. Large TiO2NPs2 and molecular TiO2 adversely affected the bacteriobiome and mycobiome, leading to an increase in autotrophic microbial groups. In contrast, medium-sized TiO2NPs1 shifted the microbiome toward chemoheterotrophy, promoting plant growth-associated bacteria, fungal saprotrophs, and potential phytopathogens, suggesting a beneficial r-strategy within the rhizosphere. Other treatments induced oligotrophic conditions, resulting in a less flexible rhizobiome with diminished root associations but an increased abundance of Trichoderma spp. Structural modelling revealed that even minor changes in operational taxonomic units (OTUs) could significantly alter the microbiota's metabolic potential. These findings highlight the importance of further research to optimize nanoparticle applications for sustainable agriculture.}, }
@article {pmid39859363, year = {2025}, author = {Merrill, AH}, title = {Don't Be Surprised When These Surprise You: Some Infrequently Studied Sphingoid Bases, Metabolites, and Factors That Should Be Kept in Mind During Sphingolipidomic Studies.}, journal = {International journal of molecular sciences}, volume = {26}, number = {2}, pages = {}, doi = {10.3390/ijms26020650}, pmid = {39859363}, issn = {1422-0067}, mesh = {*Sphingolipids/metabolism ; Animals ; Humans ; *Lipidomics/methods ; Sphingosine/metabolism/analogs &amp; derivatives ; Mass Spectrometry/methods ; Ceramides/metabolism ; }, abstract = {Sphingolipidomic mass spectrometry has provided valuable information-and surprises-about sphingolipid structures, metabolism, and functions in normal biological processes and disease. Nonetheless, many noteworthy compounds are not routinely determined, such as the following: most of the sphingoid bases that mammals biosynthesize de novo other than sphingosine (and sometimes sphinganine) or acquire from exogenous sources; infrequently considered metabolites of sphingoid bases, such as N-(methyl)n-derivatives; "ceramides" other than the most common N-acylsphingosines; and complex sphingolipids other than sphingomyelins and simple glycosphingolipids, including glucosyl- and galactosylceramides, which are usually reported as "monohexosylceramides". These and other subspecies are discussed, as well as some of the circumstances when they are likely to be seen (or present and missed) due to experimental conditions that can influence sphingolipid metabolism, uptake from the diet or from the microbiome, or as artifacts produced during extraction and analysis. If these compounds and factors are kept in mind during the design and interpretation of lipidomic studies, investigators are likely to be surprised by how often they appear and thereby advance knowledge about them.}, }
@article {pmid39859341, year = {2025}, author = {Bello-Perez, M and García-Pachón, E and Gonzalo-Jimenez, N and Ruiz-García, M and Zamora-Molina, L and Baeza-Martinez, C and Galiana, A}, title = {Gene Expression Profiles Reveal Distinct Mechanisms Driving Chronic Obstructive Pulmonary Disease Exacerbations.}, journal = {International journal of molecular sciences}, volume = {26}, number = {2}, pages = {}, doi = {10.3390/ijms26020627}, pmid = {39859341}, issn = {1422-0067}, support = {GV/2019/104//Conselleria d'Innovaci&#xf3;, Universitats, Ci&#xe8;ncia i Societat Digital/ ; }, mesh = {*Pulmonary Disease, Chronic Obstructive/genetics ; Humans ; Male ; Female ; *Sputum/metabolism/microbiology ; Aged ; *Transcriptome ; Middle Aged ; *Gene Expression Profiling ; Biomarkers ; RNA, Ribosomal, 16S/genetics ; Disease Progression ; Microbiota ; Neutrophils/metabolism ; }, abstract = {Chronic obstructive pulmonary disease (COPD) exacerbations are major contributors to morbidity and mortality, highlighting the need to better understand their molecular mechanisms to improve prevention, diagnosis, and treatment. This study investigated differential gene expression profiles and key biological processes in COPD exacerbations categorized based on sputum microbiome profiling. An observational study was performed on a cohort of 16 COPD patients, who provided blood and sputum samples during exacerbations, along with five stable-state samples as controls. Exacerbations were classified using 16S rRNA sequencing to analyze the sputum microbiota and multiplex PCR to detect respiratory viruses. Blood transcriptomic profiling was conducted using Oxford Nanopore technology, followed by differential gene expression and pathway enrichment analyses. A total of 768 regulated genes were identified across the exacerbation groups, with 35 shared genes associated with neutrophil activation. Bacterial exacerbations activated pathways related to phagocytosis and toll-like receptor signaling, while viral exacerbations were linked to pro-inflammatory responses and mitochondrial damage. Exacerbations of unknown origin showed activation of pathways involved in protozoan defense and neutrophilic asthma. Biomarkers such as IFITM3 and ISG15 for bacterial exacerbations, DEFA3 for viral, and CD47 for unknown-origin exacerbations were identified. These findings highlight distinct transcriptomic profiles and biological pathways in COPD exacerbations, emphasizing the central role of neutrophil-driven inflammation and identifying potential biomarkers for improved differential diagnosis and personalized management.}, }
@article {pmid39859327, year = {2025}, author = {Randeni, N and Xu, B}, title = {Critical Review of the Cross-Links Between Dietary Components, the Gut Microbiome, and Depression.}, journal = {International journal of molecular sciences}, volume = {26}, number = {2}, pages = {}, doi = {10.3390/ijms26020614}, pmid = {39859327}, issn = {1422-0067}, support = {UICR0400016-24//BNU-HKBU United International College/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Depression/metabolism/microbiology ; *Diet ; Brain-Gut Axis/physiology ; Animals ; }, abstract = {The complex relationship between diet, the gut microbiota, and mental health, particularly depression, has become a focal point of contemporary research. This critical review examines how specific dietary components, such as fiber, proteins, fats, vitamins, minerals, and bioactive compounds, shape the gut microbiome and influence microbial metabolism in order to regulate depressive outcomes. These dietary-induced changes in the gut microbiota can modulate the production of microbial metabolites, which play vital roles in gut-brain communication. The gut-brain axis facilitates this communication through neural, immune, and endocrine pathways. Alterations in microbial metabolites can influence central nervous system (CNS) functions by impacting neuroplasticity, inflammatory responses, and neurotransmitter levels-all of which are linked to the onset and course of depression. This review highlights recent findings linking dietary components with beneficial changes in gut microbiota composition and reduced depressive symptoms. We also explore the challenges of individual variability in responses to dietary interventions and the long-term sustainability of these strategies. The review underscores the necessity for further longitudinal and mechanistic studies to elucidate the precise mechanisms through which diet and gut microbiota interactions can be leveraged to mitigate depression, paving the way for personalized nutritional therapies.}, }
@article {pmid39859243, year = {2025}, author = {Xirouchakis, E and Pelekanos, A and Xirouchakis, S and Kranidioti, H and Manolakopoulos, S}, title = {A Systematic Review of Microbiota in Cirrhosis: A Change Towards a More Pathogenic Predisposition.}, journal = {International journal of molecular sciences}, volume = {26}, number = {2}, pages = {}, doi = {10.3390/ijms26020527}, pmid = {39859243}, issn = {1422-0067}, mesh = {Humans ; *Liver Cirrhosis/microbiology ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Bacteria/classification/genetics ; Hepatic Encephalopathy/microbiology ; Liver Neoplasms/microbiology ; Disease Susceptibility ; Carcinoma, Hepatocellular/microbiology ; }, abstract = {The microbiome of the human intestine is a regulator of health that modulates immune response and plays an important role in metabolism. The diversity, and abundance of microbiota communities in the gut have been shown to change in cirrhosis and its complications. We aimed to review the current knowledge regarding microbiota alterations in cirrhosis, its potential differences according to etiology, and its role in the development of cirrhosis complications. A systematic search of the online bibliographic database up to July 2024 was performed. Randomized controlled trials and observational and cohort studies that included a total or at least a cohort of cirrhotic adult patients were enlisted for data extraction and analysis. A total of 73 publications were included for data extraction. Alpha diversity was found to decrease in cirrhotic patients in 30/38 (78%) of the studies, while beta diversity in 20/22 (90%) presented significant differences between healthy and cirrhotic groups. Proteobacteria significantly increased in 20/27 (74%) studies, followed by Actinobacteria and Fusobacteria, while 22/25 (88%) studies found either a reduction in cirrhotic patients or increased abundance in healthy controls for Firmicutes and Bacteroidetes. The most abundant genera in hepatic encephalopathy groups were pathobionts such as Enterococcus and Streptococcus, followed by Vellionella and Escherichia. Heterogeneity was found among studies regarding Alpha diversity in hepatocellular carcinoma (HCC) as it was decreased in three studies, indifferent in five, and increased in three studies in comparison to cirrhotic non-HCC patients. The dysbiosis of the gut microbiota is associated with cirrhosis and the development of complications such as hepatic encephalopathy and hepatocellular carcinoma.}, }
@article {pmid39859161, year = {2025}, author = {Yuan, Y and Niu, X and Hao, C and Liang, L and Huang, Z and Wang, D and Hong, M and Ding, L}, title = {Dietary Taurine Regulation of the Intestinal Microbiome in Chinese Stripe-Necked Turtle (Mauremys sinensis).}, journal = {International journal of molecular sciences}, volume = {26}, number = {2}, pages = {}, doi = {10.3390/ijms26020445}, pmid = {39859161}, issn = {1422-0067}, support = {No. 32471587//Meiling Hong/ ; No. ZDYF2024SHFZ061//Li Ding/ ; No. 32271577//Li Ding/ ; }, mesh = {Animals ; *Turtles/microbiology ; *Taurine/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Dietary Supplements ; Animal Feed ; Bacteria/classification/drug effects/genetics ; Diet ; }, abstract = {Taurine is essential for sustaining the body's physiological equilibrium and is extensively utilized as a dietary supplement and immune system enhancer for aquatic creatures. The gut microbiota serves as a vital health indicator in animals. In this study, our goal was to evaluate the effects of dietary taurine on the gut microbiome of Chinese stripe-necked turtles (Mauremys sinensis). Turtles were evenly divided into three supplementation groups: a control group with no taurine in the diet, a low group with 0.1% taurine, and a high group with 0.4% taurine. High-throughput sequencing was employed to analyze the gut microbiome's composition and structure. The results showed that the impact of taurine supplementation on the α-diversity and β-diversity of the gut microbiome was not statistically significant. At the phylum level, Firmicutes and Bacteroidetes predominated the gut microbiome. At the genus level, three beneficial bacteria, Clostridium_sensu_stricto_13, Pygmaiobacter, and Terrisporobacter showed significant differences under different levels of taurine supplementation and increased in abundance with the supplementation of taurine, while the harmful bacterium Brucella decreased in abundance with the addition of taurine and exhibited significant differences. Furthermore, LEfSe analysis and functional predictions highlighted significant variations in the functional traits of gram-positive intestinal bacteria among the different taurine supplementation levels. These findings imply that dietary taurine may alter the intestinal microbiome structure in Chinese stripe-necked turtles, offering valuable insights for the scientific assessment of taurine's health benefits as a feed additive and potentially guiding the formulation of more informed and healthier feeding practices.}, }
@article {pmid39859091, year = {2025}, author = {Almonajjed, MB and Wardeh, M and Atlagh, A and Ismaiel, A and Popa, SL and Rusu, F and Dumitrascu, DL}, title = {Impact of Microbiota on Irritable Bowel Syndrome Pathogenesis and Management: A Narrative Review.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {61}, number = {1}, pages = {}, doi = {10.3390/medicina61010109}, pmid = {39859091}, issn = {1648-9144}, mesh = {Humans ; *Irritable Bowel Syndrome/therapy/microbiology/physiopathology ; *Gastrointestinal Microbiome/physiology ; *Fecal Microbiota Transplantation/methods ; *Probiotics/therapeutic use ; Brain-Gut Axis/physiology ; Dysbiosis/therapy/complications ; Quality of Life ; Synbiotics/administration &amp; dosage ; Prebiotics/administration &amp; dosage ; }, abstract = {Irritable bowel syndrome (IBS) is a prevalent gastrointestinal disorder, affecting 3-5% of the global population and significantly impacting patients' quality of life and healthcare resources. Alongside physical symptoms such as abdominal pain and altered bowel habits, many individuals experience psychological comorbidities, including anxiety and depression. Recent research has highlighted the critical role of the gut microbiota in IBS, with dysbiosis, characterized by an imbalance in microbial diversity, frequently observed in patients. The gut-brain axis, a bidirectional communication network between the gut and central nervous system, plays a central role in the development of IBS symptoms. Although interventions such as probiotics, prebiotics, synbiotics, and fecal microbiota transplantation (FMT) have demonstrated potential in modulating the gut microbiota and alleviating symptoms, their efficacy remains an area of ongoing investigation. This review examines the interactions between the gut microbiota, immune system, and brain, emphasizing the need for personalized therapeutic strategies. Future research should aim to identify reliable microbiota-based biomarkers for IBS and refine microbiome-targeted therapies to enhance patient outcomes.}, }
@article {pmid39858966, year = {2025}, author = {Moroni, F and Naya-Català, F and Hafez, AI and Domingo-Bretón, R and Soriano, B and Llorens, C and Pérez-Sánchez, J}, title = {Beyond Microbial Variability: Disclosing the Functional Redundancy of the Core Gut Microbiota of Farmed Gilthead Sea Bream from a Bayesian Network Perspective.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010198}, pmid = {39858966}, issn = {2076-2607}, support = {THINKINAZUL/2021/024//Generalitat Valenciana/ ; PID2023-146990OB-I00//Spanish MCIU project BreamHOLOBIONT/ ; PRTR-C17.I1//European Union NextGenerationEU/ ; }, abstract = {The significant microbiota variability represents a key feature that makes the full comprehension of the functional interaction between microbiota and the host an ongoing challenge. To overcome this limitation, in this study, fish intestinal microbiota was analyzed through a meta-analysis, identifying the core microbiota and constructing stochastic Bayesian network (BN) models with SAMBA. We combined three experiments performed with gilthead sea bream juveniles of the same hatchery batch, reared at the same season/location, and fed with diets enriched on processed animal proteins (PAP) and other alternative ingredients (NOPAP-PP, NOPAP-SCP). Microbiota data analysis disclosed a high individual taxonomic variability, a high functional homogeneity within trials and highlighted the importance of the core microbiota, clustering PAP and NOPAP fish microbiota composition. For both NOPAP and PAP BNs, >99% of the microbiota population were modelled, with a significant proportion of bacteria (55-69%) directly connected with the diet variable. Functional enrichment identified 11 relevant pathways expressed by different taxa across the different BNs, confirming the high metabolic plasticity and taxonomic heterogeneity. Altogether, these results reinforce the comprehension of the functional bacteria-host interactions and in the near future, allow the use of microbiota as a species-specific growth and welfare benchmark of livestock animals, and farmed fish in particular.}, }
@article {pmid39858953, year = {2025}, author = {Takasugi, S and Iimura, S and Yasuda, M and Saito, Y and Morifuji, M}, title = {Key Taxa of the Gut Microbiome Associated with the Relationship Between Environmental Sensitivity and Inflammation-Related Biomarkers.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010185}, pmid = {39858953}, issn = {2076-2607}, abstract = {Individual differences in environmental sensitivity are linked to stress-related psychiatric symptoms. In previous research, we found that high environmental sensitivity can be a risk factor for increased inflammation and gut permeability, particularly when gut microbiome diversity is low. However, the specific gut bacterial taxa involved in this interaction remain unclear. As a preliminary study, this research aimed to identify the key gut microbiome taxa associated with this relationship. Environmental sensitivity, gut microbiome composition, gut permeability (lipopolysaccharide-binding protein, LBP), and inflammation (C-reactive protein, CRP) biomarkers were evaluated in 88 participants. The interaction between environmental sensitivity and the relative abundance of the family Marinifilaceae (genus Butyricimonas) was a predictor of CRP levels. Similarly, the interaction between environmental sensitivity and relative abundance of the family Barnesiellaceae (genus Coprobacter), the family Akkermansiaceae (genus Akkermansia), the genus Family XIII AD3011 group, the genus GCA-900066225, or the genus Ruminiclostridium 1 predicted LBP levels. Individuals with high environmental sensitivity exhibited elevated CRP or LBP levels when the relative abundance of these taxa was low. Conversely, highly sensitive individuals had lower CRP or LBP levels when the relative abundance of these taxa was high. This study suggests that specific taxa serve as one of the protective factors against inflammation and gut permeability in individuals with high environmental sensitivity. Further in-depth studies are needed to confirm these associations and understand the underlying mechanisms.}, }
@article {pmid39858934, year = {2025}, author = {Wang, M and Valizadegan, N and Fields, CJ and Donovan, SM}, title = {Fecal Microbiome and Metabolomic Profiles of Mixed-Fed Infants Are More Similar to Formula-Fed than Breastfed Infants.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010166}, pmid = {39858934}, issn = {2076-2607}, support = {1R01DK107561-05A1/NH/NIH HHS/United States ; 1R01DK138032-01A1/NH/NIH HHS/United States ; }, abstract = {Many infants consume both human milk and infant formula (mixed-fed); however, few studies have investigated how mixed feeding affects the gut microbiome composition and metabolic profiles compared to exclusive breastfeeding or formula feeding. Herein, how delivery mode and early nutrition affect the microbiome and metabolome of 6-week-old infants in the STRONG Kids2 cohort was investigated. Fecal samples were collected from exclusively breastfed (BF; n = 25), formula-fed (FF; n = 25) or mixed-fed (MF; n = 25) participants. Within each feeding group, infants were either delivered vaginally (VD; n = 13) or by Cesarean section (CS; n = 12). Feeding mode affects the fecal microbiome diversity, composition, and functional potential, as well as metabolomic profiles regardless of delivery mode. Alpha and beta diversity of MF differed from that of BF (p < 0.05) but were comparable to FF infants. Functional analyses have shown 117 potential metabolic pathways differed between BF and FF, 112 between BF and MF, and 8 between MF and FF infants (p < 0.05, q < 0.10). Fecal metabolomic profiles of MF and FF clustered together and separated from BF infants. In total, 543 metabolites differed between BF and FF, 517 between BF and MF, and 3 between MF and FF (p < 0.05, q < 0.10). Delivery mode affected overall microbial composition (p = 0.022) at the genus level and 24 potential functional pathways, with 16 pathways being higher in VD than CS infants (p < 0.05, q < 0.10). Metabolomic analysis identified 47 differential metabolites between CS and VD, with 39 being lower in CS than VD (p < 0.05, q < 0.10). In summary, fecal microbiota composition and function and metabolite profiles of 6-week-old MF infants are closer to FF than BF infants.}, }
@article {pmid39858932, year = {2025}, author = {Kreouzi, M and Theodorakis, N and Nikolaou, M and Feretzakis, G and Anastasiou, A and Kalodanis, K and Sakagianni, A}, title = {Skin Microbiota: Mediator of Interactions Between Metabolic Disorders and Cutaneous Health and Disease.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010161}, pmid = {39858932}, issn = {2076-2607}, abstract = {Metabolic disorders, including type 2 diabetes mellitus (T2DM), obesity, and metabolic syndrome, are systemic conditions that profoundly impact the skin microbiota, a dynamic community of bacteria, fungi, viruses, and mites essential for cutaneous health. Dysbiosis caused by metabolic dysfunction contributes to skin barrier disruption, immune dysregulation, and increased susceptibility to inflammatory skin diseases, including psoriasis, atopic dermatitis, and acne. For instance, hyperglycemia in T2DM leads to the formation of advanced glycation end products (AGEs), which bind to the receptor for AGEs (RAGE) on keratinocytes and immune cells, promoting oxidative stress and inflammation while facilitating Staphylococcus aureus colonization in atopic dermatitis. Similarly, obesity-induced dysregulation of sebaceous lipid composition increases saturated fatty acids, favoring pathogenic strains of Cutibacterium acnes, which produce inflammatory metabolites that exacerbate acne. Advances in metabolomics and microbiome sequencing have unveiled critical biomarkers, such as short-chain fatty acids and microbial signatures, predictive of therapeutic outcomes. For example, elevated butyrate levels in psoriasis have been associated with reduced Th17-mediated inflammation, while the presence of specific Lactobacillus strains has shown potential to modulate immune tolerance in atopic dermatitis. Furthermore, machine learning models are increasingly used to integrate multi-omics data, enabling personalized interventions. Emerging therapies, such as probiotics and postbiotics, aim to restore microbial diversity, while phage therapy selectively targets pathogenic bacteria like Staphylococcus aureus without disrupting beneficial flora. Clinical trials have demonstrated significant reductions in inflammatory lesions and improved quality-of-life metrics in patients receiving these microbiota-targeted treatments. This review synthesizes current evidence on the bidirectional interplay between metabolic disorders and skin microbiota, highlighting therapeutic implications and future directions. By addressing systemic metabolic dysfunction and microbiota-mediated pathways, precision strategies are paving the way for improved patient outcomes in dermatologic care.}, }
@article {pmid39858922, year = {2025}, author = {Qiqige, B and Liu, J and Li, M and Hu, X and Guo, W and Wang, P and Ding, Y and Zhi, Q and Wu, Y and Guan, X and Li, J}, title = {Different Flooding Conditions Affected Microbial Diversity in Riparian Zone of Huihe Wetland.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010154}, pmid = {39858922}, issn = {2076-2607}, support = {No. 2020-YSKY-020//Xiao Guan/ ; No. 2020-JY-008//Xiao Guan/ ; }, abstract = {The soil microbiome plays an important role in wetland ecosystem services and functions. However, the impact of soil hydrological conditions on wetland microorganisms is not well understood. This study investigated the effects of wetted state (WS); wetting-drying state (WDS); and dried state (DS) on the diversity of soil bacteria, fungi, and archaea. The Shannon index of bacterial diversity was not significantly different in various flooding conditions (p > 0.05), however, fungal diversity and archaeal communities were significantly different in different flooding conditions (p < 0.05). Significant differences were found in the beta diversity of bacterial, fungal, and archaeal communities (p < 0.05). Additionally, the composition of bacteria, fungi, and archaea varied. Bacteria were predominantly composed of Proteobacteria and Actinobacteria, fungi mainly consisted of Ascomycota and Mucoromycota, and archaea were primarily represented by Crenarchaeota and Euryarchaeota. Bacteria exhibited correlations with vegetation coverage, fungi with plant diversity, and archaea with aboveground vegetation biomass. The pH influenced bacterial and archaeal communities, while soil bulk density, moisture, soil carbon, soil nitrogen, and plant community diversity impacted fungal communities. This study provides a scientific basis for understanding the effects of different hydrological conditions on microbial communities in the Huihe Nature Reserve; highlighting their relationship with vegetation and soil properties, and offers insights for the ecological protection of the Huihe wetland.}, }
@article {pmid39858916, year = {2025}, author = {You, T and Liu, Q and Chen, M and Tang, S and Ou, L and Li, D}, title = {Synthetic Microbial Communities Enhance Pepper Growth and Root Morphology by Regulating Rhizosphere Microbial Communities.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010148}, pmid = {39858916}, issn = {2076-2607}, support = {2022YFF1300704//Ministry of Science and Technology of the People's Republic of China/ ; 42201068//National Natural Science Foundation of China/ ; 2024RC3243//Hunan provincial Department of Science and Technology/ ; 2023JJ40647//Hunan provincial Department of Science and Technology/ ; Heke ZY220601//Guangxi provincial Department of Science and Technology/ ; }, abstract = {Synthetic microbial community (SynCom) application is efficient in promoting crop yield and soil health. However, few studies have been conducted to enhance pepper growth via modulating rhizosphere microbial communities by SynCom application. This study aimed to investigate how SynCom inoculation at the seedling stage impacts pepper growth by modulating the rhizosphere microbiome using high-throughput sequencing technology. SynCom inoculation significantly increased shoot height, stem diameter, fresh weight, dry weight, chlorophyll content, leaf number, root vigor, root tips, total root length, and root-specific surface area of pepper by 20.9%, 36.33%, 68.84%, 64.34%, 29.65%, 27.78%, 117.42%, 35.4%, 21.52%, and 39.76%, respectively, relative to the control. The Chao index of the rhizosphere microbial community and Bray-Curtis dissimilarity of the fungal community significantly increased, while Bray-Curtis dissimilarity of the bacterial community significantly decreased by SynCom inoculation. The abundances of key taxa such as Scedosporium, Sordariomycetes, Pseudarthrobacter, norankSBR1031, and norankA4b significantly increased with SynCom inoculation, and positively correlated with indices of pepper growth. Our findings suggest that SynCom inoculation can effectively enhance pepper growth and regulate root morphology by regulating rhizosphere microbial communities and increasing key taxa abundance like Sordariomycetes and Pseudarthrobacter, thereby benefiting nutrient acquisition, resistance improvement, and pathogen resistance of crops to ensure sustainability.}, }
@article {pmid39858915, year = {2025}, author = {Mohan, B and Karthik, C and Thingujam, D and Pajerowska-Mukhtar, KM and Thomas, V and Mukhtar, MS}, title = {Plasma Optimization as a Novel Tool to Explore Plant-Microbe Interactions in Climate Smart Agriculture.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010146}, pmid = {39858915}, issn = {2076-2607}, support = {IOS-2038872//National Science Foundation/ ; 2418230//National Science Foundation/ ; OIA-2148653//National Science Foundation/ ; }, abstract = {Plasma treatment has emerged as a promising tool for manipulating plant microbiomes and metabolites. This review explores the diverse applications and effects of plasma on these biological systems. It is hypothesized that plasma treatment will not induce substantial changes in the composition of plant microbiomes or the concentration of plant metabolites. We delve into the mechanisms by which plasma can regulate microbial communities, enhance antimicrobial activity, and recruit beneficial microbes to mitigate stress. Furthermore, we discuss the optimization of plasma parameters for effective microbiome interaction and the role of plasmids in plant-microbe interactions. By characterizing plasmidome responses to plasma exposure and investigating transcriptional and metabolomic shifts, we provide insights into the potential of plasma as a tool for engineering beneficial plant-microbe interactions. The review presented herein demonstrates that plasma treatment induces substantial changes in both microbial community composition and metabolite levels, thereby refuting our initial hypothesis. Finally, we integrate plasmidome, transcriptome, and metabolome data to develop a comprehensive understanding of plasma's effects on plant biology and explore future perspectives for agricultural applications.}, }
@article {pmid39858914, year = {2025}, author = {Magoutas, K and Leathersich, S and Hart, R and Ireland, D and Walls, M and Payne, M}, title = {Lower Semen Quality Among Men in the Modern Era-Is There a Role for Diet and the Microbiome?.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010147}, pmid = {39858914}, issn = {2076-2607}, abstract = {The prevalence of infertility is increasing worldwide; poor nutrition, increased sedentary lifestyles, obesity, stress, endocrine-disrupting chemicals, and advanced age of childbearing may contribute to the disruption of ovulation and influence oocyte and sperm quality and overall reproductive health. Historically, infertility has been primarily attributed to female factors, neglecting the importance of male fertility; this has resulted in an incomplete understanding of reproductive health. Male factors account for 40-50% of infertility cases. In half of these cases, the proximal cause for male infertility is unknown. Sperm contributes half of the nuclear DNA to the embryo, and its quality is known to impact fertilisation rates, embryo quality, pregnancy rates, risk of spontaneous miscarriage, de novo autosomal-dominant conditions, psychiatric and neurodevelopment conditions, and childhood diseases. Recent studies have suggested that both the microenvironment of the testes and diet quality may play an important role in fertility; however, there is limited research on the combination of these factors. This review summarises current known causes of male infertility and then focuses on the potential roles for diet and the seminal microbiome. Future research in this area will inform dietary interventions and health advice for men with poor semen quality, potentially alleviating the need for costly and invasive assisted reproduction treatments and allowing men to take an active role in the fertility conversation which has historically focussed on women individually.}, }
@article {pmid39858902, year = {2025}, author = {Bednarska, NG and Håberg, AK}, title = {Understanding Patterns of the Gut Microbiome May Contribute to the Early Detection and Prevention of Type 2 Diabetes Mellitus: A Systematic Review.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010134}, pmid = {39858902}, issn = {2076-2607}, abstract = {The rising burden of type 2 diabetes mellitus (T2DM) is a growing global public health problem, particularly prominent in developing countries. The early detection of T2DM and prediabetes is vital for reversing the outcome of disease, allowing early intervention. In the past decade, various microbiome-metabolome studies have attempted to address the question of whether there are any common microbial patterns that indicate either prediabetic or diabetic gut microbial signatures. Because current studies have a high methodological heterogeneity and risk of bias, we have selected studies that adhered to similar design and methodology. We performed a systematic review to assess if there were any common changes in microbiome belonging to diabetic, prediabetic and healthy individuals. The cross-sectional studies presented here collectively covered a population of 65,754 people, with 1800 in the 2TD group, 2770 in the prediabetic group and 61,184 in the control group. The overall microbial diversity scores were lower in the T2D and prediabetes cohorts in 86% of the analyzed studies. Re-programming of the microbiome is potentially one of the safest and long-lasting ways to eliminate diabetes in its early stages. The differences in the abundance of certain microbial species could serve as an early warning for a dysbiotic gut environment and could be easily modified before the onset of disease by changes in lifestyle, taking probiotics, introducing diet modifications or stimulating the vagal nerve. This review shows how metagenomic studies have and will continue to identify novel therapeutic targets (probiotics, prebiotics or targets for elimination from flora). This work clearly shows that gut microbiome intervention studies, if performed according to standard operating protocols using a predefined analytic framework (e.g., STORMS), could be combined with other similar studies, allowing broader conclusions from collating all global cohort studies efforts and eliminating the effect-size statistical insufficiency of a single study.}, }
@article {pmid39858891, year = {2025}, author = {Malik, PK and Kolte, AP and Trivedi, S and Tamilmani, G and Mohapatra, A and Vaswani, S and Belevendran, J and Sahoo, A and Gopalakrishnan, A and Bhatta, R}, title = {Anti-Methanogenic Potential of Seaweeds and Impact on Feed Fermentation and Rumen Microbiome In Vitro.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010123}, pmid = {39858891}, issn = {2076-2607}, support = {CRP D31031//IAEA/ ; }, abstract = {A series of in vitro studies were conducted to explore the anti-methanogenic potential of five seaweeds collected from the Indian sea and to optimize the level(s) of incorporation of the most promising seaweed(s) into a straw and concentrate diet to achieve a significant reduction in methane (CH4) production without disturbing rumen fermentation characteristics. A chemical composition analysis revealed a notable ash content varying between 55 and 70% in seaweeds. The crude protein content was highly variable and ranged between 3.25 and 15.3% of dry matter. Seaweeds contained appreciable concentrations of tannins and saponins. Among the seaweeds, Spyridia filamentosa exhibited significantly higher CH4 production, whereas the percentage of CH4 in total gas was significantly lower in the cases of Kappaphycus alvarezii and Sargassum wightii. The ranking of seaweeds in terms of CH4 production (mL/g OM) is as follows: Sargassum wightii < Kappaphycus alvarezii < Acanthophora specifera < Padina gymnospora < Spyridia filamentosa. A remarkable decrease of 31-42% in CH4 production was recorded with the incremental inclusion of Kappaphycus alvarezii at levels of 3-5% of the dry matter in the diet. The addition of Sargassum wightii led to a significant decrease of 36-48% in CH4 emissions when incorporated at levels of 4-5% of dry matter, respectively. The findings of this study revealed a significant decrease in the numbers of total protozoa and Entodinomorphs, coupled with increasing abundances of sulfate-reducing microbes and minor methanogens. Metagenome data revealed that irrespective of the seaweed and treatment, the predominant microbial phyla included Bacteroidota, Bacillota, Pseudomonadota, Actinomycetota, Fibrobacterota, and Euryarchaeota. The prevalence of Methanobrevibacter was similar across treatments, constituting the majority (~79%) of the archaeal community. The results also demonstrated that the supplementation of Kappaphycus alvarezii and Sargassum wightii did not alter the feed fermentation pattern, and therefore, the reduction in CH4 production in the present study could not be attributed to it. Animal studies are warranted to validate the extent of reduction in CH4 production and the key processes involved by supplementation with Kappaphycus alvarezii and Sargassum wightii at the recommended levels.}, }
@article {pmid39858890, year = {2025}, author = {Kuziak, A and Heczko, P and Pietrzyk, A and Strus, M}, title = {Iron Homeostasis Dysregulation, Oro-Gastrointestinal Microbial Inflammatory Factors, and Alzheimer's Disease: A Narrative Review.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010122}, pmid = {39858890}, issn = {2076-2607}, abstract = {Alzheimer's disease (AD), the most common form of dementia, is a progressive neurodegenerative disorder that profoundly impacts cognitive function and the nervous system. Emerging evidence highlights the pivotal roles of iron homeostasis dysregulation and microbial inflammatory factors in the oral and gut microbiome as potential contributors to the pathogenesis of AD. Iron homeostasis disruption can result in excessive intracellular iron accumulation, promoting the generation of reactive oxygen species (ROS) and oxidative damage. Additionally, inflammatory agents produced by pathogenic bacteria may enter the body via two primary pathways: directly through the gut or indirectly via the oral cavity, entering the bloodstream and reaching the brain. This infiltration disrupts cellular homeostasis, induces neuroinflammation, and exacerbates AD-related pathology. Addressing these mechanisms through personalized treatment strategies that target the underlying causes of AD could play a critical role in preventing its onset and progression.}, }
@article {pmid39858889, year = {2025}, author = {Balouei, F and Stefanon, B and Armone, R and Randazzo, A and Chiofalo, B}, title = {Nutritional and Microbiome Effects of a Partial Substitution of Poultry Meat with Hydrolyzed Feather Meal in Dog Diets.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010121}, pmid = {39858889}, issn = {2076-2607}, support = {Project codex N. F/200078/03/X45, CUP B41B20000280005.//BIO = C = O", PON-MISE I&amp;C 2014-2020 FESR, ASSE 6 REACT Priorit&#xe0; di investimento 13. i Azione I, "Finanziato nell'ambito della risposta dell'Unione alla pandemia di COVID-19"/ ; }, abstract = {Two extruded diets isoenergetic, isonitrogenous, and isolipidic were formulated with poultry meal (control diet) as the source of animal-origin proteins (160 g/kg of feed) or with 90 g/kg of poultry meal and 70 g/kg of hydrolyzed feather meal (treated diet) and were fed to eight dogs (four adult female and four adult male English Setters). Body condition, muscle condition, and fecal consistency scores and body weight were monitored at the beginning of the trial and after 3, 7, 15, and 45 days, and no significant differences (p > 0.05) were observed between diets and between sex. Fecal samples, collected at the same time points, were analyzed for microbiota composition. No significant difference was calculated for the alpha diversity index between control diet and treated diet, nor for the diets × times of sampling interaction and for sex. Beta diversity was different (p-value 0.001) between the control and treated groups. The beta diversity between sexes was significantly different (p-value = 0.047). Linear Discriminant analysis effect size analysis revealed significant differences between dietary groups, identifying Clostridiales, Coprococcus, Bacteroides plebeius, Eubacterium biforme, Catenibacterium, and Prevotella copri as more abundant in the CTR diet, while Fusobacterium, Bacteroides, Fusobacteriaceae, Paraprevotellaceae, Enterococcus, Faecalibacterium, Enterobacteriaceae, Peptostreptococcaceae, and Clostridium spiroforme were more abundant in the treated diet. Sex differences were also significant, with 25 taxa differing between male and female dogs. Overall, the study underscores the impact of HFM and sex on gut microbiota composition in dogs, with potential implications for dietary interventions and microbiome research.}, }
@article {pmid39858887, year = {2025}, author = {Uguz, A and Muftuoglu, C and Mert, U and Gumus, T and Ece, D and Asadi, M and Bagci, OU and Caner, A}, title = {Unveiling Microbiota Profiles in Saliva and Pancreatic Tissues of Patients with Pancreatic Cancer.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010119}, pmid = {39858887}, issn = {2076-2607}, support = {TGA-2021-22790//Ege University Scientific Research Projects Coordination Unit/ ; }, abstract = {The pancreas, previously considered a sterile organ, has recently been shown to harbor its own microbiota that may influence tumor biology and patient outcomes. Despite increasing interest in the impact of the microbiome on cancer, the relationship between pancreatic tissue and oral microbiomes in pancreatic ductal adenocarcinoma (PDAC) remains limited. In this study, the oral and pancreas tissue microbiomes of patients with PDAC were compared to patients with other periampullary cancers (DC/AC) and a healthy control group using 16S rRNA gene sequence analysis. The results showed a significant reduction in microbial diversity in the saliva of cancer patients compared to healthy controls, while the PDAC patients exhibited a distinct microbial profile in their pancreatic tissues, consisting predominantly of Firmicutes, Proteobacteria, and Actinobacter, after filtering the microbiome of the indoor environment. Notably, the presence of oral bacteria such as Anoxybacillus, Clostridium, and Bacillus in pancreatic tissues suggests potential translocation from the oral cavity. This study emphasizes the importance of understanding the role of body fluid and tissue microbiota in pancreatic cancer, proposing that oral dysbiosis may contribute to disease progression. Moreover, the results suggest that the microbiome of the indoor environment in which samples are collected and analyzed is also important in microbiota analysis studies.}, }
@article {pmid39858880, year = {2025}, author = {Athalye-Jape, G and Rath, CP and Panchal, H and Mishra, A and Graham, D and Patole, S}, title = {Evaluation of Faecal Microbiota Following Probiotics in Infants of Mothers with Gestational Diabetes Mellitus Trial: Protocol for Double-Blind Placebo-Controlled Randomized Trial.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010112}, pmid = {39858880}, issn = {2076-2607}, abstract = {(1) Background: The incidence of gestational diabetes mellitus (GDM) is rising globally. The current evidence indicates that GDM, especially in conjunction with maternal overweight, can alter the composition of infants' gut microbiota, potentially increasing the risk of inflammatory diseases, metabolic disorders, and neurodevelopmental issues later in life. Probiotic supplantation early in life might establish eubiosis and mitigate future complications. To best of our knowledge, no study has evaluated the effects of probiotics on gut dysbiosis in the infants of mothers with GDM. (2) Methods: This study will be a single-centre, double-blind, randomized, placebo-controlled trial enrolling sixty neonates born after 35 weeks of gestation to mothers with GDM. The participants will be randomly assigned to receive either a triple-strain probiotic or a placebo for four months. The primary objective is to assess the effectiveness of probiotic supplementation in correcting gut dysbiosis in the infants of mothers with GDM at four months of age. Faecal microbiome composition shall be estimated using 16SrRNA and shotgun sequencing. The secondary outcomes will include the quantification of faecal short-chain fatty acids at birth and at four months, as well as growth and developmental assessments at four, twelve, and twenty-four months. (3) Trial registration: This trial protocol is registered (ACTRN12624000930583p) in the Australian Clinical Trials registry (ANZCTR).}, }
@article {pmid39858873, year = {2025}, author = {Hu, R and Xu, X and Jia, Y and Zhu, C and Wang, L and Song, M and Xu, Q and Xia, M and He, X and Jin, Y}, title = {Phage Cocktail Alleviates Bacterial Canker of Kiwifruit by Modulating Bacterial Community Structure in Field Trial.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010104}, pmid = {39858873}, issn = {2076-2607}, support = {BLRC2023C02//5&#xb7;5 Engineering Research &amp; Innovation Team Project of Beijing Forestry University/ ; No: 2021ZY64//Fundamental Research Funds for the Central Universities/ ; }, abstract = {Bacterial canker of kiwifruit is the most destructive bacterial disease caused by Pseudomonas syringae pv. actinidiae. Bacteriophages are regarded as promising biocontrol agents against kiwifruit bacterial pathogens due to their exceptional host specificity and environmentally friendly nature. However, the underlying mechanism of phages in the control of kiwifruit bacterial canker disease remains elusive. In this study, the field trial results showed that phage cocktail could significantly reduce the incidence of bacterial canker in kiwifruit. The high throughput sequencing results showed that the phage cocktail regulated the impact of pathogen invasion on branch endophytic communities, adjusted the diversity of the bacterial community structure, regulated the composition of rare taxa and abundant taxa, and increased the proportion of deterministic processes in community assembly processes. The phage cocktail significantly reduced the relative abundance of Pseudomonadaceae, Pectobacteriaceae, and Yersiniacea. Furthermore, the application of the phage cocktail resulted in an increase in the relative abundance of Beijerinckiaceae, Sphingomonadaceae, and Xanthomonadaceae, most of which are abundant taxa of the corresponding microbial communities. Additionally, the composition of rare taxa was also altered under the influence of phages. These findings offer perspectives on the phage-mediated biocontrol of kiwifruit bacterial canker and provide practical backing for the implementation of phage cocktails in sustainable agriculture.}, }
@article {pmid39858866, year = {2025}, author = {McGrew, K and de Oca, NM and Kosten, TA}, title = {Effect of Relocation, Social Housing Changes, and Diarrhea Status on Microbiome Composition of Juvenile Cynomolgus Macaques (Macaca fascicularis).}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010098}, pmid = {39858866}, issn = {2076-2607}, abstract = {Social housing changes are likely stressful and can be associated with diarrhea, the most common health problem noted in captive macaque populations. Diarrhea may reflect a negative shift in the gut flora ("gut dysbiosis"). This study reported on changes in the gut microbiome composition of juvenile primates (Macaca fascicularis) that experienced a change in social housing and exhibited diarrhea. A matched-case-control design was utilized to compare fecal samples from gut-unhealthy animals to healthy counterparts (n = 61). Baseline samples from recently imported animals were collected during routine sedation events. When an animal experienced a housing change, the entire cohort was monitored for diarrhea. Post-relocation samples were collected from animals that exhibited diarrhea and from their matched controls. Samples were assessed via 16S rRNA next-generation sequencing for a microbiome analysis and by ELISA for cortisol levels. Fecal cortisol levels did not differ between groups or across time points. Alpha diversity increased after relocation and differed by sex with males demonstrating a greater change in alpha diversity (p < 0.01). Although exhibiting diarrhea did not affect alpha diversity levels, it was associated with increased beta diversity (p < 0.05). Understanding how the microbiome may be affected by relocation will help guide prevention strategies such as the use of specific probiotics to reduce the incidence of diarrhea.}, }
@article {pmid39858858, year = {2025}, author = {Onisiforou, A and Charalambous, EG and Zanos, P}, title = {Shattering the Amyloid Illusion: The Microbial Enigma of Alzheimer's Disease Pathogenesis-From Gut Microbiota and Viruses to Brain Biofilms.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010090}, pmid = {39858858}, issn = {2076-2607}, support = {#101031962//European Commission Marie Sk&#x142;odowska-Curie fellowship/ ; EXCELLENCE/0421/0543//Research &amp; Innovation Foundation of Cyprus - Excellence Hubs 2021/ ; NA//IDSA Foundation/ ; }, abstract = {For decades, Alzheimer's Disease (AD) research has focused on the amyloid cascade hypothesis, which identifies amyloid-beta (Aβ) as the primary driver of the disease. However, the consistent failure of Aβ-targeted therapies to demonstrate efficacy, coupled with significant safety concerns, underscores the need to rethink our approach to AD treatment. Emerging evidence points to microbial infections as environmental factors in AD pathoetiology. Although a definitive causal link remains unestablished, the collective evidence is compelling. This review explores unconventional perspectives and emerging paradigms regarding microbial involvement in AD pathogenesis, emphasizing the gut-brain axis, brain biofilms, the oral microbiome, and viral infections. Transgenic mouse models show that gut microbiota dysregulation precedes brain Aβ accumulation, emphasizing gut-brain signaling pathways. Viral infections like Herpes Simplex Virus Type 1 (HSV-1) and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) may lead to AD by modulating host processes like the immune system. Aβ peptide's antimicrobial function as a response to microbial infection might inadvertently promote AD. We discuss potential microbiome-based therapies as promising strategies for managing and potentially preventing AD progression. Fecal microbiota transplantation (FMT) restores gut microbial balance, reduces Aβ accumulation, and improves cognition in preclinical models. Probiotics and prebiotics reduce neuroinflammation and Aβ plaques, while antiviral therapies targeting HSV-1 and vaccines like the shingles vaccine show potential to mitigate AD pathology. Developing effective treatments requires standardized methods to identify and measure microbial infections in AD patients, enabling personalized therapies that address individual microbial contributions to AD pathogenesis. Further research is needed to clarify the interactions between microbes and Aβ, explore bacterial and viral interplay, and understand their broader effects on host processes to translate these insights into clinical interventions.}, }
@article {pmid39858845, year = {2025}, author = {Winters, AD and Francescutti, DM and Kracht, DJ and Chaudhari, DS and Zagorac, B and Angoa-Perez, M}, title = {The Gut Microbiome Regulates the Psychomotor Effects and Context-Dependent Rewarding Responses to Cocaine in Germ-Free and Antibiotic-Treated Animal Models.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010077}, pmid = {39858845}, issn = {2076-2607}, support = {1I21BX005850//the Department of Veterans Affairs/ ; 1I01BX004757-01A1 to M.A.-P.//the Department of Veterans Affairs/ ; }, abstract = {Cocaine use disorder remains a major global health concern, with growing evidence that the gut microbiome modulates drug-related behaviors. This study examines the microbiome's role in cocaine-induced psychomotor activation and context-dependent reward responses using germ-free (GF) and antibiotic-treated (ABX) models. In GF mice, the absence of a microbiome blunted cocaine-induced psychomotor activation (p = 0.013), which was restored after conventionalization. GF mice also showed reduced cocaine-conditioned place preference (CPP) (p = 0.002), which normalized after conventionalization. Dopaminergic function, critical for psychomotor responses and reward, was microbiome-dependent, with increased dopamine levels (p = 0.009) and normalized turnover ratios after conventionalization. In the ABX model, microbiome depletion reduced both cocaine-induced locomotion and CPP responses (p ≤ 0.009), further supporting the role of gut microbes in modulating psychomotor and reward behaviors. ABX-treated mice also showed significant declines in microbial diversity, shifts in bacterial structure, and dysregulation in metabolic, immune, and neurotransmitter pathways (p ≤ 0.0001), including alterations in short-chain fatty acids and gamma-aminobutyric acid metabolism. These findings highlight the gut microbiome's critical role in regulating cocaine's psychomotor and rewarding effects, offering insights into potential therapeutic strategies for cocaine use disorder.}, }
@article {pmid39858835, year = {2025}, author = {Shukla, S and Hsu, CL}, title = {Alcohol Use Disorder and the Gut-Brain Axis: A Narrative Review of the Role of Gut Microbiota and Implications for Treatment.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010067}, pmid = {39858835}, issn = {2076-2607}, support = {#CTORA23-208366//American Association for the Study of Liver Diseases Foundation/ ; K99AA031328/GF/NIH HHS/United States ; }, abstract = {Alcohol use disorder (AUD) affects millions of people worldwide and can lead to deleterious physical and social consequences. Recent research has highlighted not only the effect of alcohol on the gut microbiome, but also the role of the gut microbiome and the gut-brain axis in the development and maintenance of alcohol use disorder. This review provides an overview of the reciprocal relationship between alcohol consumption and the gut microbiome, including the effects of alcohol on gut microbial composition, changes in gut microbial metabolites in response to alcohol consumption, and how gut microbial metabolites may modulate alcohol use behavior. We also discuss the gut-mediated mechanisms of neuroinflammation that contribute to and result from AUD, including disruption of the intestinal barrier, toll-like receptor signaling, and the activation of glial cells and immune cells. Finally, we review the current evidence on gut microbial-directed therapies for AUD and discuss the implications of this research for our understanding of the pathophysiology of AUD and future research directions.}, }
@article {pmid39858822, year = {2025}, author = {Smith, A and Dumbrava, R and Ghori, NU and Foster, R and Campbell, J and Duthie, A and Hoyne, G and Rademaker, M and Bowen, AC}, title = {An Overview of the Skin Microbiome, the Potential for Pathogen Shift, and Dysbiosis in Common Skin Pathologies.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010054}, pmid = {39858822}, issn = {2076-2607}, abstract = {Recent interest in the diverse ecosystem of bacteria, fungi, parasites, and viruses that make up the skin microbiome has led to several studies investigating the microbiome in healthy skin and in a variety of dermatological conditions. An imbalance of the normal skin flora can cause some skin diseases, and current culture techniques are often unable to detect a microorganism to further our understanding of the clinical-microbiological correlates of disease and dysbiosis. Atopic dermatitis and rosacea are presentations that GPs often manage that may have an infective or microbiological component and can be challenging to treat. We aim to discuss the implications of the skin microbiome including the impact of dysbiosis on conditions such as these. We will also discuss some clinical pearls for initial and future directions of the management of conditions such as atopic dermatitis, rosacea, and hidradenitis suppurativa. Further research using culture-independent techniques is needed for conditions involving microbial dysbiosis to advance our knowledge of skin disease pathophysiology and guide future management.}, }
@article {pmid39858820, year = {2024}, author = {Loughrin, JH and Agga, GE}, title = {The Effect of Mono- and Di-Saccharides on the Microbiome of Dairy Cow Manure and Its Odor.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010052}, pmid = {39858820}, issn = {2076-2607}, abstract = {In a previous experiment, we showed that the odor of Bos taurus manure slurries could be improved by anaerobic incubation with the sugars glucose, lactose, and sucrose. This improvement was due to reductions in the concentrations of malodorants, including dimethyl disulfide, p-cresol, p-ethylphenol, indole, and skatole, and a shift to the production of fruity esters, including ethyl butyrate and propyl propanoate. Due to large concentrations of lactic acid produced by the sugar-amended manure slurries, we inferred that lactic acid bacteria were involved in improving the manure slurry odor. Here, through 16S rRNA amplicon sequencing for microbiome analysis, we show that lactic acid bacterial growth was promoted by the addition of all three sugars. Lactobacillus buchneri and an unknown Lactobacillus sp. were the most prominent lactic acid bacteria stimulated by sugar addition. Lactobacillales were found only in trace abundances in unamended manure slurries. The relative abundance of orders such as Clostridiales, Bifidobacteriales, and Erysipelotrichales were not noticeably affected by sugar amendment. However, the disaccharides lactose and sucrose seemed to increase the relative abundance of Bifidobacterium, whereas the monosaccharide glucose did not. We conclude that lactic acid bacteria are the primary bacteria involved in improving odor in dairy cow manure slurries and present strategies to enhance their abundance in animal wastes.}, }
@article {pmid39858814, year = {2024}, author = {Liu, Z and Cao, Q and Wang, W and Wang, B and Yang, Y and Xian, CJ and Li, T and Zhai, Y}, title = {The Impact of Lactobacillus reuteri on Oral and Systemic Health: A Comprehensive Review of Recent Research.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010045}, pmid = {39858814}, issn = {2076-2607}, support = {242102310376//Foundation of Science &amp; Technology Department of Henan Province/ ; 25A320004//Natural Science Foundation of Education Department of Henan Province/ ; }, abstract = {Oral diseases, particularly dental caries and periodontal disease, pose significant global health challenges. The imbalance of the oral microbiota plays a key role in the occurrence of these diseases, prompting researchers to seek new strategies to restore oral ecological balance. Lactobacillus reuteri is a Gram-positive rod-shaped bacterium that exists in various body parts of humans, including the gastrointestinal tract, urinary tract, skin, and so on. This species has a potentially positive impact on oral health and plays an important role in maintaining systemic health. Recent studies have explored the application of Lactobacillus reuteri in the prevention and treatment of oral diseases, and its impact on systemic health has also been preliminarily revealed. The current review summarizes the role of Lactobacillus reuteri in oral health and systemic health and outlines its potential applications in the future. Lactobacillus reuteri has shown promising prospects in treating non-communicable biofilm-dependent oral diseases, but its mechanism of action and efficacy still need further research. In addition, Lactobacillus reuteri has also displayed some potential benefits in promoting overall health. Future research should focus on revealing the specific pathways of action of Lactobacillus reuteri, screening for the most beneficial strains, determining the most effective drug delivery strategies, developing oral and systemic health products based on Lactobacillus reuteri, and ensuring their safety in clinical applications.}, }
@article {pmid39858809, year = {2024}, author = {Zhu, F and Kamiya, T and Fujiwara, T and Hashimoto, M and Gong, S and Wu, J and Nakanishi, H and Fujimoto, M}, title = {A Comparison of Rice Root Microbial Dynamics in Organic and Conventional Paddy Fields.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010041}, pmid = {39858809}, issn = {2076-2607}, support = {JPMJSP2108//Japan Science and Technology Agency (JST) SPRING/ ; 23KJ0514//Japan Society for the Promotion of Science (JSPS) KAKENHI/ ; 20H00418//Japan Society for the Promotion of Science (JSPS) KAKENHI/ ; 24H00509//Japan Society for the Promotion of Science (JSPS) KAKENHI/ ; 19KT0033//Japan Society for the Promotion of Science (JSPS) KAKENHI/ ; 20K05955//Japan Society for the Promotion of Science (JSPS) KAKENHI/ ; 23K18023//Japan Society for the Promotion of Science (JSPS) KAKENHI/ ; 24K01892//Japan Society for the Promotion of Science (JSPS) KAKENHI/ ; }, abstract = {The assembly of plant root microbiomes is a dynamic process. Understanding the roles of root-associated microbiomes in rice development requires dissecting their assembly throughout the rice life cycle under diverse environments and exploring correlations with soil properties and rice physiology. In this study, we performed amplicon sequencing targeting fungal ITS and the bacterial 16S rRNA gene to characterize and compare bacterial and fungal community dynamics of the rice root endosphere and soil in organic and conventional paddy fields. Our analysis revealed that root microbial diversity and composition was significantly influenced by agricultural practices and rice developmental stages (p < 0.05). The root microbiome in the organic paddy field showed greater temporal variability, with typical methane-oxidizing bacteria accumulating during the tillering stage and the amount of symbiotic nitrogen-fixing bacteria increasing dramatically at the early ripening stage. Redundancy analysis identified ammonium nitrogen, iron, and soil organic matter as key drivers of microbial composition. Furthermore, correlation analysis between developmental stage-enriched bacterial biomarkers in rice roots and leaf mineral nutrients showed that highly mobile macronutrient concentrations positively correlated with early-stage biomarkers and negatively correlated with later-stage biomarkers in both paddy fields. Notably, later-stage biomarkers in the conventional paddy field tended to show stronger correlations with low-mobility nutrients. These findings suggest potential strategies for optimizing microbiome management to enhance productivity and sustainability.}, }
@article {pmid39858787, year = {2024}, author = {Bernardi, F and Fanizzi, F and Parigi, TL and Zilli, A and Allocca, M and Furfaro, F and Peyrin-Biroulet, L and Danese, S and D'Amico, F}, title = {Role of Probiotics in the Management of Patients with Ulcerative Colitis and Pouchitis.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010019}, pmid = {39858787}, issn = {2076-2607}, abstract = {Acute severe ulcerative colitis (ASUC) often requires surgical intervention, such as proctocolectomy with ileal pouch-anal anastomosis (IPAA). While IPAA improves patient outcomes, it can be associated with pouchitis, a common and debilitating complication characterized by inflammation of the pouch. The development of pouchitis is closely linked to dysbiosis-an imbalance in the gut microbiota. Understanding the role of the microbiota in pouch health has spurred interest in probiotics as a therapeutic strategy. Probiotics represent a promising avenue in the management of pouchitis, offering a natural and targeted approach to improving outcomes for UC patients. This review explores the role of probiotics in the management of UC patients, with a specific focus on preventing and treating pouchitis. We compare the microbiota of healthy pouches to those with pouchitis, highlighting key microbial shifts linked to disease onset and discussing the growing evidence for probiotics as a prevention and therapeutic approach. Future directions should prioritize advancing research to optimize probiotic therapies and establish personalized approaches based on individual microbiome profiles, highlighting their significant potential as a promising treatment strategy for pouchitis.}, }
@article {pmid39858783, year = {2024}, author = {Qumsani, AT}, title = {Exploring the Effects of Imidacloprid on Liver Health and the Microbiome in Rats: A Comprehensive Study.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010015}, pmid = {39858783}, issn = {2076-2607}, abstract = {The current study investigates the systemic effects of imidacloprid, one of the most widely used neonicotinoid insecticides, on the liver and gut microbiome of rats in detail. With consideration of recent discussions on the potential harmfulness of imidacloprid to environmental and human health, the aim was to investigate the influence of this compound in the framework of controlled exposure at different dosages, namely, IMI-5, IMI-10, and IMI-30. Histopathological examination showed that liver morphology changed significantly with the dose, including in terms of cellular disorganization and signs of stress, with an alteration in the hepatic architecture. Morphological changes were related to disturbances in the activity of liver enzymes, reflecting deteriorating liver function with increased imidacloprid exposure. In parallel with this, a deep analysis of the gut microbiome revealed dramatic changes in microbial diversity and composition. Alpha diversity, represented by the Chao1 and Shannon indices, was significantly reduced with an increased dosage of imidacloprid. Subsequent beta diversity analysis, as visualized by principal component analysis, showed distinct clustering among the microbial communities, separated well between control and imidacloprid-treated groups, especially at higher dosages. Taxonomic analysis revealed an increase in the Firmicutes/Bacteroidetes ratio and a change in key phyla including Actinobacteria, Bacteroidetes, and Verrucomicrobia. A heatmap and bar charts further confirmed dose-dependent changes in microbial abundance. These changes point toward imidacloprid-induced dysbiosis, a reduction in microbial diversity, and an imbalance in the F/B ratio, usually associated with metabolic disorders. Overall, given these findings, it would seem that imidacloprid does indeed impose serious negative impacts on both liver function and gut microbiota composition and may have further impacts on health and ecological safety.}, }
@article {pmid39858781, year = {2024}, author = {Tamošiūnė, I and Hakim, MF and Buzaitė, O and Stanys, V and Vinskienė, J and Andriūnaitė, E and Baniulis, D}, title = {Diversity and Plant Growth-Promoting Properties of Rhodiola rosea Root Endophytic Bacteria.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010013}, pmid = {39858781}, issn = {2076-2607}, support = {S-MIP-22-54//Lietuvos Mokslo Taryba/ ; }, abstract = {Plants inhabiting environments with suboptimal growth conditions often have a more pronounced capacity to attract and sustain microbial communities that improve nutrient absorption and expand abiotic stress tolerance. Rhodiola rosea L. is a succulent plant of the Crassulaceae family adapted to survive in sandy or rocky soils or dry tundra. The aim of the present study was to investigate the diversity and plant growth-stimulating potential of R. rosea endophytic microbiota. Metataxonomic analysis of the bacterial diversity in the rhizome of R. rosea revealed 108 families. Among these, three families were found exclusively in the core microbiome of 1-year-old plants, while nine families were unique to the core microbiome of mature plants grown in the field for more than 4 years. Seventy-three endophytic bacteria isolates were obtained from the rhizome of R. rosea plants and were assigned into 14 distinct bacterial genera of Firmicutes (26%) or Proteobacteria (74%) phyla. Screening for functional genes related to the nitrogen cycle, phosphorus mineralisation or dissolution, and traits associated with nitrogen fixation (56% of isolates), siderophore production (40%), inorganic phosphorus solubilisation (30%), and production of indole-related compounds (51%) led to the classification of the isolates into 16 distinct clusters. Co-cultivation of 45 selected isolates with germinating Arabidopsis seedlings revealed 18 and 5 isolates that resulted in more than a 20% increase in root or shoot growth, respectively. The study results established the complexity of the succulent R. rosea endophytic microbiome and identified isolates for potential plant growth-stimulating applications.}, }
@article {pmid39858780, year = {2024}, author = {Woortman, MA and Barrett, ES and O'Connor, TG and Gill, SR and Scheible, K and Brunner, J and Sun, H and Dominguez-Bello, MG}, title = {Feeding Expressed Breast Milk Alters the Microbial Network of Breast Milk and Increases Breast Milk Microbiome Diversity over Time.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010012}, pmid = {39858780}, issn = {2076-2607}, support = {UH3OD023349/GF/NIH HHS/United States ; UG3OD023349/GF/NIH HHS/United States ; 1R01HD083369-16A1/NH/NIH HHS/United States ; P30ES005022/GF/NIH HHS/United States ; NA//The Wynne Center for Family Research/ ; UL1 TR002001/TR/NCATS NIH HHS/United States ; NA//Academy of Nutrition and Dietetics Research Practice Group Student Pilot Grant/ ; NA//CIFAR Fellow/ ; }, abstract = {Breastfeeding supplies nutrition, immunity, and hormonal cues to infants. Feeding expressed breast milk may result in de-phased milk production and feeding times, which distort the real-time circadian cues carried by breast milk. We hypothesized that providing expressed breast milk alters the microbiotas of both breast milk and the infant's gut. To test this hypothesis, we analyzed the microbiota of serial breast milk and infant fecal samples obtained from 14 mother-infant dyads who were lactating, half of which were providing expressed breast milk. Infant fecal microbiota showed lower α-diversity than breast milk microbiota. Bacterial amplicon sequence variant sharing occurred between breast milk and infant feces with no feeding group differences. However, the age-dependent gain in breast milk α-diversity was only significant in the expressed breast milk group and not in the direct breastfeeding group, suggesting that decreased contact with the infant's mouth influences the milk microbiota. Trending lower connectivity was also noted with breast milk microbes in the direct breastfeeding group, consistent with regular perturbations of the developing baby's oral microbiota by latching on the breast. The results of this preliminary study urge further research to independently confirm the effects of providing expressed breast milk and their health significance.}, }
@article {pmid39858777, year = {2024}, author = {Apostolou, K and Radea, C and Meziti, A and Kormas, KA}, title = {Bacterial Diversity Associated with Terrestrial and Aquatic Snails.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/microorganisms13010008}, pmid = {39858777}, issn = {2076-2607}, abstract = {The introduction of the holobiont concept has triggered scientific interest in depicting the structural and functional diversity of animal microbial symbionts, which has resulted in an unprecedented wealth of such cross-domain biological associations. The steadfast technological progress in nucleic acid-based approaches would cause one to expect that scientific works on the microbial symbionts of animals would be balanced at least for the farmed animals of human interest. For some animals, such as ruminants and a few farmed fish species of financial significance, the scientific wealth of the microbial worlds they host is immense and ever growing. The opposite happens for other animals, such as snails, in both the wild and farmed species. Snails are evolutionary old animals, with complex ecophysiological roles, living in rich microbial habitats such as soil and sediments or water. In order to create a stepping stone for future snail microbiome studies, in this literature review, we combined all the available knowledge to date, as documented in scientific papers, on any microbes associated with healthy and diseased terrestrial and aquatic snail species from natural and farmed populations. We conducted a Boolean search in Scopus, Web of Science, and ScienceDirect until June 2024, identifying 137 papers, of which 60 were used for original data on snail bacterial communities in the gastrointestinal tract, hepatopancreas, and feces. We provide a synthesis on how representative this knowledge is towards depicting the possible snail core microbiota, as well as the steps that need to be taken in the immediate future to increase the in-depth and targeted knowledge of the bacterial component in snail holobionts.}, }
@article {pmid39858487, year = {2025}, author = {Tahmasebi, H and Arjmand, N and Monemi, M and Babaeizad, A and Alibabaei, F and Alibabaei, N and Bahar, A and Oksenych, V and Eslami, M}, title = {From Cure to Crisis: Understanding the Evolution of Antibiotic-Resistant Bacteria in Human Microbiota.}, journal = {Biomolecules}, volume = {15}, number = {1}, pages = {}, doi = {10.3390/biom15010093}, pmid = {39858487}, issn = {2218-273X}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Microbiota/drug effects ; Methicillin-Resistant Staphylococcus aureus/drug effects/genetics ; Drug Resistance, Multiple, Bacterial/genetics ; Bacteria/drug effects/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {The growing prevalence of antibiotic-resistant bacteria within the human microbiome has become a pressing global health crisis. While antibiotics have revolutionized medicine by significantly reducing mortality and enabling advanced medical interventions, their misuse and overuse have led to the emergence of resistant bacterial strains. Key resistance mechanisms include genetic mutations, horizontal gene transfer, and biofilm formation, with the human microbiota acting as a reservoir for antibiotic resistance genes (ARGs). Industrialization and environmental factors have exacerbated this issue, contributing to a rise in infections with multidrug-resistant (MDR) bacteria, such as methicillin-resistant Staphylococcus aureus (MRSA) and carbapenem-resistant Enterobacteriaceae. These resistant pathogens compromise the effectiveness of essential treatments like surgical prophylaxis and chemotherapy, increase healthcare costs, and prolong hospital stays. This crisis highlights the need for a global One-Health approach, particularly in regions with weak regulatory frameworks. Innovative strategies, including next-generation sequencing (NGS) technologies, offer promising avenues for mitigating resistance. Addressing this challenge requires coordinated efforts, encompassing research, policymaking, public education, and antibiotic stewardship, to safeguard current antibiotics and foster the development of new therapeutic solutions. An integrated, multidimensional strategy is essential to tackle this escalating problem and ensure the sustainability of effective antimicrobial treatments.}, }
@article {pmid39858403, year = {2024}, author = {Rawani, NS and Chan, AW and Todd, KG and Baker, GB and Dursun, SM}, title = {The Role of Neuroglia in the Development and Progression of Schizophrenia.}, journal = {Biomolecules}, volume = {15}, number = {1}, pages = {}, doi = {10.3390/biom15010010}, pmid = {39858403}, issn = {2218-273X}, support = {Distinguished University Professorship Allowance RES0067002//University of Alberta (funding costs associated with preparation of this review)/ ; }, mesh = {*Schizophrenia/metabolism/pathology/etiology ; Humans ; *Neuroglia/metabolism/pathology ; Animals ; Astrocytes/metabolism/pathology ; Oligodendroglia/metabolism/pathology ; Oxidative Stress ; Microglia/metabolism/pathology ; Brain/metabolism/pathology ; Blood-Brain Barrier/metabolism/pathology ; Disease Progression ; Antipsychotic Agents/pharmacology ; Gastrointestinal Microbiome ; }, abstract = {Schizophrenia is a complex heterogenous disorder thought to be caused by interactions between genetic and environmental factors. The theories developed to explain the etiology of schizophrenia have focused largely on the dysfunction of neurotransmitters such as dopamine, serotonin and glutamate with their receptors, although research in the past several decades has indicated strongly that other factors are also involved and that the role of neuroglial cells in psychotic disorders including schizophrenia should be given more attention. Although glia were originally thought to be present in the brain only to support neurons in a physical, metabolic and nutritional capacity, it has become apparent that these cells have a variety of important physiological roles and that abnormalities in their function may make significant contributions to the symptoms of schizophrenia. In the present paper, we review the interactions of brain microglia, astrocytes and oligodendroglia with aspects such as transmitter dysregulation, neuro-inflammation, oxidative stress, synaptic function, the gut microbiome, myelination and the blood-brain barrier that appear to affect the cause, development and treatment of schizophrenia. We also review crosstalk between microglia, astrocytes and oligodendrocytes and the effects of antipsychotics on neuroglia. Problems associated with studies on specific biomarkers for glia in schizophrenia are discussed.}, }
@article {pmid39858375, year = {2025}, author = {Oladeji, OM and Mugivhisa, LL and Olowoyo, JO}, title = {Antibiotic Residues in Animal Products from Some African Countries and Their Possible Impact on Human Health.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/antibiotics14010090}, pmid = {39858375}, issn = {2079-6382}, abstract = {This review investigates the levels of antibiotic residues in animal products, types of antibiotics, and their possible impact on human health in Africa. The literature search involved the use of a systematic survey using data that were published from Africa from 2015 to 2024. The search terms used the Boolean operators with keywords such as antibiotics, antibiotic residues, antibiotics in animal products in Africa, and impact on human health. Only research conducted in Africa was used in the present study. The findings showed that the most prevalent groups of antibiotic residues were aminoglycoside, macrolides, β-lactams, fluoroquinolones, tetracyclines sulfonamides, and phenicols. Tetracycline showed the most prevalent antibiotic residue with 43% mostly from East Africa, followed by sulfonamides at 19%, and β-lactams at 16%; most of the antibiotic residue levels were higher than the World Health Organization permissible limit. Noncompliance with withdrawal periods and maximum residue limits for antibiotics used in food-producing animals may lead to negative outcomes such as allergic reactions, teratogenicity, carcinogenicity, microbiome alterations, and, most notably, antibiotic resistance. As a result, there is a need for constant monitoring of antibiotic residues in animal products in addition to the consideration of alternatives to antibiotics in order to avoid their health implications.}, }
@article {pmid39858271, year = {2025}, author = {Zhu, S and Zha, M and Xia, Y}, title = {Complex Probiotics Suppress Inflammation by Regulating Intestinal Metabolites in Kittens.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/ani15020272}, pmid = {39858271}, issn = {2076-2615}, support = {2024LHMS03043//Natural Science Foundation of Inner Mongolia, China/ ; BR22-11-05//Fundamental Research Funds of Inner Mongolia Agricultural University/ ; SPYQ202001//Cultivation Project for Excellent Youth of Inner Mongolia Agricultural University/ ; }, abstract = {Cats are popular companions for humans, and their health is of importance to a growing number of pet owners. The juvenile period is a critical stage of cat growth; in particular, the metabolic activity of the intestinal microbiome of kittens is critical for processing nutrients and supporting overall health. In this study, the effect of complex probiotics on the intestinal health of kittens was explored through a metabolomics analysis. Twenty-four healthy kittens were randomly assigned to two groups (n = 12): the control group was provided a basal diet and the probiotics group was provided the basal diet supplemented with complex probiotics (given at the same time daily). The kittens were acclimatized for 5 days, and the experiment was conducted for 14 days. We collected feces from each kitten on days 1 and 14 for metabolomic analyses. Compared to the control, the probiotics group had significantly higher (p < 0.05) methylmalonylcarnitine, lysyl-hydroxyproline, phenylpropionylglycine, and vitamin K3 levels, and significantly lower (p < 0.05) gamma-glutamyl-L-putrescine, cis-gondoic acid, myristic acid, 12,13-DiHOME, and glycodeoxycholic acid levels. The results of this study suggest that complex probiotics promote intestinal health in kittens by regulating changes in various metabolites in the intestine and may have a mitigating effect on intestinal inflammation.}, }
@article {pmid39858254, year = {2025}, author = {Romero, M and Heras-Molina, A and Muñoz, M and Calvo, L and Morales, JI and Rodríguez, AI and Escudero, R and López-Bote, C and Óvilo, C and Olivares, &#xc1;}, title = {Short- But Not Long-Term Effects of Creep Feeding Provided to Suckling Piglets.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/ani15020253}, pmid = {39858254}, issn = {2076-2615}, support = {IDI-20190857 (COPISO); IDI-20190858 (Incarlopsa) and DIN2018-009798; COPISO.//Centro para el Desarrollo Tecnol&#xf3;gico Industrial CDTI and Ministerio de Ciencia e Innovaci&#xf3;n./ ; }, abstract = {Fifty-eight litters (16 from primiparous gilts and 42 from multiparous sows) were used, with a total number of 750 piglets involved in the study. Birth weight was stratified into three groups: low (<1.02 kg; LBW), normal (1.02-1.62 kg; NBW), and high (>1.62 kg; HBW). A creep feeding diet was offered to piglets in a creep feeder in 29 litters from day 7 until their weaning. Piglet mortality was recorded daily. Traceability was ensured up to the point of carcass splitting and subsequent meat analysis. Each carcass was eviscerated and weighed individually. Sixty-nine piglets were selected for the microbiome analysis (35 from the control group and 34 from the creep feeding group). Feces samples from the rectum were obtained at three time points (three days prior weaning, a week after weaning, and before the slaughtering of the pigs). Mortality during lactation was influenced by birth weight, with LBW piglets exhibiting a six-fold higher mortality rate than HBW. Creep feeding did not impact piglet mortality. Heavier piglets demonstrated greater weight gain when subjected to creep feeding, while the growth potential of lighter piglets was reduced. Variation in creep feeding consumption based on birth weight also affected microbiome composition, with high-birth-weight piglets displaying higher alpha diversity than low- and normal-birth-weight piglets seven days after lactation. Alpha diversity is indicative of gut health, with higher values suggesting greater stability and adaptability to different feed sources. In conclusion, the immediate impacts of creep feeding appear to be most prominent during lactation and potentially early postweaning. These short-term effects are modulated by birth weight, with HBW piglets demonstrating the greatest benefits from the implementation of creep-feeding practices.}, }
@article {pmid39858248, year = {2025}, author = {Yu, Y and Fu, R and Jin, C and Han, L and Gao, H and Fu, B and Qi, M and Li, Q and Leng, J}, title = {Multi-Omics Insights into Rumen Microbiota and Metabolite Interactions Regulating Milk Fat Synthesis in Buffaloes.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/ani15020248}, pmid = {39858248}, issn = {2076-2615}, support = {32260841,U2202203//the National Natural Science Foundation of China/ ; 202201AS070063//Key Project of Basic Research Program of Science and Technology Department of Yunnan Province/ ; }, abstract = {The present study was conducted to analyze the correlation between the milk fat content of Binglangjiang buffaloes and their microbial and host metabolites. The 10 buffaloes with the highest milk fat content (HF, 5.60 ± 0.61%) and the 10 with the lowest milk fat content (LF, 1.49 ± 0.13%) were selected. Their rumen fluid and plasma were collected for rumen microbiota and metabolome analysis. The results showed that the rumen bacteria abundance of Synergistota, Quinella, Selenomonas, and Fretibacterium was significantly higher in the HF buffaloes. The abundance of 14 rumen fungi, including Candida, Talaromyces, Cyrenella, and Stilbella, was significantly higher in the HF buffaloes. The analysis of the metabolites in the rumen and plasma showed that several metabolites differed between the HF and LF buffaloes. A total of 68 and 42 differential metabolites were identified in the rumen and plasma, respectively. By clustering these differential metabolites, most of those clustered in the HF group were lipid and lipid-like molecules such as secoeremopetasitolide B, lucidenic acid J LysoPE (0:0/18:2 (9Z, 12Z)), and 5-tetradecenoic acid. Spearman's rank correlations showed that Quinella, Fretibacterium, Selenomonas, Cyrenella, and Stilbella were significantly positively correlated with the metabolites of the lipids and lipid-like molecules in the rumen and plasma. The results suggest that rumen microbiota such as Quinella, Fretibacterium, Selenomonas, and Cyrenella may regulate milk fat synthesis by influencing the lipid metabolites in the rumen and plasma. In addition, the combined analysis of the rumen microbiota and host metabolites may provide a fundamental understanding of the role of the microbiota and host in regulating milk fat synthesis.}, }
@article {pmid39858234, year = {2025}, author = {Fernández-Pinteño, A and Pilla, R and Suchodolski, J and Apper, E and Torre, C and Salas-Mani, A and Manteca, X}, title = {Age-Related Changes in Gut Health and Behavioral Biomarkers in a Beagle Dog Population.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/ani15020234}, pmid = {39858234}, issn = {2076-2615}, abstract = {The gut and the gut microbiome communicate with the nervous system through the gut-brain axis via neuroimmune and neuroendocrine mechanisms. Despite existing research, studies exploring this link in aging dogs are limited. This study aims to examine multiple blood and fecal biomarkers of intestinal health, along with various behavioral indicators based on saliva, blood, observations, and activity, in different age populations (junior: <2 y.o.; adult: 2-7 y.o.; senior: >7 y.o.) of thirty-seven Beagle dogs. In our study, Bacteroides were significantly higher in senior dogs. The relative abundance of Faecalibacterium and Blautia showed age-related trends, higher in senior and junior dogs, respectively. Fecal short-chain fatty acid concentration, especially acetate, increased with age, while propionate was higher in junior dogs. For the behavioral indicators we considered, blood thyroxine concentration, playing, exploring, and total activity were higher in junior dogs. The differences observed between the biomarkers of gut health and behavior, particularly those significant for the age correlations, emphasize the importance of considering age-related factors when studying the gut microbiome and behavior. However, further research is needed to better understand the mechanisms and specific pathways involved in the relationship between the studied biomarkers and age.}, }
@article {pmid39858228, year = {2025}, author = {Du, J and Wang, Y and Su, S and Wang, W and Guo, T and Hu, Y and Yin, N and An, X and Qi, J and Xu, X}, title = {Supplementation with Complex Phytonutrients Enhances Rumen Barrier Function and Growth Performance of Lambs by Regulating Rumen Microbiome and Metabolome.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/ani15020228}, pmid = {39858228}, issn = {2076-2615}, support = {BR230403//Outstanding Youth Science Foundation of Inner Mongolia Agricultural University/ ; 32260840//National Natural Science Foundation of China/ ; 32460843//National Natural Science Foundation of China/ ; }, abstract = {Complex phytonutrients (CPS) have attracted extensive interest due to their anti-inflammatory effects. This investigation focused on the impact of CPS on rumen health in lambs on high-concentrate diets, emphasizing growth performance, ruminal fermentation, epithelial barrier integrity, ruminal metabolism, and microbial communities. A total of 54 lambs, 3 months old and with a 30.42 ± 0.54 kg body weight, were randomly assigned to three treatment groups, with six replicates per treatment and three lambs per replicate. The lambs received a basal diet (the ratio of concentrate to forage was 75:25) without CPS supplementation (CON) or with the inclusion of 2.5 g/kg (CPS2.5) or 5.0 g/kg CPS (CPS5.0) for a total of 60 days. The CPS groups exhibited increased growth performance and improved rumen fermentation parameters. Mechanistically, CPS enhanced rumen epithelial barrier function, thereby lowering inflammation and inhibiting the overactivation of the JNK/p38 MAPK signaling pathway, and the effect of CPS5.0 was better than that of CPS2.5. Notably, CPS5.0 could optimize the composition of rumen microbiota and increase the levels of Ursolic acid and other metabolites. The strong associations between rumen bacteria and health-related indicators and differential metabolites were further highlighted. Our findings suggest that adding CPS to lambs' diets has widespread positive impacts, including improved growth performance, reduced inflammation and mRNA relative expression of apoptosis-related genes, enhanced barrier function, and beneficial changes in the rumen microbiome and metabolite profiles.}, }
@article {pmid39858218, year = {2025}, author = {Chen, G and Lu, H and Huang, S and Zhang, C and Ma, X and Li, B and Hou, L and Xu, Q and Wang, Y}, title = {Ecological and Functional Changes in the Hindgut Microbiome of Holstein Cows at High Altitudes.}, journal = {Animals : an open access journal from MDPI}, volume = {15}, number = {2}, pages = {}, doi = {10.3390/ani15020218}, pmid = {39858218}, issn = {2076-2615}, abstract = {The extreme environmental conditions of the Qinhai-Tibetan Plateau (QTP) challenge livestock survival and productivity, yet little is known about how high-altitude environments impact the gut microbiota of dairy cows. To fill this gap, we systematically investigated the differences in the hindgut microbiome between 87 plateau Holstein cows and 72 plain Holstein cows using 16S rRNA gene sequencing. Our analysis revealed that the hindgut microbiota of the plateau group exhibited lower species richness but higher evenness than that in the plain group. Additionally, significant separation in hindgut microbiota composition between the two groups was observed based on altitude, while parity, days in milk, and age did not show a comparable impact. Moreover, altitude had a lasting impact on bacterial communities and their co-occurrence networks, resulting in reduced microbial interactions and lower modularity in the plateau group. Furthermore, we identified four key microbial taxa, the Bacteroidaceae and Rikenellaceae families, as well as the Prevotella and Treponema genera, which were associated with the regulation of carbohydrate digestion and energy metabolism and might help the Holstein cows adapt to the plateau environment. Our findings provide insights into strategies for enhancing the adaptability of dairy cows to high-altitude environments through microbiota modulation, which could ultimately contribute to improving livestock management and sustainability in these extreme environments.}, }
@article {pmid39858007, year = {2025}, author = {Al-Matouq, J and Al-Ghafli, H and Alibrahim, NN and Alsaffar, N and Radwan, Z and Ali, MD}, title = {Unveiling the Interplay Between the Human Microbiome and Gastric Cancer: A Review of the Complex Relationships and Therapeutic Avenues.}, journal = {Cancers}, volume = {17}, number = {2}, pages = {}, doi = {10.3390/cancers17020226}, pmid = {39858007}, issn = {2072-6694}, abstract = {The human microbiota plays a crucial role in maintaining overall health and well-being. The gut microbiota has been implicated in developing and progressing various diseases, including cancer. This review highlights the related mechanisms and the compositions that influence cancer pathogenesis with a highlight on gastric cancer. We provide a comprehensive overview of the mechanisms by which the microbiome influences cancer development, progression, and response to treatment, with a focus on identifying potential biomarkers for early detection, prevention strategies, and novel therapeutic interventions that leverage microbiome modulation. This comprehensive review can guide future research and clinical practices in understanding and harnessing the microbiome to optimize gastric cancer therapies.}, }
@article {pmid39857870, year = {2024}, author = {Di Spirito, F and Pisano, M and Caggiano, M and De Benedetto, G and Di Palo, MP and Franci, G and Amato, M}, title = {Human Herpesviruses, Bacteria, and Fungi in Gingivitis and Periodontitis Pediatric Subjects: A Systematic Review.}, journal = {Children (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/children12010039}, pmid = {39857870}, issn = {2227-9067}, abstract = {Objectives: This systematic review assesses and compares the presence and relative abundance of periodontal pathogens, human herpesviruses (HHVs), and fungi in subgingival and/or saliva samples from pediatric subjects (≤18 years of age) with periodontally healthy status and with gingivitis and/or periodontitis. Methods: The study protocol was conducted under the PRISMA statement and registered on PROSPERO (CRD42024593007). Data from seven studies were descriptively analyzed and qualitatively assessed through the ROBINS-1 and JBI tools. Results: Pediatric subjects with clinically healthy periodontium exhibited a balanced microbiome, with early colonizers (Streptococcus species) supporting biofilm development and late colonizers like Fusobacterium nucleatum, Treponema denticola (82.35%), and Porphyromonas gingivalis (29.7%) present at low levels, suggesting subclinical dysbiosis. Viruses such as HSV-I (100%), CMV (17.8%), and EBV-I (22.09%) coexisted in a likely latent state, maintained by effective immune responses. In pediatric periodontitis, biofilms were more diverse and pathogenic, with increased prevalence of A. actinomycetemcomitans (56.09%), P. gingivalis (55.4%), and T. forsythia (35.9%). Generalized periodontitis showed higher CMV (36.36%) and EBV-I (36.24%) prevalence than gingivitis (HSV-I 18.75%). Coinfections were frequent in periodontitis, suggesting bacterial-viral synergy in exacerbating inflammation and tissue destruction. Fungi, although not studied, may also contribute under specific conditions. Conclusions: These findings highlight the role of microbial interactions in periodontal health and disease progression.}, }
@article {pmid39857809, year = {2025}, author = {Cubillejo, I and Theis, KR and Panzer, J and Luo, X and Banerjee, S and Thummel, R and Withey, JH}, title = {Vibrio cholerae Gut Colonization of Zebrafish Larvae Induces a Dampened Sensorimotor Response.}, journal = {Biomedicines}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/biomedicines13010226}, pmid = {39857809}, issn = {2227-9059}, support = {R21AI171072/GF/NIH HHS/United States ; }, abstract = {Background: Cholera is a diarrheal disease prevalent in populations without access to clean water. Cholera is caused by Vibrio cholerae, which colonizes the upper small intestine in humans once ingested. A growing number of studies suggest that the gut microbiome composition modulates animal behavior. Zebrafish are an established cholera model that can maintain a complex, mature gut microbiome during infection. Larval zebrafish, which have immature gut microbiomes, provide the advantage of high-throughput analyses for established behavioral models. Methods: We identified the effects of V. cholerae O1 El Tor C6706 colonization at 5 days post-fertilization (dpf) on larval zebrafish behavior by tracking startle responses at 10 dpf. We also characterized the larval gut microbiome using 16S rRNA sequencing. V. cholerae-infected or uninfected control groups were exposed to either an alternating light/dark stimuli or a single-tap stimulus, and average distance and velocity were tracked. Results: While there was no significant difference in the light/dark trial, we report a significant decrease in distance moved for C6706-colonized larvae during the single-tap trial. Conclusion: This suggests that early V. cholerae colonization of the larval gut microbiome has a dampening effect on sensorimotor function, supporting the idea of a link between the gut microbiome and behavior.}, }
@article {pmid39857728, year = {2025}, author = {Jaimez-Alvarado, S and López-Tenorio, II and Barragán-De Los Santos, J and Bello-Vega, DC and Gómez, FJR and Amedei, A and Berrios-Bárcenas, EA and Aguirre-García, MM}, title = {Gut-Heart Axis: Microbiome Involvement in Restrictive Cardiomyopathies.}, journal = {Biomedicines}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/biomedicines13010144}, pmid = {39857728}, issn = {2227-9059}, support = {IN212422//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; CBF2023-2024-734//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; }, abstract = {An intriguing aspect of restrictive cardiomyopathies (RCM) is the microbiome role in the natural history of the disease. These cardiomyopathies are often difficult to diagnose and so result in significant morbidity and mortality. The human microbiome, composed of billions of microorganisms, influences various physiological and pathological processes, including cardiovascular health. Studies have shown that gut dysbiosis, an imbalance in the composition of intestinal bacteria, can contribute to systemic inflammation, a key factor in many cardiovascular conditions. An increase in gut permeability, frequently caused by dysbiosis, allows bacterial endotoxins to enter the bloodstream, activating inflammatory pathways that exacerbate cardiac dysfunction. Recent reports highlight the potential role of microbiome in amyloidogenesis, as certain bacteria produce proteins that accelerate the formation of amyloid fibrils. Concurrently, advancements in amyloidosis treatments have sparked renewed hopes, marking a promising era for managing these kinds of diseases. These findings suggest that the gut-heart axis may be a potential factor in the development and progression of cardiovascular disease like RCM, opening new paths for therapeutic intervention. The aim of this review is to provide a detailed overview of the gut-heart axis, focusing on RCM.}, }
@article {pmid39857688, year = {2025}, author = {Breaza, GM and Hut, FE and Cretu, O and Abu-Awwad, SA and Abu-Awwad, A and Sima, LV and Dan, RG and Dan, CA and Closca, RM and Zara, F}, title = {Correlation Between Systemic Inflammation, Gut Microbiome Dysbiosis and Postoperative Complications After the Modified Whipple Procedure.}, journal = {Biomedicines}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/biomedicines13010104}, pmid = {39857688}, issn = {2227-9059}, support = {No Grand number//Victor Babes University of Medicine and Pharmacy Timisoara/ ; }, abstract = {(1) Background: The modified Whipple procedure, or pylorus-preserving pancreaticoduodenectomy, is a complex surgical intervention used to treat pancreatic head tumors. While preserving digestive function, it is associated with significant perioperative risks. This study explores the clinical, immunological, and microbiome-related factors influencing postoperative complications, focusing on the interplay between patient comorbidities, systemic inflammation, and gut dysbiosis. (2) Methods: A retrospective analysis was conducted on 123 patients undergoing the modified Whipple procedure for pancreatic head tumors. Patients were categorized into two groups based on the occurrence of significant postoperative complications (Group A: with complications; Group B: without complications). Data on demographics, comorbidities, inflammatory markers (CRP, IL-6, procalcitonin), and gut microbiome composition were collected. Microbial diversity was evaluated using the Shannon Index, and logistic regression was performed to identify independent predictors of complications. (3) Results: Patients in Group A had a significantly higher prevalence of diabetes mellitus (43.1% vs. 20.8%; p = 0.02) and cardiovascular disease (35.3% vs. 13.9%; p = 0.01). Elevated inflammatory markers (CRP ≥ 40 mg/L, IL-6 ≥ 30 pg/mL, procalcitonin ≥ 0.5 ng/mL) were strongly associated with higher complication rates. Microbiome analysis indicated dysbiosis in Group A, with reduced Lactobacillus and Bifidobacterium levels, increased Enterobacteriaceae abundance, and a lower Shannon Index (<2). Patients exhibiting both dysbiosis and elevated inflammation had the highest complication rate (60%). Multivariate analysis identified diabetes, elevated IL-6, and dysbiosis as independent predictors of adverse outcomes. (4) Conclusions: Postoperative complications after the modified Whipple procedure are influenced by systemic inflammation and gut dysbiosis. A systematic preoperative assessment of microbiome health and inflammatory markers enables accurate risk stratification and personalized interventions, potentially reducing the incidence of complications and improving overall surgical outcomes.}, }
@article {pmid39857684, year = {2025}, author = {Anwer, EKE and Ajagbe, M and Sherif, M and Musaibah, AS and Mahmoud, S and ElBanbi, A and Abdelnaser, A}, title = {Gut Microbiota Secondary Metabolites: Key Roles in GI Tract Cancers and Infectious Diseases.}, journal = {Biomedicines}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/biomedicines13010100}, pmid = {39857684}, issn = {2227-9059}, abstract = {The gut microbiota, a dynamic ecosystem of trillions of microorganisms, produces secondary metabolites that profoundly influence host health. Recent research has highlighted the significant role of these metabolites, particularly short-chain fatty acids, indoles, and bile acids, in modulating immune responses, impacting epigenetic mechanisms, and contributing to disease processes. In gastrointestinal (GI) cancers such as colorectal, liver, and gastric cancer, microbial metabolites can drive tumorigenesis by promoting inflammation, DNA damage, and immune evasion. Conversely, these same metabolites hold therapeutic promise, potentially enhancing responses to chemotherapy and immunotherapy and even directly suppressing tumor growth. In addition, gut microbial metabolites play crucial roles in infectious disease susceptibility and resilience, mediating immune pathways that impact pathogen resistance. By consolidating recent insights into the gut microbiota's role in shaping disease and health, this review underscores the therapeutic potential of targeting microbiome-derived metabolites for treating GI cancers and infectious diseases and calls for further research into microbiome-based interventions.}, }
@article {pmid39857680, year = {2025}, author = {Radoš, L and Golčić, M and Mikolašević, I}, title = {The Relationship Between the Modulation of Intestinal Microbiota and the Response to Immunotherapy in Patients with Cancer.}, journal = {Biomedicines}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/biomedicines13010096}, pmid = {39857680}, issn = {2227-9059}, abstract = {The intestinal microbiota is an important part of the human body, and its composition can affect the effectiveness of immunotherapy. In the last few years, the modulation of intestinal microbiota in order to improve the effectiveness of immunotherapy has become a current topic in the scientific community, but there is a lack of research in this area. In this review, the goal was to analyze the current relevant literature related to the modulation of intestinal microbiota and the effectiveness of immunotherapy in the treatment of cancer. The effects of antibiotics, probiotics, diet, and fecal microbial transplantation were analyzed separately. It was concluded that the use of antibiotics, especially broad-spectrum types or larger quantities, causes dysbiosis of the intestinal microbiota, which can reduce the effectiveness of immunotherapy. While dysbiosis could be repaired by probiotics and thus improve the effectiveness of immunotherapy, the use of commercial probiotics without evidence of intestinal dysbiosis has not yet been sufficiently tested to confirm its safety for cancer for immunotherapy-treated cancer patients. A diet consisting of sufficient amounts of fiber, as well as a diet with higher salt content positively correlates with the success of immunotherapy. Fecal transplantation is a safe and realistic adjuvant option for the treatment of cancer patients with immunotherapy, but more clinical trials are necessary. Modulating the microbiota composition indeed changes the effectiveness of immunotherapy, but in the future, more human studies should be organized to precisely determine the types and procedures of microbiota modulation.}, }
@article {pmid39857673, year = {2025}, author = {Alizadeh Bahmani, AH and Abdel-Aziz, MI and Hashimoto, S and Bang, C and Brandstetter, S and Corcuera-Elosegui, P and Franke, A and Gorenjak, M and Harner, S and Kheiroddin, P and López-Fernández, L and Neerincx, AH and Pino-Yanes, M and Potočnik, U and Sardón-Prado, O and Toncheva, AA and Wolff, C and Kabesch, M and Kraneveld, AD and Vijverberg, SJH and Maitland-van der Zee, AH and On Behalf Of The SysPharmPediA Consortium, }, title = {Association of Corticosteroid Inhaler Type with Saliva Microbiome in Moderate-to-Severe Pediatric Asthma.}, journal = {Biomedicines}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/biomedicines13010089}, pmid = {39857673}, issn = {2227-9059}, abstract = {Background/Objectives: Metered-dose inhalers (MDIs) and dry powder inhalers (DPIs) are common inhaled corticosteroid (ICS) inhaler devices. The difference in formulation and administration technique of these devices may influence oral cavity microbiota composition. We aimed to compare the saliva microbiome in children with moderate-to-severe asthma using ICS via MDIs versus DPIs. Methods: Saliva samples collected from 143 children (6-17 yrs) with moderate-to-severe asthma across four European countries (The Netherlands, Germany, Spain, and Slovenia) as part of the SysPharmPediA cohort were subjected to 16S rRNA sequencing. The microbiome was compared using global diversity (α and β) between two groups of participants based on inhaler devices (MDI (n = 77) and DPI (n = 65)), and differential abundance was compared using the Analysis of Compositions of Microbiomes with the Bias Correction (ANCOM-BC) method. Results: No significant difference was observed in α-diversity between the two groups. However, β-diversity analysis revealed significant differences between groups using both Bray-Curtis and weighted UniFrac methods (adjusted p-value = 0.015 and 0.044, respectively). Significant differential abundance between groups, with higher relative abundance in the MDI group compared to the DPI group, was detected at the family level [Carnobacteriaceae (adjusted p = 0.033)] and at the genus level [Granulicatella (adjusted p = 0.021) and Aggregatibacter (adjusted p = 0.011)]. Conclusions: Types of ICS devices are associated with different saliva microbiome compositions in moderate-to-severe pediatric asthma. The causal relation between inhaler types and changes in saliva microbiota composition needs to be further evaluated, as well as whether this leads to different potential adverse effects in terms of occurrence and level of severity.}, }
@article {pmid39857645, year = {2024}, author = {Verma, J and Anwar, MT and Linz, B and Backert, S and Pachathundikandi, SK}, title = {The Influence of Gastric Microbiota and Probiotics in Helicobacter pylori Infection and Associated Diseases.}, journal = {Biomedicines}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/biomedicines13010061}, pmid = {39857645}, issn = {2227-9059}, support = {CRG/2022/003093//Anusandhan National Research Foundation (ANRF)/ ; BA1671/16-1//German Science Foundation (DFG)/ ; }, abstract = {The role of microbiota in human health and disease is becoming increasingly clear as a result of modern microbiome studies in recent decades. The gastrointestinal tract is the major habitat for microbiota in the human body. This microbiota comprises several trillion microorganisms, which is equivalent to almost ten times the total number of cells of the human host. Helicobacter pylori is a known pathogen that colonizes the gastric mucosa of almost half of the world population. H. pylori is associated with several gastric diseases, including gastric cancer (GC) development. However, the impact of the gastric microbiota in the colonization, chronic infection, and pathogenesis is still not fully understood. Several studies have documented qualitative and quantitative changes in the microbiota's composition in the presence or absence of this pathogen. Among the diverse microflora in the stomach, the Firmicutes represent the most notable. Bacteria such as Prevotella sp., Clostridium sp., Lactobacillus sp., and Veillonella sp. were frequently found in the healthy human stomach. In contrast, H.pylori is very dominant during chronic gastritis, increasing the proportion of Proteobacteria in the total microbiota to almost 80%, with decreasing relative proportions of Firmicutes. Likewise, H. pylori and Streptococcus are the most abundant bacteria during peptic ulcer disease. While the development of H. pylori-associated intestinal metaplasia is accompanied by an increase in Bacteroides, the stomachs of GC patients are dominated by Firmicutes such as Lactobacillus and Veillonella, constituting up to 40% of the total microbiota, and by Bacteroidetes such as Prevotella, whereas the numbers of H. pylori are decreasing. This review focuses on some of the consequences of changes in the gastric microbiota and the function of probiotics to modulate H. pylori infection and dysbiosis in general.}, }
@article {pmid39857320, year = {2025}, author = {Yan, H and Wang, Y and Liang, H and Duan, Y and Wang, J and Zhou, C and Huang, Z}, title = {Effects of Lysophospholipids on the Antioxidant Capacity, Digestive Performance, and Intestinal Microbiota of Litopenaeus vannamei.}, journal = {Biology}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/biology14010090}, pmid = {39857320}, issn = {2079-7737}, support = {323MS126//Hainan province Natural Science Foundation of China/ ; 2019A1515012159//Guangdong province Rural Science and Technology Commissioners Project, Guangdong Natural Science Foundation/ ; NHYYSWZZZYKZX2020//Financial Special Project of the Ministry of Agriculture and Rural Areas/ ; 2020KX03, 2023TD97//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; 2022SPY02001//Rural Revitalization Strategy Special Fund Seed Industry Revitalization Project of Guangdong Province/ ; }, abstract = {This study seeks to assess the impact of varying concentrations of lysophospholipids on the antioxidant capacity, digestive performance, and intestinal microbiota of L. vannamei. A total of 840 shrimp, with an average initial weight of 2.22 ± 0.11 g, were randomly distributed across 28 aquaculture tanks (30 shrimp per tank), organized into 7 distinct treatment groups, each comprising 4 replicates. The control group (DL2) was administered a basal diet formula supplemented with 2% soy lecithin, whereas the experimental groups received lysophospholipids at varying concentrations of 0% (RL0), 0.1% (RL0.1), 0.5% (RL0.5), 1% (RL1), 1.5% (RL1.5), and 2% (RL2). The results revealed that the total antioxidant capacity (T-AOC) level in the RL0.1 group was significantly elevated compared to the DL2 and RL2 groups (p < 0.05). Furthermore, glutathione peroxidase (GSH-Px) and catalase (CAT) activities were markedly higher in the RL1 and RL1.5 groups relative to other groups (p < 0.05). Superoxide dismutase (SOD) activity exhibited a significant increase across all lysophospholipid-supplemented groups when compared to the DL2 group (p < 0.05). Malondialdehyde (MDA) levels were notably elevated in the RL0.5, RL1.5, and RL2 groups relative to the other groups (p < 0.05). Regarding antioxidant-related genes in the hemocytes, the relative expression levels of Nrf1, Nrf2, GPx, SOD, CAT, and Hippo were significantly higher in the RL0.5 and RL1 groups compared to the DL2 group (p < 0.05). Additionally, the relative expression levels of GPx and SOD were significantly elevated in the RL2 group compared to the DL2 group (p < 0.05). In the intestinal tract, the activities of trypsin and α-amylase (AMS) were significantly elevated in the RL0.1, RL0.5, and RL1 groups compared to the DL2 group (p < 0.05). Additionally, the RL0.1 group demonstrated significantly higher lipase (LPS) activity than the other groups supplemented with lysophospholipids (p < 0.05). Furthermore, the relative expression levels of the trypsin and α-amylase genes were significantly increased in the RL1 and RL1.5 groups in comparison to the DL2 group (p < 0.05). Sequencing analysis of the intestinal microbiota indicated that the incorporation of lysophospholipids resulted in an enhancement of the composition and structure of the intestinal microbiota. The functional abundance of the intestinal microbiome was primarily enriched in metabolic pathways. Overall, the incorporation of lysophospholipids into the diet exerted a beneficial effect on the antioxidant capacity, digestive performance, and intestinal microbiota of L. vannamei, especially with the supplementation of 0.1% lysophospholipids.}, }
@article {pmid39857318, year = {2025}, author = {Kashchenko, G and Taldaev, A and Adonin, L and Smutin, D}, title = {Investigating Aerobic Hive Microflora: Role of Surface Microbiome of Apis Mellifera.}, journal = {Biology}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/biology14010088}, pmid = {39857318}, issn = {2079-7737}, support = {No 075-15-2022-305//Ministry of Science and Higher Education of the Russian Federation within the framework of state support for the creation and development of World-Class Research Centers 'Digital Biodesign and Personalized Healthcare'./ ; }, abstract = {This study investigated the surface microbiome of the honeybee (Apis mellifera), focusing on the diversity and functional roles of its associated microbial communities. While the significance of the microbiome to insect health and behavior is increasingly recognized, research on invertebrate surface microbiota lags behind that of vertebrates. A combined metagenomic and cultivation-based approach was employed to characterize the bacterial communities inhabiting the honeybee exoskeleton. Our findings reveal a complex and diverse microbiota exhibiting significant spatial and environmental heterogeneity. The identification of antimicrobial compound producers, validated through both culture and metagenomic analyses, including potentially novel Actinobacteria species, underscores the potential impact of these microbial communities on honeybee health, behavior, and hive dynamics. This research contributes to a more profound ecological understanding of the honeybee microbiome, particularly in its winter configuration.}, }
@article {pmid39857299, year = {2025}, author = {Ramos Lopez, D and Flores, FJ and Espindola, AS}, title = {MeStanG-Resource for High-Throughput Sequencing Standard Data Sets Generation for Bioinformatic Methods Evaluation and Validation.}, journal = {Biology}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/biology14010069}, pmid = {39857299}, issn = {2079-7737}, support = {OKL03271//Oklahoma State University - Oklahoma Agricultural Experiment Station/ ; }, abstract = {Metagenomics analysis has enabled the measurement of the microbiome diversity in environmental samples without prior targeted enrichment. Functional and phylogenetic studies based on microbial diversity retrieved using HTS platforms have advanced from detecting known organisms and discovering unknown species to applications in disease diagnostics. Robust validation processes are essential for test reliability, requiring standard samples and databases deriving from real samples and in silico generated artificial controls. We propose a MeStanG as a resource for generating HTS Nanopore data sets to evaluate present and emerging bioinformatics pipelines. MeStanG allows samples to be designed with user-defined organism abundances expressed as number of reads, reference sequences, and predetermined or custom errors by sequencing profiles. The simulator pipeline was evaluated by analyzing its output mock metagenomic samples containing known read abundances using read mapping, genome assembly, and taxonomic classification on three scenarios: a bacterial community composed of nine different organisms, samples resembling pathogen-infected wheat plants, and a viral pathogen serial dilution sampling. The evaluation was able to report consistently the same organisms, and their read abundances as provided in the mock metagenomic sample design. Based on this performance and its novel capacity of generating exact number of reads, MeStanG can be used by scientists to develop mock metagenomic samples (artificial HTS data sets) to assess the diagnostic performance metrics of bioinformatic pipelines, allowing the user to choose predetermined or customized models for research and training.}, }
@article {pmid39857260, year = {2025}, author = {Shan, C and Liu, Y and Liu, S and Li, C and Ma, C and Yu, H and Li, J and Jiang, G and Tian, J}, title = {Exploring the Mechanism of Clostridium autoethanogenum Protein for Broiler Growth Based on Gut Microbiota and Serum Metabolomics.}, journal = {Biology}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/biology14010029}, pmid = {39857260}, issn = {2079-7737}, abstract = {Intestinal health is vital for poultry production, and protein plays a key role in intestinal nutrition. The present study used 16S rRNA gene sequencing and serum metabolomics to investigate the effect of CAP on the cecal microflora structure and serum metabolites in 42-day-old broiler chickens. A total of 480 one-day-old Arbor Acres broiler chickens were randomly divided into four treatments with twelve replicates comprising 10 chickens each, evenly divided by sex. The four groups were basal diet group (CAP0), treatment group 1 (CAP2), treatment group 2 (CAP3), and treatment group 3 (CAP4). The broilers in the CAP0 group were fed a basal diet (without CAP), while those in the CAP2, CAP3, and CAP4 groups received diets containing 2%, 3%, and 4% CAP, respectively. Growth performance results showed that dietary CAP supplementation significantly ameliorated the feed conversion rate (FCR) of broilers at 42 days in the CAP3 and CAP4 groups (p < 0.05). Microbial results revealed that CAP did not alter the dominant microorganisms in the cecum at the phylum, family, and genus levels. LEfSe analysis showed significantly higher relative abundances of p_Desulfobacterota, f_Desulfovibrionaceae, and g_Ruminococcus in the CAP3 group compared to the CAP0 and CAP4 groups. Metabolomic analyses indicated that the effect of incorporating CAP into the diet on serum metabolites primarily focused on organic acids and their derivatives, small peptides, amino acid derivatives, and oxidized lipids. The addition of 3% or 4% CAP to the diet can enhance metabolic pathways such as the citrate cycle (TCA cycle) and arginine and proline metabolism. In summary, incorporating CAP into the diet can increase the relative abundance of beneficial bacteria in the cecum and improve the feed conversion efficiency of broilers by enhancing amino acid and energy metabolism.}, }
@article {pmid39857242, year = {2024}, author = {Yang, C and Liu, B and Pan, L and Xia, D and Sun, C and Zheng, X and Chen, P and Hu, H and Zhou, Q}, title = {Impact of Soybean Bioactive Peptides on Growth, Lipid Metabolism, Antioxidant Ability, Molecular Responses, and Gut Microbiota of Oriental River Prawn (Macrobrachium nipponense) Fed with a Low-Fishmeal Diet.}, journal = {Biology}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/biology14010011}, pmid = {39857242}, issn = {2079-7737}, support = {BK20231138//the Natural Science Foundation of Jiangsu Province/ ; JATS[2023]470//the earmarked fund for Jiangsu Agricultural Industry Technology System/ ; CARS-48//China Agriculture Research System of MOF and MARA/ ; 2023TD63//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; }, abstract = {The substitution of fishmeal with high-level soybean meal in the diet of crustaceans usually induces lipid accumulation and oxidative stress in the hepatopancreas. Therefore, it is essential to alleviate these adverse effects. In the present study, SBPs were used to alleviate the negative effects of a fishmeal decrease on the growth performance, lipid metabolism, antioxidant capacity, and gut microbiota of oriental river prawn (Macrobrachium nipponense) in an 8-week feeding trial. Three isonitrogenic and isolipidic diets were prepared as follows: R (reference diet with 32% fishmeal), CT (control diet with 22% fishmeal), and SBP (22% fishmeal with 1.25 g/kg soybean bioactive peptides). The prawns (initial biomass per tank 17 g) were randomly divided into three groups with four replicates. The results showed that the low-fishmeal diet induced the following: (1) the inhibition of growth performance and survival of prawns; (2) an increase in triglyceride content in the hepatopancreas and hemolymph and downregulation of carnitine palmitoyl transferase 1 (cpt1) gene expression; (3) a reduction in antioxidant enzymes' activities and their genes expression levels and an increase malondialdehyde (MDA) content; and (4) an increase in the abundance of the conditional pathogen Pseudomonas in the gut. SBPs supplementation in the CT diet effectively alleviated most of the above adverse effects. SBPs enhanced inducible nitric oxide synthase (iNOS) activity to synthesize nitric oxide (NO) by activating the imd-relish pathway. Most importantly, SBPs increased the potential probiotic Rikenellaceae_RC9_gut_group abundance and decreased the abundance of the conditional pathogen Pseudomonas in the gut. In conclusion, SBPs supplementation can improve low-fishmeal-diet-induced growth inhibition by regulating the gut microbiota composition to ameliorate lipid deposition and oxidative stress and strengthen immune status in oriental river prawn.}, }
@article {pmid39856843, year = {2025}, author = {Hyży, A and Rozenek, H and Gondek, E and Jaworski, M}, title = {Effect of Antioxidants on the Gut Microbiome Profile and Brain Functions: A Review of Randomized Controlled Trial Studies.}, journal = {Foods (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/foods14020176}, pmid = {39856843}, issn = {2304-8158}, abstract = {BACKGROUND: Antioxidants are widely recognized for their potential health benefits, including their impact on cognitive function and gut microbiome modulation. Understanding these effects is essential for exploring their broader clinical applications.<br><br>OBJECTIVES: This review aims to evaluate the effects of antioxidants on the gut microbiome and cognitive function, with a focus on findings from randomized controlled trials (RCTs).<br><br>METHODS: The studies involved human participants across a range of age groups, with interventions encompassing natural antioxidant sources, such as berries, as well as specific antioxidant vitamins. An extensive search across PubMed, SCOPUS, and Web of Science databases identified six relevant RCTs, each evaluated for potential bias.<br><br>RESULTS: These studies focused on a variety of antioxidant-rich products, including both naturally derived sources and supplemental forms. Antioxidants, including vitamins C, B2, and D, along with polyphenols such as xanthohumol, fermented papaya, peanuts, and berry extracts, demonstrate the potential to support cognitive function and promote gut health through mechanisms that modulate microbiome diversity and reduce inflammation. However, observed changes in microbiome diversity were modest and inconsistent across the studies.<br><br>CONCLUSIONS: While preliminary evidence suggests that antioxidants may benefit gut health and cognitive function, the heterogeneity of existing studies limits their immediate clinical applicability. Additionally, more robust RCTs are needed to substantiate these findings and guide future interventions.}, }
@article {pmid39856758, year = {2025}, author = {Guo, F and Qiao, J and Hu, Z and Huang, J and Bi, R and Abbas, W and Zhen, W and Guo, Y and Wang, Z}, title = {Yeast cell wall polysaccharides accelerate yet in-feed antibiotic delays intestinal development and maturation via modulating gut microbiome in chickens.}, journal = {Journal of animal science and biotechnology}, volume = {16}, number = {1}, pages = {14}, pmid = {39856758}, issn = {1674-9782}, support = {32172774//the National Natural Science Foundation of China/ ; 242102110018//the Key Research and Development and Promotion of Special (Science and Technology) Project of Henan Province/ ; }, abstract = {BACKGROUND: It is important to promote intestinal development and maturation of chicks for feed digestion and utilization, intestinal health, and disease resistance. This study aimed to investigate the effects of dietary yeast cell wall polysaccharides (YCWP) addition on intestinal development and maturation of chickens and its potential action mechanism.<br><br>METHODS: 180 one-day-old male Arbor Acres broilers were randomly assigned to three groups containing control (basal diets without any antibiotics or anticoccidial drug), bacitracin methylene&#xa0;disalicylate (BMD)-treated group (50 mg/kg) and YCWP-supplemented group (100 mg/kg).<br><br>RESULTS: Compared with control group, in-feed antibiotic BMD continuous administration significantly decreased crypt depth (d 21) and villus height (d 42) along with mucosal maltase activity (d 42) in the ileum (P&#x2009;<&#x2009;0.05). Also, BMD markedly downregulated gene expression levels of &#x3b2;-catenin, lysozyme, occludin and FABP-2 (d 21) and innate immune related genes CD83 and MHC-I mRNA levels (d 42, P&#x2009;<&#x2009;0.05), and decreased goblet cell counts in the ileum of chickens (d 21 and d 42, P&#x2009;<&#x2009;0.05). While, TLR-2, TLR-6 and iNOS mRNA abundances were notably upregulated by BMD treatment (d 42, P&#x2009;<&#x2009;0.05). Nevertheless, dietary YCWP addition significantly increased the ratio of villus height to crypt depth (d 21), villus surface area (d 21 and d 42), ileal alkaline phosphatase and maltase activities as well as goblet cell (d 21 and d 42) and IgA-producing plasma cell numbers as compared to BMD treatment (d 21, P&#x2009;<&#x2009;0.05). YCWP addition also upregulated gene expression levels of Lgr5, Wnt/&#x3b2;-catenin signaling pathway related gene (Wnt3, &#x3b2;-catenin, d 21; &#x3b2;-catenin, d 42), intestinal cells proliferation marker Ki-67 and barrier function related genes (occludin, d 21 and d 42, P&#x2009;<&#x2009;0.05). Moreover, YCWP significantly increased antigen presenting cell marker related genes (MHC-II, d 21; CD83 and MHC-I, d 42), TLR-1, TLR-2 and TLR-6 mRNA levels (d 21, P&#x2009;<&#x2009;0.05). Cecal microbiome analysis showed that YCWP addition obviously improved cecal microbial composition, as indicated by increasing relative abundance of Fournierella, Psychrobacter and Ruminiclostridium on d 21, and Alistipes and Lactobacillus on d 42, which were positively related with gut development and maturation related indexes (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSION: Collectively, YCWP promoted yet antibiotic BMD delayed intestinal morphological and immunological development linked with modulating gut microbiome in chickens.}, }
@article {pmid39856742, year = {2025}, author = {Benitez, AJ and Tanes, C and Friedman, ES and Zackular, JP and Ford, E and Gerber, JS and DeRusso, PA and Kelly, A and Li, H and Elovitz, MA and Wu, GD and Zemel, B and Bittinger, K}, title = {Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {21}, pmid = {39856742}, issn = {2049-2618}, support = {KL2TR001879/TR/NCATS NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R35GM138369/GM/NIGMS NIH HHS/United States ; UL1TR001878//NIH National Center for Research Resources Clinical and Translational Science Program/ ; unrestricted donation//American Beverage Foundation for a Healthy America/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/adverse effects/pharmacology ; Infant ; *Feces/microbiology/chemistry ; Female ; *Bile Acids and Salts/metabolism ; Male ; Prospective Studies ; *Breast Feeding ; Longitudinal Studies ; Infant, Newborn ; Metagenomics ; Bacteria/classification/genetics/drug effects/isolation &amp; purification ; Child, Preschool ; Black or African American ; Amoxicillin ; Bifidobacterium/drug effects/isolation &amp; purification/genetics ; White ; }, abstract = {BACKGROUND: The evolving infant gut microbiome influences host immune development and later health outcomes. Early antibiotic exposure could impact microbiome development and contribute to poor outcomes. Here, we use a prospective longitudinal birth cohort of n = 323 healthy term African American children to determine the association between antibiotic exposure and the gut microbiome through shotgun metagenomics sequencing as well as bile acid profiles through liquid chromatography-mass spectrometry.<br><br>RESULTS: Stool samples were collected at ages 4, 12, and 24&#xa0;months for antibiotic-exposed (n&#x2009;=&#x2009;170) and unexposed (n&#x2009;=&#x2009;153) participants. A short-term substudy (n&#x2009;=&#x2009;39) collected stool samples at first exposure, and over 3&#xa0;weeks following antibiotics initiation. Antibiotic exposure (predominantly amoxicillin) was associated with minimal microbiome differences, whereas all tested taxa were modified by breastfeeding. In the short-term substudy, we observed microbiome differences only in the first 2&#xa0;weeks following antibiotics initiation, mainly a decrease in Bifidobacterium bifidum. The differences did not persist a month after antibiotic exposure. Four species were associated with infant age. Antibiotic exposure was not associated with an increase in antibiotic resistance gene abundance or with differences in microbiome-derived fecal bile acid composition.<br><br>CONCLUSIONS: Short-term and long-term gut microbiome perturbations by antibiotic exposure were detectable but substantially smaller than those associated with breastfeeding and infant age.}, }
@article {pmid39856709, year = {2025}, author = {Li, D and Chen, W and Luo, W and Zhang, H and Liu, Y and Shu, D and Wei, G}, title = {Seed microbiomes promote Astragalus mongholicus seed germination through pathogen suppression and cellulose degradation.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {23}, pmid = {39856709}, issn = {2049-2618}, support = {42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; }, mesh = {*Seeds/microbiology ; *Germination ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Cellulose/metabolism ; Astragalus Plant/microbiology ; Soil Microbiology ; Metagenome ; }, abstract = {BACKGROUND: Seed-associated microorganisms play crucial roles in maintaining plant health by providing nutrients and resistance to biotic and abiotic stresses. However, their functions in seed germination and disease resistance remain poorly understood. In this study, we investigated the microbial community assembly features and functional profiles of the spermosphere and endosphere microbiomes related to germinated and ungerminated seeds of Astragalus mongholicus by using amplicon and shotgun metagenome sequencing techniques. Additionally, we aimed to elucidate the relationship between beneficial microorganisms and seed germination through both in vitro and in vivo pot experiments.<br><br>RESULTS: Our findings revealed that germination significantly enhances the diversity of microbial communities associated with seeds. This increase in diversity is driven through environmental ecological niche differentiation, leading to the enrichment of potentially beneficial probiotic bacteria such as Pseudomonas and Pantoea. Conversely, Fusarium was consistently enriched in ungerminated seeds. The co-occurrence network patterns revealed that the microbial communities within germinated and ungerminated seeds presented distinct structures. Notably, germinated seeds exhibit more complex and interconnected networks, particularly for bacterial communities and their interactions with fungi. Metagenome analysis showed that germinated seed spermosphere soil had more functions related to pathogen inhibition and cellulose degradation. Through a combination of culture-dependent and germination experiments, we identified Fusarium solani as the pathogen. Consistent with the metagenome analysis, germination experiments further demonstrated that bacteria associated with pathogen inhibition and cellulose degradation could promote seed germination and vigor. Specifically, Paenibacillus sp. significantly enhanced A. mongholicus seed germination and plant growth.<br><br>CONCLUSIONS: Our study revealed the dynamics of seed-associated microorganisms during seed germination and confirmed their ecological role in promoting A. mongholicus seed germination by suppressing pathogens and degrading cellulose. This study offers a mechanistic understanding of how seed microorganisms facilitate successful seed germination, highlighting the potential for leveraging these microbial communities to increase plant health. Video Abstract.}, }
@article {pmid39856480, year = {2025}, author = {Tarassishin, L and Kim, T and Hu, J and Barre, A and Rendon, A and Picker, M and Chen, R and Weinstein, K and Thjømøe, A and Mørk, E and Stone, J and Torres, J and Colombel, JF and Agrawal, M and Peter, I}, title = {Elevated Fecal Lipocalin-2 Levels During Early Life Are Associated with Maternal Inflammatory Bowel Disease Diagnosis.}, journal = {Digestive diseases and sciences}, volume = {}, number = {}, pages = {}, pmid = {39856480}, issn = {1573-2568}, support = {K23DK129762-02/DK/NIDDK NIH HHS/United States ; UL1TR004419//Clinical and Translational Science Awards (CTSA)/ ; S10OD026880//Office of Research Infrastructure of the National Institutes of Health/ ; S10OD030463//Office of Research Infrastructure of the National Institutes of Health/ ; }, abstract = {BACKGROUND: Fecal lipocalin-2 (LCN2) is a biomarker of neutrophil activation, which is elevated in patients with inflammatory bowel disease (IBD); however, its dynamic changes during pregnancy and early life are largely unknown. We characterized LCN2 levels by maternal IBD diagnosis, offspring feeding behavior, and gut microbiota composition.<br><br>METHODS: In the prospective MECONIUM (Exploring Mechanisms of Disease Transmission In Utero through the Microbiome) study, we analyzed 559 fecal samples from 91 pregnant women with IBD, 78 healthy controls, and their 147 offspring for LCN2 levels at each trimester of pregnancy and multiple time points during early life using linear mixed-effects model and multiple logistic regression analyses. Gut microbiota community compositions were evaluated following 16S rRNA gene sequencing.<br><br>RESULTS: IBD cases had higher LCN2 levels throughout pregnancy compared to controls. In offspring, significantly higher LCN2 was found in babies born to mothers with IBD, compared to those without IBD, at 3&#xa0;months, 1&#xa0;year, and 4&#xa0;years (all p&#x2009;<&#x2009;0.03), with offspring LCN2 levels being predictive of maternal IBD case status with&#x2009;>&#x2009;85% accuracy at ages 1 and 4. We also detected correlations between LCN2 levels and certain IBD-associated bacterial taxa in both mothers and babies. Exclusively breastfed babies had lower LCN2 in the first weeks of life compared to formula or mixed-fed counterparts.<br><br>CONCLUSIONS: Babies born to mother with IBD had significantly higher LCN2 during early life compared to controls with exclusive breastfeeding impacting LCN2 levels early on. LCN2 levels correlated with IBD-associated microbial taxa in both mothers and babies. Future studies should identify the biological drivers and health-related consequences of elevated LCN2 during early childhood.}, }
@article {pmid39856391, year = {2025}, author = {Tisza, MJ and Lloyd, RE and Hoffman, K and Smith, DP and Rewers, M and Javornik Cregeen, SJ and Petrosino, JF}, title = {Longitudinal phage-bacteria dynamics in the early life gut microbiome.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {39856391}, issn = {2058-5276}, support = {U01 DK63829//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; U01 DK63821//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; U01 DK63865//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; }, abstract = {Microbial colonization of the human gut occurs soon after birth, proceeds through well-studied phases and is affected by lifestyle and other factors. Less is known about phage community dynamics during infant gut colonization due to small study sizes, an inability to leverage large databases and a lack of appropriate bioinformatics tools. Here we reanalysed whole microbial community shotgun sequencing data of 12,262 longitudinal samples from 887 children from four countries across four years of life as part of the The Environmental Determinants of Diabetes in the Young (TEDDY) study. We developed an extensive metagenome-assembled genome catalogue using the Marker-MAGu pipeline, which comprised 49,111 phage taxa from existing human microbiome datasets. This was used to identify phage marker genes and their integration into the MetaPhlAn 4 bacterial marker gene database enabled simultaneous assessment of phage and bacterial dynamics. We found that individual children are colonized by hundreds of different phages, which are more transitory than bacteria, accumulating a more diverse phage community over time. Type 1 diabetes correlated with a decreased rate of change in bacterial and viral communities in children aged one and two. The addition of phage data improved the ability of machine learning models to discriminate samples by country. Finally, although phage populations were specific to individuals, we observed trends of phage ecological succession that correlated well with putative host bacteria. This resource improves our understanding of phage-bacteria interactions in the developing early life microbiome.}, }
@article {pmid39856389, year = {2025}, author = {Johnson, DE and Jones, RB}, title = {Predicting child health with gut microbiome development trajectories.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {39856389}, issn = {2058-5276}, }
@article {pmid39856267, year = {2025}, author = {Daniel, H}, title = {Personalising dietary advice for disease prevention: concepts and experiences.}, journal = {Pflugers Archiv : European journal of physiology}, volume = {}, number = {}, pages = {}, pmid = {39856267}, issn = {1432-2013}, abstract = {Personalised nutrition (PN) as a new endeavour emerged in the background of the human genome project with the ease to analyse genetic heterogeneity. First commercial offers with recommendations for diet and lifestyle changes, usually based on a few polymorphisms, entered markets soon after the presentation of the human genome blueprint. Although PN has seen many attempts, meanwhile, with the inclusion of other biomedical measures such as microbiome and/or continuous glucose monitoring, scientific assessments of such approaches in various settings revealed limited success. Although personalisation improved general compliance over generic advice, particular benefits in referring to biomedical measures and individual risks did, in most cases, not provide any significant advantage. Moreover, scholars criticised such approaches as of limited impact from a public health perspective by attracting mainly technology-open individuals of high social status and proper financial capabilities. Based on these experiences, new avenues for personalising dietary advice are developed, and those are going beyond pure biomedical data by assessing the entire food environment of the individual with its capabilities and constraints in the given life setting. Embedded into digital environments for data collection but also for bidirectional communication, new possibilities emerge. Artificial intelligence methods allow for the multitude of input data and highly complex decision trees to be derived to customize advice. And that can be delivered on the spot and in time in any language whenever decisions are made on what to buy or what to eat. But systems can also be employed to increase physical activity levels and for the adoption of a more healthy lifestyle in general.}, }
@article {pmid39856229, year = {2025}, author = {Hannawayya, R and Puentes, R and Mirzadzare, N and Cirone, K and Amin, H and Soraisham, A and Alshaikh, B and Thomas, S and Cobo, ER}, title = {A multidimensional fecal microbial and inflammatory biomarker profiling in preterm and full-term neonates.}, journal = {Pediatric research}, volume = {}, number = {}, pages = {}, pmid = {39856229}, issn = {1530-0447}, abstract = {BACKGROUND: Preterm birth affects approximately one in every ten neonates. The clinical outcomes depend on care and management factors, including the birth delivery method and the use of antibiotics.<br><br>METHODS: This observational cohort study determined antimicrobial peptides, proteases, metabolomic, and microbiome profiles in fecal samples collected from 20 preterm and nine full-term neonates 48&#x2009;h after birth.<br><br>RESULTS: The results show that preterm neonates have increased levels of &#x3b1;-defensins, serine proteases, and matrix metalloproteinases. They also have distinct metabolic signatures characterized by decreased kynurenic acid and increased mevalonate levels. These neonates also exhibit reduced microbial diversity.<br><br>CONCLUSION: This study highlights that heightened immune response and proteolytic activity, marked dysbiosis, and reduced short-chain fatty acids within the preterm gastrointestinal tract immediately after birth might predispose neonates to exacerbated gut inflammation. Some of the findings, including the elevated fecal mevalonate levels, are potential biomarkers in neonatology for early identification of metabolic disturbances linked to gut inflammation, emphasizing further studies to explore its association with inflammatory conditions in preterm infants.<br><br>IMPACT: Inflammatory markers that can predict intestinal disorders are insufficiently characterized in preterm neonates. This study identified antimicrobial peptide responses, proteolytic activity, marked dysbiosis, and reduced short-chain fatty acid production in feces from preterm neonates. These critical differences in inflammatory, metabolomic, and microbial signatures may predispose to exacerbated gut inflammation in preterm neonates. Some inflammatory effectors in feces are potential biomarkers for the early detection of intestinal inflammatory conditions in preterm neonates. This study contributes to understanding the inflammatory conditions in the guts of preterm babies and identifies novel targets for timely diagnosis, interventions, and management practices in neonatal care.}, }
@article {pmid39856104, year = {2025}, author = {Özcan, E and Yu, KB and Dinh, L and Lum, GR and Lau, K and Hsu, J and Arino, M and Paramo, J and Lopez-Romero, A and Hsiao, EY}, title = {Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {987}, pmid = {39856104}, issn = {2041-1723}, support = {R01NS115537//U.S. Department of Health &amp; Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS)/ ; }, mesh = {*Diet, Ketogenic ; Animals ; *Gastrointestinal Microbiome ; *Dietary Fiber/administration &amp; dosage ; *Seizures/diet therapy/metabolism ; Mice ; Male ; Humans ; Mice, Inbred C57BL ; Disease Models, Animal ; Infant Formula ; Female ; }, abstract = {The gut microbiome modulates the anti-seizure effects of the ketogenic diet, but how specific dietary formulations differentially modify the gut microbiome in ways that impact seizure outcome is poorly understood. We find that medical ketogenic infant formulas vary in macronutrient ratio, fat source, and fiber content and differentially promote resistance to 6-Hz seizures in mice. Dietary fiber, rather than fat ratio or source, drives substantial metagenomic shifts in a model human infant microbial community. Addition of fiber to a fiber-deficient ketogenic formula restores seizure resistance, and supplementing protective formulas with excess fiber potentiates seizure resistance. By screening 13 fiber sources and types, we identify metagenomic responses in the model community that correspond with increased seizure resistance. Supplementing with seizure-protective fibers enriches microbial genes related to queuosine biosynthesis and preQ0 biosynthesis and decreases genes related to sucrose degradation and TCA cycle, which are also seen in seizure-protected mice that are fed fiber-containing ketogenic formulas. This study reveals that different formulations of ketogenic diets, and dietary fiber content in particular, differentially impact seizure outcome in mice, likely by modifying the gut microbiome. Understanding interactions between diet, microbiome, and host susceptibility to seizures could inform novel microbiome-guided approaches to treat refractory epilepsy.}, }
@article {pmid39856057, year = {2025}, author = {Hu, H and Huang, Y and Yang, F and Ma, L and Zhang, J and Deng, X and Ma, N and Wang, K and Tao, Y and Lin, Q and Li, Y and Bai, X and Pan, H}, title = {Metagenome-assembled microbial genomes (n = 3,448) of the oral microbiomes of Tibetan and Duroc pigs.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {141}, pmid = {39856057}, issn = {2052-4463}, mesh = {Animals ; *Metagenome ; Swine/microbiology ; *Mouth/microbiology ; *Microbiota ; Genome, Microbial ; Metagenomics ; Tibet ; }, abstract = {Compared with leaner breeds, local Chinese pig breeds have distinct intestinal microbial, as determined by metagenomic techniques, and the interactions between oral microorganisms and their hosts are also gradually being clarified. However, the high host genome content means that few metagenome-based oral microbiomes have been reported. Here, we combined dilution-based metagenomic sequencing and binning approaches to extract the microbial genomes from the oral microbiomes of Tibetan and Duroc pigs. The host contamination rates were reduced to 13.64%, a quarter of the normal metagenomic level (65.25% on average). Medium-high-quality metagenome-assembled genomes (MAGs; n = 3,448) spanning nine phyla were retrieved and 70.79% were novel species. Of the nonredundant MAGs, only 13.37% were shared, revealing the strong disparities between Tibetan and Duroc pigs. The oral microbial diversity of the Duroc pig was greater than that of the Tibetan pig. We present the first large-scale dilute-based metagenomic data on the pig oral microbiome, which should facilitate further investigation of the functions of oral microorganisms in pigs.}, }
@article {pmid39856008, year = {2025}, author = {Chalif, J and Goldstein, N and Mehra, Y and Spakowicz, D and Chambers, LM}, title = {The Role of the Microbiome in Cancer Therapies: Current Evidence and Future Directions.}, journal = {Hematology/oncology clinics of North America}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.hoc.2024.12.005}, pmid = {39856008}, issn = {1558-1977}, abstract = {The microbiome is essential for maintaining human health and is also a key factor in the development and progression of various diseases, including cancer. Growing evidence has highlighted the microbiome's significant impact on cancer development, progression, and treatment outcomes. As research continues to unfold, the microbiome and its modulation stand out as a promising frontier in cancer research and therapy. This review highlights current literature on the interplay between various cancer treatment modalities and human microbiotas, focusing on how the microbiome may affect treatment efficacy and toxicity and its potential as a therapeutic target to enhance future outcomes.}, }
@article {pmid39855641, year = {2025}, author = {Seear, PJ and Welsh, KG and Satchwell, J and Patel, D and Pashley, CH and Wardlaw, AJ and Gaillard, EA}, title = {Positive sputum fungal culture, fungal sensitisation and airway microbial diversity in asthmatic children.}, journal = {Medical mycology}, volume = {}, number = {}, pages = {}, doi = {10.1093/mmy/myaf005}, pmid = {39855641}, issn = {1460-2709}, abstract = {Sensitisation to thermotolerant fungi such as Aspergillus fumigatus and Candida albicans which can colonise the airways is associated with poor lung function in children with asthma. Dysbiosis of bacteria and fungi in the airway microbiome has been reported between health and asthma but has yet to be characterised for fungal sensitised asthmatic children. We investigated if microbial diversity of the airways is altered in fungal sensitised school-age asthmatic children. Sputum samples from children with asthma who were fungal sensitised (n=22) and non-fungal sensitised (n=17) along with children without asthma (n=15), aged 5-16 years were profiled by traditional microbiological culture, modified fungal culture, bacterial 16S and fungal ITS2 next generation sequencing. Microbiota were compared between groups using alpha/beta diversity and differential abundance analysis. Bacterial alpha diversity was significantly lower in asthma compared to disease controls and in stable compared to acute asthma. Fungal alpha and beta diversity did not change between asthma states and disease controls, but alpha diversity was significantly lower in asthma samples from patients with positive A. fumigatus culture. Children sensitised to fungi had similar microbial diversity compared to non-sensitised children. However, in children not sensitised to fungi, those with a positive airway fungal culture had significantly lower fungal alpha diversity and bacterial beta differences compared to children with negative fungal culture. Fungal sensitisation did not alter bacterial or fungal microbiota in the airways of asthmatic children. However, positive airway fungal culture was associated with significant changes in microbial diversity, particularly in non-fungal sensitised children with asthma.}, }
@article {pmid39855620, year = {2025}, author = {Vaziri, GJ and Caicedo, B and Dahrouge, N and Ryerson, WG and Davenport, JM and Stager, M and Jones, KR and Frost, C and Seewagen, CL and Rittenhouse, TAG and Bolnick, DI}, title = {Gut microbiomes are largely unchanged when exposed to their amphibian host's latitudinally variable upper thermal limit.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {302}, number = {}, pages = {111816}, doi = {10.1016/j.cbpa.2025.111816}, pmid = {39855620}, issn = {1531-4332}, abstract = {Climate change will increase the frequency and severity of temperature extremes. Links between host thermal physiology and their gut microbiota suggest that organisms' responses to future climates may be mediated by their microbiomes, raising the question of how the thermal environment influences the microbiome itself. Vertebrate gut microbiomes influence the physiological plasticity of their hosts via effects on immunity, metabolism, and nutrient uptake. The gut microbiota of ectothermic vertebrates in particular are responsive to long-term, sub-lethal gradual increases in environmental temperature. Whether and how the gut microbiota respond to brief exposure to temperatures at the upper limit of host physiological tolerance (CTmax) is poorly understood but could have downstream effects on host fitness. We assayed the CTmax of wood frogs (Lithobates sylvaticus) from 15 populations across a 10° latitudinal gradient. We then characterized the gut microbiota of juveniles at two time points following exposure to CTmax. Frogs from higher latitudes had lower thermal tolerance (lower CTmax) than those from lower latitudes. Unexpectedly, exposure to upper survivable temperature had little to no detectable effect on the frogs' microbiota richness, stability, or composition. Instead, we found a strong effect of time in which frogs kept in recovery conditions for four days had less diverse, but more stable gut microbiota than those that had recovered for only one day, regardless of CTmax exposure. We conclude that while wood frogs from higher latitudes have reduced thermal tolerances than those from lower latitudes, their microbial communities are largely unaffected by brief exposure to high temperatures at the edge of their physiological limits.}, }
@article {pmid39855612, year = {2025}, author = {Sutanto, H and Elisa, E and Rachma, B and Fetarayani, D}, title = {Gut Microbiome Modulation in Allergy Treatment: The Role of Fecal Microbiota Transplantation.}, journal = {The American journal of medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.amjmed.2025.01.005}, pmid = {39855612}, issn = {1555-7162}, abstract = {The prevalence of allergic diseases has been rising, paralleling lifestyle changes and environmental exposures that have altered human microbiome composition. This review article examines the intricate relationship between the gut microbiome and allergic diseases, emphasizing the potential of fecal microbiota transplantation as a promising novel treatment approach. It explains how reduced microbial exposure in modern societies contributes to immune dysregulation and the increasing incidence of allergies. The discussion also addresses immune homeostasis and its modulation by the gut microbiome, highlighting the shift from eubiosis to dysbiosis in allergic conditions. Furthermore, this article reviews existing studies and emerging research on the role of fecal microbiota transplantation in restoring microbial balance, providing insights into its mechanisms, efficacy, and safety.}, }
@article {pmid39855566, year = {2025}, author = {Zeng, Y and Jia, X and Li, H and Zhou, N and Liang, X and Liu, K and Yang, BZ and Xiang, B}, title = {Oral microbiota among treatment-naïve adolescents with depression: A case-control study.}, journal = {Journal of affective disorders}, volume = {375}, number = {}, pages = {93-102}, doi = {10.1016/j.jad.2025.01.089}, pmid = {39855566}, issn = {1573-2517}, abstract = {BACKGROUND: Adolescent depression has profound impacts on physical, cognitive, and emotional development. While gut microbiota changes have been linked to depression, the relationship between oral microbiota and depression remains elusive. Our study aims to investigate the oral microbiota in treatment-naïve adolescents experiencing depression and examine their potential associations with cognitive function.<br><br>METHODS: Our case-control study comprised two groups of adolescents aged 12-17: the depression group, including treatment-na&#xef;ve individuals diagnosed with DSM-5 major depressive disorder (MDD), and a healthy control group of non-depressed individuals (HC). Participants underwent structured neuropsychiatric assessments, and fasting morning saliva samples were collected for the 16S rRNA sequencing to investigate the oral microbiota.<br><br>RESULTS: Significant differences were identified in the &#x3b1;- and &#x3b2;-diversities of the oral microbiota between MDD and HC groups. Specific bacterial taxa, including genera Streptococcus, Neisseria, Hemophilus, Fusobacterium, and g_norank_f_norank_o_Absconditabacteriales_SR1, were significantly associated with MDD. The association extends to cognitive functions, where correlations were observed between certain oral bacteria and cognitive scores, including instant and delayed memory, visual breadth, and speech features for the combined MDD and HC individuals (p&#xa0;<&#xa0;0.05). Random forest analysis identified ten genera of oral microbes with the highest predictive values for MDD. The area under the curve (AUC) is 0.78 in the receiver operating characteristic (ROC) curve analysis.<br><br>CONCLUSION: Our results highlight the oral microbiota's role as a biomarker for adolescent depression and its impact on cognitive functions. These insights underscore the need for further research into the links between oral health, mental health, and cognitive functions.}, }
@article {pmid39855361, year = {2025}, author = {Meledathu, S and Naidu, MP and Brunner, PM}, title = {Update on Atopic Dermatitis.}, journal = {The Journal of allergy and clinical immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jaci.2025.01.013}, pmid = {39855361}, issn = {1097-6825}, abstract = {Atopic dermatitis (AD) is the most common chronic inflammatory skin condition. This review highlights most recent advances in understanding and treating this debilitating disease. We are summarizing new insights regarding molecular endotypes and clinical phenotypes that characterize AD, the role of the skin microbiome, and improvements in diagnostic tools. We also emphasize recent scientific advancements in understanding the mechanisms driving AD pathogenesis and discuss the identification and implementation of new targeted treatment approaches that have revolutionized therapeutic options for affected patients.}, }
@article {pmid39855335, year = {2025}, author = {Pasha, A and Iqbal, NT and Shafiq, Y and Khan, W and Azam, SI and Kabir, F and Muhammad, A and Nisar, I and Jehan, F}, title = {Effect of one prophylactic dose of Azithromycin on Bifidobacterium infantis colonization in infants from the Mumta Trial.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {107794}, doi = {10.1016/j.ijid.2025.107794}, pmid = {39855335}, issn = {1878-3511}, abstract = {OBJECTIVES: The effects of antibiotics on the microbiome remain incompletely understood. Azithromycin (AZ) has been shown to improve child survival and infant growth outcomes. This study aimed to assess the impact of AZ on B. infantis colonization and bacterial enteropathogen count in the infant gut.<br><br>METHODS: We analyzed clinical, biomarker, B. infantis and enteropathogen data from 150 mother-infant dyads from the MUMTA Lactating Women study. Colonization of B. infantis was assessed using quantitative PCR of fecal samples. We utilized a customized PCR-based TaqMan Array Card (TAC) for enteropathogen detection.<br><br>RESULTS: AZ administration was associated with a 1.99-fold (95% CI 1.33-2.97) increase in colonization by B. infantis. B. infantis colonization was highest when inflammatory biomarker levels were within normal range. Mode of delivery (RR 2.43; 95% CI: 1.58, 3.76) and colostrum (RR2.05; 95% CI: 1.41, 2.98) given to the infant within 24 hours of birth were associated with B. infantis colonization. A single dose of AZ on day 42 reduced bacterial enteropathogen count in the AZ group on day 56, as compared to the pre-AZ count. Bacterial enteropathogen count for infants with wasting (Weight for length Z-score WLZ<-2) was 1.43-fold higher (95% CI: 1.00-2.03) than for infants with WLZ&#x2265; -2. Over 60% of infants harboured with the macrolide resistance mph(A) gene CONCLUSIONS: AZ administration increases B. infantis colonization and reduces bacterial enteropathogen count in infants.}, }
@article {pmid39855197, year = {2025}, author = {Li, F and Armet, AM and Korpela, K and Liu, J and Quevedo, RM and Asnicar, F and Seethaler, B and Rusnak, TBS and Cole, JL and Zhang, Z and Zhao, S and Wang, X and Gagnon, A and Deehan, EC and Mota, JF and Bakal, JA and Greiner, R and Knights, D and Segata, N and Bischoff, SC and Mereu, L and Haqq, AM and Field, CJ and Li, L and Prado, CM and Walter, J}, title = {Cardiometabolic benefits of a non-industrialized-type diet are linked to gut microbiome modulation.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2024.12.034}, pmid = {39855197}, issn = {1097-4172}, abstract = {Industrialization adversely affects the gut microbiome and predisposes individuals to chronic non-communicable diseases. We tested a microbiome restoration strategy comprising a diet that recapitulated key characteristics of non-industrialized dietary patterns (restore diet) and a bacterium rarely found in industrialized microbiomes (Limosilactobacillus reuteri) in a randomized controlled feeding trial in healthy Canadian adults. The restore diet, despite reducing gut microbiome diversity, enhanced the persistence of L. reuteri strain from rural Papua New Guinea (PB-W1) and redressed several microbiome features altered by industrialization. The diet also beneficially altered microbiota-derived plasma metabolites implicated in the etiology of chronic non-communicable diseases. Considerable cardiometabolic benefits were observed independently of L. reuteri administration, several of which could be accurately predicted by baseline and diet-responsive microbiome features. The findings suggest that a dietary intervention targeted toward restoring the gut microbiome can improve host-microbiome interactions that likely underpin chronic pathologies, which can guide dietary recommendations and the development of therapeutic and nutritional strategies.}, }
@article {pmid39854991, year = {2025}, author = {Pei, Y and Lei, A and Wang, M and Sun, M and Yang, S and Liu, X and Liu, L and Chen, H}, title = {Novel tetracycline-degrading enzymes from the gut microbiota of black soldier fly: Discovery, performance, degradation pathways, mechanisms, and application potential.}, journal = {Journal of hazardous materials}, volume = {488}, number = {}, pages = {137286}, doi = {10.1016/j.jhazmat.2025.137286}, pmid = {39854991}, issn = {1873-3336}, abstract = {The antibiotic tetracycline (TC) is an emerging pollutant frequently detected in various environments. Although enzymatic remediation is a promising strategy for mitigating TC contamination, the availability of effective TC-degrading enzymes remains limited, and their mechanisms and applications are not fully understood. This study developed a comprehensive TC-degrading enzyme library from the gut microbiome of the highly TC-resistant saprophagous insect, black soldier fly larvae (BSFL), using an integrated metagenomic and comparative metatranscriptomic approach, identifying 105 potential novel TC-degradation genes. Bioinformatics analysis of 10 selected genes underscored the novelty of the identified enzymes. Among these, Trg2 demonstrated strong binding affinity and significant degradation capacity for TC. Key functional amino acid residues, including Thr231, Ala64, Ala82, Gly68, Gly79, and Ser81, were identified as essential for the interaction between TC and Trg2. Six TC degradation pathways were proposed, involving the transformation of TC into 19 metabolites through de-grouping, ring opening, oxidation, reduction, and addition reactions, effectively reducing TC toxicity. Furthermore, Trg2 exhibited resilience under harsh conditions, maintaining the capacity to remove about 45 % of the total TC in mariculture wastewater across eight successive batches. This study advances the understanding of TC degradation mechanisms and highlights the potential application of novel enzymes for bioremediation purposes.}, }
@article {pmid39854881, year = {2025}, author = {Liu, X and Wang, W and Wang, Y and Duan, W and Liu, C and Quan, P and Xiao, J and Zhang, Y and Hao, Y and Fang, L and Song, Y and Zhang, W}, title = {Biochemical strategy-based hybrid hydrogel dressing-mediated in situ synthesis of selenoproteins for DFU immunity-microbiota homeostasis regulation.}, journal = {Biomaterials}, volume = {317}, number = {}, pages = {123114}, doi = {10.1016/j.biomaterials.2025.123114}, pmid = {39854881}, issn = {1878-5905}, abstract = {Chronic consequences of diabetes that are most commonly encountered are diabetic foot ulcers (DFUs), driven by microbiota-immune system dyshomeostasis, eventually leading to delayed wound healing. Available therapies, such as systemic or topical administration of anti-inflammatory or antimicrobial agents, are limited due to antibiotic resistance and immune dysfunction. Herein, a hybrid hydrogel dressing is developed as the artificial bioadhesive barrier at wound sites to maintain microbial and immunological homeostasis locally and have potent anti-inflammatory effects. Specifically, Zero-valent selenium nanoparticles are synthesized and encapsulated into the alginate-polyacrylamide interpenetrating hydrogel networks, during which trehalose is adopted to modify the network defects. Besides, as an anti-adhesion agent, trehalose has shown the ability to prevent immune degradation by reducing bacteria binding to HUVECs. The obtained hybrid hydrogel dressing serves as a physical barrier against microbiome invasion, further regulates the composition of the wound microbiome to restore microbial immune homeostasis at the wound site, and cooperatively relieves DFU-associated symptoms. Meanwhile, the hydrogel dressing can synthesize selenoproteins in situ based on biochemical strategies and significantly reduce the secretion of proinflammatory cytokines. The proposed biochemical strategy based on the hybrid hydrogel dressings can efficiently restore microbiota-immune homeostasis in the wounds, presenting a promising approach for DFU therapy in clinics.}, }
@article {pmid39854767, year = {2025}, author = {Zhu, Y and Pan, Y and Wang, X and Wei, L and Zhu, L and Guo, Y and Jin, H and Gu, Y and Wang, Y and Chen, Y and Xu, L}, title = {Lactobacillus rhamnosus GG Combined with Metformin Alleviates Alcohol-Induced Liver Inflammation in Mice by Maintaining the Intestinal Barrier and Regulating Treg/Th1 Cells.}, journal = {Journal of medicinal food}, volume = {}, number = {}, pages = {}, doi = {10.1089/jmf.2024.k.0184}, pmid = {39854767}, issn = {1557-7600}, abstract = {Disturbances of the intestinal barrier enabling bacterial translocation exacerbate alcoholic liver disease (ALD). Lactobacillus rhamnosus GG (LGG) has been shown to exert beneficial effects in gut dysbiosis and chronic liver disease. The current study assessed the combined effects of LGG and metformin, which play roles in anti-inflammatory and immunoregulatory processes, in alcohol-induced liver disease mice. A diet comprising 5% alcohol for 4 weeks was employed to develop an alcohol-induced liver injury model. Mice were orally administered LGG, metformin, or their combination on alternate days. Tight junction (TJ) proteins, gut microbiome composition, inflammatory cytokines, Jun N-terminal kinase (JNK), and p38 signals were assessed. When compared with treatment with LGG or metformin alone, combined LGG and metformin treatment substantially lowered the symptoms of inflammation, steatosis, and elevated liver enzymes caused by alcohol administration. Combination treatment significantly improved intestinal microecology, evidenced by the recovery of intestinal flora, TJ proteins, and intestinal villi. Combination treatment reduced hepatic inflammation by blocking p38 and JNK phosphorylation. The combination of LGG and metformin corrected immune-response dysregulation and improved ALD by enhancing the intestinal microbiome, restoring mucosal barrier integrity, modulating immune function, and decreasing liver injury. These results provide information for the development of intestinal microbiota-based preventive and therapeutic agents against ALD.}, }
@article {pmid39854760, year = {2025}, author = {Chen, S and Zhang, D and Li, D and Zeng, F and Chen, C and Bai, F}, title = {Microbiome characterization of patients with Crohn disease and the use of fecal microbiota transplantation: A review.}, journal = {Medicine}, volume = {104}, number = {4}, pages = {e41262}, doi = {10.1097/MD.0000000000041262}, pmid = {39854760}, issn = {1536-5964}, support = {2021818//Hainan Province Clinical Medical Center/ ; YSPTZX202313//The specific research fund of The Innovation Platform for Academicians of Hainan Province/ ; 22A200078//Hainan Provincial Health Industry Research Project/ ; Qhyb2022-133//Hainan Provincial Postgraduate Innovation Research Project/ ; }, mesh = {Humans ; *Crohn Disease/therapy/microbiology ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; }, abstract = {Inflammatory bowel disease is a chronic inflammatory condition predominantly affecting the intestines, encompassing both ulcerative colitis and Crohn disease (CD). As one of the most common gastrointestinal disorders, CD's pathogenesis is closely linked with the intestinal microbiota. Recently, fecal microbiota transplantation (FMT) has gained attention as a potential treatment for CD, with the effective reestablishment of intestinal microecology considered a crucial mechanism of FMT therapy. This article synthesizes the findings of population-based cohort studies to enhance our understanding of gut microbial characteristics in patients with CD. It delves into the roles of "beneficial" and "pathogenic" bacteria in CD's development. This article systematically reviews and compares data on clinical response rates, remission rates, adverse events, and shifts in bacterial microbiota. Among these studies, gut microbiome analysis was conducted in only 7, and a single study examined the metabolome. Overall, FMT has demonstrated a partial restoration of typical CD-associated microbiological alterations, leading to increased α-diversity in responders and a moderate shift in patient microbiota toward the donor profile. Several factors, including donor selection, delivery route, microbial state (fresh or frozen), and recipient condition, are identified as pivotal in influencing FMT's effectiveness. Future prospective clinical studies with larger patient cohorts and improved methodologies are imperative. In addition, standardization of FMT procedures, coupled with advanced genomic techniques such as macroproteomics and culture genomics, is necessary. These advancements will further clarify the bacterial microbiota alterations that significantly contribute to FMT's therapeutic effects in CD treatment, as well as elucidate the underlying mechanisms of action.}, }
@article {pmid39854381, year = {2025}, author = {Holley, L and Creasey, HN and Bedenice, D and Reed, S and Romualdo da Silva, DR and Trautwein, V and Mazan, M and Widmer, G}, title = {Nebulization of 2% lidocaine has no detectable impact on the healthy equine respiratory microbiota.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0316079}, doi = {10.1371/journal.pone.0316079}, pmid = {39854381}, issn = {1932-6203}, mesh = {Animals ; Horses/microbiology ; *Microbiota/drug effects ; *Lidocaine/administration &amp; dosage/pharmacology ; *Bronchoalveolar Lavage Fluid/microbiology ; *Nebulizers and Vaporizers/microbiology ; Male ; Female ; Trachea/microbiology ; Cross-Over Studies ; Bacteria/genetics/classification/drug effects/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Respiratory System/microbiology ; }, abstract = {Glucocorticosteroids remain the most common pharmaceutical approach for the treatment of equine asthma but can be associated with significant side effects, including respiratory microbiome alterations. The goal of the study was to assess the impact of 2% lidocaine nebulization, a projected alternative treatment of equine asthma, on the healthy equine respiratory microbiota. A prospective, randomized, controlled, blinded, 2-way crossover study was performed, to assess the effect of 1 mg/kg 2% lidocaine (7 treatments over 4 days) on the equine respiratory microbiota compared to control horses (saline and no treatment). Clinical assessments and respiratory samples, including nasal wash, endoscopic tracheal aspirate and bronchoalveolar lavage fluid, were obtained at each sample collection timepoint. The profile of the respiratory bacterial microbiota was evaluated using 16S amplicon sequencing, and clinical data compared using related samples analyses, based on data normality. The treatment did not affect the clinical data or alter the tracheal and nasal microbiota in healthy horses. However, time explained 12.6% of microbiota variation among samples. A significant difference in bacterial composition was observed between nasal and tracheal samples, showing the greatest relative abundance of Actinobacteria and Firmicutes, respectively. Bacterial DNA from bronchoalveolar lavage fluid did not amplify with generic primers targeting the V4 variable region of the prokaryotic small subunit ribosomal RNA gene, despite attempting multiple DNA extraction methods and PCR protocols, and after excluding PCR inhibition. This observation indicates that bronchoalveolar lavage fluid of healthy horses has a low bacterial load.}, }
@article {pmid39854335, year = {2025}, author = {Hendrycks, W and Mullens, N and Bakengesa, J and Kabota, S and Tairo, J and Backeljau, T and Majubwa, R and Mwatawala, M and De Meyer, M and Virgilio, M}, title = {Deterministic and stochastic effects drive the gut microbial diversity in cucurbit-feeding fruit flies (Diptera, Tephritidae).}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0313447}, doi = {10.1371/journal.pone.0313447}, pmid = {39854335}, issn = {1932-6203}, mesh = {Animals ; *Tephritidae/microbiology/physiology ; *Gastrointestinal Microbiome ; *Larva/microbiology ; Stochastic Processes ; Bacteria/classification/genetics ; Biodiversity ; }, abstract = {Insect diversity is closely linked to the evolution of phytophagy, with most phytophagous insects showing a strong degree of specialisation for specific host plants. Recent studies suggest that the insect gut microbiome might be crucial in facilitating the dietary (host plant) range. This requires the formation of stable insect-microbiome associations, but it remains largely unclear which processes govern the assembly of insect microbiomes. In this study, we investigated the role of deterministic and stochastic processes in shaping the assembly of the larval microbiome of three tephritid fruit fly species (Dacus bivittatus, D. ciliatus, Zeugodacus cucurbitae). We found that deterministic and stochastic processes play a considerable role in shaping the larval gut microbiome. We also identified 65 microbial ASVs (Amplicon sequence variants) that were associated with these flies, most belonging to the families Enterobacterales, Sphingobacterales, Pseudomonadales and Betaproteobacterales, and speculate about their relationship with cucurbit specialisation. Our data suggest that the larval gut microbiome assembly fits the "microbiome on a leash" model.}, }
@article {pmid39854266, year = {2025}, author = {}, title = {Correction to: Microbiome characterization of skin biopsies in Spanish patients with hidradenitis suppurativa shows a decrease in D1 and H1 lineages of Cutibacterium acnes.}, journal = {The British journal of dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1093/bjd/ljaf029}, pmid = {39854266}, issn = {1365-2133}, }
@article {pmid39854190, year = {2025}, author = {Jiang, Z and Tabuchi, C and Gayer, SG and Bapat, SP}, title = {Immune Dysregulation in Obesity.}, journal = {Annual review of pathology}, volume = {20}, number = {1}, pages = {483-509}, doi = {10.1146/annurev-pathmechdis-051222-015350}, pmid = {39854190}, issn = {1553-4014}, mesh = {Humans ; *Obesity/immunology/metabolism ; Animals ; *Adipose Tissue/immunology/metabolism ; Inflammation/immunology/metabolism ; Homeostasis/immunology ; T-Lymphocytes/immunology ; Immune System/immunology/metabolism ; }, abstract = {The immune system plays fundamental roles in maintaining physiological homeostasis. With the increasing prevalence of obesity-a state characterized by chronic inflammation and systemic dyshomeostasis-there is growing scientific and clinical interest in understanding how obesity reshapes immune function. In this review, we propose that obesity is not merely an altered metabolic state but also a fundamentally altered immunological state. We summarize key seminal and recent findings that elucidate how obesity influences immune function, spanning its classical role in microbial defense, its contribution to maladaptive inflammatory diseases such as asthma, and its impact on antitumor immunity. We also explore how obesity modulates immune function within tissue parenchyma, with a particular focus on the role of T cells in adipose tissue. Finally, we consider areas for future research, including investigation of the durable aspects of obesity on immunological function even after weight loss, such as those observed with glucagon-like peptide-1 (GLP-1) receptor agonist treatment. Altogether, this review emphasizes the critical role of systemic metabolism in shaping immune cell functions, with profound implications for tissue homeostasis across various physiological contexts.}, }
@article {pmid39854186, year = {2025}, author = {Zhang, X and Chang, KM and Yu, J and Loomba, R}, title = {Unraveling Mechanisms of Genetic Risks in Metabolic Dysfunction-Associated Steatotic Liver Diseases: A Pathway to Precision Medicine.}, journal = {Annual review of pathology}, volume = {20}, number = {1}, pages = {375-403}, doi = {10.1146/annurev-pathmechdis-111523-023430}, pmid = {39854186}, issn = {1553-4014}, mesh = {Humans ; *Precision Medicine ; *Genetic Predisposition to Disease ; Gastrointestinal Microbiome ; Non-alcoholic Fatty Liver Disease/genetics/metabolism/therapy ; Risk Factors ; }, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a growing global health problem, affecting ∼1 billion people. This condition is well established to have a heritable component with strong familial clustering. With the extraordinary breakthroughs in genetic research techniques coupled with their application to large-scale biobanks, the field of genetics in MASLD has expanded rapidly. In this review, we summarize evidence regarding genetic predisposition to MASLD drawn from family and twin studies. Significantly, we delve into detailed genetic variations associated with diverse pathogenic mechanisms driving MASLD. We highlight the interplay between these genetic variants and their connections with metabolic factors, the gut microbiome, and metabolites, which collectively influence MASLD progression. These discoveries are paving the way for precise medicine, including noninvasive diagnostics and therapies. The promising landscape of novel genetically informed drug targets such as RNA interference is explored. Many of these therapies are currently under clinical validation, raising hopes for more effective MASLD treatment.}, }
@article {pmid39854185, year = {2025}, author = {Guglietta, S and Li, X and Saxena, D}, title = {Role of Fungi in Tumorigenesis: Promises and Challenges.}, journal = {Annual review of pathology}, volume = {20}, number = {1}, pages = {459-482}, doi = {10.1146/annurev-pathmechdis-111523-023524}, pmid = {39854185}, issn = {1553-4014}, mesh = {Humans ; *Neoplasms/microbiology/immunology/therapy ; *Carcinogenesis/immunology ; *Fungi/pathogenicity/physiology ; Gastrointestinal Microbiome/immunology ; Animals ; Mycobiome/immunology ; Antifungal Agents/therapeutic use ; Mycoses/microbiology/immunology/therapy ; }, abstract = {The mycobiome plays a key role in the host immune responses in homeostasis and inflammation. Recent studies suggest that an imbalance in the gut's fungi contributes to chronic, noninfectious diseases such as obesity, metabolic disorders, and cancers. Pathogenic fungi can colonize specific organs, and the gut mycobiome has been linked to the development and progression of various cancers, including colorectal, breast, head and neck, and pancreatic cancers. Some fungal species can promote tumorigenesis by triggering the complement system. However, in immunocompromised patients, fungi can also inhibit this activation and establish life-threatening infections. Interestingly, the interaction of the fungi and bacteria can also induce unique host immune responses. Recent breakthroughs and advancements in high-throughput sequencing of the gut and tumor mycobiomes are highlighting novel diagnostic and therapeutic opportunities for cancer. We discuss the latest developments in the field of cancer and the mycobiome and the potential benefits and challenges of antifungal therapies.}, }
@article {pmid39854172, year = {2025}, author = {MacCann, R and Li, J and Leon, AAG and Negi, R and Alalwan, D and Tinago, W and McGettrick, P and Cotter, AG and Landay, A and Sabin, C and O'Toole, PW and Mallon, PW and , }, title = {Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiaf043}, pmid = {39854172}, issn = {1537-6613}, abstract = {BACKGROUND: Inflammation and innate immune activation are associated with chronic HIV infection, despite effective treatment. Although gut microbiota alterations are linked to systemic inflammation, the relationships between the gut microbiome, inflammation and HIV remain unclear.<br><br>METHODS: The UPBEAT-CAD sub-study, examining cardiovascular disease (CVD) risk in HIV, enrolled participants matched on HIV status and traditional CVD risk factors. Subclinical CVD was assessed using coronary computed tomography angiography (CCTA). 34 biomarkers were measured using quantitative immunoassays. Microbiota composition was analysed by 16S rRNA sequencing of stool samples, with taxonomic assignment via the SPINGO pipeline. Differentially abundant species were identified by Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) and correlated to biomarkers, diet and CCTA outcomes using Spearman correlation.<br><br>RESULTS: Among 81 participants (median age 51 years, 73% male), people with HIV (n=44 , 54%) had a higher prevalence of hypercholesterolaemia (p <0.025) and statin use (p <0.001). A significant separation in gut microbiome &#x3b2;-diversity was observed between people with and without HIV. ANCOM-BC analysis identified 42 differentially abundant species and 10 genera in those with HIV. Enrichment of Bifidobacterium pseudocatenulatum, Megamonas hypermegale and Selenomonas ruminantium and depletion of Fusicatenenibacter correlated with lower plaque burden. Depletion of SCFA-producing Ruminococcus bromii correlated with higher plaque burden and fat intake, while depletion of Bacteroides spp and Alistepes spp correlated with elevated inflammatory biomarkers (D-dimer, CD40-ligand, CRP and IFN-&#x3b3;).<br><br>CONCLUSION: Significant gut microbiota differences in people with HIV were linked to subclinical CVD, diet, and inflammation, suggesting a role for the microbiome in cardiovascular risk in HIV infection.}, }
@article {pmid39854158, year = {2025}, author = {Lau, RI and Su, Q and Ng, SC}, title = {Long COVID and gut microbiome: insights into pathogenesis and therapeutics.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2457495}, doi = {10.1080/19490976.2025.2457495}, pmid = {39854158}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome ; Humans ; *Fecal Microbiota Transplantation ; *COVID-19/therapy/microbiology ; *Probiotics/therapeutic use ; *Dysbiosis/therapy/microbiology ; *SARS-CoV-2 ; *Post-Acute COVID-19 Syndrome ; Prebiotics/administration &amp; dosage ; }, abstract = {Post-acute coronavirus disease 2019 syndrome (PACS), following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or coronavirus disease 2019 (COVID-19), is typically characterized by long-term debilitating symptoms affecting multiple organs and systems. Unfortunately, there is currently a lack of effective treatment strategies. Altered gut microbiome has been proposed as one of the plausible mechanisms involved in the pathogenesis of PACS; extensive studies have emerged to bridge the gap between the persistent symptoms and the dysbiosis of gut microbiome. Recent clinical trials have indicated that gut microbiome modulation using probiotics, prebiotics, and fecal microbiota transplantation (FMT) led to improvements in multiple symptoms related to PACS, including fatigue, memory loss, difficulty in concentration, gastrointestinal upset, and disturbances in sleep and mood. In this review, we highlight the latest evidence on the key microbial alterations observed in PACS, as well as the use of microbiome-based therapeutics in managing PACS symptoms. These novel findings altogether shed light on the treatment of PACS and other chronic conditions.}, }
@article {pmid39854015, year = {2025}, author = {Loo, QY and Chuah, KH and Hian, WX and Khoo, XH and Lee, YY and Mahadeva, S}, title = {Impact of Positive Glucose, Lactose, and Fructose Hydrogen Breath Tests on Symptoms and Quality of Life in Irritable Bowel Syndrome.}, journal = {Journal of gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jgh.16891}, pmid = {39854015}, issn = {1440-1746}, support = {PV039-2019//UMSC C.A.R.E Fund Research Grant/ ; 304/PPSP/6150155/M145//Morinaga Milk Industry Co. Ltd./ ; }, abstract = {BACKGROUND: Gas production due to fermentation from fructose malabsorption (FM) or lactose malabsorption (LM) and small intestinal bacterial overgrowth (SIBO) contribute to the development of gastrointestinal symptoms in patients with irritable bowel syndrome (IBS). However, the impact of the carbohydrate malabsorption, unlike SIBO, is relatively unknown.<br><br>METHODOLOGY: A multicenter, prospective study of consecutive adults with IBS who underwent a hydrogen breath test (HBT) (glucose, 75&#x2009;g; lactose, 25&#x2009;g; or fructose, 25&#x2009;g) was conducted. The proportion of patients who tested positive for glucose, fructose and lactose HBT were evaluated. The symptom severity, psychology, and quality of life of subjects with SIBO were compared with those having LM and/or FM. Independent factors associated with severe IBS (IBS-symptom severity scale: IBS-SSS&#x2009;>&#x2009;300) were explored.<br><br>RESULTS: A total of 116 subjects were included (median age 56&#x2009;years, male 35.3%). Of these, 23.3% (27/116), 85.7% (24/28), and 44.4% (16/36) of them tested positive for glucose, lactose, and fructose HBT, respectively. Among those with a positive HBT (n&#x2009;=&#x2009;65), patients with SIBO were more likely to have the diarrhea-predominant subtype of IBS (77.8% vs. 47.4%, p&#x2009;=&#x2009;0.014). Severe IBS was associated with SIBO, compared with LM/FM (SIBO: 36.4% vs. LM: 9.1%/FM 13.3%, p&#x2009;=&#x2009;0.016). With multivariate analysis, SIBO (OR 5.25, p&#x2009;=&#x2009;0.028) and depression (OR 5.59, p&#x2009;=&#x2009;0.030) were independently associated with severe IBS.<br><br>CONCLUSION: Although LM and FM commonly co-exist in IBS, their clinical relevance appears to be less significant than that of SIBO. The connection between SIBO with depression reinforces the importance of the microbiome-gut-brain axis in IBS.}, }
@article {pmid39853943, year = {2025}, author = {Dyson, G and Barrett, M and Schlupp, L and Prinz, E and Hannebut, N and Szymczak, A and Brawner, CM and Jeffries, MA}, title = {Ketogenic Diet-Associated Worsening of Osteoarthritis Histologic Secerity, Increased Pain Sensitivity and Gut Microbiome Dysbiosis in Mice.}, journal = {ACR open rheumatology}, volume = {7}, number = {1}, pages = {e11794}, doi = {10.1002/acr2.11794}, pmid = {39853943}, issn = {2578-5745}, support = {K08AR070891/AR/NIAMS NIH HHS/United States ; R33AR078075/AR/NIAMS NIH HHS/United States ; R61AR078075/AR/NIAMS NIH HHS/United States ; PR191652//Congressionally Directed Medical Research Programs/ ; P20GM125528/GM/NIGMS NIH HHS/United States ; }, abstract = {OBJECTIVES: Dietary interventions are a potentially powerful treatment option for knee osteoarthritis (OA). The objective of this study was to evaluate a well-formulated ketogenic diet (KD) in the context of knee OA histology and pain using the destabilization of the medial meniscus (DMM) mouse model and correlate with gut microbiome and systemic cytokine levels.<br><br>METHODS: Adult male mice underwent unilateral DMM or sham surgery and were then fed eight weeks of KD or chow. At baseline and every two weeks, mechanical allodynia of the operated and contralateral knees was assessed via analgesiometry. Knee joints were collected for histology, gut microbiome analysis was performed on cecal material via 16S sequencing, and serum cytokines were analyzed via Bio-Plex assay.<br><br>RESULTS: KD mice had worse histopathologic OA after DMM (mean&#x2009;&#xb1;&#x2009;SEM Osteoarthritis Research Society International score: KD-DMM: 4.0&#x2009;&#xb1;&#x2009;0.5 vs chow-DMM: 2.7&#x2009;&#xb1;&#x2009;0.08; P&#xa0;=&#xa0;0.02). KD mice had increased mechanical allodynia postsurgery (P&#xa0;=&#xa0;0.005 in mixed-effects model). The gut microbiome changed substantially with KD: 59 clades were altered by KD in DMM and 39 by KD in sham (36 were shared, 25 overlapped with previous murine OA studies). Several clades were correlated on an individual-mouse level with both histology and allodynia (eg, Lactobacillus histology P&#xa0;=&#xa0;0.004, allodynia P&#xa0;=&#xa0;1&#x2009;&#xd7;&#x2009;10[-4]). Serum analysis showed four cytokines increased with KD (interleukin [IL]-1&#x3b2;, IL-2, IL-3, and IL-13).<br><br>CONCLUSION: KD started immediately after OA induction via DMM is associated with worsened histologic outcomes. KD also worsens mechanical allodynia after either DMM or sham surgery. KD induces significant gut microbiome dysbiosis in clades previously associated with murine OA.}, }
@article {pmid39853798, year = {2025}, author = {Lutz, KC and Neugent, ML and Bedi, T and De Nisco, NJ and Li, Q}, title = {A Generalized Bayesian Stochastic Block Model for Microbiome Community Detection.}, journal = {Statistics in medicine}, volume = {44}, number = {3-4}, pages = {e10291}, doi = {10.1002/sim.10291}, pmid = {39853798}, issn = {1097-0258}, support = {2113674//National Science Foundation/ ; 2210912//National Science Foundation/ ; AT-2030-20200401//Welch Foundation/ ; 1F32DK128975-01A1/NH/NIH HHS/United States ; 1R01DK131267-01/NH/NIH HHS/United States ; 1R01GM141519/NH/NIH HHS/United States ; }, mesh = {*Bayes Theorem ; Humans ; *Microbiota/genetics ; *Markov Chains ; Computer Simulation ; Female ; Monte Carlo Method ; Stochastic Processes ; Models, Statistical ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; }, abstract = {Advances in next-generation sequencing technology have enabled the high-throughput profiling of metagenomes and accelerated microbiome studies. Recently, there has been a rise in quantitative studies that aim to decipher the microbiome co-occurrence network and its underlying community structure based on metagenomic sequence data. Uncovering the complex microbiome community structure is essential to understanding the role of the microbiome in disease progression and susceptibility. Taxonomic abundance data generated from metagenomic sequencing technologies are high-dimensional and compositional, suffering from uneven sampling depth, over-dispersion, and zero-inflation. These characteristics often challenge the reliability of the current methods for microbiome community detection. To study the microbiome co-occurrence network and perform community detection, we propose a generalized Bayesian stochastic block model that is tailored for microbiome data analysis where the data are transformed using the recently developed modified centered-log ratio transformation. Our model also allows us to leverage taxonomic tree information using a Markov random field prior. The model parameters are jointly inferred by using Markov chain Monte Carlo sampling techniques. Our simulation study showed that the proposed approach performs better than competing methods even when taxonomic tree information is non-informative. We applied our approach to a real urinary microbiome dataset from postmenopausal women. To the best of our knowledge, this is the first time the urinary microbiome co-occurrence network structure in postmenopausal women has been studied. In summary, this statistical methodology provides a new tool for facilitating advanced microbiome studies.}, }
@article {pmid39853408, year = {2025}, author = {Wang, X and Yi, F and Zou, C and Yan, Q and Bashir, MH and Ahmed, W and Mahmood, SU and Wu, J and Ali, S}, title = {Exposure to spaceflight enhances the virulence of Purpureocillium lilacinum against Tetranychus cinnabarinus: modulation of the host's enzyme activities and microbiome.}, journal = {Archives of microbiology}, volume = {207}, number = {2}, pages = {43}, pmid = {39853408}, issn = {1432-072X}, mesh = {Animals ; *Tetranychidae/microbiology/genetics ; Virulence ; *Hypocreales/pathogenicity/genetics/enzymology ; Microbiota/physiology ; Antioxidants/metabolism ; }, abstract = {Multiple studies have been conducted to investigate the impact of space conditions on human, plant, and microbial life. This research investigated the virulence of spaceflight mutants of the entomopathogenic fungus Purpureocillium lilacinum (HP7, HP36, HP52) and its original strain (SP535) against Tetranychus cinnabarinus as well as examination of the T. cinnabarinus immune response, including alterations in enzyme profiles and microbiome composition post fungal application. Our observations revealed contrasting, time-specific differences in pathogenicity and tissue infection between the ground-based isolate and spaceflight mutant isolates. Analysis of detoxifying and antioxidant enzymes showed a significant reduction in enzyme activities T. cinnabarinus infected with the most virulent spaceflight mutants at 36 h post-fungal infection, compared to ground-based isolates. Additionally, the microbiota was reduced due to a fungal infection, partly due to decreased antioxidant enzyme activities. Our findings indicate that changes in the microbiota of T. cinnabarinus following infection with P. lilacinum (both ground-based and spaceflight mutant isolates) resulted in variations in metabolism and genetic information-related KEGG pathways. This data can help identify potential changes in the host immune system that drive increased virulence after spaceflight mutation.}, }
@article {pmid39853324, year = {2025}, author = {Dasinger, JH and Abais-Battad, JM and McCrorey, MK and Van Beusecum, JP}, title = {Recent Advances on Immunity and Hypertension: The New Cells on the Kidney Block.}, journal = {American journal of physiology. Renal physiology}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajprenal.00309.2024}, pmid = {39853324}, issn = {1522-1466}, support = {R00HL157549//HHS | National Institutes of Health (NIH)/ ; T32GM12055//HHS | National Institutes of Health (NIH)/ ; T32GM1523862//HHS | National Institutes of Health (NIH)/ ; IK2BX005605//U.S. Department of Veterans Affairs (VA)/ ; PTRF2023-10//Dialysis Clinics (DCI)/ ; MUSC COM-PPG//MUSC | College of Medicine, Medical University of South Carolina (College of Medicine)/ ; P30AR072582//HHS | National Institutes of Health (NIH)/ ; R56HL169434//HHS | National Institutes of Health (NIH)/ ; }, abstract = {Over the last 50 years, contribution of the immune system has been identified in the development of hypertension and renal injury. Both human and experimental animal models of hypertension have demonstrated that innate and adaptive immune cells, along with their cytokines and chemokines, modulate blood pressure fluctuations and end organ renal damage. Numerous cell types of the innate immune system, specifically monocytes, macrophages, and dendritic cells present antigenic peptides to T cells promoting inflammation and the elevation of blood pressure. These T cells and other adaptive immune cells, migrate to vascular and tubular cells of the kidney and promote end-organ fibrosis, damage, and ultimately hypertensive injury. Through the development of high throughput screening, novel renal and immune cell subsets have been identified as possible contributors and regulators of renal injury and hypertension. In this review, we will consider classical immunological cells and their contribution to renal inflammation, and novel cell subsets, including renal stromal cells, that could potentially shed new light on renal injury and hypertension. Lastly, we will discuss how interorgan inflammation contributes to the development of hypertension and hypertension-related multi-organ damage, and the clinical implications of the immunological components of renal injury and hypertension.}, }
@article {pmid39853270, year = {2025}, author = {Cardones, AR and Emiola, A and Hall, R and Sung, AD and Zhang, JY and Petty, AJ and Puza, C and Bohannon, LM and Bush, AT and Lew, MV and Fleming, E and Jin, YJ and Nichols, KR and Jain, V and Gregory, SG and Sullivan, KM and Chao, NJ and Oh, J}, title = {Cutaneous dysbiosis characterizes the post-allogeneic hematopoietic stem cell transplantation period.}, journal = {Blood advances}, volume = {}, number = {}, pages = {}, doi = {10.1182/bloodadvances.2021004792}, pmid = {39853270}, issn = {2473-9537}, abstract = {Gut dysbiosis is linked to mortality and the development of graft-versus-host disease (GVHD) after hematopoietic stem cell transplantation (HSCT), but the impact of cutaneous dysbiosis remains unexplored. We performed a pilot observational study and obtained retroauricular and forearm skin swabs from 12 adult patients prior to conditioning chemotherapy/radiation, and at 1-week, 1-month and 3-months after allogeneic HSCT, and performed shotgun metagenomic sequencing. The cutaneous microbiome among HSCT patients was enriched for gram-negative bacteria such as E coli and Pseudomonas, fungi, and viruses. Enrichment with bacteriophages and Polyomavirus sp, was observed among patients who died within 1-year, while we observed longitudinal stability of the cutaneous microbiome at the 3-month time point among those who survived beyond 1 year post-HSCT, although these may simply be a reflection of the overall medical status of the patients. There was no association with fungal abundance and any of the outcomes observed. The cutaneous microbiome may be a reservoir of pathobionts among allogeneic HSCT patients. Our findings suggest that cutaneous dysbiosis exists post-HSCT, but the ultimate implication of this to patient outcomes remains to be seen. Larger studies are required.}, }
@article {pmid39853059, year = {2025}, author = {Guo, D and Liu, C and Zhu, H and Cheng, Y and Huo, X and Guo, Y and Qian, H}, title = {Food-Induced Adverse Reactions: A Review of Physiological Food Quality Control, Mucosal Defense Mechanisms, and Gastrointestinal Physiology.}, journal = {Toxics}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/toxics13010061}, pmid = {39853059}, issn = {2305-6304}, abstract = {Although food is essential for the survival of organisms, it can also trigger a variety of adverse reactions, ranging from nutrient intolerances to celiac disease and food allergies. Food not only contains essential nutrients but also includes numerous substances that may have positive or negative effects on the consuming organism. To protect against potentially harmful components, all animals have evolved defense mechanisms, which are similar to antimicrobial defenses but often come at the cost of the organism's health. When these defensive responses are exaggerated or misdirected, they can lead to adverse food reactions, where the costs outweigh the benefits. Furthermore, due to the persistent toxicity of harmful food components, the failure of defense mechanisms can also result in pathological effects triggered by food. This article review presents a food quality control framework that aims to clarify how these reactions relate to normal physiological processes. Organisms utilize several systems to coexist with symbiotic microbes, regulate them, and concurrently avoid, expel, or neutralize harmful pathogens. Similarly, food quality control systems allow organisms to absorb necessary nutrients while defending against low-quality or harmful components in food. Although many microbes are lethal in the absence of antimicrobial defenses, diseases related to microbiome dysregulation, such as inflammatory bowel disease, have significantly increased. Antitoxin defenses also come with costs and may fail due to insufficiencies, exaggerations, or misdirected actions, ultimately leading to adverse food reactions. With the changes in human diet and lifestyle, the failure of defense mechanisms has contributed to the rising incidence of food intolerances. This review explores the mechanisms of antitoxin defenses and analyzes how their failure can lead to adverse food reactions, emphasizing the importance of a comprehensive understanding of food quality control mechanisms for developing more effective treatments for food-triggered diseases.}, }
@article {pmid39853010, year = {2024}, author = {Alexiev, A and Stretch, E and Kasschau, KD and Wilson, LB and Truong, L and Tanguay, RL and Sharpton, TJ}, title = {Clearing the Air on Pollutant Disruptions of the Gut-Brain Axis: Developmental Exposure to Benzo[a]pyrene Disturbs Zebrafish Behavior and the Gut Microbiome in Adults and Subsequent Generations.}, journal = {Toxics}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/toxics13010010}, pmid = {39853010}, issn = {2305-6304}, support = {1R01ES030226/ES/NIEHS NIH HHS/United States ; T32ES007060/ES/NIEHS NIH HHS/United States ; }, abstract = {Developmental exposure to benzo[a]pyrene (BaP), a ubiquitous environmental pollutant, has been linked to various toxic effects, including multigenerational behavioral impairment. While the specific mechanisms driving BaP neurotoxicity are not fully understood, recent work highlights two important determinants of developmental BaP neurotoxicity: (1) the aryl hydrocarbon receptor (AHR), which induces host metabolism of BaP, and (2) the gut microbiome, which may interact with BaP to affect its metabolism, or be perturbed by BaP to disrupt the gut-brain axis. We utilized the zebrafish model to explore the role of AHR, the gut microbiome, and their interaction, on BaP-induced neurotoxicity. We tested (1) how developmental BaP exposure and AHR2 perturbation in zebrafish link to adult behavior, (2) how these variables associate with the structure and function of the adult zebrafish gut metagenome, and (3) whether these associations are multigenerational. Our findings reveal a reticulated axis of association between BaP exposure, developmental AHR2 expression, the zebrafish gut metagenome, and behavior. Results indicate that AHR2 is a key modulator of how BaP elicits neurotoxicity and microbiome dysbiosis. Additionally, this axis of association manifests generationally. These findings demonstrate the importance of studying pollutant-microbiome interactions and elucidate the role of specific host genes in neurotoxicity and dysbiosis.}, }
@article {pmid39852495, year = {2025}, author = {Gómez-Lama Cabanás, C and Mercado-Blanco, J}, title = {Groundbreaking Technologies and the Biocontrol of Fungal Vascular Plant Pathogens.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {1}, pages = {}, doi = {10.3390/jof11010077}, pmid = {39852495}, issn = {2309-608X}, support = {2021ICT246//Ayudas Extraordinarias a la Incorporaci&#xf3;n de Cient&#xed;ficos Titulares OEP 2020-2021/ ; 202440E003//CSIC 'Proyecto Intramural'/ ; }, abstract = {This review delves into innovative technologies to improve the control of vascular fungal plant pathogens. It also briefly summarizes traditional biocontrol approaches to manage them, addressing their limitations and emphasizing the need to develop more sustainable and precise solutions. Powerful tools such as next-generation sequencing, meta-omics, and microbiome engineering allow for the targeted manipulation of microbial communities to enhance pathogen suppression. Microbiome-based approaches include the design of synthetic microbial consortia and the transplant of entire or customized soil/plant microbiomes, potentially offering more resilient and adaptable biocontrol strategies. Nanotechnology has also advanced significantly, providing methods for the targeted delivery of biological control agents (BCAs) or compounds derived from them through different nanoparticles (NPs), including bacteriogenic, mycogenic, phytogenic, phycogenic, and debris-derived ones acting as carriers. The use of biodegradable polymeric and non-polymeric eco-friendly NPs, which enable the controlled release of antifungal agents while minimizing environmental impact, is also explored. Furthermore, artificial intelligence and machine learning can revolutionize crop protection through early disease detection, the prediction of disease outbreaks, and precision in BCA treatments. Other technologies such as genome editing, RNA interference (RNAi), and functional peptides can enhance BCA efficacy against pathogenic fungi. Altogether, these technologies provide a comprehensive framework for sustainable and precise management of fungal vascular diseases, redefining pathogen biocontrol in modern agriculture.}, }
@article {pmid39852475, year = {2025}, author = {Obi, LU and Roopnarain, A and Tekere, M and Zhou, J and Li, H and Wang, Y and Zhang, Y and Adeleke, RA}, title = {Dynamics and Insights into the Unique Ecological Guild of Fungi in Bacteria-Bioaugmented Anaerobic Digesters.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {1}, pages = {}, doi = {10.3390/jof11010056}, pmid = {39852475}, issn = {2309-608X}, support = {WRC: Grant No. K5/2543//Water Research Commission/ ; }, abstract = {Anaerobic digesters host a variety of microorganisms, and they work together to produce biogas. While bacterial and archaeal communities have been well explored using molecular techniques, fungal community structures remain relatively understudied. The present study aims to investigate the dynamics and potential ecological functions of the predominant fungi in bacteria-bioaugmented anaerobic digesters. Eight different anaerobic digesters that contained chopped water hyacinth and cow dung as feedstock at 2% total solids were respectively inoculated with eight different bacterial strains and digested anaerobically in controlled conditions. The diversity and dynamics of the fungal community of the digesters before and after digestion were monitored using high-throughput sequencing of the fungal ITS2 sub-region of the ribosomal gene. The functional potential of the fungal community was predicted using ecological guild analysis. The dominant fungal phyla were (with relative abundance ≥1%) Ascomycota and Neocallimastigomycota. Ascomycota exhibited over 90% dominance in all treatments after anaerobic digestion (AD). Aspergillus sp. was consistently dominant across treatments during AD, while prominent anaerobic fungal genera Anaeromyces, Cyllamyces, and Caeomyces decreased. Ecological guild analysis at genus level showed that the majority of the identified fungi were saprophytes, and diversity indices indicated decreased richness and diversity after AD, suggesting a negative impact of AD on fungal communities in the anaerobic digesters. The multivariate structure of the fungal communities showed clustering of treatments with similar fungal taxa. The findings from this study provide insights into the fungal ecological guild of different bacteria-bioaugmented anaerobic digesters, highlighting their potentials in bacteria-augmented systems. Identification of an anaerobic fungal group within the phylum Ascomycota, beyond the well-known fungal phylum Neocallimastigomycota, offers a new perspective in optimizing the AD processes in specialized ecosystems.}, }
@article {pmid39852437, year = {2024}, author = {Horng, HC and Xu, JW and Kuo, YS and Chen, YS and Chiu, YH and Tsui, KH and Tung, YT}, title = {Dual Mechanisms of Action: Anti-Candida and Anti-Inflammatory Potential of Lactobacillus Fermentation Broth in Treating Vulvovaginal Candidiasis.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {11}, number = {1}, pages = {}, doi = {10.3390/jof11010018}, pmid = {39852437}, issn = {2309-608X}, abstract = {Vulvovaginal candidiasis (VVC), a condition predominantly caused by Candida albicans, affects millions of women worldwide, prompting the need for alternative treatments due to the side effects and increasing resistance associated with conventional imidazole antifungals. This study investigated VAGINNE[®], a novel fermentation broth derived from Lactobacillus species, as a potential VVC treatment. Using a BALB/c mouse model of C. albicans infection, we evaluated VAGINNE[®]'s effects on vaginal microbiome composition, inflammatory markers, and tissue integrity. Our findings revealed that VAGINNE[®] treatment enhanced the growth of beneficial Lactobacillus species while suppressing C. albicans proliferation, leading to a more balanced vaginal microbiome. Additionally, VAGINNE[®] significantly reduced pro-inflammatory cytokines (IL-17A, IL-22, IL-23) in vaginal tissues and systemic inflammatory markers (IL-6, IL-1β) in plasma. Histological analysis showed minimal fungal invasion and preserved vaginal epithelial integrity in VAGINNE[®]-treated mice compared to untreated controls. These results suggest that VAGINNE[®] could serve as an effective anti-Candida and anti-inflammatory agent for managing VVC, offering a promising alternative to traditional antifungal treatments. By promoting a healthy vaginal microbiome, reducing inflammation, and maintaining tissue health, this probiotic-based approach presents a novel strategy for addressing VVC, particularly in cases of drug resistance or adverse reactions to standard therapies. This study underscores the potential of microbiome-modulating strategies in managing vaginal infections, paving the way for more targeted and side-effect-free VVC treatments.}, }
@article {pmid39852393, year = {2025}, author = {Ou, Z and Fu, X and Norbäck, D and Lin, R and Wen, J and Sun, Y}, title = {MiMeJF: Application of Coupled Matrix and Tensor Factorization (CMTF) for Enhanced Microbiome-Metabolome Multi-Omic Analysis.}, journal = {Metabolites}, volume = {15}, number = {1}, pages = {}, doi = {10.3390/metabo15010051}, pmid = {39852393}, issn = {2218-1989}, support = {42377106//National Natural Science Foundation of China/ ; }, abstract = {Background/Objectives: The integration of microbiome and metabolome data could unveil profound insights into biological processes. However, widely used multi-omic data analyses often employ a stepwise mining approach, failing to harness the full potential of multi-omic datasets and leading to reduced detection accuracy. Synergistic analysis incorporating microbiome/metabolome data are essential for deeper understanding. Method: This study introduces a Coupled Matrix and Tensor Factorization (CMTF) framework for the joint analysis of microbiome and metabolome data, overcoming these limitations. Two CMTF frameworks were developed to factorize microbial taxa, functional pathways, and metabolites into latent factors, facilitating dimension reduction and biomarker identification. Validation was conducted using three diverse microbiome/metabolome datasets, including built environments and human gut samples from inflammatory bowel disease (IBD) and COVID-19 studies. Results: Our results revealed biologically meaningful biomarkers, such as Bacteroides vulgatus and acylcarnitines associated with IBD and pyroglutamic acid and p-cresol associated with COVID-19 outcomes, which provide new avenues for research. The CMTF framework consistently outperformed traditional methods in both dimension reduction and biomarker detection, offering a robust tool for uncovering biologically relevant insights. Conclusions: Despite its stringent data requirements, including the reliance on stratified microbial-based pathway abundances and taxa-level contributions, this approach provides a significant step forward in multi-omics integration and analysis, with potential applications across biomedical, environmental, and agricultural research.}, }
@article {pmid39852383, year = {2025}, author = {Yuan, JD and Wang, LW and Fu, SY and E, RG and Ren, XQ and Sun, H and Liu, F and Wang, B and An, JH and Zhao, MR and He, JF and He, XL}, title = {Heat Tolerance Differences Between Hu Sheep and Hu Crossbred Sheep in Microbial Community Structure and Metabolism.}, journal = {Metabolites}, volume = {15}, number = {1}, pages = {}, doi = {10.3390/metabo15010040}, pmid = {39852383}, issn = {2218-1989}, support = {2022JBGS0012//Inner Mongolia Autonomous Region Science and Technology Plan Project/ ; 2023CXYJJM03//Innovation Fund of Inner Mongolia Academy of Agricultural and Animal Husbandry Science/ ; 2023QN03019//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; ZD20232314//the Erdos Major Project of Science &amp; Technology/ ; none//the Inner Mongolia Autonomous Region Mutton Sheep industry technology system/ ; }, abstract = {BACKGROUND: The frequent occurrence of extreme temperature events causes significant economic losses to the livestock industry. Therefore, delving into the differences in the physiological and molecular mechanisms of heat stress across different sheep breeds is crucial for developing effective management and breeding strategies.<br><br>METHODS: This study explores the differences in heat tolerance mechanisms between Hu sheep and Xinggao sheep by comparing their growth performance under normal and heat stress conditions, as well as examining the differences in physiological, biochemical, and antioxidant indicators related to heat tolerance, serum metabolomics, and gut microbiomics in a heat stress environment.<br><br>RESULTS: The results indicate that with changes in the temperature-humidity index (THI), Hu sheep exhibit superior stability in respiratory rate (RR) and rectal temperature (RT) fluctuations compared to Xinggao sheep. In terms of biochemical indicators and antioxidant capacity, the levels of creatinine (Cr) and superoxide dismutase (SOD) in Hu sheep serum are significantly higher than those in Xinggao sheep. In comparison, alkaline phosphatase (ALP) and malondialdehyde (MDA) levels are significantly lower. Metabolomic results showed that, compared to Hu sheep, Xinggao sheep exhibited higher cortisol (COR) and dopamine (DA) levels under heat stress conditions, a stronger lipid mobilization capacity, and elevated levels of tricarboxylic acid (TCA) cycle-related metabolites. Furthermore, gut microbiome analysis results indicate that Hu sheep demonstrate stronger cellulose degradation capabilities, as evidenced by significantly higher abundances of microorganisms such as Ruminococcus, Fibrobacter, and Bacteroidales_RF16_group, compared to Xinggao sheep.<br><br>CONCLUSIONS: In summary, Hu sheep exhibit stronger heat tolerance compared to Xinggao sheep. These findings provide an important theoretical basis for the breeding and selection of heat-tolerant meat sheep varieties and offer strong support for the region's livestock industry in addressing the challenges posed by global warming.}, }
@article {pmid39852369, year = {2025}, author = {Lauwers, S and Weyns, AS and Breynaert, A and Van Rillaer, T and Van Huynegem, V and Fransen, E and Bittremieux, W and Lebeer, S and Tuenter, E and Hermans, N}, title = {Comparison of In Vitro Biotransformation of Olive Polyphenols Between Healthy Young and Elderly.}, journal = {Metabolites}, volume = {15}, number = {1}, pages = {}, doi = {10.3390/metabo15010026}, pmid = {39852369}, issn = {2218-1989}, abstract = {BACKGROUND: Olive leaves are a rich source of polyphenols, predominantly secoiridoids, flavonoids, and simple phenols, which exhibit various biological properties. Extracts prepared from olive leaves are associated with hypoglycemic, hypotensive, diuretic, and antiseptic properties. Upon ingestion, a substantial fraction of these polyphenols reaches the colon where they undergo extensive metabolism by the gut microbiota. Host characteristics, like age, can influence the composition of the gut microbiome, potentially affecting the biotransformation of these compounds. Therefore, it can be hypothesised that differences in the gut microbiome between young and elderly individuals may impact the biotransformation rate and the type and amount of metabolites formed.<br><br>METHODS: An in vitro biotransformation model was used to mimic the conditions in the stomach, small intestine and colon of two age groups of healthy participants (20-30 years old, &#x2265;65 years old), using oleuropein as a single compound and an olive leaf extract as test compounds. The bacterial composition and metabolite content were investigated.<br><br>RESULTS: The study revealed that, while the same metabolites were formed in both age groups, in the young age group, less metabolite formation was observed, likely due to a reduced viable cell count. Most biotransformation reactions took place within the first 24 h of colon incubation, and mainly, deglycosylation, hydrolysis, flavonoid ring cleavage, and demethylation reactions were observed. A bacterial composition analysis showed a steep drop in &#x3b1;-diversity after 24 h of colon incubation, likely due to favourable experimental conditions for certain bacterial species.<br><br>CONCLUSIONS: Both age groups produced the same metabolites, suggesting that the potential for polyphenols to exert their health-promoting benefits persists in healthy older individuals.}, }
@article {pmid39851614, year = {2025}, author = {Srila, W and Sripilai, K and Binlateh, T and Thammanichanon, P and Tiskratok, W and Noisa, P and Jitprasertwong, P}, title = {Relationship Between the Salivary Microbiome and Oral Malodor Metabolites in Older Thai Individuals with Periodontitis and the Cytotoxic Effects of Malodor Compounds on Human Oral Squamous Carcinoma (HSC-4) Cells.}, journal = {Dentistry journal}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/dj13010036}, pmid = {39851614}, issn = {2304-6767}, support = {NRIIS number 4285350//National Science, Research, and Innovation Fund (NSRF)/ ; //Thailand Science Research and Innovation/ ; //Suranaree University of Technology/ ; }, abstract = {Background/Objectives: Halitosis is primarily caused by the activity of oral microorganisms. In this study, we employed metagenomic sequencing and metabolomic approaches to investigate the differences in salivary microbiota and metabolite profiles between individuals with halitosis and periodontitis and healthy controls. Additionally, we expanded the study to examine how oral malodorous compounds interact with human oral squamous carcinoma (HSC-4) cells. Methods: Saliva samples were collected and analyzed using Ultra-High Performance Liquid Chromatography-Mass Spectrometry (UHPLC-MS) to identify metabolites. We then assessed the correlations between the microbiota and metabolites. Furthermore, the impact of oral malodorous substances on HSC-4 cells was investigated by evaluating apoptosis, antioxidant activity, and inflammatory properties. Results: The microbiota and metabolite profiles showed significant differences between the halitosis with periodontitis group and the periodontally healthy group. The halitosis with periodontitis group exhibited significantly higher relative abundances of eight genera: Tannerella, Selenomonas, Bacteroides, Filifactor, Phocaeicola, Fretibacterium, Eubacterium saphenum, and Desulfobulbus. In contrast, the periodontally healthy group showed significantly higher relative abundances of Family XIII UCG-001, Haemophilus, and Streptobacillus. Two metabolites, 2,3-dihydro-1H-indole and 10,11-dihydro-12R-hydroxy-leukotriene E4, were significantly higher in individuals with halitosis and periodontitis. In the treatment of HSC-4 cells with metabolites, dimethyl sulfide (DMS) did not show significant effects while indole appeared to induce cell death in HSC-4 cells by triggering apoptotic pathways. Additionally, both indole and DMS affected the inflammatory and antioxidant properties of HSC-4 cells. Conclusions: This study provides insights into the mechanisms of halitosis by exploring the correlations between microbiota and metabolite profiles. Furthermore, oral metabolites were shown to impact the cellular response of HSC-4 cells.}, }
@article {pmid39851512, year = {2025}, author = {Monti, E and Vianello, C and Leoni, I and Galvani, G and Lippolis, A and D'Amico, F and Roggiani, S and Stefanelli, C and Turroni, S and Fornari, F}, title = {Gut Microbiome Modulation in Hepatocellular Carcinoma: Preventive Role in NAFLD/NASH Progression and Potential Applications in Immunotherapy-Based Strategies.}, journal = {Cells}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/cells14020084}, pmid = {39851512}, issn = {2073-4409}, support = {25187//Italian Association for Cancer Research/ ; PNRR - M4C2-I1.3 Project PE_00000019 "HEAL ITALIA"//EUROPEAN UNION - NEXTGENERATIONEU/ ; }, mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/microbiology/immunology/pathology/therapy ; *Carcinoma, Hepatocellular/immunology/pathology/microbiology/therapy ; *Gastrointestinal Microbiome ; *Liver Neoplasms/immunology/pathology/microbiology/therapy ; *Immunotherapy/methods ; *Disease Progression ; Animals ; }, abstract = {Hepatocellular carcinoma (HCC) is a heterogeneous tumor associated with several risk factors, with non-alcoholic fatty liver disease (NAFLD) emerging as an important cause of liver tumorigenesis. Due to the obesity epidemics, the occurrence of NAFLD has significantly increased with nearly 30% prevalence worldwide. HCC often arises in the background of chronic liver disease (CLD), such as nonalcoholic steatohepatitis (NASH) and cirrhosis. Gut microbiome (GM) alterations have been linked to NAFLD progression and HCC development, with several investigations reporting a crucial role for the gut-liver axis and microbial metabolites in promoting CLD. Moreover, the GM affects liver homeostasis, energy status, and the immune microenvironment, influencing the response to immunotherapy with interesting therapeutic implications. In this review, we summarize the main changes in the GM and derived metabolites (e.g., short-chain fatty acids and bile acids) occurring in HCC patients and influencing NAFLD progression, emphasizing their potential as early diagnostic biomarkers and prognostic tools. We discuss the weight loss effects of diet-based interventions and healthy lifestyles for the treatment of NAFLD patients, highlighting their impact on the restoration of the intestinal barrier and GM structure. We also describe encouraging preclinical findings on the modulation of GM to improve liver functions in CLD, boost the antitumor immune response (e.g., probiotic supplementations or anti-hypercholesterolemic drug treatment), and ultimately delay NAFLD progression to HCC. The development of safe and effective strategies that target the gut-liver axis holds promise for liver cancer prevention and treatment, especially if personalized options will be considered.}, }
@article {pmid39851261, year = {2025}, author = {Zhao, X and Qiu, Y and Liang, L and Fu, X}, title = {Interkingdom signaling between gastrointestinal hormones and the gut microbiome.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2456592}, doi = {10.1080/19490976.2025.2456592}, pmid = {39851261}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Animals ; *Dysbiosis/microbiology ; *Gastrointestinal Hormones/metabolism ; *Bacteria/metabolism/classification/genetics ; Fecal Microbiota Transplantation ; Signal Transduction ; Homeostasis ; Inflammatory Bowel Diseases/microbiology/metabolism ; Gastrointestinal Tract/microbiology/metabolism ; }, abstract = {The interplay between the gut microbiota and gastrointestinal hormones plays a pivotal role in the health of the host and the development of diseases. As a vital component of the intestinal microecosystem, the gut microbiota influences the synthesis and release of many gastrointestinal hormones through mechanisms such as modulating the intestinal environment, producing metabolites, impacting mucosal barriers, generating immune and inflammatory responses, and releasing neurotransmitters. Conversely, gastrointestinal hormones exert feedback regulation on the gut microbiota by modulating the intestinal environment, nutrient absorption and utilization, and the bacterial biological behavior and composition. The distributions of the gut microbiota and gastrointestinal hormones are anatomically intertwined, and close interactions between the gut microbiota and gastrointestinal hormones are crucial for maintaining gastrointestinal homeostasis. Interventions leveraging the interplay between the gut microbiota and gastrointestinal hormones have been employed in the clinical management of metabolic diseases and inflammatory bowel diseases, such as bariatric surgery and fecal microbiota transplantation, offering promising targets for the treatment of dysbiosis-related diseases.}, }
@article {pmid39850963, year = {2024}, author = {Ciernikova, S and Sevcikova, A and Mego, M}, title = {Exploring the microbiome-gut-testis axis in testicular germ cell tumors.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1529871}, pmid = {39850963}, issn = {2235-2988}, mesh = {Humans ; *Testicular Neoplasms/microbiology ; Male ; *Neoplasms, Germ Cell and Embryonal/microbiology ; *Gastrointestinal Microbiome ; *Testis/microbiology ; *Dysbiosis/microbiology ; Microbiota ; Tumor Microenvironment ; }, abstract = {The microbiome-gut-testis axis has emerged as a significant area of interest in understanding testicular cancer, particularly testicular germ cell tumors (TGCTs), which represent the most common malignancy in young men. The interplay between the gut and testicular microbiomes is hypothesized to influence tumorigenesis and reproductive health, underscoring the complex role of microbial ecosystems in disease pathology. The microbiome-gut-testis axis encompasses complex interactions between the gut microbiome, systemic immune modulation, and the local microenvironment of the testis. Dysbiosis in the gut or testicular microbiomes may contribute to altered immune responses, inflammation, and hormonal imbalances, potentially playing a role in the pathogenesis of TGCTs. Concurrently, seminal microbiomes have been linked to variations in sperm quality, fertility potential, and possibly cancer susceptibility, underscoring the need for further evaluation. This review explores the emerging role of the microbiome-gut-testis axis in the context of testicular cancer, highlighting its implications for disease onset, progression, treatment efficacy, and toxicity. Identifying potential microbial biomarkers, followed by microbiota modulation to restore a balanced microbial community, might offer a novel supportive strategy for improving treatment efficacy in refractory TGCT patients while reducing chemotherapy-induced toxicity. We suggest a better understanding of the association between dysregulated microbial environments and TGCTs emphasizes potential pathways by which the gut microbiome might influence testicular cancer.}, }
@article {pmid39850945, year = {2024}, author = {Valitutti, F and Mennini, M and Monacelli, G and Fagiolari, G and Piccirillo, M and Di Nardo, G and Di Cara, G}, title = {Intestinal permeability, food antigens and the microbiome: a multifaceted perspective.}, journal = {Frontiers in allergy}, volume = {5}, number = {}, pages = {1505834}, pmid = {39850945}, issn = {2673-6101}, abstract = {The gut barrier encompasses several interactive, physical, and functional components, such as the gut microbiota, the mucus layer, the epithelial layer and the gut mucosal immunity. All these contribute to homeostasis in a well-regulated manner. Nevertheless, this frail balance might be disrupted for instance by westernized dietary habits, infections, pollution or exposure to antibiotics, thus diminishing protective immunity and leading to the onset of chronic diseases. Several gaps of knowledge still exist as regards this multi-level interaction. In this review we aim to summarize current evidence linking food antigens, microbiota and gut permeability interference in diverse disease conditions such as celiac disease (CeD), non-celiac wheat sensitivity (NCWS), food allergies (FA), eosinophilic gastrointestinal disorder (EOGID) and irritable bowel syndrome (IBS). Specific food elimination diets are recommended for CeD, NCWS, FA and in some cases for EOGID. Undoubtfully, each of these conditions is very different and quite unique, albeit food antigens/compounds, intestinal permeability and specific microbiota signatures orchestrate immune response and decide clinical outcomes for all of them.}, }
@article {pmid39850896, year = {2024}, author = {Deng, Y and Dong, ZX and Yang, GH and Krimsky, WS and Tai, YH and Peng, H and Huang, GT and Xu, JX and Sarkar, SA and Peng, J and Qian, K}, title = {Streptococcus intermedius promotes synchronous multiple primary lung cancer progression through apoptosis regulation.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1482084}, pmid = {39850896}, issn = {1664-3224}, mesh = {Humans ; *Lung Neoplasms/microbiology/pathology ; *Apoptosis ; Male ; *Disease Progression ; *Streptococcus intermedius ; Female ; Middle Aged ; Aged ; Microbiota ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; Lung/microbiology/pathology ; }, abstract = {BACKGROUND: Dysbiosis of the lung microbiome can contribute to the initiation and progression of lung cancer. Synchronous multiple primary lung cancer (sMPLC) is an increasingly recognized subtype of lung cancer characterized by high morbidity, difficulties in early detection, poor prognosis, and substantial clinical challenges. However, the relationship between sMPLC pathogenesis and changes in the lung microbiome remains unclear.<br><br>METHODS: In this study, 16S rRNA sequencing was performed on clinical samples to analyze lung microbiome composition. Real-time quantitative PCR (qPCR) was used to quantify bacterial abundance in lung tissues. In addition, flow cytometry was conducted to evaluate cell cycle progression and apoptosis in lung tumor cells.<br><br>RESULTS: Clinical cohort studies demonstrated that sMPLC occurrence is associated with disturbances in the lung microbiome. Notably, Streptococcus intermedius was enriched in the lungs of sMPLC patients compared with non-tumor controls and accumulated preferentially in tumor tissues. S. intermedius shortened the cell cycle and inhibited apoptosis in lung cancer cells. Analyses of oral and gut microbiomes in different patient cohorts revealed a strong correlation between oral microbiome imbalances and lung microbiome composition in sMPLC patients.<br><br>CONCLUSIONS: These findings characterize the lung microbiota in sMPLC and identify S. intermedius as a potentially influential bacterial strain. This study provides significant new insights into the diagnosis and treatment of sMPLC.}, }
@article {pmid39850876, year = {2024}, author = {Yoneda, K and Sendo, S and Okano, T and Shimizu, H and Yamada, H and Nishimura, K and Ueda, Y and Saegusa, J}, title = {Impact of dysregulated microbiota-derived C18 polyunsaturated fatty acid metabolites on arthritis severity in mice with collagen-induced arthritis.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1444892}, pmid = {39850876}, issn = {1664-3224}, mesh = {Animals ; *Arthritis, Experimental/microbiology/metabolism ; Mice ; *Gastrointestinal Microbiome ; Male ; *Fatty Acids, Unsaturated/metabolism ; Severity of Illness Index ; Linoleic Acids, Conjugated/metabolism ; Dysbiosis ; RNA, Ribosomal, 16S/genetics ; Mice, Inbred DBA ; Disease Models, Animal ; }, abstract = {OBJECTIVE: We aimed to evaluate microbiome and microbiota-derived C18 dietary polyunsaturated fatty acids (PUFAs), such as conjugated linoleic acid (CLA), and to investigate their differences that correlate with arthritis severity in collagen-induced arthritis (CIA) mice.<br><br>METHODS: On day 84 after induction, during the chronic phase of arthritis, cecal samples were analyzed using 16S rRNA sequencing, and plasma and cecal digesta were evaluated using liquid chromatography-tandem mass spectrometry. Differences in microbial composition between 10 control (Ctrl) and 29 CIA mice or between the mild and severe subgroups based on arthritis scores were identified. The cecal metabolite profile and its correlation with the microbiome were evaluated with respect to arthritis severity.<br><br>RESULTS: The hydroxy and oxo metabolite levels were higher in CIA mice than in Ctrl mice, some of which, including 10-hydroxy-cis-6-18:1, were positively correlated with arthritis scores. The 9-trans,11-trans CLA levels in CIA mice had a negative linear correlation with arthritis scores. Microbial diversity was lower in severe CIA mice than in mild CIA or Ctrl mice. The abundance of Lactobacillus relatively increased in the severe subgroup of CIA mice compared with that in the mild subgroup and was positively correlated with arthritis severity.<br><br>CONCLUSION: Alterations in gut microbiota and microbiota-derived C18 PUFA metabolites are associated in CIA mice and correlated with arthritis scores, indicating that plasma or fecal C18 PUFA metabolites can be potential biomarkers for arthritis severity and dysbiosis.}, }
@article {pmid39850838, year = {2025}, author = {Akter, A and Teddleton, H and Caldwell, M and Pighetti, G and Myer, PR and Henniger, MT and Schneider, L and Shepherd, E}, title = {Prevalence of nasopharyngeal bacteria during naturally occurring bovine respiratory disease in commercial stocker cattle.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18858}, pmid = {39850838}, issn = {2167-8359}, mesh = {Animals ; Cattle ; *Nasopharynx/microbiology ; Prevalence ; *Bovine Respiratory Disease Complex/microbiology/epidemiology ; Male ; RNA, Ribosomal, 16S/genetics ; Microbiota/drug effects ; Bacteria/isolation &amp; purification/genetics/drug effects/classification ; Cattle Diseases/microbiology/epidemiology ; }, abstract = {Bovine respiratory disease (BRD) is one of the most common economic and health challenges to the beef cattle industry. Prophylactic use of antimicrobial drugs can alter the microbial communities in the respiratory tract. Considering that the bovine upper respiratory tract microbiome has been associated with generalized health, understanding the microenvironment that influences this microbiome may provide insights into the pathogenesis of BRD. This study aimed to determine temporal variation in nasopharyngeal (NP) microbiome in naturally occurring BRD in newly received stocker calves. Mixed breed steers (n = 40) were purchased from an auction market and housed in a commercial stocker farm. Clinical signs were used to identify BRD affected animals, and calves were categorized based on the number of treatments (NumTrt) received (0, 1, 2). On days 0, 7, 14, and 21, NP samples were collected, and subsequent DNA were isolated and sequenced. After sequencing, 16S rRNA V4 gene was amplified and utilized for NP bacterial determination. The difference in relative abundance based on day and NumTrt was measured using repeated measures ANOVA (PROC GLIMMIX; SAS 9.4). Firmicutes, Proteobacteria, Actinobacteriota, Bacteroidota, and Verrucomicrobiota were the top phyla and Mycoplasma, Histophilus, Geobacillus, Saccharococcus, Lactobacillus, and Pasteurella were the top genera. In healthy calves, the relative abundance of Mycoplasma differed by day (P = 0.01), whereas on day 7, calves had five times greater abundance compared to day 0 (d 0: 0.06 ± 0.05; d 7: 0.30 ± 0.05). No differences were observed in the alpha diversity matrices based on day or NumTrt (P > 0.05). Results of this study suggest compositional variations in NP microbial populations occur during disease conditions.}, }
@article {pmid39850835, year = {2025}, author = {Zhang, Q and Zhen, M and Wang, X and Zhao, F and Dong, Y and Wang, X and Gao, S and Wang, J and Shi, W and Zhang, Y}, title = {Antibiotic exposure enriches streptococci carrying resistance genes in periodontitis plaque biofilms.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18835}, pmid = {39850835}, issn = {2167-8359}, mesh = {Humans ; *Biofilms/drug effects/growth &amp; development ; *Periodontitis/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Streptococcus/drug effects/genetics ; Female ; Male ; Adult ; *Dental Plaque/microbiology ; *Amoxicillin/pharmacology/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Drug Resistance, Bacterial/genetics ; Microbiota/drug effects/genetics ; Tetracycline/pharmacology/therapeutic use ; Metronidazole/pharmacology/therapeutic use ; Clindamycin/pharmacology/therapeutic use ; }, abstract = {BACKGROUND: Periodontitis is not always satisfactorily treated with conventional scaling and root planing, and adjunctive use of antibiotics is required in clinical practice. Therefore, it is important for clinicians to understand the diversity and the antibiotic resistance of subgingival microbiota when exposed to different antibiotics.<br><br>MATERIALS AND METHODS: In this study, subgingival plaques were collected from 10 periodontitis patients and 11 periodontally healthy volunteers, and their microbiota response to selective pressure of four antibiotics (amoxicillin, metronidazole, clindamycin, and tetracycline) were evaluated through 16S rRNA gene amplicon and metagenomic sequencing analysis. Additionally, sensitive and resistant strains were isolated and cultured in vitro for resistance evaluation.<br><br>RESULTS: Cultivation of subgingival microbiota revealed the oral microbiota from periodontitis patients were more resistant to antibiotics than that of healthy. Significant differences were also observed for the microbial community between with and without antibiotics (especially amoxicillin and tetracycline) treated in periodontitis group.<br><br>CONCLUSION: Overall, after the two antibiotics (amoxicillin and tetracycline) exposed, the oral subgingival microbiota in periodontitis patients exhibited different diversity and composition. Streptococcus may account for oral biofilm-specific antibiotic resistance in periodontitis. This provides information for personalized treatment of periodontitis.}, }
@article {pmid39850636, year = {2024}, author = {Iannotti, FA}, title = {I. IDC Key-note Lecture: Influence of gut microbiome in Duchenne muscular dystrophy.}, journal = {Journal of stem cells &amp; regenerative medicine}, volume = {20}, number = {2}, pages = {56-57}, pmid = {39850636}, issn = {0973-7154}, }
@article {pmid39850611, year = {2025}, author = {Pardali, EC and Gkouvi, A and Gkouskou, KK and Manolakis, AC and Tsigalou, C and Goulis, DG and Bogdanos, DP and Grammatikopoulou, MG}, title = {Autoimmune protocol diet: A personalized elimination diet for patients with autoimmune diseases.}, journal = {Metabolism open}, volume = {25}, number = {}, pages = {100342}, pmid = {39850611}, issn = {2589-9368}, abstract = {The autoimmune protocol diet (AIP) is a personalized elimination diet that aims to determine and exclude the foods that might trigger immune responses, leading to inflammation and symptomatology associated with autoimmune diseases. Focusing on gut health and the importance of the gut microbiome in immune regulation and overall well-being, the AIP starts by eliminating foods that might create negative effects on the patients and continues by developing a personalized and tailored diet plan for them. This comprehensive approach aims to mitigate symptoms and improve quality of life of individuals with autoimmune conditions. This review presents and critically appraises current knowledge on the AIP protocol, highlight any oversights, and discuss findings from relevant clinical trials.}, }
@article {pmid39850469, year = {2024}, author = {Leonov, G and Varaeva, Y and Livantsova, E and Vasilyev, A and Vladimirskaya, O and Korotkova, T and Nikityuk, D and Starodubova, A}, title = {Periodontal pathogens and obesity in the context of cardiovascular risks across age groups.}, journal = {Frontiers in oral health}, volume = {5}, number = {}, pages = {1488833}, pmid = {39850469}, issn = {2673-4842}, abstract = {BACKGROUND: Cardiovascular diseases (CVDs) are the leading cause of mortality and morbidity among noncommunicable diseases. Over the past decade, there has been a notable increase in the prevalence of CVDs among young individuals. Obesity, a well-known risk factor for CVDs, is also associated with various comorbidities that may contribute to cardiovascular risk. The relationship between periodontal pathogens and CVD risk factors, including obesity, smoking, lipid metabolism disorders, and inflammatory markers, remains underexplored.<br><br>METHODS: This study examined the relationship between six periodontal pathogens (Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Treponema denticola, Tannerella forsythia, Prevotella intermedia, and Fusobacterium nucleatum) and CVD risk factors among 189 subjects stratified by age and body mass index (BMI). Body composition was assessed via bioimpedance analysis, and blood samples were analyzed for lipid profiles, glucose, and proinflammatory cytokines. Oral samples were collected for polymerase chain reaction (PCR) analysis to identify periodontal pathogens. Cardiovascular and diabetes risk scores were calculated using the SCORE and FINDRISC scales.<br><br>RESULTS: The prevalence of periodontal pathogens in the population was 33.0% for P. gingivalis, 47.8% for P. intermedia, 63.4% for A. actinomycetemcomitans, 46.6% for T. forsythia, 46.6% for T. denticola, and 89.2% for F. nucleatum. Significant age- and BMI-related differences were observed in pathogen prevalence, particularly with P. gingivalis, P. intermedia, and T. denticola. Young obese individuals exhibited a higher prevalence of P. intermedia and T. forsythia. P. gingivalis was found to be associated with hypertension and dyslipidemia, while P. intermedia was linked to hypertension and obesity. T. denticola was associated with obesity, dyslipidemia and smoking, whereas T. forsythia was linked to dyslipidemia alone.<br><br>CONCLUSIONS: This study highlights the potential connection between periodontal pathogens and risk factors associated with cardiovascular disease, including smoking, elevated BMI, increased adipose tissue, hypertension, and dyslipidemia. Further research is required to determine the causal relationships between oral microbiome dysbiosis, obesity and, systemic diseases and to develop an effective strategy for preventing oral health-related CVD risk factors in young adults.}, }
@article {pmid39850273, year = {2024}, author = {Lloren, KKS and Senevirathne, A and Lee, JH}, title = {Advancing vaccine technology through the manipulation of pathogenic and commensal bacteria.}, journal = {Materials today. Bio}, volume = {29}, number = {}, pages = {101349}, pmid = {39850273}, issn = {2590-0064}, abstract = {Advancements in vaccine technology are increasingly focused on leveraging the unique properties of both pathogenic and commensal bacteria. This revolutionary approach harnesses the diverse immune modulatory mechanisms and bacterial biology inherent in different bacterial species enhancing vaccine efficacy and safety. Pathogenic bacteria, known for their ability to induce robust immune responses, are being studied for their potential to be engineered into safe, attenuated vectors that can target specific diseases with high precision. Concurrently, commensal bacteria, which coexist harmlessly with their hosts and contribute to immune system regulation, are also being explored as novel delivery systems and in microbiome-based therapy. These bacteria can modulate immune responses, offering a promising avenue for developing effective and personalized vaccines. Integrating the distinctive characteristics of pathogenic and commensal bacteria with advanced bacterial engineering techniques paves the way for innovative vaccine and therapeutic platforms that could address a wide range of infectious diseases and potentially non-infectious conditions. This holistic approach signifies a paradigm shift in vaccine development and immunotherapy, emphasizing the intricate interplay between the bacteria and the immune systems to achieve optimal immunological outcomes.}, }
@article {pmid39850178, year = {2024}, author = {Gandhi, DN and Pande, DN and Harikrishna, A and Advilkar, A and Basavan, I and Ansari, R}, title = {Beyond the Brain: Attention Deficit/Hyperactivity Disorder and the Gut-Brain Axis.}, journal = {Cureus}, volume = {16}, number = {12}, pages = {e76291}, pmid = {39850178}, issn = {2168-8184}, abstract = {Attention-deficit/hyperactivity disorder (ADHD) is a complex neurodevelopmental condition, predominantly affecting children, characterized by inattention, hyperactivity, and impulsivity. A growing body of evidence has highlighted the potential influence of the gut microbiota on the onset and presentation of ADHD symptoms. The gut microbiota, a diverse microbial ecosystem residing within the gastrointestinal tract, exerts multiple effects on systemic physiology, including immune modulation, metabolic regulation, and neuronal signalling. The bidirectional gut-brain axis serves as a conduit for communication between gut microbes and the central nervous system, implicating its disruption in neurodevelopmental disorders such as ADHD. This comprehensive literature review aims to shed light on how alterations in the gut microbiota influence the development and manifestation of ADHD symptoms. Examining potential mechanisms involving gut microbial metabolites and their impact on neurotransmitter modulation, neuro-endocrine signalling and neuroinflammation, we dissect the intricate interplay shaping ADHD pathology. Insights into these complex interactions hold promise for personalized therapeutic interventions aimed at modulating the gut microbiota to ameliorate ADHD symptoms. Discussions encompass dietary interventions, faecal microbiota-targeted therapies, and emerging probiotic approaches, underscoring their potential as adjunctive or alternative strategies in managing ADHD. Further research elucidating the precise mechanisms driving these interactions may pave the way for targeted and personalized interventions for individuals grappling with ADHD.}, }
@article {pmid39850127, year = {2024}, author = {Fakhraldeen, SA and Madhusoodhanan, R and Habibi, N and Al-Haddad, S and Alagarsamy, S and Habeebullah, SFK and Al-Zakri, WM and Thuslim, F and Fernandes, L and Al-Yamani, F and Al-Said, T}, title = {Shotgun metagenomics reveals the interplay between microbiome diversity and environmental gradients in the first marine protected area in the northern Arabian Gulf.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1479542}, pmid = {39850127}, issn = {1664-302X}, abstract = {INTRODUCTION: The northwest Arabian Gulf encounters significant anthropogenic pressures, including nutrient enrichment from coastal development and effluent discharge.<br><br>METHODS: This study presents the first shotgun metagenomics-based characterization of microbial communities in Kuwaiti waters of the northwest Arabian Gulf, focusing on Kuwait's first Marine Protected Area (MPA) in Sulaibikhat Bay, a vital nursery ground for commercially important fish.<br><br>RESULTS: Analysis revealed significantly higher microbial diversity within the MPA compared to adjacent waters, with Rhodobacteraceae (27.8%) and Flavobacteriaceae (15.3%) being dominant. Elevated inorganic phosphorus, nitrogen, and salinity were key factors driving this diversity. Multivariate analysis highlighted phosphate as a critical component affecting the MPA microbial community structure, particularly for the families Microbacteriaceae, Flavobacteriaceae, and Rhodobacteraceae.<br><br>DISCUSSION: This study underscores the ecological importance of MPAs and highlights the impact of nutrient enrichment and other environmental stressors on microbial diversity, emphasizing the need to reduce nutrient influx to mitigate eutrophication and enhance marine ecosystem resilience in stressed environments.}, }
@article {pmid39849992, year = {2025}, author = {Tamminga, SM and Van Der Wal, MM and Saager, ES and Van Der Gang, LF and Boesjes, CM and Hendriks, A and Pannekoek, Y and De Bruin, MS and Van Wijk, F and Van Sorge, NM}, title = {Single-cell sequencing of human Langerhans cells identifies altered gene expression profiles in patients with atopic dermatitis.}, journal = {ImmunoHorizons}, volume = {9}, number = {2}, pages = {}, doi = {10.1093/immhor/vlae009}, pmid = {39849992}, issn = {2573-7732}, support = {//Infection and Immunity Boost/ ; //Dutch Health Council/ ; }, mesh = {Humans ; *Dermatitis, Atopic/immunology/microbiology/genetics ; *Langerhans Cells/immunology/metabolism ; *Staphylococcus aureus/immunology/genetics ; *Single-Cell Analysis ; Skin/microbiology/pathology/immunology ; Transcriptome ; Male ; Adult ; Female ; Chemokine CCL17/genetics/metabolism ; Th2 Cells/immunology/metabolism ; T-Lymphocytes, Regulatory/immunology/metabolism ; Sequence Analysis, RNA ; Lymphocyte Activation/immunology ; }, abstract = {Atopic dermatitis (AD) is characterized by dysregulated T cell immunity and skin microbiome dysbiosis with predominance of Staphylococcus aureus, which is associated with exacerbating AD skin inflammation. Specific glycosylation patterns of S. aureus cell wall structures amplify skin inflammation through interaction with Langerhans cells (LCs). Nevertheless, the role of LCs in AD remains poorly characterized. Here, we performed single cell RNA sequencing of primary epidermal LCs and dermal T cells, isolated from skin biopsies of AD patients and healthy control subjects, alongside specific glycoanalysis of S. aureus strains isolated from the AD lesions. Our findings revealed 4 LC subpopulations ie, 2 steady-state clusters [LC1 and LC1H] and 2 proinflammatory/matured subsets [LC2 and migratory LCs]. The latter 2 subsets were enriched in AD skin. AD LCs showed enhanced expression of C-type lectin receptors, the high-affinity IgE receptor, and activation of prostaglandin and leukotriene biosynthesis pathways, upregulated transcriptional signatures related to T cell activation pathways, and increased expression of CCL17 compared with healthy LCs. Correspondingly, T helper 2 and T regulatory cell populations were increased in AD lesions. Complementary, we performed bulk RNA sequencing of primary LCs stimulated with the S. aureus strains isolated from the AD lesions, which showed upregulation of T helper 2-related pathways. Our study provides proof-of-concept for a role of LCs in connecting the S. aureus-T cell axis in the AD inflammatory cycle.}, }
@article {pmid39849986, year = {2025}, author = {Liu, Y and Geng, Y and Jiang, Y and Li, P and Li, YZ and Zhang, Z}, title = {Global microbial community biodiversity increases with antimicrobial toxin abundance of rare taxa.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf012}, pmid = {39849986}, issn = {1751-7370}, abstract = {One of the central questions in microbial ecology is how to explain the high biodiversity of communities. A large number of rare taxa in the community have not been excluded by abundant taxa with competitive advantages, a contradiction known as the biodiversity paradox. Recently, increasing evidence has revealed the central importance of antimicrobial toxins as crucial weapons of antagonism in microbial survival. The powerful effects of antimicrobial toxins result in simple combinations of microorganisms failing to coexist under laboratory conditions, but it is unclear whether they also have a negative impact on the biodiversity of natural communities. Here, we revealed that microbial communities worldwide universally possess functional potential for antimicrobial toxin production. Counterintuitively, the biodiversity of global microbial communities increases, rather than decreases, as the abundance of antimicrobial toxins in rare taxa rises. Rare taxa may encode more antimicrobial toxins than abundant taxa, which is associated with the maintenance of the high biodiversity of microbial communities amid complex interactions. Our findings suggest that the antagonistic interaction caused by antimicrobial toxins may play a positive role in microbial community biodiversity at the global scale.}, }
@article {pmid39849793, year = {2025}, author = {Gul, P and Khan, J and Li, Q and Liu, K}, title = {Moringa oleifera in a modern time: A comprehensive review of its nutritional and bioactive composition as a natural solution for managing diabetes mellitus by reducing oxidative stress and inflammation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {201}, number = {}, pages = {115671}, doi = {10.1016/j.foodres.2025.115671}, pmid = {39849793}, issn = {1873-7145}, mesh = {*Moringa oleifera/chemistry ; *Oxidative Stress/drug effects ; Humans ; *Hypoglycemic Agents/pharmacology ; *Diabetes Mellitus/drug therapy ; Animals ; *Inflammation/drug therapy ; *Plant Extracts/pharmacology ; Antioxidants/pharmacology ; Anti-Inflammatory Agents/pharmacology ; Nutritive Value ; Seeds/chemistry ; }, abstract = {Globally, diabetes mellitus (DM) and its complications are considered among the most significant public health problems. According to numerous scientific studies, Plants and their bioactive compounds may reduce inflammation and oxidative stress (OS), leading to a reduction in the progression of DM. Moringa oleifera (MO), widely used in Ayurvedic and Unani medicine for centuries because of its health-promoting characteristics, particularly its ability to control DM and its related complications. MO is a multi-purpose plant that has an impressive range of nutritional components including proteins, amino acids (Essential and non-essential amino acids), carbs, fats, fiber, vitamins, and phenolic compounds. In the modern era, scientists have paid close attention to the anti-diabetic, anti-oxidative and anti-inflammatory attributes and other medicinal properties, of MO leaves and seeds. MO leaves and seeds have modulatory effects on DM that are likely influenced by multiple mechanisms. Some of these mechanisms include direct effects, but other mechanisms involve inhibition the production of inflammatory markers, modulation of the gut microbiome, reduction of OS, enhancement of glucose metabolism through hexokinase and glucose 6-phosphate dehydrogenase, improve insulin sensitivity and glucose uptake in the liver and muscles. Overall, these findings suggest that MO may play a role in lowering the risk of DM and its related outcomes. The purpose of this review is to provide a comprehensive overview of the nutritional and bioactive profiles of MO leaves and seeds, as well as to investigate their possible anti-diabetic effects by modulating oxidative stress and inflammation. Our results indicate that MO may be a beneficial natural resource for management of DM and related issues by lowering oxidative stress and inflammation. Furthermore, studies on MO has yielded promising findings in diabetic animal models, indicating antioxidant and anti-inflammatory properties. However, human trials have shown less solid results, most likely due to a lack of studies, different techniques, and dosages. More clinical research is needed to fully understand MO's anti-diabetic potential, notably in lowering oxidative stress and inflammation, both of which are critical in controlling diabetes complications.}, }
@article {pmid39849752, year = {2025}, author = {Eg Gadegaard, IS and Eskildsen, MH and Østergaard, SK and Nielsen, JL and Rasmussen, JT}, title = {Xanthine oxidase-lactoperoxidase system: Dose-dependent antibacterial effects and global gene expression changes in infant oral microbiota.}, journal = {Food research international (Ottawa, Ont.)}, volume = {201}, number = {}, pages = {115596}, doi = {10.1016/j.foodres.2024.115596}, pmid = {39849752}, issn = {1873-7145}, mesh = {*Lactoperoxidase/metabolism/genetics ; *Xanthine Oxidase/metabolism/genetics ; Humans ; Infant ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; *Mouth/microbiology ; Saliva/microbiology/enzymology ; Reactive Oxygen Species/metabolism ; Bacteria/drug effects/genetics ; Gene Expression Regulation, Bacterial ; Milk/microbiology ; }, abstract = {Xanthine oxidase (XO) and lactoperoxidase (LPO) are highly abundant enzymes in milk. Their substrates, xanthine and thiocyanate, are found in elevated amounts in infant saliva, leading to a proposed interaction between milk and saliva referred to as the XO-LPO system. This system is suggested to generate reactive oxygen and nitrogen species with potential antibacterial effects. The antibacterial activity of the XO-LPO system was assessed on bacteria cultured from the oral cavities of five infants, where a reduction in bacterial growth rate was observed at 40 µg mL[-1] of each enzyme and with complete inhibition achieved at 200 µg mL[-1]. Gene expression analysis showed that XO-LPO treatment led to downregulation of several reactive oxygen species-related genes, suggesting a transient bacterial stress response. The study also observed downregulation of key glycolytic enzymes, indicating that XO-LPO treatment affects bacterial metabolism at transcriptional level, suggesting a possible mechanism of action for the XO-LPO system. Collectively, these findings offer new insights into the XO-LPO system, revealing novel aspects of the interaction between lactation and microbiome influence.}, }
@article {pmid39849717, year = {2025}, author = {Faubel, N and Blanco-Morales, V and Sentandreu, V and Barberá, R and Garcia-Llatas, G}, title = {Modulation of microbiota composition and markers of gut health after in vitro dynamic colonic fermentation of plant sterol-enriched wholemeal rye bread.}, journal = {Food research international (Ottawa, Ont.)}, volume = {201}, number = {}, pages = {115570}, doi = {10.1016/j.foodres.2024.115570}, pmid = {39849717}, issn = {1873-7145}, mesh = {*Bread/microbiology/analysis ; *Fermentation ; *Gastrointestinal Microbiome/physiology ; *Phytosterols/metabolism ; *Secale/chemistry ; Humans ; *Fatty Acids, Volatile/metabolism ; *Colon/microbiology/metabolism ; *Dietary Fiber/metabolism ; *Sitosterols/metabolism ; Prebiotics ; Stigmasterol/metabolism ; Bifidobacterium/metabolism ; Biomarkers ; Lactobacillus/metabolism ; Cholesterol/analogs &amp; derivatives ; }, abstract = {A human oral phase followed by a dynamic gastrointestinal digestion and colonic fermentation (simgi®) has been applied to wholemeal rye bread (WRB) and PS-enriched WRB (PS-WRB). The aim of this study was to evaluate the impact of these solid and high-fiber food matrices on the metabolism of PS, modulation of the microbiota and production of short-chain fatty acids (SCFA) and ammonium ion after a simulated chronic intake (5 days). In both breads, campesterol, campestanol, stigmasterol, β-sitosterol, sitostanol, Δ5-avenasterol, Δ5,24-stigmastadienol, Δ7-stigmastenol, and Δ7-avenasterol were identified, of which only β-sitosterol was metabolized to sitostenone after PS-WRB treatment. The presence of fiber in both breads exerted a prebiotic effect after fermentation by the increase in Firmicutes (Lactobacillus genus, maximum abundance of 89-99 %) and Actinobacteria (Bifidobacterium genus, maximum abundance of 30-31 %), reflected in an increase of SCFA content. The reduction of proteolytic activity confirmed by the decrease in ammonium ion contents is related to a reduction in the Proteobacteria phylum. Thus, PS-WRB could be considered as a healthy staple food choice since, besides the known hypocholesterolemic effect of PS, rye bread fiber preserves the beneficial microbiota and exerts a positive impact on markers of gut health.}, }
@article {pmid39849623, year = {2025}, author = {Liu, Y and Ma, J and Li, X and Zhao, H and Ai, Q and Zhang, L and Tong, Y and Meng, L and Yang, H}, title = {No microorganism was detected in amniotic fluid of healthy pregnancies from the second trimester to the delivery.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {20}, pmid = {39849623}, issn = {2049-2618}, mesh = {Humans ; Female ; Pregnancy ; *Amniotic Fluid/microbiology ; *Pregnancy Trimester, Second ; Adult ; *Bacteria/classification/isolation &amp; purification/genetics ; *RNA, Ribosomal, 16S/genetics ; Cesarean Section ; Chorioamnionitis/microbiology ; Microbiota ; Infant, Newborn ; Premature Birth/microbiology ; Pregnancy Outcome ; DNA, Bacterial/genetics ; Cohort Studies ; }, abstract = {BACKGROUND: The early colonization and establishment of the microbiome in newborns is a crucial step in the development of the immune system and host metabolism. However, the exact timing of initial microbial colonization remains a subject of ongoing debate. While numerous studies have attempted to determine the presence or absence of intrauterine bacteria, the majority of them have drawn conclusions based on sequencing data from maternal or infant samples taken at a single time point. In this study, we aimed to investigate the microbial population in amniotic fluid (AF) from the second trimester until the time of delivery using multiple microbiological methods.<br><br>METHODS: AF samples were collected during the second trimester (19-21 gestational weeks) and at the time of delivery. Cohort 1 included 51 women who underwent the term and elective cesarean section, with both their second trimester and delivery AF samples (n&#x2009;=&#x2009;55, respectively) analyzed. Cohort 2 contained 22 women who experienced infection-related adverse pregnancy outcomes (including preterm birth, histological chorioamnionitis, and stillbirth), with only their second trimester AF samples (n&#x2009;=&#x2009;24) examined. Additionally, multiple procedural negative controls and technical positive controls were applied to this study to remove potential contamination. Microbial profiles were assessed through cultivation, quantitative real-time polymerase chain reaction, 16S ribosomal RNA gene sequencing, and cytokine analysis.<br><br>RESULTS: In cohort 1, the bacterial load and community structure in the second trimester AF samples were indistinguishable from negative controls. Although marginally higher bacterial loads and different bacterial communities were observed in the delivery AF samples compared to negative controls, these bacterial DNA were not considered biologically functional due to the absence of maternal inflammatory responses. In cohort 2, the bacterial load and community structure of the second trimester AF samples differed significantly from those of negative controls, with Ureaplasma and Lactobacillus identified as the most prevalent genera against negative controls.<br><br>CONCLUSIONS: Our study demonstrates that no microorganisms were detected in the AF of healthy pregnancies from the second trimester to the delivery. The presence of Ureaplasma and Lactobacillus in the second trimester AF may be associated with infection-related adverse pregnancy outcomes. Video Abstract.}, }
@article {pmid39849517, year = {2025}, author = {Muhammad, A and Qian, Z and Li, Y and Lei, X and Iqbal, J and Shen, X and He, J and Zhang, N and Sun, C and Shao, Y}, title = {Enhanced bioaccumulation and toxicity of Fenpropathrin by polystyrene nano(micro)plastics in the model insect, silkworm (Bombyx mori).}, journal = {Journal of nanobiotechnology}, volume = {23}, number = {1}, pages = {38}, pmid = {39849517}, issn = {1477-3155}, support = {32250410276//National Natural Science Foundation of China/ ; LZ22C170001//Zhejiang Provincial Natural Science Foundation of China/ ; CARS-18-ZJ0302//China Agriculture Research System of MOF and MARA/ ; }, mesh = {Animals ; *Bombyx/metabolism ; *Polystyrenes/toxicity/chemistry ; *Bioaccumulation ; *Gastrointestinal Microbiome/drug effects ; Particle Size ; Adsorption ; Nanoparticles/toxicity/chemistry ; Pyrethrins/toxicity/metabolism ; Larva/drug effects/metabolism ; Microplastics/toxicity ; }, abstract = {BACKGROUND: Nano(micro)plastics (NMPs) and agrochemicals are ubiquitous pollutants. The small size and physicochemical properties of NMPs make them potential carriers for pollutants, affecting their bioavailability and impact on living organisms. However, little is known about their interactions in terrestrial ecosystems. This study investigates the adsorption of Fenpropathrin (FPP) onto two different sizes of polystyrene NMPs and examines their impacts on an insect model, silkworm Bombyx mori. We analyzed the systemic effects of acute exposure to NMPs and FPP, individually and combined, at organismal, tissue, cellular, and gut microbiome levels.<br><br>RESULTS: Our results showed that NMPs can adsorb FPP, with smaller particles having higher adsorption capacity, leading to size-dependent increases in the bioaccumulation and toxicity of FPP. These effects led to higher mortality, reduced body weight, delayed development, and decreased cocoon production in silkworms. Additionally, the pollutants caused physical and oxidative damage to the midgut and altered gene expression related to juvenile hormone (JH) and silk protein synthesis. The gut microbiome analysis revealed significant changes and reduced abundance of potentially beneficial bacteria. Thus, the aggravated toxicity induced by NMPs was size-dependent, with smaller particles (NPs) having a greater impact.<br><br>CONCLUSIONS: This study demonstrates the role of NMPs as carriers for contaminants, increasing their bioavailability and toxicity in terrestrial ecosystems. These findings have significant implications for ecosystem health and biodiversity.}, }
@article {pmid39849464, year = {2025}, author = {Qin, L and Lv, W}, title = {Dietary content and eating behavior in ulcerative colitis: a narrative review and future perspective.}, journal = {Nutrition journal}, volume = {24}, number = {1}, pages = {12}, pmid = {39849464}, issn = {1475-2891}, mesh = {Humans ; *Colitis, Ulcerative/physiopathology ; *Gastrointestinal Microbiome/physiology ; *Diet/methods ; *Feeding Behavior/physiology ; Dysbiosis ; Intestinal Mucosa ; Risk Factors ; }, abstract = {Ulcerative colitis (UC) has experienced a steady increase in global incidence and prevalence recently. Current research into UC pathogenesis focuses on the complex interplay of genetic and environmental factors with the immune system and gut microbiome, leading to disruption of the intestinal barrier. Normally, the microbiome, intestinal epithelium, and immune system interact to maintain intestinal homeostasis. However, when this equilibrium is disturbed, a harmful cycle of dysbiosis, immune dysregulation, and inflammation emerges, resulting in intestinal barrier dysfunction and UC progression. Among various risk factors, diet significantly influences epithelial barrier integrity and architectural stability through both direct and indirect mechanisms, shaping the entire UC continuum from pre-clinical prevention to active phase treatment and remission maintenance. This review provides insights into the impact of dietary content and eating behaviors on UC, focusing on specific food, food groups, nutrients, and intermittent fasting, while providing a detailed explanation of why the gut microbiota may mediate the sustained effects of diet across all stages of UC. Additionally, it addresses the limitations of current studies, explores underexamined areas in UC dietary research and proposes potential directions for future research and expansion.}, }
@article {pmid39849445, year = {2025}, author = {Xie, H and Chen, Z and Wu, G and Wei, P and Gong, T and Chen, S and Xu, Z}, title = {Application of metagenomic next-generation sequencing (mNGS) to describe the microbial characteristics of diabetic foot ulcers at a tertiary medical center in South China.}, journal = {BMC endocrine disorders}, volume = {25}, number = {1}, pages = {18}, pmid = {39849445}, issn = {1472-6823}, support = {[2021]76//the High-level Hospital and Clinical Specialty Discipline Construction Programme for Fujian Medical Development, China/ ; 2023J01692//Fujian Provincial Natural Science Foundation of China/ ; 2022J01243//Fujian Provincial Natural Science Foundation of China/ ; 2020Y9094//the Joint Funds for the innovation of science and Technology&#xff0c;Fujian province, China/ ; 2023Y9213//the Joint Funds for the innovation of science and Technology&#xff0c;Fujian province, China/ ; 2021Y9068//the Joint Funds for the innovation of science and Technology&#xff0c;Fujian province, China/ ; 82002034//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Diabetic Foot/microbiology/diagnosis ; China/epidemiology ; *High-Throughput Nucleotide Sequencing/methods ; *Tertiary Care Centers ; Male ; Female ; *Metagenomics/methods ; Middle Aged ; Aged ; Microbiota/genetics ; Adult ; }, abstract = {BACKGROUND: Diabetic foot ulcers (DFUs) are characterized by dynamic wound microbiome, the timely and accurate identification of pathogens in the clinic is required to initiate precise and individualized treatment. Metagenomic next-generation sequencing (mNGS) has been a useful supplement to routine culture method for the etiological diagnosis of DFUs. In this study, we utilized a routine culture method and mNGS to analyze the same DFU wound samples and the results were compared.<br><br>METHODS: Forty samples from patients with DFUs at a tertiary medical center in South China were collected, the microorganisms were identified with mNGS and routine culture method simultaneously.<br><br>RESULTS: The results showed that the positive detection rate of microorganisms in DFUs with mNGS was much higher (95% vs. 60%). Thirteen strains of microorganisms were detected with routine culture method, and seventy-seven strains were detected with mNGS. Staphylococcus aureus was the most common microorganism detected with culture method, while Enterococcus faecalis was the most common microorganism detected with mNGS. The false negative rate of the culture method was 35%, that was, 14 samples with negative results with culture method were found to be positive with mNGS.<br><br>CONCLUSION: The mNGS method had a higher positive detection rate and identified a broader spectrum of microorganisms in DFUs, thus, mNGS provided a more comprehensive understanding of the microbiome of DFUs to facilitate the development of timely and optimal treatment.<br><br>TRIAL REGISTRATION: The study was conducted in accordance with the Declaration of Helsinki and approved by the Ethical Review Committee of the Fujian Medical University Union Hospital (approval number 2021KY054).}, }
@article {pmid39849406, year = {2025}, author = {Iqbal, NT and Khan, H and Khalid, A and Mahmood, SF and Nasir, N and Khanum, I and de Siqueira, I and Van Voorhis, W}, title = {Chronic inflammation in post-acute sequelae of COVID-19 modulates gut microbiome: a review of literature on COVID-19 sequelae and gut dysbiosis.}, journal = {Molecular medicine (Cambridge, Mass.)}, volume = {31}, number = {1}, pages = {22}, pmid = {39849406}, issn = {1528-3658}, support = {3U01AI151698//Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases/ ; }, mesh = {Humans ; *COVID-19/immunology/complications ; *Dysbiosis ; *Gastrointestinal Microbiome ; *Post-Acute COVID-19 Syndrome ; *SARS-CoV-2/physiology ; *Brain-Gut Axis ; Inflammation ; }, abstract = {BACKGROUND: Long COVID or Post-acute sequelae of COVID-19 is an emerging syndrome, recognized in COVID-19 patients who suffer from mild to severe illness and do not recover completely. Most studies define Long COVID, through symptoms like fatigue, brain fog, joint pain, and headache prevailing four or more weeks post-initial infection. Global variations in Long COVID presentation and symptoms make it challenging to standardize features of Long COVID. Long COVID appears to be accompanied by an auto-immune multi-faceted syndrome where the virus or viral antigen persistence causes continuous stimulation of the immune response, resulting in multi-organ immune dysregulation.<br><br>MAIN TEXT: This review is focused on understanding the risk factors of Long COVID with a special emphasis on the dysregulation of the gut-brain axis. Two proposed mechanisms are discussed here. The first mechanism is related to the dysfunction of angiotensin-converting enzyme 2 receptor due to Severe Acute Respiratory Syndrome Corona Virus 2 infection, leading to impaired mTOR pathway activation, reduced AMP secretion, and causing dysbiotic changes in the gut. Secondly, gut-brain axis dysregulation accompanied by decreased production of short-chain fatty acids, impaired enteroendocrine cell function, and increased leakiness of the gut, which favors translocation of pathogens or lipopolysaccharide in circulation causing the release of pro-inflammatory cytokines. The altered Hypothalamic-Pituitary-Adrenal axis is accompanied by the reduced level of neurotransmitter, and decreased stimulation of the vagus nerve, which may cause neuroinflammation and dysregulation of serum cortisol levels. The dysbiotic microbiome in Long COVID patients is characterized by a decrease in beneficial short chain fatty acid-producing bacteria (Faecalibacterium, Ruminococcus, Dorea, and Bifidobacterium) and an increase in opportunistic bacteria (Corynebacterium, Streptococcus, Enterococcus). This dysbiosis is transient and may be impacted by interventions including probiotics, and dietary supplements.<br><br>CONCLUSIONS: Further studies are required to understand the geographic variation, racial and ethnic differences in phenotypes of Long COVID, the influence of viral strains on existing and emerging phenotypes, to explore long-term effects of gut dysbiosis, and gut-brain axis dysregulation, as well as the potential role of diet and probiotics in alleviating those symptoms.}, }
@article {pmid39849320, year = {2025}, author = {Taba, N and Fischer, K and Estonian Biobank Research Team,  and Org, E and Aasmets, O}, title = {A novel framework for assessing causal effect of microbiome on health: long-term antibiotic usage as an instrument.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2453616}, doi = {10.1080/19490976.2025.2453616}, pmid = {39849320}, issn = {1949-0984}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Estonia ; Irritable Bowel Syndrome/microbiology/drug therapy ; Depression/microbiology ; Microbiota/drug effects ; }, abstract = {Assessing causality is undoubtedly one of the key questions in microbiome studies for the upcoming years. Since randomized trials in human subjects are often unethical or difficult to pursue, analytical methods to derive causal effects from observational data deserve attention. As simple covariate adjustment is not likely to account for all potential confounders, the idea of instrumental variable (IV) analysis is worth exploiting. Here we propose a novel framework of antibiotic instrumental variable regression (AB-IVR) for estimating the causal relationships between microbiome and various diseases. We rely on the recent studies showing that antibiotic treatment has a cumulative long-term effect on the microbiome, resulting in individuals with higher antibiotic usage to have a more perturbed microbiome. We apply the AB-IVR method on the Estonian Biobank data and show that the microbiome has a causal role in numerous diseases including migraine, depression and irritable bowel syndrome. We show with a plethora of sensitivity analyses that the identified causal effects are robust and propose ways for further methodological developments.}, }
@article {pmid39849235, year = {2025}, author = {Scholz, KJ and Höhne, A and Wittmer, A and Häcker, G and Hellwig, E and Cieplik, F and Waidner, B and Al-Ahmad, A}, title = {Co-culture of Helicobacter pylori with oral microorganisms in human saliva.}, journal = {Clinical oral investigations}, volume = {29}, number = {1}, pages = {79}, pmid = {39849235}, issn = {1436-3771}, mesh = {Humans ; *Saliva/microbiology ; *Helicobacter pylori/isolation &amp; purification ; *Coculture Techniques ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Candida/isolation &amp; purification ; Actinomyces/isolation &amp; purification ; Streptococcus mutans/isolation &amp; purification ; Mouth/microbiology ; Colony Count, Microbial ; Streptococcus/isolation &amp; purification ; }, abstract = {OBJECTIVE: Helicobacter pylori is known for colonizing the gastric mucosa and instigating severe upper gastrointestinal diseases such as gastritis, gastroduodenal ulcers, and gastric cancer. To date, there is no data available on the oral cavity as transmission site, whether H. pylori can survive in the oral cavity or in human saliva. The aim of the study was to investigate the influence of oral microorganisms and human saliva on the survival of H. pylori in human saliva.<br><br>METHODS: H. pylori strains KE, a motile derivate of type strain H. pylori 26695, and H. pylori SS1, a clinical isolate from a gastric biopsy, were grown in human pooled saliva (pooled from 4 healthy human donors, 0.22&#xa0;&#x3bc;m filter-sterilized) or in BBF (Brucella browth formula; control) either as mono-cultures or in co-culture with Streptococcus mutans, Streptococcus oralis, Actinomyces naeslundii, Lacticaseibacillus casei and Candida dubliniensis. Bacterial survival of H. pylori and the oral microorganisms were investigated using colony forming units (CFU) assay and MALDI-TOF MS at baseline and after 24, 48 and 168&#xa0;h.<br><br>RESULTS: In saliva, H. pylori KE demonstrated enhanced survival in co-culture with S. mutans, A. naeslundii, and C. dubliniensis, enduring for at least 48&#xa0;h. In contrast, L. casei and S. oralis inhibited H. pylori KE in saliva. H. pylori KE could not be cultured after 168&#xa0;h in saliva, neither in mono- nor co-culture. In contrast, H. pylori SS1 in saliva could be cultured after 168&#xa0;h in co-culture with S. mutans and C. dubliniensis, but not in mono-culture. In BBF, H. pylori KE could be cultured after 168&#xa0;h with S. mutans, L. casei and C. dubliniensis, and H. pylori SS1 with L. casei and C. dubliniensis, but not with S. mutans. Notably, the co-cultured microorganisms survived at high CFU numbers similar to those of the monocultures.<br><br>CONCLUSION: The study suggests that H. pylori can transiently survive in human saliva and even with presence of certain oral microorganisms. However, it may not be a permanent resident of the oral microbiota. The co-survival with oral microorganisms emphasizes the necessity for studying the role of the oral microbiota in the infectious and transmission cycle of H. pylori.}, }
@article {pmid39849165, year = {2025}, author = {Sandhu, S and Kumar, S and Singh, P and Singh, BP and Jurel, SK and Lal, N and Mohit,  and Sharma, V and Rai, N and Chand, P}, title = {Metagenomic profiling of plaque microbiota in Indian subjects: identified hidden ecological tapestry.}, journal = {Current genetics}, volume = {71}, number = {1}, pages = {3}, pmid = {39849165}, issn = {1432-0983}, mesh = {Humans ; *Dental Plaque/microbiology ; *Metagenomics/methods ; Male ; *Microbiota/genetics ; Female ; India/epidemiology ; Adult ; *Metagenome ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; Young Adult ; Adolescent ; Bacteria/genetics/classification/isolation &amp; purification ; Streptococcus/genetics/isolation &amp; purification/classification ; }, abstract = {Dental plaque biofilms are the primary etiologic factor for various chronic oral infectious diseases. In recent years, dental plaque shows enormous potential to know about an individual microbiota. Various microbiome studies of oral cavity from different geographical locations reveals abundance of microbial species. Although, the representation of Indian population in this respect is limited, which make us curious to undergo this study. This study investigates the dental plaque microbiota of North Indian individuals based on their age, gender, and dietary patterns; specifically, food preference and availability of water source using 16 S rRNA metagenomics analysis. The findings from this study revealed that Streptococcus levels are high across genders, age groups, and water source, highlighting its role as a predominant dental caries associated species like Streptococcus mutans, Streptococcus pyogenes, Streptococcus sobrinus and Streptococcus oralis in the studied population groups. Additionally, the abundance of Actinomyces is observed higher in young individuals and females whereas Fusobacterium and Leptotrichia were high in elderly individuals. Moreover, non-vegetarians have higher abundance of Streptococcus and Fusobacterium, whereas vegetarians show higher abundance of Prevotella and Leptotrichia. The study also highlights the influence of water type on bacterial composition of dental plaque in the studied population i.e., individuals consuming underground water has high abundance of Streptococcus, whereas individuals consuming RO water exhibit elevated Prevotella and Leptotrichia. Insights emerged from the analysis illuminates the complex dynamics of microbiota in dental plaque among North Indians. This study also highlight that this variation of microbiome is influenced by age, gender, and dietary habits (vegetarian or non-vegetarian lifestyle). These results will fill a significant knowledge gap regarding the Indian dental plaque microbiome but also offer a foundation to conduct metagenome studies and potential therapeutic implications for future personalized oral health interventions.}, }
@article {pmid39848958, year = {2025}, author = {Escobar Marcillo, DI and Privitera, GF and Rollo, F and Latini, A and Giuliani, E and Benevolo, M and Giuliani, M and Pichi, B and Pellini, R and Donà, MG}, title = {Microbiome analysis in individuals with human papillomavirus oral infection.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2953}, pmid = {39848958}, issn = {2045-2322}, mesh = {Humans ; *Microbiota ; *Papillomavirus Infections/virology/microbiology ; Female ; Male ; Adult ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; HIV Infections/microbiology/virology/complications ; Mouth/microbiology/virology ; Papillomaviridae/genetics/isolation &amp; purification ; Bacteria/genetics/classification/isolation &amp; purification ; Human Papillomavirus Viruses ; }, abstract = {Microbiome gained attention as a cofactor in cancers originating from epithelial tissues. High-risk (hr)HPV infection causes oropharyngeal squamous cell carcinoma but only in a fraction of hrHPV+ individuals, suggesting that other factors play a role in cancer development. We investigated oral microbiome in cancer-free subjects harboring hrHPV oral infection (n = 33) and matched HPV- controls (n = 30). DNA purified from oral rinse-and-gargles of HIV-infected (HIV+) and HIV-uninfected (HIV-) individuals were used for 16S rRNA gene V3-V4 region amplification and sequencing. Analysis of differential microbial abundance and differential pathway abundance was performed, separately for HIV+ and HIV- individuals. Significant differences in alpha (Chao-1 and Shannon indices) and beta diversity (unweighted UniFrac distance) were observed between hrHPV+ and HPV-negative subjects, but only for the HIV- individuals. Infection by hrHPVs was associated with significant changes in the abundance of Saccharibacteria in HIV+ and Gracilibacteria in HIV- subjects. At the genus level, the greatest change in HIV+ individuals was observed for Bulleidia, which was significantly enriched in hrHPV+ subjects. In HIV- individuals, those hrHPV+ showed a significant enrichment of Parvimonas and depletion of Alloscardovia. Our data suggest a possible interplay between hrHPV infection and oral microbiome, which may vary with the HIV status.}, }
@article {pmid39848913, year = {2025}, author = {McLean, H and Mikaberidze, A and Deakin, G and Xu, X and Papp-Rupar, M}, title = {The interplay between scion genotype, root microbiome, and Neonectria ditissima apple canker.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf014}, pmid = {39848913}, issn = {1574-6941}, abstract = {Severity of European apple canker caused by Neonectria ditissima can vary between locations and apple genotypes. We investigated how location, cold storage/planting season, and apple scion genotype affect root-associated microbial communities. Additionally, we investigated whether differences in abundance of specific taxa could be associated with canker lesion counts. Seven scion cultivars grafted onto M9 rootstocks were inoculated with N. ditissima in the nursery and then planted in December 2018 or stored at 2 °C until planting in April 2019 at three sites in Kent, UK. We assessed canker lesions and collected root samples in June 2021. Quantitative PCR and 16S/ITS amplicon sequencing was used to analyse microbial communities. Site was the primary factor affecting microbiome size, diversity, and composition. Cold storage/planting season had small but significant effects, indicating that differences in the microbiome at planting can persist long-term. Scion genotype had a limited effect on diversity but did influence the abundance of specific root associated taxa. Bacterial α-diversity was associated with canker count in a site-dependent manner. Increased abundances of particular fungal (Rhizophagus irregularis and Epicoccum nigrum) and bacterial (Amycolatopsis and Bradyrhizobium) root associated taxa were associated with fewer cankers.}, }
@article {pmid39848566, year = {2025}, author = {Olesen, CM and Edslev, SM and Aasbjerg, GN and Yüksel, YT and Agner, T and Kamstrup, MR}, title = {Subtype specific alterations in the skin microbiome of patients with cutaneous T-cell lymphoma.}, journal = {The Journal of investigative dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jid.2025.01.009}, pmid = {39848566}, issn = {1523-1747}, }
@article {pmid39848564, year = {2025}, author = {Lewis, N and Villani, A and Lagopoulos, J}, title = {Gut dysbiosis as a driver of neuroinflammation in attention-deficit/hyperactivity disorder: A review of current evidence.}, journal = {Neuroscience}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.neuroscience.2025.01.031}, pmid = {39848564}, issn = {1873-7544}, abstract = {There is mounting evidence for the involvement of the immune system, neuroinflammation and disturbed gut microbiota, or dysbiosis, in attentive-deficit/hyperactivity disorder (ADHD). Gut dysbiosis is strongly implicated in many physical, autoimmune, neurological, and neuropsychiatric conditions, however knowledge of its particular pathogenic role in ADHD is sparse. As such, this narrative review examines and synthesizes the available evidence related to inflammation, dysbiosis, and neural processes in ADHD. Minimal differences in microbiota diversity measures between cases and controls were found, however many relative abundance differences were observed at all classification levels (phylum to strain). Compositional differences of taxa important to key gut-brain axis pathways, in particular Bacteroides species and Faecalibacterium, may contribute to inflammation, brain functioning differences, and symptoms, in ADHD. We have identified one possible model of ADHD etiopathogenesis involving systemic inflammation, an impaired blood-brain barrier, and neural disturbances as downstream consequences of gut dysbiosis. Nevertheless, studies conducted to date have varied degrees of methodological rigour and involve diverse participant characteristics and analytical techniques, highlighting a need for additional research.}, }
@article {pmid39848413, year = {2025}, author = {Koszła, O and Kukula-Koch, W and Jóźwiak, K and Jastrząb, R and Marć, MA and Mytych, J and Tabęcka-Łonczyńska, A and Skóra, B and Szychowski, KA and Sołek, P}, title = {Biotransformation of Ganoderma lucidum and Hericium erinaceus for ex vivo gut-brain axis modulation and mood-related outcomes in humans: CREB/BDNF signaling and microbiota-driven synergies.}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {119393}, doi = {10.1016/j.jep.2025.119393}, pmid = {39848413}, issn = {1872-7573}, abstract = {BACKGROUND: The human gut microbiota plays a crucial role in various aspects of health, extending beyond digestion and nutrient absorption. Ganoderma lucidum (Reishi) and Hericium erinaceus (Lion's Mane), traditional medicinal mushrooms, have garnered interest due to their potential to exert positive health effects. The aim of our study was to investigate the molecular impact of Reishi and Lion's Mane on mood regulation through the gut-brain axis.<br><br>METHODS: We utilized a dynamic simulator of the human intestinal microbial ecosystem (SHIME), followed by HPLC-ESI-QTOF-MS/MS and a series of biochemical and molecular assays, including MTT for cell viability, fluorogenic probes for redox balance (ROS and GSH), and Western blot for protein analysis.<br><br>RESULTS: Chromatographic analysis confirmed the presence of bioactive compounds in both mushrooms, including triterpenoids (ganoderic acids) and polysaccharides in G. lucidum, as well as hericenones and erinacines in H. erinaceus. We observed concentration-dependent changes in metabolic activity and redox balance due to microbiome cell-free supernatant treatment (M-CFSs). M-CFSs also influenced the Nrf2 pathway and activated heat shock proteins, which may confer neuroprotective effects. Notably, M-CFSs upregulated neurotrophic factors such as BDNF, CDNF, and MANF, crucial for neuronal function. Our study revealed alterations in intracellular signaling cascades, most notably the CREB/BDNF pathway. Moreover, the Akt/mTOR and ERK1/2 showed no significant changes, while Akt/GSK3&#x3b1;/&#x3b2; displayed only partial modifications. The overlapping effects of synaptic activity and activation of the gut-brain axis appear to contribute to mood enhancement.<br><br>CONCLUSIONS: These pilot findings suggest a potential role for G. lucidum and H. erinaceus in mood disorder regulation through multifaceted mechanisms involving the gut microbiota. The study underscores the importance of understanding the synergistic interactions between medicinal fungi, gut microbiota, and neural processes to develop novel or preventive strategies for mental health disorders.}, }
@article {pmid39848248, year = {2025}, author = {Abdill, RJ and Graham, SP and Rubinetti, V and Ahmadian, M and Hicks, P and Chetty, A and McDonald, D and Ferretti, P and Gibbons, E and Rossi, M and Krishnan, A and Albert, FW and Greene, CS and Davis, S and Blekhman, R}, title = {Integration of 168,000 samples reveals global patterns of the human gut microbiome.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2024.12.017}, pmid = {39848248}, issn = {1097-4172}, abstract = {The factors shaping human microbiome variation are a major focus of biomedical research. While other fields have used large sequencing compendia to extract insights requiring otherwise impractical sample sizes, the microbiome field has lacked a comparably sized resource for the 16S rRNA gene amplicon sequencing commonly used to quantify microbiome composition. To address this gap, we processed 168,464 publicly available human gut microbiome samples with a uniform pipeline. We use this compendium to evaluate geographic and technical effects on microbiome variation. We find that regions such as Central and Southern Asia differ significantly from the more thoroughly characterized microbiomes of Europe and Northern America and that composition alone can be used to predict a sample's region of origin. We also find strong associations between microbiome variation and technical factors such as primers and DNA extraction. We anticipate this growing work, the Human Microbiome Compendium, will enable advanced applied and methodological research.}, }
@article {pmid39848238, year = {2025}, author = {Szajewska, H}, title = {An Overview of Early-Life Gut Microbiota Modulation Strategies.}, journal = {Annals of nutrition &amp; metabolism}, volume = {}, number = {}, pages = {1-6}, doi = {10.1159/000541492}, pmid = {39848238}, issn = {1421-9697}, abstract = {BACKGROUND: The gut microbiota, or microbiome, is essential for human health. Early-life factors such as delivery mode, diet, and antibiotic use shape its composition, impacting both short- and long-term health outcomes. Dysbiosis, or alterations in the gut microbiota, is linked to conditions such as allergies, asthma, obesity, diabetes, inflammatory bowel disease, and necrotizing enterocolitis in preterm infants.<br><br>SUMMARY: This article reviews current strategies to influence the early-life gut microbiome and their potential health impacts. It also briefly summarizes guidelines on using biotics for gastrointestinal and allergic diseases in children. Key strategies include vaginal or fecal microbiota transplantation for cesarean-born infants, breastfeeding, and biotic-supplemented formulas. While vaginal microbial transfer and maternal fecal microbiota transplantation show short-term benefits, further research is needed to determine long-term safety and efficacy. Breast milk, rich in human milk oligosaccharides, promotes a healthy microbiota and offers protection against infections. Biotic-supplemented formulas can improve the gut microbiota in formula-fed infants and show clinical effects, though each biotic must be evaluated separately. Probiotics given as dietary supplements outside of infant formulas show promise for treating gastrointestinal disorders but require further investigation.}, }
@article {pmid39848217, year = {2025}, author = {Arya, S and George, AB and O'Dwyer, J}, title = {The architecture of theory and data in microbiome design: towards an S-matrix for microbiomes.}, journal = {Current opinion in microbiology}, volume = {83}, number = {}, pages = {102580}, doi = {10.1016/j.mib.2025.102580}, pmid = {39848217}, issn = {1879-0364}, abstract = {Designing microbiomes for applications in health, bioengineering, and sustainability is intrinsically linked to a fundamental theoretical understanding of the rules governing microbial community assembly. Microbial ecologists have used a range of mathematical models to understand, predict, and control microbiomes, ranging from mechanistic models, putting microbial populations and their interactions as the focus, to purely statistical approaches, searching for patterns in empirical and experimental data. We review the success and limitations of these modeling approaches when designing novel microbiomes, especially when guided by (inevitably) incomplete experimental data. Although successful at predicting generic patterns of community assembly, mechanistic and phenomenological models tend to fall short of the precision needed to design and implement specific functionality in a microbiome. We argue that to effectively design microbiomes with optimal functions in diverse environments, ecologists should combine data-driven techniques with mechanistic models - a middle, third way for using theory to inform design.}, }
@article {pmid39847963, year = {2025}, author = {Wang, S and Wang, Z and Wang, N and Wang, S and Zeng, S and Xu, Z and Liu, D and Zhao, X and Liu, F and Xu, J and Cai, Y and Ying, H}, title = {Efficient conversion of corn straw to feed protein through solid-state fermentation using a thermophilic microbial consortium.}, journal = {Waste management (New York, N.Y.)}, volume = {194}, number = {}, pages = {298-308}, doi = {10.1016/j.wasman.2025.01.023}, pmid = {39847963}, issn = {1879-2456}, abstract = {Solid-state fermentation of lignocellulosic waste to produce feed protein is a means of realising solid waste. However, low efficiency and susceptibility to microbial contamination remain significant challenges in feed protein production through room-temperature solid-state fermentation. In this study, thermophilic microbiomes were enriched. After adaptive and nitrogen acclimation, microbiomes with the combined functions of 'thermophilic-rapid decomposition-nitrogen conversion' were obtained and used for feed protein production. High-throughput sequencing and Kyoto Encyclopedia of Genes and Genomes metabolic pathway prediction techniques were used to assess the mechanisms underlying microbial involvement in substance conversion. The results showed that the microbiomes decomposed 78.21 %-81.73 % of straw within 7 days. After nitrogen acclimation, the nitrogen utilisation rate and the true protein content of the microbiomes improved by 19.22 %-26.96 % and 56.14 %-71.99 %, respectively. Fed-batch enzymatic saccharification and fermentation reduced the fermentation time by 28.5 %. Domesticated microbiomes increased the abundance of bacteria and fungi in the fermentation system, enhancing carbon metabolism and the urea cycle. This study presents a novel approach for the high-value utilisation of lignocellulose waste.}, }
@article {pmid39847933, year = {2025}, author = {Malla, MA and Nomalihle, M and Featherston, J and Kumar, A and Amoah, ID and Ismail, A and Bux, F and Kumari, S}, title = {Comprehensive profiling and risk assessment of antibiotic resistomes in surface water and plastisphere by integrated shotgun metagenomics.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137180}, doi = {10.1016/j.jhazmat.2025.137180}, pmid = {39847933}, issn = {1873-3336}, abstract = {The ever-increasing microplastics (MPs) and antibiotic-resistance genes (ARGs) in aquatic ecosystems has become a serious global challenging issue. However, the impact of different pollution sources on microbiome and antibiotic resistome in surface water (SW) and plastisphere (PS) remains largely elusive. Here, shotgun metagenomics was used to analyze microbiome structure and antibiotic resistome in SW and PS under the influence of different pollution sources. Pseudomonas were the most abundant genus, followed by Flavobacterium, Acinetobacter, Acidovorax, and Limnohabitans. However, their relative abundance varied significantly both across the sampling sites and habitats i.e. SW and PS (p < 0.05). Additionally, various ARGs were detected in SW and PS, with PS (372) having significantly more potential ARGs than SW (293). The results further showed significant variations in the relative abundance of potential pathogenic bacteria across the sampling sites and habitats (p < 0.05). Further moreover, significant differences were observed in antibiotic resistome risk scores, ARGs and MGEs across different habitats. Over all, this study suggests that pollution source and water quality parameters had a significant impact on microbiome composition and antibiotic resistome in SW and PS.}, }
@article {pmid39847486, year = {2025}, author = {Xu, H and Jia, Z and Liu, J and Liu, R and Wei, W and Li, X}, title = {Protocol for correlating the gut microbiome and metabolomics in patients with intracranial aneurysms.}, journal = {STAR protocols}, volume = {6}, number = {1}, pages = {103582}, doi = {10.1016/j.xpro.2024.103582}, pmid = {39847486}, issn = {2666-1667}, abstract = {Gut-microbiome-combined metabolomics studies in cerebrovascular disease highlight the microbiota-gut-brain axis in neurological disorders. Here, we present a protocol for correlating the gut microbiome and metabolomics in patients with intracranial aneurysms. We describe steps for sample collection, fecal genomic DNA extraction, rRNA PCR amplification, sequencing library construction, and rRNA sequencing. We then detail procedures for metabolite extraction, liquid chromatography-tandem mass spectrometry (LC-MS/MS) non-targeted metabolomics sequencing, and ELISA for cerebrospinal fluid and plasma samples. Finally, we perform combined multi-omics analysis. For complete details on the use and execution of this protocol, please refer to Xu et al.[1].}, }
@article {pmid39846984, year = {2025}, author = {Chung, V and Alistar, A and Becerra, C and Kasi, A and Borazanci, E and Jameson, GS and Roe, DJ and Wertheim, BC and Cridebring, D and Truitt, M and Downes, M and Barrett, MT and Korn, R and Lee, K and Han, H and Evans, R and Von Hoff, DD}, title = {Pembrolizumab ± paricalcitol in metastatic pancreatic cancer postmaximal cytoreduction.}, journal = {The oncologist}, volume = {30}, number = {1}, pages = {}, doi = {10.1093/oncolo/oyae323}, pmid = {39846984}, issn = {1549-490X}, support = {SU2C-AACR-CT03-16//AACR/ ; //Merck Sharp &amp; Dohme LLC/ ; //Merck &amp; Co., Inc/ ; }, mesh = {Humans ; *Ergocalciferols/pharmacology/therapeutic use/administration &amp; dosage ; *Pancreatic Neoplasms/drug therapy/pathology ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology ; Male ; Female ; Middle Aged ; Aged ; Double-Blind Method ; Cytoreduction Surgical Procedures/methods ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology ; Neoplasm Metastasis ; Adult ; }, abstract = {LESSONS LEARNED: Intravenous paricalcitol did not improve the efficacy of pembrolizumab, likely related to the short half-life.<br><br>BACKGROUND: Immunotherapy has limited benefit in the treatment of advanced pancreatic cancer with the tumor microenvironment playing a key role in immune resistance. In preclinical studies, vitamin D receptor (VDR) agonists have been shown to sensitize pancreatic tumors to PD-1 blockade.<br><br>METHODS: This was a randomized, double-blinded, placebo-controlled, phase II trial to evaluate pembrolizumab with or without paricalcitol as maintenance therapy for patients with metastatic pancreatic ductal adenocarcinoma (PDAC). Participants were &#x2265;18 years; histologically or cytologically confirmed metastatic PDAC showing no disease progression after frontline systemic therapy, and achieving maximal cytoreduction (eg, with no further antitumor effect), Eastern Cooperative Oncology Group (ECOG) status of 0 or 1; adequate organ function. Study treatment included: pembrolizumab 200&#xa0;mg IV every 3 weeks and either paricalcitol 25 mcg IV 3 times per week or placebo. The primary objective was to evaluate 6-month progression free survival (PFS). Secondary objectives include evaluating the toxicity of the combination and overall survival (OS).<br><br>RESULTS: There was no significant difference in 6-month PFS, median PFS, median OS, nor treatment-related AEs between the 2 arms.<br><br>CONCLUSIONS AND RELEVANCE: Paricalcitol did not improve the efficacy of pembrolizumab likely related to its short half-life of only 5-7 hours. Microbiome analysis revealed significant difference between long-term (>12 weeks) and short-term (<12 weeks) survival groups across treatment arms. Modulation of the tumor microenvironment will likely require more sustained VDR activity.<br><br>TRIAL REGISTRATION: Clinicaltrials.gov, ID: NCT03331562.}, }
@article {pmid39846747, year = {2025}, author = {Godsil, M and Ritz, NL and Venkatesh, S and Meeske, AJ}, title = {Gut phages and their interactions with bacterial and mammalian hosts.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0042824}, doi = {10.1128/jb.00428-24}, pmid = {39846747}, issn = {1098-5530}, abstract = {The mammalian gut microbiome is a dense and diverse community of microorganisms that reside in the distal gastrointestinal tract. In recent decades, the bacterial members of the gut microbiome have been the subject of intense research. Less well studied is the large community of bacteriophages that reside in the gut, which number in the billions of viral particles per gram of feces, and consist of considerable unknown viral "dark matter." This community of gut-residing bacteriophages, called the gut "phageome," plays a central role in the gut microbiome through predation and transformation of native gut bacteria, and through interactions with their mammalian hosts. In this review, we will summarize what is known about the composition and origins of the gut phageome, as well as its role in microbiome homeostasis and host health. Furthermore, we will outline the interactions of gut phages with their bacterial and mammalian hosts, and plot a course for the mechanistic study of these systems.}, }
@article {pmid39846536, year = {2024}, author = {Hao, N and Zhang, H and Jia, H and Zhao, Y and Li, J and Feng, X and Tang, B and Zhao, B and Liu, Y}, title = {Residual Dynamics of Chlorantraniliprole and Fludioxonil in Soil and Their Effects on the Microbiome.}, journal = {Journal of xenobiotics}, volume = {15}, number = {1}, pages = {}, doi = {10.3390/jox15010004}, pmid = {39846536}, issn = {2039-4713}, support = {2023YFD1400104//National Key Research and Development Program of China/ ; }, abstract = {The increased use of chlorantraniliprole and fludioxonil has sparked concerns about their residues and impact on the soil microbiome, highlighting an urgent issue requiring attention. This study investigates the residue dynamics of corn after chlorantraniliprole and fludioxonil treatments, as well as their effects on soil enzyme activity and microbial community structure. High-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) analysis showed a significant decrease in chlorantraniliprole and fludioxonil residues in the soil after combined application, especially with chlorantraniliprole. This application caused a temporary reduction in urease and sucrase activities. Furthermore, high-throughput sequencing of the soil microbiome revealed a decrease in the relative abundance of Talaromyces during fludioxonil application, while Mortierela and Gibberella increased. Additionally, Vicianmibacteraceae and Vicianminbactererales saw significant increases after chlorantraniliprole application. The combined application of chlorantraniliprole and fludioxonil not only decreased the population of harmful microorganisms but also lowered residue levels in the soil when compared to individual applications. This ultimately enhanced the efficacy of control measures and promoted environmental compatibility.}, }
@article {pmid39846512, year = {2025}, author = {Wang, S and Wang, X and Liu, Y and Yao, Q}, title = {Single and Synergistic Effects of Microplastics and Difenoconazole on Oxidative Stress, Transcriptome, and Microbiome Traits in Honey Bees.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.4c09141}, pmid = {39846512}, issn = {1520-5118}, abstract = {Microplastics (MPs) and pesticides are identified as two environmental pollutants. In the present study, we showed evidence of toxic effects on honey bees from chronic oral exposure to food containing difenoconazole alone (Dif) and in a binary mixture with polystyrene (PS)-MPs (Dif + PS). We observed a disrupted gut microbial community structure in bees after difenoconazole exposure, and the gut microbiota structure richness increased at the phylum and genus levels in Dif + PS group. Transcriptomic analysis revealed that difenoconazole exposure caused 98 differentially expressed genes (DEGs), while 41 DEGs were identified in Dif + PS group. PS-MPs seemed to mitigate oxidative damage and changes in the transcriptome profile in honey bees caused by difenoconazole to some extent. However, coexposure increased the disordered microbial community composition. Our study highlights the importance of investigating possible additive and synergic activities between stressors to comprehensively understand the effects of pollutants on pollinating insects.}, }
@article {pmid39846370, year = {2025}, author = {Chen, X and Guo, X}, title = {Microbiome analysis reveals the potential mechanism of herbal sitz bath complementary therapy in accelerating postoperative recovery from perianal abscesses.}, journal = {IET systems biology}, volume = {19}, number = {1}, pages = {e12114}, doi = {10.1049/syb2.12114}, pmid = {39846370}, issn = {1751-8857}, support = {2018-2020:TCM Advantage Disease Cultivation and Co//Shanghai Three-Year Action Plan for Further Accelerating the Development of Traditional Chinese Medicine/ ; JSKJ-KTZY-2021-04//Shanghai Jinshan District health special project support/ ; }, mesh = {Humans ; *Abscess/microbiology/drug therapy/therapy ; Male ; *Microbiota/drug effects ; Female ; Middle Aged ; Adult ; Wound Healing/drug effects ; Complementary Therapies/methods ; Anus Diseases/microbiology/drug therapy/surgery ; RNA, Ribosomal, 16S/genetics ; Baths ; }, abstract = {The herbal sitz bath formula, as a complementary therapy, effectively alleviates postoperative wound pain and accelerates healing time in patients with perianal abscesses. To investigate its mechanism of action, this study conducted 16S rRNA gene sequencing and bioinformatics analysis on wound exudate samples from patients after perianal abscess surgery. Patients were randomly divided into two groups: one receiving the herbal sitz bath as an adjunctive therapy and the other without this adjunctive therapy. Samples were collected on the first and eighth days after surgery to compare the differences in microbial community composition between the two groups on the eighth day and between the first and eighth days within each group. The study revealed that the herbal sitz bath significantly altered the structure of the microbial community, increasing its diversity and abundance. By reducing Enterococcus and increasing Bifidobacterium, Faecalibacterium, and Ruminococcus, the therapy enhanced the wound's anti-infective capacity and accelerated healing. This study explored the potential mechanism of the herbal sitz bath formula as an adjunctive therapy in promoting postoperative recovery from perianal abscesses, providing valuable data for further research on the role of microorganisms in wound care. These findings contribute to optimising postoperative treatment regimens and facilitating patient recovery.}, }
@article {pmid39846192, year = {2025}, author = {Yu, W and Yang, J and Teng, LW and Zhao, XL and Zhu, ZY and Cui, S and Du, WG and Liu, ZS and Zeng, ZG}, title = {Reciprocal translocation experiments reveal gut microbiome plasticity and host specificity in a Qinghai-Xizang Plateau lizard.}, journal = {Zoological research}, volume = {46}, number = {1}, pages = {139-151}, doi = {10.24272/j.issn.2095-8137.2024.284}, pmid = {39846192}, issn = {2095-8137}, mesh = {Animals ; *Lizards/microbiology/physiology ; *Gastrointestinal Microbiome/physiology ; *Altitude ; Female ; China ; Host Specificity ; }, abstract = {Animal adaptation to environmental challenges is a complex process involving intricate interactions between the host genotype and gut microbiome composition. The gut microbiome, highly responsive to external environmental factors, plays a crucial role in host adaptability and may facilitate local adaptation within species. Concurrently, the genetic background of host populations influences gut microbiome composition, highlighting the bidirectional relationship between host and microbiome. Despite this, our understanding of gut microbiome plasticity and its role in host adaptability remains limited, particularly in reptiles. To clarify this issue, we conducted a reciprocal translocation experiment with gravid females of the Qinghai toad-headed lizards (Phrynocephalus vlangalii) between high-altitude (2 600 m a.s.l.) and superhigh-altitude (3 600 m a.s.l.) environments on Dangjin Mountain of the Qinghai-Xizang Plateau, China. One year later, we assessed the phenotypes and gut microbiomes of their offspring. Results revealed significant plasticity in gut microbiome diversity and structure in response to contrasting elevations. High-altitude conditions increased diversity, and maternal effects appeared to enable high-altitude lizards to maintain elevated diversity when exposed to superhigh-altitude environments. Additionally, superhigh-altitude lizards displayed distinct gut microbiome structures with notable host specificity, potentially linked to their lower growth rates. Overall, these findings underscore the importance of the gut microbiome in facilitating reptilian adaptation to rapid environmental changes across altitudinal gradients. Furthermore, this study provides critical insights into microbial mechanisms underpinning local adaptation and adaptative plasticity, offering a foundation for future research on host-microbiome interactions in evolutionary and ecological contexts.}, }
@article {pmid39846059, year = {2025}, author = {Cyphert, EL and Clare, S and Dash, A and Nixon, JC and Raphael, J and Harrison, J and Heilbronner, A and Kim, HJ and Cunningham, M and Lebl, D and Schwab, F and Hernandez, CJ and Stein, EM}, title = {A Pilot Study of the Gut Microbiota in Spine Fusion Surgery Patients.}, journal = {HSS journal : the musculoskeletal journal of Hospital for Special Surgery}, volume = {21}, number = {1}, pages = {65-72}, pmid = {39846059}, issn = {1556-3316}, abstract = {BACKGROUND: The microbiome has been identified as a contributor to bone quality. As skeletal health is critical to success of orthopedic surgery, the gut microbiome may be a modifiable factor associated with postoperative outcomes. For spine fusion surgery in particular, de novo bone formation and sufficient bone mineral density are essential for successful outcomes. Given the prevalence and complexity of these procedures, the identification of novel factors that may be related to operative success is important.<br><br>QUESTIONS/PURPOSES: We sought to investigate how the composition of the microbiota related to bone health in a focused spinal fusion surgery cohort.<br><br>METHODS: We investigated the composition of the microbiome in a cohort of 31 patients prior to spinal fusion surgery, as well as changes in the microbiome over 6 weeks postoperatively. Preoperative areal bone mineral density (BMD) was measured by dual-energy X-ray absorptiometry.<br><br>RESULTS: Composition of gut microbiota differed among spinal fusion patients with low bone mass (T-score &#x2264; -1.0) and those with normal BMD (P = .03). There was no significant change in composition of the gut microbiota between preoperative evaluation and 6 weeks postoperatively.<br><br>CONCLUSIONS: Our findings in this small sample suggest there may be a relationship between BMD and composition of the gut microbiome in patients who undergo spinal fusion surgery. Further work is needed to investigate these relationships as well as potential interventions to foster a favorable microbial composition in spinal fusion surgery patients.}, }
@article {pmid39846052, year = {2025}, author = {Kortright-Maldonado, K and Reyes-Torres, BE and Cabrera-Lopez, LS and Rodríguez-Henríquez, P and Tenorio-Aguirre, EK and Martínez-Sánchez, FD}, title = {Navigating antiphospholipid syndrome: from personalized therapies to cutting-edge research.}, journal = {Rheumatology advances in practice}, volume = {9}, number = {1}, pages = {rkaf005}, pmid = {39846052}, issn = {2514-1775}, abstract = {APS is an autoimmune disorder characterized by thrombosis and pregnancy complications, primarily driven by aPLs such as LA, aCL and anti-β2 glycoprotein I (a-β2GPI). Despite advances in anticoagulation therapies, managing refractory APS cases remains challenging. Emerging therapies, including rituximab, eculizumab and HCQ, show potential in addressing the underlying mechanisms of APS. Additionally, research into genetic and environmental factors, particularly the gut microbiome's role through molecular mimicry, suggests new therapeutic pathways. Diagnostic advancements, such as the adjusted Global Antiphospholipid Syndrome Score (aGAPSS), metabolomic profiling and MRI, have improved risk stratification and early detection. Non-traditional biomarkers like anti-phosphatidylserine/prothrombin (aPS/PT) and anti-Domain I antibodies further enhance risk assessment. Future research should aim to validate these approaches, optimizing patient outcomes and minimizing long-term APS complications.}, }
@article {pmid39845884, year = {2024}, author = {Song, S and Ning, L and Yu, J}, title = {Elucidating the causal relationship between gut microbiota, metabolites, and diabetic nephropathy in European patients: Revelations from genome-wide bidirectional mendelian randomization analysis.}, journal = {Frontiers in endocrinology}, volume = {15}, number = {}, pages = {1391891}, pmid = {39845884}, issn = {1664-2392}, mesh = {Humans ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome ; *Diabetic Nephropathies/genetics/microbiology/metabolism ; *Genome-Wide Association Study ; Europe/epidemiology ; }, abstract = {OBJECTIVE: Previous observational studies suggest a potential link between gut microbiota, metabolites, and diabetic nephropathy. However, the exact causal relationship among these factors remains unclear.<br><br>METHOD: We conducted a two-sample bidirectional Mendelian randomization study using summary statistics from the IEU OpenGWAS Project database to investigate gut microbiota, metabolites, and diabetic nephropathy. A range of methods, including inverse variance weighting, MR-Egger, weighted median, and simple median, were applied to examine causal associations. Sensitivity analyses were performed to assess the robustness of the results. Additionally, reverse Mendelian randomization analysis was conducted, treating significant gut microbiota as the outcome, to evaluate effects and perform sensitivity testing. This comprehensive approach provided an in-depth assessment of the interactions among gut microbiota, metabolites, and diabetic nephropathy.<br><br>RESULT: The Inverse Variance Weighted estimates revealed that the abundance of Lachnospiraceae, Parasutterella, and Eubacterium exhibited negative causal effects on diabetic nephropathy, while Coprococcus, Sutterella, Faecalibacterium prausnitzii, and Bacteroides vulgatus showed protective causal effects against the condition. However, reverse Mendelian randomization analysis did not identify any significant associations between diabetic nephropathy and the identified gut microbiota. Furthermore, the estimates indicated that Cholesterol, Pyridoxate, Hexanoylcarnitine, X-12007, Octanoylcarnitine, 10-nonadecenoate (19:1n9), X-12734, and the average number of double bonds in a fatty acid chain had negative causal effects on diabetic nephropathy. In contrast, Methionine, Glycodeoxycholate, X-06351, 1-stearoylglycerol (1-monostearin), 5-dodecenoate (12:1n7), X-13859, 2-hydroxyglutarate, Glycoproteins, Phospholipids in IDL, and the concentration of small HDL particles demonstrated protective causal effects. Notably, sensitivity analyses did not detect any heterogeneity or horizontal pleiotropy, ensuring the robustness of the findings.<br><br>CONCLUSION: Modulating gut microbiota diversity and composition offers a promising strategy for improving the incidence and prognosis of diabetic nephropathy. This highlights the need for future clinical trials focusing on microbiome-based interventions, potentially utilizing microbiome-dependent metabolites. Such approaches could transform the treatment and management of diabetic nephropathy and its associated risk factors, paving the way for more effective therapeutic strategies to combat this debilitating condition.}, }
@article {pmid39845840, year = {2024}, author = {Chu, C and Behera, TR and Huang, Y and Qiu, W and Chen, J and Shen, Q}, title = {Corrigendum: Research progress of gut microbiome and diabetic nephropathy.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1549438}, doi = {10.3389/fmed.2024.1549438}, pmid = {39845840}, issn = {2296-858X}, abstract = {[This corrects the article DOI: 10.3389/fmed.2024.1490314.].}, }
@article {pmid39845646, year = {2024}, author = {Hadrich, I and Turki, M and Chaari, I and Abdelmoula, B and Gargouri, R and Khemakhem, N and Elatoui, D and Abid, F and Kammoun, S and Rekik, M and Aloulou, S and Sehli, M and Mrad, AB and Neji, S and Feiguin, FM and Aloulou, J and Abdelmoula, NB and Sellami, H}, title = {Gut mycobiome and neuropsychiatric disorders: insights and therapeutic potential.}, journal = {Frontiers in cellular neuroscience}, volume = {18}, number = {}, pages = {1495224}, pmid = {39845646}, issn = {1662-5102}, abstract = {BACKGROUND: The human gut mycobiome, a minor but integral component of the gut microbiome, has emerged as a significant player in host homeostasis and disease development. While bacteria have traditionally been the focus of gut microbiome studies, recent evidence suggests that fungal communities (mycobiota) may also play a crucial role in modulating health, particularly in neuropsychiatric disorders.<br><br>OBJECTIVE: This review aims to provide a comprehensive overview of current knowledge on the relationship between the gut mycobiome and neuropsychiatric disorders, exploring the potential of targeting fungal communities as a novel therapeutic strategy.<br><br>METHODS: We summarized recent findings from metagenomic analyses that characterize the diversity and composition of gut mycobiota and discuss how these communities interact with the host and other microorganisms via the gut-brain axis. Key methodologies for studying mycobiota, such as high-throughout sequencing and bioinformatics approaches, were also reviewed to highlight advances in the field.<br><br>RESULTS: Emerging research links gut mycobiota dysbiosis to conditions such as schizophrenia, Alzheimer's disease, autism spectrum disorders, bipolar disorder, and depression. Studies indicate that specific fungal populations, such as Candida and Saccharomyces, may influence neuroinflammation, gut permeability and immune responses, thereby affecting mental health outcomes.<br><br>CONCLUSION: Understanding the gut mycobiome's role in neuropsychiatric disorders opens new avenues for therapeutic interventions, including antifungal treatments, probiotics, and dietary modifications. Future research should integrate multi-omics approaches to unravel the complex interkingdom interactions within the gut ecosystem, paving the way for personalized medicine in mental health care.}, }
@article {pmid39845431, year = {2025}, author = {Wang, W and Xian, M and Chen, R and Li, J and Wu, L}, title = {Gradient disparities in allergy and the gut microbiome among rural, migrant, and urban populations across China.}, journal = {The World Allergy Organization journal}, volume = {18}, number = {1}, pages = {101018}, pmid = {39845431}, issn = {1939-4551}, abstract = {BACKGROUND: While much of the evidence linking the rapid urbanization and the increasing prevalence of allergen sensitization, but little is known regarding rural-to-urban migrants. The aim of this study was to identify the disparities in allergy, the gut microbiome and factors among native urban, migrating, and native rural Chinese.<br><br>METHODS: We redesigned the dataset of the China Alliance of Research on Respiratory Allergic Disease secondary survey, and after stratified sampling, a subsample of 2422 subjects were enrolled for the analysis of a questionnaire, skin prick tests (SPT), and specific immunoglobulin E (sIgE) titer measurements against 8 common allergens. Fecal microbiotal composition was also sequenced by 16S rRNA and regression-based analyses with covariate adjustment applied.<br><br>RESULTS: From urban to migrant and rural populations, IgE sensitization was predominantly directed against Dermatophagoides pteronyssinus (Der p). The titers of Der p-sIgE decreased sequentially across the 3 respective populations and co-sensitization to other allergens also showed a sequential decrease. Rural-to-urban migrants showed a low prevalence of Der p-SPT and Der p-sIgE initially, but developed substantial IgE titers and their gut microbiotal diversity, as well as species richness, appeared to change along with residential time spent in the urban area. High-fat diet, using a mattress, an SPT wheal size from Der p&#xa0;&#x2265;&#xa0;6&#xa0;mm, and duration of immigration >5 years were significantly associated with sIgE positivity in the migrants.<br><br>CONCLUSION: The Der p-sIgE responses and the composition of gut microbiota differs synchronously with extended living time in an urban area. Studies in immigrants provide a unique opportunities to evaluate the effects of environmental factors in the pathogenesis of allergic disorders.}, }
@article {pmid39845316, year = {2024}, author = {Yang, HS and Zhang, J and Feng, HX and Qi, F and Kong, FJ and Zhu, WJ and Liang, CY and Zhang, ZR}, title = {Characterizing microbial communities and their correlation with genetic mutations in early-stage lung adenocarcinoma: implications for disease progression and therapeutic targets.}, journal = {Frontiers in oncology}, volume = {14}, number = {}, pages = {1498524}, pmid = {39845316}, issn = {2234-943X}, abstract = {BACKGROUND: Lung adenocarcinoma (LUAD), the most prevalent form of lung cancer. The transition from adenocarcinoma in situ (AIS), and minimally invasive adenocarcinoma (MIA) to invasive adenocarcinoma (IAC) is not fully understood. Intratumoral microbiota may play a role in LUAD progression, but comprehensive stage-wise analysis is lacking.<br><br>METHODS: Tumor and bronchoalveolar lavage fluid (BALF) samples from patients with AIS/MIA or IAC were collected for next-generation sequencing to characterize microbial diversity and composition. DNA extraction involved lysing samples with nuclease and protease, followed by homogenization and elution. Sequencing libraries were prepared and sequenced on the Illumina platform. Whole exome sequencing was performed to identify somatic mutations and genetic variants. Bioinformatics analysis, including taxonomic annotation with Kraken2 and de novo assembly with MEGAHIT, was conducted to process metagenomic data. Correlation analysis was performed to link microbial species with mutated genes using custom R scripts.<br><br>RESULTS: Metagenomic analysis revealed a distinct microbial profile in IAC compared to AIS/MIA, with increased abundance of Bacteroidetes and Firmicutes in the IAC group. Bosea sp. and Microbacterium paludicola, were less abundant in IAC, suggesting a potential protective role in early-stage disease. Conversely, Mycolicibacterium species were more prevalent in IAC, indicating a possible contribution to disease progression. Genetic sequencing identified PTPRZ1 strongly correlating with microbial composition, suggesting a mechanistic link between microbiota and genetic alterations in LUAD.<br><br>CONCLUSION: This study characterizes microbial communities in various stages of LUAD, revealing links between microbiota and genetic mutations. The unique microbiota suggests its role in LUAD progression and as a therapeutic target.}, }
@article {pmid39845057, year = {2024}, author = {Tan, JW and Eicher, SD and Kritchevsky, JE and Bryan, KA and Dickey, A and Chitko-McKown, CG and McDaneld, TG}, title = {Insights into microbial compositions of the respiratory tract of neonatal dairy calves in a longitudinal probiotic trial through 16S rRNA sequencing.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1499531}, pmid = {39845057}, issn = {1664-302X}, abstract = {INTRODUCTION: Probiotics are a promising intervention for modulating the microbiome and the immune system, promoting health benefits in cattle. While studies have characterized the calf lung bacterial profile with and without oral probiotics, simultaneous probiotic effects on the bacterial populations of multiple sites along the respiratory tract have not been characterized.<br><br>METHODS: This study utilized the same pre-weaning diary calf group from our previous studies to characterize the bacterial populations present in the nostril and tonsil across control and treatment groups and nine sampling time points. DNA was exacted from the nostril and tonsil swabs and lung lavage fluids, and 16S ribosomal RNA gene hypervariable regions 1-3 were subsequently sequenced.<br><br>RESULTS: Temporal variation in alpha bacterial diversity within the nostril, tonsil, and lung samples was observed, indicating distinct bacterial compositions among sampling time points. Oral probiotic treatment did not change alpha diversity in any respiratory tissue, however, spatial variability in bacterial taxa composition was observed among the three respiratory tract regions. While the majority of differentially abundant taxa in probiotic treated calves were unique to their anatomical location, a few were common to two anatomical locations and one Finegoldia amplicon sequence variant was differentially abundant in all three anatomical locations.<br><br>DISCUSSION: In conclusion, these findings contribute to the understanding of the dynamic nature of bacterial diversity and the potential effects of probiotics within the bovine respiratory tract and provides insight for future studies of probiotics on animal health, disease prevention, and management.}, }
@article {pmid39845049, year = {2024}, author = {Wu, R and Mai, Z and Song, X and Zhao, W}, title = {Hotspots and research trends of gut microbiome in polycystic ovary syndrome: a bibliometric analysis (2012-2023).}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1524521}, pmid = {39845049}, issn = {1664-302X}, abstract = {INTRODUCTION: Polycystic ovary syndrome (PCOS) is a common gynecological condition affecting individuals of reproductive age and is linked to the gut microbiome. This study aimed to identify the hotspots and research trends within the domain of the gut microbiome in PCOS through bibliometric analysis.<br><br>METHODS: Utilizing bibliometric techniques, we examined the literature on the gut microbiome in PCOS from the Web of Science Core Collection spanning the period from 2012 to 2023. Analytical tools such as CiteSpace, VOSviewer, and Bibliometric R packages were employed to evaluate various metrics, including countries/regions, institutions, authors, co-cited authors, authors' H-index, journals, co-references, and keywords.<br><br>RESULTS: A total of 191 publications were identified in the field of gut microbiome in PCOS, with an increase in annual publications from 2018 to 2023. People's Republic of China was the most productive country, followed by the United States of America (USA), India. Shanghai Jiao Tong University, Fudan University, and Beijing University of Chinese Medicine were the top three most publications institutions. Thackray VG was identified as the most prolific author, holding the highest H-index, while Liu R received the highest total number of citations. The journal "Frontiers in Endocrinology" published the most articles in this domain. The most frequently co-cited reference was authored by Qi XY. The analysis of keyword burst detection identified "bile acids" (2021-2023) as the leading frontier keyword. Additionally, "gut dysbiosis," "phenotypes," "adolescents," "metabolomics," "metabolites," "fecal microbiota transplantation," and "IL-22" have emerged as the primary keywords reflecting recent research trends.<br><br>CONCLUSION: This bibliometric analysis explores how the gut microbiome influences endocrine and metabolic disorders related to PCOS, emphasizing its role in the development of PCOS and treatments targeting the gut microbiome. The findings serve as a valuable resource for researchers, enabling them to identify critical hotspots and emerging areas of investigation in this field.}, }
@article {pmid39845046, year = {2024}, author = {Almuhaideb, E and Hasan, NA and Grim, C and Rashed, SM and Parveen, S}, title = {Comparative evaluation of specimen type and processing conditions for studying oyster microbiomes.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1504487}, pmid = {39845046}, issn = {1664-302X}, abstract = {Metagenomic sequencing is increasingly being employed to understand the assemblage and dynamics of the oyster microbiome. Specimen collection and processing steps can impact the resultant microbiome composition and introduce bias. To investigate this systematically, a total of 54 farmed oysters were collected from Chesapeake Bay between May and September 2019. Six different specimen types and processing methods were evaluated for microbial community composition using shotgun metagenomics, namely fresh oyster homogenate (FOH), oyster homogenate after simulated temperature abuse (AOH), Luria broth-enriched oyster homogenate (EOH), dissected stomach homogenate (DSH), hemolymph (HLM), and stomach-gut content (SGC). In general, DSH, EOH, and FOH yielded the highest DNA concentration, while EOH had the highest microbial reads, followed by DSH, HLM, and FOH. HLM produced the highest bacterial species alpha diversity, followed by AOH, EOH, and SGC. Although alpha diversities did not differ significantly, beta-diversity measurements showed significant dissimilarity among methods (p < 0.05) indicating that the specimen types and processing steps do play an important role in representing the composition of the bacterial community. Bacterial species that had the highest log mean abundance included Cyanobium sp. PCC 7001 in FOH, Vibrio vulnificus in AOH, EOH, and DSH, and lastly Synechococcus sp. CB0205 in the DSH, HML, and SGC samples. EOH displayed higher bacterial hits, distinct microbial composition, and higher values of bacterial, phages, and antimicrobial resistance gene reads. Therefore, if studying the overall oyster microbial community, prioritizing optimum specimen collection and processing methods that align with the overall goal of the study is recommended.}, }
@article {pmid39845039, year = {2024}, author = {Du, J and Zheng, P and Gao, W and Liang, Q and Leng, L and Shi, L}, title = {All roads lead to Rome: the plasticity of gut microbiome drives the extensive adaptation of the Yarkand toad-headed agama (Phrynocephalus axillaris) to different altitudes.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1501684}, pmid = {39845039}, issn = {1664-302X}, abstract = {The gut microbiome was involved in a variety of physiological processes and played a key role in host environmental adaptation. However, the mechanisms of their response to altitudinal environmental changes remain unclear. In this study, we used 16S rRNA sequencing and LC-MS metabolomics to investigate the changes in the gut microbiome and metabolism of the Yarkand toad-headed agama (Phrynocephalus axillaris) at different altitudes (-80 m to 2000 m). The results demonstrated that Firmicutes, Bacteroidetes, and Proteobacteria were the dominant phylum, Lachnospiraceae and Oscillospiraceae were the most abundant family, and the low-altitude populations had higher richness than high-altitude populations; Akkermansiaceae appeared to be enriched in high-altitude populations and the relative abundance tended to increase with altitude. The gut microbiome of three populations of P. axillaris at different altitudes was clustered into two different enterotypes, low-altitude populations and high-altitude populations shared an enterotype dominated by Akkermansia, Kineothrix, Phocaeicola; intermediate-altitude populations had an enterotype dominated by Mesorhizobium, Bradyrhizobium. Metabolites involved in amino acid and lipid metabolism differed significantly at different altitudes. The above results suggest that gut microbiome plasticity drives the extensive adaptation of P. axillaris to multi-stress caused by different altitudes. With global warming, recognizing the adaptive capacity of wide-ranging species to altitude can help plan future conservation strategies.}, }
@article {pmid39845038, year = {2024}, author = {Peters, B and Leonhardt, SD and Schloter, M and Keller, A}, title = {Direct and indirect effects of land use on microbiomes of trap-nesting solitary bee larvae and nests.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1513096}, pmid = {39845038}, issn = {1664-302X}, abstract = {INTRODUCTION: The global decline in biodiversity and insect populations highlights the urgent need to conserve ecosystem functions, such as plant pollination by solitary bees. Human activities, particularly agricultural intensification, pose significant threats to these essential services. Changes in land use alter resource and nest site availability, pesticide exposure and other factors impacting the richness, diversity, and health of solitary bee species. In this study, we investigated yet another facet currently less well investigated in such context: Microbial communities associated with wild bees play crucial roles in larval development, metabolism, immunity and overall bee health. However, the drivers and dynamics of healthy microbiome in solitary bees are still poorly understood, especially regarding the direct and indirect effects of land use on the diversity and composition of these microbial communities.<br><br>METHODS: We examined bacterial communities in the offspring and nest materials of the Megachilid trap-nesting solitary bee, Osmia bicornis, along a gradient of land use intensification by 16S rRNA gene metabarcoding. Given that landscape composition, climatic conditions, and food resources are known to influence microbial compositions in solitary bee species, we hypothesized that land use changes would alter resources available for food and nest material collection and thereby affecting the microbiomes in offspring and their nest environments. We anticipated reduced microbial diversity and altered composition with increased land use intensification, which is known to decrease the number and diversity of resources, including the pool of floral and soil bacteria in the surrounding environment.<br><br>RESULTS: As expected, we observed significant shifts in the bacterial composition and diversity of bees and their nests across varying degrees of land use intensity, differing in management types and the availability of flowers. The Shannon diversity of bacteria in nest materials (larval pollen provision, soil nest enclosure) and larval guts decreased with increasing land use intensity. However, the pupae microbiome remained unaffected, indicating a reorganization of the microbiome during metamorphosis, which is not significantly influenced by land use and available resources.<br><br>DISCUSSION: Our findings provide new insights into the factors shaping environmental transmission and changes in solitary bee microbiomes. This understanding is crucial for comprehending the impacts of intensive land use on wild bee health and developing strategies to mitigate these effects.}, }
@article {pmid39845034, year = {2024}, author = {Meng, WJ and Wen, ZL and Kasanen, R and Sun, H and Asiegbu, FO}, title = {Microbial communities in the phyllosphere and endosphere of Norway spruce under attack by Heterobasidion.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1489900}, pmid = {39845034}, issn = {1664-302X}, abstract = {Heterobasidion annosum species complex has been regarded as the most destructive disease agent of conifer trees in boreal forests. Tree microbiome can regulate the plant-pathogen interactions by influencing both host resistance and pathogen virulence. Such information would help to improve the future health of forests and explore strategies to enhance ecosystem stability. In this study, using next-generation sequencing technology, we investigated the microbial community in different tree regions (needles, upper stem, and lower stem) of Norway spruce with and without wood decay symptoms. The primary purpose was to uncover signature characteristic microbiome harbored by asymptomatic trees compared to diseased trees. Additionally, the study was to explore the inter-kingdom and intra-kingdom interactions in microbiome (bacteria and fungi) of symptomatic versus asymptomatic trees. The results showed that in upper stem, species richness (Chao1) of fungi and bacteria were both higher in asymptomatic trees than symptomatic trees (P < 0.05). Compared to symptomatic trees, asymptomatic trees harbored a higher abundance of Actinobacteriota, bacterial genera of Methylocella, Conexibacter, Jatrophihabitans, and fungal genera of Mollisia. Fungal communities from the same anatomic region differed between the symptomatic and asymptomatic trees. Bacterial communities from the two stem regions were also distinct between the symptomatic and asymptomatic trees. The symptomatic trees possessed a less stable microbial network with more positive correlations compared to the asymptomatic trees. In the lower stem, at intra-kingdom level, the distribution of correlation numbers was more even in the bacterial network compared to the fungal network. In conclusion, the Heterobasidion attack decreased the microbial community species richness and shifted the community structure and functional structure to varying degrees. The microbial network was enlarged and became more unstable at both inter-kingdom and intra-kingdom level due to the Heterobasidion infection.}, }
@article {pmid39845032, year = {2024}, author = {Cai, Y and Tang, H and Xiang, G and Yi, H and Zhong, J and Xie, Z and Hu, Q and El Bouhi, R and Zhou, P and Zhang, Y and Yan, H}, title = {Deciphering of differences in gut microbiota and plasma metabolites profile between non-obese and obese Golden Retrievers dogs.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1514633}, pmid = {39845032}, issn = {1664-302X}, abstract = {INTRODUCTION: Golden Retrievers have a high risk of obesity, which is prevalent in dogs and is associated with inflammation and cancer, impairing the health and life expectancy of companion animals. Microbial and metabolite biomarkers have been proposed for identifying the presence of obesity in humans and rodents. However, the effects of obesity on the microbiome and metabolome of Golden Retrievers remains unknown. Therefore, this study was designed to evaluate the signatures of serum biochemistry indexes, gut microbiota and plasma metabolites in non-obese and obese Golden Retrievers, aiming to recognize potential biomarkers of canine obesity.<br><br>METHODS: A total of 8 non-obese (Ctrl group) and 8 obese (Obe group) Golden Retrievers were included in the present study to collect blood and feces samples for measurements. The fecal microbiome and plasma metabolome were determined using 16S rRNA amplicon sequencing and liquid chromatography-mass spectrometry, respectively.<br><br>RESULTS: Results showed that the alanine aminotransferase activity and total bilirubin concentration, which have been measured using serum biochemistry analysis, were higher in the Obe group than in the Ctrl group (p&#x202f;<&#x202f;0.05). Moreover, there was a significant difference in gut microbiota composition between the two groups (p&#x202f;<&#x202f;0.05). The phyla Proteobacteria, Fusobacteriota, and Bacteroidota as well as genera Fusobacterium, Prevotella, Faecalibacterium, Escherichia-Shigell, and Alloprevotella were more abundant, while phylum Firmicutes and genera Peptoclostridium, Blautia, Turicibacter, Allobaculum, and Erysipelatoclostridium were less abundant in the Obe group compared to the Ctrl group (p&#x202f;<&#x202f;0.05). Plasma concentrations of citrulline and 11-dehydrocorticosterone were significantly higher in the Obe group than those in the Ctrl group (p&#x202f;<&#x202f;0.05). Close correlations between serum biochemistry parameters, gut microbiome, and plasma metabolites were observed in the current study.<br><br>CONCLUSION: The obesity-induced shifts in serum biochemistry indexes, gut microbiota, and plasma metabolites profiles suggest that obese Golden Retrievers exhibit a different microbiome and metabolome than non-obese ones, and the certain metabolites like citrulline and 11-dehydrocorticosterone could be considered as potential biomarkers to recognize obese Golden Retrievers.}, }
@article {pmid39845029, year = {2024}, author = {Bouchez, T and Liu, B and Garza, DR}, title = {Healthy gut microbiomes are host-controllable microbiomes.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1497083}, pmid = {39845029}, issn = {1664-302X}, }
@article {pmid39844957, year = {2025}, author = {Martins, V and Abdallah, C and Teixeira, A and Moreira, C and Nóbrega, M and Lanoue, A and Gerós, H}, title = {Subregional pedoclimatic conditions with contrasted UV-radiation shape host-microbiome and metabolome phenotypes in the grape berry.}, journal = {Food chemistry: X}, volume = {25}, number = {}, pages = {102139}, pmid = {39844957}, issn = {2590-1575}, abstract = {This study used integrative omics to address the response of key elements of the grapevine holobiont to contrasted pedoclimatic conditions found in distinct subregions of Douro Valley (Portugal). A metabolic OPLS-DA model predicted with 100 % accuracy the geographic origin of berries; higher UV radiation, higher temperature and lower precipitation stimulated the accumulation of phenolic acids, flavonols and malvidin conjugates, in detriment of amino acids, organic acids, flavan-3-ols, proanthocyanidins and non-malvidin anthocyanins. Metabarcoding showed a trade-off between bacteria and fungal diversity among subregions, with Pseudomonas, Lactobacillus, Aspergillus and Penicillium acting as intraregional microbial markers. The high phenotypic plasticity of berries and the role of microbes in this process are relevant upon current projections for increased UV radiation and temperature in Southern European viticulture, in a climate change scenario, with predicted impacts on regional wine quality and on the development of adaptation strategies for resilient viticulture.}, }
@article {pmid39844919, year = {2025}, author = {Naim, W and Manetsberger, J and Lavilla Lerma, L and Benomar, N and Caballero Gómez, N and Cuesta-Bertomeu, IS and Gata Díaz, J&#xc1; and Abriouel, H}, title = {Impact of disinfection methods used in the slaughterhouse environment on microbiome diversity throughout the meat production chain.}, journal = {Current research in microbial sciences}, volume = {8}, number = {}, pages = {100336}, pmid = {39844919}, issn = {2666-5174}, abstract = {Slaughterhouse environments are prone to microbial contamination, influenced by factors like set-up, size and area as well as disinfection practices. Thus, effective control measures are crucial to prevent the spread of pathogens and their contaminant genes (antimicrobial resistance genes and virulence factors) throughout the food chain. In the present study, we assessed the microbial contamination in environmental surfaces of three slaughterhouses located in the Jaén province (Spain). We also evaluated the impact of different disinfection strategies on microbial loads and diversity by means of culture dependent and independent methods. The results revealed a statistically significant inter- and intra-specific differences in microbial loads including the most important pathogens such as pseudomonads, staphylococci, Escherichia coli, Salmonella sp. and Campylobacter jejuni. Disinfection strategies using routine disinfectant (used by the slaughterhouse), HLE disinfectant, UV, or combinations thereof showed varying effectiveness. The newly developed sustainable HLE disinfectant was most effective, while UV had the lowest disinfection strength, and routine disinfectants failed to eradicate all pathogens. Metagenomic analysis identified Pseudomonadota as the dominant phylum, followed by Actinomycetota and Bacteroidota. Results furthermore indicated shifts from sacrifice to cold rooms, with an increase in Gammaproteobacteria, particularly Moraxellaceae (represented by Psychrobacter cryohalolentis) over Acinetobacter sp. In conclusion, this study highlights the potential of HLE disinfectant (alone or in combination with the routine disinfectant) as a more effective disinfection measure on environmental surfaces, particularly for combating multi-drug resistant pathogens compared to other disinfection methods currently used.}, }
@article {pmid39844346, year = {2025}, author = {Melville, DW and Meyer, M and Kümmerle, C and Alvarado-Barrantes, KA and Wilhelm, K and Sommer, S and Tschapka, M and Risely, A}, title = {Delayed feeding disrupts diurnal oscillations in the gut microbiome of a neotropical bat in captivity.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf012}, pmid = {39844346}, issn = {1574-6941}, abstract = {Diurnal rhythms of the gut microbiota are emerging as an important yet often overlooked facet of microbial ecology. Feeding is thought to stimulate gut microbial rhythmicity, but this has not been explicitly tested. Moreover, the role of the gut environment is entirely unexplored, with rhythmic changes to gut pH rather than feeding per se possibly affecting gut microbial fluctuations. In this study, we experimentally manipulated the feeding schedule of captive lesser long-nosed bats, Leptonycteris yerbabuenae, to dissociate photic and feeding cues, and measured the fecal microbiota and gut pH every two hours. We detected strong diurnal rhythms in both microbial alpha- and beta diversity as well as in pH within the control group. However, a delay in feeding disrupted oscillations of gut microbial diversity and composition, but did not affect rhythms in gut pH. The oscillations of some genera, such as Streptococcus, which aid in metabolizing nutrients, shifted in accordance with the delayed feeding cue and were correlated with pH. For other bacterial genera, oscillations were disturbed and no connection to pH was found. Our findings suggest that the rhythmic proliferation of bacteria matches peak feeding times, providing evidence that diurnal rhythms of the gut microbiota likely evolved to optimize their metabolic support to the host's circadian phenotype.}, }
@article {pmid39844274, year = {2025}, author = {Camper, BT and Kanes, AS and Laughlin, ZT and Manuel, RT and Bewick, SA}, title = {Transgressive hybrids as hopeful holobionts.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {19}, pmid = {39844274}, issn = {2049-2618}, mesh = {*Hybridization, Genetic ; *Symbiosis ; *Microbiota ; Animals ; Biological Evolution ; Bacteria/genetics/classification ; }, abstract = {BACKGROUND: Hybridization between evolutionary lineages has profound impacts on the fitness and ecology of hybrid progeny. In extreme cases, the effects of hybridization can transcend ecological timescales by introducing trait novelty upon which evolution can act. Indeed, hybridization can even have macroevolutionary consequences, for example, as a driver of adaptive radiations and evolutionary innovations. Accordingly, hybridization is now recognized as a motor for macrobial evolution. By contrast, there has been substantially less progress made towards understanding the positive eco-evolutionary consequences of hybridization on holobionts. Rather, the emerging paradigm in holobiont literature is that hybridization disrupts symbiosis between a host lineage and its microbiome, leaving hybrids at a fitness deficit. These conclusions, however, have been drawn based on results from predominantly low-fitness hybrid organisms. Studying "dead-end" hybrids all but guarantees finding that hybridization is detrimental. This is the pitfall that Dobzhansky fell into over 80 years ago when he used hybrid sterility and inviability to conclude that hybridization hinders evolution. Goldschmidt, however, argued that rare saltational successes-so-called hopeful monsters-disproportionately drive positive evolutionary outcomes. Goldschmidt's view is now becoming a widely accepted explanation for the prevalence of historical hybridization in extant macrobial lineages. Aligning holobiont research with this broader evolutionary perspective requires recognizing the importance of similar patterns in host-microbiome systems. That is, rare and successful "hopeful holobionts" (i.e., hopeful monsters at the holobiont scale) might be disproportionately responsible for holobiont evolution. If true, then it is these successful systems that we should be studying to assess impacts of hybridization on the macroevolutionary trajectories of host-microbiome symbioses.<br><br>RESULTS: In this paper, we explore the effects of hybridization on the gut (cloacal) and skin microbiota in an ecologically successful hybrid lizard, Aspidoscelis neomexicanus. Specifically, we test the hypothesis that hybrid lizards have host-associated (HA) microbiota traits strongly differentiated from their progenitor species. Across numerous hybrid microbiota phenotypes, we find widespread evidence of transgressive segregation. Further, microbiota restructuring broadly correlates with niche restructuring during hybridization. This suggests a relationship between HA microbiota traits and ecological success.<br><br>CONCLUSION: Transgressive segregation of HA microbiota traits is&#xa0;not only limited to hybrids at a fitness deficit but also occurs in ecologically successful hybrids. This suggests that hybridization may be a mechanism for generating novel and potentially beneficial holobiont phenotypes. Supporting such a conclusion, the correlations that we find between hybrid microbiota and the hybrid niche indicate that hybridization might change host microbiota in ways that promote a shift or an expansion in host niche space. If true, hybrid microbiota restructuring may underly ecological release from progenitors. This, in turn, could drive evolutionary diversification. Using our system as an example, we elaborate on the evolutionary implications of host hybridization within the context of holobiont theory and then outline the next steps for understanding the role of hybridization in holobiont research. Video Abstract.}, }
@article {pmid39844033, year = {2025}, author = {Wang, Y and Cui, P and Cao, M and Ai, L and Zeng, L and Li, X and Chen, D and Gong, F and Fang, L and Zhou, C}, title = {Chronic restraint stress affects the diurnal rhythms of gut microbial composition and metabolism in a mouse model of depression.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {38}, pmid = {39844033}, issn = {1471-2180}, support = {YJSCX202306//Postgraduate Innovation Fund of Yongchuan Hospital Affiliated to Chongqing Medical University/ ; 82200829//National Natural Science Foundation of China/ ; 81701361//National Natural Science Foundation of China/ ; CSTB2022NSCQ-MSX0998//Natural Science Foundation of Chongqing/ ; CSTB2022NSCQ-MSX0250//Natural Science Foundation of Chongqing/ ; CSTB2022NSCQ-MSX0329//Natural Science Foundation of Chongqing/ ; KJQN202200467//Chongqing Education Commission of China/ ; KJQN202200460//Chongqing Education Commission of China/ ; YJRC202102//Science Foundation funded project of Yongchuan Hospital of Chongqing Medical University/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Depression/microbiology/metabolism/physiopathology ; *Circadian Rhythm/physiology ; Mice ; *Disease Models, Animal ; *Mice, Inbred C57BL ; *Feces/microbiology ; Male ; *Stress, Psychological/microbiology/physiopathology ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Restraint, Physical ; Dysbiosis/microbiology ; Behavior, Animal ; }, abstract = {BACKGROUND: Depression is a common mental disorder accompanied by gut microbiota dysbiosis, which disturbs the metabolism of the host. While diurnal oscillation of the intestinal microbiota is involved in regulating host metabolism, the characteristics of the intestinal microbial circadian rhythm in depression remain unknown. Our aim was to investigate the microbial circadian oscillation signature and related metabolic pathways in a mouse model with depression-like behaviours.<br><br>METHODS: Chronic restraint stress (CRS) was used to induce depressive-like behaviours in C57BL/6J mice. The open field test (OFT) and forced swimming test (FST) were used to evaluate anxiety- and depressive-like behaviours in the control and CRS groups. Afterwards, faecal samples from the two groups were collected every four hours from ZT2 (9:00 am) to ZT22 (5:00 am). Faecal 16&#xa0;S rRNA gene sequencing and metabolomics analysis were performed, and the microbial circadian rhythm was analysed via the MetaCycle package in R/RStudio.<br><br>RESULTS: CRS mice exhibited depressive-like behaviours after 4 weeks of restriction. Alpha- and beta-diversity analyses revealed that the microbial composition in control and CRS mice oscillated throughout the day. The circadian rhythm analyses revealed that at the phylum level, Bacteroidota, Firmicutes, Cyanobacteria and Patescibacteria showed circadian rhythmicity in the CRS group. At the genus level, Dubosiella and Romboutsia showed circadian rhythmicity in the control group, and Dubosiella abundance was correlated with tryptophan and galactose metabolism. In the CRS group, Bacteroides, Parabacteroides, and Rikenellaceae_RC9_gut_group showed circadian rhythmicity; among these genera, Parabacteroides was related to tryptophan metabolism, axon regeneration, phenylalanine metabolism and tyrosine metabolism.<br><br>CONCLUSION: Our data highlight the importance of observing the diurnal oscillation of the microbiome in host with depressive-like states. Rhythmicity in the microbiome may affect the host by regulating distinct metabolic pathways during the light and dark phases. A better combination of microbiota composition and oscillation would help to offer novel insight into key genera and their potential effects on depression.}, }
@article {pmid39843765, year = {2025}, author = {Zhong, L and Li, T and Zhang, X and Li, H}, title = {Clioquinol 3% Cream Improves Clinical Symptoms and Restores the Skin Microbiome in Interdigital Tinea Pedis.}, journal = {Mycopathologia}, volume = {190}, number = {1}, pages = {18}, pmid = {39843765}, issn = {1573-0832}, support = {YWJKJJHKYJJ-TY2010//Beijing&#xa0;Medical&#xa0;and&#xa0;Health&#xa0;Foundation/ ; }, mesh = {Humans ; *Microbiota/drug effects ; Male ; Female ; *Tinea Pedis/drug therapy/microbiology ; Middle Aged ; Adult ; *Clioquinol/administration &amp; dosage ; Prospective Studies ; *Skin/microbiology ; Longitudinal Studies ; Treatment Outcome ; Aged ; Fungi/drug effects/classification/isolation &amp; purification ; Young Adult ; Antifungal Agents/administration &amp; dosage/therapeutic use/pharmacology ; Administration, Topical ; Skin Cream/administration &amp; dosage ; Severity of Illness Index ; Bacteria/classification/isolation &amp; purification/drug effects/genetics ; }, abstract = {BACKGROUND: Interdigital tinea pedis is a common type of tinea pedis that occurs between toes and is easy to recur. Recently, the skin microbiome analysis of interdigital tinea pedis showed changes in bacterial microbiome in addition to fungal infection.<br><br>OBJECTIVES: To investigate the efficacy and safety of clioquinol 3% cream in treating interdigital tinea pedis as well as characterize changes in the skin microbiome during treatment.<br><br>METHODS: The clinical characteristics and skin microbiome of patients with interdigital tinea pedis were investigated in a longitudinal prospective study. In total 28 participants were rcruited to use the clioquinol 3% cream topically to the target skin lesions twice a day for 1&#xa0;week. Disease severity evaluation, fungal microscopic examination, and sample collection for skin microbiome analysis were performed at baseline, after treatment, and 1&#xa0;week post-treatment.<br><br>RESULTS: Compared with baseline, the disease severity, lesion score, pruritus score, and malodor score of the patients significantly decreased after treatment and at 1&#xa0;week post-treatment (P&#x2009;<&#x2009;0.05). The fungal profiles after treatment and 1&#xa0;week post-treatment revealed significantly decreased abundance of Trichophyton and significantly increased abundances of Cladosporium, Alternaria, and Aspergillus, which led to higher fungal diversity than pretreatment samples. The bacterial profiles after treatment and 1&#xa0;week post-treatment revealed significantly decreased abundances of Brevibacterium, Finegoldia, and Facklamia. The abundance of Streptococcus and bacterial diversity were also significantly decreased at 1&#xa0;week post-treatment. The disease severity was positively associated with the abundance of Trichophyton, Arthroderma, Finegoldia, Facklamia, Brevibacterium, Corynebacterium, and Porphyromonas.<br><br>CONCLUSIONS: The clioquinol 3% cream was efficient on treating interdigital tinea pedis by decreasing the abundance of pathogenic fungus, recovering the normal balance of the fungal and bacterial communities, and restore species diversity.}, }
@article {pmid39843757, year = {2025}, author = {Pitashny, M and Kesten, I and Shlon, D and Hur, DB and Bar-Yoseph, H}, title = {The Future of Microbiome Therapeutics.}, journal = {Drugs}, volume = {}, number = {}, pages = {}, pmid = {39843757}, issn = {1179-1950}, abstract = {The human microbiome exerts profound influence over various biological processes within the body. Unlike many host determinants, it represents a readily accessible target for manipulation to promote health benefits. However, existing commercial microbiome-directed products often exhibit low efficacy. Advancements in technology are paving the way for the development of novel microbiome therapeutics, across a wide range of indications. In this narrative review, we provide an overview of state-of-the-art technologies in late-stage development, examining their advantages and limitations. By covering a spectrum, from fecal-derived products to live biotherapeutics, phage therapy, and synthetic biology, we illuminate the path toward the future of microbiome therapeutics.}, }
@article {pmid39843735, year = {2025}, author = {Stephen-Victor, E and Kuziel, GA and Martinez-Blanco, M and Jugder, BE and Benamar, M and Wang, Z and Chen, Q and Lozano, GL and Abdel-Gadir, A and Cui, Y and Fong, J and Saint-Denis, E and Chang, I and Nadeau, KC and Phipatanakul, W and Zhang, A and Farraj, FA and Holder-Niles, F and Zeve, D and Breault, DT and Schmitz-Abe, K and Rachid, R and Crestani, E and Rakoff-Nahoum, S and Chatila, TA}, title = {RELMβ sets the threshold for microbiome-dependent oral tolerance.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {39843735}, issn = {1476-4687}, abstract = {Tolerance to dietary antigens is critical for avoiding deleterious type 2 immune responses resulting in food allergy (FA) and anaphylaxis[1,2]. However, the mechanisms resulting in both the maintenance and failure of tolerance to food antigens are poorly understood. Here we demonstrate that the goblet-cell-derived resistin-like molecule β (RELMβ)[3,4] is a critical regulator of oral tolerance. RELMβ is abundant in the sera of both patients with FA and mouse models of FA. Deletion of RELMβ protects mice from FA and the development of food-antigen-specific IgE and anaphylaxis. RELMβ disrupts food tolerance through the modulation of the gut microbiome and depletion of indole-metabolite-producing Lactobacilli and Alistipes. Tolerance is maintained by the local production of indole derivatives driving FA protective RORγt[+] regulatory T (Treg) cells[5] through activation of the aryl hydrocarbon receptor. RELMβ antagonism in the peri-weaning period restores oral tolerance and protects genetically prone offspring from developing FA later in life. Together, we show that RELMβ mediates a gut immune-epithelial circuit regulating tolerance to food antigens-a novel mode of innate control of adaptive immunity through microbiome editing-and identify targetable candidates in this circuit for prevention and treatment of FA.}, }
@article {pmid39843625, year = {2025}, author = {Jarquín-Díaz, VH and Dayaram, A and Soilemetzidou, ES and Desvars-Larrive, A and Bohner, J and Buuveibaatar, B and Kaczensky, P and Walzer, C and Greenwood, AD and Löber, U}, title = {Unraveling the distinctive gut microbiome of khulans (Equus hemionus hemionus) in comparison to their drinking water and closely related equids.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2767}, pmid = {39843625}, issn = {2045-2322}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Equidae/microbiology ; *RNA, Ribosomal, 16S/genetics ; Horses/microbiology ; *Drinking Water/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; Phylogeny ; }, abstract = {The microbial composition of host-associated microbiomes is influenced by co-evolutionary interactions, host genetics, domestication, and the environment. This study investigates the contribution of environmental microbiota from freshwater bodies to the gastrointestinal microbiomes of wild khulans (Equus hemionus hemionus, n = 21) and compares them with those of captive khulans (n = 12) and other equids-Przewalski's horse (n = 82) and domestic horse (n = 26). Using PacBio technology and the LotuS pipeline for 16S rRNA gene sequencing, we analyze microbial diversity and conduct differential abundance, alpha, and beta diversity analyses. Results indicate limited microbial sharing between wild khulans and their waterhole environments, suggesting minimal environmental influence on their gut microbiomes and low levels of water contamination by khulans. Wild khulans exhibit greater microbial diversity and richness compared to captive ones, likely due to adaptations to the harsh nutritional conditions of the Gobi desert. Conversely, captive khulans show reduced microbial diversity, potentially affected by dietary changes during captivity. These findings highlight the significant impact of environment and lifestyle on the gut microbiomes of equids.}, }
@article {pmid39843550, year = {2025}, author = {Radlinski, LC and Bäumler, AJ}, title = {Microbiome science needs more microbiologists.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {39843550}, issn = {2058-5276}, }
@article {pmid39843522, year = {2025}, author = {Bray, AS and Broberg, CA and Hudson, AW and Wu, W and Nagpal, RK and Islam, M and Valencia-Bacca, JD and Shahid, F and Hernandez, GE and Nutter, NA and Walker, KA and Bennett, EF and Young, TM and Barnes, AJ and Ornelles, DA and Miller, VL and Zafar, MA}, title = {Klebsiella pneumoniae employs a type VI secretion system to overcome microbiota-mediated colonization resistance.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {940}, pmid = {39843522}, issn = {2041-1723}, support = {AI178595//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI166642//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI173244//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {*Klebsiella pneumoniae/genetics/metabolism ; *Type VI Secretion Systems/genetics/metabolism ; Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Klebsiella Infections/microbiology ; Gene Expression Regulation, Bacterial ; Gastrointestinal Tract/microbiology ; Bacterial Proteins/metabolism/genetics ; DNA Transposable Elements/genetics ; Female ; Mice, Inbred C57BL ; }, abstract = {Microbial species must compete for space and nutrients to persist in the gastrointestinal (GI) tract, and our understanding of the complex pathobiont-microbiota interactions is far from complete. Klebsiella pneumoniae, a problematic, often drug-resistant nosocomial pathogen, can colonize the GI tract asymptomatically, serving as an infection reservoir. To provide insight on how K. pneumoniae interacts with the resident gut microbiome, we conduct a transposon mutagenesis screen using a murine model of GI colonization with an intact microbiota. Among the genes identified were those encoding a type VI secretion system (T6SS), which mediates contact-dependent killing of gram-negative bacteria. From several approaches, we demonstrate that the T6SS is critical for K. pneumoniae gut colonization. Metagenomics and in vitro killing assays reveal that K. pneumoniae reduces Betaproteobacteria species in a T6SS-dependent manner, thus identifying specific species targeted by K. pneumoniae. We further show that T6SS gene expression is controlled by several transcriptional regulators and that expression only occurs in vitro under conditions that mimic the gut environment. By enabling K. pneumoniae to thrive in the gut, the T6SS indirectly contributes to the pathogenic potential of this organism. These observations advance our molecular understanding of how K. pneumoniae successfully colonizes the GI tract.}, }
@article {pmid39843462, year = {2025}, author = {Wolf, S and Jayawickrama, C and Carlson, CA and Deutsch, C and Davis, EW and Daniels, BN and Chan, F and Giovannoni, SJ}, title = {Microbial carbon oxidation in seawater below the hypoxic threshold.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2838}, pmid = {39843462}, issn = {2045-2322}, mesh = {*Seawater/microbiology ; *Oxidation-Reduction ; *Carbon/metabolism ; *Oxygen/metabolism ; Microbiota ; Phytoplankton/metabolism ; Ecosystem ; Bacteria/metabolism/genetics ; }, abstract = {Global oxygen minimum zones (OMZs) often reach hypoxia but seldom reach anoxia. Recently it was reported that Michaelis Menten constants (Km) of oxidative enzymes are orders of magnitude higher than respiratory Km values, and in the Hypoxic Barrier Hypothesis it was proposed that, in ecosystems experiencing falling oxygen, oxygenase enzyme activities become oxygen-limited long before respiration. We conducted a mesocosm experiment with a phytoplankton bloom as an organic carbon source and controlled dissolved oxygen (DO) concentrations in the dark to determine whether hypoxia slows carbon oxidation and oxygen decline. Total oxygen utilization (TOU) in hypoxic treatment (ca. 7.1 µM O2) was 21.7% lower than the oxic treatment (ca. 245.1 µM O2) over the first 43 days of the experiment. In addition, following the restoration of fully oxic conditions to the hypoxic treatment, TOU accelerated, demonstrating that oxidative processes are sensitive to DO concentrations found in large volumes of the ocean. Microbial amplicon-based community composition diverged between oxic treatments, indicating a specialized microbiome that included Thioglobaceae (SUP05 Gammaproteobacteria), OM190 (Planctomycetota), ABY1 (Patescibacteria), and SAR86 subclade D2472, thrived in the hypoxic treatment, while the genus Candidatus Actinomarina and SAR11 alphaproteobacteria were sharply inhibited. Our findings support the hypothesis that oxygenase kinetics might slow the progression of ocean deoxygenation in oxygen-poor regions and be a factor in the evolution of microbial taxa adapted to hypoxic environments.}, }
@article {pmid39843444, year = {2025}, author = {Bechtold, EK and Ellenbogen, JB and Villa, JA and de Melo Ferreira, DK and Oliverio, AM and Kostka, JE and Rich, VI and Varner, RK and Bansal, S and Ward, EJ and Bohrer, G and Borton, MA and Wrighton, KC and Wilkins, MJ}, title = {Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {944}, pmid = {39843444}, issn = {2041-1723}, support = {EAR-2029686//National Science Foundation (NSF)/ ; PRFB-2109592//National Science Foundation (NSF)/ ; DEB-1754756//National Science Foundation (NSF)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; DE-SC000054//U.S. Department of Energy (DOE)/ ; DE-SC0007144//U.S. Department of Energy (DOE)/ ; DE-SC0012088//U.S. Department of Energy (DOE)/ ; DESC0023297//U.S. Department of Energy (DOE)/ ; DE-SC0023456//U.S. Department of Energy (DOE)/ ; DE-SC0023456//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC000054//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC000054//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; DE-SC0022191//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0021350//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0021350//U.S. Department of Energy (DOE)/ ; DESC000054//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; }, mesh = {*Methane/metabolism ; *Wetlands ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Fresh Water/microbiology ; Metagenome ; Bacteria/metabolism/genetics/classification ; Climate Change ; }, abstract = {Current estimates of wetland contributions to the global methane budget carry high uncertainty, particularly in accurately predicting emissions from high methane-emitting wetlands. Microorganisms drive methane cycling, but little is known about their conservation across wetlands. To address this, we integrate 16S rRNA amplicon datasets, metagenomes, metatranscriptomes, and annual methane flux data across 9 wetlands, creating the Multi-Omics for Understanding Climate Change (MUCC) v2.0.0 database. This resource is used to link microbiome composition to function and methane emissions, focusing on methane-cycling microbes and the networks driving carbon decomposition. We identify eight methane-cycling genera shared across wetlands and show wetland-specific metabolic interactions in marshes, revealing low connections between methanogens and methanotrophs in high-emitting wetlands. Methanoregula emerged as a hub methanogen across networks and is a strong predictor of methane flux. In these wetlands it also displays the functional potential for methylotrophic methanogenesis, highlighting the importance of this pathway in these ecosystems. Collectively, our findings illuminate trends between microbial decomposition networks and methane flux while providing an extensive publicly available database to advance future wetland research.}, }
@article {pmid39843443, year = {2025}, author = {Wu, X and Tjahyo, AS and Volchanskaya, VSB and Wong, LH and Lai, X and Yong, YN and Osman, F and Tay, SL and Govindharajulu, P and Ponnalagu, S and Tso, R and Teo, HS and Khoo, K and Fan, H and Goh, CC and Yap, CPL and Leow, MK and Henry, CJ and Haldar, S and Lim, KJ}, title = {A legume-enriched diet improves metabolic health in prediabetes mediated through gut microbiome: a randomized controlled trial.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {942}, pmid = {39843443}, issn = {2041-1723}, mesh = {Humans ; *Prediabetic State/diet therapy/metabolism/therapy/blood/microbiology ; Middle Aged ; *Gastrointestinal Microbiome ; Male ; Female ; *Fabaceae ; Aged ; *Caloric Restriction/methods ; Single-Blind Method ; Singapore ; Blood Glucose/metabolism ; Glycated Hemoglobin/metabolism ; Body Mass Index ; Cholesterol, LDL/blood/metabolism ; }, abstract = {Healthy dietary patterns rich in legumes can improve metabolic health, although their additional benefits in conjunction with calorie restriction have not been well-established. We investigated effects of a calorie-restricted, legume-enriched, multicomponent intervention diet compared with a calorie-restricted control diet in 127 Chinese prediabetes participants, living in Singapore. The study was a 16-week, single-blind, parallel-design, randomized controlled trial (n = 63 intervention group (IG), n = 64 control group (CG); mean ± SD age 62.2 ± 6.3 years, BMI 23.8 ± 2.6 kg/m[2]). Primary outcomes were markers of glycemia and all measurements were taken at 2 or 4-weekly intervals. At the end of 16 weeks, both groups had significantly lower BMI (q(Time) = 1.92 ×10[-42], β = -0.02) compared with baseline, with minimal difference between groups. The IG had significantly greater reductions in LDL cholesterol (q(Treatment×Time) = 0.01, β = -0.16), total cholesterol (q(Treatment×Time) = 0.02, β = -0.3) and HbA1c (q(Treatment×Time) = 0.04, β = -0.004) compared with CG, alongside increases in fiber degrading species in IG, mediated through metabolites such as bile acids and amino acids. A legume-enriched, multicomponent intervention diet can improve metabolic health in a prediabetes population, in addition to benefits obtained from calorie restriction alone, partially mediated through changes in gut microbial composition and function. Trial registration: Clinical Trials NCT04745702.}, }
@article {pmid39843249, year = {2025}, author = {Aqeel, A and Kay, MC and Zeng, J and Petrone, BL and Yang, C and Truong, T and Brown, CB and Jiang, S and Carrion, VM and Bryant, S and Kirtley, MC and Neshteruk, CD and Armstrong, SC and David, LA}, title = {Grocery intervention and DNA-based assessment to improve diet quality in pediatric obesity: a pilot randomized controlled study.}, journal = {Obesity (Silver Spring, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1002/oby.24205}, pmid = {39843249}, issn = {1930-739X}, support = {//Chan Zuckerberg Initiative/ ; //Burroughs Wellcome Fund Pathogenesis of Infectious Disease Award/ ; //Duke Microbiome Center/ ; 1KL2TR002554/TR/NCATS NIH HHS/United States ; UL1TR002553/TR/NCATS NIH HHS/United States ; //Duke Clinical and Translational Science Award/ ; R01-DK116187-06A1/DK/NIDDK NIH HHS/United States ; R01-DK128611-01A1/DK/NIDDK NIH HHS/United States ; }, abstract = {OBJECTIVE: We assessed the impact of a food-provisioning intervention on diet quality in children with obesity.<br><br>METHODS: Participants (n&#x2009;=&#x2009;33, aged 6-11&#x2009;years) were randomly assigned to either usual care (intensive health behavior and lifestyle treatment) or intervention (usual care + food provisioning; high-fiber, low-dairy diet) for 4&#x2009;weeks. The primary outcome was a change in child diet quality at Week 4. Secondary outcomes were changes in weight, food insecurity, gut microbiome composition (16S ribosomal RNA), and dietary intake, measured via an objective DNA-based biomarker (i.e., FoodSeq). Genomic dietary data were analyzed against a larger pediatric adolescent obesity cohort (n&#x2009;=&#x2009;195, aged 10-18&#x2009;years) from similar households.<br><br>RESULTS: Intervention demonstrated changes across all assessed diet components and was more effective than usual care in increasing whole grain (&#x3b2;&#x2009;=&#x2009;0.20, 95% CI: 0.05 to 0.34; p&#x2009;=&#x2009;0.013) and fiber (&#x3b2;&#x2009;=&#x2009;2.52, 95% CI: 1.28 to 3.76; p&#x2009;<&#x2009;0.001) and decreasing dairy (&#x3b2;&#x2009;=&#x2009;-1.31, 95% CI: -2.02 to -0.60; p&#x2009;=&#x2009;0.001). FoodSeq results, highly concordant with grocery orders (adjusted R[2]&#x2009;=&#x2009;0.65; p&#x2009;<&#x2009;0.001), indicated a dietary shift toward low-energy-density plant taxa in the intervention relative to a prior survey of diet in a related cohort (&#x3b2;&#x2009;=&#x2009;8.64, 95% CI: 5.18 to 12.14; p&#x2009;<&#x2009;0.001). No significant changes were observed in microbiome, weight, or food insecurity.<br><br>CONCLUSIONS: Our study supports the potential of dietitian-guided food provisioning for improving diet quality in children with obesity and demonstrates an objective genomic approach for evaluating dietary shifts.}, }
@article {pmid39843118, year = {2025}, author = {Liu, Y and Liu, Q and Ma, M and Zhang, J and Liu, M and Mosenthin, R and Zhao, L and Huang, S and Ma, Q}, title = {Dietary arabinogalactan modulates immunity and improves gut barrier in broilers via regulating metabolome and gut microbiome.}, journal = {Carbohydrate polymers}, volume = {352}, number = {}, pages = {123223}, doi = {10.1016/j.carbpol.2025.123223}, pmid = {39843118}, issn = {1879-1344}, mesh = {Animals ; *Galactans/chemistry/pharmacology ; *Chickens/immunology ; *Gastrointestinal Microbiome/drug effects ; *Metabolome/drug effects ; Dietary Supplements ; Animal Feed ; Larix/chemistry ; }, abstract = {The extraction of polysaccharides from wood by-products is recognized as a green re-utilization approach to shape a recycling-oriented society. In this research, we identified the structural properties of arabinogalactan (AG) extracted from Larix sibirica Ledeb wood chips and verified its efficacy as an additive in broiler framing. Results showed that the molecular weight of AG is 19.805 KDa. Methylation analysis and NMR spectra indicate that AG has a 1,6-linked Galp backbone, side residues mainly branched at C-1,3,6 on β-D-Galp. The Ara residues were substituted at C-3 of 1,6-linked Galp consisting of α-L-Araf-(1→3)-α-L-Araf-(1 → 3)-α-L-Araf (1→ and α-L-Araf-(1 → 4) β-D-Galp-(1 → 3)-β-D-Galp-(1→. As a dietary supplement in broiler model, AG treatment improved the body weight of broilers especially breast and leg muscle weight. Furthermore, AG could regulate host immune response, gut microbiota composition, and metabolic activity, especially promoting lipid metabolism. By means of serum non-targeted metabolomics analysis, enrichment of pantothenate and CoA biosynthesis and beta-alanine metabolism pathways could be determined. AG treatment led to a rise in bacteria that produce SCFAs, with elevated concentrations of acetic and butyric acids. In conclusion, AG can be considered as a potential dietary supplement to beneficially affect host's health status.}, }
@article {pmid39842720, year = {2025}, author = {Mahdavi, S and Anthony, NM and Sikaneta, T and Tam, PY}, title = {Perspective: Multi-omics and Artificial Intelligence for Personalized Nutritional Management of Diabetes in Patients Undergoing Peritoneal Dialysis.}, journal = {Advances in nutrition (Bethesda, Md.)}, volume = {}, number = {}, pages = {100378}, doi = {10.1016/j.advnut.2025.100378}, pmid = {39842720}, issn = {2156-5376}, abstract = {Managing diabetes in patients on peritoneal dialysis (PD) is challenging due to the combined effects of dietary glucose, glucose from dialysate, and other medical complications. Advances in technology that enable continuous biological data collection are transforming traditional management approaches. This review explores how multi-omics technologies and artificial intelligence (AI) are enhancing glucose management in this patient population. Continuous glucose monitoring (CGM) offers significant advantages over traditional markers like hemoglobin A1c (HbA1c). Unlike HbA1c, which reflects an average glucose level, CGM provides real-time, dynamic glucose data that allow clinicians to make timely adjustments, leading to better glycemic control and outcomes. Multi-omics approaches are valuable for understanding genetic factors that influence susceptibility to diabetic complications, particularly those related to advanced glycation end-products (AGEs). Identifying genetic polymorphisms that modify a patient's response to AGEs allows for personalized treatments, potentially reducing the severity of diabetes-related pathologies. Metabolomic analyses of peritoneal dialysis effluent are also promising, as they help identify early biomarkers of metabolic dysregulation. Early detection can lead to timely interventions and more tailored treatment strategies, improving long-term patient care. AI integration is revolutionizing diabetes management for PD patients by processing vast datasets from CGM, genetic, metabolic and microbiome profiles. AI can identify patterns and predict outcomes that may be difficult for humans to detect, enabling highly personalized recommendations for diet, medication, and dialysis management. Furthermore, AI can assist clinicians by automating data interpretation, improving treatment plans and enhancing patient education. Despite the promise of these technologies, there are limitations. CGM, multi-omics and AI require significant investment in infrastructure, training and validation studies. Additionally, integrating these approaches into clinical practice presents logistical and financial challenges. Nevertheless, personalized, data-driven strategies offer great potential for improving outcomes in diabetes management for PD patients.}, }
@article {pmid39842611, year = {2025}, author = {Erkert, L and Ruder, B and Kabisch, M and Gamez Belmonte, R and Patankar, JV and Gonzalez Acera, M and Schödel, L and Chiriac, MT and Cineus, R and Gnafakis, S and Leupold, T and Thoma, OM and Stolzer, I and Taut, A and Thonn, V and Zundler, S and Günther, C and Diefenbach, A and Kühl, AA and Hegazy, AN and Waldner, M and Basic, M and Bleich, A and , }, title = {TIFA renders intestinal epithelial cells responsive to microbial ADP-heptose and drives colonic inflammation in mice.}, journal = {Mucosal immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.mucimm.2025.01.003}, pmid = {39842611}, issn = {1935-3456}, abstract = {Intestinal immune homeostasis relies on intestinal epithelial cells (IECs), which provide an efficient barrier, and warrant a state of tolerance between the microbiome and the mucosal immune system. Thus, proper epithelial microbial sensing and handling of microbes is key to preventing excessive immunity, such as seen in patients with inflammatory bowel disease (IBD). To date, the molecular underpinnings of these processes remain incompletely understood. This study identifies TIFA as a driver of intestinal inflammation and an epithelial signaling hub between the microbiome and mucosal immune cells. TIFA was constitutively expressed in crypt epithelial cells and was highly induced in the intestine of mice and IBD patients with intestinal inflammation. We further identified IL-22 signaling via STAT3 as key mechanism driving TIFA expression in IECs. At the molecular level, we demonstrate that TIFA expression is essential for IEC responsiveness to the bacterial metabolite ADP-heptose. Most importantly, ADP-heptose-induced TIFA signaling orchestrates an inflammatory cellular response in the epithelium, with NF-κB and inflammasome activation, and high levels of chemokine production. Finally, mice lacking TIFA were protected from intestinal inflammation when subjected to a model of experimental colitis. In conclusion, our study implicates that targeting TIFA may be a strategy for future IBD therapy.}, }
@article {pmid39842557, year = {2025}, author = {Loman, BR}, title = {Communities, mysteries, and pathophysiologies - Are gut microbes key to a healthy mind?.}, journal = {Brain, behavior, and immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.bbi.2025.01.012}, pmid = {39842557}, issn = {1090-2139}, }
@article {pmid39842491, year = {2025}, author = {Rewell, SSJ and Shad, A and Chen, L and Macowan, M and Chu, E and Gandasasmita, N and Casillas-Espinosa, PM and Li, J and O'Brien, TJ and Semple, BD}, title = {A post-injury immune challenge with lipopolysaccharide following adult traumatic brain injury alters neuroinflammation and the gut microbiome acutely, but has little effect on chronic outcomes.}, journal = {Experimental neurology}, volume = {}, number = {}, pages = {115150}, doi = {10.1016/j.expneurol.2025.115150}, pmid = {39842491}, issn = {1090-2430}, abstract = {Patients with a traumatic brain injury (TBI) are susceptible to hospital-acquired infections, presenting a significant challenge to an already-compromised immune system. The consequences and mechanisms by which this dual insult worsens outcomes are poorly understood. This study aimed to explore how a systemic immune stimulus (lipopolysaccharide, LPS) influences outcomes following experimental TBI in young adult mice. Male and female C57Bl/6 J mice underwent controlled cortical impact or sham surgery, followed by 1 mg/kg i.p. LPS or saline-vehicle at 4 days post-TBI, before behavioral assessment and tissue collection at 6 h, 24 h, 7 days or 6 months. LPS induced acute sickness behaviors including weight loss, transient hypoactivity, and increased anxiety-like behavior. Early systemic immune activation by LPS was confirmed by increased spleen weight and serum cytokines. In brain tissue, gene expression analysis revealed a time course of inflammatory immune activation in TBI or LPS-treated mice (e.g., IL-1β, IL-6, CCL2, TNFα), which was exacerbated in TBI + LPS mice. This group also presented with fecal microbiome dysbiosis at 24 h post-LPS, with reduced bacterial diversity and changes in the relative abundance of key bacterial genera associated with sub-acute neurobehavioral and immune changes. Chronically, TBI induced hyperactivity and cognitive deficits, brain atrophy, and increased seizure susceptibility, similarly in vehicle and LPS-treated groups. Together, findings suggest that an immune challenge with LPS early after TBI, akin to a hospital-acquired infection, alters the acute neuroinflammatory response to injury, but has no lasting effects. Future studies could consider more clinically-relevant models of infection to build upon these findings.}, }
@article {pmid39842355, year = {2025}, author = {Li, N and Li, X and Zhao, L and Lu, ZD and Liu, YW and Wang, N}, title = {Slow sand filters with variable filtration rates for rainwater purification: Microecological differences between biofilm and water phases.}, journal = {Journal of environmental management}, volume = {375}, number = {}, pages = {124210}, doi = {10.1016/j.jenvman.2025.124210}, pmid = {39842355}, issn = {1095-8630}, abstract = {Slow sand filters (SSFs) have been increasingly applied to rainwater purification in recent years, but the response of SSFs to fluctuating rainfall, as well as the biofilm- and water-phase microecology in SSFs are still poorly understood. This study systematically evaluated the rainwater purification performance of SSFs and compared the bacterial community structure, assembly processes and molecular ecological interactions between the biofilm and water phases. The activated carbon and activated alumina filters exhibited the best performance for NH4[+]-N (18.82%∼64.00%) and TP (>90%) removal, respectively. As the filtration rate increased from 0.1 m/h to 0.3 m/h, the rainwater purification efficiencies of the three SSFs deteriorated significantly, with the enrichment of Tolumonas, Desulfovibrio and Sulfurospirillum, and reduction in Klebsiella and Enterobacter. The community diversity of biofilm phase was significantly higher than that of water phase, and filtration rate was identified as a key factor in shaping the bacterial community in both phases. The interactions of filtration rate and water quality displayed the best and significant (p < 0.01) explanation for microbiome shift, with the higher values in biofilm phase (34.70%) than in water phase (24.02%). Bacterial community assembly in SSFs was determined by stochastic ecological processes, which played a more important role in water-phase communities, with 86.34% following predictions using a neutral community model. The molecular ecological network of biofilm phase exhibited more complexity, lower modularity and more cooperative relationships than that of water phase. Disadvantaged OTUs occupied core and notable positions in the network, with the highest degree and clustering coefficient. Different keystone species were identified in biofilm- (Runella, Aquabacterium, etc) and water-network (Terrimonas) respectively, despite they processed low relative abundances (<0.1%). These results enhance the understanding of microecology in SSFs, and shed new lights on the improvement and promotion of rainwater biological treatment technology.}, }
@article {pmid39842122, year = {2025}, author = {Fan, Z and Khan, MM and Wang, K and Li, Y and Jin, F and Peng, J and Chen, X and Kong, W and Lv, X and Chen, X and Qiu, B and Wang, X}, title = {Disruption of midgut homeostasis by microplastics in Spodoptera frugiperda: Insights into inflammatory and oxidative mechanisms.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137262}, doi = {10.1016/j.jhazmat.2025.137262}, pmid = {39842122}, issn = {1873-3336}, abstract = {Microplastics have evolved as widespread contaminants in terrestrial and aquatic environments, raising significant environmental concerns due to their persistence and bioaccumulation. In this study, we investigated the toxicity of polyethylene microplastics (PE-MPs) on the agricultural insect, Spodoptera frugiperda. Maize leaves containing three sizes (0.5 μm, 5 μm, and 50 μm) of PE-MPs were fed to fall armyworm larvae for 12 days at concentrations of 1.25 g/ L, 5 g/L, and 20 g/L. The results showed that smaller size and higher concentration of microplastics led to increased toxicity. Furthermore, different sizes and maximum concentrations of PE-MPs were selected for subsequent experiments to observe changes in histological and enzymatic biomarkers, midgut microbiome, and metabolic responses. Following PE-MPs exposure, inflammation signs and oxidative stress were detected in the midgut. Significant changes were also observed in midgut microbiota and metabolomes, most related with oxidative stress, inflammatory disorders, and energy metabolism. These results provide evidence of midgut damage and alterations in the microbiota and metabolome of S. frugiperda because of PE-MPs exposure, highlighting the harm that microplastics can inflict on agricultural insects. Additionally, the study lays a theoretical foundation for future research on the transmission of microplastics through the food chain in agricultural ecosystems.}, }
@article {pmid39842118, year = {2025}, author = {Song, Y and Huang, H and Jia, K and Zou, S and Yang, Y and Yi, M}, title = {Multi-omics analysis reveals toxicity and gut-liver axis disruption induced by polychlorinated biphenyls exposure in Yellowfin Seabream (Acanthopagrus latus).}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137296}, doi = {10.1016/j.jhazmat.2025.137296}, pmid = {39842118}, issn = {1873-3336}, abstract = {Polychlorinated biphenyls (PCBs) are persistent organic pollutants known for their environmental persistence and bioaccumulation, posing significant health risks. This study examines the toxic effects of a representative PCBs (Aroclor 1254) on yellowfin seabream (Acanthopagrus latus) exposured for 30 days through a multi-omics approach. Histopathological examinations revealed structural damage to the intestinal structure and hepatic steatosis, along with elevated serum lipopolysaccharide levels, indicating compromised intestinal barrier integrity and liver inflammation. Metabolomic profiling showed significant alterations in lipid metabolites, including elevated lysophosphatidylcholines and arachidonic acid derivatives. Transcriptomic analysis unveiled 2272 differentially expressed genes in the liver, with notable changes in immune response and metabolic pathways. Gut microbiome analysis showed dysbiosis characterized by an increase in Proteobacteria and a decrease in Firmicutes and Actinobacteria. Remarkably, Tetranor-12S-HETE and LPC 15:1 emerged as key biomarkers for the disruption of the gut-liver axis, correlating with immune gene expression and gut microbiota composition. The integration of transcriptomic, metabolomic, and microbiome data highlighted the complex interplay between A1254 exposure and the gut-liver axis, emphasizing the central role played by PPAR signaling in mediating these effects. Collectively, these results indicate that exposure to A1254 results in bioaccumulation in the liver and gut, leading to severe tissue injury, microbiota dysbiosis, and dysregulation of the gut-liver axis, ultimately disrupting lipid metabolism. These findings underscore the metabolic health risks posed by PCBs exposure in aquatic environments.}, }
@article {pmid39842107, year = {2025}, author = {Zhang, Y and Song, Q and Meng, Q and Zhao, T and Wang, X and Meng, X and Cong, J}, title = {Size-dependent ecotoxicological impacts of tire wear particles on zebrafish physiology and gut microbiota: Implications for aquatic ecosystem health.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137215}, doi = {10.1016/j.jhazmat.2025.137215}, pmid = {39842107}, issn = {1873-3336}, abstract = {The ecological impact of tire wear particles (TWP), a significant source of microplastics pollution, is increasingly concerning, especially given their potential effects on the health of aquatic ecosystems. This study investigates the size-dependent ecotoxicological responses of zebrafish (Danio rerio) to TWP exposure, focusing on physiological, metabolic, and microbial community impacts over a 15-day exposure period followed by a 15-day excretion period. Through integrated analysis of gut microbiome composition, liver transcriptomics, and host physiological markers, we found that smaller TWP particles (< 120 μm) induced oxidative stress, evidenced by increased SOD and MDA levels, and inhibited growth by reducing body mass and gut length. In contrast, larger TWP particles (250-380 μm) caused more substantial disruptions in lipid and xenobiotic metabolic pathways, as shown by significant downregulation of key metabolic genes (acads, cpt2_1, hadhaa), and alterations in the gut microbiome, including the enrichment of pathogenic genera, such as Enterococcus and Fusobacterium, while depleting beneficial microbes like Acinetobacter and Methyloversatilis. These microbiome shifts led to a more complex and potentially pathogenic gut microbiome. Notably, zebrafish displayed adaptive resilience during the excretion period, with significant recovery in body mass and microbial composition, emphasizing the adaptive capacity of aquatic organisms to pollutants. Our findings underscore the broader ecological risks posed by TWP, the pivotal role of gut microbiota in host resilience to pollutants, and the need for comprehensive management strategies addressing emerging contaminants in aquatic ecosystems.}, }
@article {pmid39842104, year = {2025}, author = {Dolan, BP}, title = {Clinical trials explore altering companion animals' microbiome.}, journal = {American journal of veterinary research}, volume = {}, number = {}, pages = {1}, doi = {10.2460/ajvr.24.12.0383}, pmid = {39842104}, issn = {1943-5681}, }
@article {pmid39842075, year = {2025}, author = {Liu, J and Chen, Y and Cen, Z and Hong, M and Zhang, B and Luo, X and Wang, L and Li, S and Xiao, X and Long, Q}, title = {Ganoderma lucidum spore oil attenuates acute liver injury by modulating lipid metabolism and gut microbiota.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {256}, number = {}, pages = {116674}, doi = {10.1016/j.jpba.2025.116674}, pmid = {39842075}, issn = {1873-264X}, abstract = {The incidence of acute liver injury is increasing and poses a significant threat to human health. Ganoderma lucidum spore oil (GLSO), a lipid substance extracted from Ganoderma lucidum spore powder using supercritical CO2 technology, has been investigated for its potential to prevent acute liver injury. However, the specific mechanism underlying the protective effects of GLSO remains incompletely understood. In this study, we investigated the preventive effect of GLSO on acute liver injury in rats, focusing on the gut microbiome and serum metabolomics. GLSO effectively alleviated liver dysfunction and reduced inflammation, leading to the prevention of acute liver injury in rats. Serum metabolomics analysis revealed that GLSO primarily modulated lipid metabolic pathways related to glycerophospholipid metabolism and sphingolipid metabolism. Specifically, GLSO decreased the levels of metabolites such as lysophosphatidylcholine (LPC), glycerophosphatidylcholine (GPC), and sphinganine 1-phosphate (SA1P), while increasing the levels of phosphatidylglycerol (PG) and digalactosylceramide (DGC). Gut microbiomics data indicated that GLSO effectively regulated the composition of the gut microbiota in rats with acute liver injury. Specifically, it increased the abundance of Firmicutes and decreased the abundance of Proteobacteria. Mantel test correlation analysis revealed a close relationship between gut microbial Burkholderiales and lipid metabolites in GLSO-mediated prevention of acute liver injury. GLSO exerts its preventive effects on acute liver injury by remodeling the gut microbiota and regulating lipid metabolism. These findings provide novel insights and potential directions for the development of new drugs targeting acute liver injury.}, }
@article {pmid39842063, year = {2025}, author = {Jung, Y and Park, C and Lee, H and Yun, JI and Joo, SY and Seo, CH and Lee, ST and Kim, M and Cho, YS}, title = {Association of the skin microbiome with the biomechanical scar properties in patients with burns.}, journal = {Burns : journal of the International Society for Burn Injuries}, volume = {51}, number = {3}, pages = {107372}, doi = {10.1016/j.burns.2025.107372}, pmid = {39842063}, issn = {1879-1409}, abstract = {BACKGROUND AND OBJECTIVES: Skin microbiome dysbiosis can cause skin barrier dysfunction and stimulate scar property change. Skin barrier disruption post-burn injury leads to an imbalance in skin microbe diversity and distribution. We aimed to examine the changes in the skin microbiome of re-epithelialized burn scars.<br><br>MATERIAL AND METHODS: Twenty three patients were enrolled between January 2020 and July 2022. Twenty-six (13 Scar 1, immediately after complete wound healing; and 13 Scar 2, 3 months after complete wound healing) of seventy-eight scar skin samples (39 Scar 1 and 39 scar 2) qualified for analysis. Microbial community analysis was performed. Biomechanical scar properties of each patient and their correlation with skin microbiome were investigated.<br><br>RESULTS: The &#x3b1;-diversity of the scarred skin microbiome increased with time (Shannon's index, p&#x202f;=&#x202f;0.029; Simpson's index, p&#x202f;=&#x202f;0.009). The linear discriminant analysis effect size results showed that Bacteroides abundance decreased in scars after 3 months, whereas Campylobacter and Cutibacterium abundance increased. Campylobacter and Cutibacterium negatively and positively correlated with the final distensibility gross and biological elasticity, respectively. These results were consistent with the changes in the biomechanical properties of scars.<br><br>CONCLUSION: The scar skin microbial communities in patients with burns changed with biomechanical scar properties over time, and specific skin microorganisms correlated with biomechanical scar dynamics at the genus level.}, }
@article {pmid39841658, year = {2025}, author = {Henry, NL and Kidwell, KM and Kozar, S and Snyder, S and Zick, SM}, title = {Self-acupressure for patients with breast cancer experiencing aromatase inhibitor-associated musculoskeletal symptoms: Protocol for the AcuAIM randomized pilot trial.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0311044}, doi = {10.1371/journal.pone.0311044}, pmid = {39841658}, issn = {1932-6203}, mesh = {Humans ; Female ; *Breast Neoplasms/drug therapy ; *Aromatase Inhibitors/adverse effects/therapeutic use ; Pilot Projects ; *Acupressure/methods ; Middle Aged ; Postmenopause ; Arthralgia/therapy/chemically induced/etiology ; Quality of Life ; }, abstract = {BACKGROUND: Aromatase inhibitors (AI) reduce hormone receptor-positive breast cancer recurrence risk by about 50%. However, half of AI-treated postmenopausal women report new or worsened musculoskeletal symptoms (AIMSS), and 20% discontinue therapy prematurely. Acupuncture is effective for reducing symptoms, but many women are not able to access acupuncture therapy. We hypothesize that self-administered acupressure will reduce AIMSS.<br><br>MATERIALS AND METHODS: Postmenopausal women who have been receiving treatment with an AI for more than 3 weeks but less than 2 years, and who report new or worsened joint pain or myalgias since starting AI therapy with worst pain of at least 4 out of 10 on a numerical rating scale, are eligible. Fifty participants will be enrolled and randomized 1:1 to treatment with true or sham acupressure for 12 weeks. Participants will self-apply pressure for 3 minutes to each of the 9 acupoints daily. All participants will complete a pain assessment weekly, and a battery of symptom questionnaires every 6 weeks. Optional stool samples will be collected after 0 and 12 weeks of acupressure to examine changes in the gut microbiome. The primary endpoint is change in worst pain on the Brief Pain Inventory-Short Form with 12 weeks of the acupressure intervention, evaluated with generalized estimating equations.<br><br>CONCLUSION: Determination that self-administered acupressure reduces AIMSS in this randomized phase 2 pilot trial will lead to a larger randomized phase 3 clinical trial to confirm the efficacy of self-acupressure. Reduction of AI-related arthralgias may improve persistence with breast cancer therapy, breast cancer outcomes, and quality of life for AI-treated patients.<br><br>TRIAL REGISTRATION: Clinicaltrials.gov NCT06228768.}, }
@article {pmid39841528, year = {2025}, author = {Nicholson, TL and Stuart, KL and Bayles, DO}, title = {Streptococcus suivaginalis sp. nov., Streptococcus iners sp. nov. and Streptococcus iners subsp. hyiners subsp. nov. isolated from pigs.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {75}, number = {1}, pages = {}, doi = {10.1099/ijsem.0.006631}, pmid = {39841528}, issn = {1466-5034}, mesh = {Animals ; *Streptococcus/genetics/isolation &amp; purification/classification ; *Phylogeny ; Swine ; *RNA, Ribosomal, 16S/genetics ; *DNA, Bacterial/genetics ; *Bacterial Typing Techniques ; *Nucleic Acid Hybridization ; *Sequence Analysis, DNA ; *Genome, Bacterial ; Base Composition ; }, abstract = {Three novel strains within the genus Streptococcus (29887[T], 29892[T] and 29896[T]) were isolated from healthy pigs during routine veterinary physical exams. All three strains were non-motile and non-spore-forming Gram-positive cocci. The complete genome of each strain was attained, and phylogenetic analyses were performed. Comparison of the genomes of 29887[T], 29892[T] and 29896[T] to the genomes of other Streptococcus strains revealed digital DNA-DNA hybridization (dDDH) values between 21.2% and 53.9% and average nucleotide identity (ANI) values between 70.00% and 94.44%. Phylogenetic analyses suggested that each strain, 29896[T] (S. suivaginalis sp. nov.), 29887[T] (S. iners sp. nov.) and 29892[T] (S. iners subsp. hyiners subsp. nov.), may represent a novel species within the genus Streptococcus, while ANI analysis indicated that strains 29896[T] (S. suivaginalis sp. nov.) and 29887[T] (S. iners sp. nov.) represent novel species within the genus Streptococcus, and 29892[T] (S. iners subsp. hyiners subsp. nov.) represents a novel subspecies of 29887[T] (S. iners sp. nov.). Based upon the combined data presented in this study, two novel species, Streptococcus suivaginalis sp. nov. (type strain, 29896[T]=NRRL B-65677[T]=NCTC 14941[T]) and Streptococcus iners sp. nov. (type strain, 29887[T]=NRRL B-65675[T]=NCTC 14939[T]) are proposed, and one novel subspecies, Streptococcus iners subsp. hyiners subsp. nov. (type strain, 29892[T]=NRRL B-65676[T]=NCTC 14940[T]) is proposed.}, }
@article {pmid39841201, year = {2025}, author = {Geng, P and Zhao, N and Zhou, Y and Harris, RS and Ge, Y}, title = {Faecalibacterium prausnitzii regulates carbohydrate metabolic functions of the gut microbiome in C57BL/6 mice.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2455503}, doi = {10.1080/19490976.2025.2455503}, pmid = {39841201}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Mice, Inbred C57BL ; Mice ; *Carbohydrate Metabolism ; *Faecalibacterium prausnitzii/metabolism/genetics ; *Phylogeny ; *Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Probiotics/administration &amp; dosage ; Male ; Metagenome ; }, abstract = {The probiotic impact of microbes on host metabolism and health depends on both host genetics and bacterial genomic variation. Faecalibacterium prausnitzii is the predominant human gut commensal emerging as a next-generation probiotic. Although this bacterium exhibits substantial intraspecies diversity, it is unclear whether genetically distinct F. prausnitzii strains might lead to functional differences in the gut microbiome. Here, we isolated and characterized a novel F. prausnitzii strain (UT1) that belongs to the most prevalent but underappreciated phylogenetic clade in the global human population. Genome analysis showed that this butyrate-producing isolate carries multiple putative mobile genetic elements, a clade-specific defense system, and a range of carbohydrate catabolic enzymes. Multiomic approaches were used to profile the impact of UT1 on the gut microbiome and associated metabolic activity of C57BL/6 mice at homeostasis. Both 16S rRNA and metagenomic sequencing demonstrated that oral administration of UT1 resulted in profound microbial compositional changes including a significant enrichment of Lactobacillus, Bifidobacterium, and Turicibacter. Functional profiling of the fecal metagenomes revealed a markedly higher abundance of carbohydrate-active enzymes (CAZymes) in UT1-gavaged mice. Accordingly, UT1-conditioned microbiota possessed the elevated capability of utilizing starch in vitro and exhibited a lower availability of microbiota-accessible carbohydrates in the gut. Further analysis uncovered a functional network wherein UT1 reduced the abundance of mucin-degrading CAZymes and microbes, which correlated with a concomitant reduction of fecal mucin glycans. Collectively, our results reveal a crucial role of UT1 in facilitating the carbohydrate metabolism of the gut microbiome and expand our understanding of the genetic and phenotypic diversity of F. prausnitzii.}, }
@article {pmid39841165, year = {2025}, author = {Peters, BA and Xue, X and Hanna, DB and Wang, Y and Wang, Z and Sharma, A and Floris-Moore, M and Konkle-Parker, D and Alcaide, ML and Sheth, AN and Topper, EF and Weber, KM and Tien, PC and Merenstein, D and Vásquez, E and Chen, Y and Mimiaga, MJ and Stosor, V and Brown, TT and Erlandson, KM and Dillon, SM and Elsayed, NS and Usyk, M and Sollecito, CC and Kaplan, RC and Burk, RD and Qi, Q}, title = {Healthy Aging and the Gut Microbiome in People With and Without HIV.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiae644}, pmid = {39841165}, issn = {1537-6613}, support = {U01-HL146241/HL/NHLBI NIH HHS/United States ; //Eunice Kennedy Shriver/ ; //National Institute of Child Health and Human Development/ ; /AG/NIA NIH HHS/United States ; /DE/NIDCR NIH HHS/United States ; //National Institute of Allergy and Infectious Diseases/ ; /NS/NINDS NIH HHS/United States ; /MH/NIMH NIH HHS/United States ; /DA/NIDA NIH HHS/United States ; /NR/NINR NIH HHS/United States ; /CA/NCI NIH HHS/United States ; /AA/NIAAA NIH HHS/United States ; /DC/NIDCD NIH HHS/United States ; /DK/NIDDK NIH HHS/United States ; /MD/NIMHD NIH HHS/United States ; /NH/NIH HHS/United States ; UL1 -TR000004//Office of AIDS Research/ ; }, abstract = {BACKGROUND: Aging-related comorbidities are more common in people with human immunodeficiency virus (HIV) compared to people without HIV. The gut microbiome may play a role in healthy aging; however, this relationship remains unexplored in the context of HIV.<br><br>METHODS: 16S rRNA gene sequencing was conducted on stool from 1409 women (69% with HIV; 2304 samples) and 990 men (54% with HIV; 1008 samples) in the MACS/WIHS Combined Cohort Study. Associations of age with gut microbiome diversity, uniqueness, and genus-level abundance were examined in women and men separately, followed by examining relationships of aging-related genera with frailty (Fried frailty phenotype) and mortality risk (Veterans Aging Cohort Study [VACS] index).<br><br>RESULTS: Older age was associated with greater microbiome diversity and uniqueness, greater abundance of Akkermansia and Streptococcus, and lower abundance of Prevotella and Faecalibacterium, among others; findings were generally consistent by sex and HIV status. An aging-related microbiome score, generated via combination of 18 age-related genera, significantly increased with age in both women and men independently of demographic, behavioral, and cardiometabolic factors. In general, age was more strongly related to microbiome features (eg, diversity, microbiome score) in men without compared to with HIV, but age-microbiome associations were similar in women with and without HIV. Some age-related genera associated with healthy/unhealthy aging, such as Faecalibacterium (related to reduced frailty) and Streptococcus (related to higher VACS index).<br><br>CONCLUSIONS: Age is associated with consistent changes in the gut microbiome in both women and men with or without HIV. Some aging-related microbiota are associated with aging-related declines in health.}, }
@article {pmid39841163, year = {2025}, author = {Cherrington, T and Jordan, D and Pluske, J and Mansfield, J and Lugsomya, K and Wilkinson, S and Cadogan, D and Abraham, S and O'Dea, M}, title = {Lactobacillus and Saccharomyces fermentation products impact performance and the fecal microbiome in weanling pigs inoculated with enterotoxigenic Escherichia coli.}, journal = {Journal of animal science}, volume = {}, number = {}, pages = {}, doi = {10.1093/jas/skae394}, pmid = {39841163}, issn = {1525-3163}, abstract = {BACKGROUND: Enterotoxigenic F4 E. coli (F4-ETEC) pose an economic threat to the swine industry through reduced growth, increased mortality and morbidity, and increased costs associated with treatment. Prevention and treatment of F4-ETEC often relies on antimicrobials; however, due to the threat of antimicrobial resistance, antimicrobial use is being minimized, and hence alternative control methods are needed. This study investigated the effects of postbiotics in the form of Lactobacillus acidophilus fermentation products (LFP) and Saccharomyces cerevisiae fermentation products (SFP), on pigs challenged with an F4 ETEC strain. Eighty pigs were selected based on a pre-screening F4-ETEC susceptibility test. The animals were divided into five treatments each with four replicate pens. Pigs were assigned to five different diets: a control diet (CON); CON diet with 3,000 ppm ZnO (ZnO); CON diet with 2,000 ppm LFP (LFP); CON diet with 2,000 ppm SFP (SFP); CON diet with both 2,000 ppm LFP and 2,000 ppm SFP (LAS). Pigs were inoculated per os with F4-ETEC twice, on day 0 and day1 of the experiment.<br><br>RESULTS: No significant differences in fecal consistency scores or fecal F4-ETEC concentration in pigs supplemented with LFP and/or SFP were detected. An increased diversity and abundance of Lactobacillaceae in the fecal microbiome of pigs supplemented with LFP were detected, as well as an increased final liveweight of pigs supplemented with LFP and/or SFP.<br><br>CONCLUSION: This study demonstrated that the fecal microbiome is modified in F4-ETEC-challenged pigs supplemented with the combination of LFP and SFP, with these modifications previously associated with increased growth performance and health status in young pigs. Pigs receiving this combination of postbiotics also demonstrated an increased final liveweight, indicating that management of ETEC-associated performance loss may not require the complete removal of ETEC from a production system.}, }
@article {pmid39841008, year = {2025}, author = {Keely, SJ and Cotter, PD and Wahlstrom, A and Schellekens, H and Weinkove, D and Barrett, KE}, title = {From human to superhuman: the impact of the microbiome on physiology.}, journal = {The Journal of physiology}, volume = {}, number = {}, pages = {}, doi = {10.1113/JP287883}, pmid = {39841008}, issn = {1469-7793}, support = {SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; 16-IA-4445/SFI_/Science Foundation Ireland/Ireland ; SFI/16/RC/3835//Irish Department of Agriculture, Food and the Marine/ ; BB/H01974X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {The complex microbial community residing in the human gut has long been understood to regulate gastrointestinal physiology and to participate in digestive diseases, but its extraintestinal actions and influences are increasingly recognized. This article discusses bidirectional interactions between the gut microbiome and athletic performance, metabolism, longevity and the ability of the gut-brain axis to influence cognitive function and mental health.}, }
@article {pmid39840975, year = {2025}, author = {Ge, B and McDonald, RC and Yang, Q and Domesle, KJ and Sarria, S and Li, X and Hsu, C-H and Jarvis, KG and Tadesse, DA}, title = {Exploring animal food microbiomes and resistomes via 16S rRNA gene amplicon sequencing and shotgun metagenomics.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0223024}, doi = {10.1128/aem.02230-24}, pmid = {39840975}, issn = {1098-5336}, abstract = {As a diverse and complex food matrix, the animal food microbiota and repertoire of antimicrobial resistance (AMR) genes remain to be better understood. In this study, 16S rRNA gene amplicon sequencing and shotgun metagenomics were applied to three types of animal food samples (cattle feed, dry dog food, and poultry feed). ZymoBIOMICS mock microbial community was used for workflow optimization including DNA extraction kits and bead-beating conditions. The four DNA extraction kits (AllPrep PowerViral DNA/RNA Kit, DNeasy Blood &amp; Tissue Kit, DNeasy PowerSoil Kit, and ZymoBIOMICS DNA Miniprep Kit) were compared in animal food as well as the use of peptide nucleic acid blockers for 16S rRNA gene amplicon sequencing. Distinct microbial community profiles were generated, which varied by animal food type and DNA extraction kit. Employing peptide nucleic acid blockers prior to 16S rRNA gene amplicon sequencing was comparable with post-sequencing in silico filtering at removing chloroplast and mitochondrial sequences. There was a good agreement between 16S rRNA gene amplicon sequencing and shotgun metagenomics on community profiles in animal feed data sets; however, they differed in taxonomic resolution, with the latter superior at resolving at the species level. Although the overall prevalence of AMR genes was low, resistome analysis of animal feed data sets by shotgun metagenomics revealed 10 AMR gene/protein families, including beta-lactamases, erythromycin/lincomycin/pristinamycin/tylosin, fosfomycin, phenicol, and quinolone. Future expansion of microbiome and resistome profiling in animal food will help better understand the bacterial and AMR gene diversity in these commodities and help guide pathogen control and AMR prevention efforts.IMPORTANCEWith the growing interest and application of metagenomics in understanding the structure/composition and function of diverse microbial communities along the One Health continuum, this study represents one of the first attempts to employ these advanced sequencing technologies to characterize the microbiota and AMR genes in animal food. We unraveled the effects of DNA extraction kits on sample analysis by 16S rRNA gene amplicon sequencing and showed similar efficacies of two strategies at removing chloroplast and mitochondrial reads. The in-depth analysis using shotgun metagenomics shed light on the community compositions and the presence of an array of AMR genes in animal food. This exploration of microbiomes and resistomes in representative animal food samples by both sequencing approaches laid important groundwork for future metagenomic investigations to gain a better understanding of the baseline/core microbiomes and associated AMR functions in these diverse commodities and help guide pathogen control and AMR prevention efforts.}, }
@article {pmid39840651, year = {2025}, author = {Feng, Y and Jin, Q and Liu, X and Lin, T and Johnson, A and Huang, H}, title = {Advances in understanding dietary fiber: Classification, structural characterization, modification, and gut microbiome interactions.}, journal = {Comprehensive reviews in food science and food safety}, volume = {24}, number = {1}, pages = {e70092}, doi = {10.1111/1541-4337.70092}, pmid = {39840651}, issn = {1541-4337}, support = {//Institute for Critical Technologies and Applied Science, Virginia Tech/ ; //Virginia Agricultural Experiment Station, Virginia Polytechnic Institute and State University/ ; //National Institute of Food and Agriculture/ ; 2023-67017-39866//Foundational and Applied Science Program/ ; VA-160079//U.S. Department of Agriculture/ ; }, mesh = {*Dietary Fiber ; *Gastrointestinal Microbiome/physiology ; Humans ; Fermentation ; Bacteria ; Animals ; }, abstract = {Gut microbiota and their metabolites profoundly impact host physiology. Targeted modulation of gut microbiota has been a long-term interest in the scientific community. Numerous studies have investigated the feasibility of utilizing dietary fibers (DFs) to modulate gut microbiota and promote the production of health-beneficial bacterial metabolites. However, the complexity of fiber structures, microbiota composition, and their dynamic interactions have hindered the precise prediction of the impact of DF on the gut microbiome. We address this issue with a new perspective, focusing on the inherent chemical and structural complexity of DFs and their interaction with gut microbiota. The chemical and structural complexity of fibers was thoroughly elaborated, encompassing the fibers' molecular composition, polymorphism, mesoscopic structures, porosity, and particle size. Advanced characterization techniques to investigate fiber structural properties were discussed. Additionally, we examined the interactions between DFs and gut microbiota. Finally, we summarized processing techniques to modify fiber structures for improving the fermentability of DF by gut microbiota. The structure of fibers, such as their crystallinity, porosity, degree of branching, and pore wettability, significantly impacts their interactions with gut microbiota. These structural differences also substantially affect fiber's fermentability and capability to modulate the composition of gut microbiota. Conventional approaches are not capable of investigating complex fiber properties and their influences on the gut microbiome; therefore, it is of the essence to involve advanced material characterization techniques and artificial intelligence to unveil more comprehensive information on this topic.}, }
@article {pmid39840649, year = {2025}, author = {Pirr, S and Willers, M and Viemann, D}, title = {The neonate respiratory microbiome.}, journal = {Acta physiologica (Oxford, England)}, volume = {241}, number = {2}, pages = {e14266}, doi = {10.1111/apha.14266}, pmid = {39840649}, issn = {1748-1716}, support = {//Bundesministerium f&#xfc;r Bildung und Forschung/ ; //Deutsche Forschungsgemeinschaft/ ; //Hannover Biomedical Research School/ ; //Center for Infection Biology Hannover/ ; }, mesh = {Humans ; Infant, Newborn ; *Microbiota/physiology ; Respiratory System/microbiology/immunology ; Lung/microbiology/immunology ; }, abstract = {Over the past two decades, it has become clear that against earlier assumptions, the respiratory tract is regularly populated by a variety of microbiota even down to the lowest parts of the lungs. New methods and technologies revealed distinct microbiome compositions and developmental trajectories in the differing parts of the respiratory tract of neonates and infants. In this review, we describe the current understanding of respiratory microbiota development in human neonates and highlight multiple factors that have been identified to impact human respiratory microbiome development including gestational age, mode of delivery, diet, antibiotic treatment, and early infections. Moreover, we discuss to date revealed respiratory microbiome-disease associations in infants and children that may indicate a potentially imprinting cross talk between microbial communities and the host immune system in the respiratory tract. It becomes obvious how insufficient our knowledge still is regarding the exact mechanisms underlying such cross talk in humans. Lastly, we highlight strong findings that emphasize the important role of the gut-lung axis in educating and driving pulmonary immunity. Further research is needed to better understand the host - respiratory microbiome interaction in order to enable the translation into microbiome-based strategies to protect and improve human respiratory health from early childhood.}, }
@article {pmid39840614, year = {2025}, author = {Liu, W and Wang, J and Yang, H and Li, C and Lan, W and Chen, T and Tang, Y}, title = {The Metabolite Indole-3-Acetic Acid of Bacteroides Ovatus Improves Atherosclerosis by Restoring the Polarisation Balance of M1/M2 Macrophages and Inhibiting Inflammation.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2413010}, doi = {10.1002/advs.202413010}, pmid = {39840614}, issn = {2198-3844}, support = {82360105//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 20232ACB206001//Natural Science Foundation of Jiangxi Province/ ; 20223BBG71010//Key Research and Development Program of Jiangxi Province/ ; 2024SSY07061//Jiangxi Province Key Laboratory of bioengineering drugs/ ; }, abstract = {Emerging research has highlighted the significant role of the gut microbiota in atherosclerosis (AS), with microbiota-targeted interventions offering promising therapeutic potential. A central component of this process is gut-derived metabolites, which play a crucial role in mediating the distal functioning of the microbiota. In this study, a comprehensive microbiome-metabolite analysis using fecal and serum samples from patients with atherosclerotic cardiovascular disease and volunteers with risk factors for coronary heart disease and culture histology is performed, and identified the core strain Bacteroides ovatus (B. ovatus). Fecal microbiota transplantation experiments further demonstrated that the gut microbiota significantly influences AS progression, with B. ovatus alone exerting effects comparable to volunteer feces from volunteers. Notably, B. ovatus alleviated AS primarily by restoring the intestinal barrier and enhancing bile acid metabolism, particularly through the production of indole-3-acetic acid (IAA), a tryptophan-derived metabolite. IAA inhibited the TLR4/MyD88/NF-κB pathway in M1 macrophages, promoted M2 macrophage polarisation, and restored the M1/M2 polarisation balance, ultimately reducing aortic inflammation. These findings clarify the mechanistic interplay between the gut microbiota and AS, providing the first evidence that B. ovatus, a second-generation probiotic, can improve bile acid metabolism and reduce inflammation, offering a theoretical foundation for future AS therapeutic applications involving this strain.}, }
@article {pmid39840452, year = {2025}, author = {Jain, R and Voss, AL and Del Rosario, J and Hale, JDF}, title = {Efficacy of a topical live probiotic in improving skin health.}, journal = {International journal of cosmetic science}, volume = {}, number = {}, pages = {}, doi = {10.1111/ics.13043}, pmid = {39840452}, issn = {1468-2494}, abstract = {INTRODUCTION: Micrococcus luteus is a commensal bacterial member of the human skin and is essential in keeping the balance among the various microbial flora of the skin. M. luteus strain Q24 or BLIS Q24™ was isolated from the skin of a healthy human adult and is known to produce a unique antimicrobial spectrum that is inhibitory towards pathogens associated with skin diseases. It has been developed as a probiotic with potential applications in improving overall skin health.<br><br>OBJECTIVE: This study aimed to evaluate the perceived changes in skin quality following topical application of a formulation containing skin commensal probiotic BLIS Q24&#x2122;.<br><br>METHODS: A 28-day study involving 96 participants with self-reported normal skin with occasional blemishes or breakouts, topically applied a serum formulation containing BLIS Q24&#x2122; to the face. Participants quantitatively evaluated the probiotic serum effect on their skin at baseline Day 0 and then again on Day 10, 20 and 28 of the application. In addition, participants maintained a photo diary to record the perceived changes to their skin.<br><br>RESULTS: A total of 96 participants completed this research. In comparison to the baseline (Day 0), within 10&#x2009;days, a significant reduction in blackheads (48%), oiliness (48%), blemishes (57%), dry areas (23%), redness/rosacea (45%) and flaky and rough skin (38%) were reported. The probiotic serum was also effective in a significant reduction in fine lines and wrinkles (38%), whiteheads (41%), pimples (55%), age spots (29%), and acne (21%) by the end of 28&#x2009;days of probiotic application. Overall, there's agreement that probiotic serum delivers or exceeds consumer expectations from the concept and performs just as well, or better, than their regular moisturizer.<br><br>CONCLUSION: An approach of delivering a live probiotic packaged in an innovative formula to improve several skin conditions in otherwise healthy individuals was found to be successful. This study highlights that a serum formulation containing BLIS Q24&#x2122; has a positive impact on skin health. It is effective topically in reducing the appearance of skin blemishes, oiliness, wrinkles, redness, and dryness. BLIS Q24&#x2122; offers the potential for preventing skin health-related issues and routine maintenance of skin microbiome for healthy skin.}, }
@article {pmid39840283, year = {2024}, author = {Yan, B and Nam, Y and Li, L and Deek, RA and Li, H and Ma, S}, title = {Recent advances in deep learning and language models for studying the microbiome.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1494474}, pmid = {39840283}, issn = {1664-8021}, abstract = {Recent advancements in deep learning, particularly large language models (LLMs), made a significant impact on how researchers study microbiome and metagenomics data. Microbial protein and genomic sequences, like natural languages, form a language of life, enabling the adoption of LLMs to extract useful insights from complex microbial ecologies. In this paper, we review applications of deep learning and language models in analyzing microbiome and metagenomics data. We focus on problem formulations, necessary datasets, and the integration of language modeling techniques. We provide an extensive overview of protein/genomic language modeling and their contributions to microbiome studies. We also discuss applications such as novel viromics language modeling, biosynthetic gene cluster prediction, and knowledge integration for metagenomics studies.}, }
@article {pmid39840031, year = {2024}, author = {Lim, MY and Hong, S and Nam, YD}, title = {Understanding the role of the gut microbiome in solid tumor responses to immune checkpoint inhibitors for personalized therapeutic strategies: a review.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1512683}, pmid = {39840031}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; *Immune Checkpoint Inhibitors/therapeutic use ; *Neoplasms/immunology/therapy/drug therapy/microbiology ; *Precision Medicine ; Animals ; Immunotherapy/methods ; Treatment Outcome ; }, abstract = {Immunotherapy, especially immune checkpoint inhibitor (ICI) therapy, has yielded remarkable outcomes for some patients with solid cancers, but others do not respond to these treatments. Recent research has identified the gut microbiota as a key modulator of immune responses, suggesting that its composition is closely linked to responses to ICI therapy in cancer treatment. As a result, the gut microbiome is gaining attention as a potential biomarker for predicting individual responses to ICI therapy and as a target for enhancing treatment efficacy. In this review, we discuss key findings from human observational studies assessing the effect of antibiotic use prior to ICI therapy on outcomes and identifying specific gut bacteria associated with favorable and unfavorable responses. Moreover, we review studies investigating the possibility of patient outcome prediction using machine learning models based on gut microbiome data before starting ICI therapy and clinical trials exploring whether gut microbiota modulation, for example via fecal microbiota transplantation or live biotherapeutic products, can improve results of ICI therapy in patients with cancer. We also briefly discuss the mechanisms through which the gut microbial-derived products influence immunotherapy effectiveness. Further research is necessary to fully understand the complex interactions between the host, gut microbiota, and immunotherapy and to develop personalized strategies that optimize responses to ICI therapy.}, }
@article {pmid39840030, year = {2024}, author = {Trecarten, S and Liss, MA and Hamilton-Reeves, J and DiGiovanni, J}, title = {Obesity, dietary interventions and microbiome alterations in the development and progression of prostate cancer.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1448116}, pmid = {39840030}, issn = {1664-3224}, mesh = {Humans ; Male ; *Prostatic Neoplasms/microbiology/etiology/immunology ; *Obesity/microbiology/immunology ; *Gastrointestinal Microbiome/immunology ; *Disease Progression ; *Tumor Microenvironment/immunology ; Diet ; Animals ; Dysbiosis ; }, abstract = {PURPOSE OF REVIEW: The role of the microbiome in prostate cancer is an emerging subject of research interest. Certain lifestyle factors, such as obesity and diet, can also impact the microbiome, which has been implicated in many diseases, such as heart disease and diabetes. However, this link has yet to be explored in detail in the context of prostate cancer. The purpose of this review is to explore the cross-talk between obesity, dietary interventions, and microbiome alterations in the development and progression of prostate cancer.<br><br>RECENT FINDINGS: Many possible mechanisms exist linking obesity and dietary interventions to microbiome alterations and prostate cancer. The gut microbiome produces metabolites that could play a role in prostate cancer oncogenesis, including short-chain fatty acids, cholesterol derivatives, and folic acid. The microbiome also plays a pivotal role in the prostate tumor microenvironment (TME), contributing to inflammation, local tissue hypoxia, and epithelial-mesenchymal transition. A bidirectional relationship exists between obesity and the microbiome, and certain diets can enact changes to the microbiome, its associated metabolites, and prostate cancer outcomes.<br><br>SUMMARY: Cross-talk exists between obesity, dietary interventions, and the role of the microbiome in the development and progression of prostate cancer. To further our understanding, future human studies in prostate cancer should investigate microbiome changes and incorporate an assessment of microbiome-derived metabolites and cellular/immune changes in the TME.}, }
@article {pmid39840022, year = {2024}, author = {Voigt, RM and Engen, PA and Villanueva, M and Bambi, SA and Green, SJ and Naqib, A and Raeisi, S and Shaikh, M and Hamaker, BR and Cantu-Jungles, TM and Pridgen, SA and Held, P and Keshavarzian, A}, title = {Prebiotics as an adjunct therapy for posttraumatic stress disorder: a pilot randomized controlled trial.}, journal = {Frontiers in neuroscience}, volume = {18}, number = {}, pages = {1477519}, pmid = {39840022}, issn = {1662-4548}, abstract = {INTRODUCTION: Posttraumatic stress disorder (PTSD) is a debilitating disorder characterized by intrusive memories, avoidance, negative thoughts and moods, and heightened arousal. Many patients also report gastrointestinal symptoms. Cognitive behavioral therapy (CBT) is an evidence-based treatment approach for PTSD that successfully reduces symptoms. However, many patients still meet criteria for PTSD after treatment or continue to have symptoms indicating the need for new treatment strategies for PTSD. Patients with PTSD have a disrupted intestinal microbiome (i.e., dysbiosis) which can promote neuroinflammation; thus, modulation of the microbiome could be an alternative or adjunct treatment approach for PTSD.<br><br>METHODS: The current study was a 12-week, double-blind, placebo-controlled trial seeking to understand if CBT combined with a microbiota-modifying, prebiotic fiber intervention would beneficially impact clinical outcomes in veterans with PTSD (n = 70). This proof-of-concept, pilot trial was designed to assess: (1) the relationship between severity of PTSD symptoms and microbiota composition and SCFA levels (i.e., acetate, propionate, butyrate), (2) if CBT treatment with a concomitant prebiotic fiber intervention would beneficially impact clinical outcomes in veterans with PTSD, (3) evaluate the feasibility and acceptability of a prebiotic intervention as an adjunct treatment to CBT, and (4) assess the impact of treatment on the intestinal microbiota and stool SCFA (i.e., mechanism).<br><br>RESULTS: This study found that PTSD severity may be associated with reduced abundance of taxa capable of producing the SCFA propionate, and that a subset of individuals with PTSD may benefit from a microbiota-modifying prebiotic intervention.<br><br>CONCLUSION: This study suggests that targeting the intestinal microbiome through prebiotic supplementation could represent a promising avenue for enhancing treatment outcomes in some individuals with PTSD.<br><br>CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/, identifier NCT05424146.}, }
@article {pmid39839986, year = {2025}, author = {Hassib, L and Kanashiro, A and Pedrazzi, JFC and Vercesi, BF and Higa, S and Arruda, &#xcd; and Soares, Y and de Jesus de Souza, A and Jordão, AA and Guimarães, FS and Ferreira, FR}, title = {Should we consider microbiota-based interventions as a novel therapeutic strategy for schizophrenia? A systematic review and meta-analysis.}, journal = {Brain, behavior, &amp; immunity - health}, volume = {43}, number = {}, pages = {100923}, pmid = {39839986}, issn = {2666-3546}, abstract = {Schizophrenia is a chronic psychiatric disorder characterized by a variety of symptoms broadly categorized into positive, negative, and cognitive domains. Its etiology is multifactorial, involving a complex interplay of genetic, neurobiological, and environmental factors, and its neurobiology is associated with abnormalities in different neurotransmitter systems. Due to this multifactorial etiology and neurobiology, leading to a wide heterogeneity of symptoms and clinical presentations, current antipsychotic treatments face challenges, underscoring the need for novel therapeutic approaches. Recent studies have revealed differences in the gut microbiome of individuals with schizophrenia compared to healthy controls, establishing an intricate link between this disorder and gastrointestinal health, and suggesting that microbiota-targeted interventions could help alleviate clinical symptoms. Therefore, this meta-analysis investigates whether gut microbiota manipulation can ameliorate psychotic outcomes in patients with schizophrenia receiving pharmacological treatment. Nine studies (n = 417 participants) were selected from 81 records, comprising seven randomized controlled trials and two open-label studies, all with a low risk of bias, included in this systematic review and meta-analysis. The overall combined effect size indicated significant symptom improvement following microbiota treatment (Hedges' g = 0.48, 95% CI = 0.09 to 0.88, p = 0.004, I[2] = 62.35%). However, according to Hedges' g criteria, the effect size was small (approaching moderate), and study heterogeneity was moderate based on I[2] criteria. This review also discusses clinical and preclinical studies to elucidate the neural, immune, and metabolic pathways by which microbiota manipulation, particularly with Lactobacillus and Bifidobacterium genera, may exert beneficial effects on schizophrenia symptoms via the gut-brain axis. Finally, we address the main confounding factors identified in our systematic review, highlight key limitations, and offer recommendations to guide future high-quality trials with larger participant cohorts to explore microbiome-based therapies as a primary or adjunctive treatment for schizophrenia.}, }
@article {pmid39839897, year = {2025}, author = {Jiang, QR and Zeng, DW}, title = {Gut microbiota shifts in hepatitis B-related portal hypertension after transjugular intrahepatic portosystemic shunt: Mechanistic and clinical implications.}, journal = {World journal of gastroenterology}, volume = {31}, number = {3}, pages = {100752}, pmid = {39839897}, issn = {2219-2840}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Hypertension, Portal/diagnosis/etiology/microbiology ; *Portasystemic Shunt, Transjugular Intrahepatic/adverse effects ; *Hepatic Encephalopathy/etiology/microbiology/diagnosis ; *Liver Cirrhosis/microbiology/virology/diagnosis ; Hepatitis B virus/isolation &amp; purification ; Hepatitis B/diagnosis/complications/microbiology ; Dysbiosis ; Animals ; }, abstract = {In this article, we provide commentary on the recent article by Zhao et al. We focus on the shifts in the gut microbiota of patients with hepatitis B virus (HBV)-associated cirrhosis/portal hypertension (PH) following transjugular intrahepatic portosystemic shunt (TIPS) and the implications for understanding the mechanisms, diagnosis, and treatment. By comparing the gut microbiota composition and dynamic changes before and after TIPS in patients with and without hepatic encephalopathy, the authors found an increase in non-probiotic bacteria in those who developed hepatic encephalopathy post-TIPS, with Morganella species present only in the hepatic encephalopathy group. The gut microbiota changes post-TIPS among patients without the occurrence of hepatic encephalopathy suggest potential therapeutic benefits through prophylactic microbiome therapies. Furthermore, the specific gut microbiota alterations may hold promise to predict the risk of hepatic encephalopathy in individuals undergoing TIPS for HBV-related PH. Despite these promising findings, future studies are needed to address limitations, including a small sample size, a relatively short evaluation period for gut microbiota alterations, the absence of data on dynamic alterations in gut microbiota post-TIPS and their correlation with blood ammonia levels, and the lack of validation in animal models. In conclusion, Zhao et al's study has shed new light on the link of gut microbiota with post-TIPS hepatic encephalopathy, potentially through the intricate gut-liver axis, and has important clinical implications for improving the management of patients with HBV-related PH.}, }
@article {pmid39839888, year = {2025}, author = {Große, R and Heuser, M and Teikari, JE and Ramakrishnan, DK and Abdelfattah, A and Dittmann, E}, title = {Microcystin shapes the Microcystis phycosphere through community filtering and by influencing cross-feeding interactions.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycae170}, pmid = {39839888}, issn = {2730-6151}, abstract = {The cyanobacterium Microcystis causes harmful algal blooms that pose a major threat to human health and ecosystem services, particularly due to the prevalence of the potent hepatotoxin microcystin (MC). With their pronounced EPS layer, Microcystis colonies also serve as a hub for heterotrophic phycosphere bacteria. Here, we tested the hypothesis that the genotypic plasticity in its ability to produce MC influences the composition and assembly of the Microcystis phycosphere microbiome. In an analysis of individual colonies of a natural Microcystis bloom, we observed a significantly reduced richness of the community in the presence of MC biosynthesis genes. A subsequent synthetic community experiment with 21 heterotrophic bacterial strains in co-cultivation with either the wild-type strain Microcystis aeruginosa PCC 7806 or the MC-free mutant ΔmcyB revealed not only a tug-of-war between phototrophic and heterotrophic bacteria, but also a reciprocal dominance of two isolates of the genus Sphingomonas and Flavobacterium. In contrast, an Agrobacterium isolate thrived equally well in both consortia. In substrate utilization tests, Sphingomonas showed the strongest dependence on Microcystis exudates with a clear preference for the wild-type strain. Genome sequencing revealed a high potential for complementary cross-feeding, particularly for the Agrobacterium and Sphingomonas isolates but no potential for MC degradation. We postulate that strain-specific functional traits, such as the ability to perform glycolate oxidation, play a crucial role in the cross-feeding interactions, and that MC is one of the determining factors in the Microcystis phycosphere due to its interference with inorganic carbon metabolism.}, }
@article {pmid39839811, year = {2024}, author = {Hinton, A and Neikirk, K and Le, H and Harris, C and Oliver, A and Martin, P and Gaye, A}, title = {Estrogen receptors in mitochondrial metabolism: age-related changes and implications for pregnancy complications.}, journal = {Aging advances}, volume = {1}, number = {2}, pages = {154-171}, pmid = {39839811}, issn = {3050-6743}, abstract = {Estrogen hormones are primarily associated with their role as female sex hormones responsible for primary and secondary sexual development. Estrogen receptors are known to undergo age-dependent decreases due to age-related changes in hormone production. In the mitochondria, estrogen functions by reducing the production of reactive oxygen species in the electron transport chain, inhibiting apoptosis, and regulating mitochondrial DNA content. Moreover, estrogen receptors may be the key components in maintaining mitochondrial membrane potential and structure. Although estrogen plays a crucial role in the development of pregnancy, our understanding of how estrogen receptors change with aging during pregnancy remains limited. During pregnancy, estrogen levels are significantly elevated, with a corresponding upregulation of estrogen receptors, which play various roles in pregnancy. However, the exact role of estrogen receptors in pregnancy complications remains to be further investigated. The paper reviews the role of estrogen receptors in the regulation of mitochondrial metabolism and in pregnancy complications, with a special focus on the effect of age-related changes on estrogen levels and estrogen receptors function. We also address how estrogen maintains mitochondrial function, including reducing the production of reactive oxygen species in the electron transport chain, inhibiting apoptosis, regulating mitochondrial DNA content, and maintaining mitochondrial membrane potential and structure. However, the effects of estrogen on mitochondria-endoplasmic reticulum contacts have not been well studied. Based on these emergent roles in mitochondria, the differential roles of estrogen receptors in pregnancy complications are of great relevance. The paper emphasizes the association between maternal health and estrogen receptors and indicates the need for future research to elucidate the interdependence of estrogen receptor-regulated maternal health with mitochondrial function and their relationship with the gut microbiome. Overall, we summarize the important role of estrogen receptors during pregnancy and highlight the need for further research to better understand the role of estrogen receptors in aging and pregnancy complications. This not only helps to reveal the mechanism underlying the role of estrogen in maternal health but also has potential clinical implications for the development of new therapies targeting age-related diseases and pregnancy complications.}, }
@article {pmid39839794, year = {2024}, author = {Zhai, X and Lin, D and Shen, Y and Zhai, N and Yu, F and Zhang, J and Lin, Y and Wang, Y and Zhou, Q and Zheng, X}, title = {A novel interplay between bacteria and metabolites in different early-stage lung cancer: an integrated microbiome and metabolome analysis.}, journal = {Frontiers in oncology}, volume = {14}, number = {}, pages = {1492571}, pmid = {39839794}, issn = {2234-943X}, abstract = {BACKGROUND: The carcinogenesis mechanism of early-stage lung cancer (ESLC) remains unclear. Microbial dysbiosis is closely related to tumor development. This study aimed to analyze the relationship between microbiota dysbiosis in ESLC.<br><br>METHODS: We investigated a total of 108 surgical specimens of lung nodules, including ground glass nodules (GGN) diagnosed as lung adenocarcinoma (n = 25), solid nodules (SN) diagnosed as lung adenocarcinoma (n = 27), lung squamous carcinoma (LUSC) presenting as solid nodules (n = 26), and benign pulmonary nodules (BPD) (n = 30) that were collected. 16S rDNA amplicon sequencing and non-targeted metabolomics analysis were performed in all of the specimens.<br><br>RESULTS: We found a significantly lower microbiota richness in SN than in the GGN and LUSC. Ralstonia may be an important flora promoting the development of early lung adenocarcinoma, while Feacalibacterium and Blautia play a protective role in the progression of GGN to SN. Akkermansia, Escherichia-shigella, and Klebsiella exhibited high abundance in early lung squamous carcinoma. Compared with BPD, the differential metabolites of both early adenocarcinomas (SN and GGN) are mainly involved in energy metabolic pathways, while early LUSC is mainly involved in glutathione metabolism, producing and maintaining high levels of intracellular redox homeostasis. A correlation analysis revealed that different microbiota in GGN may function in energy metabolism via N-acetyl-1-aspartylglutamic acid (NAAG) when compared to BPD, while creatine and N-acetylmethionine were the main relevant molecules for the function of differential microbiota in LUSC.<br><br>CONCLUSION: Our study identified that early-stage lung adenocarcinoma and squamous carcinoma differ in microbial composition and metabolic status. Ralstonia may be an important flora promoting the development of early lung adenocarcinoma, while Feacalibacterium and Blautia play a protective role in the progression of GGN to SN. Conversely, Akkermansia, Escherichia-shigella, and Klebsiella exhibited high abundance in early lung squamous carcinoma. The metabolites of both early adenocarcinomas (SN and GGN) are mainly involved in energy metabolic pathways, while early LUSC is mainly involved in glutathione metabolism. Our study provides new insights into the carcinogenesis of ESLC.}, }
@article {pmid39839781, year = {2024}, author = {Artyukh, AA and Ivanov, MK and Titov, SE and Dzyubenko, VV and Krasilnikov, SE and Shumeikina, AO and Afanasev, NA and Malek, AV and Glushkov, SA and Agletdinov, EF}, title = {Detection of cervical precancerous lesions and cancer by small-scale RT-qPCR analysis of oppositely deregulated mRNAs pairs in cytological smears.}, journal = {Frontiers in oncology}, volume = {14}, number = {}, pages = {1491737}, pmid = {39839781}, issn = {2234-943X}, abstract = {BACKGROUND: Cervical screening, aimed at detecting precancerous lesions and preventing cancer, is based on cytology and HPV testing. Both methods have limitations, the main ones being the variable diagnostic sensitivity of cytology and the moderate specificity of HPV testing. Various molecular biomarkers are proposed in recent years to improve cervical cancer management, including a number of mRNAs encoded by human genes involved in carcinogenesis. Many scientific papers have shown that the expression patterns of cellular mRNAs reflect the severity of the lesion, and their analysis in cervical smears may outperform HPV testing in terms of diagnostic specificity. However, such analysis has not yet been implemented in broad clinical practice. Our aim was to devise an assay detecting severe cervical lesions (≥HSIL) via analysis of cellular mRNA expression in cytological smears.<br><br>METHODS: Through logistic regression analysis of a reverse-transcription quantitative PCR (RT-qPCR) dataset generated from analysis of six mRNAs in 167 cervical smears with various cytological diagnoses, we generated a family of linear classifiers based on paired mRNA concentration ratios. Each classifier outputs a dimensionless decision function (DF) value that increases with lesion severity. Additionally, in the same specimens, the HPV genotyping, viral load assessment, diagnosis of cervicovaginal microbiome imbalance and profiling of some relevant mRNAs and miRNAs were performed by qPCR-based methods.<br><br>RESULTS: The best classifiers were obtained with pairs of mRNAs whose expression changes in opposite directions during lesion progression. With this approach based on a five-mRNA combination (CDKN2A, MAL, TMPRSS4, CRNN, and ECM1), we generated a classifier having ROC AUC 0.935, diagnostic sensitivity 89.7%, and specificity 87.6% for &#x2265;HSIL detection. Based on this classifier, a two-tube RT-qPCR based assay was developed and it confirmed the preliminary characteristics on 120 cervical smears from the test sample. DF values weakly correlated with HPV loads and cervicovaginal microbiome imbalance, thus being independent markers of &#x2265;HSIL risk.<br><br>CONCLUSION: Thus, we propose a high-throughput method for detecting &#x2265;HSIL cervical lesions by RT-qPCR analysis of several cellular mRNAs. The method is suitable for the analysis of cervical cytological smears prepared by a routine method. Further clinical validation is necessary to clarify its clinical potential.}, }
@article {pmid39839711, year = {2025}, author = {Griffin, EF and Owens, MG}, title = {Dopaminergic neurodegeneration in C. elegans cultivated with Porphorymonas gingivalis.}, journal = {microPublication biology}, volume = {2025}, number = {}, pages = {}, pmid = {39839711}, issn = {2578-9430}, abstract = {Disruption of the human microbiome has emerged as a major contributing factor in the etiology of neurodegenerative disease. Previous work suggests a positive correlation between periodontal inflammation and Parkinson's disease. Here, we show that feeding C. elegans animals Porphorymonas gingivalis causes neurodegeneration that is not additive with neurodegeneration induced by the Parkinson's-associated protein, α-synuclein. In contrast, α-synuclein-expressing animals fed P. gingivalis show additional disruption in basal slowing, suggesting that P. gingivalis induces neurodegeneration while altering neuronal function of extant neurons. Though the mechanism is unclear, these results suggest a relationship between P. gingivalis and neurodegeneration that warrants further investigation.}, }
@article {pmid39839678, year = {2025}, author = {Modha, S and Hughes, J and Orton, RJ and Lytras, S}, title = {Expanding the genomic diversity of human anelloviruses.}, journal = {Virus evolution}, volume = {11}, number = {1}, pages = {veaf002}, pmid = {39839678}, issn = {2057-1577}, abstract = {Anelloviruses are a group of small, circular, single-stranded DNA viruses that are found ubiquitously across mammalian hosts. Here, we explored a large number of publicly available human microbiome datasets and retrieved a total of 829 anellovirus genomes, substantially expanding the known diversity of these viruses. The majority of new genomes fall within the three major human anellovirus genera: Alphatorquevirus, Betatorquevirus, and Gammatorquevirus, while we also present new genomes of the under-sampled Hetorquevirus, Memtorquevirus, and Samektorquevirus genera. We performed recombination analysis and show evidence of extensive recombination across all human anelloviruses. Interestingly, more than 95% of the detected events are between members of the same genus and only 15 inter-genus recombination events were detected. The breakpoints of recombination cluster in hotspots at the ends and outside of the ORF1 gene, while a recombination coldspot was detected within the gene. Our analysis suggests that anellovirus evolution is governed by homologous recombination; however, events between distant viruses or ones producing chimaeric ORF1s likely lead to nonviable recombinants. The large number of genomes further allowed us to examine how essential genomic features vary across anelloviruses. These include functional domains in the ORF1 protein and the nucleotide motif of the replication loop region, required for the viruses' rolling-circle replication. A subset of the genomes assembled in both this and previous studies are completely lacking these essential elements, opening up the possibility that anellovirus intracellular populations contain nonstandard viral genomes. However, low-read depth of the metagenomically assembled contigs may partly explain the lack of some features. Overall, our study highlights key features of anellovirus genomics and evolution, a largely understudied group of viruses whose potential in virus-based therapeutics is recently being explored.}, }
@article {pmid39839660, year = {2025}, author = {Mitcov, A and Ko, D and Ko, K and Kim, J and Oh, NH and Kim, HS and Choe, H and Chung, H}, title = {Composition of soil fungal communities and microbial activity along an elevational gradient in Mt. Jiri, Republic of Korea.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18762}, pmid = {39839660}, issn = {2167-8359}, mesh = {*Soil Microbiology ; *Altitude ; Republic of Korea ; *Fungi/enzymology/isolation &amp; purification ; *Soil/chemistry ; Biomass ; Hydrogen-Ion Concentration ; Ecosystem ; Mycobiome ; Climate Change ; }, abstract = {Approximately 64% of the Republic of Korea comprises mountainous areas, which as cold and high-altitude regions are gravely affected by climate change. Within the mountainous and the alpine-subalpine ecosystems, microbial communities play a pivotal role in biogeochemical cycling and partly regulate climate change through such cycles. We investigated the composition and function of microbial communities, with a focus on fungal communities, in Republic of Korea's second tallest mountain, Mt. Jiri, along a four-point-altitude gradient: 600-, 1,000-, 1,200-, and 1,400-m. Soil pH and elevation were negatively correlated, with soils becoming more acidic at higher altitude. Of the five soil enzyme activities analyzed, cellobiohydrolase, β-1,4-glucosidase, and β-1,4-xylosidase activity showed differences among the elevation levels, with lower activity at 600 m than that at 1,400 m. Soil microbial biomass correlated positively with increasing elevation and soil water content. The decrease in β-1,4-N-acetylglucosaminidase suggests a reduction in fungal biomass with increasing altitude, while factors other than elevation may influence the increase in activity of the cellobiohydrolase, β-1,4-glucosidase and β-1,4-xylosidase. Fungal alpha diversity did not exhibit an elevational trend, whereas beta diversity formed two clusters (600-1,000 m and 1,200-1,400 m). Community composition was similar among the elevations, with Basidiomycota being the most predominant phylum, followed by Ascomycota. Conversely, among the fungal communities at 1,000 m, Ascomycota was the most dominant, possibly due to increased pathotroph percentage. Elevational gradients induce changes in soil properties, vegetation, and climate factors such as temperature and precipitation, all of which impact soil microbial communities and altogether create a mutually reinforcing system. Hence, inspection of elevation-based microbial communities can aid in inferring ecosystem properties, specifically those related to nutrient cycling, and can partly help assess the oncoming direct and indirect effects of climate change.}, }
@article {pmid39839113, year = {2024}, author = {Fliegerová, KO and Mahayri, TM and Sechovcová, H and Mekadim, C and Mrázek, J and Jarošíková, R and Dubský, M and Fejfarová, V}, title = {Diabetes and gut microbiome.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1451054}, pmid = {39839113}, issn = {1664-302X}, abstract = {Diabetes mellitus represents a significant global health problem. The number of people suffering from this metabolic disease is constantly rising and although the incidence is heterogeneous depending on region, country, economic situation, lifestyle, diet and level of medical care, it is increasing worldwide, especially among youths and children, mainly due to lifestyle and environmental changes. The pathogenesis of the two most common subtypes of diabetes mellitus, type 1 (T1DM) and type 2 (T2DM), is substantially different, so each form is characterized by a different causation, etiology, pathophysiology, presentation, and treatment. Research in recent decades increasingly indicates the potential role of the gut microbiome in the initiation, development, and progression of this disease. Intestinal microbes and their fermentation products have an important impact on host metabolism, immune system, nutrient digestion and absorption, gut barrier integrity and protection against pathogens. This review summarizes the current evidence on the changes in gut microbial populations in both types of diabetes mellitus. Attention is focused on changes in the abundance of specific bacterial groups at different taxonomic levels in humans, and microbiome shift is also assessed in relation to geographic location, age, diet and antidiabetic drug. The causal relationship between gut bacteria and diabetes is still unclear, and future studies applying new methodological approaches to a broader range of microorganisms inhabiting the digestive tract are urgently needed. This would not only provide a better understanding of the role of the gut microbiome in this metabolic disease, but also the use of beneficial bacterial species in the form of probiotics for the treatment of diabetes.}, }
@article {pmid39839103, year = {2024}, author = {Hinkle, JE and Chanton, JP and Moynihan, MA and Ruff, SE and Teske, A}, title = {Complex bacterial diversity of Guaymas Basin hydrothermal sediments revealed by synthetic long-read sequencing (LoopSeq).}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1491488}, pmid = {39839103}, issn = {1664-302X}, abstract = {Hydrothermal sediments host phylogenetically diverse and physiologically complex microbial communities. Previous studies of microbial community structure in hydrothermal sediments have typically used short-read sequencing approaches. To improve on these approaches, we use LoopSeq, a high-throughput synthetic long-read sequencing method that has yielded promising results in analyses of microbial ecosystems, such as the human gut microbiome. In this study, LoopSeq is used to obtain near-full length (approximately 1,400-1,500 nucleotides) bacterial 16S rRNA gene sequences from hydrothermal sediments in Guaymas Basin. Based on these sequences, high-quality alignments and phylogenetic analyses provided new insights into previously unrecognized taxonomic diversity of sulfur-cycling microorganisms and their distribution along a lateral hydrothermal gradient. Detailed phylogenies for free-living and syntrophic sulfur-cycling bacterial lineages identified well-supported monophyletic clusters that have implications for the taxonomic classification of these groups. Particularly, we identify clusters within Candidatus Desulfofervidus that represent unexplored physiological and genomic diversity. In general, LoopSeq-derived 16S rRNA gene sequences aligned consistently with reference sequences in GenBank; however, chimeras were prevalent in sequences as affiliated with the thermophilic Candidatus Desulfofervidus and Thermodesulfobacterium, and in smaller numbers within the sulfur-oxidizing family Beggiatoaceae. Our analysis of sediments along a well-documented thermal and geochemical gradient show how lineages affiliated with different sulfur-cycling taxonomic groups persist throughout surficial hydrothermal sediments in the Guaymas Basin.}, }
@article {pmid39839099, year = {2024}, author = {Kanika, NH and Liaqat, N and Chen, H and Ke, J and Lu, G and Wang, J and Wang, C}, title = {Fish gut microbiome and its application in aquaculture and biological conservation.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1521048}, pmid = {39839099}, issn = {1664-302X}, abstract = {Understanding the diversity and function of fish gut microbiomes has advanced substantially, yet many aspects remain poorly understood, particularly the interplay among microbiota, host species, and environmental factors in the context of conservation. This review explores the composition and abundance of gut bacterial communities in key aquaculture fish groups-cyprinids, ictalurids (catfish), salmonids, and cichlids (tilapia)-alongside the model organism zebrafish, across diverse geographic regions. The findings highlight environmental habitats and host species as primary determinants of gut microbiome structure, offering a global perspective on these microbial communities. Across all fish groups, the phyla Firmicutes, Fusobacteria, and Proteobacteria consistently dominated, while temperate, sub-equatorial, and sub-tropical regions exhibited the highest microbiome diversity, underscoring the contribution of taxonomic and environmental factors. The gut bacterial diversity of farm-raised fish shows a significant divergence from that of wild-caught fish, reflecting the impacts of ecological and management differences. Understanding the dynamic responses of fish gut microbiota is vital for guiding conservation efforts, safeguarding aquatic biodiversity, and advancing sustainable aquaculture practices. Future research should leverage innovative techniques and integrative approaches, both experimental and theoretical, to uncover the functional roles of microbiomes and predict their responses to environmental changes. Expanding geographic and taxonomic coverage will be critical for creating a comprehensive framework to inform global aquaculture and conservation strategies. Collectively, this perspective highlights the transformative potential of microbiome research in addressing global challenges in aquaculture and conservation biology.}, }
@article {pmid39838826, year = {2025}, author = {Ke, X and Jiang, S and Wei, Q and Sun, M and Sun, H and Pang, M and Liu, M and Sun, L and Yang, H and Mao, Y}, title = {Unveiling the Intratumor Microbiome in Liver Cancer: Current Insights and Prospective Applications.}, journal = {Clinical and molecular hepatology}, volume = {}, number = {}, pages = {}, doi = {10.3350/cmh.2024.1039}, pmid = {39838826}, issn = {2287-285X}, abstract = {The role of the gut microbiome in the development and progression of liver cancer has long been recognized. However, the presence of microbes in tumors that were previously considered sterile has only recently been discovered. The intratumor microbiome in liver cancer likely originates from various sources, including the gut, hematogenous spread from other mucosal locations, adjacent non-cancerous tissues, and co-metastasis with the tumor cells. As a newly discovered component of the tumor microenvironment, it regulates host immune responses, promotes chronic inflammation, modulates metabolic pathways, and exerts other influences in liver cancer. These unique features offer potential new biomarkers for liver cancer prognosis and treatment response. Exploring the complex interactions between intratumor microbiome and the host to modulate or target the intratumor microbiome may provide new avenues for liver cancer treatment. This article provides a comprehensive review of our current understanding regarding the potential origins of the intratumor microbiome in liver cancer, its unique characteristics, and the underlying mechanisms by which it affects liver cancer. Furthermore, we discuss the promising clinical implications and potential challenges that remain before this knowledge can be fully integrated into clinical practice.}, }
@article {pmid39838663, year = {2025}, author = {Ma, L and Liu, Y and Ning, M and Ding, X and Shang, C and Mai, B and Hu, Z and Zhou, R}, title = {Dual Biological Effects and Mechanisms of Gut Microbiota in Breast Cancer: A Review.}, journal = {Current pharmaceutical biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113892010352725241226043912}, pmid = {39838663}, issn = {1873-4316}, abstract = {Breast cancer (BC) is a common malignant tumor. BC is serious and has a high mortality rate. The incidence of BC has increased in recent years. The incidence rate is higher in coastal cities than in inland areas and in urban areas than in rural areas. Affect the occurrence and development of BC, such as inflammation and immune response. One of the cutting- edge studies to gain insight into the pathogenesis of BC is through the gut microbiota (GM) influencing the health status of the human body. Advances in metabolomics analysis can provide a clearer picture of changes in the composition of GM. The composition and quantity of GM can affect the health of other parts of the body, and the disorder of GM can lead to the occurrence and aggravation of diseases in different parts of the body. This paper not only discusses the dual biological effects of GM on BC, the relationship between GM and its metabolites, and BC and its related mechanisms but also explores traditional treatments for BC as well as the treatment of BC through GM, providing theoretical support for the use of methods to regulate GM in the clinical study of BC.}, }
@article {pmid39838491, year = {2025}, author = {Ahmad, F and Ahmed, SH and Choucair, F and Chouliaras, S and Awwad, J and Terranegra, A and Medicine, S}, title = {A disturbed communication between hypothalamic-pituitary-ovary axis and gut microbiota in female infertility: is diet to blame?.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {92}, pmid = {39838491}, issn = {1479-5876}, mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; *Infertility, Female/microbiology/etiology ; *Hypothalamo-Hypophyseal System ; *Diet ; Ovary/microbiology ; Brain-Gut Axis/physiology ; Animals ; }, abstract = {Female infertility is a multifactorial condition influenced by various genetic, environmental, and lifestyle factors. Recent research has investigated the significant impact of gut microbiome dysbiosis on systemic inflammation, metabolic dysfunction, and hormonal imbalances, which can potentially impair fertility. The gut-brain axis, a bidirectional communication system between the gut and the brain, also plays a significant role in regulating reproductive functions. Emerging evidence suggests that the gut microbiome can influence brain functions and behavior, further emphasizing the importance of the microbiota-gut-brain axis in reproduction. Given their role as a major modulator of the gut microbiome, diet and dietary factors, including dietary patterns and nutrient intake, have been implicated in the development and management of female infertility. Hence, this review aims to highlight the impact of dietary patterns, such as the Western diet (WD) and Mediterranean diet (MD), and to decipher their modulatory action on the microbiota-gut-brain axis in infertile women. By contrasting the detrimental effects of WD with the therapeutic potential of MD, we emphasize the pivotal role of a balanced diet rich in nutrients in promoting a healthy gut microbiome. These insights underscore the potential of targeted dietary interventions and lifestyle modifications as promising strategies to enhance reproductive outcomes in subfertile women.}, }
@article {pmid39838419, year = {2025}, author = {Liu, X and Ding, H and Zhang, X and Ta, N and Zhao, J and Zhang, Q and Liu, H and Sun, M and Zhang, X}, title = {Dynamic changes in the gastrointestinal microbial communities of Gangba sheep and analysis of their functions in plant biomass degradation at high altitude.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {17}, pmid = {39838419}, issn = {2049-2618}, mesh = {Animals ; Sheep/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Altitude ; *Biomass ; Metagenome ; Animal Feed/microbiology ; Archaea/genetics/classification ; Gastrointestinal Tract/microbiology ; Plants/microbiology ; }, abstract = {BACKGROUND: While Gangba sheep being well known for their unique flavour and nutritional value, harsh environmental factors negatively affect their growth and development, leading to poor productivity. The gastrointestinal tract microbiota plays an important role in host nutrient absorption and metabolism. The identification of dynamic changes in the gastrointestinal microbial communities and their functions is an important step towards improving animal production performance and health.<br><br>RESULTS: A comprehensive multi-omics survey of the microbial communities of the Gangba sheep gastrointestinal tract was performed under three distinct feeding strategies: natural grazing, semi-grazing with supplementation, and barn feeding. The dynamic changes, cross-kingdom partnerships and functional potential profiles were analysed and the results revealed that the feeding strategies had a greater impact on the microbial communities than the site of the gastrointestinal tract. The different microbial associations among the groups were revealed by co-occurrence networks based on the amplicon sequence variants (ASVs). Moreover, a Gangba sheep gastrointestinal microbial genomic catalogue was constructed for the first time, including 1146 metagenome-assembled genomes (MAGs) with completeness&#x2009;>&#x2009;50% and contamination&#x2009;<&#x2009;10%, among which, 504 bacterial and 15 archaeal MAGs were of high quality with completeness&#x2009;>&#x2009;80% and contamination&#x2009;<&#x2009;10%. About 40% of the high-quality MAGs displaying enzyme activity were related to the microbial species that contribute to plant biomass degradation. Most of these enzymes were expressed in rumen metatranscriptome datasets, especially in Prevotella spp. and Ruminococcus spp., suggesting that gastrointestinal microbial communities in ruminants play major roles in the digestion of plant biomass to provide nutrition and energy for the host.<br><br>CONCLUSIONS: These findings suggest that feeding strategies are the primary cause of changes in the gastrointestinal microbiome. Diversification of livestock feed might be an effective strategy to maintain the diversity and ecological multifunctionality of microbial communities in the gastrointestinal tract. Additionally, the catalogue of microbial genomes and the encoded biomass-degrading enzymes identified here provide insights into the potential microbial functions of the gastrointestinal tract of Gangba sheep at high altitudes. This paves the way for microbial interventions to improve the growth performance, productivity and product quality of ruminant livestock. Video Abstract.}, }
@article {pmid39838369, year = {2025}, author = {Fan, J and Zeng, F and Zhong, H and Cai, J and Shen, W and Cheng, C and He, C and Liu, Y and Zhou, Y and Chen, S and Zhu, Y and Liu, T and Zheng, JS and Wang, L and Chen, YM and Ma, W and Zhou, D}, title = {Potential roles of cigarette smoking on gut microbiota profile among Chinese men.}, journal = {BMC medicine}, volume = {23}, number = {1}, pages = {25}, pmid = {39838369}, issn = {1741-7015}, mesh = {Humans ; Male ; *Gastrointestinal Microbiome ; *Cigarette Smoking/adverse effects ; Middle Aged ; Adult ; China ; RNA, Ribosomal, 16S/genetics ; Asian People ; Actinomyces ; Aged ; East Asian People ; }, abstract = {BACKGROUND: Cigarette smoking is posited as a potential factor in disrupting the balance of the human gut microbiota. However, existing studies with limited sample size have yielded inconclusive results.<br><br>METHODS: Here, we assessed the association between cigarette smoking and gut microbial profile among Chinese males from four independent studies (N total&#x2009;=&#x2009;3308). Both 16S rRNA and shotgun metagenomic sequencing methods were employed, covering 206 genera and 237 species. Microbial diversity and abundance were compared among non-smokers, current smokers, and former smokers.<br><br>RESULTS: Actinomyces[g], Atopobium[g], Haemophilus[g], Turicibacter[g], and Lachnospira[g] were found to be associated with smoking status (current smokers vs. non-smokers). Metagenomic data provided a higher resolution at the species level, particularly for the Actinomyces[g] branch. Additionally, serum &#x3b3;-glutamylcysteine (&#x3b3;-Glu-Cys) was found to have a potential role in connecting smoking and Actinomyces[g]. Furthermore, we revealed putative mediation roles of the gut microbiome in the associations between smoking and common diseases including cholecystitis and type 2 diabetes.<br><br>CONCLUSIONS: We characterized the gut microbiota profile in male smokers and further revealed their potential involvement in mediating the impact of smoking on health outcomes. These findings advance our understanding of the intricate association between cigarette smoking and the gut microbiome.}, }
@article {pmid39838303, year = {2025}, author = {Pan, B and Pan, Y and Huang, YS and Yi, M and Hu, Y and Lian, X and Shi, HZ and Wang, M and Xiang, G and Yang, WY and Liu, Z and Xia, F}, title = {Efficacy and safety of gut microbiome-targeted treatment in patients with depression: a systematic review and meta-analysis.}, journal = {BMC psychiatry}, volume = {25}, number = {1}, pages = {64}, pmid = {39838303}, issn = {1471-244X}, support = {2021-I2M-1-060//the CAMS Innovation Fund for Medical Sciences (CIFMS)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Depression/therapy ; Depressive Disorder/therapy ; Probiotics/therapeutic use ; Treatment Outcome ; }, abstract = {BACKGROUND: The study aimed to comprehensively analyze and establish a framework for evaluating the efficacy of microbiome-targeted treatment (MTT) for depression.<br><br>METHODS: We searched PubMed, Embase, Cochrane Library, Web of Science, and the Chinese National Knowledge Infrastructure database for randomized controlled trials (RCTs) on MTT in treating depression until October 19, 2023. A meta-analysis was conducted to evaluate the efficacy and safety of MTT. Comprehensive subgroup analyses were undertaken to explore factors influencing MTT's efficacy in treating depression. This study was registered with PROSPERO (CRD42023483649).<br><br>RESULTS: The study selection process identified 51,570 studies, of which 34 met the inclusion criteria. The overall pooled estimates showed that MTT significantly improved depression symptoms (SMD -0.26, 95% CI [-0.32, -0.19], I[2]&#x2009;=&#x2009;54%) with acceptable safety. Subgroup analyses by geography showed that effectiveness was demonstrated in Asia (SMD -0.46, 95% CI [-0.56, -0.36], I[2]&#x2009;=&#x2009;36%), while no evidence of effectiveness was found in Europe (SMD -0.07, 95% CI [-0.19, 0.05], I[2]&#x2009;=&#x2009;55%), America (SMD -0.33, 95% CI [-0.67, 0.02], I[2]&#x2009;=&#x2009;60%), and Oceania (SMD 0.00, 95% CI [-0.18, 0.18], I[2]&#x2009;=&#x2009;0%). Besides, the efficacy was shown in depressed patients without comorbidities (SMD -0.31, 95% CI [-0.40, -0.22], I[2]&#x2009;=&#x2009;0%), whereas effectiveness was poor in those with digestive disorders, such as irritable bowel syndrome (SMD -0.37, 95% CI [-0.89, 0.16], I[2]&#x2009;=&#x2009;74%), chronic diarrhea (SMD -0.34, 95% CI [-0.73, 0.05]), and chronic constipation (SMD -0.23, 95% CI [-0.57, 0.11], I[2]&#x2009;=&#x2009;0%). In perinatal depressed patients, MTT was not effective (SMD 0.16, 95% CI [0.01, 0.31], I[2]&#x2009;=&#x2009;0%). It was found that <&#x2009;8 weeks (SMD -0.33, 95% CI [-0.45, -0.22], I[2]&#x2009;=&#x2009;0%) and 8-12 weeks (SMD -0.34, 95% CI [-0.44, -0.23], I[2]&#x2009;=&#x2009;57%) MTT were effective, while&#x2009;>&#x2009;12 weeks (SMD 0.02, 95% CI [-0.12, 0.17], I[2]&#x2009;=&#x2009;68%) MTT was ineffective.<br><br>CONCLUSIONS: Despite the overall effectiveness of MTT in treating depression and its acceptable safety profile, caution is warranted in drawing this conclusion due to limitations posed by the small sample size of included studies and heterogeneity. The efficacy of MTT for depression exhibits variation influenced by geography, patient comorbidities, and duration of administration.}, }
@article {pmid39837860, year = {2025}, author = {Alser, M and Eudine, J and Mutlu, O}, title = {Taming large-scale genomic analyses via sparsified genomics.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {876}, pmid = {39837860}, issn = {2041-1723}, mesh = {*Genomics/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Algorithms ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Software ; Databases, Genetic ; }, abstract = {Searching for similar genomic sequences is an essential and fundamental step in biomedical research. State-of-the-art computational methods performing such comparisons fail to cope with the exponential growth of genomic sequencing data. We introduce the concept of sparsified genomics where we systematically exclude a large number of bases from genomic sequences and enable faster and memory-efficient processing of the sparsified, shorter genomic sequences, while providing comparable accuracy to processing non-sparsified sequences. Sparsified genomics provides benefits to many genomic analyses and has broad applicability. Sparsifying genomic sequences accelerates the state-of-the-art read mapper (minimap2) by 2.57-5.38x, 1.13-2.78x, and 3.52-6.28x using real Illumina, HiFi, and ONT reads, respectively, while providing comparable memory footprint, 2x smaller index size, and more correctly detected variations compared to minimap2. Sparsifying genomic sequences makes containment search through very large genomes and large databases 72.7-75.88x (1.62-1.9x when indexing is preprocessed) faster and 723.3x more storage-efficient than searching through non-sparsified genomic sequences (with CMash and KMC3). Sparsifying genomic sequences enables robust microbiome discovery by providing 54.15-61.88x (1.58-1.71x when indexing is preprocessed) faster and 720x more storage-efficient taxonomic profiling of metagenomic samples over the state-of-the-art tool (Metalign).}, }
@article {pmid39837844, year = {2025}, author = {Ma, Y and Zhong, Y and Tang, W and Valencak, TG and Liu, J and Deng, Z and Mao, J and Liu, D and Wang, S and Wang, Y and Wang, H}, title = {Lactobacillus reuteri ZJ617 attenuates metabolic syndrome via microbiota-derived spermidine.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {877}, pmid = {39837844}, issn = {2041-1723}, support = {2022YFD1300602//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; }, mesh = {*Limosilactobacillus reuteri/metabolism ; *Metabolic Syndrome/metabolism/microbiology ; Animals ; *Spermidine/metabolism/pharmacology ; *Probiotics ; *Gastrointestinal Microbiome ; *Diet, High-Fat/adverse effects ; Mice ; Male ; *Mice, Inbred C57BL ; Disease Models, Animal ; }, abstract = {Metabolic syndrome (MetS) is a difficult-to-manage disease that poses a significant risk to human health. Here, we show that the supplementation of Lactobacillus reuteri ZJ617 ameliorates symptoms of MetS in mice induced by the high-fat diet. L. reuteri ZJ617 modulates host metabolism by interacting with the microbiome, resulting in the production of spermidine synthesized by the microbiota. L. reuteri ZJ617 serves as a source of substrates for the microbiota to synthesize spermidine, hence preventing the decline of bacteria responsible for spermidine production. Spermidine treatment mimics the metabolic effects of L. reuteri ZJ617, whereas pharmacological inhibition of spermidine biosynthesis in mice abolishes these benefits. Our findings reveal the mechanism by which L. reuteri ZJ617 alleviates MetS symptoms and provide support for its potential use as a probiotic for promoting metabolic health.}, }
@article {pmid39837772, year = {2025}, author = {Tronson, E and Enders, L}, title = {Root microbes can improve plant tolerance to insect damage: A systematic review and meta-analysis.}, journal = {Ecology}, volume = {106}, number = {1}, pages = {e4502}, doi = {10.1002/ecy.4502}, pmid = {39837772}, issn = {1939-9170}, support = {2019-67013//National Institute of Food and Agriculture/ ; }, mesh = {*Insecta/physiology ; Animals ; *Plant Roots/microbiology ; *Herbivory ; Plants/microbiology ; Soil Microbiology ; Microbiota ; }, abstract = {To limit damage from insect herbivores, plants rely on a blend of defensive mechanisms that includes partnerships with beneficial microbes, particularly those inhabiting roots. While ample evidence exists for microbially mediated resistance responses that directly target insects through changing phytotoxin and volatile profiles, we know surprisingly little about the microbial underpinnings of plant tolerance. Tolerance defenses counteract insect damage via shifts in plant physiology that reallocate resources to fuel compensatory growth, improve photosynthetic efficiency, and reduce oxidative stress. Despite being a powerful mitigator of insect damage, tolerance remains an understudied realm of plant defenses. Here, we propose a novel conceptual framework that can be broadly applied across study systems to characterize microbial impacts on expression of tolerance defenses. We conducted a systematic review of studies quantifying the impact of rhizosphere microbial inoculants on plant tolerance to herbivory based on several measures-biomass, oxidative stress mitigation, or photosynthesis. We identified 40 studies, most of which focused on chewing herbivores (n = 31) and plant growth parameters (e.g., biomass). Next, we performed a meta-analysis investigating the impact of microbial inoculants on plant tolerance to herbivory, which was measured via differences in plant biomass, and compared across key microbe, insect, and plant traits. Thirty-five papers comprising 113 observations were included in this meta-analysis, with effect sizes (Hedges' d) ranging from -4.67 (susceptible) to 18.38 (overcompensation). Overall, microbial inoculants significantly reduce the cost of herbivory via plant growth promotion, with overcompensation and compensation comprising 25% of observations of microbial-mediated tolerance. The grand mean effect size 0.99 [0.49; 1.49] indicates that the addition of a microbial inoculant increased plant biomass by ~1 SD under herbivore stress, thus improving tolerance. This effect was influenced most by microbial attributes, including functional guild and total soil community diversity. Overall, results highlight the need for additional investigation of microbially mediated plant tolerance, particularly in sap-feeding insects and across a more comprehensive range of tolerance mechanisms. Such attention would round out our current understanding of anti-herbivore plant defenses, offer insight into the underlying mechanisms that promote resilience to insect stress, and inform the application of microbial biotechnology to support sustainable agricultural practices.}, }
@article {pmid39837716, year = {2025}, author = {Zarrabi, KK and Vaishampayan, U and Barata, PC}, title = {Enhancing the Immunogenicity of Nivolumab plus Ipilimumab with Live Bacterial Supplementation in Metastatic Renal Cell Carcinoma.}, journal = {European urology focus}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.euf.2025.01.003}, pmid = {39837716}, issn = {2405-4569}, abstract = {Dysbiosis may hinder effective tumor immunity and reduce the efficacy of therapies such as immune checkpoint blockade (ICB) in renal cell carcinoma (RCC). CBM588, a product containing live Clostridium butyricum, has shown promise in enhancing ICB effectiveness in metastatic RCC in terms of response rates and progression-free survival. Further research to confirm these findings should take factors such as diet and microbiome composition into account and include predictive biomarkers for patient selection.}, }
@article {pmid39837385, year = {2025}, author = {Pan, Y and Yang, Y and Peng, Z and Wang, W and Zhang, J and Sun, G and Wang, F and Zhu, Z and Cao, H and Lyu, Y and Zhang, Z and Yang, W}, title = {Gut microbiota may modify the association between dietary polyphenol intake and circulating levels of hippuric acid: results from a 1-year longitudinal study in China.}, journal = {The American journal of clinical nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajcnut.2025.01.018}, pmid = {39837385}, issn = {1938-3207}, abstract = {BACKGROUND: Hippuric acid (HA), a host-microbe co-metabolite, normally derives from gut microbial catabolism of dietary polyphenols.<br><br>OBJECTIVES: We investigated the potential interplay between dietary polyphenols and gut microbiota on circulating HA levels, and examined the associations between serum concentrations of HA and cardiometabolic risk markers.<br><br>METHODS: In a 1-year cohort of 754 community-dwelling adults, serum HA and its precursor [benzoic acid (BA)] and fecal microbiota were assayed using liquid chromatography-tandem mass spectrometry and 16S ribosomal RNA sequencing, respectively. Diet, blood pressure, blood glucose and lipids were measured twice, 1-year apart. Arterial stiffness [indicated by brachial-ankle pulse wave velocity (baPWV) and ankle-brachial index] and liver fat accumulation [indicated by controlled attenuation parameter (CAP)] were measured after 1 year.<br><br>RESULTS: We identified 27 microbial genera whose relative abundance was positively associated with serum HA concentrations (PFDR<0.05) and constructed a microbial score to reflect the overall HA-producing potential. In multivariate-adjusted linear models, dietary intake of catechins and chlorogenic acids was positively associated with serum HA concentrations among participants with a higher microbial score (&#x3b2;=0.26, P=0.03), but not among those with a lower score (&#x3b2;=-0.13, P=0.30, Pinteraction=0.03). Participants with higher intake of dietary catechins and chlorogenic acids had lower triglyceride (Percentage change = -5.9%, P<0.05). Each 1 &#x3bc;mol/L increase in serum HA, but not in BA, was associated with 5.7%, 1.5%, 1.7%, 1.7%, and 1.7% decrease in triglyceride, systolic blood pressure, diastolic blood pressure, baPWV, and CAP, respectively (all P<0.05).<br><br>CONCLUSIONS: The gut microbial genera that predicted circulating HA levels may modify the association between dietary polyphenol intake and circulating HA levels, and elevated serum HA concentrations are favorably associated with multiple cardiometabolic risk markers.}, }
@article {pmid39837331, year = {2025}, author = {Valdés-Mas, R and Leshem, A and Zheng, D and Cohen, Y and Kern, L and Zmora, N and He, Y and Katina, C and Eliyahu-Miller, S and Yosef-Hevroni, T and Richman, L and Raykhel, B and Allswang, S and Better, R and Shmueli, M and Saftien, A and Cullin, N and Slamovitz, F and Ciocan, D and Ouyang, KS and Mor, U and Dori-Bachash, M and Molina, S and Levin, Y and Atarashi, K and Jona, G and Puschhof, J and Harmelin, A and Stettner, N and Chen, M and Suez, J and Honda, K and Lieb, W and Bang, C and Kori, M and Maharshak, N and Merbl, Y and Shibolet, O and Halpern, Z and Shouval, DS and Shamir, R and Franke, A and Abdeen, SK and Shapiro, H and Savidor, A and Elinav, E}, title = {Metagenome-informed metaproteomics of the human gut microbiome, host, and dietary exposome uncovers signatures of health and inflammatory bowel disease.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2024.12.016}, pmid = {39837331}, issn = {1097-4172}, abstract = {Host-microbiome-dietary interactions play crucial roles in regulating human health, yet their direct functional assessment remains challenging. We adopted metagenome-informed metaproteomics (MIM), in mice and humans, to non-invasively explore species-level microbiome-host interactions during commensal and pathogen colonization, nutritional modification, and antibiotic-induced perturbation. Simultaneously, fecal MIM accurately characterized the nutritional exposure landscape in multiple clinical and dietary contexts. Implementation of MIM in murine auto-inflammation and in human inflammatory bowel disease (IBD) characterized a "compositional dysbiosis" and a concomitant species-specific "functional dysbiosis" driven by suppressed commensal responses to inflammatory host signals. Microbiome transfers unraveled early-onset kinetics of these host-commensal cross-responsive patterns, while predictive analyses identified candidate fecal host-microbiome IBD biomarker protein pairs outperforming S100A8/S100A9 (calprotectin). Importantly, a simultaneous fecal nutritional MIM assessment enabled the determination of IBD-related consumption patterns, dietary treatment compliance, and small intestinal digestive aberrations. Collectively, a parallelized dietary-bacterial-host MIM assessment functionally uncovers trans-kingdom interactomes shaping gastrointestinal ecology while offering personalized diagnostic and therapeutic insights into microbiome-associated disease.}, }
@article {pmid39837176, year = {2025}, author = {Chen, Y and Wang, Y}, title = {Innovations in intestinal organoid technology featuring an open apical surface.}, journal = {European journal of cell biology}, volume = {104}, number = {2}, pages = {151476}, doi = {10.1016/j.ejcb.2025.151476}, pmid = {39837176}, issn = {1618-1298}, abstract = {Since the development of the three-dimensional (3D) "mini-gut" culture system, adult stem cell-derived organoid technology has rapidly advanced, providing in vitro models that replicate key cellular, molecular, and physiological properties of multiple organs. The 3D intestinal organoid system has resolved many long-standing challenges associated with immortalized or cancer cell cultures, offering unparalleled capabilities for modeling gastrointestinal development and diseases. However, significant limitations remain, including restricted accessibility to the epithelial apical surface for studying host-microbe interactions, interruptions in modeling chronic gastrointestinal diseases due to frequent passaging and dissociation, and the absence of mechanical cues such as peristalsis and luminal flow, which are critical for organ development and function. To address these challenges, recent advancements have introduced Transwell-based monolayer cultures and microfluidic device-based technologies including "organ-on-a-chip" and scaffold-guided 'mini-gut' system. This review highlights these innovations, with a focus on adult stem cell-derived intestinal organoid models that feature an open apical surface and discusses their prospects and challenges for advancing basic research and clinical applications.}, }
@article {pmid39837123, year = {2025}, author = {Xu, M and Liu, X and Chen, T and Zhao, Y and Ma, L and Shi, X and Chen, X and Shi, Y and Adams, JM}, title = {Dynamics of wheat rhizosphere microbiome and its impact on grain production across growth stages.}, journal = {The Science of the total environment}, volume = {964}, number = {}, pages = {178524}, doi = {10.1016/j.scitotenv.2025.178524}, pmid = {39837123}, issn = {1879-1026}, abstract = {Crop plant microbiomes are increasingly seen as important in plant nutrition and health, and a key to maintaining food productivity. Currently, little is known of the temporal changes that occur in the wheat rhizosphere microbiome as the plant develops, and how this varies among different sites. We used a pot-based mesocosm experiment with the same modern wheat cultivar grown in eight soils from across the North China Plain, a major wheat producing area. DNA from rhizosphere soil was taken from wheat plants, from seedling up to grain harvesting stage, and amplicon sequenced for prokaryotes and microeukaryotes, followed by community analysis. Our results showed that rhizosphere diversity of prokaryotes and microeukaryotes increased over time in most sites. While there was turnover between earlier- and later-arriving species, the predominant successional model was accumulation, with early arrivals remaining in place as others colonized the rhizosphere. Rhizosphere community network modularity and stability increased during the development and maturation of the wheat plant. The abundances of certain stage-specific keystone species were correlated with eventual grain yield - suggesting a potentially important role in wheat production. Some keystone species belonged to groups previously implicated in various functions. This study provides a basis for further experimental investigation of the wheat rhizosphere microbiome, its role in determining crop yields, and the potential for microbiome engineering to promote yields. The sequential arrival and accumulation of microbiota suggests that deliberate inoculation might accelerate this process.}, }
@article {pmid39836728, year = {2025}, author = {Zhao, X and Liang, X and Zhu, Z and Yuan, Z and Yu, S and Liu, Y and Wang, J and Mason-Jones, K and Kuzyakov, Y and Chen, J and Ge, T and Wang, S}, title = {Phages Affect Soil Dissolved Organic Matter Mineralization by Shaping Bacterial Communities.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c08274}, pmid = {39836728}, issn = {1520-5851}, abstract = {Viruses are considered to regulate bacterial communities and terrestrial nutrient cycling, yet their effects on bacterial metabolism and the mechanisms of carbon (C) dynamics during dissolved organic matter (DOM) mineralization remain unknown. Here, we added active and inactive bacteriophages (phages) to soil DOM with original bacterial communities and incubated them at 18 or 23 °C for 35 days. Phages initially (1-4 days) reduced CO2 efflux rate by 13-21% at 18 °C and 3-30% at 23 °C but significantly (p < 0.05) increased by 4-29% at 18 °C and 9-41% at 23 °C after 6 days, raising cumulative CO2 emissions by 14% at 18 °C and 21% at 23 °C. Phages decreased dominant bacterial taxa and increased bacterial community diversity (consistent with a "cull-the-winner" dynamic), thus altering the predicted microbiome functions. Specifically, phages enriched some taxa (such as Pseudomonas, Anaerocolumna, and Caulobacter) involved in degrading complex compounds and consequently promoted functions related to C cycling. Higher temperature facilitated phage-bacteria interactions, increased bacterial diversity, and enzyme activities, boosting DOM mineralization by 16%. Collectively, phages impact soil DOM mineralization by shifting microbial communities and functions, with moderate temperature changes modulating the magnitude of these processes but not qualitatively altering their behavior.}, }
@article {pmid39836666, year = {2025}, author = {Gill, B and Wessels, JM and Hayes, CL and Ratcliffe, J and Wokuri, J and Ball, E and Reid, G and Kaul, R and Rana, J and Alkhaifi, M and Tharao, W and Smaill, F and Kaushic, C}, title = {Feasibility, safety and tolerability of estrogen and/or probiotics for improving vaginal health in Canadian African, Caribbean, and Black women: A pilot phase 1 clinical trial.}, journal = {PloS one}, volume = {20}, number = {1}, pages = {e0315576}, doi = {10.1371/journal.pone.0315576}, pmid = {39836666}, issn = {1932-6203}, mesh = {Humans ; Female ; *Probiotics/administration &amp; dosage/adverse effects ; Adult ; *Vagina/microbiology ; *Estrogens/administration &amp; dosage ; Middle Aged ; Young Adult ; Adolescent ; Pilot Projects ; Canada ; Black People ; Vaginosis, Bacterial/drug therapy ; Feasibility Studies ; Administration, Intravaginal ; Caribbean Region ; Prospective Studies ; HIV Infections ; }, abstract = {BACKGROUND: A dysbiotic vaginal microbiome (VMB) is associated with clinical conditions such as bacterial vaginosis (BV) and an increased risk of human immunodeficiency virus (HIV-1) infection. Considering the high prevalence of BV among African, Caribbean and Black (ACB) women, we conducted a prospective, randomized, open-label phase 1 clinical trial to determine the feasibility, safety and tolerability of administering low-dose estrogen, probiotics or both in combination to improve vaginal health and decrease HIV-1 susceptibility.<br><br>METHODS: ACB women aged 18-49 from the Greater Toronto Area (GTA) were randomized to one of four study arms: intravaginal estradiol (Estring&#xa9;; 7.5mg/day); a vaginal probiotic (RepHresh&#x2122; Pro-B&#x2122;) administered twice daily; a combination of Estring&#xa9; and vaginal RepHresh&#x2122; Pro-B&#x2122; (twice daily); or the Estring&#xa9; and oral RepHresh&#x2122; Pro-B&#x2122; (twice daily), for a duration of 30 days. Feasibility was evaluated through enrolment, retention, and adherence rates, while safety and tolerability were determined by a pre- and post-treatment blood panel and reported adverse events (AEs).<br><br>RESULTS: Overall, 63 ACB women were screened, 50 were enrolled and received the intervention while 41 completed the study, resulting in 80% enrollment and 82% retention rates. Overall adherence to the study protocol was high at 93%, with an adherence of 92% for RepHresh&#x2122; Pro-B&#x2122; and 97% for Estring&#xa9;. A total of 88 AEs were reported by 29 participants which were mild (66/88; 75%) and largely resolved (82/88;93%) by the end of the study, with no serious AEs (SAEs) noted. In addition, a panel of safety blood markers measured pre- and post-intervention confirmed no clinically significant changes in blood chemistry or blood cell count.<br><br>CONCLUSION: Overall, the administration of intravaginal estrogen and/or probiotics in pre-menopausal ACB women is feasible, safe, and well tolerated.<br><br>TRIAL REGISTRATION: The trial was registered with Clinicaltrials.gov (NCT03837015) and CIHR HIV Clinical Trials (CTN308).}, }
@article {pmid39836459, year = {2025}, author = {Li, J and King, K}, title = {Microbial Primer: Microbiome and thermal tolerance - a new frontier in climate resilience?.}, journal = {Microbiology (Reading, England)}, volume = {171}, number = {1}, pages = {}, doi = {10.1099/mic.0.001523}, pmid = {39836459}, issn = {1465-2080}, mesh = {*Microbiota/physiology ; Animals ; *Climate Change ; *Symbiosis ; Thermotolerance ; Bacteria/genetics/classification ; Host Microbial Interactions/physiology ; Temperature ; }, abstract = {Microbiome-animal host symbioses are ubiquitous in nature. Animal-associated microbiomes can play a crucial role in host physiology, health and resilience to environmental stressors. As climate change drives rising global temperatures and increases the frequency of thermal extremes, microbiomes are emerging as a new frontier in buffering vulnerable animals against temperature fluctuations. In this primer, we briefly introduce key concepts of microbiome-host symbiosis and microbial responses to temperature shifts. We then summarize the current evidence and understanding of how microbes can buffer the thermal stress faced by their hosts. We identify key challenges for future research. Finally, we emphasize the potential of harnessing microbiomes to improve conservation strategies in a rapidly changing climate, offering a concise overview of this evolving field.}, }
@article {pmid39836381, year = {2025}, author = {Zieschank, V and Muola, A and Janssen, S and Lach, A and Junker, RR}, title = {Tolerance to land-use changes through natural modulations of the plant microbiome.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf010}, pmid = {39836381}, issn = {1751-7370}, abstract = {Land-use changes threaten ecosystems and are a major driver of species loss. Plants may adapt or migrate to resist global change, but this can lag behind rapid anthropogenic changes to the environment. Our data show that natural modulations of the microbiome of grassland plants in response to experimental land-use change in a common garden directly affect plant phenotype and performance, thus increasing plant tolerance. In contrast, direct effects of fertilizer application and mowing on plant phenotypes were less strong. Land-use intensity-specific microbiomes caused clearly distinguishable plant phenotypes also in a laboratory experiment using gnotobiotic strawberry plants in absence of environmental variation. Therefore, natural modulations of the plant microbiome may be key to species persistence and ecosystem stability. We argue that a prerequisite for this microbiome-mediated tolerance is the availability of diverse local sources of microorganisms facilitating rapid modulations in response to change. Thus, conservation efforts must protect microbial diversity, which can help mitigate the effects of global change and facilitate environmental and human health.}, }
@article {pmid39836282, year = {2025}, author = {Tasoujlu, M and Sharifi, Y and Ghahremani, M and Alizadeh, K and Babaie, F and Hosseiniazar, MM}, title = {Evaluation of variations in predominant gut microbiota members in inflammatory bowel disease using real-time PCR.}, journal = {Molecular biology reports}, volume = {52}, number = {1}, pages = {143}, pmid = {39836282}, issn = {1573-4978}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; *Real-Time Polymerase Chain Reaction/methods ; Male ; Adult ; Female ; *Feces/microbiology ; Middle Aged ; *Akkermansia ; Bifidobacterium/isolation &amp; purification/genetics ; Bacteria/genetics/classification/isolation &amp; purification ; Case-Control Studies ; Lactobacillus/isolation &amp; purification/genetics ; Enterobacteriaceae/genetics/isolation &amp; purification ; }, abstract = {Inflammatory Bowel Disease (IBD) is a persistent ailment that impacts many individuals worldwide. The interaction between the immune system and gut microbiome is thought to influence IBD development. This study aimed to assess some microbiota in IBD patients compared to healthy individuals. The investigation involved a selected group of twenty patients suffering from IBD and an equal number of healthy participants. Stool specimens were obtained and analyzed for Lactobacillus, Bifidobacterium, Bacteroides, Clostridium leptum, Akkermansia muciniphila, Fusobacterium and Enterobacteriaceae using real-time PCR. The findings indicated significantly higher levels of Bifidobacterium in IBD patients (Pv = 0.009) and lower levels of A. muciniphila (Pv = 0.003) healthy individuals. Other bacteria tested did not show significant differences. The study suggests that the progression of IBD patients could be influenced by the rising of Bifidobacterium and the declining of A. muciniphila. Targeting these bacteria could lead to improved treatments and quality of life for those with IBD.}, }
@article {pmid39836273, year = {2025}, author = {Nakamura, A and Matsumoto, M}, title = {Role of polyamines in intestinal mucosal barrier function.}, journal = {Seminars in immunopathology}, volume = {47}, number = {1}, pages = {9}, pmid = {39836273}, issn = {1863-2300}, support = {23K17454//JSPS KAKENHI/ ; 22K15116//JSPS KAKENHI/ ; }, mesh = {Humans ; *Intestinal Mucosa/metabolism/immunology ; Animals ; *Polyamines/metabolism ; Cell Differentiation ; Autophagy ; Cell Proliferation ; Epithelial Cells/metabolism ; Intestinal Barrier Function ; }, abstract = {The intestinal epithelium is a rapidly self-renewing tissue; the rapid turnover prevents the invasion of pathogens and harmful components from the intestinal lumen, preventing inflammation and infectious diseases. Intestinal epithelial barrier function depends on the epithelial cell proliferation and junctions, as well as the state of the immune system in the lamina propria. Polyamines, particularly putrescine, spermidine, and spermine, are essential for many cell functions and play a crucial role in mammalian cellular homeostasis, such as that of cell growth, proliferation, differentiation, and maintenance, through multiple biological processes, including translation, transcription, and autophagy. Although the vital role of polyamines in normal intestinal epithelial cell growth and barrier function has been known since the 1980s, recent studies have provided new insights into this topic at the molecular level, such as eukaryotic initiation factor-5A hypusination and autophagy, with rapid advances in polyamine biology in normal cells using biological technologies. This review summarizes recent advances in our understanding of the role of polyamines in regulating normal, non-cancerous, intestinal epithelial barrier function, with a particular focus on intestinal epithelial renewal, cell junctions, and immune cell differentiation in the lamina propria.}, }
@article {pmid39835966, year = {2025}, author = {Levine, BH and Hoffman, JM}, title = {Microbiome transplants may not improve health and longevity in Drosophila melanogaster.}, journal = {Biology open}, volume = {14}, number = {1}, pages = {}, doi = {10.1242/bio.061745}, pmid = {39835966}, issn = {2046-6390}, support = {R00AG059920/NH/NIH HHS/United States ; //Augusta University; University of South Carolina/ ; }, mesh = {Animals ; *Drosophila melanogaster/microbiology/physiology ; *Longevity ; *Gastrointestinal Microbiome ; Female ; Male ; Microbiota ; }, abstract = {The gut microbiome, which is composed of bacteria, viruses, and fungi, and is involved in multiple essential physiological processes, changes measurably as a person ages, and can be associated with negative health outcomes. Microbiome transplants have been proposed as a method to improve gut function and reduce or reverse multiple disorders, including age-related diseases. Here, we take advantage of the laboratory model organism, Drosophila melanogaster, to test the effects of transplanting the microbiome of a young fly into middle-aged flies, across multiple genetic backgrounds and both sexes, to test whether age-related lifespan could be increased, and late-life physical health declines mitigated. Our results suggest that, overall, microbiome transplants do not improve longevity and may even be detrimental in flies, and the health effects of microbiome transplants were minor, but sex- and genotype-dependent. This discovery supports previous evidence that axenic flies, those with no gut microbiome, live healthier and longer lives than their non-axenic counterparts. The results of this study suggest that, at least for fruit flies, microbiome transplants may not be a viable intervention to improve health and longevity, though more research is still warranted.}, }
@article {pmid39835641, year = {2025}, author = {Zeky, N and LeBlanc, C and Yang, S and McDonough, E and Dhaliwal, J and Moulton, D}, title = {Food access and the severity of newly diagnosed pediatric inflammatory bowel disease.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1002/jpn3.12463}, pmid = {39835641}, issn = {1536-4801}, support = {//None/ ; }, abstract = {OBJECTIVES: Inflammatory bowel disease (IBD) results from genetic susceptibility, gut microbiome, and environmental factors. Diet, one modifiable environmental factor, has been linked to the increased prevalence of IBD. This study aimed to evaluate a potential association between food deserts and disease severity at diagnosis.<br><br>METHODS: This retrospective study included newly diagnosed IBD patients (ages of 2 and 21 years of age; diagnosed between January 1, 2019, and December 31, 2021). The United States Department of Agriculture (USDA's) Food Access Research Atlas was used to determine if patients resided in a food desert. The Modified Retail Food Environment Index (mRFEI) determined the ratio of healthy to unhealthy food options. The primary endpoint was disease severity at diagnosis based on endoscopy scores. Statistical analyses were applied as appropriate.<br><br>RESULTS: Ninety-eight patients were enrolled (75 [77%] Crohn' disease; 23 [23%] ulcerative colitis), 59 (60%) identified as Non-Hispanic White. Fifteen (15%) patients lived in a food desert. Food deserts consisted of more Black patients than White (67%; p&#x2009;=&#x2009;0.05), more public insurance (12; 80%), and lower median vitamin D (17.6 [interquartile range (IQR): 10.8-24.]). In an adjusted (sex, age, insurance, race) multivariable model mRFEI was associated with reduced odds of a living in a food desert (0.91 [95% confidence interval (CI): 0.83-0.98]). There was no difference between the severity of disease and living in a food desert or food swamp.<br><br>CONCLUSIONS: Fifteen IBD patients lived in a food desert. Food deserts have less access to healthy food retailers and higher rates of unhealthy food retailers. Further work is needed to better understand spatial disparities related to food accessibility and IBD.}, }
@article {pmid39835619, year = {2025}, author = {Campagna, RA and Kelly, EA and Vugia, DJ and Berman Watson, HF and Browne, CS and Lau, JK and Fritz, CL}, title = {Clinical and Epidemiologic Review of Capnocytophaga Spp. Infections Identified at a Public Health Reference Laboratory-California, 2005-2021.}, journal = {Zoonoses and public health}, volume = {}, number = {}, pages = {}, doi = {10.1111/zph.13209}, pmid = {39835619}, issn = {1863-2378}, abstract = {INTRODUCTION: Capnocytophaga is a genus of bacteria that are commensal to the oral microbiome of humans and some animals. Some Capnocytophaga species are found in the human oral cavity and rarely cause disease in people; the species found in animals are zoönotic and can be transmitted to people via saliva. This study describes the clinical and epidemiologic features of patients from whom Capnocytophaga spp. were isolated from blood and other clinical specimens at the California state Microbial Diseases Laboratory.<br><br>METHODS: Clinical information was obtained from laboratory submission forms and any accompanying medical records and/or from matching records in statewide hospital discharge and emergency department databases.<br><br>RESULTS: During the 17-year study period (2005-2021), Capnocytophaga spp. were isolated in 48 specimens from 47 patients. Capnocytophaga canimorsus, which is a zo&#xf6;notic species, represented 85% of the Capnocytophaga spp. identified to the species level. The median age was 67&#x2009;years (range: 30-88&#x2009;years) for the 42 patients infected with a zo&#xf6;notic species of Capnocytophaga and 36&#x2009;years (range: 12-65&#x2009;years) for the four patients infected with a non-zo&#xf6;notic species. Twenty-five (60%) patients with zo&#xf6;notic species infections were male, compared to two (50%) patients with non-zo&#xf6;notic species infections. Capnocytophaga spp. were most frequently isolated from blood (88%), and the most common case presentation was sepsis (45%). A dog or cat bite prior to diagnosis was reported for 14% of patients infected with a zo&#xf6;notic species of Capnocytophaga. Records for 45% of patients indicated at least one pre-existing health condition associated with depressed immune function.<br><br>CONCLUSIONS: This study documented that Capnocytophaga spp. can cause rare, severe, invasive disease in mostly older or immunocompromised persons, often without documentation of a dog or cat bite. Providers are encouraged to consider Capnocytophaga spp. infection in immunocompromised pet owners presenting with sepsis, even in the absence of a known animal bite.}, }
@article {pmid39835433, year = {2025}, author = {Kato, R and Obara, W}, title = {Persisting challenges in the development of predictive biomarkers for immuno-oncology therapies for renal cell carcinoma.}, journal = {Expert review of anticancer therapy}, volume = {}, number = {}, pages = {}, doi = {10.1080/14737140.2025.2457373}, pmid = {39835433}, issn = {1744-8328}, abstract = {Introduction Immuno-oncology (IO) therapies have become integral to renal cell carcinoma (RCC) management, RCC remains a complex malignancy with diverse clinical behaviors and a heterogeneous tumor microenvironment, highlighting the need for predictive biomarkers to optimize therapy. Areas covered This review synthesizes recent findings from clinical trials, translational studies, and molecular analyses to provide an updated perspective on biomarker research for IO therapies in RCC. A literature search was conducted using PubMed, Embase, and Web of Science for articles published between January 2010 and November 2024. Expert opinion IO combination therapies have demonstrated significant improvements in progression-free survival and overall survival compared with sunitinib. However, treatment outcomes vary according to the IMDC risk groups, metastatic sites, and histological subtypes, such as sarcomatoid differentiation. Advances in molecular biology have elucidated the roles of genetic alterations and immune phenotypes in modulating IO efficacy. Emerging biomarkers, including tertiary lymphoid structures, human endogenous retroviruses, and the gut microbiome, show promise but require further validation. Addressing challenges such as intratumoral heterogeneity and dynamic immune responses will be key to identifying actionable biomarkers. Continued integration of clinical and molecular insights is essential for improving patient selection and outcomes in RCC treated with IO therapies.}, }
@article {pmid39835346, year = {2025}, author = {Herzog, MK and Peters, A and Shayya, N and Cazzaniga, M and Kaka Bra, K and Arora, T and Barthel, M and Gül, E and Maurer, L and Kiefer, P and Christen, P and Endhardt, K and Vorholt, JA and Frankel, G and Heimesaat, MM and Bereswill, S and Gahan, CGM and Claesson, MJ and Domingo-Almenara, X and Hardt, WD}, title = {Comparing Campylobacter jejuni to three other enteric pathogens in OligoMM[12] mice reveals pathogen-specific host and microbiota responses.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2447832}, doi = {10.1080/19490976.2024.2447832}, pmid = {39835346}, issn = {1949-0984}, mesh = {Animals ; *Campylobacter jejuni/pathogenicity/physiology ; Mice ; *Gastrointestinal Microbiome ; *Germ-Free Life ; *Disease Models, Animal ; *Campylobacter Infections/microbiology ; Mice, Inbred C57BL ; Citrobacter rodentium/pathogenicity/physiology ; Listeria monocytogenes/pathogenicity/genetics/physiology ; Female ; }, abstract = {Campylobacter jejuni, non-typhoidal Salmonella spp., Listeria monocytogenes and enteropathogenic/enterohemorrhagic Escherichia coli (EPEC/EHEC) are leading causes of food-borne illness worldwide. Citrobacter rodentium has been used to model EPEC and EHEC infection in mice. The gut microbiome is well-known to affect gut colonization and host responses to many food-borne pathogens. Recent progress has established gnotobiotic mice as valuable models to study how microbiota affect the enteric infections by S. Typhimurium, C. rodentium and L. monocytogenes. However, for C. jejuni, we are still lacking a suitable gnotobiotic mouse model. Moreover, the limited comparability of data across laboratories is often negatively affected by variations between different research facilities or murine microbiotas. In this study, we applied the standardized gnotobiotic OligoMM[12] microbiota mouse model and compared the infections in the same facility. We provide evidence of robust colonization and significant pathological changes in OligoMM[12] mice following infection with these pathogens. Moreover, we offer insights into pathogen-specific host responses and metabolite signatures, highlighting the advantages of a standardized mouse model for direct comparisons of factors influencing the pathogenesis of major food-borne pathogens. Notably, we reveal for the first time that C. jejuni stably colonizes OligoMM[12] mice, triggering inflammation. Additionally, our comparative approach successfully identifies pathogen-specific responses, including the detection of genes uniquely associated with C. jejuni infection in humans. These findings underscore the potential of the OligoMM[12] model as a versatile tool for advancing our understanding of food-borne pathogen interactions.}, }
@article {pmid39835289, year = {2024}, author = {Toraldo, DM and Palma Modoni, A and Scoditti, E and De Nuccio, F}, title = {Obstructive sleep apnoea as a neuromuscular respiratory disease arising from an excess of central GABAergic neurotransmitters: a new disease model.}, journal = {Frontiers in cellular neuroscience}, volume = {18}, number = {}, pages = {1429570}, doi = {10.3389/fncel.2024.1429570}, pmid = {39835289}, issn = {1662-5102}, }
@article {pmid39835267, year = {2025}, author = {Laishram, B and Devi, OR and Dutta, R and Senthilkumar, T and Goyal, G and Paliwal, DK and Panotra, N and Rasool, A}, title = {Plant-microbe interactions: PGPM as microbial inoculants/biofertilizers for sustaining crop productivity and soil fertility.}, journal = {Current research in microbial sciences}, volume = {8}, number = {}, pages = {100333}, doi = {10.1016/j.crmicr.2024.100333}, pmid = {39835267}, issn = {2666-5174}, abstract = {Plant-microbe interactions play pivotal roles in sustaining crop productivity and soil fertility, offering promising avenues for sustainable agricultural practices. This review paper explores the multifaceted interactions between plants and various microorganisms, highlighting their significance in enhancing crop productivity, combating pathogens, and promoting soil health. Understanding these interactions is crucial for harnessing their potential in agricultural systems to address challenges such as food security and environmental sustainability. Therefore, the introduction of beneficial microbes into agricultural ecosystems by bio-augmentation reduces the negative effects of intensive, non-sustainable agriculture on the environment, society, and economy, into the mechanisms underlying the application of plant growth promoting microbes as microbial inoculants/biofertilizers; their interactions, the factors influencing their dynamics, and the implications for agricultural practices, emerging technologies and strategies that leverage plant-microbe interactions for improving crop yields, soil fertility, and overall agricultural sustainability.}, }
@article {pmid39835244, year = {2025}, author = {Kawabata, F and Sakai, M and Murasawa, H and Komine, Y and Mukai, K and Kawabata, Y}, title = {Taste Preference and Metabolic Rate of Trehalose in Chickens.}, journal = {The journal of poultry science}, volume = {62}, number = {}, pages = {2025005}, doi = {10.2141/jpsa.2025005}, pmid = {39835244}, issn = {1349-0486}, abstract = {Trehalose (Tre) is composed of two molecules of D-glucose joined by an α,α-1,1 glucosidic linkage. Because Tre is utilized by the gut microbiome and enhances gut immunity in chickens, it is used as a feed ingredient. However, taste preference and metabolic dynamics of Tre in chickens are not fully understood. Therefore, in this study, we investigated the taste preference in chickens for Tre and the metabolism of this disaccharide. In a short-term drinking test, chickens preferred low concentrations of Tre solution while avoiding high concentrations. Instead, in a conditioned taste aversion test, chickens did not show taste aversion to Tre, implying that chickens do not have a sufficient taste for Tre. The initial feed intake rate increased when 0.5% Tre was added. Respiratory gas analysis revealed that intragastric administration of 1.0 M Tre weakly increased the respiratory quotient. Furthermore, approximately 50% of Tre was metabolized in chickens. These results suggest that chickens slightly taste the sweetness of Tre. Moreover, adding Tre to feed increases the chickens' initial appetite, and they use approximately 50% of Tre as an energy source. This information is relevant for using Tre alone or as a supplement in poultry feed.}, }
@article {pmid39835118, year = {2024}, author = {Liang, Y and Zhao, C and Wen, Y and Sheng, D and Wei, T and Hu, T and Dai, J and Zhao, G and Yang, S and Wang, Q and Zhang, L}, title = {Corrigendum: Modulation of local immunity by the vaginal microbiome is associated with triggering spontaneous preterm birth.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1544081}, doi = {10.3389/fimmu.2024.1544081}, pmid = {39835118}, issn = {1664-3224}, abstract = {[This corrects the article DOI: 10.3389/fimmu.2024.1481611.].}, }
@article {pmid39834958, year = {2024}, author = {Suriya Luke Rathnakumar, B and Gowda, U and Guttal, C and Gautham, S}, title = {The Role of Nasal Microbiota and Sensitivity in Patients With Chronic Rhinosinusitis at a Rural Tertiary Care Hospital.}, journal = {Cureus}, volume = {16}, number = {12}, pages = {e76048}, doi = {10.7759/cureus.76048}, pmid = {39834958}, issn = {2168-8184}, abstract = {Background and aim Etiopathogeneses of chronic rhinosinusitis are poorly understood. Recent research emphasizes culture-independent molecular sequencing to identify clusters of flora that may function as drivers of inflammation. Studies also indicate that macrolides are as effective as corticosteroids in controlling chronic rhinosinusitis. In this study, we aimed to isolate microbial cultures from the middle meatus of patients suffering from chronic rhinosinusitis and assess the isolates for similarities and antibiotic sensitivity. We also sought to identify the pathogenic species disrupting the nasal microbiome and provide appropriate antibiotics based on the least minimum inhibitory concentration (MIC) from the cultures. Disease progression and response to treatment were evaluated using the Sino-Nasal Outcome Test-22 (SNOT-22) and the Lund-Kennedy endoscopy scoring system. Specifically, diagnostic nasal endoscopy (DNE) was performed in patients with chronic rhinosinusitis without nasal polyps (CRSnNP), and the pre-treatment Lund-Kennedy score was recorded, along with subjective data collected from the SNOT-22 questionnaire. After isolating cultures from the middle meatus, antibiotic treatment was provided based on these findings. A repeat DNE was conducted to calculate the post-treatment Lund-Kennedy score and collect the post-treatment SNOT-22 score. Finally, the pre- and post-treatment scores were compared to assess any statistically significant differences. Methods The patients upon arrival to the hospital and diagnosed with chronic rhinosinusitis without nasal polyposis (CRSnNP) based on the joint EPOS 2020 Criterion for the same were enrolled in the study. The patients were administered an SNOT-22 Questionnaire for subjective evaluation. The patients underwent a diagnostic nasal endoscopy (DNE) to calculate the Lund-Kennedy score, take swabs from the middle meatus for culture and sensitivity, and provide objective evaluation by the assessing physicians. The scores were recorded at the first visit and on each visit till the two weeks of antibiotic treatment were completed. The patients were treated with antibiotics as per the cultured isolates. The Lund-Kennedy scores and SNOT-22 scores before and after treatment were compared to note the response to treatment. Results The mean average Lund-Kennedy score and SNOT-22 scores dropped following a course of antibiotics. The patients also experienced symptomatic relief. The most commonly isolated organism among the samples evaluated was Pseudomonas aeruginosa. The best response to antibiotics was noted with aminoglycosides. Total resistance (100%) to macrolides and amoxicillin was also observed, which contradicts the antibiotic guidelines of EPOS 2020, ICAR 2021, and JTFPP 2014. Conclusion This study found that the invasive species disrupting the local nasal microbiome of the participants consisted of various pathogenic microorganisms. It indicated that a culture-based treatment of CRSnNP will yield better results compared to empirical antibiotics. The present study also suggests revising guidelines for antibiotic use and developing personalized antibiograms for treating chronic rhinosinusitis.}, }
@article {pmid39834942, year = {2024}, author = {Valciukiene, J and Lastauskiene, E and Laurinaviciene, A and Jakubauskas, M and Kryzauskas, M and Valkiuniene, RB and Augulis, R and Garnelyte, A and Kavoliunas, J and Silinskaite, U and Poskus, T}, title = {Interaction of human gut microbiota and local immune system in progression of colorectal adenoma (MIMICA-1): a protocol for a prospective, observational cohort study.}, journal = {Frontiers in oncology}, volume = {14}, number = {}, pages = {1495635}, doi = {10.3389/fonc.2024.1495635}, pmid = {39834942}, issn = {2234-943X}, abstract = {INTRODUCTION: The current understanding of colorectal carcinogenesis is based on the adenoma-carcinoma sequence, where genetics, intestinal microbiota changes and local immunity shifts seem to play the key roles. Despite the emerging evidence of dysbiotic intestinal state and immune-cell infiltration changes in patients with colorectal adenocarcinoma, early and advanced adenoma as precursors of colorectal cancer, and carcinoma in situ as the following progression, are rather less studied. The newly colon-site adapted AI-based analysis of immune infiltrates is able to predict long-term outcomes of colon carcinoma. Though it could also facilitate the pathologic evaluation of precancerous lesion's potential to progress. Therefore, the purpose of this prospective cohort study (MIMICA-1) is, firstly, to identify the intestinal microbiota and immune infiltration patterns around the normal bowel tissue, early and advanced adenoma, carcinoma in situ, and adenocarcinoma, and secondly, to analyze the immune - microbiome interplay along the steps of conventional colorectal tumorigenesis.<br><br>METHODS AND ANALYSES: This study aims to prospectively recruit 40 patients (10 per group) with confirmed colorectal dysplasia undergoing endoscopic polypectomy, endoscopic mucosal resection for colorectal small (&#x2264;1cm), and large (>1cm) adenoma or carcinoma in situ, or biopsy and subsequent colon resection for invasive colorectal cancer, and 10 healthy patients undergoing screening colonoscopy. Stool samples will be collected prior to bowel preparation for the analysis of fecal (luminal) microbiota composition. Biopsy specimens will be taken from the terminal ileum, right colon, left colon, and a pathological lesion in the colon (if present) to assess mucosa-associated microbiota composition and intestinal immunity response. DNA will be extracted from all samples and sequenced using the Illumina MiSeq platform. Unifrac and Bray-Curtis methods will be used to assess microbial diversity. The intestinal immune system response will be examined using digital image analysis where primarily immunohistochemistry procedures for CD3, CD8, CD20 and CD68 immune cell markers will be performed. Thereafter, the count, density and distribution of immunocompetent cells in epithelial and stromal tissue compartments will be evaluated using AI-based platform. The interaction between the microbial shifts and intestinal immune system response in adenoma-carcinoma sequence and the healthy patients will be examined. In addition, fecal samples will be explored for gut microbiota's composition, comparing fecal- and tissue-derived bacterial patterns in healthy gut and along the adenoma-carcinoma sequence.<br><br>DISCUSSION: We hypothesize that changes within the human gut microbiota led to detectable alterations of the local immune response and correlate with the progression from normal mucosa to colorectal adenoma and invasive carcinoma. It is expectable to find more severe gut immune infiltration at dysplasia site, though analyzing invasive colorectal cancer we expect to detect broader mucosa-associated and luminal microbiota changes with subsequent local immune response at near-lesion site and possibly throughout the entire colon. We believe that specific compositional differences detected around premalignant colorectal lesions are critically important for its primary role in initiation and acceleration of colorectal carcinogenesis. Thus, these microbial patterns could potentially supplement fecal immunohistochemical tests for the early non-invasive detection of colorectal adenoma. Moreover, AI-based analysis of immune infiltrates could become additional diagnostic and prognostic tool in precancerous lesions prior to the development of colorectal cancer.<br><br>REGISTRATION: The study is registered at the Australian New Zealand Clinical Trials Registry (ACTRN12624000976583) https://www.anzctr.org.au/.}, }
@article {pmid39834920, year = {2024}, author = {Styková, E and Valocký, I and Kačírová, J and Fecskeová, LK}, title = {Microbiological effect of topically applied Weissella cibaria on equine pastern dermatitis.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1493756}, doi = {10.3389/fvets.2024.1493756}, pmid = {39834920}, issn = {2297-1769}, abstract = {Equine pastern dermatitis (EPD) is a multifactorial disease with a change in the skin microbiome. The present study monitored the influence of Weissella cibaria Biocenol™ 4/8 D37 CCM 9015 stabilized on alginite on the skin microbiota of healthy horses and model patients with EPD. Based on clinical signs, EPD lesions were identified as exudative or proliferative forms. A comparison of the initial microbial community based on 16S rRNA amplicon sequencing revealed that there was a statistically significant difference between healthy vs. exudative (R = 0.52, p = 0.003) and exudative vs. proliferative communities (R = 0.78, p = 0.043). The healthy skin microbiota was dominated by the families Corynebacteriaceae (19.7 ± 15.8%) and Staphylococcaceae (15.8 ± 10.7%). Streptococcus (11.7 ± 4.1%) was the dominant genus in the exudative group together with Corynebacterium (11.0 ± 3.8%), while Staphylococcus (15.6 ± 14.5%) dominated the proliferative group. The genus Staphylococcus represented only 0.5% of the exudative skin microbial community, a major difference between EPD-affected lesion types. Upon application, there was a statistically significant shift in community composition in all the groups, including the healthy community; however, the change was the most significant in the exudative community. On average, the genus Weissella represented 80.0 ± 13.3% of the exudative and 49.0 ± 30.0% of the proliferative bacterial community during treatment. One week after the application period, richness and diversity increased and were comparable in all groups. The application of the W. cibaria strain was associated with a significant decrease of the genera Staphylococcus, Moraxella, and Rothia in the proliferative group and with a decrease of Streptococcus and Clostridium in both exudative and proliferative groups. Based on our results, we conclude that a topically applied W. cibaria RIF[R], stabilized on alginit, induced potentially beneficial shifts in the composition of the skin microbiota.}, }
@article {pmid39834755, year = {2024}, author = {Neustaeter, A and Leibovitzh, H and Turpin, W and Croitoru, K and , }, title = {Understanding Predictors of Crohn's Disease: Determinants of Altered Barrier Function in Pre-Disease Phase of Crohn's Disease.}, journal = {Journal of the Canadian Association of Gastroenterology}, volume = {7}, number = {1}, pages = {68-77}, doi = {10.1093/jcag/gwad052}, pmid = {39834755}, issn = {2515-2092}, abstract = {The pathogenesis of Crohn's disease (CD) remains unknown. The current working theory is that genetic susceptibility influences host-microbe interactions, resulting in chronic inflammation. Case-control studies fail to explain the triggers or pathogenesis of the disease, notably due to confounding factors in patients with established disease. Investigating the pre-disease phase of CD improves the capacity to assess these confounding factors and enables us to identify biomarkers associated with increased risk of CD. The Crohn's Colitis Canada-Genes, Environment, Microbial (CCC-GEM) project is a prospective cohort of healthy first-degree relatives of patients with CD, allowing us to interrogate the pre-disease phase of CD. The CCC-GEM Project has led to the identification of several demographic, serological, and microbiome composition markers associated with an increased risk of disease in pre-clinical participants. Notably, altered intestinal barrier function, as measured by the fractional urinary excretion of lactulose mannitol ratio, is associated with a significantly increased risk of CD. We review the intrinsic and external factors that are associated with altered intestinal barrier integrity, including genetic risk, subclinical inflammation, serum proteomics, intestinal microbiome composition, and environmental components, such as diet and lifestyle. Providing insights into the factors and mechanisms of altered barrier function contributes to our understanding of the pathogenic mechanisms of CD. These advances may aid in developing strategies for preventing disease in high-risk individuals. Further research and personalized strategies are needed to optimize these mitigation strategies for individuals at-risk for CD.}, }
@article {pmid39834703, year = {2024}, author = {Deng, Y and Wu, W and Huang, X and Yang, X and Yu, Y and Zhang, Z and Hu, Z and Zhou, X and Zhou, K and Liu, Y and Zhang, L}, title = {Characterization of rhizosphere bacterial communities in oilseed rape cultivars with different susceptibility to Plasmodiophora brassicae infection.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1496770}, doi = {10.3389/fpls.2024.1496770}, pmid = {39834703}, issn = {1664-462X}, abstract = {Rhizosphere microbiomes are constantly mobilized during plant-pathogen interactions, and this, in turn, affects their interactions. However, few studies have examined the activities of rhizosphere microbiomes in plants with different susceptibilities to soil-borne pathogens, especially those that cause clubroot disease. In this study, we compared the rhizosphere bacterial community in response to infection of Plasmodiophora brassicae among the four different clubroot susceptibility cultivars of oilseed rape (Brassica napus). Our results revealed obvious differences in the responses of rhizosphere bacterial community to the P. brassicae infection between the four cultivars of oilseed rape. Several bacterial genera that are associated with the nitrogen cycle, including Limnobacter, Thiobacillus, Anaeromyxobacter, Nitrosomonas, Tumebacillus, and Halomonas, showed significantly different changes between susceptible and resistant cultivars in the presence of P. brassicae infection. Moreover, increased connectedness and robustness were exhibited in the rhizosphere bacterial community co-occurrence network in clubroot-susceptible cultivars that were infected with P. brassicae, while only slight changes were observed in clubroot-resistant cultivars. Metagenomic analysis of microbial metabolism also indicated differences in the rhizosphere bacterial community between susceptible and resistant cultivars that were infected with P. brassicae. Functional analysis of the nitrogen cycle showed that genes related to nitrification (nxrB) were upregulated in susceptible cultivars, while genes related to assimilatory nitrate reduction (nasA, narB, and nirA) were upregulated in resistant cultivars that were infected with P. brassicae. These findings indicate that the synthesis and assimilation process of NO3 [-] content were promoted in susceptible and resistant cultivars, respectively. Our study revealed differences in the characteristics of rhizosphere bacterial communities in response to P. brassicae infection between clubroot-susceptible and clubroot-resistant cultivars as well as the potential impact of these differences on the plant-P. brassicae interaction.}, }
@article {pmid39834614, year = {2025}, author = {Li, R and Kurilshikov, A and Yang, S and van Oortmerssen, JAE and van Hilten, A and Ahmadizar, F and Roshchupkin, G and Kraaij, R and Duijts, L and Fu, J and Ikram, MK and Jaddoe, VWV and Uitterlinden, AG and Rivadeneira, F and Kavousi, M and Zhernakova, A and Medina-Gomez, C}, title = {Association between gut microbiome profiles and host metabolic health across the life course: a population-based study.}, journal = {The Lancet regional health. Europe}, volume = {50}, number = {}, pages = {101195}, doi = {10.1016/j.lanepe.2024.101195}, pmid = {39834614}, issn = {2666-7762}, abstract = {BACKGROUND: The human gut microbiome changes considerably over time. Previous studies have shown that gut microbiome profiles correlate with multiple metabolic traits. As disease development is likely a lifelong process, evidence gathered at different life stages would help gain a better understanding of this correlation. Therefore, we aim to investigate how the association of the gut microbiome and metabolic traits change over the lifespan.<br><br>METHODS: We identified microbiome patterns (clusters) within two population-based cohorts at different life stages, i.e., pre-adolescents of the Generation R Study (mean age 9.8 years; n&#xa0;=&#xa0;1488) and older adults of the Rotterdam Study (RS, mean age 62.7 years; n&#xa0;=&#xa0;1265) using K-Means clustering, and surveyed for host metabolic phenotypes, lifestyles and other factors driving these patterns. Analyses were replicated in the Lifelines-DEEP Study (mean age 45.0 years; n&#xa0;=&#xa0;1117). The association between microbiome clusters and host metabolic health was evaluated as well as the link between microbiome clusters and incident atherosclerotic cardiovascular disease (ASCVD) in RS during follow-up (median 6.5 years).<br><br>FINDINGS: We identified two distinct microbiome clusters (U and H) within each study population presenting contrasting metabolic statuses. Cluster U was characterized by lower microbiome diversity, increased Streptococcus, Fusicatenibacter, and decreased Prevotella_9 and Christensenellaceae_R-7_group; wherein individuals showed higher fat percentage, triglycerides, use of medications, and lower socioeconomic status. Individuals in cluster U had increased odds (between 1.10 and 1.65) of being relatively metabolically unhealthy and presented a higher 5-year ASCVD risk (mean risk 0.059&#xa0;&#xb1;&#xa0;0.071 vs 0.047&#xa0;&#xb1;&#xa0;0.042, p&#xa0;<&#xa0;0.001).<br><br>INTERPRETATION: We provide evidence of a life-course relationship between gut microbiome profiles and metabolic health.<br><br>FUNDING: R.L is supported by European UnionHorizon 2020 research and innovation program under Marie Sk&#x142;odowska-Curie grant agreement No 860898 [FIDELIO].}, }
@article {pmid39834471, year = {2024}, author = {Song, Y and Liu, S and Zhang, L and Zhao, W and Qin, Y and Liu, M}, title = {The effect of gut microbiome-targeted therapies in nonalcoholic fatty liver disease: a systematic review and network meta-analysis.}, journal = {Frontiers in nutrition}, volume = {11}, number = {}, pages = {1470185}, doi = {10.3389/fnut.2024.1470185}, pmid = {39834471}, issn = {2296-861X}, abstract = {BACKGROUND: The incidence of NAFLD is increasing. Preclinical evidences indicate that modulation of the gut microbiome could be a promising target in nonalcoholic fatty liver disease.<br><br>METHOD: A systematic review and network meta-analysis was conducted to compare the effect of probiotics, synbiotics, prebiotics, fecal microbiota transplant, and antibiotics on the liver-enzyme, metabolic effects and liver-specific in patients with NAFLD. The randomized controlled trails (RCTs), limited to English language were searched from database such as Pubmed, Embase, Web of science and Cochrane Library from inception to November 2024. Review Manager 5.3 was used to to draw a Cochrane bias risk. Inconsistency test and publication-bias were assessed by Stata 14.0. Random effect model was used to assemble direct and indirect evidences. The effects of the intervention were presented as mean differences with 95% confidence interval.<br><br>RESULTS: A total of 1921 patients from 37 RCTs were eventually included in our study. 23 RCTs evaluated probiotics, 10 RCTs evaluated synbiotics, 4 RCTs evaluated prebiotics, 3 RCTs evaluated FMT and one RCT evaluated antibiotics. Probiotics and synbiotics were associated with a significantly reduction in alanine aminotransferase [ALT, (MD: -5.09; 95%CI: -9.79, -0.39), (MD: -7.38, 95CI%: -11.94, -2.82)] and liver stiffness measurement by elastograph [LSM, (MD: -0.37;95%CI: -0.49, -0.25), (MD: -1.00;95%CI: -1.59, -0.41)]. In addition to, synbiotics was superior to probiotics in reducing LSM. Synbiotics was associated with a significant reduction of Controlled Attenuation Parameter [CAP, (MD: -39.34; 95%CI: -74.73, -3.95)]. Both probiotics and synbiotics were associated with a significant reduction of aspartate transaminase [AST, (MD: -7.81; 95%CI: -15.49, -0.12), (MD: -13.32; 95%CI: -23, -3.64)]. Probiotics and Allogenic FMT was associated with a significant reduction of Homeostatic Model Assessment for Insulin Resistance [HOMA-IR, (MD: -0.7, 95%CI: -1.26, -0.15), (MD: -1.8, 95%CI: -3.53, - 0.07)]. Probiotics was associated with a significant reduction of body mass index [BMI, MD: -1.84, 95%CI: -3.35, -0.33].<br><br>CONCLUSION: The supplement of synbiotics and probiotics maybe a promising way to improve liver-enzyme, LSM, and steatosis in patients with NAFLD. More randomized controlled trials are needed to determine the efficacy of FMT and antibiotics on NAFLD. And the incidence of adverse events of MTTs should be further explored.<br><br>https://www.crd.york.ac.uk/prospero/, CRD42023450093.}, }
@article {pmid39834377, year = {2024}, author = {Fang, M and Lu, G and Zhang, S and Liang, W}, title = {Urbanized lands degrade surrounding grasslands by deteriorating the interactions between plants and soil microbiome.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1505916}, doi = {10.3389/fmicb.2024.1505916}, pmid = {39834377}, issn = {1664-302X}, abstract = {To mitigate overgrazing on grasslands, towns were constructed in some pastoral regions of China to relocate pastoralists. Nevertheless, whether and how the urbanized lands impact the surrounding grassland ecosystem remains unclear. We assessed the impacts of urbanized lands on the plant and soil interactions within the surrounding grasslands in order to ensure an eco-sustainable pastoralist relocation. The town with 1 km radius was selected as urbanization sample and a grassland with 1 km radius was selected as nature grassland sample. Plants and soil were investigated in nature grassland (NG), and areas 1 km (T-1 km), 2 km (T-2 km), and 3 km (T-3 km) from the center of the town. In T-1 km and T-2 km, compared to the NG, plant diversity, the abundance of dominant plant species, the abundance of soil wood saprotroph fungi, soil water content (SWC), and total organic carbon (TOC) decreased, while soil plant pathogen fungi, soil pH, and total phosphatase (TP) increased. Conversely, no such changes were observed in T-3 km. The results of Mantel test and Partial least squares path model suggest that the decrease in soil TOC and SWC, along with the increase in pH and TP in T-1 km and T-2 km, lead to a decline in wood saprotroph fungi and an increase in plant pathogen fungi, ultimately resulting in reductions in plant diversity and the abundance of dominant plant species. These results indicate that towns in pastoral areas can lead to surrounding grassland degradation by deteriorating the plant-soil interactions.}, }
@article {pmid39834370, year = {2024}, author = {Maurin, A and Durand, AA and Guertin, C and Constant, P}, title = {How many do we need? Meeting the challenges of studying the microbiome of a cryptic insect in an orchard.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1490681}, doi = {10.3389/fmicb.2024.1490681}, pmid = {39834370}, issn = {1664-302X}, abstract = {The minimal sampling effort required to report the microbiome composition of insect surveyed in natural environment is often based on empirical or logistical constraints. This question was addressed with the white pine cone beetle, Conophthorus coniperda (Schwarz), a devastating insect pest of seed orchards. It attacks and stop the growth of the cones within which it will spend its life, on the ground. To survive, the bark beetle probably interacts with microorganisms involved in alimentation, cold adaptation, and dormancy stage. Deciphering the drivers and benefits of these microorganisms in an orchard first requires methodological development addressing variability of the white pine cone beetle microbiome. The number of insect guts integrated in composite samples prior to DNA extraction and the number of surveyed trees are two features expected to induce variability in recovered microbiome profiles. These two levels of heterogeneity were examined in an orchard experimental area where 12 white pine trees were sampled and 15 cones from each tree were grouped together. For each tree, 2, 3 and 4 insects were selected, their intestinal tract dissected, and the microbiome sequenced. The number of insects caused no significant incidence on the coverage of bacterial and fungal communities' composition and diversity (p > 0.8). There was more variability among the different trees. A sampling effort including up to 33 trees in an area of 1.1 ha is expected to capture 98% of the microbial diversity in the experimental area. Spatial variability has important implications for future investigations of cryptic insect microbiome.}, }
@article {pmid39834362, year = {2024}, author = {Li, T and Gao, Z and Zhou, P and Huang, M and Wang, G and Xu, J and Deng, W and Wang, M}, title = {Structures and determinants of soil microbiomes along a steep elevation gradient in Southwest China.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1504134}, doi = {10.3389/fmicb.2024.1504134}, pmid = {39834362}, issn = {1664-302X}, abstract = {Soil microbial communities play a vital role in accelerating nutrient cycling and stabilizing ecosystem functions in forests. However, the diversity of soil microbiome and the mechanisms driving their distribution patterns along elevational gradients in montane areas remain largely unknown. In this study, we investigated the soil microbial diversity along an elevational gradient from 650 m to 3,800 m above sea level in southeast Tibet, China, through DNA metabarcode sequencing of both the bacterial and fungal communities. Our results showed that the dominant bacterial phyla across elevations were Proteobacteria, Acidobacteriota and Actinobacteriota, and the dominant fungal phyla were Ascomycota and Basidiomycota. The Simpson indices of both soil bacteria and fungi demonstrated a hollow trend along the elevational gradient, with an abrupt decrease in bacterial and fungal diversity at 2,600 m a.s.l. in coniferous and broad-leaved mixed forests (CBM). Soil bacterial chemoheterotrophy was the dominant lifestyle and was predicted to decrease with increasing elevation. In terms of fungal lifestyles, saprophytic and symbiotic fungi were the dominant functional communities but their relative abundance was negatively correlated with increasing elevation. Environmental factors including vegetation type (VEG), altitude (ALT), soil pH, total phosphorus (TP), nitrate nitrogen (NO3 [-]-N), and polyphenol oxidase (ppo) all exhibited significant influence on the bacterial community structure, whereas VEG, ALT, and the carbon to nitrogen ratio (C/N) were significantly associated with the fungal community structure. The VPA results indicated that edaphic factors explained 37% of the bacterial community variations, while C/N, ALT, and VEG explained 49% of the total fungal community variations. Our study contributes significantly to our understanding of forest ecosystems in mountainous regions with large elevation changes, highlighting the crucial role of soil environmental factors in shaping soil microbial communities and their variations in specific forest ecosystems.}, }
@article {pmid39833973, year = {2025}, author = {Rampanelli, E and Romp, N and Troise, AD and Ananthasabesan, J and Wu, H and Gül, IS and De Pascale, S and Scaloni, A and Bäckhed, F and Fogliano, V and Nieuwdorp, M and Bui, TPN}, title = {Gut bacterium Intestinimonas butyriciproducens improves host metabolic health: evidence from cohort and animal intervention studies.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {15}, pmid = {39833973}, issn = {2049-2618}, mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Mice ; Feces/microbiology ; Male ; Lysine/metabolism ; Female ; Fermentation ; Butyrates/metabolism ; Cohort Studies ; Clostridiales/metabolism/classification ; Fructose/metabolism ; Mice, Inbred C57BL ; Middle Aged ; Obesity/microbiology/metabolism ; Probiotics/administration &amp; dosage/metabolism ; Disease Models, Animal ; }, abstract = {BACKGROUND: The human gut microbiome strongly influences host metabolism by fermenting dietary components into metabolites that signal to the host. Our previous work has shown that Intestinimonas butyriciproducens is a prevalent commensal bacterium with the unique ability to convert dietary fructoselysine to butyrate, a well-known signaling molecule with proven health benefits. Dietary fructoselysine is an abundant Amadori product formed in foods during thermal treatment and is part of foods rich in dietary advanced glycation end products which have been associated with cardiometabolic disease. It is therefore of interest to investigate the causal role of this bacterium and fructoselysine metabolism in metabolic disorders.<br><br>RESULTS: We assessed associations of I. butyriciproducens with metabolic risk biomarkers at both strain and functional levels using a human cohort characterized by fecal metagenomic analysis. We observed that the level of the bacterial strain as well as fructoselysine fermentation genes were negatively associated with BMI, triglycerides, HbA1c, and fasting insulin levels. We also investigated the fructoselysine degradation capacity within the Intestinimonas genus using a culture-dependent approach and found that I. butyriciproducens is a key player in the butyrogenic fructoselysine metabolism in the gut. To investigate the function of I. butyriciproducens in host metabolism, we used the diet-induced obesity mouse model to mimic the human metabolic syndrome. Oral supplementation with I. butyriciproducens counteracted body weight gain, hyperglycemia, and adiposity. In addition, within the inguinal white adipose tissue, bacterial administration reduced inflammation and promoted pathways involved in browning and insulin signaling. The observed effects may be partly attributable to the formation of the short-chain fatty acids butyrate from dietary fructoselysine, as butyrate plasma and cecal levels were significantly increased by the bacterial strain, thereby contributing to the systemic effects of the bacterial treatment.<br><br>CONCLUSIONS: I.&#xa0;butyriciproducens ameliorates host metabolism in the context of obesity and may therefore be a good candidate for new microbiota-therapeutic approaches to prevent or treat metabolic diseases. Video Abstract.}, }
@article {pmid39833942, year = {2025}, author = {Luo, Q and Chu, S and Wu, Y and Jin, L and Liu, R and Xu, Y and Yu, Y and Jin, Y and Houndekon, LOEP and Hu, H and Zou, Y and Huang, H and Chen, H}, title = {Characteristics of tongue coating microbiota in diabetic and non-diabetic kidney patients receiving hemodialysis.}, journal = {BMC oral health}, volume = {25}, number = {1}, pages = {104}, pmid = {39833942}, issn = {1472-6831}, support = {2023ZL375//Zhejiang Province Traditional Chinese Medicine Science and technology Project/ ; 2024R406A061//Zhejiang University Student Science and Technology Innovation Activity Plan/ ; LY22H280011//Zhejiang Provincial Natural Science Foundation of China/ ; }, mesh = {Humans ; *Renal Dialysis ; *Tongue/microbiology ; Male ; Female ; Middle Aged ; *Microbiota ; *Renal Insufficiency, Chronic/microbiology/therapy/complications ; Aged ; Case-Control Studies ; Adult ; RNA, Ribosomal, 16S/analysis ; Diabetes Mellitus/microbiology ; }, abstract = {BACKGROUND: Tongue-coating microbiota, especially known as the tongue microbiome, holds significant value as both a prospective clinical diagnostic biomarker and therapeutic target, which plays a crucial role in the oral microecological health. However, there is limited understanding of the composition and function of tongue coating microbiota in chronic kidney disease patients undergoing hemodialysis.<br><br>METHODS: Thirty-one non-diabetic hemodialysis patients (nonDM_HD), 29 diabetic hemodialysis patients (DM_HD) and 33 healthy controls (HC) were enrolled. Swabs from tongue coating were collected. The 16S rDNA (V3-V4 region) was sequenced to scrutinize the tongue-coating bacterial microbiome difference.<br><br>RESULTS: Both nonDM_HD and DM_HD showed distinct bacterial communities of oral microbiota compared to HC. The abundance of Streptococcus, Lactobacillus, Ruminococcaceae G1, Ligilactobacillus and Abiotrophia showed a significant increase (p&#x2009;<&#x2009;0.05) in DM_HD and nonDM_HD compared to HC, while Haemophilus, Lachnoanaerobaculum, Peptostreptococcaceae G1, Peptostreptococcus showed a significant decrease (p&#x2009;<&#x2009;0.05) respectively. Veillonella, Lactobacillus, Limosilactobacillus etc. may serve as potential biomarkers for DM_HD. While Streptococcus, Ruminococcaceae G1, Actinobacillus, Abiotrophia can be considered alternative biomarkers for nonDM_HD. Moreover, the enriched Haemophilus, Actinomyces, Lachnoanaerobaculum were prominent features of the tongue coating microbiota in HC, which could be used as the potential therapeutic targets of chronic kidney disease. Network analysis revealed a less complex interaction relationship among the tongue coating bacterial microbiota of nonDM_HD and DM_HD. Furthermore, correlations were identified between the microbiome composition and clinical parameters of the individuals.<br><br>CONCLUSION: In conclusion, deciphering the tongue coating microbiota of kidney patients undergoing hemodialysis will helpful in assessing the role of oral microbiota in pathobiology and development of kidney disease, which is expected to become a potential biomarkers and adjuvant therapeutic target.}, }
@article {pmid39833936, year = {2025}, author = {Worku, N and Sanou, A and Hartke, J and Morris, M and Cissé, F and Ouédraogo, S and Tapsoba, M and Vallon, N and Akilu, TD and Worku, L and Guelbeogo, MW and Ingham, VA}, title = {Insecticide resistant Anopheles from Ethiopia but not Burkina Faso show a microbiota composition shift upon insecticide exposure.}, journal = {Parasites &amp; vectors}, volume = {18}, number = {1}, pages = {17}, pmid = {39833936}, issn = {1756-3305}, support = {222019/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; 101075634, ReMVeC/ERC_/European Research Council/International ; TTU03.705//Deutsches Zentrum f&#xfc;r Infektionsforschung/ ; }, mesh = {*Anopheles/drug effects/microbiology ; Animals ; Burkina Faso ; Ethiopia ; *Insecticide Resistance/genetics ; *Insecticides/pharmacology ; *Microbiota/drug effects ; *Mosquito Vectors/drug effects/microbiology ; Female ; Mosquito Control/methods ; Malaria/prevention &amp; control/transmission ; }, abstract = {BACKGROUND: Malaria remains a key contributor to mortality and morbidity across Africa, with the highest burden in children under 5. Insecticide-based vector control tools, which target the adult Anopheles mosquitoes, are the most efficacious tool in disease prevention. Due to the widespread use of these interventions, insecticide resistance to the most used classes of insecticides is now pervasive across Africa. Understanding the underlying mechanisms contributing to this phenotype is necessary to both track the spread of resistance and to design new tools to overcome it.<br><br>METHODS: Here, we compare the microbiota composition of insecticide-resistant populations of Anopheles gambiae, An. coluzzii and An. arabiensis from Burkina Faso, and in the latter case additionally from Ethiopia, to insecticide-susceptible populations.<br><br>RESULTS: We show that the microbiota composition between insecticide-resistant and -susceptible populations does not differ in Burkina Faso. This result is supported by data from laboratory colonies originating in Burkina Faso across two countries. In contrast, An. arabiensis from Ethiopia demonstrates clear differences in microbiota composition in those dying from and those surviving insecticide exposure. To further understand resistance in this An. arabiensis population, we performed RNAseq and saw differential expression of detoxification genes associated with insecticide resistance and changes in respiration, metabolism and synapse-related ion channels.<br><br>CONCLUSIONS: Our results indicate that, in addition to changes in the transcriptome, microbiota can contribute to insecticide resistance in certain settings.}, }
@article {pmid39833926, year = {2025}, author = {Li, Z and Zhao, C and Mao, Z and Zhang, F and Dong, L and Song, C and Chen, Y and Fu, X and Ao, Z and Xiong, Y and Hui, Q and Song, W and Penttinen, P and Zhang, S}, title = {Structure and metabolic function of spatiotemporal pit mud microbiome.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {10}, pmid = {39833926}, issn = {2524-6372}, support = {2022HX04//Youth Fund of Postdoctor/ ; 2021JDJQ0038//Youth Fund of Sichuan Province/ ; }, abstract = {BACKGROUND: Pit mud (PM) hosts diverse microbial communities, which serve as a medium to impart flavor and quality to Baijiu and exhibit long-term tolerance to ethanol and acids, resulting in a unique ecosystem. However, the ecology and metabolic functions of PM remain poorly understood, as many taxa in PM represent largely novel lineages. In this study, we used a combination of metagenomic analysis and chemical derivatization LC-MS analysis to provide a comprehensive overview of microbial community structure, metabolic function, phylogeny, horizontal gene transfer, and the relationship with carboxyl compounds in spatiotemporal PM samples.<br><br>RESULTS: Our findings revealed three distinct stages in the spatiotemporal changes of prokaryotic communities in PM: an initial phase dominated by Lactobacillus, a transitional phase, and a final state of equilibrium. Significant variations in &#x3b1;- and &#x3b2;-diversity were observed across different spatial and temporal PM samples. We identified 178 medium- and high-quality non-redundant metagenome-assembled genomes (MAGs), and constructed their phylogenetic tree, depicting their roles in the carbon, nitrogen, and sulfur cycles. The Wood-Ljungdahl pathway and reverse TCA cycle were identified as the main carbon fixation mechanisms, with both hydrogenotrophic and aceticlastic methanogens playing a major role in methane production, and methylotrophic pathway observed in older PM. Furthermore, we identified relationships between prokaryotes and 29 carboxyl metabolites, including medium- and long-chain fatty acids. Horizontal gene transfer (HGT) was widespread in PM, particularly among clostridia, Bacteroidota, Bacilli, and Euryarchaeota, and was shown to play critical roles in fermentation dynamics, carbon fixation, methane production, and nitrogen and sulfur metabolism.<br><br>CONCLUSION: Our study provides new insights into the evolution and function of spatiotemporal PM, as well as its interactions with carboxyl metabolites. Lactobacillus dominated in new PM, while methanogens and clostridia were predominant in older or deeper PM layers. The three distinct stages of prokaryotic community development in PM and HGT played critical roles in metabolic function of spatiotemporal PM. Furthermore, this study highlights the importance of &#x3b1;-diversity, &#x3b2;-diversity, methanogens, and Clostridium as useful indicators for assessing PM quality in the production of high-quality Baijiu.}, }
@article {pmid39833701, year = {2025}, author = {Burrows, PB and Godoy-Santos, F and Lawther, K and Richmond, A and Corcionivoschi, N and Huws, SA}, title = {Decoding the chicken gastrointestinal microbiome.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {35}, pmid = {39833701}, issn = {1471-2180}, mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; DNA, Bacterial/genetics ; Gastrointestinal Tract/microbiology ; Biodiversity ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {Metataxonomic studies have underpinned a vast understanding of microbial communities residing within livestock gastrointestinal tracts, albeit studies have often not been combined to provide a global census. Consequently, in this study we characterised the overall and common 'core' chicken microbiota associated with the gastrointestinal tract (GIT), whilst assessing the effects of GIT site, bird breed, age and geographical location on the GIT resident microbes using metataxonomic data compiled from studies completed across the world. Specifically, bacterial 16S ribosomal DNA sequences from GIT samples associated with various breeds, differing in age, GIT sites (caecum, faeces, ileum and jejunum) and geographical location were obtained from the Sequence Read Archive and analysed using the MGnify pipeline. Metataxonomic profiles produced across the 602 datasets illustrated the presence of 3 phyla, 25 families and 30 genera, of which core genera (defined by presence in over 90% of datasets) belonged to Lactobacillus, Faecalibacterium, Butyricicoccus, Eisenbergiella, Subdoligranulum, Oscillibacter, Clostridium &amp; Blautia. PERMANOVA analysis also showed that GIT site, bird breed, age and geographical location all had a significant effect on GIT microbial diversity, regardless of dietary factors, which were not considered in this study. On a genus level, Faecalibacterium was most abundant in the caeca, Lactobacillus was most abundant in the faeces, ileum and jejunum, with the data showing that the caeca and faeces were most diverse. AIL F8 progeny, Ross 308 and Cobb 500 breeds GIT bacteria were dominated by Lactobacillus, and Eisenbergiella, Megamonas and Bacteroides were most abundant amongst Sasso-T451A and Tibetan chicken breeds. Microbial communities within each GIT site develop with age, from a Lactobacillus and Streptococcus dominated community during the earlier stages of growth, towards a Faecalibacterium, Eisenbergiella, Bacteroides, Megamonas, and Lactobacillus dominated community during the later stages of life. Geographical locations, and thus environmental effectors, also impacted upon gastrointestinal tract microbiota, with Canadian and European datasets being dominated by Lactobacillus, whilst UK and Chinese datasets were dominated by Eisenbergiella and Bacteroides respectively. This study aids in defining what 'normal' is within poultry gastrointestinal tract microbiota globally, which is imperative to enhancing the microbiome for productive and environmental improvements.}, }
@article {pmid39833681, year = {2025}, author = {Guodong, W and Yinhang, W and Xinyue, W and Hong, S and Jian, C and Zhanbo, Q and Shuwen, H}, title = {Fecal occult blood affects intestinal microbial community structure in colorectal cancer.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {34}, pmid = {39833681}, issn = {1471-2180}, support = {2022C03026//the Key research and development project of Science and Technology Department of Zhejiang Province/ ; No.2021YZ22//Public Welfare Technology Application Research Program of Huzhou/ ; No.2024ZL1018//Zhejiang Province Traditional Chinese Medicine Science and Technology Project/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms/microbiology ; *Occult Blood ; Male ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; Middle Aged ; *Feces/microbiology ; *RNA, Ribosomal, 16S/genetics ; Aged ; Adult ; Support Vector Machine ; Early Detection of Cancer/methods ; }, abstract = {BACKGROUND: Gut microbes have been used to predict CRC risk. Fecal occult blood test (FOBT) has been recommended for population screening of CRC.<br><br>OBJECTIVE: To analyze the effects of fecal occult blood test (FOBT) on gut microbes.<br><br>METHODS: Fecal samples from 107 healthy individuals (FOBT-negative) and 111 CRC patients (39 FOBT-negative and 72 FOBT-positive) were included for 16&#xa0;S ribosomal RNA sequencing. Based on the results of different FOBT, the community structure and diversity of intestinal bacteria in healthy individuals and CRC patients were analyzed. Characteristic gut bacteria were screened, and various machine learning algorithms were applied to construct CRC risk prediction models.<br><br>RESULTS: The gut microbiota of healthy people and CRC patients with different fecal occult blood were mapped. There was no statistical difference in diversity between CRC patients with negative FOBT and positive FOBT. Bacteroides, Blautia and Escherichia-Shigella were more correlated to healthy individuals, while Streptococcus showed higher correlation with CRC patients with negative FOBT. The accuracy of CRC risk prediction model based on the support vector machines (SVM) algorithm was the highest (89.71%). Subsequently, FOBT was included as a characteristic element in the model construction, and the prediction accuracy of the model was all increased. Similarly, the CRC risk prediction model based on SVM algorithm had the highest accuracy (92%).<br><br>CONCLUSION: FOB affects the community composition of gut microbes. When predicting CRC risk based on gut microbiome, considering the influence of FOBT is expected to improve the accuracy of CRC risk prediction.}, }
@article {pmid39833573, year = {2025}, author = {Ling, X and Zhang, XJ and Bui, CHT and Chan, HN and Yau, JWK and Tang, FY and Kam, KW and Ip, P and Young, AL and Hon, KL and Tham, CC and Pang, CP and Chen, LJ and Yam, JC}, title = {Multi-cohort analysis identifying core ocular surface microbiome and bacterial alterations in eye diseases.}, journal = {Eye (London, England)}, volume = {}, number = {}, pages = {}, pmid = {39833573}, issn = {1476-5454}, support = {07180826//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/ ; 21220251//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/ ; 5160836//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/ ; 5160836//Food and Health Bureau of the Government of the Hong Kong Special Administrative Region | Health and Medical Research Fund (HMRF)/ ; 178662514//Chinese University of Hong Kong (CUHK)/ ; 2015.1.056//Chinese University of Hong Kong (CUHK)/ ; 4054193//Chinese University of Hong Kong (CUHK)/ ; 4054121//Chinese University of Hong Kong (CUHK)/ ; }, abstract = {PURPOSE: Inconsistency exists among reported studies on the composition of human ocular surface microbiome (OSM). The roles of OSM in ocular diseases remain uncertain. In this study, we aimed to determine the composition of OSM and to evaluate its potential roles and functions from multiple cohorts.<br><br>METHODS: Raw 16&#x2009;s sequencing data were obtainable from publicly available repositories, sourced from 17 published studies. Employing a standardized method, we processed the data and conducted a cross-cohort analysis. Through bioinformatics pipelines QIIME2 and PICRUSt2, we processed a total of 1875 ocular surface samples. Core microbiome analyses, genera comparisons, and MetaCyc pathway analyses were performed within each cohort independently. The results were then combined to identify shared patterns across different datasets.<br><br>RESULTS: The core OSM comprised seven genera: Corynebacterium, Staphylococcus, Acinetobacter, Streptococcus, Pseudomonas, Cutibacterium and Bacillus. Corynebacterium and Staphylococcus are the most abundant genera on ocular surface. Most ocular diseases showed OSM alterations and eight genera demonstrated a non-specific, shared response among two or more ocular diseases. Moreover, changes in various metabolic pathways were predicted following OSM alteration, indicating potential roles of OSM in biological processes.<br><br>CONCLUSION: We refined the core OSM candidates combining multiple cohorts. The common pattern shared by different cohorts is worth further investigation. Changes in metabolic pathways based on bioinformatic analysis indicated a role of OSM on ocular diseases. Our results help extend the knowledge and encourage further investigations on the associations between OSM and ocular diseases.}, }
@article {pmid39833403, year = {2025}, author = {Liu, G and Liu, K and Ji, L and Li, Y}, title = {Intratumoral microbiota, fatty acid metabolism, and tumor microenvironment constitute an unresolved trinity in colon adenocarcinoma.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2568}, pmid = {39833403}, issn = {2045-2322}, mesh = {Humans ; *Tumor Microenvironment ; *Colonic Neoplasms/microbiology/metabolism/pathology ; *Adenocarcinoma/microbiology/metabolism/pathology ; *Fatty Acids/metabolism ; Microbiota ; Prognosis ; Male ; Female ; Transcriptome ; }, abstract = {The intratumoral microbiota, fatty acid metabolism (FAM), and tumor microenvironment (TME) all provide insights into the management of colon adenocarcinoma (COAD). But the biological link among the three remains unclear. Here, we analyzed intratumoral microbiome samples and matched host transcriptome samples from 420 patients with COAD in The Cancer Genome Atlas (TCGA). All patients were divided into two subtypes (FAM_high and FAM_low) based on the Gene set variation analysis (GSVA) score of FAM pathway. Furthermore, we found significant difference in the intratumoral microbiota signatures between the two subtypes. In-depth analysis suggested that specific microbes in tumors may indirectly modify the TME, particularly stromal cell populations, by modulating the FAM process. More importantly, the crosstalk between the three can have a significant impact on prognosis, response to immunotherapy, and drug sensitivity of patients. Pathological image profiling showed that changes in the TME originating from intratumoral microbiota disturbance could be reflected in pathological image features. In summary, our study provides novel insights into the biological links among the intratumoral microbiota, FAM, and the TME in COAD, and offer guidance for the therapeutic opportunities that target intratumoral microbes.}, }
@article {pmid39833377, year = {2025}, author = {Fischer, S and Neurath, MF}, title = {[Update on the pathophysiology, prediction and prevention of inflammatory bowel diseases].}, journal = {Innere Medizin (Heidelberg, Germany)}, volume = {}, number = {}, pages = {}, pmid = {39833377}, issn = {2731-7099}, abstract = {BACKGROUND: The pathophysiology of inflammatory bowel diseases is not fully understood. In a staged model by the European Crohn's and Colitis Organization (ECCO) regarding disease development, it is assumed that there is a population at risk for manifestation of disease following subtle changes over time.<br><br>OBJECTIVE: This work aims to summarize the current state of knowledge regarding the pathophysiology, prediction and prevention of chronic inflammatory bowel diseases.<br><br>MATERIALS AND METHODS: Selective literature research via PubMed.<br><br>RESULTS: Several genetic, biochemical, and microbiome scores have the potential to identify individuals at increased risk of developing inflammatory bowel disease, possibly up to a&#xa0;decade before onset.<br><br>DISCUSSION: The growing knowledge regarding the pathogenesis of inflammatory bowel diseases makes prediction before disease onset a&#xa0;possible future diagnostic goal. Hypothetically, early changes before the disease manifests could be reversible and may be amenable to prevention programs.}, }
@article {pmid39833341, year = {2025}, author = {Zhang, C and Yu, Y and Yue, L and Chen, Y and Chen, Y and Liu, Y and Guo, C and Su, Q and Xiang, Z}, title = {Gut microbiota profiles of sympatric snub-nosed monkeys and macaques in Qinghai-Tibetan Plateau show influence of phylogeny over diet.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {95}, pmid = {39833341}, issn = {2399-3642}, support = {32171487//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31870509//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32400413//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Phylogeny ; *Diet ; Tibet ; RNA, Ribosomal, 16S/genetics ; Colobinae/microbiology ; Macaca mulatta ; Macaca/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {The unique environment of the Qinghai-Tibetan Plateau provides a great opportunity to study how primate intestinal microorganisms adapt to ecosystems. The 16S rRNA gene amplicon and metagenome analysis were conducted to investigate the correlation between gut microbiota in primates and other sympatric animal species living between 3600 and 4500 m asl. Results showed that within the same geographical environment, Macaca mulatta and Rhinopithecus bieti exhibited a gut microbiome composition similar to that of Tibetan people, influenced by genetic evolution of host, while significantly differing from other distantly related animals. The gut microbiota of plateau species has developed similar strategies to facilitate their hosts' adaptation to specific environments, including broadening its dietary niche and enhancing energy absorption. These findings will enhance our comprehension of the significance of primate gut microbiota in adapting to specific habitats.}, }
@article {pmid39833301, year = {2025}, author = {Yang, F and Henniger, MT and Izzo, AS and Melchior, EA and Clemmons, BA and Oliver, MA and Gaffney, JR and Martino, C and Ault-Seay, TB and Striluk, ML and Embree, JJ and Cordero-Llarena, JF and Mulon, PY and Anderson, DE and Embree, MM and Myer, PR}, title = {Performance improvements and increased ruminal microbial interactions in Angus heifers via supplementation with native rumen bacteria during high-grain challenge.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {2289}, pmid = {39833301}, issn = {2045-2322}, mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; Female ; *Animal Feed ; *Edible Grain ; Dietary Supplements ; Bacteria/classification/metabolism ; Gastrointestinal Microbiome ; Microbial Interactions ; Diet/veterinary ; }, abstract = {Feedlot cattle may be subjected to digestive disorders, including ruminal acidosis, due to high concentration of grain in their diet. Therefore, novel feeding strategies are required to maximize animal performance and mitigate economic losses in the operation. This study employed a two-period crossover design to assess the effect of direct ruminal administration of native rumen microorganisms (NRM) inoculation on cattle that underwent a high-grain challenge. The NRM inoculation consisted of six microorganisms (1.70 M CFU /day/animal) isolated from the rumen of healthy feedlot cattle: Succinivibrio dextrinosolvens ASCUSBF53, Prevotella albensis ASCUSBF41, Chordicoccus furentiruminis ASCUSBF65, Bacteroides xylanisolvens ASCUSBF52, Clostridium beijerinckii ASCUSBF26, and Syntrophococcus sp. ASCUSBF60. The trial consisted of 16 Angus heifers receiving NRM (n = 8) or a CON (CON = Carrier Buffer; n = 8) inoculation daily for 14-days as pre-challenge while on a high-grain diet and continued daily for a 21-day treatment period. The combined 35 days of microbial supplementation resulted in an improved average daily gain (ADG) of 29% (P = 0.037) and a tendency toward a 19% decrease in the feed efficiency metric, gain to feed ratio (G: F) (P = 0.055). Additionally, administration of NRM to animals on a high-grain diet, improved ruminal microbiome stability (P < 0.001), potentially encouraging the conversion of rumen lactate to propionate over time via the succinate pathway and alleviating metabolic stress.}, }
@article {pmid39832809, year = {2025}, author = {Miebach, J and Green, D and Strittmatter, M and Mallinger, C and Garrec, LL and Zhang, QY and Foucault, P and Kunz, C and Gachon, CMM}, title = {Importance, structure, cultivability, and resilience of the bacterial microbiota during infection of laboratory-grown Haematococcus spp. by the blastocladialean pathogen Paraphysoderma sedebokerense: evidence for a domesticated microbiota and its potential for biocontrol.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf011}, pmid = {39832809}, issn = {1574-6941}, abstract = {Industrial production of the unicellular green alga Haematococcus lacustris is compromised by outbreaks of the fungal pathogen Paraphysoderma sedebokerense (Blastocladiomycota). Here, using axenic algal and fungal cultures and antibiotic treatments, we show that the bacterial microbiota of H. lacustris is necessary for the infection by P. sedebokerense and that its modulation affects the outcome of the interaction. We combined metagenomics and laboratory cultivation to investigate the diversity of the bacterial microbiota associated to three Haematococcus species and monitor its change upon P. sedebokerense infection. We unveil three types of distinct, reduced bacterial communities, which likely correspond to keystone taxa in the natural Haematococcus spp. microbiota. Remarkably, the taxonomic composition and functionality of these communities remained stable during infection. The major bacterial taxa identified in this study have been cultivated by us or others, paving the way to developing synthetic communities to experimentally explore interactions within this tripartite system. We discuss our results in the light of emerging evidence concerning the structuring and domestication of plant and animal microbiota, thus providing novel experimental tools and a new conceptual framework necessary to enable the engineering of Haematococcus spp. microbiota toward the biocontrol of P. sedebokerense.}, }
@article {pmid39832807, year = {2025}, author = {Bekris, F and Papadopoulou, E and Vasileiadis, S and Karapetsas, N and Theocharis, S and Alexandridis, TK and Koundouras, S and Karpouzas, DG}, title = {Vintage and terroir are the strongest determinants of grapevine carposphere microbiome in the viticultural zone of Drama, Greece.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaf008}, pmid = {39832807}, issn = {1574-6941}, abstract = {The role of microbial terroir for enhancing the geographical origin of wines is well appreciated. Still, we lack a good understanding of the assembly mechanisms driving carposphere grapevine microbiota. We investigated the role of cultivar, vintage, terroir units (TUs) and vineyard geographic location on the composition of the carpospheric microbiota of three important cultivars in the viticultural zone of Drama, Greece using amplicon sequencing. Our strategy to define TUs based on georeferencing analysis allowed us to disentangle the effects of TU and vineyards geographic location, considered as a lumped factor in most studies to date. We hypothesized that: (i) these factors contribute differently on the assembly of the carposphere microbiome and that (ii) fungal and bacterial communities follow different assembly mechanisms. Vintage and TU were the stronger determinants of the carposphere fungal and bacterial communities, although the latter showed weaker response. The stronger effect of TU over vineyard geography and cultivar reinforces the role of microbial terroir in viticulture. We identified fungi (Cladosporium, Aureobasidium, Alternaria) and bacteria (Pseudomonas, Methylobacterium, Sphingomonadaceae) as main members of the core microbiome. These microorganisms were associated with specific cultivars and TUs, a feature that could be pursued towards a new microbiome-modulated paradigm of viticulture.}, }
@article {pmid39832641, year = {2025}, author = {Beaver, LM and Jamieson, PE and Wong, CP and Hosseinikia, M and Stevens, JF and Ho, E}, title = {Promotion of healthy aging through the nexus of gut microbiota and dietary phytochemicals.}, journal = {Advances in nutrition (Bethesda, Md.)}, volume = {}, number = {}, pages = {100376}, doi = {10.1016/j.advnut.2025.100376}, pmid = {39832641}, issn = {2156-5376}, abstract = {Aging is associated with the decline of tissue and cellular functions, which can promote the development of age-related diseases like cancer, cardiovascular disease, neurodegeneration, and disorders of the musculoskeletal and immune systems. Healthspan is the length of time an individual is in good health and free from chronic diseases and disabilities associated with aging. Two modifiable factors that can influence healthspan, promote healthy aging, and prevent the development of age-related diseases, are the diet and microbiota in the gastrointestinal tract (gut microbiota). This review will discuss how dietary phytochemicals and gut microbiota can work in concert to promote a healthy gut and healthy aging. First an overview is provided of how the gut microbiota influences healthy aging through its impact on gut barrier integrity, immune function, mitochondria function and oxidative stress. Next, the mechanisms by which phytochemicals effect gut health, inflammation, and nurture a diverse and healthy microbial composition are discussed. Lastly, the gut microbiota can directly influence health by producing bioactive metabolites from phytochemicals in food like urolithin A, equol, hesperetin and sulforaphane. These and other phytochemical derived microbial metabolites that may promote healthspan are discussed. Importantly, an individual's capacity to produce health promoting microbial metabolites from cruciferous vegetables, berries, nuts, citrus and soy products will be dependent on the specific bacteria present in the individual's gut.}, }
@article {pmid39832517, year = {2025}, author = {Peno, C and Jagne, YJ and Clerc, M and Balcazar Lopez, C and Armitage, EP and Sallah, H and Drammeh, S and Senghore, E and Goderski, G and van Tol, S and Meijer, A and Ruiz-Rodriguez, A and de Steenhuijsen Piters, W and de Koff, E and Jarju, S and Lindsey, BB and Camara, J and Bah, S and Mohammed, NI and Kampmann, B and Clarke, E and Dockrell, DH and de Silva, TI and Bogaert, D}, title = {Interactions between live attenuated influenza vaccine and nasopharyngeal microbiota among children aged 24-59 months in The Gambia: a phase 4, open-label, randomised controlled trial.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {100971}, doi = {10.1016/j.lanmic.2024.100971}, pmid = {39832517}, issn = {2666-5247}, abstract = {BACKGROUND: Live attenuated influenza vaccines (LAIVs) alter nasopharyngeal microbiota in adults. It is poorly understood why LAIV immunogenicity varies across populations, but it could be linked to the microbiome. We aimed to investigate the interactions between intranasal immunisation with LAIV and nasopharyngeal microbiota composition in children from The Gambia.<br><br>METHODS: We conducted a phase 4, open-label, randomised controlled trial in Sukuta, The Gambia. Children aged 24-59&#xa0;months with no underlying illness or history of respiratory illness for at least 14&#xa0;days before recruitment were eligible. Participants were randomly assigned (2:1) by use of a computer-generated sequence in permuted blocks of 15, stratified by sex, to receive trivalent LAIV either on day 0 (intervention group) or after active follow-up at day 21 (control group). The investigator team was initially masked to block size and randomisation sequence; however, group allocation was later revealed to the team. Microbiome profiles were characterised from nasopharyngeal samples collected from all participants on days 0, 7, and 21&#xa0;by use of 16S rRNA sequencing. The primary outcomes were the effect of LAIV on nasopharyngeal microbiome profiles on day 7&#xa0;and day 21, and the association between the nasopharyngeal microbiome at baseline and LAIV-induced mucosal IgA responses at day&#xa0;21, assessed with permutational ANOVA tests. Asymptomatic respiratory viral co-infection at baseline and year of recruitment (2017 or 2018) were included as covariates. This trial is registered with ClinicalTrials.gov (NCT02972957) and is closed.<br><br>FINDINGS: Between Feb 8&#xa0;and April 12, 2017, and Jan 15&#xa0;and March 28, 2018, 343&#xa0;children were screened for eligibility, of whom 220 (64%) children were randomly assigned to the intervention group and 110 (32%) to the control group. 213 (97%) children in the intervention group and 108 (98%) in the control group completed the study and were included in the final analysis. Although we did not observe an independent effect of LAIV on microbial community composition at days 7&#xa0;or 21, we found that LAIV had an effect dependent on the year of recruitment. LAIV affected microbial community composition in 2018 (R[2] 1&#xb7;97% [95% CI 0&#xb7;85-5&#xb7;94]; p=0&#xb7;037), but not in 2017 (1&#xb7;23% [0&#xb7;49-4&#xb7;46]; p=0&#xb7;091). We also found that viral co-infection at baseline had an effect on microbial composition at day 7, regardless of recruitment year (R[2]&#xa0;1&#xb7;01% [95% CI 0&#xb7;28-3&#xb7;01]; p=0&#xb7;026). Nasopharyngeal microbial community composition at baseline had no effect on mucosal IgA responses to LAIV administration (R[2] 0&#xb7;51% [95% CI 0&#xb7;23-2&#xb7;49]; p=0&#xb7;46).<br><br>INTERPRETATION: Our findings suggest that the effect of LAIVs on nasopharyngeal microbiota composition in children is modest and temporary; therefore, LAIVs could be used as an intervention to curb influenza in children from low-income and middle-income countries, without causing long-lasting perturbations in nasopharyngeal microbiota. However, nasopharyngeal microbiota at the time of vaccination might not explain the variability observed between individuals in LAIV-induced IgA responses.<br><br>FUNDING: The Wellcome Trust, UK National Institute for Health Research, and Chief Scientist Office Scotland.}, }
@article {pmid39832471, year = {2025}, author = {Wu, T and Liu, K and Chen, S and Ye, Z and Xia, J and He, J and Xing, P and Yang, J and Qian, Y and Chen, M}, title = {Pulmonary microbiota disruption by respiratory exposure to carbon quantum dots induces neuronal damages in mice.}, journal = {Journal of hazardous materials}, volume = {487}, number = {}, pages = {137255}, doi = {10.1016/j.jhazmat.2025.137255}, pmid = {39832471}, issn = {1873-3336}, abstract = {Given the fact that carbon quantum dots (CQDs) have been commercially produced in quantities, it is inevitable to make their ways into environment and interact closely with the public. Even though CQDs in the environment have been reported to damage the central nervous system, the underlying mechanisms of neurotoxic effects of CQDs following respiratory exposure is still not clear. Intranasal instilled CQDs, mimicking respiratory exposure, induces neurobehavioral impairments associated with neuronal cell death of ferroptosis and disulfidptosis that is regulated by metabolic reprogramming of glutathione and cysteine pathways in the cortex and hippocampus where CQDs were hardly accumulated. Therefore, further exploration found that dysbiosis in the lung microbiome was found specifically manipulated by CQDs, which correlated with systemic and neuroinflammatory responses, implicating a lung-brain axis other than gut-brain axis as a critical pathway through which microbiota dysbiosis may impact neurological health after respiratory exposure to CQDs. This study pioneers the exploration of the neurological consequences of inhaled CQDs in the environment through the regulation of microbiome-lung-brain axis, which is key in understanding the mechanistic link between CQDs exposure and neurotoxicity. The findings could develop potential strategies for mitigating the neurological effects of CQDs even other types of nanoparticles.}, }
@article {pmid39832301, year = {2025}, author = {Kebbe, M and Leung, K and Perrett, B and Reimer, RA and Adamo, K and Redman, LM}, title = {Effects of Infant Formula Supplemented With Prebiotics on the Gut Microbiome, Gut Environment, Growth Parameters, and Safety and Tolerance: A Systematic Review and Meta-Analysis.}, journal = {Nutrition reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/nutrit/nuae184}, pmid = {39832301}, issn = {1753-4887}, abstract = {CONTEXT: Prebiotics are often added to infant formulas to mimic the benefits of oligosaccharides found in human milk.<br><br>OBJECTIVE: This systematic review and meta-analysis evaluated the effects of prebiotic-supplemented cow's milk-based formula on the gut microbiota, gut environment, growth parameters, and safety and tolerance in infants &#x2264;6&#x2009;months old, compared with a standard formula or human milk comparator.<br><br>DATA SOURCES: Searches were performed in the PubMed, Embase, Cochrane Central Register of Controlled Trials, and ProQuest Dissertations &amp; Theses databases. Articles were included that reported on randomized controlled trials, were published from inception until April 2024, and met prespecified inclusion and exclusion criteria.<br><br>DATA EXTRACTION: Outcomes included gut microbiota (eg, diversity; taxa at phylum, family, genus and species levels), gut environment (eg, pH, secretory immunoglobulin A, fecal calprotectin, fecal metabolites), growth parameters (eg, z scores), and safety and tolerance. Fixed or random effects models were used and mean differences (MDs) with 95% CIs were calculated to assess pooled effects. Risk of bias was assessed using the Cochrane Collaboration Tool (RoB 2).<br><br>DATA ANALYSIS: A total of 30 articles met inclusion criteria, with 5290 infants included. Whereas effects on Lactobacillus were inconsistent, prebiotic formula supplementation increased Bifidobacterium counts (k&#x2009;=&#x2009;7 [MD: 0.49; 95% CI, 0.27-0.71]; I2&#x2009;=&#x2009;13%; P&#x2009;<&#x2009;.00001) and decreased fecal pH (k&#x2009;=&#x2009;7 [MD: -0.39; 95% CI, -0.57 to -0.20]; I2&#x2009;=&#x2009;0%; P&#x2009;<&#x2009;.0001) compared with standard formula. Prebiotic formula supplementation increased total bacteria compared with human milk (MD: 0.41 [95% CI, 0.17-0.65]; I2&#x2009;=&#x2009;8%; P&#x2009;=&#x2009;.0006). In terms of growth parameters, weight-for-age z scores favored the prebiotic formula group compared with the human milk group (k&#x2009;=&#x2009;2 [MD: 0.23; 95% CI, 0.04-0.42]; I2&#x2009;=&#x2009;7%; P&#x2009;=&#x2009;.02).<br><br>CONCLUSIONS: Prebiotic supplementation in infant formula can positively alter the gut microbiota, particularly Bifidobacterium, without negative impacts on growth. Standardized, high-quality research is needed to confirm the study findings and inform guidelines for prebiotic use in infant nutrition.<br><br>PROSPERO registration no. CRD42021253589.}, }
@article {pmid39832278, year = {2025}, author = {Wang, Y and Wengler, J and Fang, Y and Zhou, J and Ruan, H and Zhang, Z and Han, L}, title = {Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources.}, journal = {Genomics, proteomics &amp; bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1093/gpbjnl/qzaf001}, pmid = {39832278}, issn = {2210-3244}, abstract = {Tumor-specific antigens, also known as neoantigens, have potential utility in anti-cancer immunotherapy, including immune checkpoint blockade (ICB), neoantigen-specific T cell receptor-engineered T (TCR-T), chimeric antigen receptor T (CAR-T), and therapeutic cancer vaccines (TCVs). After recognizing presented neoantigens, the immune system becomes activated and triggers the death of tumor cells. Neoantigens may be derived from multiple origins, including somatic mutations (single nucleotide variants, insertion/deletions, and gene fusions), circular RNAs, alternative splicing, RNA editing, and polymorphic microbiome. An increasing amount of bioinformatics tools and algorithms are being developed to predict tumor neoantigens derived from different sources, which may require inputs from different multi-omics data. In addition, calculating the peptide-major histocompatibility complex (MHC) affinity can aid in selecting putative neoantigens, as high binding affinities facilitate antigen presentation. Based on these approaches and previous experiments, many resources were developed to reveal the landscape of tumor neoantigens across multiple cancer types. Herein, we summarized these tools, algorithms, and resources to provide an overview of computational analysis for neoantigen discovery and prioritization, as well as the future development of potential clinical utilities in this field.}, }
@article {pmid39832034, year = {2025}, author = {Arulvasan, W and Greenwood, J and Ball, ML and Chou, H and Coplowe, S and Birch, O and Gordon, P and Ratiu, A and Lam, E and Tardelli, M and Szkatulska, M and Swann, S and Levett, S and Mead, E and van Schooten, FJ and Smolinska, A and Boyle, B and Allsworth, M}, title = {Optimized breath analysis: customized analytical methods and enhanced workflow for broader detection of VOCs.}, journal = {Metabolomics : Official journal of the Metabolomic Society}, volume = {21}, number = {1}, pages = {17}, pmid = {39832034}, issn = {1573-3890}, mesh = {*Breath Tests/methods ; *Volatile Organic Compounds/analysis ; Humans ; *Gas Chromatography-Mass Spectrometry/methods ; Workflow ; Biomarkers/analysis ; Male ; ROC Curve ; Adult ; }, abstract = {INTRODUCTION: Breath Volatile organic compounds (VOCs) are promising biomarkers for clinical purposes due to their unique properties. Translation of VOC biomarkers into the clinic depends on identification and validation: a challenge requiring collaboration, well-established protocols, and cross-comparison of data. Previously, we developed a breath collection and analysis method, resulting in 148 breath-borne VOCs identified.<br><br>OBJECTIVES: To develop a complementary analytical method for the detection and identification of additional VOCs from breath. To develop and implement upgrades to the methodology for identifying features determined to be "on-breath" by comparing breath samples against paired background samples applying three metrics: standard deviation, paired t-test, and receiver-operating-characteristic (ROC) curve.<br><br>METHODS: A thermal desorption (TD)-gas chromatography (GC)-mass spectrometry (MS)-based analytical method utilizing a PEG phase GC column was developed for the detection of biologically relevant VOCs. The multi-step VOC identification methodology was upgraded through several developments: candidate VOC grouping schema, ion abundance correlation based spectral library creation approach, hybrid alkane-FAMES retention indexing, relative retention time matching, along with additional quality checks. In combination, these updates enable highly accurate identification of breath-borne VOCs, both on spectral and retention axes.<br><br>RESULTS: A total of 621 features were statistically determined as on-breath by at least one metric (standard deviation, paired t-test, or ROC). A total of 38 on-breath VOCs were able to be confidently identified from comparison to chemical standards.<br><br>CONCLUSION: The total confirmed on-breath VOCs is now 186. We present an&#xa0;updated methodology for high-confidence VOC identification, and a new set of VOCs commonly found on-breath.}, }
@article {pmid39831966, year = {2025}, author = {Butkovich, LV and Vining, OB and O'Malley, MA}, title = {New approaches to secondary metabolite discovery from anaerobic gut microbes.}, journal = {Applied microbiology and biotechnology}, volume = {109}, number = {1}, pages = {12}, pmid = {39831966}, issn = {1432-0614}, support = {W911NF-19-2-0026//Institute for Collaborative Biotechnologies/ ; W911NF-19-1-0010//Institute for Collaborative Biotechnologies/ ; DE-AC02-05CH11231//Biological and Environmental Research/ ; DE-SC0020420//Biological and Environmental Research/ ; DE-SC0022142//Biological and Environmental Research/ ; DBI - 2400327//Directorate for Biological Sciences/ ; }, mesh = {*Gastrointestinal Microbiome ; *Secondary Metabolism ; Animals ; Anaerobiosis ; Fungi/metabolism/genetics ; Bacteria/metabolism/genetics/classification ; Archaea/metabolism/genetics ; Multigene Family ; }, abstract = {The animal gut microbiome is a complex system of diverse, predominantly anaerobic microbiota with secondary metabolite potential. These metabolites likely play roles in shaping microbial community membership and influencing animal host health. As such, novel secondary metabolites from gut microbes hold significant biotechnological and therapeutic interest. Despite their potential, gut microbes are largely untapped for secondary metabolites, with gut fungi and obligate anaerobes being particularly under-explored. To advance understanding of these metabolites, culture-based and (meta)genome-based approaches are essential. Culture-based approaches enable isolation, cultivation, and direct study of gut microbes, and (meta)genome-based approaches utilize in silico tools to mine biosynthetic gene clusters (BGCs) from microbes that have not yet been successfully cultured. In this mini-review, we highlight recent innovations in this area, including anaerobic biofoundries like ExFAB, the NSF BioFoundry for Extreme &amp; Exceptional Fungi, Archaea, and Bacteria. These facilities enable high-throughput workflows to study oxygen-sensitive microbes and biosynthetic machinery. Such recent advances promise to improve our understanding of the gut microbiome and its secondary metabolism. KEY POINTS: • Gut microbial secondary metabolites have therapeutic and biotechnological potential • Culture- and (meta)genome-based workflows drive gut anaerobe metabolite discovery • Anaerobic biofoundries enable high-throughput workflows for metabolite discovery.}, }
@article {pmid39831637, year = {2025}, author = {Wang, C and Tang, Y and Yang, T and Wang, Y and Niu, Z and Zhang, K and Lin, N and Li, Q}, title = {Causal Relationship Between Intestinal Microbiota, Inflammatory Cytokines, Peripheral Immune Cells, Plasma Metabolome and Parkinson's Disease: A Mediation Mendelian Randomization Study.}, journal = {The European journal of neuroscience}, volume = {61}, number = {2}, pages = {e16665}, doi = {10.1111/ejn.16665}, pmid = {39831637}, issn = {1460-9568}, support = {2022e07020069//Anhui Provincial Key Research and Development Plan/ ; }, mesh = {*Parkinson Disease/blood/immunology/microbiology ; Humans ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome ; *Cytokines/blood ; *Metabolome ; *Genome-Wide Association Study ; }, abstract = {Parkinson's disease (PD) is a neurodegenerative disease involving multiple factors. We explored the connection between intestinal microbiome levels and PD by examining inflammatory cytokines, peripheral immune cell counts and plasma metabolomics as potential factors. By obtaining the Genome-Wide Association Study (GWAS) data needed for this study from GWAS Catalog, including summary data for 473 intestinal microbiota traits (N = 5959), 91 inflammatory cytokine traits (N = 14,824), 118 peripheral immune cell count traits (N = 3757), 1400 plasma metabolite traits (N = 8299) and PD traits (N = 482,730). We used two-step Mendelian randomization (MR) mediated analysis to investigate possible pathways from intestinal microbiota to PD mediated by inflammatory cytokines, peripheral immune cells and plasma metabolites. MR has revealed the causal effects of 19 intestinal microbiota, 1 inflammatory cytokine and 12 plasma metabolites on PD, whereas there is no significant causal relationship between immune cell count characteristics and the occurrence of PD. Mediation analysis showed that the associations between the genus Demequina and PD were mediated by tryptophan with mediated proportions of 17.51% (p = 0.0393). Our study demonstrates that genus Demequina may promote the occurrence of PD by reducing the levels of tryptophan.}, }
@article {pmid39831120, year = {2024}, author = {Duan, D and Wang, M and Han, J and Li, M and Wang, Z and Zhou, S and Xin, W and Li, X}, title = {Advances in multi-omics integrated analysis methods based on the gut microbiome and their applications.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1509117}, doi = {10.3389/fmicb.2024.1509117}, pmid = {39831120}, issn = {1664-302X}, abstract = {The gut microbiota actually shares the host's physical space and affects the host's physiological functions and health indicators through a complex network of interactions with the host. However, its role as a determinant of host health and disease is often underestimated. With the emergence of new technologies including next-generation sequencing (NGS) and advanced techniques such as microbial community sequencing, people have begun to explore the interaction mechanisms between microorganisms and hosts at various omics levels such as genomics, transcriptomics, metabolomics, and proteomics. With the enrichment of multi-omics integrated analysis methods based on the microbiome, an increasing number of complex statistical analysis methods have also been proposed. In this review, we summarized the multi-omics research analysis methods currently used to study the interaction between the microbiome and the host. We analyzed the advantages and limitations of various methods and briefly introduced their application progress.}, }
@article {pmid39831114, year = {2024}, author = {Kourkoutas, Y and Kopsahelis, N and Koutelidakis, A and Tzakos, AG}, title = {Editorial: Innovations in microbiome applications for health-promoting and sustainable food systems.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1538798}, doi = {10.3389/fmicb.2024.1538798}, pmid = {39831114}, issn = {1664-302X}, }
@article {pmid39830903, year = {2025}, author = {Cambray, GA and Kalinski, JJ}, title = {Microbial Characterization of a Zambian Honey Vinegar.}, journal = {Food science &amp; nutrition}, volume = {13}, number = {1}, pages = {e4549}, doi = {10.1002/fsn3.4549}, pmid = {39830903}, issn = {2048-7177}, abstract = {Forest Fruits Organic Honey Vinegar (FFOHV) is a spontaneously fermented (yeast) and acetified (Acetic Acid Bacteria-AAB) Miombo Woodland honey vinegar developed in Zambia. Live vinegars containing live microbial cultures are marketed for their probiotic health benefits. The correlation between a well-developed gut microbiome and human health is well studied and fermented products such as live vinegar containing AAB contribute to a healthy gut microbiome. This study details a metagenomic analysis of stable, bottled FFOHV (Zambia) alongside two commercially available live vinegar products: Bragg Organic Apple Cider Vinegar (BOACV) and Nature's Source Apple Cider Vinegar (NSACV). FFOHV contained representatives of five bacterial and nine fungal genera, compared to BOACV with two bacterial and five fungal, and NSACV containing no bacterial and six fungal genera. FFOHV and BOACV showed a dominance of Komagataeibacter bacterial species. The dominant yeast was Vanrija humicola present in all three vinegar samples. FFOHV contained greater diversity of genera, with the notable species Monascus purpureus-a microbe that produces several health-enhancing compounds. The analysis showed that FFOHV is a microbially diverse product containing several potentially health-enhancing microbes. Graphical Abstract Text: This study presents a metagenomic analysis of Forest Fruits Organic Honey Vinegar (FFOHV) from Zambia, compared with two commercial live cider vinegars: Bragg Organic Apple Cider Vinegar (BOACV) and Nature's Source Apple Cider Vinegar (NSACV). FFOHV exhibited a richer microbial diversity, containing five bacterial and nine fungal genera, including the health-promoting species Monascus purpureus. Both FFOHV and BOACV were dominated by Komagataeibacter species, with Vanrija humicola as the prevalent yeast across all samples. This confirmed FFOHV's unique potential probiotic benefits.}, }
@article {pmid39830577, year = {2024}, author = {Almabruk, BA and Bajafar, AA and Mohamed, AN and Al-Zahrani, SA and Albishi, NM and Aljarwan, R and Aljaser, RA and Alghamdi, LI and Almutairi, TS and Alsolami, AS and Alghamdi, JK}, title = {Efficacy of Probiotics in the Management of Irritable Bowel Syndrome: A Systematic Review and Meta-Analysis.}, journal = {Cureus}, volume = {16}, number = {12}, pages = {e75954}, doi = {10.7759/cureus.75954}, pmid = {39830577}, issn = {2168-8184}, abstract = {Irritable bowel syndrome (IBS) significantly impacts quality of life. Probiotics offer relief by modulating gut microbiota, but variability in outcomes necessitates a systematic evaluation of their efficacy. This study aims to evaluate the efficacy of probiotics in improving symptoms of IBS through a systematic review and meta-analysis. A comprehensive search of PubMed and Google Scholar identified studies published between 2014 and 2018. Inclusion criteria focused on randomized controlled trials evaluating probiotics in adult IBS patients diagnosed using standardized criteria. Statistical analysis utilized random effects models to account for heterogeneity, with subgroup analysis performed for IBS subtypes. This review included 23 studies involving 3,288 participants. Probiotics significantly reduced abdominal pain (mean difference = -1.66, 95% CI = -2.39 to -0.93, p < 0.0001) and bloating (mean difference = -2.13, 95% CI = -3.96 to -0.30, p = 0.0224). Improvement in stool habits was significant (mean difference = -1.52, 95% CI = -2.15 to -0.88, p < 0.0001), particularly in diarrhea-predominant IBS. Quality of life improved significantly, with a mean increase of 8.77 points (95% CI = 0.91 to 16.64, p = 0.028). Adverse events were mild and infrequent. However, heterogeneity was high (I[2] > 90%), reflecting variability in study protocols. Probiotics are effective in reducing IBS symptoms and improving quality of life, mainly in diarrhea-predominant IBS. More research should be conducted that focuses on standardized, long-term trials to refine treatment strategies.}, }
@article {pmid39830544, year = {2024}, author = {Keil, E}, title = {A Warning Against Antibiotic Treatment for Gastrointestinal Non-Typhoidal Salmonella Infections in Immunocompetent Adults: A Case Report and Review of the Literature.}, journal = {Cureus}, volume = {16}, number = {12}, pages = {e75953}, doi = {10.7759/cureus.75953}, pmid = {39830544}, issn = {2168-8184}, abstract = {Salmonella enterica is a common pathogen that causes foodborne illness worldwide. There is limited evidence describing the treatment of gastrointestinal non-typhoidal Salmonella (NTS). Clinicians are inclined to treat these infections with antibiotics, but the use of antibiotics may paradoxically worsen gastrointestinal symptoms and prolong bacterial stool shedding. This is a case of gastrointestinal NTS in 30-year-old immunocompetent female patient. She experienced prolonged diarrhea for six weeks following food poisoning with Salmonella enterica Serovar Enteritidis and received antibiotics as a treatment for her symptoms. The antibiotics worsened her symptoms, and she continued to have positive stool tests. At week 11 following the initial infection, she was advised by her infectious diseases physician to avoid further antibiotic use and take probiotics including Saccharomyces boulardii and kefir probiotics. These improved her gastrointestinal symptoms; however, she continued to have bacterial stool shedding for a total of 25 weeks. Antibiotics should be avoided for the treatment of gastrointestinal NTS in immunocompetent adults due to their lack of benefit and their potential for worsening and/or prolonging symptoms. Treatment should instead focus on recovering the gut microbiome.}, }
@article {pmid39830521, year = {2024}, author = {Nielsen, SM and Johnsen, KK and Hansen, LBS and Rikvold, PD and Møllebjerg, A and Palmén, LG and Durhuus, T and Schlafer, S and Meyer, RL}, title = {Large-scale screening identifies enzyme combinations that remove in situ grown oral biofilm.}, journal = {Biofilm}, volume = {8}, number = {}, pages = {100229}, doi = {10.1016/j.bioflm.2024.100229}, pmid = {39830521}, issn = {2590-2075}, abstract = {Bacteria in the oral cavity are responsible for the development of dental diseases such as caries and periodontitis, but it is becoming increasingly clear that the oral microbiome also benefits human health. Many oral care products on the market are antimicrobial, killing a large part of the oral microbiome but without removing the disease-causing biofilm. Instead, non-biocidal matrix-degrading enzymes may be used to selectively remove biofilm without harming the overall microbiome. The challenge of using enzymes to degrade biofilms is to match the narrow specificity of enzymes with the large structural diversity of extracellular polymeric substances that hold the biofilm together. In this study, we therefore perform a large-scale screening of single and multi-enzyme formulations to identify combinations of enzymes that most effectively remove dental biofilm. We tested >400 different treatment modalities using 44 different enzymes in combinations with up to six enzymes in each formulation, on in vitro biofilms inoculated with human saliva. Mutanase was the only enzyme capable of removing biofilm on its own. Multi-enzyme formulations removed up to 69 % of the biofilm volume, and the most effective formulations all contained mutanase. We shortlisted 10 enzyme formulations to investigate their efficacy against biofilms formed on glass slabs on dental splints worn by 9 different test subjects. Three of the ten formulations removed more than 50 % of the biofilm volume. If optimal enzyme concentration and exposure time can be reached in vivo, these enzyme combinations have potential to be used in novel non-biocidal oral care products for dental biofilm control.}, }
@article {pmid39830328, year = {2024}, author = {Mao, X and Paerhati, G and Wu, Y and Cheng, LF}, title = {Modulation of gut microbiota, up-regulation of ZO-1, and promotion of metabolism as therapeutic mechanisms of indole-3-carbinol against obesity in mice.}, journal = {Frontiers in pharmacology}, volume = {15}, number = {}, pages = {1499142}, doi = {10.3389/fphar.2024.1499142}, pmid = {39830328}, issn = {1663-9812}, abstract = {BACKGROUND: Indole-3-carbinol (I3C) is a compound derived from Cruciferous vegetables. We aim to ascertain whether I3C mediates the relations between mouse gut microbiota, intestinal barrier function, and metabolism to treat obesity in mice.<br><br>METHODS: The experimental analyses focused on the changes in lipid distribution, inflammatory cytokines, glucose tolerance, gut microbiota composition, and serum metabolomics of 60 C57BL/6N mice.<br><br>RESULTS: The experimental results demonstrated that I3C reduced body weight, hepatic steatosis, and systemic inflammation and improved insulin resistance in mice on a high-fat diet (HFD). Furthermore, I3C remarkably enhanced the enrichment of probiotics Akkermansia and Ligilactobacillus as well as SCFA-producing bacteria (Eubacterium, Lactococcus, and Coprococcus), while reducing the abundance of Eisenbergiella and Rikenellaceae_RC9_gut_group. Also, I3C notably up-regulated the levels of Claudin4, Occludin, and ZO-1 proteins and modulated the metabolism of argininosuccinic acid and galactose.<br><br>CONCLUSION: The aforementioned findings suggest that I3C exerts a significant anti-obesity effect in mice by regulating abnormal gut microbiome, enhancing intestinal barrier function, and improving metabolic disorders.}, }
@article {pmid39830252, year = {2025}, author = {Hafeez, S and Khalid, A and Ahmed, S and Umrani, F and Qureshi, AK and Ahmed, K and Shaheen, F and Hotwani, A and Kabir, F and Moore, SR and Ali, SA and Iqbal, J and Iqbal, NT}, title = {The Role of Fermented Pickles in Shaping Gut Microbiota and Immune Response in Women: A Community-Based Trial in Pakistan.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.10.25320071}, pmid = {39830252}, abstract = {A gut microbiome-targeted diet can potentially mitigate chronic diseases like malnutrition. In a prospective 12-week intervention trial, we evaluated the effects of six different plant-based fermented pickles (∼50g/day) on clinical, inflammatory, and gut-microbiome parameters in women (n=230) in a rural setting with a high prevalence of undernutrition. Blood was collected at two, whereas stool was collected at three timepoints. Among fecal biomarkers, myeloperoxidase (MPO), Lipocalin-2 (LCN2), and 16S rRNA sequencing were measured at baseline, 8 [th,] and 12 [th] weeks. Overall compliance rate was >70%. WBC and neutrophils significantly decreased among radish (p=0.002, p=0.01) and carrot (p=0.005, p=0.006) groups compared to controls. In lemon-chili groups, platelets significantly decreased (p<0.001) while MCV increased (p=0.02). In onion and lemon-chili groups, the alpha (р=0.001 and p=0.0005, respectively) and beta diversities (p=9e-04 and p=0.0223, respectively) were significantly increased. Post-intervention linear discriminant analysis (LDA) identified 25 bacterial taxa markers at 8 [th] and 12 [th] week, that included Eggerthellaceae and Oscillospiraceae, Erysipelatoclostridiaceae and Subdoligranumlum, predominantly in lemon-chili group. Correlation analysis revealed six taxa negatively associated with inflammatory markers such as CRP, LCN2, and platelets. Our study provides preliminary information about consumption of culturally acceptable fermented pickles exerting beneficial changes in hematological and gut microbiome profiles of women, post-intervention.}, }
@article {pmid39830242, year = {2025}, author = {Carter, MM and Zeng, X and Ward, CP and Landry, M and Perelman, D and Hennings, T and Meng, X and Weakley, AM and Cabrera, AV and Robinson, JL and Nguyen, T and Higginbottom, S and Maecker, HT and Sonnenburg, ED and Fischbach, MA and Gardner, CD and Sonnenburg, JL}, title = {A gut pathobiont regulates circulating glycine and host metabolism in a twin study comparing vegan and omnivorous diets.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.08.25320192}, pmid = {39830242}, abstract = {Metabolic diseases such as type 2 diabetes and obesity pose a significant global health burden. Plant-based diets, including vegan diets, are linked to favorable metabolic outcomes, yet the underlying mechanisms remain unclear. In a randomized trial involving 21 pairs of identical twins, we investigated the effects of vegan and omnivorous diets on the host metabolome, immune system, and gut microbiome. Vegan diets induced significant shifts in serum and stool metabolomes, cytokine profiles, and gut microbial composition. Notably, vegan diet subjects exhibited elevated serum glycine levels despite lower dietary glycine intake, linked to reduced abundance of the gut pathobiont Bilophila wadsworthia . Functional studies demonstrated that B. wadsworthia metabolizes glycine via the glycine reductase pathway and modulates host glycine availability. Removing B. wadsworthia from gnotobiotic mice elevated glycine levels and improved metabolic markers. These findings reveal a previously underappreciated mechanism by which the gut microbiota regulates host metabolic status through diet.}, }
@article {pmid39830094, year = {2025}, author = {Lin, J and Dai, Z and Lei, M and Qi, Q and Zhou, W and Ma, LQ and Dahlgren, RA and Xu, J}, title = {Arsenic modifies the microbial community assembly of soil-root habitats in Pteris vittata.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycae172}, doi = {10.1093/ismeco/ycae172}, pmid = {39830094}, issn = {2730-6151}, abstract = {Pteris vittata, renowned for its ability to hyperaccumulate arsenic, presents a promising solution to the escalating issue of global soil arsenic contamination. This fern cultivates a unique underground microbial community to enhance its environmental adaptability. However, our understanding of the assembly process and the long-term ecological impacts of this community remains limited, hindering the development of effective soil remediation strategies. This study addresses this gap by investigating soil-root habitats from three geographically diverse fields comprising a gradient of arsenic contamination, complemented by a time-scale greenhouse experiment. Field investigations reveal that arsenic stress influences community assembly dynamics in the rhizosphere by enhancing processes of homogeneous selection. Greenhouse experiments further reveal that arsenic exposure alters the assembly trajectory of rhizosphere communities by promoting key microbial modules. Specifically, arsenic exposure increases the enrichment of a core taxon (i.e. Rhizobiaceae) in the rhizosphere, both in field and greenhouse settings, boosting their abundance from undetectable levels to 0.02% in the soil after phytoremediation. Notably, arsenic exposure also promotes a pathogenic group (i.e. Spirochaetaceae) in the rhizosphere, increasing their abundance from undetectable levels to 0.1% in the greenhouse. This raise concerns that warrant further investigation in future phytoremediation studies. Overall, this study elucidates the assembly dynamics of the soil microbiome following the introduction of a remediation plant and emphasizes the often-overlooked impacts on soil microbial community following phytoremediation. By probing the ecological impacts of remediation plants, this work advances a more nuanced understanding of the complex ecological implications inherent in phytoremediation processes.}, }
@article {pmid39830093, year = {2025}, author = {Yu, J and Yang, J and Qu, L and Huang, X and Liu, Y and Jiang, P and Wang, C}, title = {Soil microbial carbon use efficiency differs between mycorrhizal trees: insights from substrate stoichiometry and microbial networks.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycae173}, doi = {10.1093/ismeco/ycae173}, pmid = {39830093}, issn = {2730-6151}, abstract = {The role of mycorrhizal associations in controlling forest soil carbon storage remains under debate. This uncertainty is potentially due to an incomplete understanding of their influence on the free-living soil microbiome and its functions. In this study, rhizosphere and non-rhizosphere soils were collected from eight arbuscular mycorrhizal (AM) and seven ectomycorrhizal (ECM) tree species in a temperate forest. We employed high-throughput sequencing and [18]O-H2O labeling to analyze the soil microbial community and carbon use efficiency (CUE), respectively. We find microbial respiration rates are higher in rhizosphere than that in non-rhizosphere soils for ECM trees, whereas microbial growth rates show no significant differences. Consequently, microbial CUE is lower in rhizosphere compared to non-rhizosphere soils for ECM trees. In addition, we find that non-rhizosphere soils from ECM trees exhibited higher CUE compared to those from AM trees. Furthermore, we observe that bacterial-fungal co-occurrence networks in ECM soils exhibit greater complexity relative to AM ones. Using random forest and structural equation modeling analyses, we find that microbial stoichiometric carbon/nitrogen imbalance and network complexity are key predictors of soil microbial CUE for AM and ECM trees, respectively. Our findings shed new light on the pivotal role of mycorrhizal associations in shaping free-living microbial communities and their metabolic characteristics in the studied soils. These insights are critical for predicting soil carbon sequestration in response to shifts in ECM and AM species within temperate forest under climate change.}, }
@article {pmid39829898, year = {2025}, author = {Ni, M and Fan, Y and Liu, Y and Li, Y and Qiao, W and Davey, LE and Zhang, XS and Ksiezarek, M and Mead, E and Touracheau, A and Jiang, W and Blaser, MJ and Valdivia, RH and Fang, G}, title = {Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.11.632565}, pmid = {39829898}, issn = {2692-8205}, abstract = {The human gut microbiome within the gastrointestinal tract continuously adapts to variations in diet, medications, and host physiology. A central strategy for genetic adaptation is epigenetic phase variation (ePV) mediated by bacterial DNA methylation, which can regulate gene expression, enhance clonal heterogeneity, and enable a single bacterial strain to exhibit variable phenotypic states. Genome-wide and site-specific ePV have been well characterized in human pathogens' antigenic variation and virulence factor production. However, the role of ePV in facilitating adaptation within the human microbiome remains poorly understood. Here, we comprehensively cataloged genome-wide and site-specific ePV in human infant and adult gut microbiomes. First, using long-read metagenomic sequencing, we detected genome-wide ePV mediated by complex structural variations of DNA methyltransferases, highlighting the ones associated with antibiotics or fecal microbiota transplantation. Second, we analyzed an extensive collection of public short-read metagenomic sequencing datasets, uncovering a greater prevalence of genome-wide ePV in the human gut microbiome. Third, we quantitatively detected site-specific ePVs using single-molecule methylation analysis to identify dynamic variations associated with antibiotic treatment or probiotic engraftment. Finally, we performed an in-depth assessment of an Akkermansia muciniphila isolate from an infant, highlighting that ePV can regulate gene expression and enhance the bacterial adaptive capacity by employing a bet-hedging strategy to increase tolerance to differing antibiotics. Our findings indicate that epigenetic modifications are a common and broad strategy used by bacteria in the human gut to adapt to their environment.}, }
@article {pmid39829854, year = {2025}, author = {Ghazi, AR and Thompson, KN and Bhosle, A and Mei, Z and Yan, Y and Wang, F and Wang, K and Franzosa, EA and Huttenhower, C}, title = {Quantifying Metagenomic Strain Associations from Microbiomes with Anpan.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.06.631550}, pmid = {39829854}, issn = {2692-8205}, abstract = {Genetic and genomic variation among microbial strains can dramatically influence their phenotypes and environmental impact, including on human health. However, inferential methods for quantifying these differences have been lacking. Strain-level metagenomic profiling data has several features that make traditional statistical methods challenging to use, including high dimensionality, extreme variation among samples, and complex phylogenetic relatedness. We present Anpan, a set of quantitative methods addressing three key challenges in microbiome strain epidemiology. First, adaptive filtering designed to interrogate microbial strain gene carriage is combined with linear models to identify strain-specific genetic elements associated with host health outcomes and other phenotypes. Second, phylogenetic generalized linear mixed models are used to characterize the association of sub-species lineages with such phenotypes. Finally, random effects models are used to identify pathways more likely to be retained or lost by outcome-associated strains. We validated our methods by simulation, showing that we achieve more accurate effect size estimation and a lower false positive rate compared to alternative methodologies. We then applied our methods to a dataset of 1,262 colorectal cancer patients, identifying functionally adaptive genes and strong phylogenetic effects associated with CRC status, sometimes complementing and sometimes extending known species-level microbiome CRC biomarkers. Anpan's methods have been implemented as a publicly available R library to support microbial community strain and genetic epidemiology in a variety of contexts, environments, and phenotypes.}, }
@article {pmid39829850, year = {2025}, author = {Kajihara, KT and Yuan, M and Amend, AS and Cetraro, N and Darcy, JL and Fraiola, KMS and Frank, K and McFall-Ngai, M and Medeiros, MCI and Nakayama, KK and Nelson, CE and Rollins, RL and Sparagon, WJ and Swift, SOI and Téfit, MA and Yew, JY and Yogi, D and Hynson, NA}, title = {Diversity, connectivity and negative interactions define robust microbiome networks across land, stream, and sea.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.07.631746}, pmid = {39829850}, issn = {2692-8205}, abstract = {In this era of rapid global change, factors influencing the stability of ecosystems and their functions have come into the spotlight. For decades the relationship between stability and complexity has been investigated in modeled and empirical systems, yet results remain largely context dependent. To overcome this we leverage a multiscale inventory of fungi and bacteria ranging from single sites along an environmental gradient, to habitats inclusive of land, sea and stream, to an entire watershed. We use networks to assess the relationship between microbiome complexity and robustness and identify fundamental principles of stability. We demonstrate that while some facets of complexity are positively associated with robustness, others are not. Beyond positive biodiversity x robustness relationships we find that the number of "gatekeeper" species or those that are highly connected and central within their networks, and the proportion of predicted negative interactions are universal indicators of robust microbiomes. With the potential promise of microbiome engineering to address global challenges ranging from human to ecosystem health we identify properties of microbiomes for future experimental studies that may enhance their stability. We emphasize that features beyond biodiversity and additional characteristics beyond stability such as adaptability should be considered in these efforts.}, }
@article {pmid39829831, year = {2025}, author = {Austin, GI and Korem, T}, title = {Compositional transformations can reasonably introduce phenotype-associated values into sparse features.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.02.19.581060}, pmid = {39829831}, issn = {2692-8205}, abstract = {It was recently argued [1] that an analysis of tumor-associated microbiome data [2] is invalid because features that were originally very sparse (genera with mostly zero read counts) became associated with the phenotype following batch correction [1] . Here, we examine whether such an observation should necessarily indicate issues with processing or machine learning pipelines. We show counterexamples using the centered log ratio (CLR) transformation, which is often used for analysis of compositional microbiome data [3] . The CLR transformation has similarities to Voom-SNM [4,5] , the batch-correction method brought into question [1,2] , yet is a sample-wise operation that cannot, in itself, "leak" information or invalidate downstream analyses. We show that because the CLR transformation divides each value by the geometric mean of its sample, common imputation strategies for missing or zero values result in transformed features that are associated with the geometric mean. Through analyses of both synthetic and vaginal microbiome datasets we demonstrate that when the geometric mean is associated with a phenotype, sparse and CLR-transformed features will also become associated with it. We re-analyze features highlighted by Gihawi et al. [1] and demonstrate that the phenomenon of sparse features becoming phenotype-associated can also be observed after a CLR transformation, which serves as a counterexample to the claim that such an observation necessarily means information leakage. While we do not intend to address other concerns regarding tumor microbiome analyses [1,6] , validate Poore et al.'s [2] results, or evaluate batch-correction pipelines, we conclude that because phenotype-associated features that were initially sparse can be created by a sample-wise transformation that cannot artifactually inflate machine learning performance, their detection is not independently sufficient to demonstrate information leakage in machine learning pipelines. Microbiome data is multivariate, and as such, a value of zero carries a different meaning for each sample. Many transformations, including CLR and other batch-correction methods, are likewise multivariate, and, as these issues demonstrate, each individual feature should be interpreted with caution.}, }
@article {pmid39829744, year = {2025}, author = {Tang, G and Carr, AV and Perez, C and Ramos Sarmiento, K and Levy, L and Lampe, JW and Diener, C and Gibbons, SM}, title = {Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.01.07.631807}, pmid = {39829744}, issn = {2692-8205}, abstract = {Absolute bacterial biomass estimation in the human gut is crucial for understanding microbiome dynamics and host-microbe interactions. Current methods for quantifying bacterial biomass in stool, such as flow cytometry, qPCR, or spike-ins (i.e., adding cells or DNA from an organism not normally found in a sample), can be labor-intensive, costly, and confounded by factors like water content, DNA extraction efficiency, PCR inhibitors, and other technical challenges that add bias and noise. We propose a simple, cost-effective approach that circumvents some of these technical challenges: directly estimating bacterial biomass from metagenomes using bacterial-to-host (B:H) read ratios. We compare B:H ratios to the standard methods outlined above, demonstrating that B:H ratios are useful proxies for bacterial biomass in stool and possibly in other host-associated substrates. We show how B:H ratios can be used to track antibiotic treatment response and recovery in both mice and humans, which showed 403-fold and 45-fold reductions in bacterial biomass during antibiotic treatment, respectively. Our results indicate that host and bacterial metagenomic DNA fractions in human stool fluctuate longitudinally around a stable mean in healthy individuals, and the average host read fraction varies across healthy individuals by < 8-9 fold. B:H ratios offer a convenient alternative to other absolute biomass quantification methods, without the need for additional measurements, experimental design considerations, or machine learning algorithms, enabling retrospective absolute biomass estimates from existing stool metagenomic data.}, }
@article {pmid39829685, year = {2025}, author = {Melenovský, V and Hošková, E and Velebová, K and Veleba, J and Borlaug, BA and Benes, J and Kuda, O and Čajka, T and Segeťová, M and Thieme, L and Kopecký, J and Kopecký, J and Pelikánová, T and Haluzík, M and Hill, M and Kahleová, H}, title = {Metformin Improves Glycemic Control and Postprandial Metabolism and Enhances Postprandial Glucagon-Like Peptide 1 Secretion in Patients With Type 2 Diabetes and Heart Failure: A Randomized, Double-Blind, Placebo-Controlled Trial.}, journal = {Clinical diabetes : a publication of the American Diabetes Association}, volume = {43}, number = {1}, pages = {23-32}, doi = {10.2337/cd24-0003}, pmid = {39829685}, issn = {0891-8929}, abstract = {This randomized trial tested the effect of metformin on glycemic control and cardiac function in patients with heart failure (HF) and type 2 diabetes while evaluating intestinal effects on selected gut microbiome products reflected by trimethylamine-N-oxide (TMAO) and gut-derived incretins. Metformin treatment improved glycemic control and postprandial metabolism and enhanced postprandial glucagon-like peptide 1 (GLP-1) secretion but did not influence cardiac function or the TMAO levels. Metabolic effects of metformin in HF may be mediated by an improvement in intestinal endocrine function and enhanced secretion of the gut-derived incretin GLP-1.}, }
@article {pmid39829414, year = {2025}, author = {Gomes, SIF and Gundersen, P and Bezemer, TM and Barsotti, D and D'Imperio, L and Georgopoulos, K and Justesen, MJ and Rheault, K and Rosas, YM and Schmidt, IK and Tedersoo, L and Vesterdal, L and Yu, M and Anslan, S and Aslani, F and Byriel, DB and Christiansen, J and Hansen, SH and Kasal, N and Kosawang, C and Larsen, H and Larsen, KS and Lees, J and van Dijke, ACP and Kepfer-Rojas, S}, title = {Soil Microbiome Inoculation for Resilient and Multifunctional New Forests in Post-Agricultural Landscapes.}, journal = {Global change biology}, volume = {31}, number = {1}, pages = {e70031}, doi = {10.1111/gcb.70031}, pmid = {39829414}, issn = {1365-2486}, support = {NNF20OC0059948//Novo Nordisk Fonden/ ; }, mesh = {*Soil Microbiology ; *Forests ; *Microbiota ; *Agriculture ; *Biodiversity ; Conservation of Natural Resources ; Trees/microbiology ; }, abstract = {Afforestation is increasingly recognized as a critical strategy to restore ecosystems and enhance biodiversity on post-agricultural landscapes. However, agricultural legacies, such as altered soil structure, nutrient imbalances, and depleted microbial diversity, can slow down forest establishment or cause ecosystems to deviate from expected successional trajectories. In this opinion paper, we explore the potential of soil inoculations as a tool to overcome these challenges by introducing beneficial microbial communities that can accelerate ecosystem recovery and forest development. Restoring soil biodiversity is a crucial aspect of this process that drives broader ecosystem functionality and resilience. We highlight the need to carefully consider the type and timing of inoculations and to ensure compatibility between the inoculum and recipient site characteristics to optimize the establishment of introduced species. While tree productivity is often a central focus of afforestation efforts, the restoration of soil biodiversity, which will also contribute to increased ecosystem-level functions, should also be a priority for long-term forest resilience. Agricultural legacies add complexities to the restoration process, creating unique challenges that need to be addressed in restoration planning. Thus, successful inoculation strategies require a thorough understanding of both donor and recipient site characteristics, also in relation to potential mismatches related to soil physiochemical properties to avoid unintended consequen