@article {pmid41265504,
year = {2025},
author = {McKee, KS and Bassis, CM and Golob, J and Palazzolo, B and Comstock, SS and Rosas-Salazar, C and Stanford, JB and Ananda, S and O'Connor, T and Gern, JE and Paneth, N and Dunlop, AL and , },
title = {Vaginal microbiome structure in pregnancy and host factors predict preterm birth: Results from the ECHO Cohort.},
journal = {Annals of epidemiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.annepidem.2025.11.003},
pmid = {41265504},
issn = {1873-2585},
abstract = {PURPOSE: The vaginal microbiome is dynamic, typically shifting during pregnancy toward enrichment of Lactobacillus. However, proliferation of Lactobacillus may be absent among women with preterm births (PTBs). We sought to identify robust vaginal microbiota signatures along with host factors that predicted PTB across diverse U.S. cohorts.

METHODS: We meta-analyzed 16S rRNA gene amplicon sequence data from the Environmental influences on Child Health Outcomes Cohort. We classified community state types (CSTs) and employed penalized logistic regression models to assess the association between vaginal CST and PTB. We generated supervised random forest models and validated them using a train-and-test approach to identify the most predictive vaginal taxa and host factors.

RESULTS: Of 683 births, 12% were preterm. Overall, 26% had a non- L. iners Lactobacillus-dominant CST (I, II, V), 43% had a L. iners-dominant CST (III), and 30% had a diverse, non-Lactobacillus-dominant (IV-B, IV-C) CST. Vaginal CST was strongly associated with PTB (adjusted odds ratio [aOR], 3.86, 95% confidence interval [CI], 1.57-11.3 for diverse, non-Lactobacillus-dominant communities and aOR, 3.03, 95% CI, 1.25-8.78 for L. iners-dominant compared to L. crispatus-dominant communities). The model with the highest area under the curve (AUC=.77) included Gardnerella vaginalis, age, Prevotella timonensis, and L. crispatus.

CONCLUSIONS: Along with host factors, vaginal microbiota could be used for predictive risk scoring for PTB across different U.S. cohorts.},
}

@article {pmid41265489,
year = {2025},
author = {Akhirini, N and Suprayogi, WPS and Saraswati, PN and Ratriyanto, A and Irawan, A},
title = {Fermented soybean meal using Bacillus subtilis and Aspergillus oryzae positively enhances cecal microbial composition and broiler performance.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.250400},
pmid = {41265489},
issn = {2765-0189},
abstract = {OBJECTIVE: This study investigated the effect of fermented SBM (FSBM) prepared through solid-state fermentation using Bacillus subtilis (BS) and Aspergillus oryzae (AO) to replace SBM in broiler chickens' diets on production, digestibility, and cecal microbial profile.

METHODS: In total, 160 sex-mixed day-old chicks of Cobb 500 broiler chickens were randomly assigned to four groups, four pens (replicates; 10 birds each pen), and were raised for 35 days under tropical conditions. The treatments were control (basal diet; CON) or SBM replaced by FSBM produced using AO (AO group), BS (BS group), and their combination (AO+BS group).

RESULTS: Birds fed AO+BS diet resulted in higher (p=0.003) BW while BS diet tended (p=0.063) to have higher final BW than CON or AO. Similarly, birds fed FSBM prepared under either BS or AO+BS had higher feed intake (p<0.01) than the CON group. No difference was found on feed conversion ratio (FCR). Relative organ weights including heart, liver, abdominal fat, and total inner organs were lower (p<0.01) on birds fed AO+BS diet than CON, but relative carcass weight was unaffected (p>0.05). Treatments with BS or AO+BS increased dry matter (DM) (p=0.032), organic matter (OM) (p=0.016), and crude protein (CP) (p=0.044) digestibility, while AO did not affect DM and CP digestibility. Broilers fed AO+BS diet showed greater abundance of Firmicutes phylum and Bacteroides genus than CON group. Several microbial taxa biomarkers were identified via LEfSE analysis, including higher abundance of Enterococcus and Bacillus in AO+BS group but lower abundance of Erysipelatoclostridium, Odoribacter, Ruminococcaceae bacterium, Staphylococcus, and Clostridium methylpentosum group in CON group.

CONCLUSION: B. subtilis and A. oryzae could synergistically enhance the nutritional quality of SBM, positively alter cecal microbiota, and improve the production performance of broiler chickens.},
}

@article {pmid41265441,
year = {2025},
author = {Xu, Y and Wang, Z and Wu, J and Yue, Y and Ren, Y and Pan, Y and Li, J and Liu, C and Borriss, R and Liu, X and Qiao, J and Lee, YW and Wu, H and Dini-Andreote, F and Shen, Q and Xiong, W and Gao, X and Berendsen, RL and Gu, Q},
title = {Keystone Pseudomonas species in the wheat phyllosphere microbiome mitigate Fusarium head blight by altering host pH.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.10.016},
pmid = {41265441},
issn = {1934-6069},
abstract = {Phyllosphere microbiota play crucial roles in supporting host performance. However, the dynamic changes of phyllosphere-associated microbiome during pathogen infections and their impacts on plant health remain unknown. Here, we found phyllosphere microbes can mitigate wheat Fusarium head blight (FHB), a severe disease caused by Fusarium graminearum (F. graminearum) pathogen that promotes infection by inducing host alkalinization. Using wheat head microbial community profiling and metatranscriptomics, we found Pseudomonas spp. significantly enriched on infected wheat heads. Through isolating 595 bacterial strains from infected wheat heads-including 196 Pseudomonas isolates-we identified certain enriched Pseudomonas isolates capable of producing organic acids that counteract pathogen-induced pH upshift. In vitro experiments confirm the selective promotion of specific host-acidifying Pseudomonas in wheat heads. Field trials confirmed that host-acidifying Pseudomonas strains effectively controlled FHB. These findings highlight the pivotal role of plant-beneficial microbes in host pH regulation and offer innovative avenues for sustainable plant disease control.},
}

@article {pmid41265342,
year = {2025},
author = {Uyeda, KS and Borovik, AS},
title = {Forged in O2: Transition metal ions and the rise of aerobic life.},
journal = {Journal of inorganic biochemistry},
volume = {275},
number = {},
pages = {113147},
doi = {10.1016/j.jinorgbio.2025.113147},
pmid = {41265342},
issn = {1873-3344},
abstract = {The evolution of oxidative metabolism has shaped life on Earth, from ancient anaerobic microorganisms to modern eukaryotes. Central to aerobic life is the ability of metalloproteins to regulate and utilize dioxygen through tightly controlled biochemical processes. Beginning with the emergence of oxygenic photosynthesis and aerobic respiration, the pivotal roles of metalloenzymes in dioxygen activation, utilization and detoxification are then highlighted. Bridging perspectives from bioinorganic chemistry, enzymology, synthetic biology and microbiome science, we discuss how studies of biomimetic molecular complexes and natural and artificial metalloproteins illuminate the structural and functional strategies used to manage dioxygen reactivity. We further consider the systemic roles of metal ions in maintaining redox balance, shaping host-microbe interactions, and contributing to pathological outcomes when misregulated. A foundation is established for understanding the critical roles that metal ions play in dioxygen chemistry that underpins both healthy metabolism and oxidative stress related diseases.},
}

@article {pmid41265278,
year = {2025},
author = {Tian, Y and Hao, F and Xu, G and Qian, Y and Liu, J and Pan, N and Yang, T},
title = {Causal effects of gut microbiome on aortic dissection: A mendelian randomization study.},
journal = {Clinics (Sao Paulo, Brazil)},
volume = {80},
number = {},
pages = {100811},
doi = {10.1016/j.clinsp.2025.100811},
pmid = {41265278},
issn = {1980-5322},
abstract = {INTRODUCTION: Aortic Dissection (AD) is a severe vascular disease with high mortality. While its progression is rapid, the development of AD is a chronic disease process. The gut microbiome may play a crucial role in this process. This study aims to explore the potential causal association between gut microbiome and AD using Mendelian Randomization (MR).

METHODS: This study employed a two-sample MR approach using Genome-Wide Association Study (GWAS) data from the Finnish population to investigate the causal association between gut microbiota and AD. Single Nucleotide Polymorphisms (SNPs) associated with 473 gut microbiota taxa were selected as instrumental variables, and various MR methods were applied to evaluate the causal effects. Sensitivity analyses were conducted to assess the robustness of the results, and a reverse MR analysis was performed to validate the directionality of the associations.

RESULTS: The MR analysis confirmed that Actinomycetales, Bacillales A, Lawsonibacter sp002161175, Prevotella sp002933775, Saccharomonospora, Acidaminococcus fermentans, CAG-110, CAG-177 sp002451755, CAG-177 sp003514385, and Eisenbergiella sp900066775 may exert protective effects, whereas koll11, Magnetospirillum A, Poseidoniaceae, Pseudomonas aeruginosa, Bacteroides eggerthii, CAG-269 sp002372935, and Dorea phocaeense may increase the risk of AD. Sensitivity analyses confirmed the robustness of these findings.

CONCLUSION: This study provides new insights into the role of gut microbiome in AD, identifying specific taxa that may serve as protective or risk factors. Further research is needed to validate these findings in broader populations.},
}

@article {pmid41265274,
year = {2025},
author = {Eichinger, J and Seifert, J and Sáenz, JS and Amin, N and Lorenz, S and Eckel, F and Zollfrank, C and Windisch, W and Brugger, D},
title = {The interaction of microplastics with the ruminal ecosystem in vitro.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140481},
doi = {10.1016/j.jhazmat.2025.140481},
pmid = {41265274},
issn = {1873-3336},
abstract = {Mismanaged plastic waste contaminates marine and terrestrial environments, so farm animals are increasingly exposed to microplastics (MP) in feed. Yet their interactions with the rumen microbiome are largely unknown. We evaluated these interactions in vitro with the Hohenheim Gas Test. Five MP chemical species - polylactide, polyhydroxybutyrate, high‑density polyethylene, polyvinyl chloride and polypropylene - were tested in two particle‑size classes (<125 µm and 125-500 µm) and six doses (0-70 mg per incubation cylinder). Each MP variant was incubated with rumen fluid plus hay or barley. We recorded cumulative gas production, pH and dry‑matter (DM) disappearance, followed by volatile‑fatty‑acid profiling, metaproteomics and metabolomics. MP consistently reduced cumulative gas output independent of polymer type, particle size or dose, but enhanced total DM degradation dose-dependently. In barley incubations, metaproteomics revealed a shift from Bacteroidetes toward Firmicutes and higher abundance of protein categories "replication & repair" and "translation", while "carbohydrate metabolism & transport" and "amino‑acid metabolism" declined. The results show that MPs interact with, and are at least partly degraded by, the ruminal microbiota. Progressive size reduction in the rumen could facilitate MP translocation into animal tissues, underscoring the need for in‑vivo studies on animal health and food‑safety implications.},
}

@article {pmid41265266,
year = {2025},
author = {Fernández-Triana, I and Rubilar, O and Fincheira, P and Fernández-Baldo, MA and Saldivar-Diaz, M and Lora-Peña, OA and Benavides-Mendoza, A and Schoebitz, M and Tighe-Neira, R and Leiva, S and Tortella, GR},
title = {Abiotic multi-stressor co-exposure to hazardous pollutants reveals drought as the primary driver of soil microbiome shifts.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140515},
doi = {10.1016/j.jhazmat.2025.140515},
pmid = {41265266},
issn = {1873-3336},
abstract = {Soil microbial communities are essential for ecosystem functioning, yet their responses to combined abiotic stressors remain unclear, as most studies focus on single-stressor effects. In this work, the combined effects of different drought levels and co-contamination with copper nanoparticles and the fungicide carbendazim on microbial community structure and function in an agricultural soil over 120 days were evaluated. Enzymatic activities, potential nitrification rate, and functional gene abundances (16S and amoB) were measured. Moreover, 16S rRNA metabarcoding was applied to explore microbial diversity and community dynamics comprehensively. Pesticide dissipation kinetics were also assessed. General metabolic and nutrient-cycling enzymes were susceptible to combined stress under SD and ED. Although alpha and beta diversity showed limited differences at the end of the experiment, co-occurrence networks revealed progressive increases in microbial connectivity and negative correlations, indicating structural reorganization. Functional predictions highlighted a shift from nitrogen and phosphorus cycling toward carbon-degradation pathways, suggesting stress-induced trade-offs. Significantly, pesticide dissipation was markedly reduced under SD, with prolonged half-lives and higher residues, reflecting impaired microbial degradation capacity. Collectively, our results demonstrate that drought is the dominant driver of microbial reorganization, amplifying the effects of emerging contaminants on microbial interactions, functional potential, and pollutant fate.},
}

@article {pmid41265168,
year = {2025},
author = {Jiang, Y and Xie, Y and Liu, F and Qin, Y and Zhang, Y and Tang, L and Dong, X and Li, L and Chen, S and Yuan, B and You, Y and Qiu, R},
title = {Biological Validation of the PSC-MCAT: Analyzing Dental Plaque Microbiota Across Caries Risk Levels in Preschoolers.},
journal = {International dental journal},
volume = {76},
number = {1},
pages = {104007},
doi = {10.1016/j.identj.2025.104007},
pmid = {41265168},
issn = {1875-595X},
abstract = {OBJECTIVE: Although Caries Risk Assessment (CRA) tools are widely recognised in preventive dentistry for predicting dental caries risk in children, there is a notable lack of studies addressing CRA within the Chinese population. This study aimed to evaluate the biological validity of the modified caries-risk assessment tool for preschool children (PSC-MCAT) by analysing the oral microbiome of children stratified by caries risk.

MATERIALS AND METHODS: A comprehensive analysis of the oral microbiome was conducted on 72 preschool children categorised into low- (L), moderate- (M), and high-risk (H) groups based on the PSC-MCAT criteria. Next-generation sequencing was employed to assess microbial diversity and structure. Statistical analyses were performed to identify significant differences among the risk groups.

RESULTS: The analysis revealed statistically significant differences in microbial diversity and structure among the caries risk groups (P < .05). Specific caries risk biomarkers, including Scardovia, Prevotella, and Megasphaera, were significantly enriched in the H group (P < .05). Co-occurrence network analysis showed that the M group exhibited a more complex microbial network compared to the H group, while the L group displayed sparse ecological interactions. KEGG pathway analysis identified 8 differentially abundant metabolic pathways among the risk groups. Furthermore, certain biomarkers in the H group, such as Scardovia and Megasphaera, were associated with D-arginine and D-ornithine metabolic pathways (P < .05) and were closely linked to children's oral health behaviours, including sweet food intake frequency and regular fluoride application (P < .05).

CONCLUSION: This study provides the first biological validation of the PSC-MCAT's risk stratification capacity, establishing a mechanistic link between clinical risk tiers and the dynamics of acidogenic pathobionts as well as host-microbe metabolic interactions. These findings offer valuable insights for prognostic predictions and targeted caries management strategies.},
}

@article {pmid41264973,
year = {2025},
author = {See, MS and Ching, XL and Razali, N and Asri, IS and Abdullah, MM and Bidai, J and Rusli, MU and Ma, NL},
title = {Blood heavy metals content and gut microbiota profile in immature and nesting wild green turtles (Chelonia mydas).},
journal = {Marine environmental research},
volume = {213},
number = {},
pages = {107688},
doi = {10.1016/j.marenvres.2025.107688},
pmid = {41264973},
issn = {1879-0291},
abstract = {Sea turtles live in habitats where they experience chronic exposure to pollutants, such as heavy metals, over the course of their long lifespan. This makes them valuable model organisms for studying the long-term biological impacts of persistent environmental contaminants. Morphological changes are often insufficient to capture the impacts of low-dose exposures, whereas gut microbiota profiling can offer critical insights into host health and adaptive responses to environmental stressors. This study investigated the relationship between heavy metal exposure and gut microbiota composition in green turtles (Chelonia mydas) at immature (IM, n = 10) and nesting (NT, n = 9) stages. Metal concentrations in whole blood were measured using inductively coupled plasma mass spectrometry (ICP-MS), while gut microbiota were characterized via 16S rRNA gene sequencing. The blood of immature turtles exhibited significantly higher concentrations of manganese (Mn), whereas nesting turtles had elevated arsenic (As), lead (Pb), barium (Ba), and strontium (Sr). Analysis of gut microbiota revealed significant differences in both α-Shannon and β-diversity associated with different pollutants, indicate restructuring of microbial communities. PICRUSt2 revealed alteration of carbohydrate, nucleotide, vitamin, and xenobiotic metabolisms among growth stages. Correlation analysis (LEfSe and CCA) further showed that bacterial genera such as Methylophaga and Thermomonas were positively associated with Cd, Pb, and Sr, whereas Lactobacillus and Rodentibacter displayed negative correlations with these metals. Collectively, this highlights the potential of pollutants to compromise host health through microbiome-mediated mechanisms.},
}

@article {pmid41264968,
year = {2025},
author = {Yang, C and Bao, L and Shi, Z and Xv, X and Li, J and Jiang, D and You, L},
title = {Jingning formula alleviates ADHD by restoring gut microbiota dysbiosis and tryptophan metabolic dysfunction.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {269},
number = {},
pages = {117256},
doi = {10.1016/j.jpba.2025.117256},
pmid = {41264968},
issn = {1873-264X},
abstract = {Jingning Fang (JNF), a clinically used herbal medicine for attention deficit hyperactivity disorder (ADHD), demonstrates significant efficacy in alleviating core symptoms such as hyperactivity and impulsivity in pediatric patients. To systematically investigate its therapeutic mechanisms, we implemented an integrated approach encompassing UPLC-Q-TOF/MS-based untargeted metabolomics profiling of brain, serum, and fecal specimens, targeted quantification of tryptophan pathway metabolites across these biological compartments, and gut microbiome characterization via 16S rRNA sequencing. Our analysis revealed a prominently dysregulated metabolic pathway in ADHD, characterized by perturbations in tryptophan metabolism that were particularly pronounced in feces (P < 0.05). Notably, the kynurenic acid (KYNA)/quinolinic acid (QUINA) ratio, a pivotal indicator of kynurenine pathway homeostasis, exhibited robust correlations with both behavioral manifestations and gut microbial ecology. These findings provide a mechanistic basis for JNF's clinical efficacy in ADHD management by highlighting its role in restoring gut microbiome balance and tryptophan metabolic homeostasis.},
}

@article {pmid41264233,
year = {2025},
author = {Yun, Y and Duan, C and He, X and Tang, R and Lan, Y and Lu, M and Liu, T and Fan, X and Fan, Z and Ran, J},
title = {Gut microbiome plasticity explains the altitudinal distribution pattern and adaptability in a small mammal species (Apodemus draco).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0238825},
doi = {10.1128/spectrum.02388-25},
pmid = {41264233},
issn = {2165-0497},
abstract = {Altitudinal distribution patterns of species, a central focus of ecology, predominantly focus on environmental factors and only rarely on the host's intrinsic adaptive capacity. Particularly, the role of gut microbiota has not yet been studied. Here, we used the wild South China Field Mouse (Apodemus draco), a widely distributed small mammal species, as the study subject to investigate the altitudinal distribution pattern of the species and assess how gut microbiota contributes to the formation of this pattern. A total of 219 wild samples were captured in the middle section of the Qionglai Mountains, China, and 121 adult individuals were selected for metagenomic sequencing (e.g., gut microbial diversity, network topology, composition, and functional profiles). Vegetation cover of each sampling quadrat was assessed using Normalized Difference Vegetation Index. Our results indicate that A. draco exhibited a hump-shaped altitudinal distribution, but the peak abundance of A. draco corresponds to lower vegetation cover of habitats. Gut microbial diversity, complexity, robustness, energy harvesting ability, and carbohydrate utilization capacity all peaked at the mid-altitude zone, matching the host's spatial distribution pattern. Furthermore, the gut microbiome in high-altitude A. draco populations facilitates host acclimatization in extreme high-altitude niches by enhancing energy harvesting, hypoxia tolerance, and pathogen resistance.IMPORTANCEWe propose for the first time that the gut microbiome serves as a pivotal factor in structuring the altitudinal distribution pattern of species and further reveal a gut microbiota-mediated adaptive strategy underlying mammalian high-altitude adaptation. These results demonstrate that the gut microbiome fundamentally facilitates host adaptation to ecological niches. The study provides a novel insight into the factors of species' spatial distribution from a gut microbiota perspective.},
}

@article {pmid41264189,
year = {2025},
author = {Mohamad Zain, N and Mohd Amin, I and Abdul Razak, F and Abu Hassan, MI},
title = {Preliminary screening of pomegranate-derived compounds for antimicrobial and anti-virulence effects against cariogenic streptococci.},
journal = {The Saudi dental journal},
volume = {37},
number = {10-12},
pages = {84},
pmid = {41264189},
issn = {1013-9052},
abstract = {As a biofilm-mediated disease, dental caries is primarily attributed to the activity of Streptococcus mutans and Streptococcus sobrinus, key contributors to enamel mineral loss under acidic conditions. Current broad-spectrum antimicrobials disrupt the oral microbiota and carry undesirable side effects, prompting interest in targeted, microbiome-friendly alternatives. This study evaluated the antimicrobial, anti-cariogenic, and cytotoxic properties of pomegranate (Punica granatum) derived compounds, corilagin, ellagic acid, gallocatechin, kaempferol-7-O-glucoside, punicalagin, punicalin, and rutin against cariogenic S. mutans and S. sobrinus, and the commensal S. gordonii. Antibacterial activity was assessed using disc diffusion, minimum inhibitory concentration (MIC), and minimum bactericidal concentration (MBC) methods. Anti-virulence effects were evaluated through glycolytic pH drop and cell surface hydrophobicity assays. Cytotoxicity was determined using the brine shrimp lethality assay. Punicalagin, punicalin, and ellagic acid showed strong, selective bactericidal activity against S. mutans and S. sobrinus, with low MICs and MBC/MIC ratios, while sparing S. gordonii. These compounds significantly suppressed acid production, maintaining pH above the critical demineralisation threshold, and reduced surface hydrophobicity in cariogenic strains without affecting the commensal. Most compounds exhibited low toxicity (LC50 > 500 µg/mL), indicating a favourable safety profile. Overall, punicalagin and punicalin demonstrated dual antimicrobial and anti-virulence activity with selective targeting of cariogenic pathogens. These findings support the potential inclusion of punicalagin and punicalin in oral care formulations aimed at preventing dental caries while preserving beneficial oral microbiota. As this is a preliminary screening study, the results should be interpreted cautiously, and further biofilm and host-cell assays are needed to confirm translational potential.},
}

@article {pmid41264167,
year = {2025},
author = {Baek, KW and Yun, K and He, MT and Kim, NK and Kim, JS and Ahn, K and Kim, JH},
title = {Integrated transcriptomic and 16S rRNA analyses reveal colon and brain barrier-preserving effects of red radish (Raphanus sativus L.) sprout supplementation in high-fat diet-fed mice.},
journal = {Genes & genomics},
volume = {},
number = {},
pages = {},
pmid = {41264167},
issn = {2092-9293},
abstract = {BACKGROUND: Radish sprouts (Raphanus sativus L.) are rich in dietary fibers and phytochemicals with antioxidant and anti-inflammatory activities. However, their whole-food effects on the gut-brain axis remain poorly defined.

OBJECTIVE: This study examined the preventive potential of whole-food red radish sprout (RS) powder against high-fat diet (HFD)-induced obesity and cognitive decline in mice, focusing on its effects on barrier integrity, inflammation, oxidative stress, and gut microbiota.

METHODS: Male C57BL/6 mice were fed an HFD for 16 weeks with or without RS powder (low or high dose). Assessments included body and tissue indices, oral glucose tolerance, serum leptin, cognitive performance, oxidative stress in brain, gene expression of tight junction and inflammatory markers in colon and brain, and fecal microbiota profiling using 16S rRNA sequencing.

RESULTS: RS supplementation attenuated HFD-induced weight gain, improved glucose tolerance, and reduced leptin levels, with stronger effects at the higher dose. Cognitive deficits were rescued by RS, accompanied by alleviation of brain oxidative stress and reduced expression of neuroinflammatory genes (Tnf, Il6, Il1b, Aif1, Gfap). RS restored tight-junction genes (Tjp1, Ocln, Cldn1, Jam2, Cdh5) while simultaneously decreasing Cldn2 and pro-inflammatory transcripts, and upregulating Il10. Although alpha diversity was unchanged, beta diversity differed significantly; RS reduced the Firmicutes/Bacteroidota ratio, enriched Akkermansia and Lactobacillus, and suppressed Oscillibacter and Desulfovibrio.

CONCLUSION: Whole-food RS powder prevents HFD-induced obesity and cognitive decline by reinforcing barrier integrity, reducing inflammation and oxidative stress, and reshaping gut microbiota. These findings support RS as a practical functional food for early obesity intervention via gut-brain axis regulation.},
}

@article {pmid41263968,
year = {2025},
author = {Brennan, AA and Renshaw, CP and Tata, SC and Campanella, A and Hartman, R and Carlotz, R and Downs, M and Yurtola, A and Baum, J and Rodriguez, KM and Bertucci, MA and Tal-Gan, Y},
title = {The Quorum Sensing-Controlled Competence Regulon Drives H2O2 Production in Streptococcus gordonii.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.5c00926},
pmid = {41263968},
issn = {2373-8227},
abstract = {Streptococcus gordonii sp. firmicutes is an early colonizer of the oral microbiome and contributes positively to oral health. While this species has been found to produce hydrogen peroxide by spxB expression, the relationship of this expression to the competence regulon has not yet been explored. To this end, this study sought to investigate the connection of the S. gordonii competence regulon quorum sensing (QS) circuitry with downstream proliferative phenotypic expression resulting from competence-stimulating peptide (CSP) exposure, with specific attention to peroxide formation. Following confirmation of the native CSP, RNA-seq was completed to gain insights into transcriptomic variations resulting from CSP incubation. Later, structure-activity relationship (SAR) analyses of the native CSP were completed. The results revealed residues integral to CSP:ComD binding and activation, while indicating which residues were considered dispensable to this process. Phenotypic assessment revealed that peroxide formation was modulated via the competence regulon. Finally, interspecies competition assays were carried out to understand the interactions between S. gordonii and S. mutans, with S. gordonii demonstrating a profound capability of antagonizing S. mutans growth and proliferation. Our results support that this antagonism is mainly attributed to hydrogen peroxide production by S. gordonii. This finding suggests that S. gordonii may be exploited for its beneficial proliferative phenotypes downstream of the competence regulon.},
}

@article {pmid41263913,
year = {2025},
author = {Merrick, B and Prossomariti, D and Kertanegara, M and Wyatt, D and Goldenberg, S},
title = {Facilitators and barriers to recruitment and retention in a feasibility trial of encapsulated faecal microbiota transplant to eradicate carriage of antibiotic-resistant bacteria at an academic hospital in central London: a nested qualitative study.},
journal = {BMJ open},
volume = {15},
number = {11},
pages = {e104783},
doi = {10.1136/bmjopen-2025-104783},
pmid = {41263913},
issn = {2044-6055},
mesh = {Humans ; London ; *Fecal Microbiota Transplantation/methods ; Male ; Female ; Feasibility Studies ; Middle Aged ; Qualitative Research ; Adult ; Focus Groups ; *Patient Selection ; COVID-19/epidemiology ; Aged ; *Carrier State/therapy ; },
abstract = {OBJECTIVES: This nested qualitative study (NQS) aimed to identify facilitators and barriers to the delivery of a substantive randomised controlled trial investigating the eradication of gastrointestinal tract carriage of antibiotic-resistant organisms using encapsulated faecal microbiota transplant (FMT).

DESIGN: NQS within a participant-blinded, randomised, placebo-controlled, single-centre, feasibility trial (RCT)-Feasibility of ERadicating gastrointestinal carriage of Antibiotic-Resistant Organisms (FERARO) (ISRCTN reg. no. 34 467 677)-with data collected via focus groups and analysed using thematic analysis.

SETTING: RCT participants were recruited from a large academic tertiary referral hospital in central London. Focus groups were held at the hospital or via videoconferencing for those unable to travel.

PARTICIPANTS: This study included 13 FERARO study participants across two focus groups. 11 participants were under RCT follow-up and unaware of their treatment allocation, two participants had completed 6-month follow-up and knew whether they had received FMT or matched placebo. Additional data were opportunistically collected on reasons for declining RCT participation.

RESULTS: Participants found FMT to be an acceptable and holistic management strategy and noted positive impacts from RCT participation including enhanced personal health awareness and valuable support from the research team. The time and travel commitment presented the most substantial barrier to RCT participation. Many participants were motivated by a desire to give something back to the UK National Health Service and/or research. Patients' current health status also influenced the decision-making process, and, while infrequently cited, the COVID-19 pandemic added extra complexity likely impacting individuals' willingness to participate.

CONCLUSIONS: While FMT is generally acceptable to participants, logistical barriers such as the time and travel commitment associated with RCT participation need consideration. Effective communication, personal connections and participant education on antimicrobial resistance are likely to be crucial for enhancing recruitment and retention in future trials.

TRIAL REGISTRATION NUMBER: ISRCTN registration number 34 467 677 and EudraCT number 2019-001618-41.},
}

Humans
London
*Fecal Microbiota Transplantation/methods
Male
Female
Feasibility Studies
Middle Aged
Qualitative Research
Adult
Focus Groups
*Patient Selection
COVID-19/epidemiology
Aged
*Carrier State/therapy

@article {pmid41263680,
year = {2025},
author = {Jakubczyk-Słabicka, A and Kasprzak, J and Skonieczna-Żydecka, K and Sławek, J and Górska-Ponikowska, M},
title = {Gut and skin microbiome profiles as promising biomarkers in Parkinson's disease - preliminary results.},
journal = {Neurologia i neurochirurgia polska},
volume = {},
number = {},
pages = {},
doi = {10.5603/pjnns.108273},
pmid = {41263680},
issn = {0028-3843},
}

@article {pmid41263597,
year = {2025},
author = {Ku, M and Taibi, A and Wu, D and Chen, YT and Lopez-Dominguez, L and Yang, Y and Chen, S and Liang, F and Liu, R and Tsao, R and Power, KA and Thompson, LU and Comelli, EM},
title = {Altered mouse cecal microbiome-serum enterolignans relationships in response to dietary lignans ingested through whole flaxseed or flaxseed hull.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo03558a},
pmid = {41263597},
issn = {2042-650X},
abstract = {Flaxseed (FS) is rich in bioactive compounds, including fiber and lignans, which provide health benefits largely mediated by gut microbial metabolism. However, gut microbiota responses, including their relationship with fiber- and lignan-derived microbial metabolites (short chain fatty acids (SCFA) and enterolignans enterodiol and enterolactone), remain unclear. We addressed this through administration of an isocaloric flaxseed (FS) or flaxseed hull (FH) diet to female mice, where FH provided a higher amount of fiber and lignan secoisolariciresinol diglucoside compared to FS. Both diets increased cecal SCFA and serum enterolignans concentrations compared to the basal control diet (BD). Compared to FS, FH increased serum secoisolariciresinol, enterodiol, and total lignans, but not SCFA concentrations. FS and FH increased α- and β-diversity and altered microbiota composition and functional potential compared to BD, but no differences were observed between FS and FH, except for altered abundance of select taxa and a limited number of functions. However, the two diets altered the microbial network structure, including keystone species shifts from Intestinimonas in FS to Carnobacterium in FH, and taxa relationships with enterolignans and SCFA. Our findings suggest that while intestinal microbiota composition responses to whole flaxseed result in increased circulating enterolignans and intestinal SCFA production, FH can further elevate serum enterolignans via reorganization of interactions among taxa.},
}

@article {pmid41263574,
year = {2025},
author = {Tang, L and Xie, P and Wang, H and Hong, X and Gong, Z and Zhao, G and Yue, M},
title = {The sex hormone-gut microbiome axis: mechanistic drivers of sex-disparate bacterial infection outcomes and precision clinical interventions.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0023625},
doi = {10.1128/cmr.00236-25},
pmid = {41263574},
issn = {1098-6618},
abstract = {SUMMARYSex disparities in bacterial infections pose significant challenges in clinical microbiology, influencing diagnostic approaches, antimicrobial stewardship, and patient outcomes. Males frequently exhibit heightened severity in conditions like Helicobacter pylori-associated gastritis and Vibrio cholerae outbreaks, whereas females face amplified risks during reproductive phases for pathogens, such as Listeria monocytogenes and Salmonella spp. Beyond genetic and behavioral factors, the bidirectional sex hormone-gut microbiome axis emerges as a key mechanistic driver: estrogens bolster innate immunity and microbial diversity (e.g., enriching short-chain fatty acid-producing taxa like Bifidobacterium), while androgens and progesterone impose immunosuppressive effects, altering colonization resistance and virulence modulation. Microbial contributions-via β-glucuronidase-mediated hormone deconjugation, bile acid biotransformations, and metabolite signaling-further calibrate host responses, as evidenced in Clostridioides difficile recurrence and enterohemorrhagic Escherichia coli virulence upregulation. This review synthesizes epidemiological, preclinical, and emerging clinical data, highlighting the axis's role in pathogen-specific immune evasion and dysbiosis-driven exacerbations. Clinically, these insights advocate for sex-stratified microbiome diagnostics (e.g., 16S rRNA sequencing for risk profiling) and targeted therapies, including hormone-modulated probiotics to restore barrier function, fecal microbiota transplantation to curb antibiotic-associated vulnerabilities, and selective estrogen receptor modulators to enhance clearance in high-risk cohorts. Despite advances, gaps in human longitudinal studies and pathogen-strain interactions limit translation. Future research integrating multi-omics with clinical trials could refine precision interventions, optimizing infection management in diverse populations and aligning with evolving demands for personalized microbiology.},
}

@article {pmid41263569,
year = {2025},
author = {Ding, W and Ling, Z and Liu, X and Zhang, J and Cheng, Y and Zhu, Z and Wu, L and Xu, X and Gao, Y and Hu, X},
title = {Impact of carbapenem-resistant Klebsiella pneumoniae infection on gut microbiota and host immunity: a case-control study.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0297525},
doi = {10.1128/spectrum.02975-25},
pmid = {41263569},
issn = {2165-0497},
abstract = {Carbapenem-resistant Klebsiella pneumoniae (CRKP) represents a critical global health threat with limited treatment options. While the gut microbiota is a reservoir for opportunistic pathogens and a regulator of host immunity, the reciprocal impact of systemic CRKP infection on gut microbial ecology and immune responses remains poorly defined. In a prospective case-control study, 38 patients with confirmed CRKP infection and 38 matched hospitalized controls without CRKP were enrolled. Fecal samples underwent 16S rRNA gene sequencing to characterize microbial profiles, and serum cytokine levels were quantified using multiplex immunoassays. CRKP infection was associated with significantly reduced microbial diversity and a distinct shift in community structure, characterized by depletion of beneficial commensals (Bacteroides, Faecalibacterium, Roseburia) and enrichment of pathobionts (Klebsiella, Enterococcus). Enterotype analysis revealed a predominance of a Klebsiella/Enterococcus-dominated enterotype in CRKP patients. Functional predictions indicated impaired carbohydrate and butyrate metabolism alongside increased virulence- and resistance-associated pathways. Systemically, patients exhibited elevated pro-inflammatory cytokines (IL-6, TNF-α, IFN-γ) and chemokines (IP-10, MCP-1, RANTES). Correlation analyses linked opportunistic taxa with heightened inflammatory markers, while beneficial short-chain fatty acid producers showed inverse associations. Systemic CRKP infection is associated with profound gut dysbiosis and a hyper-inflammatory immune response. The strong microbiota-immune correlations suggest that the gut microbiota may serve as a biomarker and a potential therapeutic target for mitigating CRKP-associated immune dysfunction, though the directional relationship (cause vs. consequence) between dysbiosis and CRKP infection remains to be elucidated.IMPORTANCECarbapenem-resistant Klebsiella pneumoniae (CRKP) is a critical global threat with limited therapeutic options. This study reveals that systemic CRKP infection is associated with profound gut dysbiosis-characterized by loss of beneficial commensals (e.g., Faecalibacterium) and expansion of pathobionts (e.g., Klebsiella, Enterococcus)-as well as a hyperinflammatory immune response. We demonstrate strong correlations between specific microbial taxa and host cytokines, suggesting that the gut microbiome may hold potential as a biomarker and therapeutic target. These findings enhance our understanding of host-microbe interactions in CRKP infection and support the exploration of microbiota-based therapies. However, further studies, including longitudinal and animal models, are needed to clarify whether gut dysbiosis directly influences CRKP outcomes or is a secondary consequence.},
}

@article {pmid41263392,
year = {2025},
author = {Zhao, R and Lu, Y and Xu, Q and Ren, H and Li, H and Gao, J and Cui, H and Yuan, Z and Cao, B and Wei, B},
title = {Gut blautia coccoides-derived 5Z-dodecenoic acid attenuates chronic psychological stress-induced gastric cancer progression.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000004080},
pmid = {41263392},
issn = {1743-9159},
abstract = {BACKGROUND: Chronic psychological stress is a critical oncogenic factor of gastric cancer (GC). However, the mechanisms underlying stress-induced malignant progression remain largely unknown. Gut microbiota dysregulation is tightly associated with cancer development and metabolism.

MATERIALS AND METHODS: Chronic unpredictable mild stress (CUMS) modeling was used to prepare mice suffering from chronic psychological stress. 16s rRNA sequencing and Q300 targeted metabolite quantification were jointly conducted to depict landscapes of gut microbiome and metabolomics of CUMS mice. Fecal microbiota transplantation was employed to investigate the functions of gut microbial communities in regulating CUMS-mediated GC growth. Drug affinity responsive target stability, surface plasmon resonance and molecular docking assays were performed to screen direct target proteins of 5Z-dodecenoic acid. The interactions between RIOK2 and BYSL were verified with co-immunoprecipitation and GST pull-down and fluorescent co-localization analysis. A series of experiments for malignant behaviors and glycolysis and subcutaneous tumor transplantation were employed to detect alterations of GC cell phenotypes ex vivo and in vivo, respectively.

RESULTS: Microbiome and metabolomics collectively demonstrated disrupted gut microbial communities and metabolic patterns. Particularly, Blautia coccoides-derived 5Z-dodecenoic acid was predominately declined by CUMS. Supplementation with Blautia coccoides or 5Z-dodecenoic acid effectively mitigated the negative effects of CUMS on glycolysis and malignancy. Mechanistically, 5Z-dodecenoic acid directly inhibits the functions of RIOK2, which maintained ectopic glycolysis and malignant behaviors. RIOK2 further interacted with BYSL and maintained its properties of potentiation of GC progression and metabolism.

CONCLUSION: Our findings advance the insights of Blautia coccoides-derived 5Z-dodecenoic acid implicated in chronic psychological stress-induced GC progression and provide novel strategies for dampening GC progression.},
}

@article {pmid41263210,
year = {2025},
author = {Zhukova, NG and Sayfitdinkhuzhaev, ZF and Israilova, GM and Bustonov, OY and Nasriddinova, NA and Gaponova, OV and Zhukova, IA and Masenko, AY},
title = {[«Brain-gut-microbiome» axis in patients with Parkinson's disease].},
journal = {Zhurnal nevrologii i psikhiatrii imeni S.S. Korsakova},
volume = {125},
number = {11. Vyp. 2},
pages = {18-23},
doi = {10.17116/jnevro202512511218},
pmid = {41263210},
issn = {1997-7298},
mesh = {Humans ; *Parkinson Disease/microbiology/metabolism/physiopathology ; *Gastrointestinal Microbiome ; *Brain/metabolism ; alpha-Synuclein/metabolism ; *Brain-Gut Axis ; },
abstract = {Parkinson's disease (PD) is one of the most common motor neurological diseases. The clinical presentation of PD includes both motor symptoms (hypokinesia, muscle rigidity, and tremor) and non-motor manifestations (asthenia, depression, hyposmia), as well as cognitive disorders. The primary link in PD pathogenesis is considered to be the accumulation of pathological α-synuclein; however, neuroinflammation, oxidative stress, mitochondrial dysfunction, and dysregulation of the Brain-gut microbiome axis also contribute to the pathological processes. This review of modern medical literature, encompassing domestic and foreign authors, summarizes recent studies on the significance of gastrointestinal tract changes in PD patients. The analysis revealed the involvement of the microbiome and specific bacterial taxonomic groups in the development of PD. In addition, the accumulation of α-synuclein, according to recent data, begins specifically in the nerve plexuses of the intestine and then spreads along the nerves upward into the central nervous system, affecting the substantia nigra, in particular.},
}

Humans
*Parkinson Disease/microbiology/metabolism/physiopathology
*Gastrointestinal Microbiome
*Brain/metabolism
alpha-Synuclein/metabolism
*Brain-Gut Axis

@article {pmid41263129,
year = {2025},
author = {Mesiha, M and Cumbermack, M and Kim, J and White, R and Lin, T and Rubin, J and Jotwani, R},
title = {How pro-inflammatory diets influence perioperative outcomes.},
journal = {Pain management},
volume = {},
number = {},
pages = {1-6},
doi = {10.1080/17581869.2025.2591598},
pmid = {41263129},
issn = {1758-1877},
abstract = {Recent evidence shows that pro-inflammatory diets-high in saturated fats, added sugars, and ultra processed foods-have been linked to elevated levels of cytokines like interleukin-6 (IL-6) and tumor necrosis factor (TNF), showing a marked increase in systemic inflammation, disrupted immune function and altered anesthetic drug metabolism. These effects have been linked to prolonged recovery, impaired wound healing, and increased complication rates. Additionally, a pro-inflammatory diet changes the gut microbiome, impacting pain perception, opioid sensitivity and stress response by the gut-brain axis. On the contrary, an anti-inflammatory diet reduces inflammatory markers and is associated with a shorter hospital stay. This review synthesizes data from randomized controlled trials (RCT), meta-analyses, and mechanistic studies from 2000-2025, emphasizing literature on omega-3 fatty acids, specialized pro-resolving mediators (SPMs), and short-chain fatty acids (SCFAs). Targeted interventions such as education on nutrition and dietary assessment risk could enhance surgical recovery. Perioperative interventions discussed include pre/probiotic supplementation, omega-3 fatty acid administration, and also dietary counseling as part of Enhanced Recovery After Surgery (ERAS) pathways.},
}

@article {pmid41263038,
year = {2025},
author = {Wang, M and Sun, H and Wang, X and Zhang, X and Huang, Y and Cui, R and Sun, Y and Yao, H and Wan, JY},
title = {Tangerine Peel-Based Herbal Formula Ameliorates Metabolic Syndrome via Gut Microbiota-Mediated Bile Acid Remodeling and TGR5 Activation.},
journal = {The American journal of Chinese medicine},
volume = {},
number = {},
pages = {1-19},
doi = {10.1142/S0192415X25500946},
pmid = {41263038},
issn = {1793-6853},
abstract = {The growing global burden of metabolic syndrome (MetS), a key driver of multiple chronic diseases, highlights the limited treatment options for its multifactorial pathophysiology. Tanshi-Tiaoti Decoction (TTD), a Chinese herbal formula comprised of Citri Reticulatae Pericarpium (Tangerine peel), Coicis Semen (Raw coix seed/Job's tears), Raphani Semen (Radish seed), Nelumbinis Folium (Lotus leaf), Eckloniae/Laminariae thallus (Kelp), and Crataegi Fructus (Raw hawthorn fruit), demonstrates efficacy in the clinical management of MetS. However, its underlying molecular mechanisms remain incompletely elucidated. This study indicates that TTD restored gut microbiota homeostasis and bile acid (BA) profiles in high-fat diet (HFD)-induced MetS mice. TTD significantly attenuated body weight gain, fasting glucose levels, serum triglycerides, and hepatic steatosis. TTD corrected gut microbiota dysbiosis, most notably by reducing the Firmicutes/Bacteroidetes ratio. Fecal microbiota transplantation (FMT) validated the fact that the gut microbiome mediates TTD's therapeutic effects. TTD regulated BA biosynthesis through this microbial modulation, and thus specifically increased hyodeoxycholic acid (HDCA). HDCA, which has been identified as the signature BA during TTD treatment, phenocopied TTD's therapeutic effects against MetS by both activating the BA receptor TGR5 and subsequently promoting beige adipocyte browning. Collectively, TTD ameliorates MetS by reshaping microbial-mediated BA pools, and in particular elevates HDCA levels to thereby activate TGR5 and induce beige adipocyte browning. These findings support TTD as a promising herbal-based therapeutic strategy for the treatment of MetS.},
}

@article {pmid41262934,
year = {2025},
author = {Herath Dissanayakalage, SS and Kaur, J and Mann, RC and Sawbridge, TI},
title = {Host genotype-driven shifts in the Medicago seed microbiome reveal domestication-linked diversity loss in lucerne (Medicago sativa).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1660250},
pmid = {41262934},
issn = {1664-302X},
abstract = {Seed microbiomes represent a critical yet underexplored dimension of plant-associated microbial communities, with potential to enhance crop resilience and sustainability. While plant microbiomes have gained prominence, the diversity and composition of seed-associated bacteria-especially across wild and domesticated lineages-remain poorly characterised. Here, we profiled the bacterial seed microbiome of lucerne (Medicago sativa L.) and its crop wild relatives using an integrative approach combining amplicon sequencing, culture-based recovery, and whole-genome analysis of representative isolates. Amplicon profiling revealed a conserved core microbiome across all accessions, alongside host-genotype-specific patterns and markedly higher bacterial diversity in wild relatives. Culture-based methods recovered over half of the abundant amplicon sequence variants (ASVs), validating the representativeness of the isolate library. The whole genome sequencing of selected isolates uncovered substantial intra-species variation, including genomically distinct strains within the same species. Core taxa such as Pantoea, Paenibacillus, and Pseudomonas were consistently recovered, while several genera enriched in wild relatives-Massilia, Duganella, Sphingomonas-were absent or rare in domesticated lines. Comparative microbiome analysis revealed that domestication has reduced both taxonomic richness and microbial variability in the lucerne seed microbiome. The dominance of conserved taxa alongside the exclusion of wild-enriched groups suggests that breeding history influences microbial assembly and may constrain microbiome function. The consistent presence of core taxa across accessions is consistent with the possibility that, vertical transmission, together with host genotype, contributes to seed microbiome structure. By linking plant genotype with seed microbiome composition and culturability, this study provides a high-resolution view of seed microbial assembly shaped by evolutionary history. The resulting culture-based microbial resource, supported by genome-level characterisation of representative taxa, offers a robust foundation for microbiome-informed strategies in lucerne breeding and pasture improvement.},
}

@article {pmid41262932,
year = {2025},
author = {Meng, F and Zhao, Y and Guo, Y and Guo, X and Zhang, Q and Li, S and Chi, Y and Li, L and Hui, F and Tong, M and Yan, S},
title = {Optimization of Artemisia ordosica crude polysaccharides on milk fatty acid composition in lactating donkeys and their effects on rectal microbiome and lactation performance.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1682805},
pmid = {41262932},
issn = {1664-302X},
abstract = {INTRODUCTION: This study evaluated the effects of dietary Artemisia ordosica crude polysaccharides (AOCP; 0.5 g/kg DM) supplementation on milk fatty acid profiles, rectal microbiota, enzymes related to lipid metabolism, and lactation performance in lactating Dezhou donkeys.

METHODS: A single-factor completely randomized design was used, with 14 lactating Dezhou donkeys (6.16 ± 0.67 years old, 250.06 ± 25.18 kg, parity 2.82 ± 0.48, 39.11 ± 7.42 days in lactation, each with a foal) randomly divided into two groups (n = 7/group). The CON group was fed a diet with a concentrate to forage ratio of 3:7, while the AOCP group received the same diet supplemented with 0.5 g/kg DM of AOCP. The trial lasted 10 weeks (including a 2-week adaptation period).

RESULTS AND DISCUSSION: Compared with the CON group, AOCP supplementation significantly enhanced lactation performance (milk yield, fat, lactose) and the digestibility of DM, ADF, NDF, and elevated oleic acid, linoleic acid, eicosapentaenoic acid, as well as the unsaturated-to-saturated (U/S) and polyunsaturated-to-saturated (P/S) fatty acid ratios, while reducing saturated fatty acids and the c index. AOCP elevated acetate and butyrate in the rectum and the activity of enzymes related to lipid metabolism such as stearoyl-CoA desaturase, and increased the relative abundance of beneficial bacteria (Eubacterium hallii group, Prevotella, Ruminococcus), while decreasing potentially pathogenic bacteria Streptococcus and norank_f_Lachnospiraceae. In summary, AOCP may optimize the fatty acid composition of donkey milk and enhance lactation performance by modulating rectal bacteria structure, enzymes related to lipid metabolism, and nutrient utilization.},
}

@article {pmid41262931,
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 = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1704392},
pmid = {41262931},
issn = {1664-302X},
abstract = {INTRODUCTION: Despite durable viral suppression, neuroinflammation and neurocognitive complications remain common yet poorly understood in people with HIV (PWH). HIV alters human viromes, and virome perturbations have been linked to neurocognitive issues in people without HIV. Recently characterized, the brain and cerebrospinal fluid (CSF) viromes represent a new avenue to understand brain and mental health in PWH.

METHODS: 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 and RNA viruses. Taxonomic composition (reads and contigs), diversity, and relative abundance (RA) of prokaryotic (PV), human eukaryotic (hEV), and non-human eukaryotic viruses (nhEV) were evaluated in relation to HIV status, markers of neuroinflammation/neurodegeneration, cognitive functions, and depressive symptoms. Sensitivity analyses and post-hoc cluster analysis on the RA of hEV, non-human viruses (NHV) and blood-brain barrier permeability were performed. Multivariable models assessed the relationship between cognition and clusters.

RESULTS: Of 46 read-positive CSF samples, 93.5% contained PV sequences, 47.8% hEV, and 45.6% nhEV. PWH displayed lower α diversity, although p > 0.05. At β diversity analysis, HIV status explained 3.4% of the variation in viral composition (p = 0.016). Contigs assembly yielded 13 samples positive for 8 hEV, 2 nhEV, and 6 PV. Higher RA of PV was correlated with higher CSF S100β (rho 0.36, p = 0.002) and β-Amyloid 1-42 fragment (βA-42, rho 0.27, p = 0.026), whereas higher RA of nhEV with poorer cognitive performance (rho 0.26, p = 0.022). Conversely, higher RA of hEV correlated with better cognition (rho -0.38, p = 0.003) and lower βA-42 (rho -0.30, p = 0.012). Sensitivity analyses restricted to only CSF samples with detectable reads 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 NHV-enriched CSF (all p < 0.05).

CONCLUSION: 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 {pmid41262929,
year = {2025},
author = {Asatulloev, T and Yusupov, Z and Cai, L and Chen, Q and Gurung, B and Tojibaev, KS and Sun, W},
title = {Comparative root associated microbial community analysis of Oreocharis mileensis, a resurrection plant species with extremely small populations.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1692695},
pmid = {41262929},
issn = {1664-302X},
abstract = {Plants dynamically interact with their microbiomes through phytohormonal signaling and defense responses, shaping microbial diversity and ecosystem function. While resurrection plants host growth-promoting and drought associated microbes, prior studies on different resurrection plants have been limited to localized sampling, potentially underestimating microbial diversity. We analyzed bacterial and fungal communities across five populations of Oreocharis mileensis, a resurrection plant, during hydrated and dehydrated states to examine population-level microbiome differences or affinity, identify microorganisms that may assist during plant desiccation, and assess their conservation across populations. We found that microbial composition was strongly influenced by compartment (bulk soil, rhizosphere, and endosphere) but exhibited only moderate drought-induced changes, suggesting that O. mileensis maintains a stable microbiome under stress. Core phyla (e.g., Proteobacteria, Actinobacteriota, Ascomycota) were conserved across populations, but genus-level core taxa varied relatively between populations, reflecting niche specialization and host genotype. Drought increased bacterial alpha diversity while reducing beta diversity, indicating homogenization driven by stress-tolerant taxa such as Actinobacteriota. Fungal responses differed, with increased beta diversity suggesting drought-enhanced compositional turnover. Key bacterial genera (e.g., Burkholderia-Caballeronia-Paraburkholderia, Bacillus, Rhizobium) dominated hydrated states, while drought enriched Actinobacteria (e.g., Microlunatus, Rubrobacter) and other drought-resistant taxa. Fungal communities shifted from saprotroph-dominated hydrated states to symbiotic taxa (e.g., Paraboeremia, Helotiales) under drought conditions. Functional profiling revealed compartment-specific metabolic specialization, with drought enriching stress-response pathways (e.g., secondary metabolite biosynthesis, signal transduction). These findings demonstrate that O. mileensis microbiomes are structured by compartmental filtering and exhibit drought-driven functional plasticity, with conserved stress-adapted taxa potentially supporting host resilience. Overall, this study expands our understanding of microbiome assembly in resurrection plants and highlights candidate microbes for microbiome engineering to enhance crop stress tolerance.},
}

@article {pmid41262927,
year = {2025},
author = {González-Chávez, SA and Alvarado-Jáquez, MF and Salas-Leiva, JS and Mohl, JE and Chaparro-Barrera, E and Prieto-Carrasco, R and Loya-Rivera, M and Pacheco-Silva, C and Pacheco-Tena, C},
title = {Joint Microbiota Suggests Articular Dysbiosis in Experimental Murine Spondyloarthritis and Histological Detection of Bacteria in Human SpA Joints.},
journal = {International journal of inflammation},
volume = {2025},
number = {},
pages = {9982583},
pmid = {41262927},
issn = {2090-8040},
abstract = {BACKGROUND: Recent studies have provided evidence supporting the presence of a commensal joint microbiome; however, its role in the pathogenesis of spondyloarthritis (SpA) remains unclear. This study aimed to characterize the joint microbiome and assess its role in bacterial dissemination and systemic involvement.

METHODS: DBA/1 mice with spontaneous arthritis (SpAD) and healthy BALB/c mice, as well as biopsies from SpA patients, were analyzed by histology (Gram staining and IHC), short-read next-generation sequencing of the 16S rRNA gene amplicons, and transcriptomics. Shared bacterial species were evaluated across tissues, including the liver and heart, and the colocalization of bacterial and inflammatory markers was assessed using double indirect immunofluorescence (IIF).

RESULTS: Bacteria were detected in the joints of healthy and SpAD mice, with significantly greater abundance in the latter. Microbiome analysis revealed distinct bacterial communities, with genera, such as Pelomonas and Aerococcus uniquely identified in the joints of SpAD mice, indicating a state of dysbiosis. Several bacterial species, including Prevotella sp., Ruminococcus gnavus, Lactobacillus johnsonii, and Limosilactobacillus reuteri, were detected in both the gut and joints of SpAD mice. Additionally, bacterial DNA from these taxa was also amplified from liver and heart tissues, indicating systemic dissemination. Transcriptomic analysis revealed dysregulated bacterial response pathways in SpAD joints, with an inflammatory profile distinct from that observed in gut tissues. Double IIF confirmed the colocalization of bacterial components with proinflammatory cytokines in joint cells. In human SpA biopsies, Gram staining and IHC also identified bacteria in sacroiliac and tarsal tissues.

CONCLUSIONS: These findings confirm the presence of bacteria in the joints of healthy and SpAD mice, as well as SpA patients. The joint microbiome differs between healthy and diseased mice, contributing to inflammation through dysregulated bacterial responses. Additionally, the identification of shared bacterial species between the gut and joints, as well as their detection in the liver and heart, supports the hypothesis of bacterial dissemination consistent with translocation and systemic involvement.},
}

@article {pmid41262831,
year = {2025},
author = {Murthy D, K and Soman, RJ and Soman, D and Pv, K},
title = {Testing the Immunomodulatory Effects of Probiotic Bacillus coagulans SNZ 1969® in Healthy Adults: A Randomized, Double-Blind, Placebo-Controlled Trial.},
journal = {Cureus},
volume = {17},
number = {10},
pages = {e94845},
pmid = {41262831},
issn = {2168-8184},
abstract = {BACKGROUND: The immune system and the gastrointestinal tract are intricately linked. The intestinal barrier, microbiome, and immune system are in constant communication, shaping immune responses and maintaining homeostasis. Imbalances in the gut microbiome can affect the intestinal barrier and increase susceptibility to infections, along with a decline in immune function (both innate and adaptive immunity). Maintaining optimal immune function is crucial for protecting against infections and supporting overall health, particularly in populations that may be more vulnerable to seasonal respiratory and gastrointestinal infections. Probiotics, particularly spore-forming strains, demonstrate potential for improving natural killer (NK) cell function and mucosal immunity through gut-associated lymphoid tissue interactions. This study evaluated the immunomodulatory effects of Bacillus coagulans SNZ 1969[®] in adults.

METHODS: This randomized, double-blind, placebo-controlled clinical trial enrolled adults aged 60-65 years who were susceptible to seasonal infections. Participants were randomized 1:1 to receive either B. coagulans SNZ 1969[®] (2 billion CFU/day) or placebo for 12 weeks. Primary endpoints included NK cell activity, absolute NK cell count (CD3⁻/CD16⁺/CD56⁺), and immunoglobulin levels (serum IgM, IgG, and IgA and salivary IgA). Secondary outcomes assessed respiratory and gastrointestinal infection incidence, inflammatory markers (C-reactive protein), and safety parameters.

RESULTS: Of 60 enrolled participants, 50 completed the study (25 per group). B. coagulans SNZ 1969[®] significantly enhanced NK cell activity compared to placebo, with a net increase of 42.07% between groups (44.59% versus 2.52% increase from baseline; p = 0.0002). NK cell activity improvements were consistent across both genders in exploratory subgroup analyses (limited by small female n = 7-8 per arm; males: 36.75% versus 2.52%; p = 0.00004; females: 63.64% versus 2.71%; p = 0.01155). Significant improvements were observed in serum IgA (25.00% versus 2.30% change; p = 0.0016) and salivary IgA (27.70% versus 0.60% change; p = 0.0002). No significant changes occurred in absolute NK cell counts, serum IgM, IgG, or C-reactive protein levels. Secondary analyses showed numerical reduction trends in upper respiratory tract infections (20% versus 32%; p = 0.11), gastrointestinal infections (8% versus 28%), and total illness days (23 days versus 35 days), favoring the probiotic group, though statistical significance was not achieved. The probiotic was well-tolerated with no serious adverse events.

CONCLUSIONS:  B. coagulans SNZ 1969[®] supplementation significantly enhanced NK cell activity and mucosal IgA production in adults, suggesting its potential role in strengthening the innate immune defense mechanisms. These findings support the role of B. coagulans SNZ 1969[®] as a safe dietary supplement for augmenting innate cellular immune function and thereby potentially contributing to a reduced trend to infection susceptibility; however, these preliminary findings require more extensive investigation in a larger study population.},
}

@article {pmid41262520,
year = {2026},
author = {Yang, X and Jin, Y and Wu, Y and Zhou, F and Qu, Z and Zhou, Q and He, J and Tao, Y and Zhuang, J and Han, S},
title = {Gut microbiome-metabolome-ionome network spectrum mapping of colorectal cancer.},
journal = {Genes & diseases},
volume = {13},
number = {1},
pages = {101566},
pmid = {41262520},
issn = {2352-3042},
}

@article {pmid41262449,
year = {2025},
author = {Huang, X and Mo, W and Wang, X},
title = {Metabolomics in autoimmune hepatitis: progress and perspectives.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1667391},
pmid = {41262449},
issn = {2296-858X},
abstract = {This review summarizes recent advances in applying metabolomics to autoimmune hepatitis (AIH). AIH is a chronic liver disease characterized by immune-mediated hepatocellular injury, with complex pathogenesis involving genetic, immunological, and environmental factors. Metabolomics, a system-wide approach analyzing small molecule metabolites, offers potential in early diagnosis, prognosis, and therapeutic evaluation of AIH. Current studies identify alterations in amino acid, lipid, carbohydrate, and bile acid metabolism, as well as changes in the gut microbiome and specific metabolite markers that distinguish AIH from other liver diseases. Techniques such as liquid chromatography-mass spectrometry (LC-MS), and bioinformatics facilitate biomarker discovery and enhance understanding of disease mechanisms. Despite challenges such as standardization and data integration, metabolomics holds promise for developing personalized treatment strategies and advancing disease management. Future prospects include combining multi-omics approaches, large-scale cohort studies, and artificial intelligence (AI)-based data analysis to deepen insights into AIH pathology and improve clinical outcomes.},
}

@article {pmid41262252,
year = {2025},
author = {Pang, X and Huang, P and Huang, S and Liu, X},
title = {The gut-lung axis: a new perspective on the impact of atmospheric particulate matter exposure on chronic obstructive pulmonary disease.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1657675},
pmid = {41262252},
issn = {1664-3224},
mesh = {Humans ; *Particulate Matter/adverse effects ; *Pulmonary Disease, Chronic Obstructive/etiology/metabolism/microbiology/immunology ; *Gastrointestinal Microbiome/drug effects/immunology ; *Lung/immunology/metabolism/drug effects ; Oxidative Stress ; Animals ; *Environmental Exposure/adverse effects ; *Air Pollutants/adverse effects ; },
abstract = {Environmental pollution is a serious public health problem closely related to various chronic respiratory diseases, such as chronic obstructive pulmonary disease (COPD), bronchial asthma, and lung malignancies. Atmospheric particulate matter (PM) is an important component of environmental pollution, and its influence on COPD has been shown to be related to inflammation, oxidative stress, immune imbalance, abnormal cell death, and cell aging. A growing body of evidence has shown that an imbalance of the lung and intestinal microbiota, as well as changes in metabolites, is closely related to the occurrence and development of PM-induced COPD. PM exposure damages the respiratory system and alters the structure and activity of the gut microbiome. The metabolites produced by the gut microbiome, in turn, disrupt airway immunity and exacerbate respiratory inflammation. Therefore, the bidirectional influence of PM on the gut-lung axis has attracted widespread attention. This review explores the mechanisms by which PM causes oxidative stress damage to the lungs and intestines, as well as the characteristics of the resultant immune imbalance and changes in the microbiota and metabolite products. It also describes how PM disrupts barrier function through microecological imbalance and how it participates in the progression of COPD via the gut-lung axis. These mechanisms highlight the potential of targeting the microbial flora as a new approach for treating COPD caused by environmental pollution.},
}

Humans
*Particulate Matter/adverse effects
*Pulmonary Disease, Chronic Obstructive/etiology/metabolism/microbiology/immunology
*Gastrointestinal Microbiome/drug effects/immunology
*Lung/immunology/metabolism/drug effects
Oxidative Stress
Animals
*Environmental Exposure/adverse effects
*Air Pollutants/adverse effects

@article {pmid41262070,
year = {2025},
author = {Ganamurali, N and Sabarathinam, S},
title = {Integrative Network Analysis of Antioxidant Nutrients Targeting 7-Ketocholesterol-Induced Lipotoxicity via Sterol Metabolism and Organelle Protection Pathways.},
journal = {Lipids},
volume = {},
number = {},
pages = {},
doi = {10.1002/lipd.70024},
pmid = {41262070},
issn = {1558-9307},
abstract = {7-Ketocholesterol (7-KC), a cytotoxic oxysterol, contributes to atherosclerosis, neurodegeneration, and metabolic disorders by promoting oxidative stress, inflammation, and dysfunction of organelles including mitochondria, peroxisomes, lysosomes, and the endoplasmic reticulum, ultimately leading to cell death. Nutritional biomedicine offers potential strategies to counteract these effects using antioxidant nutrients and probiotics. In this study, genes associated with 7-KC toxicity were retrieved from GeneCards, and targets of quercetin, luteolin, butyrate, Docosahexaenoic Acid (DHA), and vitamin E were predicted using SwissTargetPrediction. Overlapping targets were identified via an interactive Venn tool and analyzed through STRING protein-protein interaction networks, CytoHubba hub ranking, and Gene Ontology (GO)/ClueGO pathway enrichment. Twenty shared genes were identified, with Peroxisome Proliferator-Activated Receptor Gamma (PPARG), AKT Serine/Threonine Kinase 1 (AKT1), Amyloid Precursor Protein (APP), and Matrix Metalloproteinase-9 (MMP9) as key hubs. Enriched processes included sterol metabolism, cholesterol efflux, inflammatory regulation, and organelle protection, indicating multi-target modulation. These findings support that combinatorial nutrient interventions can restore sterol homeostasis, mitigate oxidative stress, and attenuate 7-KC-induced pathologies.},
}

@article {pmid41261931,
year = {2025},
author = {Lindner, N and Leibman-Markus, M and Gupta, R and Anand, G and Marash, I and Dolgov, T and Kleiman, M and Bar, M},
title = {Leaf Developmental Stage Influences Disease Resistance in Tomato.},
journal = {Molecular plant pathology},
volume = {26},
number = {11},
pages = {e70162},
doi = {10.1111/mpp.70162},
pmid = {41261931},
issn = {1364-3703},
support = {1759/20//Israel Science Foundation/ ; },
mesh = {*Plant Leaves/growth & development/microbiology/immunology/metabolism ; *Solanum lycopersicum/microbiology/growth & development/immunology/metabolism ; *Disease Resistance/physiology ; *Plant Diseases/microbiology/immunology ; Cyclopentanes/metabolism ; Oxylipins/metabolism ; Salicylic Acid/metabolism ; },
abstract = {The processes of morphogenesis and differentiation are crucial for leaf development, with the duration of the morphogenetic window influencing final leaf shape. Leaves at different developmental stages exhibit distinct morphological and physiological characteristics that may influence their ability to resist pathogens, and disease resistance has been linked to developmental stage in many plant species. To understand how leaf development impacts disease resistance, we examined the immunity of leaves at distinct developmental stages, exploring the role of hormonal pathways and the impact of leaf structure and microbial interactions on disease resistance. Our findings reveal that leaves of different developmental stages exhibit distinct disease responses to various pathogens, determined primarily by the ratio between salicylic acid and jasmonic acid. Higher relative jasmonic acid content in later developing leaves was found to result in increased disease resistance to necrotrophs, while higher relative salicylic acid content in earlier developing leaves rendered them more resistant to biotrophs. This phenomenon occurred across plant ages, in several species, and also impacted the plants' response to biocontrol agents, depending on the pathway being primed. We found that structural variations among leaves can also affect disease response, due to differential recognition by the invading pathogen, and possibly also due to alterations in the leaf microbiome. Our results uncover some of the factors influencing developmental immunity in tomato, and highlight the importance of considering plant development when managing disease resistance.},
}

*Plant Leaves/growth & development/microbiology/immunology/metabolism
*Solanum lycopersicum/microbiology/growth & development/immunology/metabolism
*Disease Resistance/physiology
*Plant Diseases/microbiology/immunology
Cyclopentanes/metabolism
Oxylipins/metabolism
Salicylic Acid/metabolism

@article {pmid41261800,
year = {2025},
author = {},
title = {Yuting Liang.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70754},
pmid = {41261800},
issn = {1469-8137},
}

@article {pmid41261325,
year = {2025},
author = {Miková, E and Krčmářová, E and Černý, V and Sklenářová, L and Avramová, P and Protivová, E and Slunéčková, B and Akhtar, M and Věcek, J and Procházka, J and Kubik-Zahorodna, A and Petrásková, P and Novotná, O and Pelantová, H and Kuzma, M and Schabussova, I and Hrdý, J},
title = {The Ability of Probiotic Strain Escherichia coli O83:K24:H31 to Modulate Gut Homeostasis and Immune Function After Antibiotic-Induced Dysbiosis.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41261325},
issn = {1867-1314},
support = {6121//GAUK/ ; CZ.02.01.01/00/22_010/0008115//MSCA fellowship CZ/ ; CZ 04/2024 and CZ 07/2023//OeAD-GmbH/ ; IMMU207032//Cooperatio/ ; },
abstract = {A healthy microbiome and a homeostatic interaction between the microbiome and the host immune system are essential for proper nutrition and overall health. Excessive use of antibiotics (ATB) can disrupt the healthy gut microenvironment, leading to dysbiosis, a condition linked to a wide range of disorders and diseases. Alterations in the composition and function of the microbiota have been associated with a broad spectrum of pathological conditions. In this work, we investigated the effect of ATB administration on microbiota composition and immune modulation, with a particular focus on neutrophil dynamics. We evaluated the capacity of the probiotic strain Escherichia coli O83:K24:H31 (EcO83) to mitigate ATB-induced dysbiosis and restore immune function. As expected, ATB treatment reduced microbiota diversity, which was partially restored by EcO83 supplementation. Furthermore, ATB administration affected the expression of tight junction proteins in the small intestine, an effect reversed by EcO83 treatment. Notably, our data indicate that ATB-induced dysbiosis accelerates neutrophil aging and reduces the release of neutrophils from the bone marrow. EcO83 supplementation counteracts these effects by promoting the influx of newly generated neutrophils into circulation. Overall, our findings confirm that ATB treatment disrupts gut microbiota homeostasis, adversely affecting immune function, including neutrophil turnover. However, probiotic supplementation with EcO83 can at least partially restore microbiome composition and immune homeostasis, highlighting its potential therapeutic application in mitigating ATB-induced dysbiosis.},
}

@article {pmid41261182,
year = {2025},
author = {Prusty, G and Prasad, BR and Polaki, S and Mereddy, S},
title = {Integrative multi-omics characterization of the gut microbiome in Pila globosa: functional insights into nutrient cycling and detoxification potential.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {12},
pages = {464},
pmid = {41261182},
issn = {1573-0972},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenomics/methods ; Proteomics/methods ; *Snails/microbiology ; Phylogeny ; Metagenome ; Multiomics ; },
abstract = {Pila globosa, a freshwater snail endemic to Indian aquatic ecosystems, plays a pivotal role in nutrient cycling and organic matter turnover. In this study, we present the first integrative multi-omics characterization of its gut microbiome using shotgun metagenomics, metaproteomics, and genome-resolved analyses. The gut microbiota was taxonomically diverse yet compositionally stable, dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with core genera including Pseudomonas, Clostridium, Bacillus, and Streptomyces. Alpha diversity metrics (Shannon = 4.22 ± 0.15; Simpson = 0.90 ± 0.01) and low Bray-Curtis dissimilarity (0.12-0.15) indicated a conserved core microbiome across replicates. Functional profiling through HUMAnN2 and metaproteomic validation revealed enrichment of pathways related to carbohydrate metabolism, short-chain fatty acid (SCFA) synthesis, amino-acid biosynthesis, and oxidative phosphorylation, reflecting the community's contribution to host nutrition and metabolic balance. Genes and proteins associated with xenobiotic degradation (benzoate, toluene metabolism) and oxidative stress response (superoxide dismutase, catalase, glutathione S-transferase) were abundant, suggesting microbial support for redox regulation and detoxification. Twelve high-quality metagenome-assembled genomes (MAGs) reconstructed from dominant taxa encoded traits for secondary metabolite production, metal resistance, and stress tolerance, underscoring their ecological versatility. Together, these results establish a foundational reference for understanding the functional potential of the P. globosa gut microbiome and its possible role in nutrient transformation and pollutant processing in freshwater systems. The study provides baseline data for future comparative and ecotoxicological investigations of gastropod holobionts.},
}

*Gastrointestinal Microbiome/genetics
Animals
*Bacteria/classification/genetics/metabolism/isolation & purification
Metagenomics/methods
Proteomics/methods
*Snails/microbiology
Phylogeny
Metagenome
Multiomics

@article {pmid41260935,
year = {2025},
author = {Peláez-Vico, MÁ and Rillig, MC and Mittler, R},
title = {Plant-to-plant signaling: building networks for resilience to stress, or merely eavesdropping?.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2025.10.021},
pmid = {41260935},
issn = {1878-4372},
abstract = {The overall function of an ecosystem is determined by the richness of its biodiversity and the complex interactions formed between the different species that inhabit it. Understanding how global change factors (including climate change), and their combinations, are affecting the intricate species-to-species relationships formed within different ecosystems and agro-ecosystems is becoming therefore increasingly important to our future. Here, we discuss how improved plant-to-plant and plant-to-microbiome signaling, achieved via research, intervention, and altered practices, can be used to form resilient plant communities that will help us shape our environment and successfully address some of our current and future anthropogenically generated critical challenges.},
}

@article {pmid41260765,
year = {2026},
author = {Rojanasopondist, P and Kaz, A and Yu, M and Grady, WM},
title = {Emerging Biomarkers for Managing Barrett's Esophagus.},
journal = {Gastrointestinal endoscopy clinics of North America},
volume = {36},
number = {1},
pages = {149-170},
doi = {10.1016/j.giec.2025.05.005},
pmid = {41260765},
issn = {1558-1950},
mesh = {Humans ; *Barrett Esophagus/genetics/metabolism/diagnosis/pathology/therapy ; *Adenocarcinoma/genetics/metabolism/diagnosis ; *Esophageal Neoplasms/genetics/diagnosis/metabolism ; *Biomarkers, Tumor/metabolism/genetics ; DNA Methylation ; Biomarkers ; MicroRNAs ; },
abstract = {Comparative analyses of normal esophageal tissue, Barrett's Esophagus (BE), and esophageal adenocarcinoma have identified distinctive molecular alterations in genomic DNA, epigenetics, non-coding RNA, and proteins that have shown promise as disease-specific biomarkers. Some of the best characterized and promising biomarkers for managing BE are multi-target esophageal cytology DNA assays based on methylated-DNA and immunohistochemical staining of Trefoil factor 3. Additional biomarkers including microRNA, measures of genomic instability, mixed-method panels, and other novel biomarkers (e.g. volatile organic compounds and saliva microbiome) remain in early development and will need further validation in large, prospective studies prior to clinical use.},
}

Humans
*Barrett Esophagus/genetics/metabolism/diagnosis/pathology/therapy
*Adenocarcinoma/genetics/metabolism/diagnosis
*Esophageal Neoplasms/genetics/diagnosis/metabolism
*Biomarkers, Tumor/metabolism/genetics
DNA Methylation
Biomarkers
MicroRNAs

@article {pmid41260570,
year = {2025},
author = {Deb, S and Zhang, Y and An, Y and Xia, Y and Sun, J},
title = {Loss of intestinal endosome associated protein sorting nexin 27 disrupts epithelial barrier and promotes inflammation.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {},
number = {},
pages = {101682},
doi = {10.1016/j.jcmgh.2025.101682},
pmid = {41260570},
issn = {2352-345X},
abstract = {BACKGROUNDS AND AIMS: SNX27, member of the sorting nexin (SNX) family, carries a unique PDZ domain and mediates recycling of endocytosed transmembrane proteins. SNX27 is critical for neurodevelopmental processes, however its role in intestine remains unexplored. We aim to determine the previously unknown roles of SNX27 in regulating intestinal homeostasis, epithelial barrier integrity, and inflammatory responses.

METHODS: We used available NCBI GEO and Single Cell RNA Sequencing datasets to analyze SNX27 expression in human IBD. We generated a novel mouse model of SNX27 conditional deletion from intestinal epithelial cells (SNX27[ΔIEC]) and challenged these mice with Dextran Sulfate Sodium (DSS).

RESULTS: SNX27 expression was significantly lower in human IBD, including UC and CD. SNX27[ΔIEC] mice had significantly lower bodyweight and exhibited increased proliferation and poor differentiation of secretory Paneth and Goblet cells. We found reduced mucin layer and downregulation of crucial epithelial barrier proteins β-catenin, E-cadherin, ZO-1, ZO-2, and Claudin10 in SNX27[ΔIEC] mice. SNX27[ΔIEC] mice showed high intestinal permeability and spontaneously developed intestinal inflammation. Moreover, SNX27[ΔIEC] mice were more susceptible towards DSS-induced colitis, compared to the SNX27[Loxp] mice.

CONCLUSION: Overall, deletion of intestinal epithelial SNX27 weakens barrier functions and promotes inflammation. Our results indicate a novel role of SNX27 in regulating intestinal physiology and protecting against intestinal disorders. Thus, understanding the mechanisms of SNX27 downregulation in IBD will provide insights into new prevention and targets against chronic inflammation.},
}

@article {pmid41260531,
year = {2025},
author = {Siracusano, M and Arturi, L and Riccioni, A and Medoro, A and Savino, R and Scapagnini, G and Davinelli, S and Mazzone, L},
title = {Feeding Difficulties, Eating Disorders and Therapeutic Approaches in Autism Spectrum Disorder: An Overview.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {108040},
doi = {10.1016/j.phrs.2025.108040},
pmid = {41260531},
issn = {1096-1186},
abstract = {Feeding problems are highly prevalent in individuals with autism spectrum disorder (ASD) from early developmental stages. Difficulties during the transition to solid foods, limited dietary variety, and reluctance to try new foods since infancy, combined with gastrointestinal disorders, represent significant concerns for both parents and clinicians from diagnostic and, more importantly, therapeutic perspectives. The primary clinical link between atypical eating behaviors and core autistic symptoms lies in aberrant sensory processing and an insistence on sameness, which have important implications for intervention strategies. Additionally, the increased risk of gastrointestinal disorders and altered gut microbiome composition in individuals with ASD constitute another critical factor, opening avenues for novel therapeutic approaches. Therefore, the aim of this review is to summarize the existing literature on therapeutic approaches for feeding problems in ASD, with a focus on evidence-based practices across pharmacological, psychological, and nutritional domains.},
}

@article {pmid41260454,
year = {2025},
author = {Tarique, I and Haider, A and Nawazish, F},
title = {Complementary Therapeutic Actions of Shikonin and Indolepropionic Acid Ameliorate Diabetic Infertility via Distinct Antioxidant and Metabolic Pathways.},
journal = {F&S science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.xfss.2025.11.001},
pmid = {41260454},
issn = {2666-335X},
abstract = {OBJECTIVE: To evaluate the effect of Shikonin, a potent direct ROS scavenger, and Indolepropionic acid (IPA), a microbiome-derived metabolite, on epididymis and sperm morphology and function in diabetic rats.

DESIGN: A rat model of Type 2 diabetes mellitus (T2DM) was induced in male Wistar rats using a high-fat diet and streptozotocin (50 mg/kg). The animals were subsequently divided into seven groups: Control, T2DM, T2DM + IPA (50 mg/kg), T2DM + Shikonin (0.5 mg/kg), T2DM + Metformin (50 mg/kg), IPA-only, and Shikonin-only. Treatments were administered orally for four weeks. We assessed histological integrity, sperm motility and viability (via CASA), serum lipid profiles, epididymal antioxidant activity (SOD, MDA, catalase), and apoptotic marker (cytochrome C, caspase-9, caspase-3) and metabolic signature (FGF21) expression via qRT-PCR.

SETTING: University ANIMAL(S): Male Wistar albino rats (n = 42, Age: 8-12 weeks old, 200 ± 2.4 g) INTERVENTION(S): Streptozotocin, Shikonin, Indolepropionic Acid MAIN OUTCOME MEASURE(S): T2DM profoundly impairs male fertility, with oxidative stress in the epididymis being a key driver of sperm damage.

RESULT(S): Streptozotocin-induced diabetic rats exhibited increased oxidative damage, characterized by an impaired antioxidant system, high expression of apoptotic markers, and reduced metabolic gene expression. These effects ultimately damaged epididymis tissue and resulted in poor sperm quality. Shikonin and Indolepropionic Acid treatments significantly attenuated oxidative stress and apoptosis, restored antioxidant activity and lipid profiles, and improved sperm parameters. Both treatments enhanced metabolic balance, as indicated by improved FGF-21 expression, and restored epididymal histoarchitecture. Shikonin was superior in improving the epididymal somatic index and sperm motility, whereas IPA was more effective in normalizing FGF21 expression and lipid profiles, highlighting its primary metabolic role.

CONCLUSION(S): Our findings reveal that Shikonin and IPA protect against diabetic reproductive damage through complementary pathways. This work not only introduces promising natural therapeutic strategies but also provides a mechanistic framework for their combined or targeted use in managing diabetic infertility.},
}

@article {pmid41260449,
year = {2025},
author = {Chen, YF and Fan, CS and Hung, YC and Chien, PJ and Tsai, WH and Yeh, YT and Jhong, JH and Hsieh, YN and Huang, YH and Jan, MS and Chang, CF and Yang, CY and Chang, WW},
title = {Heat-killed Lacticaseibacillus paracasei GMNL-346 exerts anti-oral cancer effect by suppressing cancer stem cell activity and rebalancing gut microbiota dysbiosis.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {149033},
doi = {10.1016/j.ijbiomac.2025.149033},
pmid = {41260449},
issn = {1879-0003},
abstract = {Oral squamous cell carcinoma (OSCC) presents a major therapeutic challenge, necessitating novel treatments. This study investigated heat-killed Lacticaseibacillus paracasei GMNL-346 as a potential therapeutic agent for OSCC, targeting tumor progression and gut microbiota dysbiosis. In OSCC cell lines, GMNL-346 selectively inhibited proliferation by disrupting the cell cycle and suppressing cancer stemness proteins, while sparing normal gingival epithelial cells. In OSCC xenograft mouse models, the treatment enhanced survival rates and reversed tumor-induced gut microbiota dysbiosis, increasing beneficial metabolites such as propionic and isobutyric acids, which are associated with reduced OSCC progression. Whole-genome sequencing identified a heat-stable antimicrobial peptide that replicated GMNL-346's ability to suppress OSCC cell proliferation and cancer stemness protein expression. These findings suggest that heat-killed L. paracasei GMNL-346 may represent a promising and safe therapeutic candidate for OSCC, potentially acting through direct tumor suppression and microbiota modulation, which supports further exploration of its role in microbiome-based cancer therapy.},
}

@article {pmid41260222,
year = {2025},
author = {Wang, Y and Wu, J and Yao, J and Chen, J and Cheng, KKY and Ho, MY and Lee, CH and Lam, KS and Tse, MA and Panagiotou, G and Xu, A},
title = {Gut microbiome-adipose crosstalk modulates soluble IL-6 receptor influencing exercise responsiveness in glycemic control and insulin sensitivity.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2025.10.013},
pmid = {41260222},
issn = {1932-7420},
abstract = {Exercise is an effective intervention for the prevention and management of diabetes, but the high interpersonal variability in response to exercise impedes its widespread implementation. Herein, we identify adipocyte-derived soluble interleukin-6 receptor (sIL-6R) as a key exerkine determining exercise efficacy in improving metabolic health. In individuals with obesity who underwent a 12-week exercise intervention, circulating sIL-6R level exhibits dichotomous changes between exercise responders (Rs) and non-responders (NRs), in close association with exercise-mediated alterations in insulin sensitivity and glycemic control. Mechanistically, elevated gut microbiome-mediated leucine in NR acts on white adipocytes to promote disintegrin and metalloproteinase 17 (ADAM17)-mediated sIL-6R production via the mammalian target of rapamycin (mTOR)-hypoxia-inducible factor 1α (HIF1α) pathway, which in turn impairs the metabolic benefits of exercise through interleukin (IL)-6 trans-signaling-induced adipose inflammation. Adipocyte-selective ablation of ADAM17 prevents the effects of fecal microbiota transplantation from NR on elevation of sIL-6R, thereby restoring the efficacy of exercise-shaped gut microbiome in counteracting glucose intolerance and insulin resistance in obese mice. Thus, therapeutic interventions targeting adipocyte-derived sIL-6R represent a promising strategy for maximizing exercise efficacy in personalized diabetes prevention.},
}

@article {pmid41260126,
year = {2025},
author = {Sójka, O and van der Mei, HC and van Veelen, HPJ and van Rijn, P and Gagliano, MC},
title = {Investigating the role of physicochemical surface properties of polymeric pipe materials and a nanogel-based coating on microbial adhesion in unchlorinated drinking water.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124941},
doi = {10.1016/j.watres.2025.124941},
pmid = {41260126},
issn = {1879-2448},
abstract = {Past research focused on the effect that different polymeric pipe materials have on biofilm formation in drinking water distribution systems (DWDS), to determine the best one to deliver safe drinking water to customers. However, results are often contradictory. Here, we studied the influence of five polymeric pipe materials and a surface modification with the anti-adhesive poly(N-isopropylmethacrylamide)-based nanogel coating on early-stage biofilms formation in unchlorinated drinking water in simulated DWDS conditions. Coupons made from two high-density polyethylene (HDPE-1 and HDPE-2), two unplasticized polyvinyl chloride (PVC-1 and PVC-2), and a molecularly oriented polyvinyl chloride (PVCO) were characterized in terms of surface topography, roughness, chemistry, and hydrophilicity. Biofilms were grown from real drinking water on the selected materials in a flow-chamber setup simulating DWDS conditions, with and without nutrient supplementation. Biofilm growth for 72 h with nutrient addition led to the same extensive biofilm formation on all surfaces. Without nutrients supplementation, 35-days experiments showed significant biofilm development on HDPE-1 only, despite comparable surface properties and chemistry to HDPE-2, and smoother and more homogeneous topography than PVCs. Application of the nanogel coating on HDPE-1 resulted in an average reduction of 87 % in biofilm development regardless under which condition. Microbial community analysis of biofilms by means of 16S rRNA gene sequencing showed a common core microbiome on all included materials in both nutrient-rich and oligotrophic conditions, with a high variability even within duplicates of the same material. Presented findings in combination with multiple studies available in the literature suggest that no conclusion can be made of whether PVC or PE is ultimately better in preventing biofilm formation in DWDS, because it is mainly due to the manufacturer. The suggested application of a surface modification with the anti-adhesive nanogel coating could uniform materials behaviour, acting as a localized biofilm control strategy for DWDS sections (hotspots) especially prone to biofilm development.},
}

@article {pmid41260114,
year = {2025},
author = {Ahmad, W and Ray, R and Khan, AL},
title = {Can silicate types regulate plant defense and rhizospheric microbiome diversity differently during heat stress conditions?.},
journal = {The Science of the total environment},
volume = {1007},
number = {},
pages = {180812},
doi = {10.1016/j.scitotenv.2025.180812},
pmid = {41260114},
issn = {1879-1026},
abstract = {Silicates (Si) improve plant growth; however, how different types of silicate sources influence plant growth and rhizosphere microbiome remains underexplored. We compare two Si types (pure and bioavailable silicic acid (Si) and mineral magnesium silicate (MgSi)) applied to the soybean (Glycine max L.) rhizosphere to determine whether two silicate types (Si-types) differently impact plant growth, defense responses, and microbiome diversity and function during heat stress. Under heat stress, Si-type treatments improved biomass (86 % with Si and 82 % with MgSi), reduced H2O2 (26 % phyllosphere; 33 % rhizosphere), and enhanced β-glucosidase activity (2.6-fold rhizosphere) compared to heat-only treatment and increased Proteobacteria relative abundance from ∼65 % (heat-only) to ∼74 % in Si-type-treated rhizospheric soil. Si-types showed downregulation of heat shock transcription factors, suggesting regulatory defense effects during heat stress. Metagenome-assembled genomes (MAGs) analysis revealed significant bacterial shifts across the Si-treatments, with Proteobacteria and Bacteroidetes being the dominant phyla in the rhizospheric soil. Under heat stress, the core microbiome comprised 14 rhizosphere genera (including Pelomonas, Achromobacter, Paracoccus, Nocardioides), whereas Pelomonas was the sole core root genus, and Pelomonas puraquae core species in both compartments. MAGs analysis revealed Si-based shifts in microbial metabolic pathways and enrichment of auxin biosynthesis in Si-treated roots during heat stress. Because MgSi supplies both Mg and Si, effects observed with MgSi are interpreted as combined Si + Mg effects. In conclusion, both Si-types caused shifts in microbiome diversity and function, and impacted plant growth and defense responses under heat stress, providing a foundation for improving thermotolerance in plants.},
}

@article {pmid41256388,
year = {2025},
author = {King, AC and Seiler, K and Swanson, K and Ciorba, MA and Alvarado, DM},
title = {IBD risk locus rs1077773 is a pharmacogenomic eQTL for aryl hydrocarbon receptor activity and modulates immune cell function.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41256388},
issn = {2692-8205},
abstract = {INTRODUCTION: The inflammatory bowel diseases (IBD) Crohn's disease (CD) and ulcerative colitis (UC) are disorders that cause chronic inflammation of the gastrointestinal tract. Both genetic and environmental factors contribute to the pathogenesis of IBD. There are currently >200 known genetic susceptibility loci for the development of IBD. The physiological impact of the majority of these loci remain a gap in our knowledge. One such locus is the single nucleotide polymorphism rs1077773, located ~56kbp downstream from the aryl hydrocarbon receptor (AHR) gene. AHR is a ligand-activated transcription factor that is crucial to maintaining intestinal homeostasis. We hypothesized that rs1077773 enhances AHR activity to regulate mucosal immune response and maintain intestinal homeostasis.

METHODS: All study procedures and reagents were approved by the Washington University Institutional Review Board (#202011003). Patient biopsies were collected at Barnes Jewish Hospital and genotyped using the IBD Genetics Consortium custom GSA SNP chip (Broad Institute) followed by imputation using TopMed Imputation Server at University of Michigan. Patient derived organoids (PDOs; N=3 G/G, N=4 G/A, N=5 A/A) were derived and maintained in 3D culture and supplemented with 50% L-WRN conditioned medium with passage every 3-4 days as previously described. PDOs were treated with AHR agonist 6-Formylindolo[3,2-b]carbazole (FICZ) or vehicle for 48h. Expression of AHR and its transcriptional targets Cytochrome P450 1A1 (CYP1A1) and CYP1B1 was assessed by RT-qPCR. Blood was collected from pediatric patients undergoing intestinal resection at St. Louis Children's Hospital and was genotyped with custom TaqMan SNP assay (N=3 G/G, N=5 G/A). Peripheral blood monocyte-derived macrophages (MDMϕs) were treated with lipopolysaccharide in the presence or absence of AHR ligands FICZ or indole-3-carboxaldehyde for 24h. Cytokine levels in culture supernatant were measured via using the ProcartaPlex human cytokine, chemokine, and growth factor 45-plex (ThermoFisher) on a Luminex FLEXMAP3D instrument.

RESULTS: AHR expression was similar across genotypes and treatments. PDOs homozygous for rs1077773 demonstrate enhanced CYP1A1 expression in response to AHR activation. In PBMϕs, cytokine secretion was stimulated by LPS treatment and was abrogated by FICZ treatment. PBMϕs with rs1077773 alternate allele demonstrated significant reduction in secretion of 17 cytokines and chemokines.

CONCLUSIONS: This work demonstrates that rs1077773 is an expression quantitative trait locus (eQTL) for AHR activity and modulates epithelial and immune cell function in vitro. Further mechanistic understanding of this locus and its correlates could improve our understanding of the molecular mechanisms of IBD susceptibility and may lead to novel personalized therapeutic approaches in IBD.},
}

@article {pmid41260033,
year = {2025},
author = {Zhang, Q and Zhang, S and Cao, X and Zhi, Y and Guo, Y},
title = {The gut microbiota in post-stroke depression: A systematic review of microbial mechanisms and therapeutic targeting of neuroinflammation.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128391},
doi = {10.1016/j.micres.2025.128391},
pmid = {41260033},
issn = {1618-0623},
abstract = {Post-stroke depression (PSD), a frequent and debilitating complication after stroke, severely hinders rehabilitation. Emerging evidence underscores the role of neuroinflammation and the gut microbiota in PSD pathogenesis. This review systematically elaborates the mechanisms by which gut dysbiosis contributes to PSD-related neuroinflammation via immune cell regulation (e.g., Treg/Th17 balance), microbial metabolites (e.g., SCFAs, tryptophan derivatives), and neural pathways (vagus nerve, HPA axis). A key focus is the comparative analysis of the gut microbiota in PSD against major depressive disorder (MDD) and Alzheimer's disease (AD), revealing a unique, stroke-induced microbial signature characterized by a loss of protective symbionts and a bloom of pro-inflammatory taxa. We further discuss the translational potential of microbiota-targeted interventions (e.g., probiotics, prebiotics) for PSD. By integrating clinical microbial ecology with mechanistic insights, this review synthesizes evidence suggesting that the gut microbiome may represent a promising diagnostic and therapeutic target for PSD, offering a distinct perspective from previous literature.},
}

@article {pmid41259916,
year = {2025},
author = {Shi, R and Liu, W and Shi, X and Li, X and Ge, Y and Liu, J and Zeb, A and Zhao, Y and Sun, Y and An, J},
title = {Earthworm intestine orchestrates dual host-microbiome detoxification of 6PPD-quinone.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140527},
doi = {10.1016/j.jhazmat.2025.140527},
pmid = {41259916},
issn = {1873-3336},
abstract = {The highly toxic tire-derived compound N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine-quinone (6PPD-Q) poses emerging environmental risks, yet its fate within soil invertebrates remains unclear. Here, we investigate the tissue distribution, elimination kinetics, biotransformation, and detoxification of 6PPD-Q in earthworms. 6PPD-Q showed tissue-specific accumulation, with the highest levels in the lipid-rich intestine (48.30 ± 4.06 ng/g; bioaccumulation factor (BAF) = 0.489 ± 0.156). We identified 17 metabolites generated through classical phase I and II detoxification pathways, mainly mediated by cytochrome P450 (CYP450) enzymes. 6PPD-Q exposure enriched detoxifying microbes (e.g., Paenibacillus and Pseudarthrobacter) and shifted microbial dynamics from deterministic to stochastic processes. Network analysis revealed enhanced microbial connectivity and functional resilience, which correlated strongly with degradation efficiency (p < 0.001). In vitro assays further confirmed microbial transformations yielding unique hydroxylated, acetylated, and methylated products. These findings highlight the intestine as both a reservoir and a bioreactor, emphasizing host-microbiota synergy in 6PPD-Q detoxification and offering new insights into contaminant bioremediation in soil invertebrates.},
}

@article {pmid41259824,
year = {2025},
author = {Fan, X and Wei, Y and Zang, T and Tu, Y and Liu, L and Tian, H and Li, X and Cheng, H and Bai, J and Liu, Y},
title = {Gut feelings: Dysbiosis of gut microbiota and short-chain fatty acids associated with prenatal depression, pregnancy-related anxiety, and prenatal combined depression and anxiety.},
journal = {Psychoneuroendocrinology},
volume = {184},
number = {},
pages = {107686},
doi = {10.1016/j.psyneuen.2025.107686},
pmid = {41259824},
issn = {1873-3360},
abstract = {OBJECTIVES: The role of the gut microbiota and short-chain fatty acids (SCFAs) in psychiatric disorders in pregnant women has not been fully elucidated. Therefore, this study aimed to investigate the association between the gut microbiota and its metabolite SCFAs and prenatal depression, pregnancy-related anxiety, and prenatal combined depression and anxiety.

METHODS: In total 200 pregnant women in the third trimester were recruited for this study. The Edinburgh Postnatal Depression Scale and Pregnancy-Related Anxiety Questionnaire Revised-2 were used to evaluate pregnant women's anxiety and depression, and stool samples were collected for gut microbiome and SCFAs.

RESULTS: This study found that reduced abundance of Allobaculum and Cetobacterium were associated with pregnancy-related anxiety in women. Furthermore, the enrichment of Anaerofustis, Gemella, and Staphylococcus and the reduction of Tyzzerella and unclassified_f_UCG-011 were associated with prenatal depression. This study was the first to indicate that women with comorbid prenatal anxiety and depression share similarities in gut microbiota and SCFAs with women with prenatal depression (Anaerofustis, Gemella, Staphylococcus, Tyzzerella, and isohexanoic acid). This study also found that certain gut microbial profiles were associated with prenatal comorbid anxiety and depression. While receiver operating characteristic analysis suggests a limited ability of the gut microbiota alone to predict prenatal psychological distress problems, the integration of phenotypic variables into the model significantly improved the model's predictive ability.

CONCLUSION: Our findings suggested that dysbiosis of gut microbiota and SCFAs are associated with prenatal psychiatric disorders. Alterations of the gut microbiota may have the potential as biomarkers for distinguishing prenatal psychiatric disorders.},
}

@article {pmid41259688,
year = {2025},
author = {Alizon, S and Tamarelle, J},
title = {[The scientific, health et social significance of the vaginal microbiome].},
journal = {Medecine sciences : M/S},
volume = {41},
number = {10},
pages = {760-769},
doi = {10.1051/medsci/2025139},
pmid = {41259688},
issn = {1958-5381},
mesh = {Humans ; Female ; *Microbiota/physiology ; *Vagina/microbiology/physiology ; Sexually Transmitted Diseases/microbiology/epidemiology ; },
abstract = {The vaginal microbiome is an ideal study system given the diversity of bacteria it harbors, its communities that can be structured into large, stable types, the ease of sampling, and the well-characterized environment. The microbiome is also dynamic and varying according to life stage, biological mechanisms such as hormonal cycles or menstruation, and specific exposures (e.g.; antibiotics, sexual practices). The associations between vaginal microbiota and health are strong, including its role in sexually transmitted infections, fertility, and general well-being. This raises questions about prevention and therapies, while avoiding the risk of excessive pathologization.},
}

Humans
Female
*Microbiota/physiology
*Vagina/microbiology/physiology
Sexually Transmitted Diseases/microbiology/epidemiology

@article {pmid41259558,
year = {2025},
author = {Issilbayeva, A and Jarmukhanov, Z and Kozhakhmetov, S and Bakytgul, Y and Chulenbayeva, L and Muniz-Terrera, G and Furukawa, M and Nikawa, H and Supiyev, A and Kushugulova, A and Zhumadilova, A},
title = {Oral microbiome patterns of dental caries in Kazakhstani adolescents.},
journal = {Journal of applied oral science : revista FOB},
volume = {33},
number = {},
pages = {e20250476},
doi = {10.1590/1678-7757-2025-0476},
pmid = {41259558},
issn = {1678-7765},
mesh = {Humans ; *Dental Caries/microbiology ; Adolescent ; Male ; *Microbiota/genetics ; Female ; Child ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; DMF Index ; Reference Values ; },
abstract = {OBJECTIVE: The oral microbiome is one of the most complex microbial ecosystems in the host. This study aimed to investigate and characterize the oral microbiome composition in Kazakhstani adolescents associated with dental caries.

METHODOLOGY: The study included 312 adolescents, with 241 individuals presenting with caries and 71 caries-free, aged 12-15 years. Dental caries assessment was performed using DMFT (Decayed, missed, filled teeth) index. Oral samples were collected, and 16S rRNA (16S ribosomal ribonucleic acid) gene sequencing targeting the V3-V4 hypervariable regions on an Illumina MiSeq platform was performed to profile the microbial communities. Functional metagenomic predictions were generated using PICRUSt2 v2.5.0, using the KEGG database for bacterial pathway abundance estimation. Data analysis was conducted using Python 3.9.16 and R 4.2.2.

RESULTS: The alpha diversity was insignificant, while beta diversity analysis demonstrated clear distinctions by Bray-Curtis (F=2.5, p=0.003) and weighted UniFrac distances (F=4.4, p=0.002). The Neisseria and Prevotella genera, and Gammaproteobacteria class showed significant associations with dental caries (MaAsLin2 p≤0.05, LDA≥2), stronger predictive power (AUC=0.65, F1=0.83), and higher predicted functional activity through glutathione metabolism, RNA degradation, and unsaturated fatty acid metabolism pathways.

CONCLUSIONS: This study identified specific oral microbiome patterns associated with dental caries in Kazakhstani adolescents, revealing interactions between key bacterial taxa and metabolic pathways.},
}

Humans
*Dental Caries/microbiology
Adolescent
Male
*Microbiota/genetics
Female
Child
RNA, Ribosomal, 16S/genetics
*Mouth/microbiology
DMF Index
Reference Values

@article {pmid41259413,
year = {2025},
author = {Triadafilopoulos, G},
title = {Lessons learned: endoscopy with 96-hour ambulatory esophageal pH monitoring as a tool to avoid proton pump inhibitor use in cancer patients with refractory gastroesophageal reflux.},
journal = {Diseases of the esophagus : official journal of the International Society for Diseases of the Esophagus},
volume = {38},
number = {6},
pages = {},
doi = {10.1093/dote/doaf102},
pmid = {41259413},
issn = {1442-2050},
mesh = {Humans ; *Proton Pump Inhibitors/therapeutic use/adverse effects ; *Gastroesophageal Reflux/drug therapy/etiology/complications/diagnosis ; Male ; Female ; Retrospective Studies ; Middle Aged ; *Esophageal pH Monitoring/methods ; Aged ; *Neoplasms/complications ; *Heartburn/etiology/drug therapy ; *Esophagoscopy/methods ; Adult ; },
abstract = {The proton pump inhibitors (PPIs) are extensively prescribed for the empirical treatment of epigastric pain and heartburn in cancer patients. However, they carry the potential for drug interactions with antineoplastic agents during active cancer therapy, and osteopenia, opportunistic infections, adverse cardiovascular outcomes, and altered gut microbiome in long-term users in survivorship. Herein, we examined the use of endoscopy with esophageal 96-hour ambulatory pH monitoring in guiding clinicians in safely prescribing PPI in 21 such patients. We retrospectively studied patients with active cancer or in survivorship, presenting with PPI-refractory heartburn. All underwent an endoscopy with esophageal ambulatory pH monitoring performed "off" PPI therapy for 96 hours, following a "liberal diet" for the first 48, and a "restrictive diet" for the latter 48 hours. Acid exposure time (AET) ≥ 6% per 24 hours was defined as abnormal. For each patient, the average AET from the first 2 days was considered as baseline and was compared with that from the latter 2 days (on restrictive diet). We concluded that ambulatory 96-hour pH monitoring, identifies 48% of patients with normal AET, who may not need PPI. Esophageal pH monitoring on restrictive diet normalizes AET in 73% of patients, thereby allowing esophageal acid control to be achieved with diet alone.},
}

Humans
*Proton Pump Inhibitors/therapeutic use/adverse effects
*Gastroesophageal Reflux/drug therapy/etiology/complications/diagnosis
Male
Female
Retrospective Studies
Middle Aged
*Esophageal pH Monitoring/methods
Aged
*Neoplasms/complications
*Heartburn/etiology/drug therapy
*Esophagoscopy/methods
Adult

@article {pmid41259398,
year = {2025},
author = {Yadav, A and Ali, R and Devi, P and Kumari, P and Soni, J and Garima, and Tarai, B and Budhiraja, S and Shamim, U and Pandey, R},
title = {Non-canonical Metatranscriptomic analysis of COVID-19 and Dengue reveals an expanded microbial and AMR landscape in COVID-19 mortality patients.},
journal = {PLoS pathogens},
volume = {21},
number = {11},
pages = {e1013703},
doi = {10.1371/journal.ppat.1013703},
pmid = {41259398},
issn = {1553-7374},
mesh = {Humans ; *COVID-19/mortality/microbiology ; *Dengue/microbiology/mortality ; *Microbiota/genetics ; SARS-CoV-2 ; Female ; Male ; Middle Aged ; Transcriptome ; Adult ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Drug Resistance, Bacterial/genetics ; },
abstract = {AMR is a growing concern in viral infections, where microbiome shifts contribute to resistance gene dissemination. While dengue and COVID-19, caused by ssRNA viruses, are not bacterial-driven, their resistome and microbial communities influence disease progression and AMR burden. This study analyzes the resistome and microbiome in 251 COVID-19 and 112 dengue patients using non-canonical metatranscriptomics. By mapping antimicrobial resistance genes (ARGs) and their transcriptionally active microbes (TAMs) hosts, we uncover greater ARG burden in COVID-19, particularly during mortality, with a diverse set of associated TAMs compared to dengue. MDR genes were prevalent, with beta-lactamase ARGs commonly detected in both infections. COVID-19 exhibited higher carbapenemase resistance genes (NDM, OXA, VIM), while dengue was associated with TEM variants. Escherichia coli and Klebsiella pneumoniae were dominant ARG hosts, with Acinetobacter baumannii in COVID-19 mortality and Bacillus cereus in severe dengue. These findings highlight resistome dynamics and emphasize the need for AMR surveillance in high-burden infections.},
}

Humans
*COVID-19/mortality/microbiology
*Dengue/microbiology/mortality
*Microbiota/genetics
SARS-CoV-2
Female
Male
Middle Aged
Transcriptome
Adult
Anti-Bacterial Agents/pharmacology/therapeutic use
*Drug Resistance, Bacterial/genetics

@article {pmid41259328,
year = {2025},
author = {Custodio, R and Alseth, EO and Brockhurst, MA and Brown, SP and Westra, ER},
title = {Bacterial immune systems as causes and consequences of microbiome structure.},
journal = {PLoS biology},
volume = {23},
number = {11},
pages = {e3003489},
doi = {10.1371/journal.pbio.3003489},
pmid = {41259328},
issn = {1545-7885},
mesh = {*Microbiota/immunology/genetics ; *Bacteria/immunology/genetics ; Humans ; Interspersed Repetitive Sequences ; Animals ; },
abstract = {Attacks from molecular parasites such as mobile genetic elements (MGEs) have driven the evolution of defense systems in bacterial genomes. Yet, despite significant advances in understanding the molecular mechanisms of these bacterial immune systems, we have only a rudimentary understanding of their ecology and evolution. Bacteria exist as part of complex microbiomes, but community ecology and microbiome research has yet to characterize the impacts of interactions between MGEs and defense mechanisms upon the structure, dynamics and evolution of microbiomes. This Essay introduces and discusses the interplay between bacterial community dynamics and bacterial immune systems, speculating about how these reciprocal interactions may shape microbial community structure and function.},
}

*Microbiota/immunology/genetics
*Bacteria/immunology/genetics
Humans
Interspersed Repetitive Sequences
Animals

@article {pmid41259124,
year = {2025},
author = {Todt, T and van Bussel, I and Afman, L and Brennan, L and Ivanova, DG and Kiselova-Kaneva, Y and Thomas, EL and Rühl, R},
title = {Transcriptome-driven Health-status Transversal-predictor Analysis for health, food, microbiome and disease markers for understanding of lifestyle diseases.},
journal = {Physiological genomics},
volume = {},
number = {},
pages = {},
doi = {10.1152/physiolgenomics.00026.2025},
pmid = {41259124},
issn = {1531-2267},
support = {EU FP7 nutritech//all except Tilman/ ; },
abstract = {We developed a novel artificial intelligence (AI) approach based on machine-learning to predict general health and food-intake parameters. This approach, named Transcriptome-driven Health-status Transversal-predictor Analysis (THTA) is relevant for markers of diabesity and is based on a non-transcriptomic, mathematics-driven approach. The prediction was based on values derived from food consumption, dietary lipids and their bioactive metabolites, peripheral blood mononuclear cell (PBMC) mRNA-based transcriptome signatures, magnetic resonance imaging (MRI), energy metabolism measurements, microbiome analyses, and baseline clinical parameters, as determined in a cohort of 72 subjects. Our novel machine learning approach incorporated transcriptome data from PBMCs as a "one-method" approach to predict 77 general health-status markers for the broad stratification of the diabesity phenotype. These markers would usually necessitate measurements using 16 different methods. The PBMC transcriptome was used to determine these 77 basic and background health markers with very high accuracy in a transversal-predictor establishment group (Pearson correlations are r = 0.98 ranging from 0.94 to 0.99). These collected variables provide valuable insides into which individual factor(s) are mainly target diabesity. Based on the "establishment group" prediction approach a further "confirmation group" prediction approach was performed, achieving a predictive potential r = 0.59 (ranging from 0.19 to 0.98) for these 77 variables. This "one-method" approach enables the simultaneous monitoring of a large number of health-status variables relevant to diabesity and may facilitate the monitoring of therapeutic and preventive strategies. In summary, this novel technique, which is based on PBMC transcriptomics from human blood, can predict a wide range of health-related markers.},
}

@article {pmid41258884,
year = {2025},
author = {Ni, D and Pinget, G and Santner-Nanan, B and Tan, J and Reyes, JGA and Lai, CL and Wang, Y and Tran, C and Clarke, JM and Macia, L and Campbell, DE and Hsu, P and Nanan, R},
title = {Effects of Butyrylated High Amylose Maize Starch (HAMSB) as an Adjuvant for Oral Immunotherapy.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70161},
pmid = {41258884},
issn = {1398-9995},
support = {//National Health and Medical Research Council/ ; //Norman Ernest Bequest Fund/ ; },
}

@article {pmid41258872,
year = {2025},
author = {Scheelings, TF and Kodikara, S and Beale, DJ and Van, TTH and Moore, RJ and Skerratt, LF},
title = {Unravelling the impacts of captivity on saltwater crocodile (Crocodylus porosus) cloacal bacterial communities and physiology.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf114},
pmid = {41258872},
issn = {1574-6941},
abstract = {This study addresses a significant research gap in understanding the impacts of captivity on the bacteriome and physiology of saltwater crocodiles (Crocodylus porosus). Despite their ecological and cultural significance, crocodilians are a taxon that remains underexplored in microbiome research. We investigated cloacal bacteriome samples from both wild and captive populations to identify compositional and functional differences resulting from captivity. Our findings reveal significant alterations in bacterial diversity and community structure in captive crocodiles, with notable shifts at both phylum and family levels; specifically, Bacteroidota and Fusobacteriota dominate in captivity, whereas wild crocodiles exhibit a higher prevalence of Pseudomonadota and Bacillota. The Shannon diversity index indicates a significant reduction in bacterial diversity among captive individuals, likely due to husbandry practices that foster a microbially depauperate environment. Additionally, serum metabolomics analysis shows an enrichment of alcohol sugars in captive crocodiles, alongside a decrease in pantothenic acid. While this is the first study to characterize these traits in saltwater crocodiles, further research is necessary to determine the physiological consequences of these bacterial and metabolic changes on host fitness and adaptability. Longitudinal studies are essential for understanding how bacterial communities evolve over time and in response to environmental factors, which will inform conservation strategies and improve the management of captive populations of crocodilians intended for reintroduction into the wild.},
}

@article {pmid41258857,
year = {2025},
author = {Wang, M and Hou, H and Sang, W and Li, P and Yang, X and Qi, P and Ma, Y},
title = {Bile Microbiome and Metabolic Characteristics in Primary Common Bile Duct Stone Patients with Juxtapapillary Duodenal Diverticula: A Clinical Investigation.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf280},
pmid = {41258857},
issn = {1365-2672},
abstract = {OBJECTIVE: This study aimed to characterize the bile microbiome and metabolome in patients with common bile duct stones (CBDs), with versus without juxtapapillary duodenal diverticulum (JPDD), to identify potential factors associated with stone formation.

METHODS: From January to May 2024, CBDs patients undergoing endoscopic retrograde cholangiopancreatography at our hospital were prospectively enrolled. Bile samples were collected for 16SrRNA sequencing and LC-MS/MS metabolomics analysis. Patients were divided into JPDD (n = 15) and CBDs (n = 15) groups.

RESULTS: The JPDD group had larger stone and bile duct diameters (P < 0.05). Although Proteobacteria dominated the bile microbiota in both groups, the JPDD group showed higher abundances of Escherichia-Shigella, Enterococcus, and Escherichia coli. Beta diversity differed significantly between groups (P < 0.05), and LEfSe identified 25 differentially abundant bacterial taxa. Enterococcus, Klebsiella, and Gemellaceae were more abundant in the JPDD group, while Peptococcaceae, Roseburia, and Alistipes were more prevalent in the CBDs group. Enterococcaceae and Enterococcus abundances were positively correlated with stone and duct sizes in the JPDD group (P < 0.05), whereas Peptococcaceae and Acinetobacter showed negative correlations. Metabolomic analysis identified ten differentially enriched pathways-including phenylalanine and alanine metabolism-and higher levels of bilirubin glucuronide and taurochenodeoxycholic acid in the JPDD group. Enterococcus abundance was correlated with bile acid metabolites such as chenodeoxycholylasparagine (P < 0.05).

CONCLUSIONS: JPDD is associated with distinct microbial and metabolic profiles in bile. Enrichment of Enterococcus and Klebsiella in the JPDD group, along with changes in metabolic pathways and bile acid metabolites, suggests a potential link to CBD stone formation and growth.},
}

@article {pmid41258716,
year = {2025},
author = {Marsh, CC and Nel Van Zyl, K and Babalola, OO and Böhmer, R and Cowan, DA and Moganedi, KLM and Moroenyane, I and Naidoo, J and Nieves Delgado, A and Posma, JM and Segal, LN and Setati, ME},
title = {From description to implementation: key takeaways from the 3rd African Microbiome Symposium.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0068325},
doi = {10.1128/msphere.00683-25},
pmid = {41258716},
issn = {2379-5042},
abstract = {The 3rd African Microbiome Symposium was held in Cape Town, South Africa, from 20 to 22 November 2024. The symposium featured a diverse range of local and international microbiome research and provided a platform for 79 researchers, students, and industry members to engage in discussions on the microbiome within an African context and focusing on translational research. This meeting review shares highlights, findings, and recommendations derived from the event. Insights from two panel discussions revealed key barriers to microbiome research in Africa, including limited funding, infrastructure gaps, and a shortage of trained local scientists. Recommendations centered on increased investment, institutional training, adherence to ethical guidelines, and the fostering of equitable global partnerships.},
}

@article {pmid41258692,
year = {2025},
author = {Lukacz, ES and McDonald, D and Bryant, M and Putnam, S and Rudser, K and Brennan, C and Meister, M and Fok, CS and Mueller, MG and Knight, R and Brubaker, L and , },
title = {Concordance of Urogenital Microbiome From Sequentially Self-collected Specimens.},
journal = {Urogynecology (Philadelphia, Pa.)},
volume = {31},
number = {11},
pages = {1033-1042},
pmid = {41258692},
issn = {2771-1897},
mesh = {Humans ; Female ; *Microbiota ; Longitudinal Studies ; Middle Aged ; Adult ; RNA, Ribosomal, 16S ; *Specimen Handling/methods ; *Urogenital System/microbiology ; Aged ; },
abstract = {IMPORTANCE: Population-based research is necessary to understand the relationship between the urobiome and bladder health.

OBJECTIVE: Using advanced contamination controls and ecological metrics, we aimed to evaluate the concordance of microbiota in self-collected urogenital specimens from home versus a clinical research setting.

STUDY DESIGN: A subset of community-dwelling women was enrolled in a longitudinal cohort study, self-collected urogenital samples at 3 time points: 1-day prior, the day of and during an in-person evaluation. Samples were sequenced with V4 16S rRNA and KatharoSeq removed samples indistinguishable from background contamination. Data were matched to Greengenes2-2022.10 and rarefied to 1000 seqs/sample. Intersample concordance pairs above the KatharoSeq threshold were assessed between samples. Unweighted UniFrac distances, Mantel Pearson correlations, Kruskal-Wallis, and chi-square tests were used for comparisons.

RESULTS: Detectable sequences were obtained in 261 samples from the 114 participants with 186 (71%) above the KatharoSeq threshold. Escherichia_710834, Lactobacillus, and Prevotella were most prevalent. Intersample concordance was determined for samples above the threshold from 38 participants with 2 home samples and 47 with home and clinic samples. Correlations between 2 home and between home and clinic were significant (r = 0.43, P = 0.001; r = 0.362, P = 0.001, respectively). There were no significant differences across time points (X2 = 2.72, P = 0.256).

CONCLUSIONS: Home-collected urine samples for urogenital microbiome ecological analysis have sufficient short-term similarity and concordance with self-collected urine samples from a research clinic setting for use in population-based research, which may facilitate inclusion of participants with limited access to clinic-based research.},
}

Humans
Female
*Microbiota
Longitudinal Studies
Middle Aged
Adult
RNA, Ribosomal, 16S
*Specimen Handling/methods
*Urogenital System/microbiology
Aged

@article {pmid41258538,
year = {2025},
author = {Brubaker, L and Horsley, H and Khasriya, R and Wolfe, AJ},
title = {Microbiologist in the Clinic: Pregnant Microbiologist with Asymptomatic Bacteriuria.},
journal = {International urogynecology journal},
volume = {},
number = {},
pages = {},
pmid = {41258538},
issn = {1433-3023},
abstract = {In this fourth episode of the Microbiologist in the Clinic series, clinicians and laboratory scientists share their perspectives about a 26-year-old microbiologist G1P0 who is 20 weeks pregnant. She is questioning her obstetrician's recommendation to take systemic antibiotics for a positive urine culture obtained, as her research work focuses on the effect of antibiotics on young children. She hopes to avoid exposing her child to systemic antibiotics if possible.},
}

@article {pmid41258495,
year = {2025},
author = {Gutiérrez-Sarmiento, W and Fosado-Mendoza, M and Lozano-Flores, C and Varela-Echavarría, A},
title = {The Body Wall Microbiome of the Terrestrial Slug Deroceras laeve Reveals Potential Endosymbionts and Shares Core Organisms with Other Mollusks.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02652-8},
pmid = {41258495},
issn = {1432-184X},
support = {CBF2023-2024-834//SECIHTI/ ; IN211322//DGAPA-UNAM PAPIIT/ ; },
abstract = {The marsh slug Deroceras laeve is an invasive mollusk found in gardens, field crops, and wetlands. It lacks a protective shell, suggesting that microbial communities are associated with its adaptability to the environment. Here, we used a whole shotgun metagenomic approach to analyse the complex microbiome of D. laeve and compared it to that of other mollusks. This demonstrated the presence in D. laeve of bacteriophages such as Erwinia phage, Certrevirus, and Machinavirus, which target plant pathogen bacteria. In the Archaea domain the halophilics Halovivax and Halobaculum predominated, but also present were the methanogens Methanobacterium, Methanobrevibacter, Methanocaldococcus, Methanococcus, and Methanosarcina, involved in phosphate solubilization and methanogenesis during decomposition of organic matter. The Bacteria domain was dominated by γ-Pseudomonadota such as Buttiauxella, Citrobacter, Enterobacter, Klebsiella, Kluyvera, Leclercia, and Pseudomonas which are producers of enzymes that degrade biomass and complex carbohydrates. Regarding the fungal community, filamentous or yeast ascomycetes predominated such as Debaryomyces, Puccina, and Pyricularia known as plant pathogens or associated with decaying organic matter. Consistent with these findings, functional analysis revealed enrichment in genes involved in fermentation and carbohydrate metabolism. Remarkably, regardless of species, ecosystem, and tissue type, we found that the core microbiome of the mollusks in this study is mainly structured by the Phyla Uroviricota, Euryarchaeaota, Pseudomonadota, and Ascomycota, with diversity at the genus level. This suggests ancient symbiotic interactions of these mollusks with specific types of microbes which may have been critical for adaptability to their environment.},
}

@article {pmid41258493,
year = {2025},
author = {Xu, Q and Lin, A and Jiang, A and Chen, L and Zhu, L and Mou, W and Liu, Z and Zhang, J and Cheng, Q and Miao, K and Luo, P},
title = {Circadian rhythms as a modulator of gut microbiota-tumor microenvironment crosstalk.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {82},
number = {1},
pages = {409},
pmid = {41258493},
issn = {1420-9071},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Circadian Rhythm/physiology ; *Tumor Microenvironment ; Animals ; *Neoplasms/microbiology/pathology/therapy ; Dysbiosis/microbiology ; },
abstract = {Circadian rhythms play a pivotal role in regulating diverse physiological functions, notably the composition and activity of gut microbiota. Accumulating evidence indicates that circadian rhythm disruption can induce dysbiosis of the gut microbiome, which in turn is implicated in influencing the tumor microenvironment (TME) and facilitating cancer progression. This review integrates and analyzes recent advances elucidating the complex interplay where circadian rhythms modulate gut microbiota, and how these circadian-driven microbial changes affect the TME. This review analyzes recent advances in elucidating the complex interplay among circadian rhythms, gut microbiota, and the TME. We examine how circadian disruption modifies the diversity and metabolic functions of gut microbiota, resulting in alterations of microbial metabolites, including but not limited to short-chain fatty acids and secondary bile acids. These metabolic alterations have the potential to modulate immune cell function, vascular remodeling, and tumor cell metabolism within the TME. We investigate the potential mechanisms through which gut microbial dysbiosis induced by circadian misalignment could promote an immunosuppressive TME and accelerate tumor growth. Additionally, we evaluate emerging therapeutic strategies that leverage the circadian-microbiome axis, encompassing chronotherapy, probiotic supplementation, and fecal microbiota transplantation. The integration of circadian biology, microbiology, and cancer immunology presents promising avenues for the development of novel diagnostic and therapeutic approaches. However, significant challenges persist in translating these findings into viable clinical applications. Further research is imperative to elucidate the molecular pathways interconnecting circadian rhythms, gut microbiota, and the TME, and to develop personalized chronobiological interventions for cancer prevention and treatment.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Circadian Rhythm/physiology
*Tumor Microenvironment
Animals
*Neoplasms/microbiology/pathology/therapy
Dysbiosis/microbiology

@article {pmid41258378,
year = {2025},
author = {Liu, L and Wang, H and Minichino, A and Xiao, R and Du, Y and Wang, L and He, D and Guo, S and Mo, X and Xiang, Y and Wu, J and McGuire, P and Yue, W and Lu, L and Cipriani, A and Xie, P},
title = {Mapping the reciprocal interactions between antidepressants and the gut microbiome: novel targets for the personalisation and optimization of drug response.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {41258378},
issn = {1476-5578},
support = {82201683//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82401814//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82288101//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Although accumulating evidence suggests a role of the gut microbiome in the response to antidepressant medications, its mechanistic basis is largely unknown. We performed a comprehensive analysis and presented an up-to-date atlas of the relationship between antidepressants and gut microbiome. The main findings were: 1. Treatment with antidepressants increases the abundance of anti-inflammatory species (e.g., Bifidobacterium) and decreases that of pro-inflammatory species (e.g., Escherichia_coli); 2. The nature of microbiome at baseline and of its changes following the start of treatment can be used to predict the efficacy of individual antidepressants. 3. Two sets of bacterial taxa (termed "Microhancers" and "Microlencers") are candidate pre-treatment targets for optimizing the therapeutic response. Two mechanisms that appear to underlie the modulation of the antidepressant treatment response are biotransformation and bioaccumulation, and these appear to be mediated by specific bacterial strains. These findings could support the personalisation of treatment by informing the selection of the best antidepressant for each individual. In addition, they suggest that the therapeutic response to antidepressants may be optimised by manipulating the gut microbiome prior to treatment.},
}

@article {pmid41258153,
year = {2025},
author = {Cheng, YC and Krieger, M and Korves, AM and Camarinha-Silva, A},
title = {The chicken gut microbiome in conventional and alternative production systems.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {153},
pmid = {41258153},
issn = {1674-9782},
support = {FKZ 2821OE034//Bundesministerium für Ernährung und Landwirtschaft/ ; },
abstract = {The poultry gut microbiome plays a key role in nutrient digestion, immune function, and overall health. Differences among various farming systems, including conventional, antibiotic-free, free-range, and organic systems, influence microbial composition and function through variations in diet, genetic selection, environmental exposure, and antibiotic use. Conventional systems typically rely on formulated diets and controlled housing conditions, often with routine antimicrobial use. In contrast, organic systems emphasize natural feed ingredients, including roughage, outdoor access, and strict limitations on the use of antibiotics. These divergent practices shape the gut microbiota differently, with organic systems generally associated with greater exposure to environmental microbes and, consequently, greater microbial diversity. However, the implications of this increased diversity for poultry health and performance are complex, as organic systems may also carry a higher risk of pathogen exposure. This review summarizes current findings on the chicken gut microbiome across conventional and alternative production systems (antibiotic-free, free-range, and organic), focusing on microbial diversity, functional potential, and disease resilience. The need for standardized methodologies and consistent nomenclature in microbiome research is also discussed to improve comparability across studies. Understanding how production systems influence the gut microbiota is essential for improving poultry health and productivity while addressing challenges related to antimicrobial resistance and sustainable farming practices.},
}

@article {pmid41258106,
year = {2025},
author = {Zhang, Y and Ju, M and Chen, S and Yang, W and Cai, Y and Yu, X and Chen, G and Shen, Z and Bai, Y and Ren, H and Li, Y and Shen, L and Li, J and Shi, P and Yuan, Y and Han, B and Yao, H},
title = {Migration of CD8 + TSCM cells into intestine via PPBP-CXCR2 axis increases host stress susceptibility by inhibiting gut microbiome-derived homovanillic acid.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10165},
pmid = {41258106},
issn = {2041-1723},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *CD8-Positive T-Lymphocytes/immunology/metabolism ; Humans ; Mice ; Male ; Mice, Inbred C57BL ; *Stress, Psychological/immunology/metabolism ; Female ; Cell Movement ; *Memory T Cells/immunology/metabolism ; *Intestines/immunology/microbiology ; Adoptive Transfer ; },
abstract = {Psychosocial stress impacts immune system and brain function, yet mechanisms linking peripheral immune dysregulation to major depressive disorder remain unclear. Here, we demonstrate that a specific subset of T cells, the stem cell-like memory CD8[+] T (TSCM) cells, is elevated in patients and stress-susceptible mice. CD8[+] TSCM cells from patients display unique transcriptional programs and correlated with depression severity. Adoptive transfer of stress-derived CD8[+] TSCM cells induced depressive-like behavior and neuroinflammation in recipients, without brain migration. Employing a whole-body immunolabeling technology, we discover CD8[+] TSCM cells migrated to intestine via the interaction of pro-platelet basic protein and C-X-C motif chemokine receptor 2. CD8[+] TSCM cells decrease the abundance of tyrosine-metabolizing bacteria to reducing homovanillic acid production, triggered neuroinflammation and depressive symptoms. Thus, our findings uncover a complex interplay between CD8[+] TSCM cells and gut microbial metabolism, shedding light on potential mechanisms underlying depression and suggesting avenues for therapeutic intervention.},
}

Animals
*Gastrointestinal Microbiome/immunology
*CD8-Positive T-Lymphocytes/immunology/metabolism
Humans
Mice
Male
Mice, Inbred C57BL
*Stress, Psychological/immunology/metabolism
Female
Cell Movement
*Memory T Cells/immunology/metabolism
*Intestines/immunology/microbiology
Adoptive Transfer

@article {pmid41257857,
year = {2025},
author = {Knudsen, KS and Husebø, G and Nielsen, R and Paytuvi-Gallart, A and Malinverni, R and Sanseverino, W and Lehmann, S and Eagan, TM},
title = {Whole genome sequencing of the pulmonary microbiome in interstitial lung disease subtypes.},
journal = {Respiratory research},
volume = {26},
number = {1},
pages = {324},
pmid = {41257857},
issn = {1465-993X},
mesh = {Humans ; Male ; *Lung Diseases, Interstitial/microbiology/genetics/diagnosis ; Female ; Middle Aged ; *Microbiota/genetics ; *Lung/microbiology ; Aged ; *Whole Genome Sequencing/methods ; Bronchoalveolar Lavage Fluid/microbiology ; Dysbiosis/genetics ; },
abstract = {BACKGROUND: Interstitial lung diseases (ILDs) represent a heterogeneous group of lung disorders, some of which remain unclassifiable. The pulmonary microbiome may contribute to ILD pathogenesis, yet research is limited. Whole genome sequencing (WGS) offers enhanced microbial characterization. Here we evaluate the dysbiosis index (DI) as a potential biomarker to refine the classification of unclassifiable ILD.

METHODS: Protected bronchoalveolar lavage (PBAL) samples were collected from the right middle lobe of 12 IPF patients, 34 sarcoidosis patients, 11 unclassifiable ILD patients and 100 healthy controls. WGS was performed with the Illumina NovaSeq platform. Operational Taxonomic Units (OTU) were identified with GAIA 2.0 software, and statistical analyses were performed in R. The DI was calculated based on differential abundant species.

RESULTS: Alpha diversity was significantly higher in IPF and sarcoidosis patients compared to healthy controls. Beta diversity analysis revealed distinct microbial composition in IPF, sarcoidosis and unclassifiable ILD groups relative to controls. Differential abundance analysis identified several taxa with significant variation across groups. Notably, the dysbiosis index demonstrated high sensitivity and specificity in distinguishing IPF and sarcoidosis from healthy controls and provided further insight into the microbial characterization of unclassifiable ILD.

CONCLUSIONS: The pulmonary microbiome in unclassifiable ILD patients differed from healthy controls, and the dysbiosis index may provide exploratory insights for future ILD characterization.},
}

Humans
Male
*Lung Diseases, Interstitial/microbiology/genetics/diagnosis
Female
Middle Aged
*Microbiota/genetics
*Lung/microbiology
Aged
*Whole Genome Sequencing/methods
Bronchoalveolar Lavage Fluid/microbiology
Dysbiosis/genetics

@article {pmid41257762,
year = {2025},
author = {Linton, S and Hossenbaccus, L and Davis, A and Thiele, J and Garvey, S and Botting, H and Steacy, L and Sheth, PM and Ellis, AK},
title = {Staphylococcus aureus nasal carriage is associated with faster symptom resolution following nasal allergen challenge in ragweed-allergic participants: a subset of the Allergic Rhinitis Microbiome Study.},
journal = {Allergy, asthma, and clinical immunology : official journal of the Canadian Society of Allergy and Clinical Immunology},
volume = {21},
number = {1},
pages = {48},
pmid = {41257762},
issn = {1710-1484},
abstract = {In this letter, we report that ragweed-allergic participants with nasal Staphylococcus aureus carriage (n = 7) exhibited significantly smaller reductions in Peak Nasal Inspiratory Flow from baseline at 3 h (P = 0.013) and 5 h (P = 0.008) post-nasal allergen challenge compared to non-carriers (n = 12). There was no significant difference between carriers and non-carriers in the initial response within the first three hours following the challenge (all P > 0.05). Carriers also reported significantly lower Total Nasal Symptom Scores (P = 0.015) and Total Rhinoconjunctivitis Symptom Scores (P = 0.021) at 48 h. These findings suggest that S. aureus carriage does not exacerbate allergic responses and may instead be associated with more rapid symptom resolution.},
}

@article {pmid41257759,
year = {2025},
author = {Flintham, L and Dack, C and Koumanov, F and Feil, E and Ainsworth, B},
title = {A qualitative evaluation of older people's perceptions towards optimal diet management in the context of antimicrobial resistance.},
journal = {BMC public health},
volume = {25},
number = {1},
pages = {4060},
pmid = {41257759},
issn = {1471-2458},
}

@article {pmid41257564,
year = {2025},
author = {Zou, F and Chen, H and Yu, X and Hu, D and Dong, Y and Zhou, X and Si, X},
title = {Oral microbial profile polymorphisms predict early Siewert II adenocarcinoma of esophagogastric junction.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {764},
pmid = {41257564},
issn = {1471-2180},
support = {JSPH-MB-2021-13//the Clinical Capacity Enhancement Project of the First Affiliated Hospital of Nanjing Medical University/ ; },
mesh = {Humans ; *Esophagogastric Junction/pathology/microbiology ; Male ; Female ; Middle Aged ; *Adenocarcinoma/microbiology/pathology/diagnosis ; *Esophageal Neoplasms/microbiology/pathology/diagnosis ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Aged ; *Microbiota/genetics ; *Mouth/microbiology ; *Stomach Neoplasms/microbiology ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: Dysbiosis of the oral microbiota has been shown to be associated with the development of esophageal and gastric cancer. Nevertheless, little research explores how oral microbiota might contribute to the occurrence and progression of adenocarcinoma of the esophagogastric junction (AEG).

METHOD: 16 S rRNA V3-V4 amplicon sequencing was performed on 106 oral microbiota samples from 55 AEG patients and 51 controls. To determine key microbial indicators, Linear Discriminant Analysis Effect Size (LEfSe) analysis, Random Forest model, and species composition heatmaps were utilised. Spearman correlation analysis assessed the relationship between oral microbiota and clinicopathological variables. PICRUSt2 was employed to predict microbial functions and investigate the association with KEGG metabolic pathways.

RESULTS: A total of 584 oral genera and 647 oral species were observed in AEG and controls, excluding unidentified species. The abundance of 24 oral genera significantly increased in AEG patients, with Neisseria, Streptococcus, Rothia, Gemella, and Capnocytophaga being the five most abundant. Lefse, RF model and Species composition heatmap identified that genera enriched in the AEG group including Streptococcus, Neisseria, Rothia, Gemella, and genera depleted including Prevotella, Veillonella, Centipeda, Nanosynbacter were determined as biological markers to distinguish AEG from healthy controls. The genera with decreased abundance in AEG patients showed a positive association with WBC levels, neutrophil levels, and CA724 levels in the Mantel correlation test. PICRUSt analysis revealed significant differences in the abundance of 12 KEGG pathways. Carbohydrate metabolism, drug resistance, infectious diseases, lipid metabolism, nucleotide metabolism, and membrane transport pathways were positively correlated with genera enriched in the AEG group such as Streptococcus and Rothia, while negatively correlated with depleted genera like Prevotella.

CONCLUSION: Our research may suggest that dysbiosis of the oral microbiota and alterations in the KEGG metabolic pathway are linked to the development of AEG. In the future, we will conduct comprehensive verification through animal experiments and large-scale multicentre studies.},
}

Humans
*Esophagogastric Junction/pathology/microbiology
Male
Female
Middle Aged
*Adenocarcinoma/microbiology/pathology/diagnosis
*Esophageal Neoplasms/microbiology/pathology/diagnosis
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Aged
*Microbiota/genetics
*Mouth/microbiology
*Stomach Neoplasms/microbiology
Dysbiosis/microbiology

@article {pmid41257545,
year = {2025},
author = {Vazquez-Ortiz, K and Rivera-Orduña, FN and Zúñiga, G},
title = {Comparative genomics of dominant members of the gut core microbiome of the bark beetle, Dendroctonus rhizophagus (Curculionidae: Scolytinae) reveals potential functional complementarity in the detoxification process.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {1064},
pmid = {41257545},
issn = {1471-2164},
support = {891748//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; },
}

@article {pmid41256608,
year = {2025},
author = {Wang, Y and Chang, HW and Cheng, J and Webber, DM and Lynn, HM and Hibberd, MC and Kao, C and Mostafa, I and Ahmed, T and Barratt, MJ and Gordon, JI},
title = {Using gnotobiotic mice to decipher effects of gut microbiome repair in undernourished children on tuft and goblet cell function.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.02.680046},
pmid = {41256608},
issn = {2692-8205},
abstract = {UNLABELLED: Studies have implicated perturbations in the postnatal development of the gut microbiome as a contributing factor to childhood undernutrition. Compared to a standard ready-to-use supplementary food, a microbiome-directed complementary food (MDCF-2) designed to repair these perturbations produced superior improvements in ponderal and linear growth in clinical trials of Bangladeshi children with moderate acute malnutrition. Here, 'reverse translation' experiments are performed where intact fecal microbiomes collected from trial participants prior to and at the end of treatment are introduced into female gnotobiotic mice just after delivery of their pups. Pups received diets designed to resemble those consumed by children in the trials to recreate "unrepaired" and "repaired" gut ecosystems. Analyses of the abundances of bacterial strains (metagenome-assembled genomes), their expressed genes and metabolic products, combined with assessments of ponderal growth and intestinal epithelial lineage transcriptomes (single-nucleus RNA-Seq with follow-up immunocytochemistry) disclosed effects of MDCF-2 associated microbiome repair that cannot be determined, in part because 'no treatment' control arms cannot be ethically incorporated into these trials. Specifically, microbiome repair in these mice produced significant increases in ponderal growth, changes microbial gene expression consistent with a less virulent gut ecosystem and changes in expression of (i) components of gut epithelial cell junctions in the enterocytic and goblet cell lineages, (ii) pathways for synthesis and secretion of eicosanoid immune effectors in chemosensory tuft cells, and (iii) goblet cell pathways involved in glycosylation and secretion of mucin. Experiments of the type described can help formulate and test hypotheses about how microbiome repair affects host biology.

SIGNIFICANCE STATEMENT: Undernutrition is a global health problem. Recent clinical trials of a gut microbiome-directed complementary food (MDCF-2) designed to repair the perturbed gut microbiomes of undernourished Bangladesh children produced superior growth outcomes versus a standard nutritional supplement. Given ethical considerations and tissue sampling constraints associated with these types of studies, we colonized gnotobiotic mice postnatally with microbiome samples obtained from trial participants before and after treatment to model "unrepaired" and "repaired" gut ecosystems. Using a multi-omics approach, we uncover heretofore unappreciated changes in expressed chemosensory tuft cell, mucus-producing goblet cell and absorptive enterocytic functions and interactions accompanying microbiome repair. Extending microbiome clinical trials back to preclinical models ('reverse translation') provides mechanistic insights that can inform design/interpretation of future interventions.},
}

@article {pmid41256588,
year = {2025},
author = {Chakrawarti, A and Cromarty, RT and Basting, CM and Anderson, J and Schroeder, TA and Escandon, K and Shields-Cutler, R and Langat, R and Swanson, E and Soon-Shiong, P and Safrit, JT and Sender, LS and Reddy, S and Miller, JS and Rhein, J and Schacker, TW and Klatt, NR},
title = {Pre-treatment Microbiome Diversity and Function is associated with Expansion of Cytotoxic and Regulatory Immune Populations after N-803 treatment in People with HIV.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.01.679827},
pmid = {41256588},
issn = {2692-8205},
abstract = {BACKGROUND: N-803, an IL-15 superagonist, is currently being studied in clinical trials as a treatment to reverse HIV latency. However, its effects on the gut microbiome are not well understood.

METHODS: In this longitudinal metagenomic study, we analyzed fecal microbiomes from ART-suppressed people with HIV at four different timepoints before, during, and after N-803 treatment.

RESULTS: Overall taxonomic and functional diversity did not change significantly, yet beneficial microbial taxa and pathways were enriched after N-803. Specifically, the relative abundance of Faecalibacterium prausnitzii increased significantly after N-803, whereas histidine degradation pathways, often associated with pro-inflammatory mucosal state, decreased. A higher baseline microbial diversity correlated with stronger CD8 [+] and natural killer (NK) cells activation and reduced frequency of rectal HIV RNA [+] cells. MaAsLin2 analyses further associated short-chain fatty acid (SCFA)-producing taxa and pathways with increased immune activation markers.

CONCLUSIONS: These results indicate that gut microbiome diversity prior to immunotherapy influences host response and suggest that microbiome-based strategies could improve efforts to cure HIV.},
}

@article {pmid41256397,
year = {2025},
author = {Chakraborty, M and Shi, SM and Porter, IE and Richard, DJ and Marinov, GK and Moore, AA and Blum, JLE and Natarajan, A and Jahng, JW and Wu, JC and Lu, SX and Davidson, SM and Greenleaf, WJ and Saw, NL and Shamloo, M and Brunet, A and Wyss-Coray, T and Bhatt, AS},
title = {Age-related microbiome metabolites alter RNA splicing and chromatin accessibility in the brain.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.03.680371},
pmid = {41256397},
issn = {2692-8205},
abstract = {The gut microbiome generates diverse metabolites that can enter the bloodstream and alter host biology, including brain function. Hundreds of physiologically relevant, gut-brain signaling molecules likely exist; however, there has been no systematic, high-throughput effort to identify and validate them. Here, we integrate computational, in vitro , and in vivo approaches to pinpoint microbiome-derived metabolites whose blood levels change during aging, and that induce corresponding changes in the mouse brain. First, we mine large-scale metabolomics datasets from human cohorts (each n ≥ 1200) to identify 30 microbiome-associated metabolites whose blood levels change with age. We then screen this panel in an in vitro transcriptomic assay to identify metabolites that perturb genes linked to age-related neurodegeneration. We then test four metabolites in an acute-exposure mouse model, and use multi-omic approaches to evaluate their impact on cellular functions in the brain. We confirm the known neurodegeneration-promoting effects of trimethylamine N-oxide (TMAO), including mitochondrial dysfunction, and further discover its disruptive impact on the pathways of glycolysis, GABAergic signaling, and RNA splicing. Additionally, we identify glycodeoxycholic acid (GDCA), a microbiome-derived secondary bile acid, as a potent regulator of chromatin accessibility and suppressor of genes that protect the brain from age-related, neurodegeneration-promoting insults. GDCA also acutely reduces mobility. In summary, we present a scalable framework for linking microbiome metabolites to host pathologies, and apply it to identify microbial metabolites that induce molecular changes related to neurodegeneration.},
}

@article {pmid41256368,
year = {2025},
author = {Gao, A and Newhart, V and Flory, M and Alam, A},
title = {Pro-restitutive Bacteroides thetaiotaomicron reprograms the transcriptome of intestinal epithelial cells by modulating the expression of genes essential for proliferation and migration.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.30.679439},
pmid = {41256368},
issn = {2692-8205},
abstract = {The mammalian intestine harbors a highly complex, very diverse, and numerically vast community of symbiotic microorganisms, which profoundly influence the development and maintenance of the intestinal barrier function. Alterations in microbial composition, known as dysbiosis, are observed in Inflammatory Bowel Disease (IBD), colorectal cancer (CRC), and gastrointestinal infections; however, the exact causal relationship between these changes and the resolution of intestinal inflammation and the repair of damaged mucosa remains unclear. Notably, IBD is not only marked by dysbiosis but also by changes in microbial metabolic pathways and metabolite landscape in the intestinal lumen. The small molecules and microbial metabolites present in the intestinal lumen have emerged as potential regulators of gut pathology, cancer, and mucosal repair. Investigating how altered microbiota and microbial metabolic activities influence intestinal epithelial cells (IEC) can provide insights into their role in the regeneration of mucosal epithelia and restoration of gut barrier functions. This knowledge can be harnessed to promote intestinal homeostasis, prevent relapse, and prolong remission of IBD. To dissect the complex interplay between the gut microbiome and IEC, we focused on the overrepresented bacterium Bacteroides thetaiotaomicron . Here, we show that B. thetaiotaomicron and Akkermansia muciniphila , the dominant members of gut microbiota, expand during the repair & resolution phase of the chemically induced acute murine colitis. Furthermore, our bioinformatics analysis demonstrated that the elevated relative abundance of B. thetaiotamicron was also accompanied by rewiring of bacterial metabolic programs towards the essential amino acid metabolism, polyamine synthesis and utilization, stress response mechanisms, cell envelope biogenesis, and nutrient scavenging. Our RNA sequencing and transcriptomic analysis of primary human colonic epithelial cells cocultured with B. thetaiotaomicron showed that B. thetaiotaomicron stimulates the expression of genes and pathways involved in different cellular functions, including proliferation, differentiation, adhesion, lipid metabolism, migration, chemotaxis, and receptor expression. Our study emphasizes the crucial functions of the gut microbiome and metabolic activities in regulating the functions of intestinal epithelial cells during the repair of injured gut mucosa. Thus, these microorganisms and their metabolism hold promise as potential therapeutic agents.},
}

@article {pmid41256293,
year = {2025},
author = {Agrawal, H and Agarwal, N and Gupta, N},
title = {Impact of gut microbiome on outcomes following endoscopic interventions in gastrointestinal disease.},
journal = {World journal of gastrointestinal endoscopy},
volume = {17},
number = {11},
pages = {110207},
pmid = {41256293},
issn = {1948-5190},
abstract = {BACKGROUND: Endoscopic interventions play a vital role in diagnosing and managing gastrointestinal diseases, but complications such as bleeding, infection, and delayed healing can adversely affect patient outcomes. The influence of the gut microbiome on these outcomes is increasingly being recognized.

AIM: To evaluate the role of the gut microbiome in influencing clinical outcomes after endoscopic interventions, focusing on microbial diversity, specific taxa, metabolic functions, and emerging predictive models.

METHODS: A systematic literature search was conducted in PubMed, EMBASE, and Cochrane databases up to May 2025, selecting human studies that analyzed gut microbiome composition or function in relation to endoscopic interventions and clinical outcomes. Microbiome analysis techniques included 16S rRNA gene sequencing, metagenomics, and metabolomics.

RESULTS: Forty-two studies met the inclusion criteria. Our review identifies key beneficial microbes, such as Faecalibacterium prausnitzii and Bacteroides spp., which support mucosal healing. In contrast, dysbiosis (e.g., an increased abundance of Proteo bacteria) is associated with poorer healing and higher complication rates. Notably, microbiome-informed predictive models have shown strong potential for forecasting post-procedural complications, offering a pathway to personalized treatment strategies. Probiotics have also emerged as a promising intervention, helping to restore microbial balance and reduce complications such as infection and delayed healing.

CONCLUSION: The gut microbiome plays a significant role in recovery after endoscopy. Integrating microbiome analysis into clinical decision-making could improve outcomes through personalized predictions and targeted therapies. Future research should focus on standardizing microbiome assessment protocols and validating predictive models to optimize patient care.},
}

@article {pmid41256169,
year = {2025},
author = {Band, VI and LaPoint, P and Levy, S and Krausfeldt, L and Lacroix, IS and Chong, A and Brandes, NT and Schwarz, B and Mistry, S and Burns, AS and Bacorn, M and Banks, K and Strength, R and Chen, Q and Romero-Soto, HN and Prasad, R and Apps, R and Wang, L and Douagi, I and Polanco, JJ and Kotekar, A and Mukherjee, A and Koroleva, G and Compean, A and Sellers, B and Langowski, T and Rose, K and Roy, S and Namasivayam, S and Perez-Chaparro, PJ and Chau, J and Stacy, A and Belkaid, Y and Hourigan, SK},
title = {Bismuth subsalicylate profoundly alters gut microbiome and immunity with increased susceptibility to infection.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.10.01.25337000},
pmid = {41256169},
abstract = {Bismuth subsalicylate (BSS) is a commonly used over-the-counter medication for a variety of gastrointestinal symptoms. BSS sequesters gut sulfides, which have been shown in murine studies to be key regulators of gut microbiota. Here, we investigated the impact of BSS on human gut microbiome, immunity and susceptibility to enteric pathogens. We observed a significant shift in microbiome composition after BSS usage, with a profound expansion in bacteria with pathogenic potential including Pseudomonadota. Metabolite composition was greatly altered with increased amino acid levels and decreased short chain fatty acids and secondary bile acids. Notably, there was a collapse of key CD4 T cell subsets in the ileum. Finally, mouse and ex vivo human models revealed that BSS treatment increases susceptibility to colonization with the enteric pathogen Salmonella enterica . This study underlines the key role of sulfides in human gut microbiome and immunity and warrants further investigation into commonly used sulfide-depleting drugs.},
}

@article {pmid41255946,
year = {2025},
author = {Cui, L and Wang, Q and Sun, S and Li, W and Li, L and Sun, K and Zhou, Y and Tu, G and Liu, R and Li, L and Yu, Z and Zhang, C and Wu, X and Pan, T},
title = {The Role of Semi-Wild Habitats in the Physical Conditions of Juvenile Alligators: Implications for Conservation.},
journal = {Ecology and evolution},
volume = {15},
number = {11},
pages = {e72451},
pmid = {41255946},
issn = {2045-7758},
abstract = {The number and survival rate of juveniles play a key role in the recovery of Chinese alligators (Alligator sinensis). The differences between artificial and semi-wild environments can directly affect the growth and development of juvenile alligators. This study analyzed the physical conditions (lengths and weights) and cloacal microbial communities of juvenile alligators in both artificial breeding (DJ, ZX) and semi-wild (GJM) environments to reveal the significant effects of environmental pressure on their physiological state and microbiome. The results revealed that the body length (23.15 ± 1.06 cm) and weight (22.8 ± 3.08 g) of juvenile alligators in the GJM were significantly lower than those in the artificial environment (body length = 29.5 cm, weight = 68.6 g; p < 0.01). Moreover, the microbial α diversity (ACE, Shannon) of the GJM was significantly reduced, and the community structure was significantly separated (NMDS analysis), suggesting that the pressure of the semi-wild environment inhibited growth. In terms of microbial composition, the relative abundance of Actinobacteria in the GJM group was significantly, increased, whereas that of Bacteroidetes was decreased, and Microbacteria and Cyanobacteria were unique; at the genus level, environmentally specific marker genera were identified (such as Limnohabitans and Pseudomonas in GJM and Fluviicola and Deinococcus in the artificial environments). LEfSe analysis further elucidated the differential marker microbiota (such as Actinobacteria/Cyanobacteria in GJM). In summary, stress (such as food shortages) in semi-wild environments affects the growth and development of juvenile alligators by changing their microbial communities (such as enriched actinomycetes), This finding provides a microbial ecological basis for optimizing the conservation strategy of the Chinese alligator.},
}

@article {pmid41255677,
year = {2025},
author = {Devulapalli, CS},
title = {Modulatory role of vitamin D in atopic dermatitis and allergic rhinitis.},
journal = {World journal of clinical pediatrics},
volume = {14},
number = {4},
pages = {112145},
pmid = {41255677},
issn = {2219-2808},
abstract = {Vitamin D, beyond its classical role in calcium homeostasis, has emerged as a key regulator of immune function and epithelial barrier integrity. Its deficiency during early childhood-a critical period for immune maturation-has been increasingly implicated in the development of atopic diseases. While extensively studied in asthma, its role in non-respiratory allergic conditions such as atopic dermatitis (AD) and allergic rhinitis (AR) remains comparatively underexplored. This minireview synthesizes current mechanistic and clinical evidence on vitamin D in pediatric AD and AR. In AD, vitamin D promotes epidermal barrier function through upregulation of filaggrin and ceramide synthesis, and enhances antimicrobial defense via induction of antimicrobial peptides. Observational studies consistently report lower serum 25-hydroxyvitamin D in affected children, particularly those with allergic sensitization. Select randomized controlled trials suggest clinical improvement with supplementation, especially at doses > 2000 IU/day in deficient individuals. In AR, epidemiological data indicate stronger inverse associations with seasonal (pollen-induced) disease. Proposed mechanisms include modulation of dendritic cells, regulatory T cells, T helper 2 cytokines, and mucosal barrier integrity. The shared immunopathogenesis of AD and AR underscores vitamin D's relevance. Although promising, clinical evidence remains heterogeneous. Future research should prioritize phenotype-stratified trials to clarify optimal dosing, timing, and individual response determinants, including genetics and microbiome composition.},
}

@article {pmid41255658,
year = {2025},
author = {Nagoba, BS and Dhotre, SV and Sonar, MN and Mumbre, SS and Gavkare, AM and Dhotre, PS},
title = {Neonatal and pediatric sepsis: Microbiological insights, diagnostic innovations, and antimicrobial challenges.},
journal = {World journal of clinical pediatrics},
volume = {14},
number = {4},
pages = {107974},
pmid = {41255658},
issn = {2219-2808},
abstract = {Neonatal and pediatric sepsis remains a major global health concern, contributing significantly to morbidity and mortality among children under 5 years of age. The clinical and microbiological characteristics of sepsis differ markedly in neonates and children, necessitating tailored diagnostic and treatment approaches. This mini-review explores the evolving microbiological landscape, recent advancements in diagnostic methodologies, and challenges posed by antimicrobial resistance (AMR) in managing neonatal and pediatric sepsis. Emerging pathogens, including multidrug-resistant Gram-negative bacilli and fungal organisms, are reshaping the epidemiology of sepsis. Innovations in molecular diagnostics, including polymerase chain reaction-based platforms, next-generation sequencing, and artificial intelligence-integrated tools, are revolutionizing early pathogen detection and resistance profiling. However, implementation gaps persist, particularly in low- and middle-income countries. Therapeutic challenges are compounded by limited pediatric data on newer antimicrobials and rising AMR rates. Infection prevention strategies, especially in intensive care units, are crucial to outbreak containment. An integrated approach combining microbiological surveillance, rapid diagnostics, and antimicrobial stewardship is critical for improving sepsis outcomes. Future research should focus on context-specific implementation of diagnostic tools and optimizing treatment strategies for resource-limited settings.},
}

@article {pmid41255540,
year = {2025},
author = {Tseyslyer, Y and Malyi, V and Saifullina, M and Tsyryuk, O and Shvets, Y and Penchuk, Y and Kovalchuk, I and Kovalchuk, O and Korotkyi, O and Bulda, V and Lazarieva, O},
title = {Harnessing gut-derived bioactives and AI diagnostics for the next generation of type 2 diabetes solutions.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1699954},
pmid = {41255540},
issn = {1664-2392},
mesh = {Humans ; *Diabetes Mellitus, Type 2/diagnosis/therapy/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; *Artificial Intelligence ; Quality of Life ; },
abstract = {INTRODUCTION: The prevalence of type 2 diabetes (T2D) has significantly increased over the past 20 years, currently affecting over 500 million people worldwide. Projections suggest that this number could rise to over 700 million in the next two decades. Despite advancements in medication and global health strategies that promote healthy lifestyles, T2D remains a complex disease that impacts the quality of life. Traditional treatment methods are becoming less effective, highlighting the need for innovative approaches to prevention, diagnosis, and treatment.

METHODS: Two promising areas of research that could transform the management of T2D are the use of biologically active substances derived from the intestines and the integration of artificial intelligence (AI) in clinical diagnostics. The human intestinal microbiota plays a crucial role in metabolic processes, including glucose regulation and insulin sensitivity. Microbial metabolites, including bile acids and short-chain fatty acids, have potential as therapeutic agents for metabolic disorders. As digital medicine advances, AI is increasingly utilized for real-time monitoring and personalized risk assessments. The medical field is evolving from merely using biosensors for glucose tracking to employing machine learning to analyze various biological indicators and electronic medical records.

RESULTS: Recent research at the intersection of microbiome studies and AI may improve diagnostic accuracy and support tailored treatment strategies. This study aims to analyze global experiences with the implementation of bioactive substances from the intestines and the diagnostic potential of AI in developing a new approach to enhancing the quality of life and treating T2D.

DISCUSSION: We examine the diverse functions of microbial metabolites and the current landscape of their therapeutic applications. Additionally, the review examines the current state of AI in diagnostics, with a particular focus on microbiome parameters. As a result, we propose a novel model that combines these two fields into an adaptive and personalized approach to treating patients with T2D and improving their quality of life.},
}

Humans
*Diabetes Mellitus, Type 2/diagnosis/therapy/microbiology/metabolism
*Gastrointestinal Microbiome/physiology
*Artificial Intelligence
Quality of Life

@article {pmid41255529,
year = {2025},
author = {Horiachok, M and Potapova, K and Ivanykovych, T and Yerokhovych, V and Ilkiv, Y and Sokolova, L},
title = {Integrating gut microbiota into multidisciplinary perspectives on diabetic neuropathy.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1710868},
pmid = {41255529},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetic Neuropathies/microbiology/therapy/metabolism ; *Dysbiosis/microbiology ; Animals ; Probiotics/therapeutic use ; },
abstract = {Diabetic neuropathy (DN) is one of the most common and debilitating complications of diabetes mellitus, yet its precise pathogenesis remains incomplete. Emerging evidence highlights the gut microbiome as a key factor linking metabolic dysfunction, immune activation, and neuronal damage. Even minor dysbiosis may interfere with microbial metabolite balance and disrupt intestinal integrity, leading to local and, consequently, systemic inflammation, which in turn drives altered pain response via the gut-brain-immune axis. Recent clinical and preclinical data show that reduced short-chain fatty acid availability, altered bile acid and tryptophan metabolism, let alone expansion of pro-inflammatory species collaboratively contribute to DN onset and progression. Moreover, advances in metagenomics and metabolomics reveal reproducible microbiome-derived biomarkers that could predict neuropathy risk and pain phenotypes independent of glycemic control, supporting the microbiome as both a mechanistic driver and a measurable potential diagnostic tool. In the context of management, microbiota-affected interventions, such as probiotics, synbiotics, omega-3 supplementation, and fecal microbiota transplantation, show early promise in alleviating symptoms and improving nerve function. This mini-review synthesizes current evidence on the microbiome's role in DN, emphasizing its dual potential as a biomarker for early diagnosis and a therapeutic target for precision microbiome-based interventions.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Diabetic Neuropathies/microbiology/therapy/metabolism
*Dysbiosis/microbiology
Animals
Probiotics/therapeutic use

@article {pmid41255342,
year = {2025},
author = {Miller, DM and McCauley, KF and Dunham-Snary, KJ},
title = {Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD): Mechanisms, Clinical Implications and Therapeutic Advances.},
journal = {Endocrinology, diabetes & metabolism},
volume = {8},
number = {6},
pages = {e70132},
doi = {10.1002/edm2.70132},
pmid = {41255342},
issn = {2398-9238},
support = {202303PJT-190103/CAPMC/CIHR/Canada ; CRC-2020-00192//Tier II Canada Research Chair in Mitochondrial and Metabolic Regulation in Health and Disease/ ; 41511//Canada Foundation for Innovation/ ; 6035577//Banting Research Foundation and Mitacs/ ; 6032495//Queen's University, Kingston, Ontario, Canada/ ; 6034430//Queen's University, Kingston, Ontario, Canada/ ; },
mesh = {Humans ; *Fatty Liver/therapy/epidemiology/etiology/metabolism ; *Metabolic Syndrome/complications/epidemiology ; *Non-alcoholic Fatty Liver Disease/therapy/epidemiology ; Prevalence ; Insulin Resistance ; },
abstract = {INTRODUCTION: Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) has emerged as the most prevalent chronic liver disease worldwide, affecting ~25%-30% of the adult population, with higher prevalence observed in individuals with obesity and type 2 diabetes. Among reported MASLD cases, prevalence is consistently higher in men than in women, and global incidence has risen by ~50% over the past two decades, mirroring the global rise in obesity and metabolic syndrome. MASLD encompasses a spectrum of hepatic pathologies ranging from simple steatosis to steatohepatitis, fibrosis and cirrhosis. Despite its high prevalence, the heterogeneity in disease progression and relative absence of approved pharmacological therapies pose challenges for effective clinical management.

METHODS AND RESULTS: This review synthesises current literature on MASLD across epidemiology, pathophysiology, clinical presentation and treatment. Key molecular mechanisms, including lipid metabolism dysregulation, insulin resistance and mitochondrial dysfunction, are examined with a focus on understanding the basis for progression to metabolic dysfunction-associated steatohepatitis (MASH). Clinical manifestations, diagnostic tools and risk stratification systems for MASLD are summarised. Current and emerging therapies such as lifestyle interventions, pharmacological agents and microbiome-targeted strategies are reviewed. The review also highlights ongoing challenges, including diagnostic limitations, disease heterogeneity and disparities in care.

CONCLUSION: MASLD is a complex, multifactorial liver disease with a growing public health impact, driven by the rising prevalence of metabolic syndrome. Mitochondrial dysfunction is a critical nexus linking genetic susceptibility to metabolic stress and inflammatory responses. Preclinical models that capture these mitochondrial contributions are vital for therapeutic discovery and for advancing personalised medicine approaches in MASLD care.},
}

Humans
*Fatty Liver/therapy/epidemiology/etiology/metabolism
*Metabolic Syndrome/complications/epidemiology
*Non-alcoholic Fatty Liver Disease/therapy/epidemiology
Prevalence
Insulin Resistance

@article {pmid41255157,
year = {2025},
author = {Chen, J and Wu, C and Yang, R and Chen, Z and Yang, X and Xu, Y and Cheng, X and Sui, H and Zhang, S and Zhu, X and Wu, M and Huang, Y and Chen, X and Liu, H and Yang, J and Tan, X and Chen, F and Cheng, C and Shao, D and Han, X and Shi, B and Yang, C and Leong, KW and Huang, H},
title = {LPS-Binding Hydrogel for TLR4-Mediated Microbiota-Immune Modulation.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e14484},
doi = {10.1002/adma.202514484},
pmid = {41255157},
issn = {1521-4095},
support = {82301148//National Natural Science Foundation of China/ ; 82470955//National Natural Science Foundation of China/ ; 2024T170605//China Postdoctoral Science Foundation/ ; RD-02-202511//Research and Develop Program, West China Hospital of Stomatology Sichuan University/ ; 2025ZNSFSC0758//Sichuan Province Science and Technology Support Program/ ; RCDWJS2024-7//West China School of Stomatology, Sichuan University/ ; 24QNMP060//Health Commission of Sichuan Province/ ; TB2022005//Sichuan Provincial Postdoctoral Science Foundation/ ; },
abstract = {Lipopolysaccharide (LPS), a conserved component of Gram-negative bacteria, is a potent immune activator that disrupts tissue repair when released during microbial dysbiosis. LPS-scavenging strategies are often limited by the poor accessibility of lipid A, the bioactive core of LPS, which is shielded by variable oligosaccharide structures and embedded in bacterial membranes. To address this, a synergistic LPS-binding hydrogel (OCMC-PMBP) is developed, combining polymyxin B (PMB) for lipid A-targeted bacterial lysis and polyethyleneimine (PEI) for electrostatic LPS capture. This system is applied to oronasal-perforating wounds, a complex and infection-prone condition associated with cleft palate repair. Clinical microbiome analysis and murine models reveal that LPS-TLR4 signaling contributes to immune dysregulation and impaired healing. OCMC-PMBP treatment reduces LPS levels, restores microbiota balance, suppresses inflammation, and accelerates epithelial regeneration and collagen remodeling. Integrated 16S rRNA sequencing, metagenomics, and single-cell transcriptomics show that the hydrogel reprograms immune cell phenotypes and modulates macrophage interactions with neutrophils, epithelial cells, and fibroblasts across healing phases. This study introduces a biomaterials design combining antimicrobial and immunomodulatory functions to resolve dysbiosis-induced inflammation and enhance regenerative healing in complex mucosal wounds.},
}

@article {pmid41255097,
year = {2025},
author = {van Heule, M and Verstraete, M and Norris, JK and Graniczkowsa, KB and Scoggin, KE and Ali, HE and Ball, BA and De Spiegelaere, W and Daels, P and Weimer, BC and Dini, P},
title = {Beyond nocardioform: Transcriptionally active microbes and host responses in equine mucoid placentitis.},
journal = {Equine veterinary journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/evj.70112},
pmid = {41255097},
issn = {2042-3306},
support = {//UC Davis Center for Equine Health/ ; //Special Research Fund at University of Ghent (BOF)/ ; //Clay Endowment at UKY/ ; //John Hughes Endowment at UCDavis/ ; //Foundation for the Horse/ ; //Grayson-Jockey Club Research Foundation/ ; },
abstract = {BACKGROUND: Nocardioform placentitis (NP) is an understudied form of equine placentitis historically attributed to nocardioform bacteria, yet it remains uncertain whether these organisms are the sole pathogens involved.

OBJECTIVES: To elucidate the pathophysiology of NP and the host-pathogen interaction.

STUDY DESIGN: In vivo clinical multi-omics study.

METHODS: Dual RNA sequencing was performed to profile transcriptionally active microbial communities and concurrent placental transcriptome responses in samples from 31 placentas with and without NP. Untargeted metabolomics was performed to study the associated metabolites in the placenta.

RESULTS: The most abundant microbial transcripts belonged to Amycolatopsis, Crossiella, Lentzea, Enterococcus, and Mycobacterium. Bacterial gene expression in NP-affected placentas was enriched in pathways related to ribosomal activity and metabolic processes involving amino acid, carbohydrate, and glycosphingolipid metabolism. Concurrently, placental transcripts demonstrated significant upregulation of inflammatory pathways and downregulation of pathways associated with blood vessel formation. Untargeted metabolomics highlighted an elevated abundance of metabolites such as beta-D-fucose, nervonic acid, and zymostenol in the placentitis samples. Significant correlations were found between microbial genes (mraW, rlmB, amy, afuA, and cysC) and host inflammation genes (CXCL14, IL15RA, TASL, and IFIH1). Additionally, elevated beta-D-fucose, a microbe-specific metabolite, showed a strong correlation with microbial genes involved in stress-adaptive metabolism and DNA repair (ydhP, ybgC, serC, puuE, and radA). The bacterial enzymes involved in beta-D-fucose were notably upregulated and predominantly expressed by Amycolatopsis and Lentzea.

MAIN LIMITATIONS: Classification based on RNA abundance limited the number of Crossiella cases (n = 3).

CONCLUSIONS: Both nocardioform and non-nocardioform bacteria are involved in NP-diagnosed cases, challenging the current generalisation of the term 'nocardioform placentitis' and supporting the need to broaden diagnostic protocols for mucoid placentitis. Multi-omics profiling revealed potential host-microbe interactions mediated by microbial metabolites, offering mechanistic insights and opportunities for improved diagnostic strategies.},
}

@article {pmid41254816,
year = {2025},
author = {Chen, CY and Kuo, HC and Fang, YT and Lu, CW and Chen, SK and Hung, CM},
title = {Microbiota-gut-brain axis in avian parenting: gut microbiome associates with nest-construction behavior and neural gene expression in a songbird.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {120},
pmid = {41254816},
issn = {2524-4671},
support = {NSTC 112-2311-B-001-039-MY3//National Science and Technology Council/ ; NSTC 112-2811-B-001-025//National Science and Technology Council/ ; AS-CDA-108-L05//Academia Sinica/ ; },
}

@article {pmid41254708,
year = {2025},
author = {Liu, Y and Liu, Y and Huang, W and Liu, Y and Sun, J},
title = {An inflammation-responsive therapeutic gel for precise microbiota modulation in colitis.},
journal = {Journal of nanobiotechnology},
volume = {23},
number = {1},
pages = {719},
pmid = {41254708},
issn = {1477-3155},
support = {82304903//National Natural Science Foundation of China/ ; 82204678//National Natural Science Foundation of China/ ; 22202206//National Natural Science Foundation of China/ ; XYD2024GR03//National Research Innovation Talents Cultivation Project/ ; },
mesh = {Animals ; Mice ; *Colitis/drug therapy/microbiology/chemically induced ; Gels/chemistry/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Inflammation/drug therapy ; Nanofibers/chemistry ; Humans ; Tungsten/chemistry/pharmacology ; Male ; Cytokines/metabolism ; Leukocyte L1 Antigen Complex/metabolism ; Dextran Sulfate ; },
abstract = {Microbiome dysbiosis is a hallmark of inflammatory bowel disease (IBD), and its reprogramming represents a promising intervention strategy. Existing treatments are often limited by gastrointestinal instability and non-specific microbial toxicity, leading to suboptimal outcomes and potential aggravation of IBD symptoms. Herein, we construct a calcium phosphotungstate gel (CPW), characterized by tortile nanofibers (length > 5 μm, diameter ~ 20 nm) forming a stable 3D network, which remains structurally intact in gastrointestinal fluid for over 24 h and exhibits commendable resistance to gastric acid and digestive enzymes. Furthermore, CPW disintegrates specifically in response to the inflammatory biomarker calprotectin (CAL), releasing over 54% of tungsten payloads within 12 h (versus < 6% without CAL). The locally released tungsten ions selectively inhibit nitrate respiratory enzymes and induce apoptosis in approximately 50% of nitrate-dependent pathogens within 24 h, enabling precise microbiome modulation. As a versatile carrier, CPW demonstrated exceptional protection for diverse therapeutics (DIO, peptides, nucleic acids) against digestive enzymes, enabling > 70% cargo release specifically at inflamed sites. In DSS-induced colitis mice, DEX-loaded CPW (DEX@CPW) significantly improved colon length (comparable to healthy controls), reduced pro-inflammatory cytokines (IL-1β, IL-6, TNF-α by 2.1-3.3 fold), and restored beneficial microbiota. Crucially, CPW reduced systemic tungsten exposure by 62.7% in kidneys while increasing intestinal tungsten retention by 1.67-fold, demonstrating superior targeting. This dual-function platform-integrating pathogen-selective metallotherapy and inflammation-triggered drug release-represents a promising clinical approach for IBD by simultaneously modulating dysbiosis and ameliorating inflammation.},
}

Animals
Mice
*Colitis/drug therapy/microbiology/chemically induced
Gels/chemistry/pharmacology
*Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
*Inflammation/drug therapy
Nanofibers/chemistry
Humans
Tungsten/chemistry/pharmacology
Male
Cytokines/metabolism
Leukocyte L1 Antigen Complex/metabolism
Dextran Sulfate

@article {pmid41254590,
year = {2025},
author = {Schwob, G and Delleuze, M and Motreuil, S and Marschal, C and Saucède, T and Orlando, J and Poulin, E and Cabrol, L},
title = {Gut microbiome plasticity and host resistance in response to ocean warming in sub-Antarctic sea urchins.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {343},
pmid = {41254590},
issn = {1741-7007},
support = {program No. 1044 PROTEKER//French Polar Institute-IPEV/ ; Millennium Institute BASE, grant #ICN2021_002//Millennium Science Initiative Program - Chilean National Agency of Research and Innovation (ANID)/ ; 1211672//Regular FONDECYT - Chilean National Agency of Research and Innovation (ANID)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Climate Change ; *Sea Urchins/microbiology/physiology ; Antarctic Regions ; RNA, Ribosomal, 16S/genetics ; Seawater ; Acclimatization ; *Global Warming ; Oceans and Seas ; Temperature ; },
abstract = {BACKGROUND: Sub-Antarctic marine ecosystems are highly vulnerable to climate change, with rising ocean temperatures threatening key benthic species. Abatus cordatus, an endemic sea urchin of the Kerguelen Islands with limited dispersal capacity, has been hypothesised to possess a narrow thermal niche, which would render it particularly susceptible to environmental shifts. However, microbiome-mediated acclimation may provide a potential mechanism of resilience to ocean warming. To test these hypotheses, this study evaluates host survival and gut microbiome responses of A. cordatus to medium-term seawater warming under near-future temperature scenarios using 16S rRNA gene sequencing to compare these changes with those observed in sediment microbiomes.

RESULTS: Host mortality remained relatively low across all temperatures, showing no association with warming intensity and thereby suggesting thermal tolerance. While gut microbiome alpha-diversity remained stable, its composition shifted and variability increased with experiment duration and temperature, leading to greater inter-individual divergence and a decline in both the richness and abundance of core taxa. In contrast, sediment microbiomes remained more stable, exhibiting more deterministic assembly and increased core stability over time. At the taxonomic level, specific gut bacterial ASVs showed temperature-dependent abundance shifts, with greater flexibility at moderate thermal stress. Notably, the depleted and enriched ASVs were affiliated to known sulphate-reducing and fermentative taxa, respectively, suggesting a possible functional shift.

CONCLUSIONS: Overall, our findings suggest that A. cordatus can tolerate medium-term warming, with gut microbiome plasticity representing a potential mechanism supporting host resilience.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Climate Change
*Sea Urchins/microbiology/physiology
Antarctic Regions
RNA, Ribosomal, 16S/genetics
Seawater
Acclimatization
*Global Warming
Oceans and Seas
Temperature

@article {pmid41254344,
year = {2025},
author = {Distante, A and Garino, D and Cerrato, C and Perez-Ardavin, J and Flores, FQ and Lopetuso, L and Mir, MC},
title = {The role of the human microbiome in prostate cancer: a systematic review from diagnosis to treatment.},
journal = {Prostate cancer and prostatic diseases},
volume = {},
number = {},
pages = {},
pmid = {41254344},
issn = {1476-5608},
abstract = {BACKGROUND: Prostate cancer (PC) heterogeneity and treatment resistance remain major clinical challenges, with emerging evidence implicating the microbiome as a key modulator of disease pathogenesis. While microbial dysbiosis has been linked to PC diagnosis, progression, and therapeutic outcomes, the mechanisms underlying these associations are poorly understood. This review synthesizes current evidence on the diagnostic, prognostic, and therapeutic potential of the microbiome in PC.

METHODS: A systematic search of PubMed, Embase, and Cochrane Central Register of Controlled Trials (through April 2024) was conducted following PRISMA guidelines (PROSPERO: CRD42024534899). Controlled and observational studies investigating microbial roles in PC diagnosis (e.g., ISUP grading group), prognosis, or treatment response were included. Data extraction and quality assessment used the QUIPS tool. From 810 screened records, 42 studies met inclusion criteria.

RESULTS: Distinct microbial profiles differentiated PC from controls, with Mycoplasma genitalium and Staphylococcus spp. enriched in prostate tumors (3.1- and 2.7-fold, respectively) and correlated with inflammation (IL-6: r = 0.38, p = 0.002). Urinary microbiota showed diagnostic potential (sensitivity: 58-82%), though sampling methods influenced variability. Prognostically, Betaproteobacteria gut enrichment predicted earlier castration-resistant progression (5.2 months; HR 1.8, 95% CI 1.3-2.5), while ADT-induced dysbiosis (e.g., Klebsiella overgrowth) accelerated resistance (2.1-fold risk). Therapies altered microbial ecology: radiotherapy depleted Bacteroides (linked to proctitis; OR 3.1), and immunotherapy responders harbored higher Akkermansia muciniphila. Microbial androgen synthesis and endotoxin production emerged as resistance mechanisms.

CONCLUSIONS: The microbiome influences PC detection, aggressiveness, and treatment efficacy through direct (tissue-resident) and indirect (gut-derived) mechanisms. Standardized profiling and microbiome-modulating strategies (e.g., probiotics during ADT) may personalize management. Prospective trials are needed to validate causality and translate microbial biomarkers into clinical practice.},
}

@article {pmid41254308,
year = {2025},
author = {Nicola, T and Wenger, NM and Seidman, K and Evans, M and Yang, Y and Chen, D and Van Der Pol, WJ and Walia, A and Lefkowitz, EJ and Wang, J and LeMoire, A and Lin, L and Morrow, C and Ambalavanan, N and Gaggar, A and Lal, CV},
title = {Double-Blind Randomized Placebo-Controlled Trial of a Lactobacillus Probiotic Blend in Chronic Obstructive Pulmonary Disease.},
journal = {Pulmonary therapy},
volume = {},
number = {},
pages = {},
pmid = {41254308},
issn = {2364-1746},
support = {K08 HL141652/HL/NHLBI NIH HHS/United States ; R44HL164156/HL/NHLBI NIH HHS/United States ; UM1TR004771/TR/NCATS NIH HHS/United States ; },
abstract = {INTRODUCTION: Gut microbiota modulate systemic anti-inflammatory and immune responses in the lungs, suggesting a potential to support lung health through probiotic supplementation. We hypothesized that a probiotic blend (Lactobacilli) combined with herbal extracts (resB[®]) could improve quality of life in patients with chronic obstructive pulmonary disease (COPD).

METHODS: We conducted a randomized, double-blinded, placebo-controlled study (NCT05523180) evaluating the safety and impact of resB[®] on quality of life in volunteers with COPD. Participants took resB[®] or placebo (two capsules daily) for 12 weeks. The primary endpoint was change in quality of life by Saint George's Respiratory Questionnaire (SGRQ). Secondary outcomes included safety, serum and sputum biomarkers, and microbiome analysis. resB[®] was well tolerated with no related adverse events.

RESULTS: Participants receiving resB[®] showed significant improvement in SGRQ symptom scores (P < 0.05), while placebo recipients did not. In the resB[®] group, serum and sputum levels of matrix metalloproteinase 9, C-reactive protein, and interleukin 6 decreased (P < 0.05), correlating with increased stool Lactobacilli. Additionally, Veillonella abundance increased in both stool and sputum.

CONCLUSION: These findings suggest that resB[®] improves respiratory symptoms and reduces inflammation in patients with COPD, potentially by modulating gut and lung microbiota.

TRIAL REGISTRATION: ClinicalTrials.gov identifier NCT05523180.},
}

@article {pmid41254244,
year = {2025},
author = {Mekadim, C and Mrázek, J and Vodička, M and Ergang, P and Fliegerová, KO and Mahayri, TM and Chawengsaksophak, K and Pácha, J},
title = {Impact of Sex, Gonadectomy, and Repeated Restraint Stress on Gut Microbiome in Mice.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {80},
pmid = {41254244},
issn = {1559-1182},
support = {Grant 21-10845S//Czech Science Foundation/ ; PPLZ Project: L200112201//Czech Academy of Science/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; *Restraint, Physical ; *Stress, Psychological/microbiology/blood ; *Sex Characteristics ; Mice, Inbred C57BL ; Mice ; *Castration ; Corticosterone/blood ; RNA, Ribosomal, 16S/genetics ; Cecum/microbiology ; Colon/microbiology ; },
abstract = {Recently, the bidirectional connection between the gastrointestinal microbiota and the brain has gained interest in many research studies. Findings have highlighted the potential role of stress and sex hormones in modulating the gut microbiome. To our knowledge, no study has investigated the effect of sex hormone perturbations on the gut microbiota in response to stress. To understand how stress may alter the gut microbiota differently depending on sex, gonadectomized and sham-operated male and female mice were subjected to 2 h of daily restraint stress for seven consecutive days. Body weight and plasma level of corticosterone were evaluated. Bacterial diversity and composition of colon and cecum were analyzed by sequencing of 16S rRNA gene. The bacterial communities were strongly altered by stress in the colon than in the cecum. A profound dysregulation of several metabolic and functional pathways was observed in sham mice. Alterations in the gut microbiome diversity and its functional pathways due to stress were more pronounced in males than in females. The present results provide potential sex-specific biomarkers and novel metabolic signatures in the gut microbiota related to stress disorders which may be used as potential targets in diagnostic and therapeutic approaches in neurogastroenterological diseases.},
}

Animals
*Gastrointestinal Microbiome/physiology
Male
Female
*Restraint, Physical
*Stress, Psychological/microbiology/blood
*Sex Characteristics
Mice, Inbred C57BL
Mice
*Castration
Corticosterone/blood
RNA, Ribosomal, 16S/genetics
Cecum/microbiology
Colon/microbiology

@article {pmid41254155,
year = {2025},
author = {Ayayee, P and Custer, G and Clayton, JB and Price, J and Ramer-Tait, A and Larsen, T},
title = {Assessing gut microbial provisioning of essential amino acids to host in a mouse model with reconstituted gut microbiomes.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1604},
pmid = {41254155},
issn = {2399-3642},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Amino Acids, Essential/metabolism ; Mice, Inbred C57BL ; Male ; Carbon Isotopes ; },
abstract = {Gut microbial provisioning of essential amino acids (EAAs) represents a critical but poorly understood aspect of mammalian nutrition, with direct implications for host metabolism, growth, and disease resistance. While advances in microbiome research have highlighted the potential significance of these microbial-host nutritional interactions, direct empirical evidence quantifying actual microbial contributions to host EAA supply remains surprisingly limited, particularly under controlled experimental conditions. Here, we show using stable carbon isotope analysis of six EAAs across brain, kidney, liver, and muscle tissues that germ-free mice maintained on a high-protein diet and conventionalized mice with reconstituted gut microbiomes fed a low-protein diet for twenty days exhibit no significant differences in δ[13]C-EAA values. Our results reveal no detectable microbial contribution to host EAA pools, as δ[13]C-EAA patterns remain nearly identical between treatment groups across all organs examined. Microbial profiling confirms that conventionalized mice successfully established diverse gut microbiota communities dominated by typical Firmicutes and Bacteroidetes phyla. These findings contrast with recent δ[13]C-EAA based studies that reported substantial microbial EAA contributions in wild-type mice, raising important questions about functional restoration of reconstituted gut microbiomes and underscoring the need to critically revisit experimental designs and analytical frameworks to better understand microbial nutrient provisioning dynamics.},
}

Animals
*Gastrointestinal Microbiome/physiology
Mice
*Amino Acids, Essential/metabolism
Mice, Inbred C57BL
Male
Carbon Isotopes

@article {pmid41254023,
year = {2025},
author = {Liu, Y and Wu, W and Liang, Q and Diao, J and Yang, W and Zheng, S and Han, Y and Yuan, C},
title = {Metabolic and microbial alterations in oral potentially malignant disorders versus oral squamous cell carcinoma.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40637},
pmid = {41254023},
issn = {2045-2322},
support = {PKUSS-2023CRF304//Peking University School and Hospital of Stomatology series of clinical research projects/ ; 2022YFE0118300//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Mouth Neoplasms/metabolism/microbiology/diagnosis/pathology ; Male ; Female ; Middle Aged ; Saliva/metabolism ; *Carcinoma, Squamous Cell/metabolism/microbiology ; Aged ; Metabolomics/methods ; Biomarkers, Tumor/metabolism ; Adult ; Microbiota ; Metabolome ; },
abstract = {Oral potentially malignant disorders (OPMDs) are oral mucosal conditions associated with an increased risk of oral squamous cell carcinoma (OSCC), and their clinical manifestations may be subtle and insidious. The primary aim of this study was to identify metabolite-based biomarkers for early, non-invasive detection of tumor-related metabolic signals in this at-risk population. We enrolled 21 OPMD and 46 OSCC patients, collecting saliva and plasma from all participants and tissue samples from a subset of the same cohort (12 OPMD and 5 OSCC). Untargeted metabolomics identified 491 and 303 differential metabolites in saliva and plasma, respectively. Five metabolites-dodecanoic acid, tetradecanedioic acid, porphobilinogen, uridine, and isocitrate-were significantly altered in both biofluids. Tissue validation showed significant alterations in dodecanoic acid, tetradecanedioic acid, and isocitrate. Using all biologically annotated differential metabolites, AUCs were 0.888 (saliva) and 0.994 (plasma), while the tissue-anchored three-metabolite classifier yielded 0.694 (saliva) and 0.852 (plasma). Full-length 16S rDNA sequencing and integrative microbiome-metabolome analysis indicated potential correlations between microbial shifts and metabolite profiles. Our findings highlight metabolic alterations and cross-compartment associations across saliva, plasma, and tissue in OPMDs and OSCC. Notably, despite the higher internal discrimination of all-differential models, the tumor-informed three-metabolite model captures tissue-aligned metabolic changes detectable in saliva and plasma, providing a specific, non-invasive readout for early detection.},
}

Humans
*Mouth Neoplasms/metabolism/microbiology/diagnosis/pathology
Male
Female
Middle Aged
Saliva/metabolism
*Carcinoma, Squamous Cell/metabolism/microbiology
Aged
Metabolomics/methods
Biomarkers, Tumor/metabolism
Adult
Microbiota
Metabolome

@article {pmid41253982,
year = {2025},
author = {Chiba, N and Limviphuvadh, V and Ng, CH and Koyagi, R and Kino, Y and Nakamura, Y and Yamada, T},
title = {Preliminary study of gut microbiome influence on black Ivory coffee fermentation in Asian elephants.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40548},
pmid = {41253982},
issn = {2045-2322},
support = {KAKENHI JP16H06279//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Elephants/microbiology ; *Fermentation ; *Coffee/metabolism ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; *Coffea/metabolism ; },
abstract = {Black Ivory Coffee (BIC), produced through the digestion of Arabica coffee beans by Asian elephants, is recognized for its smooth, chocolaty flavor and low bitterness. However, the biological mechanisms underlying its unique taste remain poorly understood. In this study, we conducted a preliminary analysis of the gut microbiome of BIC-producing elephants and compared it with that of control elephants. 16S rRNA gene sequencing analysis revealed significant differences in microbial community structure, including the enrichment of specific bacterial genera such as Acinetobacter and family such as Izemoplasmataceae in the BIC group. Functional prediction using PICRUSt2 indicated that the BIC elephant gut microbiome harbors key enzymes involved in the degradation and utilization of pectin and cellulose-major components of coffee cherries and beans. Notably, genes related to pectin transport and downstream metabolism, including K08191 and K01812, were significantly more abundant in BIC elephants. These pathways may contribute to the degradation of specific compounds, such as 2-furfuryl furan, which has been previously shown to decrease after gastrointestinal passage. Comparative analysis with other animals revealed that only elephants harbored a complete set of pectin-degrading genes. Our findings suggest that the gut microbiota of BIC elephants facilitates microbial fermentation of coffee components, potentially influencing the chemical profiles of Black Ivory Coffee.},
}

Animals
*Gastrointestinal Microbiome
*Elephants/microbiology
*Fermentation
*Coffee/metabolism
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
*Coffea/metabolism

@article {pmid41253951,
year = {2025},
author = {Palladino, G and Marangi, M and Scicchitano, D and Turroni, S and Rampelli, S and Candela, M},
title = {Gut microbiome structure in asylum seekers newly arrived in Italy from Africa.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40596},
pmid = {41253951},
issn = {2045-2322},
mesh = {Humans ; *Refugees ; Italy ; *Gastrointestinal Microbiome/genetics ; Africa ; Adult ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; Middle Aged ; Young Adult ; Feces/microbiology ; },
abstract = {The global landscape of migration has evolved significantly, with international migrants tripling since 1970, reaching approximately 281 million by 2020. This rise includes a notable surge in forcibly displaced individuals due to conflicts, wars, and human rights violations. Additionally, climate change is reshaping migration patterns by environmental degradation and extreme weather events, with projections indicating that 143 million individuals may be uprooted by climate catastrophes over the next three decades. In this context, migrants experience chronic stress due to the uncertainties of their journey, exposure to trauma, and changes in living conditions, possibly exacerbating health issues, including through impairment of the gut microbiome. Our study focuses on the characterization-by 16 S rRNA gene amplicon sequencing-of intestinal microbiome in 79 asylum seekers newly arrived in Italy from African countries through their comparison with publicly available datasets of worldwide populations encompassing different origin and lifestyle. This microbiological surveillance, conducted as cross-sectional sampling over one year, aimed to provides some glimpses on how the forced migration journey and the associated stressors affect refugees' gut microbiome composition. Our findings suggest significant deviations in the gut microbiome composition of refugees compared to traditional rural populations, possibly driven by stressors such a psychological trauma and dietary changes. The loss of microbial diversity may increase susceptibility to health issues, highlighting the need for targeted public health strategies for refugee populations.},
}

Humans
*Refugees
Italy
*Gastrointestinal Microbiome/genetics
Africa
Adult
Male
Female
RNA, Ribosomal, 16S/genetics
Cross-Sectional Studies
Middle Aged
Young Adult
Feces/microbiology

@article {pmid41253868,
year = {2025},
author = {Li, J and Yu, L and Wang, Y and Yuan, C and Wang, K and Ma, X},
title = {Alterations in urinary microbiota composition in children with overactive bladder: insights from 16S rRNA gene sequencing.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40455},
pmid = {41253868},
issn = {2045-2322},
support = {2024NSFSC1499//Natural Science Foundation of Sichuan Province/ ; 2023YFS0101//Sichuan Science and Technology Program/ ; },
mesh = {Humans ; Child ; *RNA, Ribosomal, 16S/genetics ; Female ; Male ; *Urinary Bladder, Overactive/microbiology/urine ; *Microbiota/genetics ; Adolescent ; Child, Preschool ; *Bacteria/genetics/classification ; Case-Control Studies ; },
abstract = {This study aimed to characterize the urinary microbiota profiles in pediatric patients with overactive bladder (OAB) compared to healthy controls, identify differentially enriched microbial taxa, and explore their associations with clinical symptoms and functional pathways. Urine samples were collected from 87 children (39 OAB patients, 48 controls) aged 5-14 years. Microbial DNA was extracted, and the V3-V4 regions of the 16 S rRNA gene were sequenced using the Illumina NovaSeq6000 platform. To delineate microbial community variations and functional associations, bioinformatics pipelines and statistical approaches-including permutational multivariate ANOVA (PERMANOVA), principal coordinates analysis (PCoA), linear discriminant analysis effect size (LEfSe), and Spearman's correlation-were applied to assess α/β-diversity, taxon-specific disparities, and clinical phenotype linkages in 16 S rRNA sequencing datasets. Clinical parameters, such as urinary urgency severity, nocturnal enuresis, and residual urine, were correlated with microbial composition. While no significant differences in α-diversity were observed between groups, β-diversity analysis revealed distinct clustering of microbial communities (ANOSIM, P = 0.001). OAB patients (OABs) exhibited enrichment in Proteobacteria, Gammaproteobacteria, Enterobacterales, Sphingomonas, and Escherichia-Shigella, whereas controls showed higher abundances of Clostridia, Bacteroidales, and Prevotella. Positive correlations were detected among Defluviitoga, Escherichia-Shigella, and Ligilactobacillus, while Defluviitoga negatively correlated with Bacteroides. Functional prediction highlighted OAB-associated upregulation of antibiotic resistance, biofilm formation, and bacterial secretion pathways. Subgroup analyses further linked severe OAB symptoms to elevated inflammatory taxa (e.g., Enterobacteriaceae) and residual urine to Gammaproteobacteria dominance. Pediatric OAB is associated with a dysbiotic urinary microbiota characterized by pro-inflammatory bacteria and altered metabolic functions. Specific microbial signatures, such as Escherichia-Shigella and Enterobacterales, may contribute to pathogenesis, while Prevotella and Clostridia in controls suggest protective roles. Specific microbial signatures associate with disease severity and possess functional capacities linked to inflammation, urothelial invasion, and immune evasion. Our findings underscore the urinary microbiome's contribution to pediatric OAB pathogenesis, suggesting promise for microbiome-informed diagnostic and therapeutic strategies.},
}

Humans
Child
*RNA, Ribosomal, 16S/genetics
Female
Male
*Urinary Bladder, Overactive/microbiology/urine
*Microbiota/genetics
Adolescent
Child, Preschool
*Bacteria/genetics/classification
Case-Control Studies

@article {pmid41253756,
year = {2025},
author = {Knoll, RL and Brauny, MM and Robert, E and Cloos, L and Waser, L and Hilbert, K and Ulmer, N and Hillen, B and Birkner, T and Bartolomaeus, TUP and Nitsche, O and Jarquín-Díaz, VH and Lynch, S and Gehring, S and Maier, L and Poplawska, K and Forslund-Startceva, SK},
title = {CFTR modulator therapy drives microbiome restructuring through improved host physiology in cystic fibrosis: the IMMProveCF phase IV trial.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10111},
pmid = {41253756},
issn = {2041-1723},
support = {551589343//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FO 1279/6-1, Project ID 431232613 - SFB 1449 (//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Humans ; *Cystic Fibrosis/drug therapy/microbiology/genetics/physiopathology ; *Cystic Fibrosis Transmembrane Conductance Regulator/genetics/metabolism ; *Quinolones/therapeutic use/pharmacology ; Male ; Female ; *Aminophenols/therapeutic use/pharmacology ; Adult ; Sputum/microbiology ; Gastrointestinal Microbiome/drug effects ; *Benzodioxoles/therapeutic use/pharmacology ; Indoles/therapeutic use/pharmacology ; Feces/microbiology ; Longitudinal Studies ; Young Adult ; *Microbiota/drug effects/genetics ; *Pyrroles/therapeutic use/pharmacology ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Adolescent ; Pyridines/therapeutic use/pharmacology ; Drug Combinations ; Dysbiosis/drug therapy/microbiology ; Pyrrolidines/therapeutic use/pharmacology ; Pyrazoles ; },
abstract = {Cystic fibrosis (CF) is a genetic disorder caused by mutations in the CFTR gene, leading to impaired CFTR function, mucus accumulation, chronic infections, and inflammation. The triple combination elexacaftor/tezacaftor/ivacaftor (ETI) has transformed CF treatment by restoring CFTR function. However, how ETI-induced physiological improvements affect long-standing dysbiosis and pathogen colonization across microbiome habitats remains poorly understood. In this prospective longitudinal study (DRKS00023862), we analyzed sputum, throat, and stool microbiomes of pwCF (n = 35) before and after ETI initiation, alongside healthy controls (n = 49). The primary endpoint was longitudinal change in diversity, species richness, and microbial composition in the respiratory and intestinal microbiome, profiled by 16S rRNA gene sequencing. Secondary endpoints included changes in lung function, systemic and gastrointestinal inflammation. We show how improved CFTR function and direct antibacterial effects of ETI create a niche disadvantage for Staphylococcus in the sputum microbiome. Respiratory microbiome shifts were immediate, while gut changes emerged gradually. Escherichia abundance in stool, initially elevated in pwCF, decreased post-ETI and correlated with lower fecal calprotectin. These findings demonstrate that ETI can partially reverse CF-associated dysbiosis through improved host physiology. They offer insights into host-microbiome dynamics under therapeutic modulation and emphasize the need for confounder-aware models in complex clinical populations.},
}

Humans
*Cystic Fibrosis/drug therapy/microbiology/genetics/physiopathology
*Cystic Fibrosis Transmembrane Conductance Regulator/genetics/metabolism
*Quinolones/therapeutic use/pharmacology
Male
Female
*Aminophenols/therapeutic use/pharmacology
Adult
Sputum/microbiology
Gastrointestinal Microbiome/drug effects
*Benzodioxoles/therapeutic use/pharmacology
Indoles/therapeutic use/pharmacology
Feces/microbiology
Longitudinal Studies
Young Adult
*Microbiota/drug effects/genetics
*Pyrroles/therapeutic use/pharmacology
RNA, Ribosomal, 16S/genetics
Prospective Studies
Adolescent
Pyridines/therapeutic use/pharmacology
Drug Combinations
Dysbiosis/drug therapy/microbiology
Pyrrolidines/therapeutic use/pharmacology
Pyrazoles

@article {pmid41253509,
year = {2025},
author = {Acire, PV and Brown, SC and Day, AS},
title = {The role of the Mediterranean diet in the management of inflammatory bowel disease: a narrative review.},
journal = {Intestinal research},
volume = {},
number = {},
pages = {},
doi = {10.5217/ir.2025.00043},
pmid = {41253509},
issn = {1598-9100},
abstract = {Inflammatory bowel disease (IBD) is characterized by the presence of gastrointestinal inflammation, that in some individuals leads on to complications, including strictures. IBD can be associated with significant morbidity with disruption of daily activities. Although the precise cause of IBD is unknown, epidemiologic studies indicate that diet is one contributory factor. Furthermore, various specific nutritional interventions have roles in the management of IBD. While the contribution of the Mediterranean diet (MedDiet) to the development or management of IBD has not yet been clearly delineated, available data are generally supportive. The MedDiet includes the consumption of a pattern of particular foods, such as plentiful vegetables, fruit, seafood, and olive oil, along with lifestyle features. Adherence to a MedDiet is associated with enrichment of beneficial components of the intestinal microbiome and enhanced barrier function: outcomes that are likely beneficial to individuals with IBD. The focus of this review was to highlight the evidence for the MedDiet in the setting of IBD, whilst giving an overview of the underlying health impacts of the MedDiet and the putative mechanisms of this dietary approach.},
}

@article {pmid41253445,
year = {2025},
author = {Chen, YL and Meng, LL and Wu, JY and Yang, XY and Ouyang, L and Wu, BF and Xu, HX and Gu, JL and Wang, YL and Jing, XY and Lu, SF and Fu, SP},
title = {Electroacupuncture Reprograms Gut Microbiota and Confers Cerebral Protection After Stroke through Enhanced Regulatory T Cell Response.},
journal = {The American journal of Chinese medicine},
volume = {},
number = {},
pages = {1-24},
doi = {10.1142/S0192415X25500855},
pmid = {41253445},
issn = {1793-6853},
abstract = {Ischemic stroke seriously endangers both the health and quality of life of patients. The gut microbiota, which plays a crucial role in modulating communication between the gut and the nervous system, has emerged as a promising target for therapeutic interventions in stroke. Electroacupuncture (EA), which is associated with intestinal immunity, has been proven to exert significant beneficial effects in ischemic stroke, but its exact mechanism remains unclear. In this study, we investigated the regulatory mechanism of EA on the microbiome-gut-brain axis following ischemic stroke. In rat models of ischemic stroke, EA treatment significantly reduced cerebral infarct volume and neuronal damage following cerebral ischemia-reperfusion injury, and also modulated the composition, diversity, and taxonomic distribution of the gut microbiota. Fecal microbiota transplantation from EA-treated donors significantly reduced cerebral infarct volume and neuronal damage in the ischemic hemisphere of recipient mice, and likewise upregulated Treg cell expression to suppress immune-inflammatory responses in the brain. These results indicate that, through modulation of the gut microbiota, which in turn regulates Treg-mediated immune-inflammatory responses, EA ameliorates cerebral ischemic injury to thereby improve the prognosis of ischemic stroke patients. This study provides new perspectives on the efficacy of EA in the treatment of ischemic stroke.},
}