@article {pmid41115624,
year = {2025},
author = {Mishra, R and Harvey, A and Guo, A and Tillotson, G and Feuerstadt, P and Khanna, S and Shannon, WD and Blount, KF},
title = {Microbiome and metabolome changes after fecal microbiota, live-jslm, administration are associated with health-related quality of life improvements.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {103006},
doi = {10.1016/j.anaerobe.2025.103006},
pmid = {41115624},
issn = {1095-8274},
abstract = {OBJECTIVES: Increasing evidence indicates a gut microbiome-brain axis, but more robust statistical methods are needed to solidify this connection. In a large phase 3, randomized, placebo-controlled clinical trial (PUNCH CD3; NCT03244644), fecal microbiota, live-jslm (REBYOTA; RBL, previously RBX2660), was effective in preventing recurrent Clostridium difficile infections, and trial participants had significant gut microbiome and metabolome shifts concurrent with significant changes in health-related quality of life (HRQOL). Advanced statistical methods were applied to data from this trial to further explore and demonstrate associations between changing HRQOL and microbiome or metabolome changes.

METHODS: A categorical statistical analysis queried whether patient-reported Cdiff32 HRQOL scores were more likely to improve after RBL than after placebo among PUNCH CD3 participants, and a Dirichlet-multinominal recursive partitioning model assessed whether mental domain Cdiff32 HRQOL scores were linked to participants' fecal microbiome or bile acid compositions.

RESULTS: Cdiff32 mental domain HRQOL scores were more likely to be improved after RBL administration compared with placebo among treatment responders. Cdiff32 mental domain scores were associated with changing gut microbiome and metabolome compositions, with a gradient of increased Clostridia and Bacteroidia and increased secondary bile acid predominance associated with better Cdiff32 scores.

CONCLUSIONS: The microbiota-gut-brain axis is posited to modulate health-related quality of life, microbiome, and metabolome changes through immune, gastrointestinal, and central nervous system functions in patients with recurrent C. difficile infection following RBL administration. These analyses provide a novel approach for investigating multi-omics data and categorical health-related quality of life questionnaires and generate new insights for further clinical studies.

CLINICAL TRIAL REGISTRATION: NCT03244644.},
}

@article {pmid41114648,
year = {2025},
author = {Graf, T and Moser, F and Embleton, H and Niklaus, PA and Grabenweger, G},
title = {Which factors influence the virulence of entomopathogenic fungi? Effect of spore type, oosporein, application method, and pathway of entry on the infectiveness of Beauveria brongniartii against Melolontha melolontha.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf259},
pmid = {41114648},
issn = {1365-2672},
abstract = {AIMS: The control of the common cockchafer Melolontha melolontha using the entomopathogenic fungus (EPF) Beauveria brongniartii is one of the most successful biological control systems. This study aimed to identify factors influencing the outcome of laboratory bioassays, which are crucial early steps in the development of biocontrol products, by using this system as a role model.

METHODS AND RESULTS: We combined spray and injection applications of conidio- and blastospores of the host-specific pathogen B. brongniartii BIPESCO2 (Bip2) and the generalist EPF Metarhizium brunneum Ma 43 and applied the treatments to cockchafer adults and larvae. Furthermore, the mycotoxin oosporein was tested alone or with Bip2 blastospores, as well as Bip2 conidiospores, in immersion, spray, and injection treatments of larvae. The most efficient spore suspension was applied to different larval body parts and to their food. Bip2 and Ma 43 infected adults frequently, but larvae resisted topical spray applications. Injection treatments revealed that adult cuticles offered limited protection, whereas the larval cuticle acted as an effective barrier. Larval thorax and legs, with articulations and intersegmental membranes, were more susceptible than the abdomen. Oosporein synergized with blastospores in larval immersion treatments, but alone had no effect. We propose that oosporein's antibiotic activity disrupts the larval cuticle microbiome, facilitating infection.

CONCLUSION: Contrary to the assumption that laboratory bioassays overestimate EPF performance under field conditions, we found the opposite. We therefore argue that more elaborate studies are required for realistic evaluation of candidate biocontrol agents, considering host-pathogen traits and test conditions.},
}

@article {pmid41114647,
year = {2025},
author = {Basso, TO and Venturini, AM and Ceccato-Antonini, SR and Gombert, AK},
title = {Microbial Ecology Applied to Fuel Ethanol Production from Sugarcane.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf100},
pmid = {41114647},
issn = {1574-6941},
abstract = {The production of fuel ethanol in sugarcane biorefineries is a non-aseptic industrial operation, which employs cell recycling and the use of adapted Saccharomyces cerevisiae strains. Microbial contaminants are present and, depending on the conditions, may lead to process performance deterioration. Past studies have identified the main microbial species present in this environment, using culture-dependent techniques. A few recent studies started to deploy culture-independent techniques to better understand this microbiota and its dynamics. In both cases, lactic acid bacteria have been identified as the main contaminating microorganisms. Less than a handful of reports are available on the interactions between yeast and contaminating bacteria, using synthetic microbial communities, proposing that interactions are not necessarily always detrimental. The present mini-review aims at systematizing the current knowledge on the microbiota present in the alcoholic fermentation environment in sugarcane biorefineries and setting the ground and claiming the need for a microbial ecology perspective to be applied to this system, which in turn might lead to future process improvements.},
}

@article {pmid41114585,
year = {2025},
author = {Aries Marchington, M and Gasvoda, H and Michelotti, M and Rodriguez-Caro, F and Gooman, A and Perez, A and Hensley-McBain, T},
title = {APOE genotype and sex drive microbiome divergence after microbiome standardization in APOE-humanized mice.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0042925},
doi = {10.1128/msphere.00429-25},
pmid = {41114585},
issn = {2379-5042},
abstract = {The APOE4 allele is the greatest known genetic factor for sporadic or late-onset Alzheimer's Disease (LOAD). Gut microbiome (GMB) dysbiosis can lead to poorer outcomes in disease. The intersection of sex, APOE genotype, inflammation, and gut microbiota is incompletely understood. Previous studies in humans and humanized APOE mice have demonstrated APOE-genotype-specific differences in the GMB. However, most of these studies were unable to resolve bacteria to the species level. It remains unclear how GMB changes with age and sex in the context of APOE genotype. In this study, humanized male mice with either APOE 2, 3, or 4 genotype were bred with the same two C57BL/6J sisters to standardize microbiomes across lines and monitor divergence based on APOE allele. Stool samples were collected at breeder set up and from the heterozygous (F1) and homozygous (F2) generations at wean and 6 months old. Stool was assessed via shallow shotgun sequencing to enable species and strain-level taxonomic resolution. The heterozygous pups' microbiome resembled each other at wean across all genotypes. However, the heterozygous pups and their homozygous offspring continued to diverge, particularly the APOE2 females. In homozygous mice, the GMB demonstrated significant divergence at 6 months of age based on sex and APOE genotype. In comparison to their APOE3 and APOE4 counterparts, APOE2 females and males demonstrated an increased quantity of bacteria associated with anti-inflammatory profiles, including in the Lachnospiraceae family (Lachnospiraceae bacterium UBA3401) and decreased quantities in the Turicibacteraceae family (higher levels are associated with LOAD).IMPORTANCEThe APOE4 allele is implicated as a significant risk factor for many diseases, including cardiovascular disease (responsible for more deaths than any other disease) and sporadic or late-onset Alzheimer's Disease (accounts for an estimated 60%-80% of all dementia cases). It is known that the gut microbiome (GMB) is affected by different genotypes and disease states. Mouse model studies have environmental and genetic controls, allowing a specific gene to be studied. This study aims at discovering key GMB species differences allowing for future therapeutic targets. The GMB of the experimental mice was standardized, and genotype and sex-specific divergence was observed with species and even strain level taxonomic resolution. Reported here are the first data demonstrating GMB divergence over time driven by APOE genotype from an inherited source and the first data to identify APOE genotype-specific bacteria species that may serve as therapeutic targets in APOE-driven disease.},
}

@article {pmid41114583,
year = {2025},
author = {Xia, Y and Yang, J and Lu, S and Cheng, W and Ren, M and Liu, Z and Yang, L and Shen, Q and Liang, Y and Huang, H and Chen, M and Zhou, X and Yu, M and Ji, F and Xu, C},
title = {Microbial changes resulting from VSG attenuate MASLD by modulating bile acid metabolism and the intestinal FXR-FGF19 axis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0063425},
doi = {10.1128/msystems.00634-25},
pmid = {41114583},
issn = {2379-5077},
abstract = {UNLABELLED: Vertical sleeve gastrectomy (VSG) is a highly effective intervention for metabolic dysfunction-associated steatotic liver disease (MASLD) and is associated with significant alterations in the gut microbiota. However, the precise mechanisms underlying its metabolic benefits remain poorly understood. In this study, we revealed that VSG mitigates MASLD by reshaping gut microbiota-mediated bile acid metabolism. Through integrated 16S rRNA sequencing, targeted metabolomics, and functional validation experiments, we demonstrated that VSG markedly enhances bile salt hydrolase (BSH) activity within the gut microbiota, resulting in elevated levels of unconjugated bile acids. These unconjugated bile acids serve as potent agonists for the intestinal farnesoid X receptor (FXR), thereby activating the intestinal FXR-fibroblast growth factor 19 signaling pathway. This activation leads to significant improvements in metabolic health, including enhanced glucose regulation and attenuated hepatic lipid accumulation. Fecal microbiota transplantation (FMT) from VSG-treated rats replicated these metabolic improvements, whereas antibiotic treatment abolished these beneficial effects, highlighting the indispensable role of the gut microbiota in mediating the anti-MASLD effects of VSG. Importantly, inhibition of intestinal FXR signaling negated the metabolic benefits of FMT, further emphasizing the critical role of the gut microbiota-BSH-FXR axis. Our findings reveal a novel mechanism by which VSG alleviates MASLD through gut microbiota-dependent activation of intestinal FXR, offering new perspectives for microbiome-targeted therapeutic strategies in MASLD.

IMPORTANCE: Fecal transplantation from bariatric surgery patients and mice to germ-free mice has shown that the gut microbiota may contribute to metabolic benefits after bariatric surgery. However, the mechanisms by which the gut microbiota contributes to metabolic benefits after bariatric surgery require further investigation. To address this gap, we investigated the effects of the vertical sleeve gastrectomy (VSG) gut microbiota on metabolic dysfunction-associated steatotic liver disease (MASLD) in vivo and elucidated its underlying mechanisms. Our study demonstrated that VSG significantly improved the gut microbiota, especially by increasing bile salt hydrolase (BSH) activity, in MASLD rats. Increased BSH activity significantly increased the proportion of FXR-agonistic bile acids and further activated the intestinal FXR-FGF19 axis, thereby improving MASLD. These findings explored the key roles and mechanisms of the gut microbiota in the metabolic benefits of VSG, offering new microbiome-based treatment strategies.},
}

@article {pmid41114579,
year = {2025},
author = {Powell, CE and McCurry, MD and Quevedo, SF and Ventura, L and Krishnan, K and Dave, M and Mahmood, SD and Specht, K and Bordia, R and Sargen, MR and Pratt, DS and Korzenik, JR and Devlin, AS},
title = {Cultured bacteria isolated from primary sclerosing cholangitis patient bile induce inflammation and cell death.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0055025},
doi = {10.1128/msphere.00550-25},
pmid = {41114579},
issn = {2379-5042},
abstract = {Primary sclerosing cholangitis (PSC) is a chronic liver disease characterized by inflammation and progressive fibrosis of the biliary tree. PSC pathogenesis remains poorly understood, and there are no effective therapies. Previous studies have observed associations between colonic and biliary microbiome alterations and PSC. We aimed to determine whether bacterial isolates cultured from PSC patient bile induce disease-associated phenotypes in cells, specifically cell death, epithelial permeability, inflammation, and changes in host-protective pathways. Bile was collected from PSC patients by endoscopic retrograde cholangiography and from non-PSC controls undergoing cholecystectomies. Biliary bacteria were cultured anaerobically, and 50 colonies per sample were identified by 16S sequencing. No bacteria were isolated from non-PSC controls, while bacteria were cultured from most PSC patients. The PSC bile microbiomes exhibited reduced diversity compared to the gut or oral cavity, with one or two species predominating. The effects of supernatants from seven PSC-associated bacterial isolates on cellular phenotypes were characterized using human colonic (Caco-2), hepatic (HepG2), and biliary (EGI-1) cells. Overall, PSC-associated bacteria produced factors cytotoxic to hepatic and biliary cells. An Enterococcus faecalis isolate, and to a lesser extent a Veillonella parvula isolate, induced epithelial permeability, while Escherichia coli, Fusobacterium necrophorum, and Klebsiella pneumoniae isolates induced inflammatory cytokines in biliary cells. Our data suggest that bacteria cultured from PSC bile induce cellular changes characteristic of PSC pathogenesis, with different isolates inducing distinct cellular responses. Our work provides a starting point for future research into bacterial contributions to PSC with the eventual goal of developing therapies for this disease.IMPORTANCEPrimary sclerosing cholangitis (PSC) is a chronic liver disease in which inflammation and scarring of the bile ducts cause bile to build up in the liver, leading to liver damage and eventually liver failure. The causes of this disease are poorly understood, and the only current treatment is a liver transplant. To develop new treatments, we must first better understand what leads to this disease. We examined whether bacteria isolated from PSC patient bile can cause disease-related responses in human biliary, liver, and intestinal cells. We observed that different PSC-associated bacteria can induce distinct disease-related cellular changes, including inflammation and cell death. These data suggest that the microbial community in PSC patients may indeed be linked to disease development. Our findings provide new starting points for further exploration into the poorly understood origins of PSC.},
}

@article {pmid41114526,
year = {2025},
author = {Schroll, M and Amar, Y and Krüger, P and Neuhaus, K and Djabali, K},
title = {Baricitinib Augments Lonafarnib Therapy to Preserve Colonic Homeostasis and Microbial Balance in a Mouse Model of Progeria.},
journal = {Aging cell},
volume = {},
number = {},
pages = {e70273},
doi = {10.1111/acel.70273},
pmid = {41114526},
issn = {1474-9726},
support = {2022-82//Progeria Research Foundation/ ; },
abstract = {Hutchinson-Gilford Progeria Syndrome (HGPS) is a fatal genetic disorder caused by progerin, a mutant lamin A variant that disrupts nuclear architecture and drives systemic cellular dysfunction. Gastrointestinal (GI) involvement in HGPS remains poorly understood, despite growing evidence of gut abnormalities and microbial dysbiosis in progeroid mouse models. Here, we provide the first comprehensive characterization of colonic pathology in Lmna[G609G/G609G] mice and assess the therapeutic impact of baricitinib (Bar), a JAK-STAT inhibitor, lonafarnib (FTI), the only FDA-approved therapy, and their combination on colonic health. Bar + FTI combination therapy most effectively lowered progerin levels, preserved colonic architecture and epithelial regeneration markers, while also reducing inflammation, cellular senescence, and early fibrotic changes. Notably, FTI monotherapy aggravated inflammation via STAT1 activation, an effect reversed by Bar co-administration. Bar also emerged as the primary driver in mitigating colonic tissue senescence, highlighting its role in supporting intestinal homeostasis. In addition, we observed marked microbial dysbiosis in HGPS mice, particularly in late-stage disease. While both monotherapies induced distinct shifts in gut microbiota, combination therapy preserved a profile more closely resembling healthy controls. These findings expand the current understanding of GI involvement in HGPS and identify the colon as a site where JAK-STAT inhibition enhances the therapeutic profile of FTI.},
}

@article {pmid41114510,
year = {2025},
author = {Leao, L and Esmail, GA and Miri, S and Mottawea, W and Hammami, R},
title = {In vitro modeling of the female gut microbiome: effects of sex hormones and psychotropic drugs.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0235025},
doi = {10.1128/spectrum.02350-25},
pmid = {41114510},
issn = {2165-0497},
abstract = {Sex hormones play a crucial role in shaping gut microbiome composition and metabolism, with significant implications for mental health. This study investigated the effects of sex hormones and the psychotropic drug aripiprazole on the gut microbiome, using a novel in vitro colonic fermentation model adapted from the PolyFermS system. Fecal samples from four male and female donors were used to develop sexually divergent models, with the female model subjected to hormonal treatments mimicking different phases of the menstrual cycle. Microbiome composition and short-chain fatty acid (SCFA) metabolism were analyzed. The results demonstrated that sex hormones significantly influenced microbiota structure and diversity, with the female model exhibiting reduced α-diversity and distinct bacterial associations with SCFAs. Hormonal fluctuations across menstrual phases induced specific shifts in bacterial composition, notably increasing Bacteroidota while decreasing Bacillota and Pseudomonadota. In the female model, aripiprazole treatment led to increased microbial diversity and altered SCFA profiles, although the changes in SCFAs were not statistically significant (P > 0.05). Differential abundance analysis revealed sex-specific enrichment of bacterial genera, such as Eubacterium coprostanoligenes and Agathobacter. These findings underscore the importance of considering sex-specific microbiome profiles and hormonal influences when optimizing psychotropic treatments for mental health disorders.IMPORTANCEThe gut microbiome plays a crucial role in human health, affecting metabolism, immunity, and brain function. However, the role of sex hormones in shaping the gut microbiome composition and metabolism remains largely unexplored. This study introduces a novel in vitro colonic fermentation model to investigate the effects of sex hormone fluctuations and psychotropic drug exposure on the gut microbiome. By simulating a sexually divergent human colon environment and mimicking hormonal variations throughout the menstrual cycle, this model provides a controlled setting for studying microbiome response to external stimuli. Our findings revealed that sex hormones, such as estrogen, progesterone, and testosterone, shape microbial diversity and alter the microbiome composition compared to the control group. Additionally, this study examined the effect of psychotropic drug exposure on the microbiota of a simulated female colon, revealing alterations in the microbial composition and metabolism. These results highlight the importance of considering the role of the gut microbiome in drug response, given the widespread use of psychiatric medications, particularly among women. This novel colonic fermentation model offers a valuable tool for studying sex-specific microbiome dynamics and their broader implications for health.},
}

@article {pmid41114501,
year = {2025},
author = {Gou, L and Luo, G and Xia, Z and Zhang, W and Li, S and Ji'e, K and Gao, T and Abi, K and Yang, F},
title = {Influence of breast milk microbiota on the composition of the early intestinal microbial community in goat kids: a study of composition and correlations.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0264224},
doi = {10.1128/spectrum.02642-24},
pmid = {41114501},
issn = {2165-0497},
abstract = {Colonization of gut microbes in young ruminants plays a fundamental role in their lifelong health. Although the relationship between breast milk (BM) and the gut microbiota of young animals has been reported, its specific impact on goats has yet to be thoroughly explored. Therefore, this study aimed to comprehensively reveal the influence of breast milk feeding on the development of intestinal microorganisms in goat kids and the interactions between breast milk microbiome and fecal microbiome. The results showed that there was a significant difference in the richness of breast milk microbiota between the BMD1, BMD7, and BMD14 groups (P < 0.05). At the genus level, the bacterial microbiota in breast milk across different days of age was predominantly composed of Pseudomonas, Asticcacaulis, Mannheimia, Sphingomonas, and Staphylococcus. In contrast, the fecal microbiota of goat kids was primarily dominated by Escherichia-Shigella, Butyricicoccus, Bacteroides, Lactobacillus, and Limosilactobacillus. Significant correlations (P < 0.05) were observed between the microbial communities of breast milk and the fecal microbiota of goat kids. Specifically, Delftia in breast milk was positively correlated with Limosilactobacillus and Lactobacillus and negatively correlated with Lachnoclostridium in the rectal feces of goat kids, and Lactobacillus in breast milk was positively correlated with Ruminococcus_gnavus_group. These results suggest that the structure of the breast milk microbiota may influence the colonization of the intestinal microbiota in goat kids, especially for some probiotic genera such as Lactobacillus. In conclusion, this study elucidates the dynamic changes in breast milk microbiota and the shifts in goat kid fecal microbiota following breast milk feeding, as well as the correlations between them. These findings provide a scientific foundation for enhancing goat kid growth, development, and health through early microbiota modulation in practical production.IMPORTANCEThe gastrointestinal (GI) microbiota has a profound effect on host health, especially in resisting pathogen colonization and promoting intestinal function (T. Zhong, Y. Wang, X. Wang, A. Freitas-de-Melo, et al., Front Microbiol 13:1020657, 2022, https://doi.org/10.3389/fmicb.2022.1020657). The results show that the stability of rumen microbial communities and their associated functions in lambs is not achieved until they reach at least 20 days of age (B. Brooks, B. A. Firek, C. S. Miller, I. Sharon, et al., Microbiome 2, 2014, https://doi.org/10.1186/2049-2618-2-1). From a nutritional perspective, young animals, such as lambs, can be considered non-ruminants (Y. Li, L. Ren, Y. Wang, J. Li, et al., Nutrients, 14, 2022, https://doi.org/10.1017/S1751731119003148). The gut is not only a key organ for digestion and absorption of nutrients, but also plays a variety of important roles in maintaining overall health. Thus, udder feeding may have a significant effect on the construction of the gut microbiota in lambs until 20 days of age. Although the relationship between breast milk (BM) and the gut microbiota of young animals has been reported, its specific impact on goats has yet to be thoroughly explored. Therefore, this study aimed to comprehensively reveal the influence of breast milk feeding on the development of intestinal microorganisms in goat kids and the interaction relationships between breast milk microbiome and fecal microbiome.},
}

@article {pmid41114498,
year = {2025},
author = {Tarquinio, KM and Farrell, J and Varga, JJ and Zhao, C and Mehlferber, E and Brown, SP},
title = {Mapping the respiratory microbiome in intubated children over time.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0044825},
doi = {10.1128/spectrum.00448-25},
pmid = {41114498},
issn = {2165-0497},
abstract = {Children who require airway intubation are almost always treated with empiric antibiotics, pending clinical microbiology results. Positive pathogen results are near inevitable, due to the frequent presence of potential opportunistic pathogens, whether they are causing disease or not. This pattern leads to potential antibiotic over-prescribing, to the detriment of both patients who do not require antibiotics and to antimicrobial stewardship goals. To assess our hypothesis that opportunistic pathogens are more common in children with prior lung disease, we prospectively profiled tracheal aspirate (TA) microbiome samples in children with and without prior lung disease. An IRB approval was obtained, and TAs were collected longitudinally. Samples were analyzed using 16S rDNA sequencing and conventional cultures. Patient demographics and clinical courses were obtained using electronic medical records. Thirteen subjects were included, producing 39 TA samples. Microbiome analysis identified 98 bacterial genera, dominated by Pseudomonas and Streptococcus. Patient identity was a significant determinant of TA sample variation, indicating a robust individual TA microbiome despite the presence of substantial antibiotic exposures. In contrast, clinical category and time since intubation were not significant predictors, in the context of substantial inter-patient variation. Our results reveal substantial inter-patient variation in TA microbiome structure, limiting our ability to test for significant impacts of clinical category on microbiome structure. Our results provide information for the design of larger-scale studies to evaluate the role of clinical history and specific taxa in governing the interplay between antibiotics and pathogen dynamics in critically ill children.IMPORTANCEClinicians often prescribe empirical antibiotics for critically ill, intubated children with suspected respiratory infections, contributing to antibiotic overuse and challenging antimicrobial stewardship. Our longitudinal tracheal aspirate analysis of cultures and 16S rDNA sequencing revealed significant inter-patient variability, regardless of the primary reason for intubation. We observed both concordance and discrepancies between clinical microbiology and sequencing results-gram-negative organisms aligned well between methods, whereas Streptococcus was detected in 34 of 39 samples by 16S rDNA but only once by culture. Our findings emphasize the value of longitudinal airway microbiome analysis in pediatric patients. Given the heterogeneous pathologies and diverse age groups in pediatric intensive care, future large-scale studies should account for antibiotic exposure, commensal bacterial interactions, and clinical conditions that influence microbiome dynamics. Expanding research in this area could improve our understanding of microbial shifts in critically ill children and inform more targeted treatment strategies.},
}

@article {pmid41114153,
year = {2025},
author = {Bera, S and Fouladi, F and Peddada, S},
title = {Cluster Based Association Measures with Applications.},
journal = {Sankhya. Series B. [Methodological.]},
volume = {},
number = {},
pages = {},
pmid = {41114153},
issn = {0581-5738},
abstract = {It is well recognized that relationships between variables are not always linear or even monotonic. For example, the expressions of cell-cycle, or circadian clock genes, or the abundance of microbes in a dynamic ecology are not expected to be linear. Furthermore, unknown to the researcher, there may be heterogeneous subgroups or clusters in the data. Researchers may be interested in discovering those clusters and derive an overall measure of association between variables of interest accounting for the different clusters as well as deriving associations within each cluster. Although standard concepts of correlations, such as the Pearson or Spearman, are widely used to describe overall associations, they can be misleading in such situations. As researchers continue to generate complex high dimensional data with hidden substructures or clusters, there is an urgent need for a measure that correctly quantifies associations between variables while agnostically accounting for hidden clusters in the data. Using clustering algorithms which are able to detect hidden clusters and association measures which are suitable for quantifying arbitrary relationships within each clusters, we develop a novel association procedure called CLuster based Association Measures (CLAM) to describe association between pairs of univariate as well as multivariate variables. The method is not limited to any specific form of association and is well-suited for heterogeneous data with hidden clusters, which are common in biomedical research. Performance of CLAM is evaluated using a synthetic data as well as real data from diverse applications, such as fission yeast (S. pombe) cell-cycle genes data, intestinal microbiome data from IBD patients, and three well-known imaging data sets, namely DrivFace data, Landsat data, and COIL data.},
}

@article {pmid41114144,
year = {2025},
author = {Shoaib, M and Li, G and Liu, X and Arshad, M and Zhang, H and Asif, M and Brestic, M and Skalicky, M and Wu, J and Zhang, S and Hu, F and Li, H},
title = {Nanoplastic alters soybean microbiome across rhizocompartments level and symbiosis via flavonoid-mediated pathways.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1676933},
pmid = {41114144},
issn = {1664-462X},
abstract = {Plastic pollution, particularly its breakdown into nanoplastics (NPs), poses a significant threat to ecosystem services, with notable effects on soil-plant-microbe interactions in agricultural systems. However, there is limited understanding of how NPs influence the soil microbiome and plant symbiotic functions. In this study, we applied polypropylene (PP) and polyethylene (PE) NPs, measuring 20 to 50 nm, to soybean growing conditions. We evaluated soil physicochemical properties, nodule counts, nitrogenase activity, and bacterial community composition in nodule, rhizosphere, and bulk soil under different concentrations of these NPs (200, 500, and 1000 mg/kg of soil w/w). Our results revealed that the impact of NPs on soil physicochemical properties was type-dependent, with PE-NPs exerting a more pronounced effect on soil enzyme activities than PP-NPs. Both NPs treatments accelerated nodulation and increased nitrogenase activity, with lower doses inducing more significant effects. Furthermore, PE and PP-NPs enriched bacterial species such as Ensifer and Arthrobacter, which positively interact with diazotrophs such as Bradyrhizobium, supporting symbiosis and biological nitrogen fixation. NPs treatments also significantly affected the bacteriome assembly process in the bulk soil, rhizosphere, and nodule, with an increased source ratio from the rhizosphere to the nodule and homogenous selection in the nodule bacteriome, likely benefiting bacteria involved in nodulation. Exposure to 500 mg/kg of both NPs caused alterations in the metabolic exudation profile of the plant rhizosphere, particularly influencing the biosynthesis pathways of flavonoids and isoflavonoids. Metabolites such as genistein and naringenin emerged as key mediators of plant-microbe interactions, further enhancing plant symbiotic processes under NPs exposure. This study demonstrates that NPs influence plants' symbiotic potential both directly, by altering the composition of the soil bacteriome, and indirectly, by affecting exudation potential. It provides strong evidence that NPs, especially those smaller than a micrometer, can have long-term effects on the stability and functionality of agricultural ecosystems.},
}

@article {pmid41114113,
year = {2025},
author = {Wu, TT and Zhou, X and Huang, Q and Yang, Q},
title = {Effectiveness of multi-region 16S rRNA gene sequencing in studying the microbiome of gastric cancer tissues.},
journal = {World journal of gastrointestinal oncology},
volume = {17},
number = {10},
pages = {110997},
pmid = {41114113},
issn = {1948-5204},
abstract = {BACKGROUND: The gastric microbiome is closely associated with gastric cancer, and single-region 16S rRNA sequencing has limitations in analyzing its characteristics, necessitating the search for a better sequencing method.

AIM: To evaluate the effectiveness of multi-region 16S rRNA gene sequencing in studying the microbiome of gastric cancer tissues.

METHODS: Patients with gastric cancer (n = 118) who underwent surgery at Liyang People's Hospital from January 2022 to December 2024 were enrolled. Fifty-nine paraffin-embedded and 59 fresh tissue samples were obtained. The ZymoBIOMICS[TM] microbial community standard and Escherichia coli ATCC 25922 were used as positive controls. Multi-region and single-region 16S rRNA gene sequencing were performed. Species identification, detection rates at varying microbial abundances, operational taxonomic unit (OTU) counts, and alpha diversity indices in gastric cancer tissues were compared between the two methods.

RESULTS: Multi-region 16S rRNA sequencing identified more species (eight species and eight genera) in the positive controls compared with single-region sequencing (one species and six genera). Detection rates at concentrations of 10[3], 10[2], and 10 CFU/mg were significantly higher using multi-region sequencing (P < 0.05). Multi-region sequencing also revealed significantly higher OTU counts and alpha diversity indices (Shannon, Simpson, and Chao1) in gastric cancer tissues (P < 0.05).

CONCLUSION: Compared with single-region sequencing, multi-region 16S rRNA gene sequencing demonstrates superior species resolution and detection sensitivity, providing a more comprehensive profile of microbial diversity in gastric cancer tissues.},
}

@article {pmid41114103,
year = {2025},
author = {Liu, XX and Yang, B and Tang, DX},
title = {Bidirectional regulation of the gut microbiome-immune axis in the immune microenvironment of colorectal cancer and targeted interventions.},
journal = {World journal of gastrointestinal oncology},
volume = {17},
number = {10},
pages = {109503},
pmid = {41114103},
issn = {1948-5204},
abstract = {The initiation and progression of colorectal cancer (CRC) are profoundly influenced by the complex interplay between the gut microbiota and the immune system, underscoring the clinical importance of exploring the bidirectional regulatory mechanisms of the microbiota-immune axis within the CRC immune microenvironment. Emerging evidence indicates that the composition and functional capacity of the gut microbiota play a vital role in modulating the host's immune responses, while the immune system, in turn, can reciprocally regulate the structure and function of the microbiota. Despite significant insights into the role of the microbiota-immune axis in CRC progression, several critical questions remain unanswered-including how microbial heterogeneity affects therapeutic outcomes and the specific consequences of dysregulated regulatory mechanisms on the immune microenvironment. This review aims to provide a comprehensive analysis of the compositional features of the CRC immune microenvironment, examine the bidirectional molecular mechanisms underpinning the microbiota-immune axis, and evaluate the potential of targeted therapeutic strategies, thereby offering novel research perspectives and clinical applications for CRC treatment.},
}

@article {pmid41114048,
year = {2025},
author = {Andermann, TM and Zeng, K and Guirales-Medrano, S and Groth, A and Ramachandran, BC and Sun, S and Sorgen, AA and Hill, L and Bush, AT and Liu, H and Jones, C and Roach, J and Conlon, BP and Rao, G and Chao, NJ and Fodor, AA and Sung, AD},
title = {Duration of Hospitalization is Associated with the Gut Microbiome in Patients Undergoing Hematopoietic Stem Cell Transplantation: Early Results from a Randomized Trial of Home Versus Hospital Transplantation.},
journal = {OBM transplantation},
volume = {9},
number = {3},
pages = {},
pmid = {41114048},
issn = {2577-5820},
abstract = {Home-based hematopoietic stem cell transplantation (HCT) is an innovative care model with growing interest, but its impact on the gut microbiome remains unexplored in a randomized setting. We present interim results from the first randomized controlled trials (RCT) evaluating the effect of HCT location-home versus hospital-on gut microbial diversity and antimicrobial resistance (AMR) gene carriage. We hypothesize that patients randomized to undergo home HCT would have higher gut taxonomic diversity and lower AMR gene abundance compared to those undergoing standard hospital HCT. We analyzed stool samples from the first 28 patients enrolled in ongoing Phase II RCTs comparing home (n = 16) and hospital (n = 12) HCT at Duke University using shotgun metagenomic sequencing to compare taxa and AMR gene composition between groups. We also performed a secondary analysis comparing patients who received transplants at outpatient infusion clinics versus inpatient standard HCT to evaluate the influence of hospitalization duration. In the primary RCT analysis, taxonomic and AMR gene α- and β-diversity were comparable between home and hospital groups, reflecting similar durations of hospitalization despite group allocation. In contrast, secondary analyses demonstrated that patients transplanted in outpatient infusion clinics who experienced significantly reduced hospitalization had higher gut taxonomic α-diversity and differential β-diversity, although AMR gene diversity remained unchanged. In summary, randomization by transplant location did not impact the gut microbiota to the same extent as the duration of hospitalization, although secondary analyses were heavily confounded. Even when taxonomic differences were observed, AMR genes were similar between groups. This RCT represents a novel investigation into how care setting influences the gut microbiome during HCT. Our findings suggest that hospital duration, rather than randomization allocation alone, is the primary driver of microbial disruption. These results underscore the potential for reducing hospital duration to mitigate microbiome injury, thereby informing future interventions to reduce infection risk and improve patient outcomes.},
}

@article {pmid41114005,
year = {2025},
author = {Sun, R and Xu, W and Xu, Y and Xu, Z and Tan, Y and Li, J and Liu, H and Yung, CCM},
title = {Environmental gradients shape viral-host dynamics in the Pearl River estuary.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf164},
pmid = {41114005},
issn = {2730-6151},
abstract = {Marine viruses play critical roles in shaping microbial communities and driving biogeochemical cycles, yet their dynamics in estuarine systems are not well characterized. Here, we conducted a comprehensive metagenomic analysis of viral communities and virus-host interactions across the Pearl River estuary, a dynamic subtropical estuary in southern China. Using 24 metagenomic libraries from eight sampling sites, we identified 29,952 viral populations, with Uroviricota and potential Uroviricota accounted for 80.48% of taxa, underscoring their ecological importance. A key finding of our integrated analysis is the unexpectedly high abundance of nucleocytoplasmic large DNA viruses in offshore waters, which suggests a more significant role for eukaryotic viruses in coastal ecosystems than previously acknowledged and correlates with elevated levels of their eukaryotic hosts. Environmental variables, particularly salinity and nutrient availability, emerged as key drivers of viral and host distribution patterns. By linking environmental gradients to distinct community "envirotypes" and their underlying genomic features, we revealed novel virus-host interactions and highlighted the impact of environmental gradients on microbial ecology. Additionally, viral auxiliary metabolic genes linked to phosphorus and nitrogen metabolism suggest critical roles in modulating host metabolic pathways and influencing nutrient cycling. Our findings demonstrate how spatial heterogeneity and environmental gradients shape viral and microbial ecology in estuarine ecosystems. Our findings provide a holistic, multi-domain view of microbial and viral ecology, demonstrating how integrating prokaryotic, eukaryotic, and viral community analyses offers a more complete understanding of ecosystem function in these critical transition zones.},
}

@article {pmid41113903,
year = {2025},
author = {Cheng, CH and Hung, CC and Wu, CY and Lin, CM and Fang, JT and , },
title = {Beyond the Pillow: Linking Subjective and Objective Sleep Measures to Gut Microbiome Composition in Community-Dwelling Older Adults.},
journal = {Nature and science of sleep},
volume = {17},
number = {},
pages = {2657-2668},
pmid = {41113903},
issn = {1179-1608},
abstract = {BACKGROUND: Sleep-related complaints are common among older adults, and recent research indicates that changes in sleep patterns may be associated with alterations in the composition of the gut microbiome (GM). However, investigations into the relationship between sleep measures and GM abundance among older adults have been limited thus far. This study represents the first large-scale effort to comprehensively explore the connection between GM composition and both subjective and objective sleep measures in older adults.

METHODS: The study included 279 cognitively-normal older adults from the community who had not used sleep medication, antibiotics, or probiotics for at least one month before providing stool samples. Participants were categorized as good sleepers (GS) or poor sleepers (PS) based on the Pittsburgh Sleep Quality Index (PSQI) scores. GM diversity and relative abundance were compared between both groups, and their associations with PSQI scores and objective sleep measures were also examined.

RESULTS: Alpha and beta diversity did not show significant differences between the GS and PS groups. However, significant differences in GM relative abundance across various taxonomic levels were found between the GS and PS groups. In the overall sample, higher PSQI scores were linked to lower abundance of the species Hungatella_hathewayi (p = 0.005, false discovery rate = 0.035). However, there were no significant associations between GM abundance and objective sleep measures after corrections for multiple comparisons.

CONCLUSION: These findings suggest that specific gut microbial taxa are associated with subjective sleep disturbances in older adults.},
}

@article {pmid41113721,
year = {2025},
author = {Ou, Y and Wang, H and Zhou, C and Chen, Y and Lyu, J and Feng, M and Huang, X},
title = {Endometriosis-associated infertility: Multi-omics insights into pathogenesis and precision therapeutics.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1613334},
pmid = {41113721},
issn = {1664-2392},
mesh = {Humans ; *Endometriosis/complications/therapy/metabolism/genetics ; Female ; *Infertility, Female/etiology/therapy/metabolism ; *Precision Medicine/methods ; Multiomics ; },
abstract = {INTRODUCTION: Endometriosis is a prevalent, estrogen-dependent, inflammatory disease that impairs fertility via hormonal dysregulation, immune dysfunction, oxidative stress/ferroptosis, genetic and epigenetic alterations, and microbiome imbalance. We summarize multi-omics insights and clinical implications for endometriosis-associated infertility.

METHODS: This article is a Systematic Review that synthesizes recent multi-omics and clinical evidence on mechanisms (hormonal, immune-inflammatory, oxidative stress/ferroptosis, genetic/epigenetic, microbiome/metabolic) and appraises therapeutic strategies spanning surgery, hormonal suppression, assisted reproductive technologies (ART), and emerging adjuncts. Mechanistic and clinical findings are integrated to map targets, biomarkers, and precision-care opportunities across disease phenotypes.

RESULTS: Evidence indicates local estrogen dominance with progesterone resistance, pervasive immune dysregulation, and oxidative stress with iron-driven ferroptosis that particularly injures granulosa cells, alongside disease-relevant genetic/epigenetic regulators and reproductive-tract/gut microbiome dysbiosis. Clinically, endometriosis detrimentally affects ovarian reserve and oocyte competence, disrupts endometrial receptivity/decidualization, and remodels pelvic anatomy through adhesions and fibrosis, cumulatively reducing fecundity. Current management includes laparoscopic excision/ablation, hormonal suppression (e.g., progestins, GnRH analogs/antagonists), and ART tailored to goals and disease severity. Adjunctive antioxidant and immune-modulating approaches show promise but require robust clinical validation. Biomarker discovery-including epigenetic regulators and microbiome-derived signals-may enable earlier diagnosis and personalization. Innovative avenues include immunotherapy targeting nociceptor-immune crosstalk, ferroptosis modulation, microbiota manipulation, and diet-based metabolic strategies.

DISCUSSION: The pathogenesis of endometriosis-associated infertility is multifactorial and interconnected. While current treatments offer benefits, their efficacy is variable. The integration of multi-omics data is unveiling novel diagnostic biomarkers and therapeutic targets. Future management requires a patient-centered, multidisciplinary precision medicine approach that combines mechanistic insights with individualized treatment strategies to improve reproductive outcomes across the disease spectrum.},
}

Humans
*Endometriosis/complications/therapy/metabolism/genetics
Female
*Infertility, Female/etiology/therapy/metabolism
*Precision Medicine/methods
Multiomics

@article {pmid41113655,
year = {2025},
author = {Mote, S and De, K and Nanajkar, M and Gupta, V},
title = {Unraveling the bacterial composition of a coral and bioeroding sponge competing in a marginal coral environment.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1550446},
pmid = {41113655},
issn = {1664-302X},
abstract = {The newly described bioeroding sponge Cliona thomasi, part of the Cliona viridis complex, is contributing to coral decline in the central eastern Arabian Sea, the West Coast of India. While its morphological and allelopathic mechanisms in coral invasion are well investigated, the role of its microbial communities in spatial competition is underexplored. This study focuses on the coral Turbinaria mesenterina and sponge C. thomasi, both known for their distinct symbiotic associations with Symbiodiniaceae. A 16S rRNA V3-V4 amplicon next-generation sequencing approach, followed by processing through the DADA2 algorithm, was used to analyze the bacterial composition. The results showed higher bacterial richness and diversity in coral samples, identifying 30 distinct phyla, compared to 14 in sponge samples. The coral samples were dominated by Proteobacteria, Actinobacteria, Firmicutes, Cyanobacteria, Planctomycetes, Chloroflexi, and Patescibacteria, while Proteobacteria, Cyanobacteria, Planctomycetes, and Actinobacteria were dominant in the sponge. Enrichment analysis revealed higher dominance of Acidobacteria, Actinobacteria, Chloroflexi, Dadabacteria, Firmicutes, Fusobacteriota, and Patescibacteria in the coral samples, while the sponge samples showed enrichment for Cyanobacteria, Planctomycetes, and Bdellovibrionota. Beta-diversity analysis (PERMANOVA and nMDS) showed significant differences, with an average dissimilarity of 81.44% between sponge and coral samples (SIMPER). These differences highlight variations in microbial profiles between sponges and corals, competing in the same vulnerable environment. Exploring the microbiome aspect, therefore, may elucidate physiological and ecological functions of the holobiont while also representing a health status biomarker for corals, supporting their conservation.},
}

@article {pmid41113651,
year = {2025},
author = {Lan, R and De Paula Ramos, L and Chen, Z and Carrouel, F},
title = {Editorial: Exploring the oral-gut microbiome interactions: pathways to therapeutic strategies and implications for systemic health.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1691238},
pmid = {41113651},
issn = {1664-302X},
}

@article {pmid41113648,
year = {2025},
author = {Dong, L and Du, Y and Qiu, F and Zhang, M and Wang, X and Zhu, X and Yao, Y and Li, J and Ji, X and Zhu, X},
title = {Metagenomic insights reveal the differences in the community composition and functional characteristics of the sea turtle microbiomes based on host species and tissue region.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1652229},
pmid = {41113648},
issn = {1664-302X},
abstract = {INTRODUCTION AND METHODS: Sea turtles have been proposed as health indicators of marine ecosystems for their characteristic of longevity and migratory, but they are facing serious threats due to various factors. The microbial communities within animals play an important role in health and disease. Our study aims to explore a thorough evaluation of the sea turtle microbiome by examining the oral, nasal, and cloacal microbial communities of three species: green turtles, hawksbills, and loggerheads, through metagenomic sequencing.

RESULTS: Utilizing approximately 705.81 GB of metagenomic sequencing data from 63 samples collected from different turtle species and tissue regions, we created a nonredundant sea turtle microbial gene catalog (STMGC) containing 10,733,232 unique genes through the de-redundancy of open reading frames (ORFs). Our findings revealed that the sea turtle microbiomes were primarily composed of Pseudomonadota (formerly Proteobacteria) and Bacteroidota (formerly Bacteroidetes). The tissue region was a key factor affecting the variability in the sea turtle microbiome, with green turtles showing notable differences among the three turtle species. Pseudomonadota was significantly more abundant in oral samples, while Bacteroidota was more prevalent in nasal samples. Campylobacterota was identified as significantly more abundant in cloacal samples. Importantly, we discovered 389 genera and 1,445 species of potential pathogens within the sea turtle microbiome, indicating potential pathogenic risks that warrant further investigation alongside culturomics. Additionally, our study highlighted significant functional differences among the three turtles and tissue regions. It is worth noting that among the three sea turtles, antibiotic resistance genes are more prevalent in hawksbills, while virulence genes are more abundant in loggerheads. Moreover, within the three tissue regions, antibiotic resistance genes are higher in oral samples, while virulence genes are more extensive in cloacal samples.

CONCLUSION: The findings in our study demonstrate that the microbial composition and function in these sea turtles exhibit both species-specific and region-specific variations. The implications of these associations and the underlying mechanisms not only provide valuable insights for future studies on the microbial communities of turtles, but also lay the foundation for further research on the health interrelationships among sea turtles, marine and terrestrial animals, humans and the environment, and for defining "One Health" factors.},
}

@article {pmid41113646,
year = {2025},
author = {Chen, X and Wu, J and Fan, D and Zhang, P and Li, Y and Cao, Y and Cao, M},
title = {Gut viral metagenomics identifies viral signatures and their role in depression.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1573851},
pmid = {41113646},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiome has been implicated in the onset and progression of depression. Yet, the role of the gut virome in depression remains unexplored, and a diagnostic model has not been satisfactorily constructed.

METHODS: Herein, we analysed the gut virome profiles of 29 patients with depression and 33 healthy controls using bulk metagenome sequencing.

RESULTS: A total of 45 differentially abundant viral taxa were identified, among which four, s_Stenotrophomonas_virus_Pokken, g_Pokkenvirus, s_Dickeya_virus_AD1, and g_Alexandravirus, demonstrated strong diagnostic potential (AUCs > 0.8). These four viruses also exhibited strong correlations, suggesting they may constitute a synergistic ecological cluster. Function annotation revealed seven metabolic pathways with significant differences, including alanine, aspartate, and glutamate metabolism, branched-chain amino acid (BCAA) biosynthesis, and energy metabolism in patients with depression.

CONCLUSION: This study identified four distinct viral signatures for depression and proposes novel viral biomarkers for the diagnosis of depression, offering a robust diagnostic approach and new insights into the pathological mechanisms of depression.},
}

@article {pmid41113645,
year = {2025},
author = {Durán-González, E and Ramírez-Tejero, JA and Pérez-Sánchez, M and Morales-Torres, C and Gómez-Morano, R and Díaz-López, C and Martínez-Lara, A and Cotán, D},
title = {Fibromyalgia diagnosis from a multi-omics approach: a gut feeling.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1641185},
pmid = {41113645},
issn = {1664-302X},
abstract = {BACKGROUND: Fibromyalgia is a complex disorder whose main symptoms are chronic widespread pain and fatigue and affects between 0.2 and 6.6% of the world population. Nowadays, there are no molecular biomarkers that could facilitate diagnosis. The latest efforts by researchers have focused on studying problems at the level of central nervous system sensitivity, inflammation, and oxidative disorders.

METHODS: A total of 892 women were initially enrolled in the study. For individuals who met the inclusion criteria, a plasma proteome analysis was conducted using blood samples. Briefly, blood was collected, centrifuged, and analyzed by liquid nano-chromatography coupled to tandem mass spectrometry. After the raw data analysis, proteins with statistically significant differential abundance and a fold change over 1.2 (20% increase in fibromyalgia compared with control samples) or under 0.8 (20% decrease in fibromyalgia compared with control samples) in fibromyalgia were selected. For fecal metagenome analysis, fecal samples were collected and processed for DNA extraction. Amplicon sequencing of V3-V4 regions from the 16S ribosomal RNA gene was performed using the Illumina MiSeq platform. The statistical analysis was conducted using R v4.3.2 base packages.

RESULTS: After applying exclusion criteria, 242 women (199 patients and 43 age- and environmentally paired controls) provided plasma and feces samples, as well as properly filled health questionnaires. A total of 30 proteins and 19 taxa were differentially expressed in fibromyalgia patients, and their integration into an algorithm allows for discrimination between cases and controls. The multi-omic approach for biomarker discovery in this study proposes a multifactorial connection between gut microbiota and mitochondria-derived oxidative stress and inflammation.

CONCLUSIONS: Plasma and fecal multi-omics analysis suggest an intricate and multifactorial connection between gut microbiota and mitochondria-derived oxidative stress and inflammation in FM patients, with glyceraldehyde-3-phosphate dehydrogenase and Streptococcus salivarius as leading actors.

TRIAL REGISTRATION: NCT05921409.},
}

@article {pmid41113638,
year = {2025},
author = {Verma, D and Zhang, Z and Liu, J},
title = {Editorial: Tobacco disease and biological control.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1694523},
pmid = {41113638},
issn = {1664-302X},
}

@article {pmid41113630,
year = {2025},
author = {Ngari, C and Poulet, V and Percoco, G and Peno-Mazzarino, L and Seyer, D},
title = {Early skin colonization by Staphylococcus epidermidis and Staphylococcus aureus reveals environment-dependent synergistic effects.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1677214},
pmid = {41113630},
issn = {1664-302X},
abstract = {INTRODUCTION: The skin microbiome is crucial for skin health and homeostasis. It contributes to immune defense, promotes epidermal differentiation, and supports a robust skin barrier function. Despite its importance, few studies have used model skin systems to examine how simple bacterial communities interact and how they impact the skin.

METHODS: We studied the interaction between a skin commensal, Staphylococcus epidermidis, and a pathogen, Staphylococcus aureus, by performing inoculations and co-inoculations on Reconstructed Human Epidermis (RHE) models maintained under classical humid conditions (>90% relative humidity) or dry conditions (<25% RH). In parallel, inoculations were conducted on human skin explants using a novel culture setup preserving physiological humidity levels (40-60% RH). Bacterial attachment was assessed 4 h post-inoculation. At 24 h, histology was examined, three natural moisturizing factors (NMFs) were quantified. Filaggrin (FLG) and ceramide levels were analyzed to assess the skin barrier function.

RESULTS: In contrast to previous findings at 24 h, co-inoculation increased S. epidermidis and S. aureus attachment in RHEs, but only under humid conditions. Only RHE maintained in dry conditions and skin explant revealed an effect of co-inoculation on filaggrin (FLG), yet an increase in RHEs and a decrease in skin explants. In both RHEs maintained in dry conditions and skin explants, NMF levels were consistently reduced following co-inoculation. In RHEs and skin explants, inoculation with S. aureus alone also lowered NMFs, with co-inoculation further amplifying this effect. Finally, ceramide levels increased similarly across both inoculations and co-inoculation.

DISCUSSION: Revealing unexpected early interactions between S. epidermidis, S. aureus, and the skin, our results could suggest that co-inoculation may trigger a synergetic disruption of the barrier function. Alternatively, it could imply that co-inoculation might reinforce the epidermal barrier via a S. aureus-mediated stimulation of the protective functions of S. epidermidis. Further studies are needed to confirm these effects and determine whether they are strain-specific or more broadly applicable.},
}

@article {pmid41113141,
year = {2025},
author = {Waseem, MH and Abideen, ZU and Shoaib, A and Rehman, N and Osama, M and Sajid, B and Ahmad, R and Fahim, Z and Ansari, MW and Aimen, S and Cheema, AH and Thada, PK},
title = {Fecal Microbiota Transplantation for Treatment of Parkinson's Disease: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.},
journal = {Journal of central nervous system disease},
volume = {17},
number = {},
pages = {11795735251388781},
pmid = {41113141},
issn = {1179-5735},
abstract = {BACKGROUND: Emerging evidence has indicated gut dysbiosis as a potential modifiable contributor to the pathogenesis of Parkinson's disease (PD). Fecal microbiota transplantation (FMT), a microbiome-centric model aimed at modulating the intestinal microbial taxa, represents a novel therapeutic approach. However, its safety and efficacy profile in improving PD symptoms remains inadequately researched.

METHODS: PubMed, ScienceDirect, and the Cochrane Central Registry were searched to retrieve relevant articles from inception till February 2025. Risk ratios (RR) and Mean differences (MD), along with 95% confidence intervals (CI), were pooled under the random-effect model for dichotomous and continuous outcomes, respectively. The primary outcomes of interest were change in Movement Disorder Society Unified Parkinson's Disease Rating Scale part 1 (MDS-UPDRS 1), change in MDS-UPDRS 2. Secondary endpoints of interest were change in MDS-UPDRS 3 (on medication), change in MDS-UPDRS 3 (off medication), change in MDS-UPDRS 4, change in Irritable Bowel Severity Scoring System (IBS-SSS), change in Montreal Cognitive Assessment (MoCA), change in Parkinson Disease Questionnaire Summary Index (PDQ-39 SI), and GI adverse events. The Cochrane Risk of Bias 2.0 (RoB 2.0) tool was used for the quality assessment of the included randomized controlled trials (RCTs). A Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) assessment was done for the certainty of evidence.

RESULTS: This systematic review and meta-analysis included 145 patients across 3 RCTs. FMT and placebo were comparable regarding the primary outcomes that include MDS-UPDRS Part I (MD = -0.36; 95% CI:[-2.18,1.45]; P = .70; I[2] = 33%), Part II (MD = -0.46; 95% CI:[-1.91,0.99]; P = .53; I[2] = 0%). The secondary outcomes, involving MDS-UPDRS Part III on-medication (MD = 1.41; 95% CI:[-2.14,4.42]; P = .50; I[2] = 17%), Part III off-medication (MD = 1.26; 95% CI:[-2.27,4.79]; P = .48; I[2] = 0%), and Part IV (MD = -0.39; 95% CI:[-1.63,0.85]; P = .54; I[2] = 24%) were also comparable between the two groups. No significant changes were observed in IBS-SSS (MD = -15.91; 95% CI:[-63.17,31.89]; P = .51; I[2] = 76%), PDQ-39 SI (MD = -2.13, 95% CI:[-5.62,1.36]; P = .23; I[2] = 0%), and MOCA scores (MD = 0.11; 95% CI:[-1.34,1.57]; P = .88; I[2] = 68%). However, the FMT group had more frequent adverse gastrointestinal events (RR = 3.32; 95% CI: [1.01,10.87]; P = .05; I[2] = 39%).

CONCLUSION: FMT shows no evidence of superiority compared to placebo. Variations in the findings of existing studies suggest that donor fecal composition, host-microbiota interactions, and methodological heterogeneity may determine outcomes. Further RCTs employing tailored microbiota and standardized endpoint metrics are required to establish a correlation between FMT and PD.},
}

@article {pmid41113084,
year = {2025},
author = {Curto, A and Iamello, RG and Lynch, EN and Galli, A},
title = {Advancing the management of primary biliary cholangitis: From pathogenesis to emerging therapies.},
journal = {World journal of clinical cases},
volume = {13},
number = {30},
pages = {109028},
pmid = {41113084},
issn = {2307-8960},
abstract = {Primary biliary cholangitis is a chronic cholestatic autoimmune liver disease that progressively damages the bile ducts, leading to cholestasis and, in advanced stages, cirrhosis. While it primarily affects middle-aged women, recent data indicate a rising incidence in men. The interplay between genetic susceptibility, environmental exposures, and gut microbiome alterations is thought to drive disease onset. Diagnosis relies on persistent cholestatic enzyme elevation, disease-specific autoantibodies, and, in select cases, liver biopsy. Ursodeoxycholic acid remains the cornerstone of treatment, but many patients show an incomplete response. The recent withdrawal of obeticholic acid from the market, due to insufficient evidence of long-term benefit, has highlighted the urgent need for effective second-line therapies. Agonists of peroxisome proliferator- activated receptors, such as elafibranor and seladelpar, have demonstrated promising biochemical improvements and may reshape the therapeutic landscape. Future research is focused on refining risk assessment, optimizing treatment combinations, and addressing symptoms such as fatigue and pruritus to enhance patient well-being. A shift toward early intervention and personalized treatment strategies may further improve long-term outcomes in primary biliary cholangitis.},
}

@article {pmid41112829,
year = {2025},
author = {Tansarawut, P and Boonsoongnern, P and Kamlangdee, A and Woonwong, Y and Boonsoongnern, A},
title = {Gut Health Evaluation Using Gut Microbiome and Intestinal Alkaline Phosphatase Levels in Postweaning Diarrhoea.},
journal = {Veterinary medicine international},
volume = {2025},
number = {},
pages = {4499017},
pmid = {41112829},
issn = {2090-8113},
abstract = {Postweaning diarrhoea (PWD) poses a significant threat to the swine industry by causing notable declines in productivity and mortality. Gut health diagnosis in pigs typically involves complex methods such as gut microbiome analysis, which can be costly and can require specialised skills. This study aimed to assess gut health in postweaning piglets by measuring and comparing gut microbiome profiles and levels of intestinal alkaline phosphatase (IALP) in faecal samples from pigs with and without PWD. This study revealed significant differences between the nondiarrhoea and diarrhoea groups of piglets in terms of IALP levels and gut microbiome composition. Nondiarrhoeal piglets had greater IALP levels than did diarrhoeal piglets (p=0.003). Additionally, faecal flora richness (observed (p=0.0007) and Chao1 (p=0.0007)) indices of the faecal microflora in the nondiarrhoeal pigs. At the phylum level, Firmicutes and Bacteroidetes were predominantly abundant in both groups, while Firmicutes (p=0.0008) and Patescibacteria (p=0.0334) showed significantly lower abundances in the nondiarrhoea group and Bacteroidetes (p=0.0003) exhibited greater abundance. The Clostridia class was significantly more abundant in the diarrhoea group than the nondiarrhoea group (p=0.0159). The diarrhoea group had a significantly greater relative abundance of the Clostridiaceae family than did the nondiarrhoea group (p=0.0007). At the genus level, the relative abundance of Prevotellaceae NK3B31 was significantly greater in the nondiarrhoea group than the diarrhoea group (p=0.0032). Moreover, the relative abundances of some pathogenic bacteria, including Clostridium sensu stricto (Clostridiaceae) 1, were significantly greater in the diarrhoea group than in the nondiarrhoea group (p=0.0007). IALP levels and gut microbiome diversity in faecal samples can be used to assess the gut health of nursery pigs. These results contribute to the understanding and manipulation of postweaning piglet gut health.},
}

@article {pmid41112728,
year = {2025},
author = {Zhou, Z and Liu, B and Shen, J and Yan, C and Yang, G and Zhang, Y and Zhao, J and Chen, L},
title = {Milk fat globule membrane supplementation in formula modulates the gut microbiome and metabolic status of piglets and normalizes intestinal development.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1632519},
pmid = {41112728},
issn = {2296-861X},
abstract = {Milk fat globule membrane (MFGM) supplementation of infant formula demonstrates potential efficacy in modulating gut microbiota and metabolic profiles. However, the associated site-specific effects on intestinal microbial composition remain unclear. In this study, we used a neonatal piglet model to investigate the mechanisms associated with the metabolic regulation of supplemental MFGM and characterized the compartment-specific modulatory effects on intestinal microbial communities. A total of 20 piglets were randomly allotted to one of the following three groups: breastfed (BF), standard formula (SF), and MFGM-supplemented formula (EF). These diets were administered until weaning, with subsequent provision of commercial feed until euthanasia. Morphometric, microbial, and serum metabolomic analyses revealed that compared to piglets in the SF group, those in the EF group were characterized by significantly enhanced jejunal villus height (p < 0.05) and reduced cecal Oxalobacter (p < 0.05) and Pasteurella abundances, which were comparable to the levels detected in the BF group. Metabolically, piglets in the SF group demonstrated significantly lower levels of tyrosine, phenylalanine, and β-alanine (p < 0.05) and higher levels of 3-methyl-2-oxovalerate (p < 0.05) than those in BF piglets. In contrast, compared to the SF piglets, EF piglets exhibited significantly elevated levels of betaine (p < 0.05) and lysine. Spearman's correlation analysis revealed significant positive associations between Oxalobacter abundance and creatinine, dimethyl sulfone, phenylalanine, tyrosine, and β-alanine concentrations, with inverse correlations observed for 3-methyl-2-oxovalerate and lysine levels. In conclusion, these findings revealed that MFGM supplementation contributes to maintaining a normal intestinal architecture, modulates site-specific microbiota, and mitigates metabolic disparities between formula-fed and breastfed neonates. Notably, these effects are primarily mediated via choline pathway regulation and competitive inhibition of pathogenic bacteria.},
}

@article {pmid41112578,
year = {2025},
author = {Chen, J and Xu, Q and Zhang, L and Zhang, D and Wu, X},
title = {Enrichment of prevotella melaninogenica in the lower respiratory tract links to checkpoint inhibitor pneumonitis and radiation pneumonitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1594460},
pmid = {41112578},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; Middle Aged ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; *Radiation Pneumonitis/microbiology ; *Prevotella/isolation & purification/genetics/classification ; Microbiota ; Lung Neoplasms/drug therapy ; *Immune Checkpoint Inhibitors/adverse effects ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Pneumonia/microbiology ; Lung/microbiology ; },
abstract = {BACKGROUND: Checkpoint inhibitor pneumonitis (CIP) and radiation pneumonitis (RP) lead to anti-cancer therapy discontinuation and poor diagnosis. The human microbiome is related to various respiratory diseases. However, the role of the lung microbiome in CIP and RP remains unknown. Our study aimed to explore the lower respiratory tract (LRT) microbiome in CIP/RP patients.

METHODS: The study enrolled 61 patients with pneumonitis or pneumonia, including 23 with CIP/RP, and 38 with lung cancer with pneumonia (LC-P). Metagenomic next-generation sequencing (mNGS) was performed to identify the microbiota in bronchoalveolar lavage fluid (BALF), and bioinformatics methods were used to compare the microbial differences between CIP/RP and LC-P groups. Correlation analysis was conducted to explore the relationship between LRT microbiota and clinical features.

RESULTS: The Prevotella was the dominant genus in both groups. The Prevotella melaninogenica, which belongs to the Prevotella genus, was the dominant species in the CIP/RP group and the second most abundant species in the LC-P group. Compared to the LC-P group, the CIP/RP group had significantly high levels of Prevotella melaninogenica species and lymphocyte percentage in BALF but significantly low levels of lymphocytes, eosinophils and albumin in peripheral blood. In addition, the Prevotella melaninogenica species had a negative correlation with peripheral blood lymphocytes.

CONCLUSION: The enrichment of Prevotella melaninogenica species in LRT and a decreased level of peripheral blood lymphocytes are associated with CIP/RP.},
}

Humans
Male
Female
Middle Aged
Aged
Bronchoalveolar Lavage Fluid/microbiology
*Radiation Pneumonitis/microbiology
*Prevotella/isolation & purification/genetics/classification
Microbiota
Lung Neoplasms/drug therapy
*Immune Checkpoint Inhibitors/adverse effects
High-Throughput Nucleotide Sequencing
Metagenomics
*Pneumonia/microbiology
Lung/microbiology

@article {pmid41112491,
year = {2025},
author = {Kumari V S, S and Potdar, V and Shinde, M and Parashar, D and Alagarasu, K and Cherian, S and Lavania, M},
title = {Dysbiosis of the oropharyngeal microbiota in COVID-19: distinct profiles in patients with severe respiratory symptoms.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2569523},
pmid = {41112491},
issn = {2000-2297},
abstract = {BACKGROUND: COVID-19 has been strongly associated with alterations in the oropharyngeal microbiota, yet the microbial features linked to disease severity remain unclear.

OBJECTIVE: This study aimed to elucidate the microbial signatures associated with COVID-19 disease severity.

DESIGN: 16S rRNA gene sequencing was employed to profile the oropharyngeal microbiota of patients with varying degrees of COVID-19 severity.

RESULTS: A significant reduction in alpha diversity suggests a major microbial dysbiosis in critically ill patients compared to less severe cases and healthy individuals, whereas beta diversity analysis revealed a broadly conserved community structure across different groups. Comparative analysis showed significant depletion of the phylum Fusobacteriota and enrichment of bacterial families, including Corynebacteriaceae, Methylobacteriaceae, Acetobacteraceae, Bradyrhizobiaceae, Lactobacillaceae, Staphylococcaceae, Propionibacteriaceae, and Moraxellaceae. Rothia mucilaginosa was notably enriched in patients with severe respiratory symptoms, and many of the enriched taxa are known opportunistic pathogens associated with respiratory infections.

CONCLUSION: The marked dysbiosis and enrichment of opportunistic pathogens in the oropharyngeal microbiota of critically ill patients indicate their possible role in respiratory complications. The identified microbial patterns highlight the potential of microbiome profiling as a tool for disease prognosis and guide further research into the role of microbes in COVID-19 pathogenesis and implications for treatment protocols.},
}

@article {pmid41112298,
year = {2025},
author = {Ma, T and Zhang, T and Peng, C and Liu, K and Xiong, Y and Chen, K and Peng, N and Wei, Z and Kuang, J and Ou, L},
title = {Immune cells: the key mediator between the gut microbiota and osteoporosis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1680021},
pmid = {41112298},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Osteoporosis/immunology/microbiology/metabolism/therapy/etiology ; Animals ; Bone and Bones/immunology/metabolism ; Probiotics ; },
abstract = {As the body's largest immunological interface, the intestine harbors a complex ecosystem of gut microbiota (GM) that orchestrates mucosal immune maturation while sustaining local immunological equilibrium. Emerging evidence reveals the gut's influence on skeletal homeostasis via neuro-immune-endocrine pathways-termed the gut-bone axis-though its mechanistic intricacies remain incompletely defined. Since the concept of osteoimmunology was proposed in 2000 by Arron & Choi, immune-skeletal interactions have garnered significant research traction. Immune cells primarily contribute to the maintenance of bone homeostasis through the release of pro- and anti-inflammatory factors. Consequently, the immune system represents a crucial intermediary in understanding the relationship between GM and metabolic bone diseases. This review synthesizes the interrelationships among gut microbiota, immune cells, and osteoporosis, and elucidates how GM modulate bone metabolism in osteoporosis through this critical intermediary. Furthermore, building upon the microbiome-immune-bone axis, we highlight several emerging microbiota-targeted interventions-such as probiotics, prebiotics, dietary modifications, fecal microbiota transplantation, and engineered microbes-and evaluate their clinical translational potential, with the aim of advancing diagnostic and therapeutic strategies for metabolic bone disorders.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Osteoporosis/immunology/microbiology/metabolism/therapy/etiology
Animals
Bone and Bones/immunology/metabolism
Probiotics

@article {pmid41112283,
year = {2025},
author = {Pei, X and Yu, M and Wang, Y and Zong, S and Qi, F and Wang, K},
title = {What is the relationship between microorganisms in the human body and upper tract urothelial carcinoma?.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1636782},
pmid = {41112283},
issn = {1664-3224},
mesh = {Humans ; *Microbiota/immunology ; *Urologic Neoplasms/microbiology ; Tumor Microenvironment/immunology ; *Carcinoma, Transitional Cell/microbiology ; },
abstract = {Upper Tract Urothelial Carcinoma (UTUC) is a highly malignant tumor originating from the epithelium of the upper urinary tract with diverse pathogenesis, but currently available diagnostic and therapeutic strategies have some limitations. In recent years, human microbiome-related studies have provided new ideas for the exploration of the pathogenesis and treatment of UTUC. In this paper, we review the research progress of human microbiome related to UTUC. Focusing on the urinary microbiome, the role of the microbiome in the pathogenesis of UTUC is investigated through the mechanisms of chronic inflammation, genotoxic damage, immune microenvironmental imbalance and metabolic reprogramming. The pyelo-ureteric microbiome of healthy populations is dominated by commensal bacteria such as Lactobacillus and Streptococcus, whereas pathogenic bacteria such as Escherichia coli (E. coli) and Enterococcus faecalis are significantly enriched in patients with UTUC, which results in the development of DNA damage, inflammatory response and immunosuppression. In addition, microbiome metabolites (e.g., short-chain fatty acids, tryptophan derivatives) can influence tumor progression by modulating immune checkpoints (e.g., PD-1/PD-L1, B7-H4) and metabolic pathways (e.g., Warburg effect). In diagnostic and therapeutic applications, urinary microbial markers (e.g., E. coli-specific gene clusters) can be combined with circulating tumor DNA (ctDNA) assays to improve diagnostic sensitivity and specificity, and indices of intestinal flora diversity (e.g., Simpson's index) are significantly correlated with the response rate to chemotherapy and prognostic course. In the future, we need to overcome the challenges of difficult sample acquisition, unknown causal mechanisms, and etiologic heterogeneity interference, and promote multi-omics joint modeling as well as cross-ethnicity and geographic research, and bidirectional regulation mechanisms of the gut-kidney axis in order to develop more accurate UTUC diagnosis and treatment strategies.},
}

Humans
*Microbiota/immunology
*Urologic Neoplasms/microbiology
Tumor Microenvironment/immunology
*Carcinoma, Transitional Cell/microbiology

@article {pmid41112258,
year = {2025},
author = {Filippi Xavier, L and Gacesa, R and da Rocha, GHO and Broering, MF and Scharf, P and Lima, FDS and Faber, KN and Harmsen, H and Hoffmann, C and Farsky, SHP},
title = {Annexin A1 levels affect microbiota in health and DSS-induced colitis/inflammatory bowel disease development.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1679071},
pmid = {41112258},
issn = {1664-3224},
mesh = {Animals ; *Annexin A1/genetics/metabolism ; *Gastrointestinal Microbiome ; Humans ; Mice ; Mice, Knockout ; *Colitis/chemically induced/microbiology/metabolism ; Mice, Inbred C57BL ; Dextran Sulfate ; Male ; *Inflammatory Bowel Diseases/microbiology/metabolism ; Female ; Disease Models, Animal ; Dysbiosis ; Feces/microbiology ; Adult ; Middle Aged ; },
abstract = {BACKGROUND: Inflammatory Bowel Diseases (IBDs) are characterized by intestinal dysbiosis and immune dysregulation. Annexin A1 (AnxA1) promotes epithelial repair and inhibits immune responses during IBD. However, AnxA1's impact on gut microbiota during IBD remains unclear. Here, we experimentally investigated the microbiota profile during colitis in wild-type (WT) and AnxA1-deficient mice (AnxA1[-/-]), and evaluated an observational cohort in IBD patients with high or low AnxA1 expression.

METHODS: Colitis was induced in C57BL/6 WT and AnxA1 [[-]/[-]] mice via oral administration of 2% DSS for six days. Fecal samples were collected at baseline, peak inflammation (day 6), and during the recovery phase (day 10) for 16S rRNA sequencing. Human microbiota data from the Lifelines Dutch Microbiome Project cohort, including IBD and healthy subjects, were analyzed for AnxA1 expression using R software.

RESULTS: Healthy AnxA1[-/-] mice exhibited reduced microbial richness and a distinct gut microbiota composition, marked by increased Proteobacteria and Parasutterella, and reduced Deferribacterota, Campylobacterota, and Verrucomicrobiota. During DSS-induced colitis, AnxA1[-/-] mice showed greater weight loss and heightened inflammation, displaying earlier and more pronounced microbial shifts, including increased Proteobacteria, Cyanobacteria, Parabacteroides, Bacteroides, and Escherichia-Shigella. In contrast, WT mice exhibited delayed changes, with expansion of Alloprevotella, Akkermansia, and Faecalibaculum after day 6. In human IBD samples, Crohn's disease (CD) patients with low AnxA1 expression and active inflammation presented an altered microbiota enriched in Lachnoclostridium and Parabacteroides, while ulcerative colitis (UC) patients showed phylum-level shifts modulated by AnxA1 levels. Notably, non-inflamed CD and UC patients with low AnxA1 differed significantly in microbiota composition. Moreover, inflamed CD patients with high AnxA1 expression showed microbial profiles resembling those of healthy controls, while low AnxA1 expression was associated with a more pronounced dysbiotic state.

CONCLUSION: AnxA1 is implicated in microbiota control under healthy and IBD conditions. Accordingly, the microbiota of healthy AnxA1[-/-] mice, colitic AnxA1[-/-] mice, and IBD patients with low AnxA1 expression exhibit dysbiosis compared to their respective controls. Together, these unprecedented findings reveal AnxA1 as a potential regulatory protein in the immune-microbiota axis involved in IBD pathogenesis.},
}

Animals
*Annexin A1/genetics/metabolism
*Gastrointestinal Microbiome
Humans
Mice
Mice, Knockout
*Colitis/chemically induced/microbiology/metabolism
Mice, Inbred C57BL
Dextran Sulfate
Male
*Inflammatory Bowel Diseases/microbiology/metabolism
Female
Disease Models, Animal
Dysbiosis
Feces/microbiology
Adult
Middle Aged

@article {pmid41112171,
year = {2025},
author = {Muneer, MA and Huang, R and Xiaojun, Y and Pang, Z and Munir, MZ and Ji, B and Wu, L and Zheng, C},
title = {Mg-enriched nutrient management enhances phyllosphere bacterial diversity, community structure, and functional traits in pomelo orchards.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100476},
pmid = {41112171},
issn = {2666-5174},
abstract = {Phyllosphere, the aerial surface of plants, harbors a tremendous diversity of microbes that significantly influences plant health and ecosystem functionality. Nevertheless, a holistic understanding of the effects of nutrient management, particularly magnesium (Mg) supplementation, on phyllosphere endophytes remains elusive. Herein, we conducted a five-year field experiment to investigate the impact of different nutrient management practices, including farmer practice of high N.P.K input (FP), reduced N.P.K input (OPT), and OPT supplemented with Mg (OPT+Mg), on the phyllosphere endophytic bacterial community (Illumina 16S sequencing) associated with fruit and leaf of pomelo trees across different growth stages, i.e., June (S1), July (S2), and September (S3). The results demonstrated that Mg-enriched nutrient management (OPT+Mg), significantly enhanced microbial diversity and restructured community composition, with notable increases in the relative abundance of beneficial phyla such as Actinobacteriota, Bacteroidota, and Chloroflexi compared with FP across all growing seasons. Similarly, both OPT and OPT+Mg generally supported higher microbial diversity than FP in fruit and leaf samples. Principal Coordinate Analysis (PCoA) and PERMANOVA confirmed significant differences in bacterial community structures among treatments. Ternary plot analysis further indicated the enrichment of beneficial genera under OPT and OPT+Mg treatments, which can play key roles in promoting plant growth and enhancing resilience against various stresses. In addition, Mg application was associated with more complex co-occurrence networks, highlighting its impact on promoting robust microbial communities in leaf and fruit samples. Functional predictions (FAPROTAX) suggested that Mg application was associated with higher predicted carbon and nitrogen cycling functions and lower predicted relative abundances of potential plant pathogens and intracellular parasites. This study is the first to provide long-term field-based evidence of how Mg supplementation modulates phyllosphere microbiota in fruit orchards, offering critical insights into microbiome-informed nutrient strategies. These findings highlight the unexplored role of Mg in shaping aerial plant microbiomes and present a novel avenue for enhancing sustainable pomelo production through targeted nutrient-microbiome interventions.},
}

@article {pmid41112052,
year = {2025},
author = {Xu, J and Dai, D and Yang, Y and Gao, S and Yang, J and Dong, C and Yang, W and Yuan, J and Wang, T and Tian, T and Yang, Y and Luo, F and Jiang, P and Wu, C and Sun, X and Sui, Y and Gao, G and Ma, W and Wu, Y and Zhang, J and Li, J and Guo, C and Cui, C and Guo, T and Zhao, X and Yuan, J and Qiao, S and Hu, F and Gao, X and Luo, X and Peng, H and Wang, D and Wu, J and Wu, C and He, J and Chen, WH and Yang, Y and Fu, J},
title = {Distinct microbial and metabolic shifts characterize acute coronary syndrome and recovery.},
journal = {iMeta},
volume = {4},
number = {5},
pages = {e70079},
pmid = {41112052},
issn = {2770-596X},
abstract = {Early identification of patients at risk of acute coronary syndrome (ACS) remains a major unmet need, particularly among those with stable coronary artery disease (sCAD), where timely intervention could markedly improve outcomes. The gut microbiota has been implicated in coronary artery disease (CAD), but its ability to distinguish ACS from sCAD is not well defined. Here, we performed cross-sectional multi-omics profiling of fecal microbiota and plasma metabolites in 548 individuals, including participants with normal coronary arteries (N = 175), primary sCAD (N = 161), and ACS (N = 212). To assess whether disease-associated changes resolve with treatment, we further analyzed an independent cohort of ACS patients (N = 52) who transitioned to sCAD following standard therapy. We identified profound ACS-associated alterations in gut microbial composition and systemic metabolism, marked by enrichment of pro-inflammatory taxa such as Streptococcus spp. and elevated circulating levels of 3-hydroxybutyrate (3-HB). Strikingly, many of these ACS-specific microbial and metabolic signatures, including 3-HB and related microbial functional pathways, were restored toward sCAD-like levels after clinical recovery. Integrative models combining microbial taxa, metabolites, and clinical biomarkers robustly discriminated ACS from healthy controls (AUC = 0.91) and from sCAD (AUC = 0.83), significantly outperforming clinical markers alone (AUC = 0.69 for NCA vs. ACS; 0.59 for sCAD vs. ACS). These findings establish the gut microbiome and its metabolic outputs as key discriminators of ACS, reveal their dynamic resolution during disease recovery, and highlight their potential as biomarkers and therapeutic targets for cardiovascular risk stratification and management.},
}

@article {pmid41112047,
year = {2025},
author = {Xu, M and Guan, S and Zhong, C and Ma, M and Tao, L and Huang, G},
title = {Characterizing the microbiome of "sterile" organs in experimental mice and evidence of translocation of bacteria from the gut to other internal organs.},
journal = {iMeta},
volume = {4},
number = {5},
pages = {e70081},
pmid = {41112047},
issn = {2770-596X},
abstract = {Using culturomics and metagenomics, we demonstrate the existence of non-pathogenic microbiota in the internal organs of healthy experimental mice, challenging the traditional dogma of organ sterility. Based on the analysis of 104 commercially sourced mice (C57BL/6J, BALB/c, ICR), the study reveals that over 20% of the analyzed mice harbored a high microbial burden in the internal organs and identified a total of 463 microbial species. Several species, including Ligilactobacillus murinus, Alcaligenes faecalis, Micrococcus luteus, Pseudochrobactrum asaccharolyticum, Escherichia coli, and Microbacterium sp., were frequently identified and were abundant in the mouse tissues. Further investigation implies that microorganisms in the "sterile" tissues could be associated with the gut microbiota. Given the wide use of experimental mice in medical and biological research, these findings of resident microorganisms in the animal's internal organs raise concerns about potential variability in experimental outcomes.},
}

@article {pmid41112042,
year = {2025},
author = {Lin, A and Xiong, M and Jiang, A and Huang, L and Wong, HZH and Feng, S and Zhang, C and Li, Y and Chen, L and Chi, H and Zhang, P and Ye, B and Zhang, H and Zhang, N and Zhu, L and Mou, W and Shen, J and Li, K and Xu, W and Ying, H and Zhang, C and Zeng, D and Xie, J and Deng, X and Wang, Q and Xu, J and Shi, W and Qi, C and Qu, C and Huang, X and Hajdu, A and Li, C and Peng, C and Cao, X and Pei, G and Zhang, L and Huo, Y and Xu, J and Glaviano, A and Szöllősi, AG and Bian, S and Li, Z and Tang, H and Tang, B and Liu, Z and Zhang, J and Miao, K and Cheng, Q and Wei, T and Yuan, S and Luo, P},
title = {The microbiome in cancer.},
journal = {iMeta},
volume = {4},
number = {5},
pages = {e70070},
pmid = {41112042},
issn = {2770-596X},
abstract = {The human microbiome is now recognized as a central regulator of cancer biology, intricately shaping tumor development, immune dynamics, and therapeutic response. This comprehensive review delineates the multifaceted roles of bacteria, viruses, and fungi in modulating the tumor microenvironment and systemic immunity across diverse cancer types. We synthesize current evidence on how microbial dysbiosis promotes carcinogenesis via chronic inflammation, metabolic reprogramming, genotoxic stress, immune evasion, and epigenetic remodeling. This review emphasizes organ-specific microbiome signatures and highlights their potential as non-invasive biomarkers for early detection, treatment stratification, and prognosis. Furthermore, we explore the impact of intratumoral microbiota on cancer therapies, uncovering how microbial metabolites and host-microbe interactions shape therapeutic efficacy and resistance. Finally, advances in microbiome-targeted strategies, such as probiotics, fecal microbiota transplantation, and engineered microbes offer new avenues for adjunctive cancer therapy. This review provides a roadmap for future investigation and underscores the transformative promise of microbiome modulation in cancer prevention and treatment.},
}

@article {pmid41112009,
year = {2025},
author = {Guo, YC and Hong, Y and Huang, L and Xu, XW and Sun, JQ and Ji, KK and Li, CN},
title = {Beyond biomarkers: An integrated traditional Chinese medicine-machine learning approach predicts hepatic steatosis in high metabolic risk populations.},
journal = {World journal of gastroenterology},
volume = {31},
number = {38},
pages = {112166},
pmid = {41112009},
issn = {2219-2840},
mesh = {Humans ; *Machine Learning ; *Medicine, Chinese Traditional/methods ; Biomarkers/blood/analysis ; Risk Assessment/methods ; *Non-alcoholic Fatty Liver Disease/diagnosis ; Risk Factors ; Predictive Value of Tests ; Liver/pathology ; },
abstract = {Tian et al present a timely machine learning (ML) model integrating biochemical and novel traditional Chinese medicine (TCM) indicators (tongue edge redness, greasy coating) to predict hepatic steatosis in high metabolic risk patients. Their prospective cohort design and dual-feature selection (LASSO + RFE) culminating in an interpretable XGBoost model (area under the curve: 0.82) represent a significant methodological advance. The inclusion of TCM diagnostics addresses metabolic dysfunction-associated fatty liver disease (MAFLD's) multisystem heterogeneity-a key strength that bridges holistic medicine with precision analytics and underscores potential cost savings over imaging-dependent screening. However, critical limitations impede clinical translation. First, the model's single-center validation (n = 711) lacks external/generalizability testing across diverse populations, risking bias from local demographics. Second, MAFLD subtyping (e.g., lean MAFLD, diabetic MAFLD) was omitted despite acknowledged disease heterogeneity; this overlooks distinct pathophysiologies and may limit utility in stratified care. Third, while TCM features ranked among the top predictors in SHAP analysis, their clinical interpretability remains nebulous without mechanistic links to metabolic dysregulation. To resolve these gaps, we propose external validation in multiethnic cohorts using the published feature set (e.g., aspartate aminotransferase/alanine aminotransferase, low-density lipoprotein cholesterol, TCM tongue markers) to assess robustness. Subtype-specific modeling to capture MAFLD heterogeneity, potentially enhancing accuracy in high-risk subgroups. Probing TCM microbiome/metabolomic correlations to ground tongue phenotypes in biological pathways, elevating model credibility. Despite shortcomings, this work pioneers a low-cost screening paradigm. Future iterations addressing these issues could revolutionize early MAFLD detection in resource-limited settings.},
}

Humans
*Machine Learning
*Medicine, Chinese Traditional/methods
Biomarkers/blood/analysis
Risk Assessment/methods
*Non-alcoholic Fatty Liver Disease/diagnosis
Risk Factors
Predictive Value of Tests
Liver/pathology

@article {pmid41112002,
year = {2025},
author = {Saadeh, M and Donohue, S and Ailawadi, S and Hong, G and Johnson, DA},
title = {Oral microbiome and inflammatory bowel disease: New understanding and call to action.},
journal = {World journal of gastroenterology},
volume = {31},
number = {38},
pages = {111210},
pmid = {41112002},
issn = {2219-2840},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/immunology/therapy ; *Dysbiosis/microbiology/immunology ; *Mouth/microbiology/immunology ; *Microbiota/immunology ; Gastrointestinal Microbiome ; },
abstract = {The oral microbiome is the second largest microbial community in the human body after the gut microbiome. It includes an array of fungi, bacteria, amoebae, flagellates, archaea, and viruses, all of which are potential pathogens. This microbiome can act as a facilitator not only for protection but also for aggravation when dysbiosis occurs. Although conventional thought is this is primarily in terms of oral health issues, such as dental caries and gingival disease. The systemic effects of the oral microbiome however, are relevant to both gastrointestinal (GI) disease and non-GI disease. These systemic risks occur for several reasons, including upregulation of cytokines, adhesion cell-like processes, toll-like receptors, reactive oxidative species or generation of mutation inducing DNA changes. Additionally, there is translocation risk of potential active pathogens or their metabolic byproducts. There is a substantial and growing body of evidence that the oral microbiome influences diseases including Barrett's esophagus, metabolic-associated steatosis liver disease, and GI cancers. Additionally, there is burgeoning evidence of a causal association with systemic inflammatory diseases, including inflammatory bowel disease. This report discusses the most recent evidence of this association and highlights new approaches to potentially enhance our "best practice" strategies for optimal care of patients with inflammatory bowel disease.},
}

Humans
*Inflammatory Bowel Diseases/microbiology/immunology/therapy
*Dysbiosis/microbiology/immunology
*Mouth/microbiology/immunology
*Microbiota/immunology
Gastrointestinal Microbiome

@article {pmid41110993,
year = {2025},
author = {Jang, KB and Seo, E and Kim, Y},
title = {Dynamic Interactions between the Gut Microbiome, Health, and Metabolic Disorders in Preterm Infants.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2508033},
doi = {10.4014/jmb.2508.08033},
pmid = {41110993},
issn = {1738-8872},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Infant, Premature/growth & development ; Infant, Newborn ; Dysbiosis/microbiology ; *Metabolic Diseases/microbiology ; Probiotics ; Gastrointestinal Tract/microbiology ; },
abstract = {Preterm birth, which occurs before the entire gestation is completed, causes serious health challenges for newborns. The gastrointestinal tract often shows delayed development and poor function in nutrient utilization and immune response. Preterm neonates are faced with difficulties in growth, are more vulnerable to infections, and have a higher risk of developing inflammatory diseases. One key factor in these outcomes is the abnormal development of intestinal microbiota. In premature neonates, gut microbes tend to show lower diversity and changes in several bacteria. The gut dysbiosis can disrupt gut function and contribute to complications like necrotizing enterocolitis, sepsis, and even long-term metabolic and neurodevelopmental disorders. This review brings together current research on how premature birth affects the growth, gut development, and overall health of infants, with a focus on changes in microbial colonization. In addition, we discuss how gut microbiota plays a role in shaping the immune system and influencing brain development. There is growing interest in using breast milk, specialized nutrition, and probiotics to improve microbial balance in premature infants. Preterm birth alters intestinal development and microbial colonization, making infants vulnerable to gut dysbiosis and disease. These changes contribute to a heightened risk of neonatal diseases such as NEC, sepsis, and long-term neurodevelopmental and metabolic disorders. Evidence highlights the critical role of commensal microbes and their metabolites in promoting epithelial maturation, immune balance, and gut-brain signaling. Advancing neonatal care will require precision approaches based on microbial profiling, targeted nutritional strategies, and a deeper understanding of host-microbe interactions to improve health in preterm infants. Therefore, this review focuses on integrating recent evidence of microbial development and preterm infant health, highlighting the gut-brain axis in relation to metabolic disorders, and emphasizing how gut dysbiosis links clinical outcomes with mechanistic insights in neonatal care.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Infant, Premature/growth & development
Infant, Newborn
Dysbiosis/microbiology
*Metabolic Diseases/microbiology
Probiotics
Gastrointestinal Tract/microbiology

@article {pmid41110987,
year = {2025},
author = {Hong, HH and Lee, SY and Jang, DH and Ju, SE and Shim, JE and Kim, TH and Kang, HS and Kim, SM},
title = {Multiomics Integration Reveals Microbial Gene Interactions Shaping Host Responses in a DSS-Induced Colitis Mouse Model.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2507010},
doi = {10.4014/jmb.2507.07010},
pmid = {41110987},
issn = {1738-8872},
mesh = {Animals ; Dextran Sulfate ; *Colitis/microbiology/chemically induced/immunology/genetics ; Disease Models, Animal ; Mice ; *Gastrointestinal Microbiome/genetics ; Inflammatory Bowel Diseases/microbiology/immunology ; Mice, Inbred C57BL ; Amino Acyl-tRNA Synthetases/genetics/metabolism ; Metabolic Networks and Pathways/genetics ; *Bacteria/genetics/classification ; Transcriptome ; Multiomics ; },
abstract = {Inflammatory bowel disease (IBD) has been studied with a multi-omics approach to identify key contributors and unravel the biological complexity of its pathogenesis, aiding in the development of early diagnostic markers and therapeutic targets. The dextran sulfate sodium (DSS)-induced colitis mouse model, a widely used system for studying IBD, induces gut barrier disruption and proinflammatory responses, making it an ideal model for investigating host-microbiome interactions. This study emphasizes the intricate relationship between microbial transcriptomic changes and host immune responses, revealing regulation of microbial genes, particularly in metabolic pathways related to carbohydrate metabolism, nucleotide metabolism, and aminoacyl-tRNA biosynthesis under inflammatory conditions. We identified key hub microbes and microbial genes that are closely associated with host immunological pathways, with particular focus on microbial aminoacyl-tRNA synthetases (aaRSs), which play significant roles in immune cell activation and inflammatory pathways. These findings offer valuable insights into the microbial contributions to inflammation and immune modulation in IBD, highlighting the potential role of aaRSs in regulating immune responses beyond their traditional function in translation. This lays the foundation for future research into host-microbiome interactions in inflammatory diseases and the development of novel therapeutic strategies that target microbial aaRSs to manipulate immune response.},
}

Animals
Dextran Sulfate
*Colitis/microbiology/chemically induced/immunology/genetics
Disease Models, Animal
Mice
*Gastrointestinal Microbiome/genetics
Inflammatory Bowel Diseases/microbiology/immunology
Mice, Inbred C57BL
Amino Acyl-tRNA Synthetases/genetics/metabolism
Metabolic Networks and Pathways/genetics
*Bacteria/genetics/classification
Transcriptome
Multiomics

@article {pmid41110985,
year = {2025},
author = {Lee, HW and Ha, JH},
title = {High-Resolution Characterization of the Bacterial Microbiome in Chili Pepper Powder Using SMRT Sequencing.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2506003},
doi = {10.4014/jmb.2506.06003},
pmid = {41110985},
issn = {1738-8872},
mesh = {*Capsicum/microbiology ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; Powders ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; China ; Republic of Korea ; Food Microbiology ; Phylogeny ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; },
abstract = {Chili pepper powder is an essential ingredient of Korean cuisine and kimchi products. As such, ensuring its microbiological safety is crucial from a public health perspective. In this study, the bacterial microbiomes of Korean and Chinese chili pepper powder samples were compared using high-resolution single-molecule real-time sequencing. Nine samples each from Korea and China were analyzed, yielding high-quality sequencing data with N50 values exceeding 1,460 bp and quality scores greater than Q30. Based on alpha diversity analysis, Chinese samples exhibited higher microbial diversity, whereas Korean samples had a more selective and clustered microbial structure, composed predominantly of Bacillus. Taxonomically, Chinese samples contained a wider range of genera, including Pantoea, Weissella, and Klebsiella, in contrast, Korean samples were dominated by Firmicutes, primarily Bacillus species. Although Salmonella enterica was detected in some Korean samples, viability was not confirmed. This may have indicated residual DNA or viable but nonculturable cells due to the low water activity of chili powders. Beta diversity analysis indicated moderate separation between the two groups, with Korean samples showing tighter clustering and Chinese samples displaying greater variability. Linear discriminant analysis effect size identified Bacillus altitudinis and Bacillus safensis as biomarkers for Korean samples, and Pantoea agglomerans and Weizmannia coagulans as biomarkers for Chinese samples. Overall, despite slightly lower microbial diversity, Korean chili pepper powder samples exhibited a more stable microbial community structure. Selection of chili pepper powder characterized by a stable and controlled microbiome could play an essential role in promoting the hygienic production and microbial safety of kimchi.},
}

*Capsicum/microbiology
*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification
Powders
RNA, Ribosomal, 16S/genetics
DNA, Bacterial/genetics
China
Republic of Korea
Food Microbiology
Phylogeny
Sequence Analysis, DNA
High-Throughput Nucleotide Sequencing

@article {pmid41110780,
year = {2025},
author = {Sreekutti, S and Ndomondo, S and Sharma, P and Patel, R and Mevada, V},
title = {Forensic application of metagenomics: Methods and future directions.},
journal = {Journal of microbiological methods},
volume = {239},
number = {},
pages = {107300},
doi = {10.1016/j.mimet.2025.107300},
pmid = {41110780},
issn = {1872-8359},
abstract = {The microbial communities are found commonly in our environment, making it impossible to touch any surface without interfering with them. The human microbiome, primarily bacteria in the saliva, skin, and gut, can be used for forensic purposes. Human-associated and environmental samples, such as soil, water, etc., carry the microbiome, which can be used for geolocation inference. These microbiomes have considerable potential for use in forensic investigations, including many instances of sexual violence, post-mortem examinations, individual identification, and location identification. Recent developments in metagenomic sequencing have greatly contributed to microbial analysis. Yet, because of certain issues and challenges, the forensic application of microbiomes is still in its infancy. This article reviewed the use of metagenomics in forensic science and some of the main obstacles that are faced by experts in this area. The first and foremost issues noted were the lack of standardization protocols and a poor reference database for research studies. Some limitations, such as storage sensitivity and limited samples, are also indicated. Future research studies should concentrate on more standardized investigations to overcome these difficulties and explore the enormous potential of microbiomes for beneficial applications in forensic contexts.},
}

@article {pmid41110769,
year = {2025},
author = {Alqudah, S and DeLucia, B and Osborn, LJ and Markley, RL and Bobba, V and Preston, SM and Thambidurai, T and Nia, LH and Fulmer, CG and Sangwan, N and Nemet, I and Claesen, J},
title = {The diet-derived gut microbial metabolite 3-phenylpropionic acid reverses insulin resistance and obesity-associated metabolic dysfunction.},
journal = {Molecular metabolism},
volume = {},
number = {},
pages = {102272},
doi = {10.1016/j.molmet.2025.102272},
pmid = {41110769},
issn = {2212-8778},
abstract = {Obesity-associated metabolic disorders, including type 2 diabetes and metabolic dysfunction associated fatty liver disease (MAFLD), are major global health burdens. While dietary polyphenols have shown promise in ameliorating these conditions, their efficacy is dependent on specialized gut microbial metabolism, and the underlying molecular mechanisms remain mostly elusive. Here, we demonstrate that dietary supplementation with polyphenol-rich elderberry (Eld) extract abrogates the effects of an obesogenic diet in a gut microbiota-dependent manner, preventing insulin resistance and reducing hepatic steatosis in mice. We developed a targeted, quantitative liquid chromatography-tandem mass spectrometry method for detection of gut bacterial polyphenol catabolites and identified 3-phenylpropionic acid as a key microbial metabolite in the portal plasma of Eld supplemented animals. Next, we showed that 3-phenylpropionic acid potently activates hepatic AMP-activated protein kinase α, explaining its role in improved liver lipid homeostasis. We further uncovered the metabolic pathway cumulating in 3-phenylpropionic acid for the common gut commensal Clostridium sporogenes. Our findings establish 3-phenylpropionic acid as a diet-derived, microbiota-dependent metabolite with insulin-sensitizing and anti-steatotic activities and provide a molecular basis for prebiotic interventions to improve host metabolic health.},
}

@article {pmid41110752,
year = {2025},
author = {Hong, G and Zhao, Y and Hou, X},
title = {Impact of four-week rifaximin treatment on abdominal symptoms, psychological state and gut microbiome in diarrhea-predominant irritable bowel syndrome: a pilot study.},
journal = {European journal of pharmacology},
volume = {1007},
number = {},
pages = {178271},
doi = {10.1016/j.ejphar.2025.178271},
pmid = {41110752},
issn = {1879-0712},
abstract = {Previous studies have revealed the effect of two-week rifaximin treatment on abdominal symptoms and gut microbiota in diarrhea-predominant irritable bowel syndrome (IBS-D), but they failed to observe the influence of rifaximin intervention for a longer period. This pilot study is designed to describe gut microbial profiles in IBS-D and to evaluate the impact of four-week rifaximin treatment on IBS-associated symptoms and gut microbiota for the first time. IBS-D patients who fulfilled the Rome III criteria and healthy controls (HC) were enrolled in the study. Then, 400 mg rifaximin was orally administered to IBS-D patients three times daily for four weeks. Abdominal symptoms and mental state were evaluated before treatment, after two weeks of treatment, and after four weeks of treatment. Fecal samples were collected to characterize the gut microbiota by performing 16S rRNA sequencing. A total of 40 healthy volunteers and 33 IBS-D patients were recruited, and all IBS-D patients agreed to receive rifaximin treatment. IBS-D patients exhibited decreased microbial diversity and a different microbial structure compared with HC. Microbial composition differed between HC and IBS-D at the phylum and genus levels. Administration of rifaximin for four weeks improved abdominal symptoms and anxiety in IBS-D patients. Potential enteropathogens including Haemophilus, Escherichia, and Veillonella were inhibited by rifaximin. Rifaximin upregulated arginine and proline metabolism in the gut microbiota. This is the first study demonstrating that four-week rifaximin treatment exerts good efficacy in relieving abdominal symptoms and anxiety in IBS-D, possibly through suppressing three potential enteropathogens and enhancing arginine and proline metabolism.},
}

@article {pmid41110468,
year = {2025},
author = {Maqsood, S and Asif, M and Shakoor, S and Saddiqa, A},
title = {Modulating Metabolism and Reproductive Health through Microbiome Driven Gut-Brain Axis Therapies.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108113},
doi = {10.1016/j.micpath.2025.108113},
pmid = {41110468},
issn = {1096-1208},
abstract = {The gut microbiome plays a crucial role in regulating metabolic and reproductive health through the gut-brain axis. This review underscores the therapeutic potential of modulating gut microbiota to alleviate conditions such as obesity and polycystic ovarian syndrome (PCOS). Gut dysbiosis as an imbalance microbiome, has direct effect on insulin resistance, hormonal imbalances, and systemic inflammation. It contributes to metabolic and reproductive disparities. This study reveals the coordination between dysbiosis and obesity, and PCOS. Alterations in gut-microbiota is the major contributor of insulin-resistance, menstrual dysfunction, and hormonal imbalances. It also focuses on the efficacy of probiotic and relevant microbes. Considering the literature, microbiome-potential and its role in treating the interventions is significantly important. Outcomes recommend that gut-dysbiosis aggravates metabolic and reproductive health illnesses by making worse hormonal inequalities and inflammation. The therapy probiotic has indicated favorable outcomes in enhancing insulin-resistance and menstrual cycle regulation, highlighting its capability as a reliable treatment for PCOS and obesity. Nevertheless, well-monitored clinical trials are necessary on large scale to make it optimized microbiome-focused treatments for long-term results and safety.},
}

@article {pmid41110352,
year = {2025},
author = {Yuan, Y and Hu, J and Lu, X and Han, H and Wang, M and Zhang, W and Jiao, Y and Li, Y and Lin, Z and Liang, C and Yu, Y and Xie, C and Li, J and Mao, T},
title = {Oral rhein attenuate nonalcoholic steatohepatitis in mice through the modulation of gut microbiota and Th17 cell differentiation.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {148},
number = {},
pages = {157409},
doi = {10.1016/j.phymed.2025.157409},
pmid = {41110352},
issn = {1618-095X},
abstract = {BACKGROUND: Non-alcoholic steatohepatitis (NASH) is an important clinical issue and a challenge in the field of global public health. However, there are very few clinically approved drugs that can effectively treat NASH. Rhein is a natural organic compound with anti-inflammatory and antioxidant properties, but the specific role and mechanism on NASH remain unexplored.

PURPOSE: This study investigated the role and associated mechanism of rhein in NASH mice.

METHODS: The effects of rhein on lipid accumulation were evaluated in NASH mice through systemic signs of obesity, biochemical parameters, and histological changes. Network pharmacology was employed to determine the main bioactive compounds and key targets of rhein for the NASH treatment. Additionally, antibiotics treatment and fecal microbiota transplantation (FMT) were performed to investigate the role of microbiota in the treatment of NASH with rhein. Bacterial 16S rRNA amplicon sequencing, LC-MS/MS analysis and flow cytometric were employed to investigate the mechanisms underlying rhein's regulatory effects on gut microbiota, BA metabolism and immune balance. Finally, in vitro cell experiments were conducted to explore the effects of metabolites on Th17 cell differentiation.

RESULTS: Our results showed that mice treated with rhein showed a significant alleviating effect from high-fat diet (HFD)-induced liver lipid accumulation and pathological changes compared to those in HFD group. The protective effects of rhein are gut microbiota dependent, as demonstrated by fecal microbiome transplantation and antibiotics treatment. Microbiota transferred from rhein-treated mice displayed a similar role in attenuating hepatic lipid deposition as rhein on NASH in mice, and depletion of the gut microbiota through antibiotics treatments diminished the protective effects of rhein on NASH mice. Moreover, the results from bacterial 16S rRNA sequencing suggested that rhein partially attenuated HFD-induced gut dysbiosis in NASH mice. Network pharmacology analyses was implemented and showed that Th17 cell differentiation might be the potential target in the treatment of rhein against NASH, which was confirmed by flow cytometric analysis showing markedly decrease of the percentage of Th17 cells, corresponded with upregulated Treg cells in rhein-treated NASH mice. Furthermore, targeted bile acid metabolomics analysis showed that supplement with rhein greatly increased the levels of primary bile acids β-MCA and AlloLCA, positively correlated with the relative abundances of Bifidobacterium_choerinum, which may play the key role by which rhein-altered gut microbiota promoted the restoration of Th17/Treg balance in NASH mice. Subsequent in vitro experiments confirmed that AlloLCA directly inhibits Th17 cell differentiation, with suppression of glycolysis potentially serving as the underlying mechanism for the immunomodulatory effects of AlloLCA.

CONCLUSIONS: Collectively, our results suggested that orally administrated rhein reduced hepatic lipid deposition through the modulation of dysregulated gut microbiota and bile acids metabolism, thus regulating Th17/Treg immune balance. This study uncovers a novel mechanistic axis in NASH pathogenesis and providing new research directions for microbiota-targeted clinical strategies.},
}

@article {pmid41110294,
year = {2025},
author = {Muthukumar, S and Suresh Babu, HW and George, A and Maurya, BM and Mahalaxmi, I and Yadav, MK and HariKrishna Reddy, D and Arvinder Wander, and Narayanasamy, A and Ganesan, R and Lakhanpal, V and Vellingiri, B},
title = {The role of cytochrome P450 and gut microbiome in drug metabolism: Insights into Parkinson disease treatment.},
journal = {Drug metabolism and disposition: the biological fate of chemicals},
volume = {53},
number = {11},
pages = {100166},
doi = {10.1016/j.dmd.2025.100166},
pmid = {41110294},
issn = {1521-009X},
abstract = {Parkinson disease (PD) is a complex neurodegenerative condition marked by progressive motor and nonmotor symptoms. Cytochrome P450 (P450) enzymes, notably those from the CYP1 and CYP2 families, are increasingly recognized as significant factors in the development of PD. This review examines the role of P450 enzymes in PD, covering genetic variations, copy number variations, and single nucleotide polymorphisms linked to PD pathogenicity. It also explores the regulatory mechanisms controlling P450 expression in PD and the influence of the gut microbiome and metabolites on P450 activity. Additionally, the review discusses how P450 enzymes metabolically activate drugs used to treat PD and investigates the intricate relationship between P450s and mitochondrial dysfunction. Finally, it underscores the therapeutic potential of targeting P450 enzymes for PD treatment. Understanding the diverse roles of P450 enzymes in PD may lead to innovative treatment approaches and personalized interventions for this challenging neurological disorder. SIGNIFICANCE STATEMENT: Cytochrome P450 (P450) enzymes significantly influence Parkinson disease (PD) development through their roles in drug metabolism and detoxification. Single nucleotide polymorphisms in P450 genes can alter enzyme activity, affecting PD susceptibility and progression. Gut microbiota modulates P450 function, impacting detoxification of PD-related toxins and influencing gut and blood-brain barrier integrity. Additionally, P450-mitochondrial interactions contribute to energy deficits and oxidative stress, exacerbating neurodegeneration in PD. Understanding these pathways may uncover novel therapeutic targets and personalized treatment strategies.},
}

@article {pmid41109629,
year = {2025},
author = {Vahed, A and Molanouri Shamsi, M and Siadat, SD and Behmanesh, M and Negaresh, R and Agh-Mohammadi, S and Ebrahimi, M},
title = {Effects of home-based exercise training on gut microbiota and possible relations with cognitive function and metabolic health in postmenopausal women with type 2 diabetes mellitus: a randomized control trial.},
journal = {Diabetes research and clinical practice},
volume = {},
number = {},
pages = {112908},
doi = {10.1016/j.diabres.2025.112908},
pmid = {41109629},
issn = {1872-8227},
abstract = {AIM: Evidence suggests that the gut microbiome is involved in type 2 diabetes mellitus (T2DM). This study investigates the association between gut microbiota composition, cognitive function, and metabolic health in postmenopausal women with T2DM following a 12-week home-based multi-task exercise intervention.

METHODS: Seventy postmenopausal women with T2DM were randomly assigned to either an intervention group, which performed home-based multi-task exercises, or a control group. Gut microbiota, cognitive function, physical fitness, and metabolic indices were assessed before and after the intervention.

RESULTS: Exercise training significantly increased Akkermansia muciniphila and Faecalibacterium levels, and reduced Lactobacillus abundance (p < 0.05). Participants showed improvements in HDL levels, cognitive function, and physical fitness (p < 0.05). Among the microbial changes, an increased abundance of Akkermansia was significantly correlated with improvements in high-density lipoprotein (HDL) levels (r = 0.41) and cognitive function (r = 0.49).

CONCLUSION: This study supports the potential effectiveness of multi-task exercise programs in enhancing physical fitness and metabolic health in postmenopausal women with T2DM. The findings also suggest a possible connection between the gut and the brain, with Akkermansia muciniphila emerging as a potential mediator. Investigating the Akkermansia-to-brain pathway represents a promising and emerging area of research that warrants further exploration.},
}

@article {pmid41109625,
year = {2025},
author = {Rattanapitoon, NK and Thanchonnang, C and Padchasuwan, NH and Rattanapitoon, SK},
title = {Extracellular vesicles and PET microplastics: toward a biomarker framework for systemic endocrine-microbiome disruption.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {127281},
doi = {10.1016/j.envpol.2025.127281},
pmid = {41109625},
issn = {1873-6424},
}

@article {pmid41109441,
year = {2025},
author = {Yu, Q and Liao, H and Tan, W and Xu, L and Lin, G and Ai, Z and Xie, Q and Liu, Y and Li, Y and Yang, X and Su, Z and Ma, G and Xie, J and Lai, Z},
title = {Mechanistic insights into metformin's anti-hyperuricemic effect: Targeting PPP/DNPB/XOD-mediated purine pathway, purinosome assembly, and gut microbiota homostasis in rats.},
journal = {Chemico-biological interactions},
volume = {},
number = {},
pages = {111783},
doi = {10.1016/j.cbi.2025.111783},
pmid = {41109441},
issn = {1872-7786},
abstract = {Hyperuricemia has become a public threat to human health, and conventional medical treatment only aims to inhibit xanthine oxidase (XOD). Endogenous purine biosynthesis and purinosome formation are neglected in research of medical mechanism. In this study, the therapeutic effect and mechanism of metformin was explored in chronic high-fructose-induced hyperuricemic rats. Results indicated that four weeks of metformin administration effectively reduced uric acid (UA), creatinine, and urea levels, ameliorated renal and hepatic injuries, and promoted glycogen synthesis in hyperuricemic rats. Furthermore, metformin remarkedly downregulated the mRNA and protein expression of core enzymes in pentose phosphate pathway (PPP), and de novo purine biosynthesis (DNPB) of endogenous purine. Metformin was found to markedly inhibit the purine salvage pathway (PSP) and XOD to retard purine recycling and metabolism. Additionally, metformin effectively restored physiological purinosome architecture, preventing aberrant enzyme clustering and subcellular redistribution. The hepatic levels of IMP, inosine, hypoxanthine and xanthine in hyperuricemic rats were remarkably decreased by metformin. Besides, metformin favorably maintained the gut microbiome homeostasis and normalized purine metabolism to lower purine levels in intestine. Taken together, the results for the first time indicated that metformin exerted appreciable anti-hyperuricemic effect, at least partly, via inhibiting original biosynthetic and metabolic pathways of endogenous purine simultaneously mediated by PPP/DNPB/XOD, purinosome assembly, and modulating gut microflora profile. This work provided a scientific basis for its potential application in hyperuricemia therapy beyond its classical use in diabetes.},
}

@article {pmid41109435,
year = {2025},
author = {Rao, Z and Shi, Y and She, M and Liu, C and Zhu, J and Yu, Y},
title = {Associations among microbial enterotype, brain structure, and working memory: A combined structural and diffusion MRI study.},
journal = {NeuroImage},
volume = {},
number = {},
pages = {121536},
doi = {10.1016/j.neuroimage.2025.121536},
pmid = {41109435},
issn = {1095-9572},
abstract = {BACKGROUND: Enterotype analysis classifies individuals based on gut microbial community composition using clustering techniques. Despite evidence suggesting the important role of enterotype in affecting brain function and working memory, little is known about the brain structural substrates.

METHODS: We collected fecal samples and utilized 16S rDNA amplicon sequencing to identify three enterotypes (Bacteroides, Prevotella, and Ruminococcaceae) among 511 healthy young adults through unsupervised clustering. Structural and diffusion MRI techniques were adopted to assess gray matter morphology and white matter integrity. Inter-enterotype differences in brain structure were tested, followed by correlation and mediation analyses to investigate the potential relationships among enterotype, brain structure, and working memory.

RESULTS: The three enterotypes exhibited significant differences in cortical thickness of the prefrontal cortex and mean diffusivity of the cerebral peduncle and cingulum. Moreover, prefrontal cortical thickness was correlated with working memory and further acted as a significant mediator of the association between enterotype and working memory.

CONCLUSIONS: Our findings may contribute to the growing literature on the microbiota-brain-cognition relationship, setting the stage for for future longitudinal and interventional research.},
}

@article {pmid41109419,
year = {2025},
author = {Li, J and Zhang, W and Li, X and Liu, Z and Yan, H},
title = {Bupropion administration significantly impacts the gut microbiome, serum metabolites, and immune factors in chronic stress depression rats.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {120457},
doi = {10.1016/j.jad.2025.120457},
pmid = {41109419},
issn = {1573-2517},
abstract = {Emerging evidence suggests that the gut microbiota plays a crucial role in the pathogenesis of depression through the microbiota-gut-brain axis. Our previous research demonstrated that oral antidepressants were potent in regulating gut microbiome in depressive rats. Bupropion is a common antidepressant, but its regulatory mechanisms on the gut microbiota in the treatment of depression remain unclear. Here, we evaluated the potential mechanisms underlying the microbe-mediated behavioral effects of oral and injectable bupropion in chronic restraint stress (CRS)-induced depressive rat model through integrated microbiome, metabolome, and biochemical techniques. Oral bupropion modulated the gut microbiota composition in favor of beneficial bacteria such as Romboutsia and Muribaculum, while reducing potentially harmful bacteria, including Staphylococcus, Streptococcus, and Bacteroides. Metabolomic results revealed that oral bupropion improved the abnormal levels of acetic acid, butyric acid, tryptophan and its derivatives, nicotinamide, and biotin. Moreover, oral bupropion significantly reduced the percentage of CD4[+] T lymphocytes and the levels of IL-1β and CXCL2. In comparison, injectable administration may not fully replicate the effects of oral administration on these alterations. Moreover, significant changes in the gut microbiota composition, particularly Muribaculum and Bacteroides, as well as tryptophan metabolites (L-tryptophan, 5-hydroxy-L-tryptophan, and indole-3-acetic acid), and immune indicators (CXCL2 levels and CD4[+] T lymphocyte percentages), were correlated. Notably, bupropion administration may also selectively exert negative effects on the gut microbiota, metabolites, and immune factors. Collectively, this study presents the first comprehensive overview of changes in the gut microbiome, metabolome, and immune indicators after bupropion treatment, highlighting their role in mediating antidepressant effects.},
}

@article {pmid41109237,
year = {2025},
author = {Dorsey, ER and De Miranda, BR and Hussain, S and Bloem, BR and Elbaz, A and Llibre-Guerra, J and Lo, RY and Goldman, SM and Tanner, CM},
title = {Environmental toxicants and Parkinson's disease: recent evidence, risks, and prevention opportunities.},
journal = {The Lancet. Neurology},
volume = {24},
number = {11},
pages = {976-986},
doi = {10.1016/S1474-4422(25)00287-X},
pmid = {41109237},
issn = {1474-4465},
mesh = {Humans ; *Parkinson Disease/prevention & control/etiology/epidemiology ; *Environmental Exposure/adverse effects/prevention & control ; Pesticides/adverse effects ; Risk Factors ; *Environmental Pollutants/adverse effects ; },
abstract = {The global burden of Parkinson's disease is rising. Large-scale genetic studies have confirmed that extrinsic or environmental factors, rather than genetic predisposition, play a dominant role in its cause. Increasing evidence implicates three classes of toxicants-certain pesticides, the dry-cleaning chemicals trichloroethylene and perchloroethylene, and air pollution-in the development of Parkinson's disease. These toxicants are widely prevalent, impair mitochondrial or lysosomal function, or both, and contribute to, if not cause, the disease. Parkinson's disease could be thus largely preventable. Uncertainties remain regarding the relevant doses, timing, and routes of exposure, the nature of genetic and environmental interactions, the effects of combined exposures, the role of the microbiome, and the identity of other environmental risks. Methodological limitations and structural challenges hinder our understanding. However, improved measurement of toxicant exposure in individuals and the environment, long-term prospective studies, increased funding for prevention, and policy changes can precipitate the fall of the burden of Parkinson's disease.},
}

Humans
*Parkinson Disease/prevention & control/etiology/epidemiology
*Environmental Exposure/adverse effects/prevention & control
Pesticides/adverse effects
Risk Factors
*Environmental Pollutants/adverse effects

@article {pmid41109046,
year = {2025},
author = {Xu, S and Wang, R and Liu, X and Zhang, P and Luo, C and Zou, K and Xiang, C and Huan, X and Yao, W and Li, X and Zhang, J and Wu, Z},
title = {Yiqi Huayu Jiedu decoction enhances pathological response in neoadjuvant chemotherapy-treated gastric cancer patients: A prospective, randomized controlled trial.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {148},
number = {},
pages = {157410},
doi = {10.1016/j.phymed.2025.157410},
pmid = {41109046},
issn = {1618-095X},
abstract = {BACKGROUND: While neoadjuvant chemotherapy (NAC) shows suboptimal pathological responses in advanced gastric cancer (GC), Yiqi Huayu Jiedu decoction (YHJD) demonstrates potential as a synergistic agent.

METHODS: This study represents an interim analysis of a prospective, double-arm, single-center, randomized controlled clinical trial (ChiCTR2300072742) conducted at Jiangsu Provincial Hospital of Traditional Chinese Medicine. A total of 122 patients with locally advanced GC were enrolled between June 2023 and December 2024. The study aimed to evaluate the efficacy and safety of YHJD in enhancing the neoadjuvant FLOT regimen. The primary endpoint was tumor pathological regression (TRG).

RESULTS: The YHJD group demonstrated superior pathological responses (TRG 1-3: YHJD group vs CON group: 44/68 [68.8%] vs 29/58 [50.0%], p = 0.043) while maintaining a safety profile comparable to chemotherapy alone. Gut microbiota analysis revealed that YHJD significantly reduced the abundance of Lactobacillus salivarius (L.salivarius) during NAC, with lower levels correlating with improved treatment response. Notably, depletion of intratumoral L.salivarius in the YHJD paralleled enhanced NAC efficacy. Further analysis revealed that enrichment of L. salivarius was associated with immunosuppressive microenvironment, it showed positive correlations with T regulatory cells (Tregs; r = 0.512, p < 0.0001) and M2 macrophages (r = 0.411, p = 0.002).

CONCLUSIONS: YHJD enhanced the pathological response rates in GC patients receiving FLOT-based NAC, possibly through modulation of the immuno-oncology-microbiome axis, potentially by downregulating L. salivarius-mediated immunosuppression.},
}

@article {pmid41108937,
year = {2025},
author = {Yang, MT and Xie, LH and Wang, L and Gao, YQ and Liu, R and Ma, H and Lei, CC and Jiang, J and Su, JW and Zhang, XX and Ni, HB and Nan, FL},
title = {Metagenomic analysis of bile acid biotransformation by gut microbiota in wild birds.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {105956},
doi = {10.1016/j.psj.2025.105956},
pmid = {41108937},
issn = {1525-3171},
abstract = {Although gut microbiota-mediated bile acid (BA) metabolism is well characterized in mammals, its mechanisms in wild birds remain largely unknown, hindering our understanding of their ecological adaptation and health. In this study, metagenomic analysis was performed on 10,455 metagenome-assembled genomes (MAGs) derived from 718 wild bird gut samples, from which 1,034 high-quality non-redundant MAGs were selected for further analysis. Functional annotation analysis identified 755 MAGs encoding genes associated with BA biotransformation pathways, primarily derived from the phyla Bacillota_A, Bacteroidota, and Bacillota, with dominant genera including Helicobacter_G and Ligilactobacillus. Subsequent genomic analysis identified 379 MAGs encoding bile salt hydrolase (BSH), with phylogenetic classification demonstrating predominant affiliation to the Bacteroidota and Bacillota_A phyla. Compared to the BSH-producing microbiota in the human and chicken gut, the phylum Bacillota exhibited a notably higher relative abundance in wild birds. Within the wild bird gut microbiome, Helicobacter_G was identified as the predominant BSH-encoding genus, whereas its relative abundance was substantially lower in both humans and chickens. Moreover, migratory birds (MB) displayed significantly higher diversity of BA biotransformation genes than resident birds (RB), with Helicobacter_G being notably enriched at the genus level in MB, potentially associated with their heightened energy and nutritional demands during migration. Notably, in addition to residency status, host species emerged as the most influential factor shaping the compositional variation of BA biotransformation genes, followed by environmental factors and dietary habits. In summary, this study systematically elucidates the potential functions of gut microbiota in BA metabolism and their close associations with host ecological traits in wild birds, not only advancing our understanding of host-microbe interactions and metabolic adaptation mechanisms but also providing a theoretical foundation for future interventions targeting gut microbiota to improve wildlife health.},
}

@article {pmid41108672,
year = {2025},
author = {Thelen, AC and Andreani, N and Korten, NM and Neumann, M and Verspohl, V and van Egmond, M and Kneisel, L and Voelz, C and Blischke, L and Baines, JF and Baier, J and Schumacher, J and Kiessling, F and Herpertz-Dahlmann, B and Beyer, C and Keller, L and Seitz, J and Trinh, S},
title = {The Influence of Omega-3 Fatty Acids and Probiotics on Hippocampal Inflammation and Glial Cells in a Chronic Anorexia Nervosa Rat Model.},
journal = {The International journal of eating disorders},
volume = {},
number = {},
pages = {},
doi = {10.1002/eat.24574},
pmid = {41108672},
issn = {1098-108X},
support = {START 16/22//University Hospital Aachen, RWTH Aachen/ ; //Bundesministerium für Bildung und Forschung/ ; 01EW1906A-01EW1906B//EU (European Research Association (ERA-)NET NEURON)/ ; //Deutsche Forschungsgemeinschaft/ ; },
abstract = {OBJECTIVE: Anorexia nervosa (AN) is a severe eating disorder associated with brain volume reduction, glial cell loss, microbiome alterations, and dysregulated pro-inflammatory mechanisms. However, the underlying cellular mechanisms remain inadequately elucidated, and interventions addressing these alterations are lacking.

METHOD: This study employed a chronic activity-based anorexia (ABA) rat model to investigate hippocampal glial and neuronal cell alterations, inflammation, and microbial modifications in the gut. Omega-3 fatty acids and a multi-strain probiotic were examined as potentially protective agents. Cell count, proliferation, and apoptosis rates of microglia, neurons, astrocytes, and oligodendrocytes were analyzed in the hippocampus. Furthermore, local gene expression of pro-inflammatory cytokines and microRNA was measured. The hippocampal volume was determined longitudinally using 7-Tesla MRI scans before and after starvation. Finally, the fecal microbiome was analyzed to identify potential associations with brain and clinical characteristics.

RESULTS: Results confirmed the previously described reduction in astrocytes and newly demonstrated a decrease in oligodendrocytes in the hippocampus. Increased levels of IBA1-positive cells and pro-inflammatory cytokines suggest microglial activation in this region. Administering omega-3 and probiotics to starved animals reduced neuroinflammation and microglial activation in the hippocampus, resulting in significantly increased neuronal cell counts in the omega-3 group. Microbiome composition was primarily affected by the ABA model, and to a lesser extent by omega-3 and probiotics.

DISCUSSION: These findings support the involvement of microglial activation in the pathogenesis of AN, potentially relevant to hippocampal re-learning and thus important for psychotherapy. Further, omega-3 and probiotics may serve as adjunct therapeutic strategies by modifying inflammation.},
}

@article {pmid41108591,
year = {2025},
author = {Officer, A and Meng, W and Spellman, D and Martin, J and Bracci, PM and McGrath, M and Huang, Y and Gao, SJ},
title = {Oral Microbiome and Inferred Functions Predict Kaposi's Sarcoma Progression.},
journal = {Journal of medical virology},
volume = {97},
number = {10},
pages = {e70647},
doi = {10.1002/jmv.70647},
pmid = {41108591},
issn = {1096-9071},
support = {//National Institutes of Health./ ; //This study was supported by grants from the National Institutes of Health (CA096512, CA284554, CA278812, CA291244 and CA124332 to S.-J. Gao), UPMC Hillman Cancer Center Startup Fund to S.-J. Gao, S10OD028483 to the Center for Research Computing of the University of Pittsburgh, and in part by award P30CA047904. A. Officer is supported by T32CA186873./ ; },
mesh = {Humans ; *Sarcoma, Kaposi/microbiology/pathology/virology ; *Microbiota ; Disease Progression ; RNA, Ribosomal, 16S/genetics ; Male ; *Mouth/microbiology ; Female ; Middle Aged ; Adult ; Herpesvirus 8, Human ; Sequence Analysis, DNA ; Bacteria/classification/genetics/isolation & purification ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/genetics/chemistry ; AIDS-Related Opportunistic Infections ; },
abstract = {Kaposi's sarcoma (KS) is a common cancer among people living with HIV and is caused by infection with Kaposi's sarcoma-associated herpesvirus (KSHV). While previous studies have linked the oral microbiome to KSHV infection and KS development, its role in KS progression remains poorly defined. We performed 16S rRNA gene sequencing targeting the V1-V2 and V3-V4 hypervariable regions to characterize the microbiome in 20 patients with AIDS-associated KS, including 10 with nonprogressive disease and 10 with progressive disease. Samples were obtained from three anatomical sites: oral cavity, peripheral blood, and tumor biopsies. The highest number of microbes were identified in the oral cavity at species, genus, and family levels. Beta diversity analysis revealed significant compositional differences in the oral microbiome between progressive and nonprogressive KS (p value = 0.044). Differential abundance analysis identified 16 species in the oral cavity associated with disease progression, compared to only three species in tumors and one in blood (p value < 0.05). Notably, Prevotella pallens and Megasphaera micronuciformis, both known producers of short-chain fatty acids, were significantly enriched in the oral microbiome of patients with progressive KS (log-fold changes = 2.8 and 2.4, respectively). Functional pathway inference revealed 39 differentially abundant microbial pathways in the oral cavity, including pathways related to denitrification, ubiquinone biosynthesis, and arginine metabolism (all p values < 0.05). Our findings provide the first evidence that specific oral microbiome alterations are associated with KS progression. The enrichment of short-chain fatty acid-producing bacteria and changes in microbial metabolic pathways may promote inflammation and KSHV lytic replication, offering potential mechanistic insights into KS pathogenesis and highlighting novel microbiome-based prognostic markers.},
}

Humans
*Sarcoma, Kaposi/microbiology/pathology/virology
*Microbiota
Disease Progression
RNA, Ribosomal, 16S/genetics
Male
*Mouth/microbiology
Female
Middle Aged
Adult
Herpesvirus 8, Human
Sequence Analysis, DNA
Bacteria/classification/genetics/isolation & purification
DNA, Bacterial/genetics/chemistry
DNA, Ribosomal/genetics/chemistry
AIDS-Related Opportunistic Infections

@article {pmid41108536,
year = {2025},
author = {Siddiqui, S and Siddiqui, H and Riguene, E and Nomikos, M},
title = {Zebrafish: A Versatile and Powerful Model for Biomedical Research.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {},
number = {},
pages = {e70080},
doi = {10.1002/bies.70080},
pmid = {41108536},
issn = {1521-1878},
support = {//NPRP-Blue Skies Research Award/ ; NPRP-BSRA1-0504-210082//Qatar Research Development and Innovation Council (QRDI), Doha, Qatar/ ; },
abstract = {Zebrafish (Danio rerio) have become a versatile model in precision medicine, bridging fundamental biology with translational applications. Their optical transparency, rapid development, and high genetic conservation with humans enable real-time imaging and cost-efficient high-throughput screening. Advances in CRISPR/Cas9, prime editing, and morpholino approaches have expanded their utility for modeling diverse human diseases. In addition to well-established roles in cardiovascular, neurological, metabolic, oncological, and infectious disease research, emerging applications include non-invasive larval urine assays, functional validation of rare human variants, host-microbiome interactions, and automated behavioral profiling for neuropsychiatric conditions. Limitations such as species-specific lipid metabolism and limited antibody availability remain, yet recent integration of single-cell transcriptomics, computational modeling, and machine learning is enhancing translational relevance. Collectively, these innovations position zebrafish as a scalable and powerful platform for disease modeling and personalized therapeutic strategies, underscoring their growing impact in the evolving landscape of precision medicine.},
}

@article {pmid41108334,
year = {2025},
author = {Chang, A and Oh, J and Shin, A and Oser, M and Manitius, N and Ghaffari, A and Limketkai, BN},
title = {Similar Symptoms, Distinct Syndromes: Multi-modal Approach to the Patient with an IBD-IBS Overlap.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {41108334},
issn = {1573-2568},
abstract = {Inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) are distinct gastrointestinal conditions, but they frequently share overlapping clinical symptoms such as abdominal pain, bloating, and altered bowel habits. IBD is defined by the presence of chronic immune-mediated inflammation, and IBS is characterized by gastrointestinal symptoms in the absence of endoscopic and histologic inflammation. When patients with IBD continue to experience IBS-like symptoms despite remission of inflammation, this phenomenon is commonly referred to as IBD-IBS overlap. These patients pose diagnostic and therapeutic challenges, as symptom persistence may reflect lingering immune activation, disrupted barrier function, visceral hypersensitivity, gut-brain axis dysfunction, or microbiome alterations. This review synthesizes emerging evidence on the shared mechanisms underlying IBD and IBS and outlines a multimodal treatment approach that includes pharmacologic management, dietary interventions, mind-body therapies, and microbiome-directed strategies such as probiotics and fecal microbiota transplantation.},
}

@article {pmid41108224,
year = {2025},
author = {Agrawal, R and Lathia, T},
title = {Obesity during pregnancy: contemporary evidence and clinical implications.},
journal = {Current opinion in endocrinology, diabetes, and obesity},
volume = {},
number = {},
pages = {},
doi = {10.1097/MED.0000000000000936},
pmid = {41108224},
issn = {1752-2978},
abstract = {PURPOSE OF REVIEW: Obesity during pregnancy is a growing global health concern with implications for maternal, fetal, and intergenerational outcomes. This review highlights pathophysiological mechanisms, clinical risks, and evidence-based management strategies across the preconception, antenatal, and postpartum periods.

RECENT FINDINGS: Maternal obesity amplifies pregnancy-associated insulin resistance, disrupts adipokine balance, and promotes inflammation, placental hormone dysregulation, and aberrant mTOR signaling. These mechanisms increase risks of gestational diabetes, hypertensive disorders, cesarean delivery, and macrosomia. Epigenetic modifications contribute to fetal metabolic programming, raising offspring risk of obesity, type 2 diabetes, and cardiovascular disease. Recent advances emphasize early risk stratification using continuous glucose monitoring, lipid and inflammatory biomarkers, and integration of telehealth-based lifestyle interventions. Precision medicine and microbiome-targeted therapies represent emerging frontiers.

SUMMARY: Management of obesity in pregnancy requires a continuum of care. Preconception optimization through lifestyle interventions and, in select cases, bariatric surgery improves outcomes. Antenatal care demands individualized metabolic monitoring, adherence to gestational weight gain targets, and pharmacologic interventions such as metformin when indicated. Postpartum priorities include structured weight management, diabetes prevention, and lactation support. Multidisciplinary, culturally tailored strategies are essential to mitigate the global burden of maternal obesity and its intergenerational consequences.},
}

@article {pmid41108133,
year = {2025},
author = {Wang, YF and Dong, SS and Chen, Y and Zeng, YH and Chen, ZX and Zhang, LL},
title = {Caries Control by CAPE Toothpaste: In Vitro, In Vivo, and In Situ Analysis.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345251374959},
doi = {10.1177/00220345251374959},
pmid = {41108133},
issn = {1544-0591},
abstract = {Dental caries is closely associated with microbiome dysbiosis. Incorporating antimicrobial agents can enhance the efficacy of fluoride toothpaste. Our previous studies showed that caffeic acid phenethyl ester (CAPE), derived from propolis, effectively inhibited cariogenic bacteria. To formulate a novel CAPE-containing fluoridated toothpaste and establish a multistage evaluation system assessing its caries-controlling efficacy. The CAPE toothpaste's physicochemical properties were characterized. Its in vitro antimicrobial activity against Streptococcus mutans was examined using quantitative suspension and checkerboard microdilution assays. In vivo anticaries efficacy and biosafety were evaluated in a rat caries model (n = 9/group) comparing 5 groups: untreated control (group NC), base toothpaste without CAPE (group B, 600 ppm F[-]), CAPE-fluoride toothpaste (group C, 0.16 mg/mL CAPE + 600 ppm F[-]), fluoride control (group F, DARLIE[®], 600 ppm F[-]), and propolis nonfluoride control (group P, Red Seal[®]). Caries severity was scored using the Keyes method. Finally, in situ enamel repair (n = 24 enamel blocks) and plaque microbiome modulation (n = 6 samples) were assessed in a 7-d clinical study (ChiCTR2400089643) with 4 groups (groups NC, C, F, and P). The novel formulation showed stable physicochemical properties. Group C reduced S. mutans by 1.5-log10 within 3 min (P = 0.0062 vs NC), and CAPE plus fluoride exhibited additive antibacterial properties (fractional inhibitory concentration index = 0.75). In rats, group C showed the lowest smooth-surface score (21.0 ± 1.7, P < 0.005 vs. all) and reduced sulcal lesion severity (slight dentinal lesions: P = 0.0181 vs. NC and P = 0.0318 vs. F). In situ, group C achieved 27.58% surface microhardness recovery (P < 0.01 vs. all), with significant reductions in mineral loss and lesion depth (P < 0.001 vs. all). Microbiome analysis revealed a preserved microbial diversity, increased Streptococcus oralis, and reduced cariogenic populations. The novel CAPE-containing fluoridated toothpaste effectively inhibited the onset and development of caries. Wider-ranging and longer-term clinical investigations are still needed.},
}

@article {pmid41108124,
year = {2025},
author = {Manzoor, M and Putaala, J and Zaric, S and Leskelä, J and Dong, A and Könönen, E and Lahti, L and Paju, S and Pussinen, PJ},
title = {Oral Microbial Determinants of Saliva and Serum Lipopolysaccharide Activity.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345251370995},
doi = {10.1177/00220345251370995},
pmid = {41108124},
issn = {1544-0591},
abstract = {Lipopolysaccharide (LPS) is a virulence factor of gram-negative bacteria, and endotoxemia or translocation of LPS in serum plays a significant role in oral and systemic pathologies. The contribution of the oral microbiome composition to saliva LPS activity and endotoxemia remains unclear. We investigated whether salivary and serum LPS levels are associated with oral microbiome diversity, taxonomic profiles, and functional characteristics. The oral microbiome was analyzed using metagenomic sequencing of saliva from 298 individuals enrolled in a multicenter case-control study, SECRETO (NCT01934725). Serum and salivary LPS activities were measured, and multiple linear regression models were fitted to identify the microbial taxa that predicted LPS levels. MaAsLin2 (Microbiome Multivariable Associations with Linear Models) was used to determine the associations of microbial functional features and LPS levels. Salivary alpha diversity was positively associated with serum LPS but negatively associated with salivary LPS, smoking, and antibiotic use in the preceding 1 to 6 mo. Community composition (beta diversity) differed between the salivary LPS tertiles (P = 0.001) but not between serum LPS tertiles. In total, 10 oral taxa associated with serum LPS tertiles and 59 with salivary LPS tertiles were identified. Prevotella, Neisseria, Leptotrichia, and Porphyromonas had significant positive associations with salivary LPS, whereas Fusobacterium had a negative association. Among these genera, Prevotella sp. E13_17, P. gingivalis, L. wadei, and F. nucleatum were the species with the strongest associations. Among the 1,016 oral microbiome metabolic features, several were linked to the biosynthesis of LPS, lipid A, and O-antigen pathways. The oral microbiome composition was strongly associated with salivary LPS activity in addition to weaker links to serum LPS. Oral microbiota-derived LPS activity in saliva was associated with microbial metabolism characterized by the predominance of proliferation and biosynthesis pathways. Our study indicates that dysbiosis of the oral microbiome is a source of increased salivary and serum LPS activity.},
}

@article {pmid41108123,
year = {2025},
author = {Boubsi, F and Anckaert, A and Argüelles-Arias, A and Ongena, M},
title = {Pectin-derived oligogalacturonides shape mutualistic interactions between Bacillus and its host plant.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf232},
pmid = {41108123},
issn = {1751-7370},
abstract = {Certain beneficial bacteria of the root-associated microbiome such as B. velezensis protect plants against diseases and are promising biocontrol agents exploited in sustainable agriculture. Unveiling the molecular dialogue governing mutualistic interactions between these beneficials and their host is essential to better understand their ecological behavior and to optimize their use as bioprotectants. However, the chemical diversity and functionality of mediators involved in this interkingdom crosstalk remain largely unexplored. In this study, we uncover a strategy by which B. velezensis exploits the root cell wall polymer pectin to prime its host for enhanced resistance against phytopathogens and to ensure a safe environment enabling its efficient root establishment. Thanks to the activity of its two conserved pectinolytic enzymes, the bacterium generates a specific pattern of short oligogalacturonides that act as efficient triggers of plant systemic defense against leaf pathogens. Moreover, these oligomers induce only weak immune responses in root cells and dampen local defense reaction in response to the perception of the bacterium itself. Our data emphasize the key role of short oligogalacturonides as mediators in the intricate interplay between plants and their bacterial associates, providing new insights into the mechanisms that enable beneficial bacteria to coexist with their host plant.},
}

@article {pmid41108012,
year = {2025},
author = {Woolley, CSC and Muwonge, A and de C Bronsvoort, BM and Schoenebeck, JJ and Handel, IG and Chamberlain, K and Rose, E and Clements, DN},
title = {The gut microbiota of Labrador retriever puppies: a longitudinal cohort study.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {108},
pmid = {41108012},
issn = {2524-4671},
support = {BB/ J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/ J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/ J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/ J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/ J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/ J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/ J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/ J004235/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {BACKGROUND: Most research into the development of the canine gut microbiota has featured cross-sectional studies, and there has been limited exploratory research into how it is affected by external factors. We aimed to longitudinally characterise the gut microbiota and its development in Labrador Retriever puppies and identify whether alterations in the gut microbiota are associated with factors related to demography, lifestyle, antibiotic usage and gastrointestinal health.

RESULTS: 76 Labrador Retriever puppies were recruited via Dogslife, a UK-based online cohort study. Faecal samples were collected at three to four, seven, and 12 months of age and analysed using 16 S rRNA gene sequencing alongside questionnaire data. Alpha and beta diversity were assessed using linear mixed effects models and permutational multivariate analysis, accounting for repeated measures. Differential abundance was evaluated using multivariable association with linear models. Associations were identified between puppies' gut microbiota and age, sex, coat colour, household smoking status, dietary indiscretions (e.g. household waste, coprophagia), contact with other dogs and horses, recent oral/injected antibiotic use, and recent vomiting and diarrhoea. The greatest source of variation was individual identity, explaining approximately 25% of alpha diversity and 50% of beta diversity. Alpha diversity declined between three and 12 months, with age-related shifts in community composition and dispersion. Coprophagia was associated with increased alpha diversity and contributed to variation in community structure. Antibiotic use was associated with reduced alpha diversity, altered composition, and changes in taxa across Firmicutes, Proteobacteria, and Tenericutes. These effects were largely transient, with the largest shifts occurring within one week of treatment. Puppies with recent diarrhoea showed increased alpha diversity and differential abundance in several taxa within four weeks of the episode. Helicobacter was more frequently detected in samples from puppies with recent diarrhoea.

CONCLUSIONS: This longitudinal study characterises the development of gut microbiota in Labrador Retriever puppies and identifies associations with demographic, environmental, and health-related factors. These findings underscore the value of longitudinal sampling in microbiome research, offer novel insights for owners and veterinarians, and lay a foundation for future studies investigating causal mechanisms and potential interventions.},
}

@article {pmid41107739,
year = {2025},
author = {Wu, F and Jiang, X and Chen, G and Zhang, L},
title = {Integrated Microbiome and metabolome analysis reveals Microbial-Metabolic interactions in psoriasis pathogenesis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {665},
pmid = {41107739},
issn = {1471-2180},
support = {82370785//National Natural Science Foundation of China/ ; ZR2024MH220//Shandong Provincial Natural Science Foundation/ ; },
mesh = {Humans ; *Psoriasis/microbiology/metabolism ; Female ; Male ; *Skin/microbiology/metabolism ; *Metabolome ; *Microbiota ; Adult ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metabolomics ; Corynebacterium ; Lipid Metabolism ; },
abstract = {BACKGROUND: Psoriasis is a chronic inflammatory skin disorder with unclear etiology. The roles of skin microbiome and metabolic dysregulation in psoriasis pathogenesis are not yet fully understood.

METHODS: We conducted an integrated microbiome and untargeted metabolomic analyses on skin samples from 29 patients with psoriasis and 31 healthy controls. The skin microbiota was characterized using 16 S rRNA gene sequencing, and untargeted metabolomic profiling was performed using LC-MS/MS. Multivariate statistical analyses were used to identify differential microbes and metabolites, followed by correlation analyses to explore microbe-metabolite interactions.

RESULTS: Psoriatic lesions exhibited significantly higher skin microbial alpha diversity compared to healthy controls. Principal component analysis revealed distinct microbial community structures between the two groups. At the genus level, Corynebacterium and Staphylococcus were significantly enriched in psoriatic lesions, while Cutibacterium was notably reduced. Metabolomic analysis identified 63 differential metabolites, with 39 upregulated and 24 downregulated in psoriatic lesions. These metabolites were primarily involved in lipid metabolism (particularly phospholipids and sphingolipids), amino acid metabolism, and inflammatory mediator pathways. Correlation analysis revealed significant associations between microbial alterations and metabolic dysregulation. Cutibacterium abundance was negatively correlated with inflammatory lipids and positively correlated with antioxidant metabolites, whereas Staphylococcus and Corynebacterium exhibited the opposite pattern. Notably, the abundance of Propionibacteriaceae strongly correlated with glutathione levels (r = 0.821, P < 0.001), indicating a potential role of microbiome-mediated oxidative stress in psoriasis.

CONCLUSIONS: This study highlights significant alterations in both the skin microbiome and metabolome in patients with psoriasis, revealing complex microbe-metabolite interaction networks. The findings suggest that microbial dysbiosis, particularly the decreased abundance of Cutibacterium and the increased abundance of Staphylococcus/Corynebacterium, may contribute to psoriasis pathogenesis by modulating lipid metabolism, inflammatory pathways, and oxidative stress responses.},
}

Humans
*Psoriasis/microbiology/metabolism
Female
Male
*Skin/microbiology/metabolism
*Metabolome
*Microbiota
Adult
Middle Aged
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/metabolism/isolation & purification
Metabolomics
Corynebacterium
Lipid Metabolism

@article {pmid41107717,
year = {2025},
author = {Khan, MSI and Wu, J and Hou, S and Ji, S and Li, H and Chang, Y and Sui, B and Tan, D and Yin, J},
title = {Bile modulates phage-host interactions in multidrug-resistant Pseudomonas aeruginosa.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {666},
pmid = {41107717},
issn = {1471-2180},
support = {2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; 2021-243//People's Government of Dalian Municipality/ ; },
mesh = {*Pseudomonas aeruginosa/virology/drug effects/genetics/physiology ; *Bile/metabolism ; *Drug Resistance, Multiple, Bacterial ; Biofilms/growth & development/drug effects ; *Pseudomonas Phages/physiology ; Lipopolysaccharides/biosynthesis ; Pseudomonas Infections/microbiology ; *Host-Pathogen Interactions ; },
abstract = {Biliary tract infections (BTIs) arise within a bile-rich environment that profoundly shapes microbial ecology and pathogen adaptation. Pseudomonas aeruginosa, a major opportunistic pathogen in nosocomial settings, exhibits remarkable physiological plasticity, that enable persistence in such challenging niches. However, the influence of bile on P. aeruginosa's adaptive responses and phage-host interactions remains largely unexplored. Here, we demonstrate that ox-bile imposes concentration-dependent stress on P. aeruginosa strain ZS-PA-35, indicative of host-derived selective pressure. Notably, ox-bile enhances biofilm formation and promotes swarming and twitching motilities while concurrently suppressing swimming motility. Moreover, ox-bile modulates phage susceptibility, likely through altered receptor expression: exposure to ox-bile sensitizes P. aeruginosa to the type IV pili (T4P)-dependent phage phipa2, whereas susceptibility to the lipopolysaccharide (LPS)-targeting phage phipa10 remains unchanged. Genome-wide mutagenesis identified resistance-conferring mutations affecting T4P structures, LPS biosynthesis, and associated regulatory pathways. Among these, phage-resistant mutants ΔpilT and ΔgalU retained high fitness under ox-bile stress, accompanied by enhanced swarming and swimming motilities. Furthermore, in a lysogenic context, ox-bile markedly suppressed prophage accumulation in the T4P-dependent strain ZS-PA-05. These findings reveal that bile acts as a critical environmental cue shaping both adaptive physiology and phage susceptibility in P. aeruginosa, with broad implications for microbiome dynamics and the development of phage-based therapies targeting bile-impacted infections.},
}

*Pseudomonas aeruginosa/virology/drug effects/genetics/physiology
*Bile/metabolism
*Drug Resistance, Multiple, Bacterial
Biofilms/growth & development/drug effects
*Pseudomonas Phages/physiology
Lipopolysaccharides/biosynthesis
Pseudomonas Infections/microbiology
*Host-Pathogen Interactions

@article {pmid41107577,
year = {2025},
author = {Meng, L and Liu, J and Ong, HH and Wang, DY and Shi, L},
title = {MUC1 in the upper-lower airway inflammatory continuum: an endotype-centered perspective.},
journal = {Inflammation research : official journal of the European Histamine Research Society ... [et al.]},
volume = {74},
number = {1},
pages = {143},
pmid = {41107577},
issn = {1420-908X},
support = {82371117//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Mucin-1/immunology ; Animals ; *Inflammation/immunology ; *Respiratory Tract Diseases/immunology ; },
abstract = {Emerging evidence indicates that upper and lower airway diseases share anatomical and pathophysiological features. Infections often begin in the upper airway and progress downward, suggesting common immunological mechanisms. Mucin 1 (MUC1), a membrane-bound glycoprotein abundantly expressed in airway epithelial cells, has attracted increasing attention for its immunoregulatory and barrier functions. This review summarizes recent findings on MUC1's involvement in airway inflammation driven by Th1, Th2, and Th17 immune responses. In Th1-type inflammation, MUC1 negatively regulates Toll-like receptor (TLR)-NF-κB signaling pathways, thereby limiting excessive inflammatory responses to bacterial and viral infections. In Th2-type inflammation, MUC1 influences eosinophil survival, maintains epithelial integrity, and modulates glucocorticoid sensitivity, exerting both protective and pathological effects. In Th17-type inflammation, characterized by neutrophil infiltration and elevated IL-17A and IL-22, MUC1 expression alleviates chronic inflammation and may impact microbiome dysbiosis. While MUC1's roles in lower airway disorders are increasingly understood, its specific function and regulatory mechanisms in upper airway diseases remain unclear. This review adopts the unified airway disease (UAD) framework to examine the endotype-specific roles of MUC1 across the upper and lower airways. Rather than providing a disease-by-disease summary, we synthesize evidence through Th1/Th2/Th17 endotypes, link shared mechanisms to biomarker-based patient stratification, and outline MUC1-targeted therapeutic strategies. By applying an endotype- and UAD-centered perspective, the review distinguishes itself from previous work and highlights actionable opportunities for precision medicine. Furthermore, we emphasize the translational potential of MUC1 as both a diagnostic biomarker and a therapeutic target, focusing on advances in small peptides, monoclonal antibodies, RNA interference, and natural compounds that modulate MUC1-related pathways. These developments may ultimately enable the creation of personalized therapies for airway inflammation.},
}

Humans
*Mucin-1/immunology
Animals
*Inflammation/immunology
*Respiratory Tract Diseases/immunology

@article {pmid41107300,
year = {2025},
author = {Urrutia-Angulo, L and Ocejo, M and Yergaliyev, T and Oporto, B and Aduriz, G and Camarinha-Silva, A and Hurtado, A},
title = {Exploring colostrum microbiota and its influence on early calf gut microbiota development using full-length 16S rRNA gene metabarcoding.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {36350},
pmid = {41107300},
issn = {2045-2322},
support = {PRE2020-096275//MICIU/AEI/10.13039/501100011033 and ESF Investing in your future/ ; },
mesh = {*Colostrum/microbiology ; Animals ; Cattle ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; DNA Barcoding, Taxonomic/methods ; Female ; Phylogeny ; },
abstract = {The early gut microbiota of calves is seeded by colostrum and shaped by diet, environment, disease, and antibiotic treatments. This study analyzed the colostrum microbiota of 42 cows and tracked their calves' gut microbiota during early life (days d1, d16, and d57), assessing the impact of antimicrobial dry cow therapy and infection treatments. The full-length 16S rRNA gene was sequenced using Oxford Nanopore, enabling taxonomic classification down to species level. Microbial richness and diversity were lowest at d1 and increased afterwards. Beta diversity analysis showed that d16 samples had microbial profiles intermediate to those of d1 and d57. The most abundant phyla (Pseudomonadota, Bacillota, and Bacteroidota) were common to all sample categories, while genus-level composition showed greater variability. Colostrum was dominated by Paraclostridium, Romboutsia, and Staphylococcus, while Escherichia/Shigella and Clostridium were more abundant in d1 feces, later replaced by Succinivibrio and Faecalibacterium at d16 and d57. Notably, 56.2% of species in d1 feces were also present in colostrum, and 37.4% of colostrum species persisted in feces at d57, highlighting colostrum´s role in bacterial gut colonization. Interindividual variability in gut microbiota decreased over time as richness and diversity increased. Antimicrobial treatments did not significantly alter microbiota diversity or composition, suggesting a limited long-term impact.},
}

*Colostrum/microbiology
Animals
Cattle
*RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome/genetics
*Bacteria/genetics/classification/isolation & purification
Feces/microbiology
DNA Barcoding, Taxonomic/methods
Female
Phylogeny

@article {pmid41107061,
year = {2025},
author = {Carraro, P and Naeem, Y and Girardi, F and Botton, A and Varotto, S and Ruperti, B and Bonghi, C},
title = {A Rootstock-Centered Perspective on the Regulation of Alternate Bearing in Fruit Trees.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/eraf460},
pmid = {41107061},
issn = {1460-2431},
abstract = {Alternate bearing in most perennial fruit tree species refers to the phenomenon where high-yielding on-years are followed by low or nearly no fruiting off-years. This variability complicates orchard management, especially under unpredictable weather patterns. Alternate bearing is regulated by both endogenous and environmental signals, and recent studies suggest that rootstocks could play a role on its modulation. Beyond affecting scion growth and nutrient status, rootstocks influence developmental behavior through long-distance signaling. They participate in hormonal metabolism, nutrient uptake, water transport, and chromatin conformation in scion tissues. Epigenetic changes, including DNA methylation and histone marks, have been implicated in regulating flowering-related genes in response to environmental and developmental cues. This review explores possible contributions of the rootstock to alternate bearing through physiological, molecular, and epigenetic signals-such as signaling molecules and chromatin states associated with flowering-as working hypotheses. The role of rootstocks in shaping source-sink dynamics, interpreted throughout the resource budget model, and their potential influence on stress responses are also discussed in relation to the AB rhythmicity. Finally, emerging strategies aimed at mitigating alternate bearing intensity, including genome editing, marker-assisted selection, and microbiome-based strategies, are highlighted as promising for stabilizing productivity under changing climate conditions.},
}

@article {pmid41107018,
year = {2025},
author = {Marietta, E and Rubio-Tapia, A},
title = {Intestinal Bacteria and Gluten Interactions in Celiac Disease.},
journal = {Gastrointestinal endoscopy clinics of North America},
volume = {35},
number = {4},
pages = {869-880},
doi = {10.1016/j.giec.2025.02.012},
pmid = {41107018},
issn = {1558-1950},
mesh = {Humans ; *Celiac Disease/microbiology ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/complications ; *Glutens/immunology/metabolism ; Probiotics/therapeutic use ; Intestinal Mucosa/microbiology ; },
abstract = {Dysbiosis exists in both the small intestinal mucosa, as well as the fecal microbiome of patients with celiac disease. However, no clear signal has been associated with every patient with celiac disease. Rather, the intestinal microbiome of each patient with celiac disease differs from the controls. Clinical trials with probiotics have not demonstrated any consistent reversals of intestinal pathology, but they have shown promising results with amelioration of symptoms. It is unlikely that intestinal dysbiosis plays a direct role in the pathogenesis of celiac disease. Instead, it may play an aggravating role in either the pathogenesis or healing.},
}

Humans
*Celiac Disease/microbiology
*Gastrointestinal Microbiome
*Dysbiosis/microbiology/complications
*Glutens/immunology/metabolism
Probiotics/therapeutic use
Intestinal Mucosa/microbiology

@article {pmid41107011,
year = {2025},
author = {Weekley, K and Gardinier, D and Lee, AR and Weisbrod, V},
title = {The Gluten-Free Diet for Celiac Disease.},
journal = {Gastrointestinal endoscopy clinics of North America},
volume = {35},
number = {4},
pages = {753-773},
doi = {10.1016/j.giec.2025.01.009},
pmid = {41107011},
issn = {1558-1950},
mesh = {Humans ; *Celiac Disease/diet therapy/psychology ; *Diet, Gluten-Free/adverse effects/psychology ; Quality of Life ; Micronutrients/deficiency ; },
abstract = {A gluten-free diet (GFD) is the only treatment of celiac disease (CeD). A GFD is free from any food or substance with wheat, rye, and barley. CeD can be associated with micronutrient deficiencies including iron, folate, vitamin B12, vitamin D, zinc, and copper. Foods that are high in fat, added sugars, total calories are more often consumed, increasing the risk of obesity and a poor microbiome. There are psycho-social demands of a GFD including emotional burden, anxiety, social isolation, and relationship strain. People with CeD on a GFD should be monitored for nutrient deficiencies, other comorbidities, and overall quality of life.},
}

Humans
*Celiac Disease/diet therapy/psychology
*Diet, Gluten-Free/adverse effects/psychology
Quality of Life
Micronutrients/deficiency

@article {pmid41106736,
year = {2025},
author = {Tampanna, N and Lim, SJ and Rahman, HA and Sofian-Seng, NS and Razali, NSM and Mustapha, WAW and Wichienchot, S},
title = {Human gut microbiome modulation and butyrogenic effects of fucoidan from Sargassum binderi: A prebiotic activity in in vitro simulated digestion and human fecal fermentation.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {148327},
doi = {10.1016/j.ijbiomac.2025.148327},
pmid = {41106736},
issn = {1879-0003},
abstract = {The fucoidan extract from Sargassum binderi, a brown algae-derived marine polysaccharide, is rich in fucose, and are a potent candidate for functional food, and nutraceutical applications. This study uniquely investigated the prebiotic potential of S. binderi fucoidan through in vitro simulated digestion and human fecal fermentation. The fucoidan extract demonstrated higher resistance to simulated upper gastrointestinal digestion (88.27 %) than inulin (81.13 %), allowing a substantial portion to reach the colon, which was metabolized by gut microbiota into beneficial metabolites. Fucoidan selectively modulated the gut microbiome by increasing the relative abundance of Megamonas and decreasing Bacteroides. Our current findings proved that the Megamonas enrichment, a carbohydrate-fermenting genus, contributed to a substantial rise in short-chain fatty acid (SCFA) production, including butyric acid (10.24-fold), acetic acid (5.89-fold), and propionic acid (4.92-fold), higher than those produced by inulin, indicating a strong butyrogenic effect. These microbiome shifts and enhanced SCFA production suggest that S. binderi fucoidan may help maintain gut microbiome balance. Overall, the current findings highlight the potential of S. binderi-derived fucoidan to formulate functional foods with a butyrogenic effect, for promoting gut health.},
}

@article {pmid41106731,
year = {2025},
author = {Kamath, S and Ariaee, A and Abdelhafez, A and Asif, Z and Chan, NSL and Collins, K and Hunter, A and Joyce, P},
title = {Microbiome-active drug delivery systems (MADDS): Leveraging microbial stimuli for controlled drug release.},
journal = {Advanced drug delivery reviews},
volume = {},
number = {},
pages = {115720},
doi = {10.1016/j.addr.2025.115720},
pmid = {41106731},
issn = {1872-8294},
abstract = {The human microbiome comprises diverse microbial communities that inhabit tissues and biofluids throughout the body, including the gastrointestinal tract, lungs, vagina, and skin. These sites create dynamic microenvironments rich in enzymes, metabolites, and chemical gradients that act both as biological barriers and as localised targets for drug delivery. This review provides an overview of Microbiome-Active Drug Delivery Systems (MADDS), an emerging class of platforms that exploit microbial stimuli for site-specific therapeutic release. Unlike conventional systems that simply coexist with the microbiome, MADDS harness resident microbes and their metabolites to trigger drug activation, retention, or release. This enables spatially precise delivery of small molecules, biologics, and live biotherapeutic products (LBPs). Key strategies include enzyme-, environment-, metabolite-, biofilm-, and receptor-responsive designs, each tailored to microbial niches and applied across infectious, inflammatory, and metabolic disorders. However, challenges remain, including microbiome variability between individuals, regulatory uncertainty around hybrid biologic-material systems, and the need for scalable GMP-compliant manufacturing. This review therefore outlines the current approaches for engineering MADDS and the future steps required for clinical translation. By exploiting microbial cues for controlled drug release, MADDS offer a practical route to more targeted and patient-specific therapies.},
}

@article {pmid41106704,
year = {2025},
author = {Heckmann, ND and Culler, M and Atallah, LM and Mont, MA and Lieberman, JR and Parvizi, J},
title = {Emerging Concepts in Periprosthetic Joint Infection Research: Infection Recurrence and Microbe Persistence.},
journal = {The Journal of arthroplasty},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.arth.2025.10.033},
pmid = {41106704},
issn = {1532-8406},
abstract = {Recurrent periprosthetic joint infection (PJI) is a highly morbid complication following total joint arthroplasty (TJA). Despite appropriate medical and surgical management with targeted antimicrobial therapies, many patients who suffer from a PJI experience clinically relevant episodes of recurrence. Though the majority of these recurrent infections are due to microbes that are different from the species initially isolated at the index infection, approximately 15 to 50% of subsequent PJIs are attributed to recurrence with the same causative organism. Treatment resistance, contamination during revision surgery, hematogenous spread of bacteria from a distant source, and the presence of resilient biofilms have long been implicated in these recurrent infections. However, recent preclinical and clinical evidence has demonstrated that certain organisms that commonly cause PJI, namely staphylococcal species, can undergo phenotypic transformation into viable, but non-culturable (VBNC) and quasi-dormant small colony variant (SCV) forms that may persist intracellularly and lead to recurrent infection. Moreover, some organisms are known to infiltrate the osteocyte lacuno-canalicular network (OLCN) and invade eukaryotic cells to avoid targeting by the host immune system and antimicrobial agents. In doing so, they create microbial reservoirs that may be capable of reactivating to cause symptomatic infection locally or after being transported to the joint by circulating phagocytic cells. Commensal species present in the human microbiome may also become pathogenic and lead to recurrent PJI. Evidence suggests dysbiosis, a pathological imbalance in the composition and function of the microbiome, may induce the translocation of resident organisms from the gut into the bloodstream. Recent studies have also identified joint microbiota signatures that vary in accordance with the presence or absence of certain pathologies, including PJI.},
}

@article {pmid41106636,
year = {2025},
author = {Chen, T and Tang, Q and Yu, B and Tang, L and Lin, J and Zhang, L and Shan, W and Yu, H},
title = {Investigation of the mechanism involved in high-fat diet-induced depressive behavior based on energy metabolism.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {120505},
doi = {10.1016/j.jad.2025.120505},
pmid = {41106636},
issn = {1573-2517},
abstract = {BACKGROUND: The specific mechanisms underlying high-fat diet (HFD) and depressive behaviors remain elusive. Meanwhile, the impact of calorie restriction (CR) on the development of depression has not been explored in-depth. Thus, we aimed to examine the pathways underlying how long-term HFD intake leads to depression, focusing on energy metabolism.

METHODS: C57BL/6J mice were randomly divided into four groups-control (CK) group, CR group, HFD group, and chronic unpredictable mild stress (CUMS) group. Enzyme-linked immunosorbent assay, western blot, metabolomics and 16s rRNA gene sequencing analysis were undertaken to investigate the 5-hydroxytryptamine system, glucolipid metabolism, brain energy metabolism and gut microbiome.

RESULTS: Mice with HFD- and CUMS-induced depressive-like symptoms exhibited a significant decrease in serotonergic activity in the hippocampus. The behaviors of CR mice did not differ significantly from CK mice. Fasting blood glucose levels, fatty acid contents, and reactive oxygen species (ROS) levels were all negatively affected in unrestricted HFD and CUMS mice, suggestive of energy metabolism disruption. Metabolomic analysis revealed that tricarboxylic acid cycle activity was inhibited in the HFD and CUMS groups but not in the CR group. Additionally, analysis of the gut microbiome revealed that [Ruminococcus] gnavus exhibited higher predictive potential for HFD-induced depression, while Allobaculum showed greater predictive potential for stress-induced depression.

LIMITATIONS: Causal relationship between brain energy metabolism and gut microbiome unclear.

CONCLUSION: An unrestricted HFD promotes dysbiosis of the gut microbiota, impairs energy metabolism in the brain, affects the serotonergic system, and ultimately induces depressive-like behaviors.},
}

@article {pmid41106616,
year = {2025},
author = {Israel, A and Weizman, A and Israel, S and Stokar, J and Ashkenazi, S and Vinker, S and Magen, E and Merzon, E},
title = {Systematic screening Identifies medication and disease factors associated with Schizophrenia risk.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106135},
doi = {10.1016/j.bbi.2025.106135},
pmid = {41106616},
issn = {1090-2139},
abstract = {Schizophrenia (SCZ) is a severe psychiatric disorder with a complex and poorly understood etiology. Previous studies have linked Toxoplasma gondii infection to SCZ, though its clinical relevance remains uncertain. To identify factors associated with SCZ risk, we analyzed electronic health records from a national Israeli health provider, retrospectively comparing 3,273 individuals with SCZ to 32,730 matched controls. We systematically screened all medication purchases and medical diagnoses recorded from 10 years to 30 days before SCZ onset. Significant associations, adjusted for residual confounding, were further evaluated in the TriNetX network, where large propensity score-matched cohorts were compared for incident SCZ following medication exposure. Among all medication classes screened, strong protective associations were detected for specific antimicrobials, notably atovaquone/proguanil, clindamycin, and ophthalmic fluoroquinolones. Nonsteroidal anti-inflammatory drugs, particularly COX-2 inhibitors, were also linked to reduced SCZ risk, whereas neomycin, tramadol, and desmopressin were associated with increased risk. Key associations were confirmed within TriNetX with high statistical significance. These observational findings, reproduced across two national cohorts, are hypothesis-generating and may reflect multiple, non-exclusive mechanisms, including antimicrobial, anti-inflammatory, and microbiome-related pathways, with T. gondii elimination through antiprotozoal activity representing one compelling explanatory hypothesis that warrants further investigation.},
}

@article {pmid41106336,
year = {2025},
author = {Pereira, G and Wise, CM and Pagenkopp Lohan, KM and Noyce, GL and Lopes, ML and Magalhães, L},
title = {Trait-mediated effects of Macoma balthica (L.) on nitrogen and carbon biogeochemistry in estuarine ecosystems.},
journal = {Marine environmental research},
volume = {213},
number = {},
pages = {107621},
doi = {10.1016/j.marenvres.2025.107621},
pmid = {41106336},
issn = {1879-0291},
abstract = {Coastal ecosystems rely on microbially mediated biogeochemical processes for ecosystem functioning, particularly carbon (C) and nitrogen (N) cycling across the water-sediment interface, supported by bivalves through bioturbation activity. Here, we conducted an 8-week coastal microcosm experiment using Macoma balthica sampled from the Rhode River (Chesapeake Bay) to assess how bivalve presence and individual traits (burial position and shell length) influence the N cycle (NH3 and NOX) and C cycle (CDOM, measured as aCDOM 250 m[-1]) in the water column and interstitial water. Our results show that bivalve presence significantly affected N cycling: NH3 initially rose in the water column before declining, followed by exponential increases in NOx in both water and interstitial water. Burial position influenced NH3 and NOx concentrations throughout the experiment, and larger individuals were associated with higher NOx levels. Additionally, aCDOM 250 m[-1] increased over time regardless of bivalve presence, likely due to daily feeding with artificial algae, suggesting that future studies should include additional C parameters such as dissolved and particulate forms of organic and inorganic C. Overall, our findings show that M. balthica's influence on N cycling is shaped by individual traits and temporal dynamics, creating functional heterogeneity with implications for Rhode River nutrient fluxes and ecosystem functioning. While microbiomes might contribute to the nitrification processes observed, future research should clarify the pathways of bivalve-microbiome interactions in M. balthica.},
}

@article {pmid41106321,
year = {2025},
author = {Wang, X and Wang, Y and Guo, C and Guo, R and Zuo, W and Liu, C and Wang, J and Gao, C and Zhang, L and Yuan, W and Ma, J},
title = {Targeted depletion of intratumoral bacteria using PEGylated metronidazole to augment cancer treatment efficacy.},
journal = {Biomaterials},
volume = {327},
number = {},
pages = {123772},
doi = {10.1016/j.biomaterials.2025.123772},
pmid = {41106321},
issn = {1878-5905},
abstract = {Since the infiltration of intratumoral microbiota is associated with aggressive phenotypes of cancer, eliminating bacteria within tumors has become an attractive approach to cancer treatment. By self-assembly of PEGylated metronidazole (MTI-PEG), we developed a nanosized antibiotic that effectively eliminates intratumoral bacteria without causing gut microbiome dysbiosis. In Fusobacterium nucleatum spp (Fn) colonized tumor models, we observed significant adjuvant effects of MTI-PEG on chemotherapy, immunotherapy and targeted therapy through reversing drug resistance through the modulation of autophagy, the human T-cell immunoglobulin and ITIM domain (TIGIT) and the phosphatidylinositol-3-kinase/protein kinase B (PI3K-AKT) signaling pathway, respectively, while reshaping immune landscape of tumor microenvironment. The encouraging results indicate a promising future for MTI-PEG in microbiome-infiltrated tumors, with potential to improve the overall therapeutic efficacy of current cancer treatments.},
}

@article {pmid41106256,
year = {2025},
author = {Wang, S and Song, F and Yang, Y and Liu, B and Zhou, C and Wang, C and Wang, Y and Luo, H},
title = {Exploring the forensic skin and 'touched' bacterial community through full-length and variable region sequencing of the 16S rRNA gene.},
journal = {Forensic science international. Genetics},
volume = {81},
number = {},
pages = {103374},
doi = {10.1016/j.fsigen.2025.103374},
pmid = {41106256},
issn = {1878-0326},
abstract = {The human skin microbiome is unique to each individual, and the microbial exchange between human skin and their touched objects could aid in tracing individuals. However, the microbial transfer and deposition on transiently touched items, and their forensic potential application remain insufficiently understood. Therefore, we simulate a scenario where a suspect holds a knife for a brief time to investigate the transfer of skin-associated microbiota from the hand to the touched object's surface using sequencing of the 16S rRNA gene full length and variable region. The results showed the full-length 16S rRNA gene sequencing (V1-V9) achieved significantly higher taxonomic resolution (species-level) and enriched α-diversity in both skin and contact-objects microbiomes compared to the variable region (V3-V4) sequencing approach. The skin bacterial community exhibited greater biodiversity than the "touched" bacterial communities, and there was no significant similarity between the skin and "touched" bacterial communities for each individual. The intra-individual β diversity of "touched" bacterial communities was close to 1, while the β diversity within individuals (ranging from 0.7 to 0.9) was significantly lower than that observed between individuals in the skin bacterial community. Skin bacterial communities were individual-specific, and the efficacy in discriminating individuals through individual-specific amplicon sequence variants was 100 % using the support vector machine model, in both of the two sequencing datasets. Individual-specific amplicon sequence variants were observed within high relative abundance bacterial taxa (e.g., Staphylococcus epidermidis, Streptococcus mitis, and Streptococcus parasanguinis), but the number of skin individual-specific amplicon sequence variants detectable in "touched" bacterial communities was low. Only a small fraction of skin-derived taxa was detectable on objects and detectability couldn't be explained by robust individual-specific signatures. The dominant bacterial genera and species identified in the shared amplicon sequence variants between skin and "touched" bacterial communities were among the relatively high-abundance taxa within the skin microbiome, like Streptococcus, Staphylococcus, Corynebacterium, Staphylococcus epidermidis, Streptococcus mitis, Corynebacterium bovis, Streptococcus parasanguinis, etc. Such high relative abundance bacterial species showed both individual-specific, easy-to-transfer, and easy-to-deposit in touch events, which may be new marks in forensic identification.},
}

@article {pmid41106100,
year = {2025},
author = {Wang, H and Nie, Y and Luo, Y and Sun, Z and He, Y and Yang, J},
title = {Daidzein alleviates chronic restraint stress-induced depression-like behavior by regulating neuroinflammation and synaptic plasticity via microbiota-gut-brain axis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {148},
number = {},
pages = {157394},
doi = {10.1016/j.phymed.2025.157394},
pmid = {41106100},
issn = {1618-095X},
abstract = {BACKGROUND: Depression is one of the most serious psychological disorders worldwide. Growing evidence suggests that the gut-brain axis plays a pivotal role in its pathophysiology. Daidzein, a naturally occurring isoflavone compound, exhibits neuroprotective properties and can be metabolized by gut microbiota into highly bioactive secondary metabolites.

PURPOSE: This study aims to evaluate the antidepressant effects of daidzein and to investigate its underlying mechanisms, particularly mediated by the gut microbiome.

STUDY DESIGN AND METHODS: We employed the chronic restraint stress (CRS) mice models and classic behavioral tests to investigate the therapeutic effect of daidzein. Furthermore, we used 16S rRNA sequencing and metabolomics methods to explore the regulatory effects of daidzein on key functional bacteria and metabolites after CRS exposure. Intestinal barrier function was evaluated by histopathology and FITC-dextran detection. Neuroinflammatory responses, neuronal morphology, and plasticity were also evaluated using immunofluorescence staining, western blotting, and Nissl staining. Finally, we employed an antibiotic intervention experiment to validate the pivotal role of gut microbiota in the antidepressant effect of daidzein.

RESULTS: Our data demonstrate that daidzein administration mitigated the depression-like behaviors in CRS mice, with gut microbiota composition playing a potentially critical mediating role. Specifically, daidzein induced significant modulations in gut microbial communities (Rikenella, Enterococcus, Akkermansia, and Ruminococcus) and associated metabolic profiles, particularly affecting short-chain fatty acid biosynthesis (valeric acid and acetic acid) and bile acid metabolism (cholic acid/allocholic acid, taurine-deoxycholic acid, and 3-dehydrocholic acid). Mechanistic investigations revealed that daidzein exerted protective effects on intestinal barrier integrity while concurrently reducing pro-inflammatory cytokine levels in both serum and hippocampus. At the neurobiological level, daidzein exhibited multifaceted regulatory effects, including attenuation of glial cell activation (microglia and astrocytes), normalization of FXR/NF-κB/NLRP3 inflammasome signaling, and enhancement of BDNF/TrkB neurotrophic pathways. These molecular changes were further associated with improved neuronal morphological complexity and upregulated expression of synaptic plasticity markers (SYP and PSD95) in the hippocampus.

CONCLUSION: These data propose a gut-brain axis-mediated mode of action for daidzein's antidepressant-like effects, highlighting its promise as a potential candidate for depression, while further investigations are required to elucidate the specific microbial and metabolic drivers of these effects.},
}

@article {pmid41105996,
year = {2025},
author = {Chen, ZY and Gao, FZ and Bai, H and He, LY and Liu, YS and Ying, GG},
title = {Airborne free DNA in chicken farms: The overlooked traits in microbial diversity, viral composition, and antimicrobial resistance risk.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140144},
doi = {10.1016/j.jhazmat.2025.140144},
pmid = {41105996},
issn = {1873-3336},
abstract = {The enrichment of DNA from total suspended particulates (TSP) onto 0.22 µm pore size filters (intracellular DNA, iDNA) is a critical step in characterizing the airborne microbiome. However, free DNA (< 0.22 µm, fDNA) may harbor unrecognized microbial and genetic components. In this study, metagenomic analysis was employed to compare airborne fDNA and iDNA from eight chicken houses. Overall, the average concentration of fDNA was 5.6-fold higher than that of iDNA. A total of 587 genera spanning 28 phyla were identified in fDNA, including 162 genera absent from iDNA. Notably, 39.7 % of open reading frames were unique to fDNA, involving key metabolic and regulatory pathways. A total of 50.2 % viral contigs were only detected in fDNA, carrying mobile genetic elements, virulence factor genes, and resistance genes against antibiotics, biocides, and metals. The total absolute abundance of the antibiotic resistome was higher in fDNA, with 79.2 % of significantly varied genes enriched therein, including 16 high-risk genes. Metagenomic binning further supported that fDNA harbors broader microbial diversity and functional traits. These findings underscore airborne fDNA as an underexplored reservoir of microbial and genetic diversity, meriting further investigation for its ecological and public health implications.},
}

@article {pmid41105994,
year = {2025},
author = {Diambra, L},
title = {Network-based community analysis of microbial composition: Insights into dysbiosis and assembly.},
journal = {Computers in biology and medicine},
volume = {198},
number = {Pt A},
pages = {111190},
doi = {10.1016/j.compbiomed.2025.111190},
pmid = {41105994},
issn = {1879-0534},
abstract = {Traditional analyses of the human gut microbiome, often relying on differential abundance of individual taxa, face significant challenges due to the inherent complexity of microbial communities and frequently yield inconsistent findings. This study introduces a novel network-based approach to overcome these limitations by reducing data dimensionality and facilitating the identification of biologically relevant patterns. Our method constructs microbial association networks, applies community detection algorithms to identify robust groups of co-occurring species, and defines 'community strength variables' as the aggregated abundance of these communities, serving as a reduced-dimension framework for downstream analysis. We applied this approach to two distinct publicly available human gut microbiome datasets: a longitudinal study of infant gut microbiome assembly in Bangladeshi children and an obesity-control study in Danish adults. In the infant cohort, our analysis revealed key community transitions linked to developmental stages, highlighting the dynamic interplay between host growth and microbial colonization. For instance, Community 1 showed a strong positive correlation with age, while the Bifidobacterium-dominated Community 4 declined with age. In the Danish obesity study, our method identified distinct community profiles associated with obesity, effectively circumventing the inconsistencies observed in traditional differential abundance comparisons. Notably, Communities C1 and C19 showed significantly higher fractional abundances in lean participants compared to obese individuals. These findings underscore the context-specificity of microbial associations and demonstrate the power of community-level analysis. Despite limitations such as reliance on correlation-based networks, our framework offers a valuable tool for investigating microbiome structure and function, providing a promising avenue for developing robust microbiome-based biomarkers and therapeutic interventions through the quantification of key microbial consortia.},
}

@article {pmid41105671,
year = {2025},
author = {Thompson, RN and Blumenthal, A and Morrison, M and Thomson, RM},
title = {The microbiome and gut-lung axis in nontuberculous mycobacterial pulmonary disease.},
journal = {PLoS pathogens},
volume = {21},
number = {10},
pages = {e1013603},
doi = {10.1371/journal.ppat.1013603},
pmid = {41105671},
issn = {1553-7374},
mesh = {Humans ; *Mycobacterium Infections, Nontuberculous/microbiology/immunology ; *Gastrointestinal Microbiome/physiology ; *Lung/microbiology/immunology ; *Lung Diseases/microbiology/immunology ; Animals ; Nontuberculous Mycobacteria ; },
abstract = {Nontuberculous mycobacterial pulmonary disease (NTM-PD) is increasingly recognised as a significant global health concern. It is characterised by a highly heterogenous clinical course and remains poorly understood, from host susceptibility to disease pathophysiology, and is notoriously difficult to treat. Recent advances highlight the microbiome as a critical modulator of host physiology, with site-specific 'microbiota' influencing the delicate balance between health, infection and disease. While microbial populations vary across discrete anatomical sites, there is a growing recognition that they are interconnected. For example, gut microbes can influence immune cell functions in the lung via the gut-lung axis (GLA). Drawing parallels with other related chronic respiratory diseases, it is hypothesised that microbiota-host-interactions shape susceptibility and manifestation of NTM-PD. This review synthesises current knowledge of some key host susceptibility factors in NTM-PD, and their potential interactions with host microbiota. With only recently emerging studies, we explore the potential role of the GLA in NTM-PD, given its promising links to microbial communities and immunological and metabolic pathways. We assess the limited, but growing body of research on the lung microbiota in NTM-PD and evaluate the small number of studies on faecal microbiota in NTM-PD. By considering insights across anatomical sites, this review aims to contextualise the microbiome within multiple dimensions of NTM-PD, including host susceptibility, disease progression, treatment responsiveness, and the effects of antibiotic therapy. A better understanding of the microbiome in NTM-PD could hold promise in uncovering the complex and multifactorial mechanisms that contribute to the heterogenous clinical course and challenging management of NTM-PD.},
}

Humans
*Mycobacterium Infections, Nontuberculous/microbiology/immunology
*Gastrointestinal Microbiome/physiology
*Lung/microbiology/immunology
*Lung Diseases/microbiology/immunology
Animals
Nontuberculous Mycobacteria

@article {pmid41105587,
year = {2025},
author = {Nikam, B and Jha, SN and Thakare, Y and Coshic, P and Gupta, N},
title = {Short-Chain Fatty Acid Sodium Butyrate Suppresses Protective Humoral Immunity by Inhibiting Follicular T Helper Cell Differentiation.},
journal = {European journal of immunology},
volume = {55},
number = {10},
pages = {e70076},
doi = {10.1002/eji.70076},
pmid = {41105587},
issn = {1521-4141},
support = {//National Institute of Immunology/ ; },
mesh = {Animals ; Mice ; *Butyric Acid/pharmacology ; *Cell Differentiation/drug effects/immunology ; *Immunity, Humoral/drug effects ; *T Follicular Helper Cells/immunology/drug effects ; Germinal Center/immunology ; *Orthomyxoviridae Infections/immunology ; *Fatty Acids, Volatile ; Mice, Inbred C57BL ; B-Lymphocytes/immunology ; Gastrointestinal Microbiome/immunology ; *T-Lymphocytes, Helper-Inducer/immunology ; Lymphocyte Activation/drug effects/immunology ; },
abstract = {The gut microbiome and its metabolites are critical regulators of intestinal homeostasis, with emerging evidence highlighting their influence on humoral immune responses and vaccine efficacy. The development of effective humoral immunity depends on the magnitude and quality of germinal centers (GCs), which are driven by follicular T helper (Tfh) cells. Here, we investigate the role of short-chain fatty acids (SCFAs) in shaping humoral immunity, with a particular focus on Tfh cells. In ex vivo assays, we found that sodium butyrate, not sodium acetate or sodium propionate, directly suppresses Tfh cells differentiation and helper functions. Using antigen-specific and influenza virus infection models, we further demonstrate that sodium butyrate impairs Tfh cell differentiation, leading to diminished GC B cell responses and compromised humoral immunity during systemic infection. Notably, mice treated with sodium butyrate succumbed to virus infection, underscoring its effect on impairing protective immunity. Mechanistically, our findings reveal that sodium butyrate mediates these suppressive effects on Tfh cells via histone deacetylase (HDAC) inhibition. Together, our findings establish sodium butyrate as a negative regulator of humoral immunity by directly suppressing the Tfh-cell differentiation and Tfh-derived GC responses. These insights provide a mechanistic link between gut microbiome-derived metabolites and humoral immunity, with potential implications for vaccine efficacy and therapeutic interventions.},
}

Animals
Mice
*Butyric Acid/pharmacology
*Cell Differentiation/drug effects/immunology
*Immunity, Humoral/drug effects
*T Follicular Helper Cells/immunology/drug effects
Germinal Center/immunology
*Orthomyxoviridae Infections/immunology
*Fatty Acids, Volatile
Mice, Inbred C57BL
B-Lymphocytes/immunology
Gastrointestinal Microbiome/immunology
*T-Lymphocytes, Helper-Inducer/immunology
Lymphocyte Activation/drug effects/immunology

@article {pmid41105342,
year = {2025},
author = {Lu, L and Li, Z and Qiang, P and Shao, Y},
title = {Gut microbiota and risk of cervical cancer: a Mendelian multivariable randomization study.},
journal = {Discover oncology},
volume = {16},
number = {1},
pages = {1912},
pmid = {41105342},
issn = {2730-6011},
abstract = {BACKGROUND AND HYPOTHESIS: Epidemiological evidence demonstrates associations between gut microbial dysbiosis and cervical cancer, though causal inference remains limited by potential confounding.

STUDY DESIGN: A meta-analysis of the largest available genome-wide association study (GWAS) meta-analysis using the MiBioGen consortium (n = 14,306 individuals; 8,107,040 SNPs analyzed) was conducted for the summary statistics of the gut microbiome. A two-sample Mendelian randomization study was performed using the statistics of cervical cancer from BioBank Japan (BBJ) and the European Bioinformatics Institute (EBI) GWAS Catalog. The causal relationship between the gut microbiome and cervical cancer was examined using inverse variance weighting, maximum likelihood, MR-Egger, weighted median, weighted model, and MR-PRESSO methods. The Cochran Q statistic was used to quantify the heterogeneity of the instrumental variables.

STUDY RESULTS: The odds ratio (OR) values obtained by the IVW method indicate that the consistent microbial communities in the validation results from two different cervical cancer datasets are: Actinomyces (BBJ OR = 0.52, 95% CI: 0.29-0.92, P < 0.05), (EBI OR = 0.55, 95% CI: 0.29-0.87, P < 0.05) It has a protective effect on the occurrence of cervical cancer, Lachnospiraceae UCG001 (BBJ OR = 2.00, 95% CI: 1.11-3.58, P < 0.05), (EBI OR = 1.91, 95% CI: 1.16-3.13, P < 0.05) It has a promoting risk effect on the occurrence of cervical cancer, and there is no significant heterogeneity or horizontal pleiotropy.

CONCLUSIONS: Both datasets consistently showed that Actinomyces was protective against cervical cancer (BBJ OR = 0.52; EBI OR = 0.55), while Lachnospiraceae UCG001 increased risk (BBJ OR = 2.00; EBI OR = 1.91), with no evidence of heterogeneity or pleiotropy in these robust MR analyses.},
}

@article {pmid41105100,
year = {2025},
author = {Arellano, AA and Prack, JL and Coon, KL},
title = {Host-mediated niche construction of bacterial communities in an aquatic microecosystem.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf233},
pmid = {41105100},
issn = {1751-7370},
abstract = {Microbes coordinate homeostasis in host-associated and environmental ecosystems alike, but the connectivity of these biomes is seldom considered. Hosts exert controls on the composition and function of their internally associated symbionts, but an underappreciated modality of microbiome curation is external to the host through changes to the environmental species pool from which they recruit microbial symbionts. Niche construction theory describes how organisms alter their environment and the selective landscape of their offspring and conspecifics. We hypothesize that host-driven manipulation of environmental microbial communities is an underexplored form of this concept. Using the pitcher plant mosquito (Wyeomyia smithii) as a model, we tested how hosts shape microbial communities across developmental stages and gradients of pre-existing community complexity. We report three lines of evidence supporting host-mediated niche construction, leveraging amplicon sequencing and microbiota manipulation experiments with germ-free (axenic) and selectively recolonized (gnotobiotic) mosquitoes. First, single female egg-laying assays showed repeatable adult inoculation of sterile water with beneficial bacteria capable of sustaining robust larval development. Second, increasing larval density in assays inoculated with complex, field-derived microbial communities selected for environmental and host-associated bacteria that correlated with increased larval fitness. Finally, exposing axenic larvae to mixtures of parentally and environmentally derived microbiota demonstrated that prior conditioning by conspecifics enhanced offspring fitness. Although the bacterial taxa associated with mosquito structuring varied, members of the Actinobacteriota and Acetobacteraceae were consistently associated with increased fitness. Overall, our results provide an example of host-mediated niche construction to favor environmental microbial communities that positively impact host fitness.},
}

@article {pmid41104927,
year = {2025},
author = {Anwar, S and Lamaudiere, M and Hassall, J and Dehinsilu, J and Bhuller, RK and Hold, GL and Vázquez-Campos, X and Mahnert, A and Moissl-Eichinger, C and Gallé, B and Kainz, G and Pjevac, P and Hausmann, B and Schwarz, J and Kohl, G and Berry, D and Vancuren, SJ and Allen-Vercoe, E and Nielsen, N and Sørensen, N and Eklund, A and Nielsen, HB and Riedel, R and Krause, JL and Chang, H-D and Park, S and Song, H-Y and Seo, H and Ul-Haq, A and Kim, S and Kwon, Y and Park, S and Soberon, X and Silva-Herzog, E and Verlouw, JAM and Arp, P and Jhamai, M and Kraaij, R and Geelen, AR and Ducarmon, QR and Smits, WK and Kuijper, EJ and Zwittink, RD and van Best, N and Penders, J and Le, G and Driessen, C and Kool, J and Shetty, SA and Fuentes, S and Demirci, M and Yigin, A and Whalley, C and Beggs, AD and Quince, C and James, R and Raguideau, S and Gordon, M and Mate, R and Fritzsche, M and Danckert, NP and Blanco, JM and Marchesi, JR and Rauch, M and Williamson, RA and Van't Wout, AB and Kritz, A and Rosecker, S and Stevens, R and Laws, L and Sayavedra, L and Romano, S and Telatin, A and Baker, D and Narbad, A and Servetas, SL and Kralj, JG and Forry, SP and Hunter, ME and Dootz, JN and Jackson, SA and Mason, CE and Butler, DJ and Mozsary, C and Foox, J and Damle, N and Resh, A and Busswitz, A and Lenz, P and Sontag, S and Cross, A and Sanchez, C and Guo, M and Olson, K and Smith, EA and La Reau, AJ and Ward, T and Kuersten, S and Hyde, F and Khrebtukova, I and Schroth, G and Rijpkema, S and Amos, GCA and Sergaki, C},
title = {DNA reference reagents isolate biases in microbiome profiling: a global multi-lab study.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0046625},
doi = {10.1128/msystems.00466-25},
pmid = {41104927},
issn = {2379-5077},
abstract = {When profiling the human gut microbiome, technical biases introduced by analytical approaches impede translational research, reducing data reliability and study comparability. Here, through a global study involving 23 labs, we analyzed a wide range of sequencing and bioinformatic approaches for the taxonomic profiling of two well-defined DNA reference reagents (RRs) comprised of 20 common gut bacteria. Through both shotgun and 16S rRNA gene amplicon sequencing, we aimed to isolate sources of bias and understand their impact on microbiome profiling accuracy. Importantly, minimum quality criteria (MQC) were established and are used to evaluate profiling performance. We found that the variability of shotgun sequencing data sets was greater than that of 16S rRNA gene amplicon sequencing and isolated sources of bias in wet and dry lab steps, such as sequencing depth, primer and database choices, rarefaction, and 16S copy number adjustment. This study presents well-defined RRs and MQC to combat technical bias, paving the way for reliable and comparable microbiome research.IMPORTANCEThis benchmark paper highlights the true level of variability in microbiome data across the world and across sectors, underscoring the critical need for the use of WHO International DNA Gut Reference Reagents (RRs) to elevate the quality of data in microbiome research. This global study is the first of its kind, revealing the reality of the bias in the field, comprehensively testing methodologies used by leading laboratories across the world, but also providing avenues for workflow optimization, to accelerate innovation and translational research and move the field forward.},
}

@article {pmid41104769,
year = {2025},
author = {Chapman, PA and Day, RC and Hudson, DT and Ward, JM and Morgan, XC and Beck, CW},
title = {Commensal skin bacteria interact with the innate immune system to promote tail regeneration in Xenopus laevis tadpoles.},
journal = {Developmental dynamics : an official publication of the American Association of Anatomists},
volume = {},
number = {},
pages = {},
doi = {10.1002/dvdy.70088},
pmid = {41104769},
issn = {1097-0177},
support = {MFP-UOO1910//Royal Society Te Apārangi/ ; },
abstract = {BACKGROUND: Tadpoles of the clawed frog Xenopus laevis can regenerate their tails following partial amputation, replacing the missing spinal cord, muscles, and fin. However, for a brief period of development this response becomes unstable, leading to a proportion of tadpoles that undergo wound healing rather than regenerative programme. Inspired by a growing number of links between the microbiome and human inflammatory disease, we asked how the tadpole skin microbiome and innate immunity influence the regeneration of a complex appendage. We previously showed that tadpoles raised in antibiotics such as gentamicin or penicillin/streptomycin or with reduced Toll-like receptor 4 signaling regenerated tails poorly, while adding exogenous lipopolysaccharide promoted or rescued tail regeneration.

RESULTS: Here, we show that CRISPR/Cas9 knockdown of Toll-like receptor 2 also reduces tadpole tail regeneration. Conversely, addition of the pathogen-associated molecular pattern peptidoglycan to the medium at the time of amputation increases the likelihood of regeneration. While we have previously shown that tadpoles acquire most of their early skin microbiome from their mothers, analysis of mitochondrial haplotypes did not support a genetic maternal explanation of regenerative bias. Levels of endogenous lipopolysaccharides on tail tips were also not predictive of regenerative success, and shotgun sequencing indicated that there was no difference in bacterial loads. To see if the composition of native microbiome was associated with regenerative success, we sequenced the 16S rRNA genes of 503 tadpole tail tips from 12 sibships and mapped these to the regenerative outcome of each tadpole. While no one taxon was found to be associated with regenerative success, higher proportions of Gram-positive genera overall correlated with improved regeneration outcomes. Supporting this finding, when tadpoles were raised with the antibiotic vancomycin, to select against Gram-positive bacteria, the number of individuals undergoing tail regeneration was significantly decreased.

CONCLUSIONS: Taken together, our results suggest a previously undocumented role for Tlr2, possibly activated by peptidoglycan from Gram-positive commensal skin bacteria, in tipping the balance from wound repair to regenerative programmes in Xenopus laevis refractory stage tadpoles.},
}

@article {pmid41104650,
year = {2025},
author = {Yasinzai, AQK and Jalali, P and Syaj, S and Sahin, IH and Nassour, I and George, TJ and Saeed, A},
title = {Trends and Projected Burden of Early-Onset Gastrointestinal Malignancies in the United States: A Population-Based Analysis (2001-2021).},
journal = {Journal of the National Cancer Institute},
volume = {},
number = {},
pages = {},
doi = {10.1093/jnci/djaf304},
pmid = {41104650},
issn = {1460-2105},
abstract = {BACKGROUND: Early-onset colorectal cancer (eoCRC) has become a serious public health concern in recent years. This study aims to contribute to the growing body of evidence on the rise in early onset gastrointestinal cancers (eoGIC), anatomical sub-sites of eoCRC, and explore racial and gender disparities in these trends.

METHODS: We analyzed data from the NPCR-SEER database (2001-2021) for people aged 20 to 49 with gastrointestinal (GI) cancers. The dataset covers cancer incidence rates for about 98% of United States population. Joinpoint regression was used to calculate average annual percent change (AAPC), and polynomial regression was applied to forecast rates from 2021 to 2031.

RESULTS: A total of 527,411 cases were analyzed. Colorectal comprised of the highest cases (n = 313,513) followed by pancreatic (n = 50,448). Intrahepatic bile duct had the highest AAPC (+6.24%, 95% CI +5.20 to + 7.45) followed by small intestine (+3.19%, 95% CI: +2.69 to + 3.72), eoCRC (+1.65%, 95% CI: +1.45 to + 1.92), pancreatic (+1.52, 95% CI: +1.37 to + 1.66), and stomach (+1.20, 95% CI: +0.89 to + 1.53). In colorectum, rectum had the highest AAPC (+2.09%). Females (+1.81%) experienced disproportionate rise when compared to males (+0.83%). Projection suggests a demographic shift with female surpassing males in the overall age adjusted rate of eoGIC.

CONCLUSION: The study highlights that eoCRC is not an isolated phenomenon but part of a broader epidemiologic shift across gastrointestinal malignancies. The parallel rise in other sites suggests shared upstream risk factors or exposures and supports investigations into potential environmental, dietary, microbiome, or hormonal risk factors.},
}

@article {pmid41104481,
year = {2025},
author = {},
title = {Laila P. Partida-Martínez.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70665},
pmid = {41104481},
issn = {1469-8137},
abstract = {Laila P. Partida-Martínez, Cinvestav-Irapuato (Mexico).},
}

@article {pmid41104474,
year = {2025},
author = {Piekiełko-Witkowska, A and Elisei, R and Leger, J and Bendlová, B and Pekova, BB and Caron, P and Durante, C and Fassnacht, M and Feldt-Rasmussen, U and Nyström, HF and Jansen, H and Köhrle, J and Kuś, A and Ludgate, M and Mertens, J and Oczko-Wojciechowska, M and Peters, C and Schoenmakers, N and Stoupa, A and van Santen, H and Trimboli, P and van Trotsenburg, P and Edward Visser, W},
title = {EndoCompass project: research roadmap for thyroid endocrinology.},
journal = {European journal of endocrinology},
volume = {193},
number = {Supplement_2},
pages = {ii117-ii127},
doi = {10.1093/ejendo/lvaf010},
pmid = {41104474},
issn = {1479-683X},
mesh = {Humans ; *Endocrinology/trends/organization & administration/methods ; *Thyroid Diseases/therapy/diagnosis/epidemiology ; *Biomedical Research/trends ; European Union ; Databases, Factual ; },
abstract = {BACKGROUND: Endocrine science remains underrepresented in European Union research programs despite the fundamental role of hormone health in human well-being. Analysis of the CORDIS database reveals a persistent gap between the societal impact of endocrine disorders and their research prioritization. At national funding level, endocrine societies report limited or little attention of national research funding toward endocrinology. The EndoCompass project-a joint initiative between the European Society of Endocrinology and the European Society of Paediatric Endocrinology, aimed to identify and promote strategic research priorities in endocrine science to address critical hormone-related health challenges.

METHODS: Research priorities were established through comprehensive analysis of the EU CORDIS database covering the Horizon 2020 framework period (2014-2020). Expert consultation in thyroid endocrinology was conducted to identify key research priorities, followed by broader stakeholder engagement including society members and patient advocacy groups.

RESULTS: For thyroid disorders, research priorities encompass neoplastic and nonneoplastic conditions, focusing on disease mechanisms, improved diagnostics and treatments, and the impact of environmental and metabolic factors. Key areas include personalized medicine approaches, artificial intelligence applications, and the establishment of pan-European registries to advance understanding of rare thyroid conditions.

CONCLUSIONS: The thyroid component of the EndoCompass project provides an evidence-based roadmap for strategic research investment. This framework identifies crucial investigation areas into thyroid disease pathophysiology, prevention, and treatment strategies, ultimately aimed at reducing the burden of thyroid disorders on individuals and society. The findings support the broader EndoCompass objective of aligning research funding with areas of highest potential impact in endocrine health.},
}

Humans
*Endocrinology/trends/organization & administration/methods
*Thyroid Diseases/therapy/diagnosis/epidemiology
*Biomedical Research/trends
European Union
Databases, Factual

@article {pmid41104472,
year = {2025},
author = {Mathieu, C and Meireles, M and Pagotto, U and Wabitsch, M and Banerjee, I and Bartolomé, A and Battelino, T and Beck, J and Chiarelli, F and De Leon, DD and Dovč, K and El Ghoch, M and Galderisi, A and Gevers, E and Gillard, P and Haliloglu, B and Hoermann, H and Mankovsky, B and Mertens, J and Mohnike, K and Oram, R and Pasquini, T and Pearson, E and Pieber, TR and Polovina, S and Raskin, J and Roeper, M and Ruck, L and Salomon Estebanez, M and Tankova, T and Thornton, P and van Rossum, EFC and Vukovic, R and Worth, C and Zachurzok, A},
title = {EndoCompass project: research roadmap for diabetes, obesity, and metabolism.},
journal = {European journal of endocrinology},
volume = {193},
number = {Supplement_2},
pages = {ii47-ii71},
doi = {10.1093/ejendo/lvaf065},
pmid = {41104472},
issn = {1479-683X},
mesh = {Humans ; *Obesity/therapy/metabolism/epidemiology ; *Endocrinology ; *Biomedical Research/trends ; *Diabetes Mellitus/therapy ; European Union ; *Metabolic Diseases/therapy ; },
abstract = {BACKGROUND: Endocrine science remains underrepresented in European Union research programmes despite the fundamental role of hormone health in human well-being. Analysis of the CORDIS database reveals a persistent gap between the societal impact of endocrine disorders and their research prioritization. At national funding level, endocrine societies report limited or little attention of national research funding towards endocrinology. The EndoCompass project-a joint initiative between the European Society of Endocrinology and the European Society of Paediatric Endocrinology, aimed to identify and promote strategic research priorities in endocrine science to address critical hormone-related health challenges.

METHODS: Research priorities were established through comprehensive analysis of the EU CORDIS database covering the Horizon 2020 framework period (2014-2020). Expert consultation was conducted to identify key research priorities, followed by broader stakeholder engagement including society members and patient advocacy groups.

RESULTS: Research priorities include: genetic/epigenetic factors, brain-periphery communication, and environmental influences. Key therapeutic areas include innovative approaches for monogenic disorders, incretin mimetics, dual receptor agonists, microbiome analysis, and improved behavioural interventions. For type 1 diabetes, priorities focus on early detection, insulin delivery systems, and disease-modifying therapies.

CONCLUSIONS: This component of the EndoCompass project provides an evidence-based roadmap for strategic research investment. This framework identifies crucial investigation areas into diabetes and obesity pathophysiology, prevention, and treatment strategies, ultimately aimed at reducing the burden of metabolic disorders on individuals and society. The findings support the broader EndoCompass objective of aligning research funding with areas of highest potential impact in endocrine health.},
}

Humans
*Obesity/therapy/metabolism/epidemiology
*Endocrinology
*Biomedical Research/trends
*Diabetes Mellitus/therapy
European Union
*Metabolic Diseases/therapy

@article {pmid41104433,
year = {2025},
author = {Pandey, AK and Vurukonda, SSKP and Giovanardi, D},
title = {Editorial: Unraveling pathogen-plant-microbiome interactions in horticultural crops through omics approaches.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1696789},
pmid = {41104433},
issn = {1664-462X},
}

@article {pmid41104285,
year = {2025},
author = {Ji, K and Lei, S and Wang, L and Tian, L and Wen, Z and Shi, R and Liu, L and Liu, J and Shi, B and Wang, J},
title = {Synergistic effects of multi-strain probiotics and Chinese herbal medicine on growth performance and gut health in weaned piglets.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1677127},
pmid = {41104285},
issn = {2297-1769},
abstract = {BACKGROUND: Weaning stress represents a considerable challenge in global swine production. While probiotics and Chinese herbal medicine have been extensively studied as individual interventions, their combined application as alternative feed additives in swine production requires further investigation.

METHODS: Forty-five weaned piglets (35 ± 3 days old) were randomly allocated to five treatment groups (n = 9 per group) for a 28-day feeding trial: control (CON), antibiotic (A), probiotic (PRO), Chinese herbal medicine (CHM), and probiotic plus Chinese herbal medicine (PROC). Growth performance, serum antioxidant levels, and immune parameters were assessed alongside 16S rRNA microbiome sequencing and liquid chromatography-mass spectrometry metabolomics analysis.

RESULTS: The PROC group significantly improved growth performance compared to controls (p < 0.05), showing 8.91% higher final body weight, significantly increased average daily gain, and the most efficient feed conversion ratio (1.55) among treatments. Serum analysis indicated a significant increase in total antioxidant capacity (T-AOC) in the PROC group relative to the other groups. The probiotic (PRO) and PROC groups enhanced superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) activities, while reducing malondialdehyde (MDA) levels (p < 0.05). Pro-inflammatory cytokines IL-2 and IL-6 were significantly reduced in the PRO and PROC groups, while immunoglobulins IgA and IgG levels were increased (p < 0.05). Microbiota analysis revealed increased α-diversity (Shannon and Chao1 indices) and altered community structure in the PROC group. Metabolomic profiling identified 5,090 metabolites with distinct profiles between groups based on OPLS-DA. KEGG pathway analysis indicated that the PRO group exhibited enrichment in nucleotide and purine metabolism, whereas the PROC group activated supplementary pathways, including purine and lipid metabolism.

CONCLUSION: These findings suggest that combined probiotic and Chinese herbal medicine supplementation may serve as an effective feed strategy for promoting intestinal health and alleviating weaning stress, providing valuable insights for developing antibiotic alternatives in swine production.},
}

@article {pmid41104042,
year = {2025},
author = {Yassin, LK and Skrabulyte-Barbulescu, J and Alshamsi, SH and Saeed, S and Alkuwaiti, SH and Almazrouei, S and Alnuaimi, A and BaniYas, S and Aldhaheri, D and Alderei, M and Shehab, S and Hamad, MIK},
title = {The microbiota-gut-brain axis in mental and neurodegenerative disorders: opportunities for prevention and intervention.},
journal = {Frontiers in aging neuroscience},
volume = {17},
number = {},
pages = {1667448},
pmid = {41104042},
issn = {1663-4365},
abstract = {The microbiota-gut-brain axis (MGBA) is increasingly recognized as a critical regulator of brain health, influencing both neurodevelopment and age-related neurological decline. Disruptions in this axis, driven by gut dysbiosis, have been implicated in the pathogenesis of a wide range of neurodegenerative and neuropsychiatric disorders. This review synthesizes current evidence linking microbiota alterations to Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), multiple sclerosis (MS), and stroke-including post-stroke cognitive impairment (PSCI), as well as major depressive disorder (MDD), bipolar disorder (BD), anxiety disorders, post-traumatic stress disorder (PTSD), and chronic fatigue syndrome (CFS). Common findings include reduced microbial diversity, depletion of short-chain fatty acid (SCFA)-producing genera, and enrichment of pro-inflammatory taxa. These changes contribute to neuroinflammation, blood-brain barrier (BBB) dysfunction, microglial activation, and neurotransmitter imbalances. The review further explores the neurotoxic effects of external factors such as radiation and xenobiotics on the MGBA. Despite disorder-specific variations, shared microbial and immunological mechanisms emerge across the spectrum of conditions. Importantly, we present current and emerging strategies aimed at restoring gut-brain communication, including dietary interventions such as fiber-rich and Mediterranean diets, SCFA supplementation, probiotics, and fecal microbiota transplantation (FMT). These approaches show promise in alleviating cognitive and emotional symptoms, modulating immune responses, and potentially slowing disease progression. By integrating mechanistic insights with therapeutic perspectives, this review underscores the gut microbiota as a modifiable factor in neuropsychiatric and neurodegenerative disease. Targeting the MGBA offers a novel, translational approach to intervention that may ultimately contribute to healthier brain aging and improved outcomes across the lifespan.},
}

@article {pmid41103946,
year = {2025},
author = {Zhou, L and Li, B and Ren, J and Wang, S and Wang, J},
title = {Microbiome-mediated regulation of chemoradiotherapy response.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1659467},
pmid = {41103946},
issn = {2234-943X},
abstract = {The gut microbiota critically influences patient responses to chemoradiotherapy through bidirectional interactions with host physiology, modulating both therapeutic efficacy and toxicity. Radiotherapy and chemotherapy disrupt microbial homeostasis, exacerbating intestinal damage, systemic inflammation, and immune dysfunction, while specific commensals and metabolites enhance treatment response via metabolic reprogramming, DNA repair regulation, and immune activation. Key mechanisms include microbiota-mediated TLR/NF-κB signaling, SCFA-dependent epigenetic modifications, and microbial enhancement of immune checkpoint inhibitors. Clinical interventions such as probiotics, fecal microbiota transplantation, and targeted antibiotics demonstrate potential to mitigate toxicity and overcome resistance. This review summarizes emerging evidence on how microbial dysbiosis induced by radiotherapy and chemotherapy exacerbates intestinal damage, systemic inflammation, and immune dysfunction, while specific commensals and metabolites enhance chemoradiotherapy response via metabolic reprogramming, DNA repair modulation, and immune activation. These findings underscore the gut microbiota as a critical determinant of chemoradiotherapy precision, offering actionable targets for microbiome-guided therapeutic optimization.},
}

@article {pmid41103764,
year = {2025},
author = {Jiang, T and Yang, X and Wu, B and Tao, R and Chen, R and Jin, L and Sun, D and Weng, H},
title = {Gut microbiota in hypothyroidism: pathogenic mechanisms and opportunities for precision microbiome interventions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1661211},
pmid = {41103764},
issn = {1664-302X},
abstract = {Hypothyroidism is a common endocrine disorder characterized by insufficient thyroid hormone synthesis or secretion, most frequently caused by Hashimoto's thyroiditis, an autoimmune condition that leads to chronic thyroid gland damage. Despite the widespread use of levothyroxine replacement therapy, a substantial proportion of patients continue to experience persistent symptoms and metabolic dysregulation even after achieving biochemical euthyroidism. These observations have prompted growing interest in non-hormonal contributors to hypothyroidism, particularly the role of the gut microbiota. Recent studies indicate that gut microbial dysbiosis may influence the onset and progression of hypothyroidism through mechanisms involving immune dysregulation, increased intestinal permeability, chronic low-grade inflammation, and impaired nutrient absorption. Additionally, microbial metabolites such as short-chain fatty acids and bile acids are increasingly recognized as modulators of thyroid hormone metabolism, tissue sensitivity, and enterohepatic circulation. The bidirectional interactions between thyroid function and the gut microbiota constitute the emerging concept of the gut-thyroid axis, providing a novel framework for understanding the disease. Microbiota-targeted interventions, including probiotics, prebiotics, synbiotics, and dietary modulation, have demonstrated potential to improve microbial composition, alleviate systemic inflammation, enhance thyroid hormone utilization, and reduce autoantibody levels. This review systematically explores the mechanistic links between gut microbiota and hypothyroidism, critically evaluates current microbiota-based therapeutic strategies, and highlights future opportunities for personalized, microbiome-driven interventions to optimize the management of hypothyroidism.},
}

@article {pmid41103759,
year = {2025},
author = {Khelfaoui, I and Wang, W and Meskher, H and Shehata, AI and El Basuini, MF and Abouelenein, MF and Degha, HE and Alhoshy, M and Teiba, II and Mahmoud, SS},
title = {Beyond just correlation: causal machine learning for the microbiome, from prediction to health policy with econometric tools.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1691503},
pmid = {41103759},
issn = {1664-302X},
abstract = {The human microbiome is increasingly recognized as a key mediator of health and disease, yet translating microbial associations into actionable interventions remains challenging. This review synthesizes advances in machine learning (ML) and causal inference applied to human microbiome research, emphasizing policy-relevant applications. Explainable ML approaches, have identified microbial drivers, guiding targeted strategies. Econometric tools, including instrumental variables, difference-in-differences, and panel data models, provide robust frameworks for validating causal relationships, while hybrid methods like Double Machine Learning (Double ML) and Deep Instrumental Variables (Deep IV) address high-dimensional and non-linear effects, enabling precise evaluation of microbiome-mediated interventions. Policy translation is further enhanced by federated learning, standardized analytical pipelines, and model visualization frameworks, which collectively improve reproducibility, scalability, and data privacy compliance. By integrating predictive power with causal rigor, microbiome research can move beyond observational associations to generate interventions that are biologically grounded, clinically actionable, and policy-ready. This roadmap provides a blueprint for translating mechanistic microbial insights into real-world health solutions, emphasizing interdisciplinary collaboration, standardized reporting, and evidence-based policymaking.},
}