@article {pmid41207099,
year = {2025},
author = {Torres, AHF and Soares, TA and Pereira, RB and Gomes, P and Garrido, SS},
title = {Interplay between the immune system and the microbiome of human skin and its modulation by antimicrobial peptides.},
journal = {International immunopharmacology},
volume = {168},
number = {Pt 1},
pages = {115754},
doi = {10.1016/j.intimp.2025.115754},
pmid = {41207099},
issn = {1878-1705},
abstract = {The cutaneous immune system is essential for protecting the body against pathogens and regulating the skin's immune response, which can be further influenced by the skin's microbiome and also by exogenous bioactive compounds. As such, innovative approaches based on use of antimicrobial peptides and/or probiotics show a promising potential for restoring skin homeostasis and alleviating dermatological conditions. In this connection, herein we revise the immune functions of the skin, covering its structural and cellular components, interactions with the microbiome, and defense mechanisms as well as their modulation by antimicrobial peptides. We further address recent developments in this topic, providing an up-to-date perspective that paves the way for advancing both skin immunology knowledge and new therapeutic interventions for a healthy skin.},
}

@article {pmid41207093,
year = {2025},
author = {Li, Y and Yu, R and Tan, S and Sun, L and Yan, Y and Huang, J and Waseem, MH and Wang, Z and Li, C},
title = {Alterations in the profiles of rumen microbiota and metabolites in Holstein and Jersey dairy cows under heat stress.},
journal = {Journal of thermal biology},
volume = {134},
number = {},
pages = {104327},
doi = {10.1016/j.jtherbio.2025.104327},
pmid = {41207093},
issn = {0306-4565},
abstract = {High temperature impacts the performance and health of dairy cows in summer, causing considerable financial burden in the dairy industry. Differences in physiological changes, rumen microbial diversity and metabolites of Holstein and Jersey dairy cows under heat stress and normal environment were investigated. The present study demonstrates that oxidative stress levels in Holstein and Jersey cows are significantly elevated under conditions of heat stress, while the pro-inflammatory cytokine levels were elevated only in heat-stressed Holstein cows. 16S rDNA gene sequencing showed that heat stress markedly altered the abundance, homogeneity and makeup in the bovine rumen microbiome. Moreover, the significant abundance of Rikenellaceae_RC9_gut_group exhibited a positive association with malondialdehyde (MDA) in Holstein cows, Pseudobutyrivibrio was positively correlated with tumor necrosis factor-α (TNF-α) in the Jersey cows. Metabolomics profiling based on liquid chromatography-mass spectrometry (LC-MS) revealed that totally 1065 metabolites in Holstein cows and 571 metabolites in Jersey cows were significantly changed. The differential metabolites Leucine and Prostaglandin i2 were negatively associated with interleukin (IL)-6, Erucamide was positively related to IL-1β and MDA in Holstein cows. And 9,10-dihydroxy-12z-octadecenoic acid showed a negative correlation with IL-6 and TNF-α in Jersey cows. Besides, the changed rumen microbiome displayed remarkable associations with metabolites. Our results indicated that heat stress caused remarkable alterations of rumen microbiome and metabolism both in Holstein and Jersey dairy cows, the altered ruminal bacteria and metabolic profiles could consecutively affect physiological responses in dairy cows.},
}

@article {pmid41206954,
year = {2025},
author = {Mao, Y and Jiang, Z and Wang, T and Hu, Y and Zhan, X},
title = {TCVS: Tree-guided compositional variable selection analysis of microbiome data.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf617},
pmid = {41206954},
issn = {1367-4811},
abstract = {MOTIVATION: Studies of microbial communities, represented by the relative abundances of taxa at various taxonomic levels, have underscored the significance of microbiota in numerous aspects of human health and disease. A pivotal challenge in microbiome research lies in pinpointing microbial taxa associated with disease outcomes, which could play crucial roles in prevention, detection, and treatment of various health conditions. Alongside these relative abundance data, taxonomic information sometimes offers a unique lens to explore the impact of shared evolutionary histories on patterns of microbial abundance.

RESULTS: In pursuit of this goal, we utilize the tree structure to more flexibly identify taxa associated with disease outcomes. To enhance the accuracy of our selection process, we introduce auxiliary knockoff copies of microbiome features designated as noise. This approach allows for the assessment of false positives in the selection process and aids in refining it towards more precise outcomes. Extensive numerical simulations demonstrate that our methodology outperforms several existing methods in terms of selection accuracy. Furthermore, we demonstrate the practicality of our approach by applying it to a widely used gut microbiome dataset, identifying microbial taxa linked to body mass index.

TCVS R code is available at https://github.com/Yicong1225/TCVS.},
}

@article {pmid41206936,
year = {2025},
author = {Borman, T and Sannikov, A and Finn, RD and Limborg, MT and Rogers, AB and Kale, V and Hanhineva, K and Lahti, L},
title = {HoloFoodR: a statistical programming framework for holo-omics data integration workflows.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf605},
pmid = {41206936},
issn = {1367-4811},
abstract = {SUMMARY: Holo-omics is an emerging research area that integrates multi-omic datasets from the host organism and its microbiome to study their interactions. Recently, curated and openly accessible holo-omic databases have been developed. The HoloFood database, for instance, provides nearly 10,000 holo-omic profiles for salmon and chicken under controlled treatments. However, bridging the gap between holo-omic data resources and algorithmic frameworks remains a challenge. Combining the latest advances in statistical programming with curated holo-omic data sets can facilitate the design of open and reproducible research workflows in the emerging field of holo-omics.

HoloFoodR R/Bioconductor package and the source code are available under the open-source Artistic License 2.0 at the package homepage https://doi.org/10.18129/B9.bioc.HoloFoodR.

SUPPLEMENTARY INFORMATION: Available in the package vignette https://ebi-metagenomics.github.io/HoloFoodR/articles/case_study.html.},
}

@article {pmid41206876,
year = {2025},
author = {Catano, CP and DuBose, JG and Fuller-Hall, L and Chavez, J and de Roode, JC},
title = {Experimental Immigration Mediates Ecological Selection and Drift in Monarch Microbiome Assembly.},
journal = {Ecology letters},
volume = {28},
number = {11},
pages = {e70252},
doi = {10.1111/ele.70252},
pmid = {41206876},
issn = {1461-0248},
support = {IOS-2202255//National Science Foundation/ ; },
abstract = {The distribution of biodiversity depends on processes operating across scales, yet multiscale paradigms have struggled to permeate host-microbiome research. Instead, host-microbiome research has focused on host selection and has struggled to explain the high variation in microbial composition across individuals. By integrating multi-scale ecological theory with experimental manipulation of bacteria colonizing monarch butterfly caterpillars, we test the hypothesis that immigration from the regional species pool alters the importance of niche selection and drift in causing variation in gut bacterial communities across individuals and through ontogeny. Higher immigration increased the dominance of certain bacteria, causing greater convergence in bacterial composition across the caterpillar life stage. Conversely, limited immigration made colonization more stochastic, resulting in more unpredictable variability in bacterial composition across individuals. Our study reveals that immigration mediates the balance between host selection and drift, demonstrating that processes operating at scales beyond the individual are underappreciated but critical for structuring host-microbiome symbioses.},
}

@article {pmid41206864,
year = {2025},
author = {Docherty, JAD and Cook, R and Kiu, R and Dyball, X and Brown, TL and Kujawska, M and Smith, RL and Phillips, S and Watt, R and Telatin, A and Tiwari, SK and Hall, LJ and Adriaenssens, EM},
title = {Diverse defense systems and prophages in human-associated Bifidobacterium species reveal coevolutionary "arms race" dynamics.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116542},
doi = {10.1016/j.celrep.2025.116542},
pmid = {41206864},
issn = {2211-1247},
abstract = {Bacteria of the genus Bifidobacterium are pivotal for human health, especially in early life, where they dominate the gut microbiome in healthy infants. Bacteriophages, as drivers of gut bacterial composition, can affect bifidobacterial abundance. Here, we use a bioinformatics approach to explore direct interactions between human-associated Bifidobacterium spp. and prophages, as evidenced by their genomes. Analysis of 1,086 bifidobacterial genomes reveals the presence of complex systems that prevent viral invasion, with 34 defense systems and 56 subtypes detected, including several different CRISPR-Cas systems. CRISPR spacers target almost three-quarters of bifidobacteria-derived prophages, indicating dynamic interactions. At least one prophage is present in ∼67% of strains, with phages exhibiting high genomic diversity and evidence of historical recombination. These prophages encode various defense and anti-defense systems, such as anti-CRISPR genes and restriction-modification mechanisms. Overall, this investigation reveals that coevolutionary "arms race" dynamics drive genomic diversity in both bifidobacteria and their phages.},
}

@article {pmid41206708,
year = {2025},
author = {Royer, FP and Schlick-Steiner, JS and Klammsteiner, T and Kopf, T and Schlick-Steiner, BC and Steiner, FM},
title = {Bacterial communities of wild bee species and the western honey bee (Apis mellifera) (Hymenoptera: Apoidea): Alpine insights.},
journal = {Journal of insect science (Online)},
volume = {25},
number = {6},
pages = {},
doi = {10.1093/jisesa/ieaf095},
pmid = {41206708},
issn = {1536-2442},
abstract = {Wild bees are decreasing in species diversity and populations due to human impact. The abundance of the western honey bee (Apis mellifera L.) experiences an inverse trend, enhancing competition with wild bees and the probability of microbiome exchange. Addressing this exchange, we studied the gut microbiome composition of wild and honey bees, focusing on patterns indicating honey bee influence. Three solitary wild bee species (large scabious mining bee [Andrena hattorfiana F.], grey-backed mining bee (Andrena vaga Panzer), and European orchard bee [Osmia cornuta Latreille]) as well as bumble bees as representatives of eusocial wild bees (Bombus spp. Latreille) and honey bees were sampled in the Austrian Alps. Subsequent 16S ribosomal DNA sequencing revealed the composition of the bacterial communities. The bee groups differed concerning their bacterial composition, with honey bees having the least variation among individuals and a low number of exclusive bacterial taxa and bumble bees the highest bacterial diversity. High honey bee densities corresponded with lower bacterial diversity in wild bees and a higher bacterial similarity between wild and honey bees. Some bacterial taxa were found for the first time in the studied bee groups. Furthermore, the composition of bacterial communities differed between solitary and social bees. We found the first hints that high honey bee density negatively impacts wild bees through alterations of wild bee microbiomes. Future studies should focus on understanding microbiome transmission mechanisms and their consequences for wild bees. Suggestions on how to consider wild bee fitness are indispensable in halting the biodiversity crisis.},
}

@article {pmid41206461,
year = {2025},
author = {Kifushi, M and Nishikawa, Y and Hosokawa, M and Anai, T and Takeyama, H},
title = {Strain-level dissection of complex rhizoplane and soil bacterial communities using single-cell genomics and metagenomics.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {},
number = {},
pages = {},
doi = {10.1093/dnares/dsaf032},
pmid = {41206461},
issn = {1756-1663},
abstract = {Root exudates shape root-associated microbial communities that differ from those in soil. Notably, specific microorganisms colonize the root surface (rhizoplane) and strongly associate with plants. Although retrieving microbial genomes from soil and root-associated environments remains challenging, single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are essential for studying these microbiomes. This study compared SAGs and MAGs constructed from short-read metagenomes of the same soil samples to clarify their advantages and limitations in soil and root-associated microbiomes, and to deepen insights into microbial dynamics in rhizoplane. We demonstrated that SAGs are better suited than MAGs for expanding the microbial tree of life in soil and rhizoplane environments, due to their greater gene content, broader taxonomic coverage, and higher sequence resolution of quality genomes. Metagenomic analysis provided sufficient coverage in the rhizoplane but was limited in soil. Additionally, integrating SAGs with metagenomic reads enabled strain-level analysis of microbial dynamics in the rhizoplane. Furthermore, SAGs provided insights into plasmid-host associations and dynamics, which MAGs failed to capture. Our study highlights the effectiveness of single-cell genomics in expanding microbial genome catalogs in soil and rhizosphere environments. Integrating high-resolution SAGs with comprehensive rhizoplane metagenomes offers a robust approach to elucidating microbial dynamics around plant roots.},
}

@article {pmid41206083,
year = {2025},
author = {Jain, SG and Vennam, SS and Dharmatti, G and Huey, SL and Kaur, P and Krishnan, S and Nandi, BK and Puri, S and Sesikaran, B and Srinivasan, S and Udipi, S and Voruganti, VS},
title = {Principles and Guidelines for the Practice of Precision Nutrition in the Indian Context: A Narrative Review.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuaf177},
pmid = {41206083},
issn = {1753-4887},
support = {//International Life Sciences Institute India (ILSI INDIA)/ ; },
abstract = {Precision and personalized nutrition represent a transformative shift in dietary recommendations, moving away from a one-size-fits-all approach to a more individualized strategy that considers genetics, epigenetics, the microbiota, and socio-cultural, environmental, and lifestyle factors. As the field of precision medicine evolves, clear principles and guidelines are essential for its application in clinical and public health settings. In this narrative review we aimed to provide the current principles and guidelines governing personalized nutrition to establish a comprehensive and standardized framework for effective application and development of personalized nutrition strategies. In this review we also emphasized the importance of involving regional and cultural perspectives while formulating nutritional plans with a particular focus on individuals with an Indian background. A comprehensive search of key databases spanning the past two decades identified several core principles of precision nutrition and their integration with sociocultural factors. The guidelines emphasize interdisciplinary approaches and technological advancements like AI and big data and also point toward the applicability and generalizability of these approaches across cultures and populations, specifically Indian. However, the integration of multiple data sources and the requirement for uniform protocols are major challenges. Notwithstanding these challenges, the field of individualized nutrition has great promise for the future of nutrition. Future research should focus on refining these guidelines and addressing existing gaps to enhance their efficacy and applicability in real-world settings.},
}

@article {pmid41206012,
year = {2025},
author = {Tan, EK and Wang, JDJ and Pettersson, S and Wang, Q and Takahashi, R and Poewe, W and Jankovic, J and Rascol, O},
title = {Faecal microbiota transplant for Parkinson's disease: promises and future directions.},
journal = {Brain : a journal of neurology},
volume = {},
number = {},
pages = {},
doi = {10.1093/brain/awaf419},
pmid = {41206012},
issn = {1460-2156},
abstract = {There is considerable evidence linking alterations in gut microbiome composition with Parkinson's disease (PD), leading to several recent randomized controlled fecal microbiota transplantation (FMT) trials in PD patients targeting gut dysbiosis with the aim to modulate the gut-brain axis. Some FMT trials have observed motor and non-motor symptoms improvements in PD patients, possibly through microbiota linked enhanced short-chain fatty acid or other metabolite effects and reduced systemic inflammation. While the findings are exciting and can potentially open a new treatment paradigm, crital questions on donor selection, the optimal screening and selection of the donor microbiome, delivery routes and the timing and frequency of transplantation need to be addressed. We suggest that future FMT trials should incorporate blood, metabolites, urine and functional neuroimaging biological markers and control dietary, lifestyle comorbidities, medication intake and/or other potential variables, and to ensure optimal evaluation of interactions between the gut microbes and brain outcomes prospectively over a longer time frame.},
}

@article {pmid41205933,
year = {2025},
author = {Favaron, A and Sangfuang, N and McCoubrey, LE and Awad, A and Ghyselinck, J and Marzorati, M and Verstrepen, L and De Munck, J and De Medts, J and Basit, AW and Orlu, M},
title = {Assessing the effects of tofacitinib on the gut microbiome in inflammatory bowel disease.},
journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences},
volume = {},
number = {},
pages = {107365},
doi = {10.1016/j.ejps.2025.107365},
pmid = {41205933},
issn = {1879-0720},
abstract = {Gut microbiota dysbiosis and impaired epithelial barrier function play a key role in inflammatory bowel disease (IBD). Tofacitinib citrate, a Janus kinase (JAK) inhibitor approved for IBD, modulates immune responses via the JAK-STAT (Janus kinase-signal transducer and activator of transcription) pathway, yet its effects on the gut microbiome remain unclear. Here, we employed the short-term colon model (ProDigest, BE) containing human microbiota from three Crohn's Disease donors to assess fermentative and metabolic activities and microbial composition following 48 h of tofacitinib treatment. A Caco-2/THP1 co-culture system was used to assess the impact of tofacitinib on epithelial immunomodulation and barrier integrity. Tofacitinib did not significantly affect microbiota composition and fermentative or metabolic activity. However, it consistently reduced pro-inflammatory chemokines motif chemokine ligand 10 (CXCL10) and monocyte chemoattractant protein-1 (MCP-1), and interleukin-6 (IL-6) in specific donors, indicating targeted immunomodulatory effects. These findings suggest that while tofacitinib may have a minimal impact on microbiota function, it may exert anti-inflammatory effects via microbiota-derived metabolites. The short-term colon model represents a robust platform for investigating microbiome-drug interactions relevant to IBD.},
}

@article {pmid41205808,
year = {2025},
author = {Cohen, S and Donovan, M and Gardner, D and Sambo, D and Karagoz, SB and Cinar, R and Goldman, D and Gardner, JD and Pacher, P and Paloczi, J},
title = {Selective Depletion of Gut Gram-Negative Bacteria Attenuates Alcohol-Binge-Induced Cardiovascular Dysfunction by Lowering Cardiac Anandamide Levels.},
journal = {The American journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajpath.2025.10.010},
pmid = {41205808},
issn = {1525-2191},
abstract = {Binge drinking contributes to a rising number of emergency room visits in the United States. Our previous work demonstrated that an alcohol binge impairs cardiac performance and exerts complex hemodynamic effects through the activation of the endocannabinoid-mediated cannabinoid receptor 1 (CB1R) signaling pathway. Anandamide (AEA), an endogenous CB1R agonist, is synthesized in response to various stressors and tissue injury. However, the role of binge drinking in increasing myocardial AEA levels, which leads to CB1R-dependent cardiodepression, remains unclear. Here, we studied how endotoxins from intestinal Gram-negative bacteria affect myocardial AEA levels, which further induce CB1R-dependent cardiac dysfunction following acute alcohol intoxication. Using a murine model of a single alcohol binge (5 g/kg orally), we observed reduced mesenteric microcirculation concurrent with elevated circulating endotoxin levels. Selective depletion of gut Gram-negative bacteria by antibiotics partially ameliorated alcohol-induced gut barrier dysfunction, significantly lowered circulating endotoxins, coinciding with reduced cardiac AEA levels at 3 hours post-binge. These changes were paralleled with moderately improved cardiac performance, and vascular tone. Cardiac RNA levels of genes involved in AEA synthesis increased after alcohol binge, but not in antibiotic-pretreated mice. However, acute alcohol-induced cardiac AEA formation was unrelated to Toll-like receptor-4 signaling. These findings provide novel insights that highlight the pivotal role of intestinal Gram-negative bacteria in modulating cardiac AEA levels after an alcohol binge, leading to cardiovascular dysfunction.},
}

@article {pmid41205786,
year = {2025},
author = {Weltz, TK and Peng, S and Larsen, A and Bak, EEF and Tran, JVQ and Hemmingsen, MN and Ørholt, M and Mielke, LV and Trillingsgaard, J and Elberg, JJ and Hölmich, LR and Jensen, LT and Vester-Glowinski, P and Fritz, B and Bjarnsholt, T and Trivedi, U and Li, X and Sørensen, SJ and Herly, M},
title = {Breast Implant microbiome profile correlates with foreign body response severity.},
journal = {Acta biomaterialia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.actbio.2025.11.008},
pmid = {41205786},
issn = {1878-7568},
abstract = {Biomedical implants significantly enhance quality of life for millions of individuals worldwide. However, maintaining long-term implant function remains challenging, and it is often due to a severe foreign body response, characterized by fibrosis and functional impairment, clinically referred to as capsular contracture for breast implants. Colonization of implant surfaces by low-virulent bacteria has been proposed as a potential driver of severe foreign body response, but evidence from large-scale human studies has been lacking. We found that the implant microbiome composition is significantly associated with the foreign body response severity based on an extensive characterization of the breast implant microbiome using 16S rRNA gene amplicon sequencing. We analyzed 339 explanted breast implants from 206 patients undergoing revisional surgery without any symptoms of a clinical infection. We detected a diverse community of bacteria on the implants and demonstrated that an increased relative abundance of Staphylococcus was associated with a severe foreign body response. This pattern was supported by a within-patient analysis of 20 individuals with unilateral severe versus contralateral mild foreign body response. These findings suggest that the implant microbiome plays a role in the development of a severe foreign body response and may guide strategies to improve implant biocompatibility. STATEMENT OF SIGNIFICANCE: : This study identified a diverse microbiome on breast implants from patients without any symptoms of infection and demonstrated a clear association between microbiome composition and the severity of the foreign body response (FBR), a significant complication affecting implant function. Notably, implants with severe FBR showed lower microbial diversity and higher relative abundance of Staphylococcus compared to those with mild FBR. Additionally, a paired analysis within patients with severe FBR in one breast and mild FBR in the contralateral breast further supported higher relative Staphylococcus abundance on the severe FBR implant. These findings provide insights into microbial factors influencing implant biocompatibility, which may guide strategies to improve implant biocompatibility and reduce complications for patients.},
}

@article {pmid41205726,
year = {2025},
author = {Tao, H and Mao, K and Zhang, Z and Wei, W and Huang, X and Chen, Y and Mei, S and Tian, X},
title = {Applications of traditional Chinese medicine in cancer immunotherapy via gut microbiota modulation: Current status, mechanisms, challenges and perspectives.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {108020},
doi = {10.1016/j.phrs.2025.108020},
pmid = {41205726},
issn = {1096-1186},
abstract = {Cancer immunotherapy faces significant limitations due to therapeutic resistance. Emerging evidences have identified the gut microbiota (GM) as a crucial regulator of antitumor immunity through its effects on the tumor immune microenvironment (TIME). Guided by the principle of "fu zheng qu xie" (fortifying healthy qi to reinforce immune homeostasis and eliminating pathogenic factors to promote immune clearance), traditional Chinese medicine (TCM) exerts multi-target systemic regulation. Specifically, TCM modulates gut microecology, which in turn regulates the production of microbial metabolites (e.g., short-chain fatty acids, bile acids), ultimately reprogramming TIME by enhancing immune cell infiltration into the tumor parenchyma, optimizing T-cell cytotoxicity and differentiation, improving antigen presentation, and alleviating immunosuppression. This review systematically summarizes the causal chain of "TCMGMmetabolitesimmune cellsTIME" across different immune phenotypes, emphasizing how bioactive TCM components and classical formulas reshape microbial communities, enrich beneficial bacteria, and regulate metabolic pathways to potentiate cancer immunotherapy. Despite promising preclinical data, challenges persist due to mechanistic complexity, the lack of standardization, and limited clinical translation. Potential solutions include multi-omics integration, intelligent screening of herbal compounds, and targeted delivery systems. With advancing pharmacological insights, TCM-derived microbiome modulators (TMMs), defined as phytochemicals and formulations that systematically modulate gut microecology, may overcome immunotherapy resistance, representing a novel strategy for enhancing cancer immunotherapy.},
}

@article {pmid41205590,
year = {2025},
author = {Golob, JL and Oskotsky, TT and Tang, AS and Roldan, A and Chung, V and Ha, CWY and Wong, RJ and Flynn, KJ and Chai, R and Dubin, C and Parraga-Leo, A and Wibrand, C and Minot, SS and Oskotsky, B and Andreoletti, G and Kosti, I and Bletz, J and Nelson, A and Gao, J and Wei, Z and Chen, G and Tang, ZZ and Novielli, P and Romano, D and Pantaleo, E and Amoroso, N and Monaco, A and Vacca, M and De Angelis, M and Bellotti, R and Tangaro, S and Wang, Z and Yao, J and Goel, A and Mao, J and Wang, H and Zhang, Y and Tewari, A and Kuntzleman, A and Bigcraft, I and Techtmann, S and Bae, D and Kim, E and Jeon, J and Joe, S and , and Theis, KR and Ng, S and Lee, YS and Diaz-Gimeno, P and Bennett, PR and MacIntyre, DA and Stolovitzky, G and Lynch, SV and Albrecht, J and Gomez-Lopez, N and Romero, R and Stevenson, DK and Aghaeepour, N and Tarca, AL and Costello, JC and Sirota, M},
title = {Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102428},
doi = {10.1016/j.xcrm.2025.102428},
pmid = {41205590},
issn = {2666-3791},
}

@article {pmid41205569,
year = {2025},
author = {Mayr, AV and Weinhold, A and Nolzen, A and Keller, A and Ayasse, M},
title = {The neonicotinoid Acetamiprid alters the chemical profile of the primitive eusocial bee Lasioglossum malachurum.},
journal = {Ecotoxicology and environmental safety},
volume = {306},
number = {},
pages = {119311},
doi = {10.1016/j.ecoenv.2025.119311},
pmid = {41205569},
issn = {1090-2414},
abstract = {The widespread use of agrochemicals, particularly neonicotinoids, poses a significant threat to the health of (pollinating) insects. Various health traits are affected, but the impact on the chemical communication of wild bees remains a poorly studied aspect. Here, we assessed how field-realistic exposure to the 'honeybee-safe' neonicotinoid Acetamiprid affects the behaviour, cuticular lipids and microbiome of Lasioglossum malachurum, a small ground-nesting sweat bee. L. malachurum is an important, abundant pollinator of several crop plants with primitive social behaviour which relies on cuticular lipids for communication. We collected bees in the field for a controlled pesticide treatment in the lab. Pesticide-treated individuals increased their sugar-water consumption rate compared to the control group. After 7 days of experiment, the treatment group showed a trend towards less developed ovaries and an increased amount of odour with significantly altered queen pheromones. While the microbiome was not affected by the treatment, a comparison with field individuals showed an erosion of their gut microbiome with a reduction in Apilactobacillus during laboratory keeping. Our findings indicate that neonicotinoids may disturb chemical communication in L. malachurum and thus might impair social behaviour. This raises concerns about the threats of currently approved pesticides to wild pollinators.},
}

@article {pmid41205563,
year = {2025},
author = {Bautzmann, R and Waelchli, J and Schürch, S and Schlaeppi, K and Rentsch, D},
title = {Biodegradable plastics impair maize growth and reshape bacterial communities associated with roots and sand or soil.},
journal = {Ecotoxicology and environmental safety},
volume = {306},
number = {},
pages = {119353},
doi = {10.1016/j.ecoenv.2025.119353},
pmid = {41205563},
issn = {1090-2414},
abstract = {Biodegradable plastics entering terrestrial ecosystems raise environmental and food safety concerns, as they impact soil-plant systems either directly by releasing compounds during degradation, or indirectly, by altering soil biophysical properties and/or microbial communities. Here, we examined the impact of biodegradable micro- and macroplastics made from Mater-Bi, and starch (a simple carbon [C] source present in the plastic studied) on the growth of Zea mays seedlings and bacterial communities associated with roots or with the growth substrates, i.e., sand or silt loam soil. Increasing concentrations of biodegradable plastics and starch reduced plant biomass and chlorophyll content in a dose-dependent manner. Additionally, nitrogen (N) content was reduced, accompanied by lower transcript levels of genes commonly downregulated under N-limiting conditions. Biodegradable plastics and starch altered the bacterial community composition, resulting in decreased bacterial diversity in the growth substrates and increased diversity within maize roots. The effects on maize and bacteria were consistent but generally stronger in sand than in silt loam soil. A follow-up experiment confirmed that plastics- or starch-associated microbes did not affect maize growth when no plastics or starch was present. Our results suggest that biodegradable plastics significantly impair soil-plant systems through their C inputs.},
}

@article {pmid41205502,
year = {2025},
author = {Song, HW and An, J and Sha, JQ and Hu, FY and Liu, WT},
title = {Ca(II) alleviates microplastic toxicity to Microcystis aeruginosa via cyanobacteria induced carbonate precipitation.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140341},
doi = {10.1016/j.jhazmat.2025.140341},
pmid = {41205502},
issn = {1873-3336},
abstract = {Microplastics (MPs), as a globally emerging contaminant, present significant and increasing threats to aquatic ecosystem health and adversely impact cyanobacterial physiology. Ca(II) are ubiquitous essential ions in natural waters, yet their influence on MPs toxicity to cyanobacteria remains insufficiently understood. This study systematically investigated the mitigating effects and mechanisms of Ca(II) on MPs-induced toxicity in Microcystis aeruginosa through an integrated approach involving toxicological assays, microscopic characterization, and microbiome analysis. Both low (2 mg L[-1]) and high (10 mg L[-1]) concentrations of MPs induce oxidative stress and inhibit the growth of M. aeruginosa. However, the addition of Ca(II) significantly mitigated these adverse effects. Mechanistically, Ca(II) promoted cyanobacteria induced carbonate precipitation (CICP), leading to the immobilization of approximately 32.3-34.7 % of MPs, thereby reducing cellular exposure to MPs. Consequently, this attenuated MPs-induced stress on glucosiolate biosynthesis and 2-oxocarboxylic acid metabolism pathways, while mitigating damage to photosynthetic components, including photosystem II (PSII), photosystem I (PSI), and the photosynthetic electron transport chain (PETC). This study provides evidence that Ca(II) protects M. aeruginosa from MPs toxicity by activating the CICP pathway to establish a calcite-based defense system. These findings enhance our understanding of cyanobacteria-MPs interactions under environmentally relevant ionic conditions.},
}

@article {pmid41205302,
year = {2025},
author = {Camille, E and Sébastien, B and Virginie, B},
title = {The hidden players: The mycobiome of pancreatic ductal adenocarcinoma tumors.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128392},
doi = {10.1016/j.micres.2025.128392},
pmid = {41205302},
issn = {1618-0623},
abstract = {The microorganisms that inhabit the human body are known to play a role in human health and disease. Continuing to elucidate their specific role in disease progression is, however, necessary. The imbalance of these microorganisms-known as dysbiosis-has been linked to a myriad of intestinal diseases, and more recently to cancer. Despite making up less than 0.1 % of the human microbiome, dysbiosis of the fungal component of the microbiome-the mycobiome-has been found to contribute to the tumorigenesis and progression of certain types of tumors, pancreatic ductal adenocarcinoma (PDAC) included. The quantity and composition of the mycobiome was found to differ between healthy pancreatic tissue, the gut mycobiome of PDAC patients and PDAC tissue. Moreover, in a murine model of PDAC, it was shown that fungal ablation had a protective effect on tumor growth, and that specific fungal species, such as Malassezia globosa, contribute to tumor growth as well as to the inflammatory environment observed in PDAC tumors which promotes tumor progression. Research shows that fungal presence contributes to shaping the immune microenvironment through the activation of the complement system and/or by eliciting a type 2 immune response. Despite these preliminary findings, given the novelty of the field and of the bioinformatics pipelines used to analyze sequencing data, standardized approaches are still under development, thus leading to disagreement on the reliability of these results. The purpose of this review is to provide an up-to-date overview of the current research regarding the contribution of the fungal mycobiome in PDAC tumor progression and the overall tumor microenvironment (TME) of PDAC tumors.},
}

@article {pmid41205272,
year = {2025},
author = {Ai, Y and Davis, AB and Basta, NT and Lee, J},
title = {Unveiling profiles: Dredged materials from Lake Erie harbors are reservoirs for toxic cyanobacteria, antimicrobial resistance, and nutrients.},
journal = {The Science of the total environment},
volume = {1005},
number = {},
pages = {180879},
doi = {10.1016/j.scitotenv.2025.180879},
pmid = {41205272},
issn = {1879-1026},
abstract = {The beneficial use of dredged materials (DMs) as an agricultural resource has gained popularity. Lake Erie shorelines are the most dredged of the Great Lakes in the United States, which is also affected by anthropogenic-driven harmful algal blooms (HAB) and other pollutants like antibiotic resistance genes (ARGs). This study focused on characterizing the DMs from six harbors along the southwest shore of Lake Erie, focusing on the toxic cyanobacteria, toxins, nutrients, microbiome, resistome, and their bacterial hosts. Dominated toxic cyanobacteria genera in DMs are Microcystis, Dolichospermum, Nostoc, Aphanizomenon, and Planktothrix. with microcystin (MC)-producing Microcystis being the major toxin producer. In line with the spatial bloom distribution in Lake Erie, from the central to western basin, the concentration of MC and toxic cyanobacteria in DMs increased. The same spatial trend was observed regarding the ARG, nitrogen, and phosphorus concentrations in DMs. The concentration of clinically relevant ARGs (blaKPC, blaNDM, blaOXA-48, tetQ, and sul1) was positively correlated with the toxic cyanobacteria, N, and P concentrations. Overall, this study provides valuable information on DMs from cyanobacteria- and AR-affected eutrophicated lakes, so safe DM management plan and dredging operations can be possible to sustain beneficial use of DMs in the HAB-affected areas.},
}

@article {pmid41205133,
year = {2025},
author = {Ghafoor, DD and Ahmad, DO and Najmuldeen, HH and Mohammed, SJ and Jalal, PJ and Mustafa, FS and Alghofaili, F and Zangana, BA and Al-Bajalan, SJ},
title = {Multiple sclerosis pathophysiology: a comprehensive review of genetic, environmental, and immunological drivers.},
journal = {Inflammopharmacology},
volume = {},
number = {},
pages = {},
pmid = {41205133},
issn = {1568-5608},
abstract = {Multiple sclerosis (MS) is a complex, chronic neuroinflammatory and neurodegenerative disorder of the central nervous system. This comprehensive review synthesizes evidence to argue that the paramount challenge in MS is bridging the disconnect between anti-inflammatory therapies and ineffective neuroprotective strategies, necessitating a dual-target approach. The paper discusses the crucial roles of genetic predisposition, highlighting the HLA-DRB1*15:01 allele and other non-HLA loci, and environmental triggers, such as Epstein-Barr virus infection, vitamin D deficiency, and smoking. We detail the dysregulation of both T-cells (Th1 and Th17 subsets) and B-cells in the autoimmune attack on myelin, as well as the intricate mechanisms of neurodegeneration, axonal damage, and the challenges of remyelination. The review also incorporates emerging insights into the role of the gut microbiome and epigenetic modifications, underscoring the necessity of an integrative model to understand MS pathogenesis. Ultimately, this review provides a foundational understanding of converging biological drivers of MS. Therapeutically, currently approved disease-modifying therapies (DMTs)-including interferon-β, glatiramer acetate, oral S1P modulators, fumarates, teriflunomide, cladribine, natalizumab, and anti-CD20 monoclonals-reduce relapse frequency and MRI activity but do not eliminate disability progression, particularly in progressive MS. Acute relapses are treated with high-dose corticosteroids, with plasma exchange reserved for steroid-refractory cases. We therefore argue that future success requires integrated strategies that couple sustained control of peripheral inflammation with CNS-intrinsic neuroprotection and remyelination. Therapeutically, modern disease-modifying therapies (interferon-β, glatiramer acetate, oral S1P modulators, fumarates, teriflunomide, cladribine, natalizumab, anti-CD20 monoclonals including ocrelizumab, ofatumumab, and ublituximab) reduce relapse rates and MRI activity yet do not consistently prevent disability progression-particularly in non-active progressive MS. Acute relapses are treated with high-dose corticosteroids; plasma exchange is reserved for steroid-refractory attacks. These realities motivate mechanism-informed strategies that pair sustained immune control with CNS-intrinsic neuroprotection and remyelination.},
}

@article {pmid41205097,
year = {2025},
author = {Lee, SJ and Lee, YS and Kim, YR and Jeon, MH and Noh, DI and Jeong, SM and Kim, KW and Lee, EW and Jang, WJ},
title = {Development of Novel Host-Associated Low-Temperature Probiotics (HALP) Tailored to Aquaculture Applications.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41205097},
issn = {1867-1314},
support = {R2025038//National Institute of Fisheries Science/ ; 2022R1A2C1012655//National Research Foundation of Korea/ ; RS-2024-00403688//Korea Basic Science Institute/ ; },
abstract = {Aquaculture temperatures vary depending on the fish species, and probiotics used in aquaculture must remain effective under these conditions. Therefore, our study developed host-associated low-temperature probiotics (HALP) adapted to temperature conditions relevant to aquaculture. Three bacterial strains, Rahnella inusitata NBL2302 (RI), Pseudoalteromonas arctica NBL2303 (PA), and Lactiplantibacillus plantarum NBL2306 (LP), were isolated from the gastrointestinal tract of Korean rockfish (Sebastes schlegelii). Safety assessments, in vitro probiotic characterization (including antioxidant activity, acid/salt/bile tolerance, antimicrobial activity, and adhesion), and a feeding trial were conducted. All three strains were confirmed to be safe, exhibiting no hemolytic or cytotoxic activity. Among the three strains, LP exhibited the highest adhesion to intestinal epithelial cells and showed antimicrobial activity against fish pathogens. RI supplementation significantly enhanced innate immune markers such as serum total protein (TP), triglycerides (TG), and myeloperoxidase (MPO), along with the upregulation of immune-related genes (HSP70, IL-1β, TNF-α) (p < 0.05). PA supplementation resulted in the greatest weight gain and significantly improved specific growth rate (SGR), likely due to increased digestive enzyme activity. LP promoted immunostimulatory responses (elevated expression of MPO, TP, HSP70, and TNF-α) and pronounced changes in the beta diversity of the gut microbiota. Microbiome analysis revealed that LP-fed fish harbored higher abundances of beneficial genera such as Pseudomonas, Ralstonia, and Sphingomonas. Overall, each strain displayed unique characteristics and exerted distinct effects during feeding trials. These findings, which take host temperature preferences into account, underscore the potential of HALP in aquaculture and highlight the need for further research into optimized combination strategies.},
}

@article {pmid41204383,
year = {2025},
author = {Issifu, S and Elango, AV and Michl, K and David, C and Cernava, T and Wilhelm, RC and Rasche, F},
title = {Perennial Kernza cropping promotes rhizosphere microbiome stability and endophyte recruitment compared to annual wheat.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {139},
pmid = {41204383},
issn = {2524-6372},
support = {RA 1717/8-1//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Perennial cropping systems are increasingly recognized for their potential to enhance microbial biodiversity and beneficial soil functions compared to annual crops. The impact of perennialization on the rhizomicrobiome and endophyte community was assessed by comparing intermediate wheatgrass (Thinopyrum intermedium, commercialized as Kernza®, hereafter called 'Kernza') and annual wheat (Triticum aestivum) associated communities across a north-south European agroclimatic gradient (Sweden, Belgium, and France) over two growing seasons and at two depths.

RESULTS: Between the 2 years, the Kernza-associated rhizomicrobiome was more stable and exhibited greater homogeneity across depths compared to annual wheat. Kernza harboured a significantly more diverse set of crop-associated amplicon sequence variants (ASVs) and had a higher number of core ASVs than annual wheat. Furthermore, Kernza had a significantly higher proportion of rhizobacterial populations in root tissues than annual wheat. Environment-wide association analyses revealed that the Kernza rhizosphere had higher proportions of grassland-associated and rhizosphere-dwelling microbiomes compared to annual wheat. Despite these noteworthy differences, the greatest variation in the rhizomicrobiome composition was driven by factors such as country, year, and depth, rather than crop type. For instance, Actinobacteriota dominated rhizobacterial communities in both Kernza and annual wheat.

CONCLUSIONS: Overall, Kernza conferred modest yet clear improvements in rhizomicrobiome community stability and selective endophyte recruitment, supporting its ability to enhance sustainable, microbially-mediated soil functions. Moreover, Kernza hosted significant grassland-associated taxa, suggesting a similarity between Kernza fields and grassland ecosystems.},
}

@article {pmid41204381,
year = {2025},
author = {Villette, R and Sunyer, JO and Novikova, PV and Aho, VTE and Petrov, VA and Hickl, O and Busi, SB and De Rudder, C and Kunath, BJ and Heintz-Buschart, A and Trezzi, JP and Halder, R and Jäger, C and Lebrun, LA and Daujeumont, A and Schade, S and Janzen, A and Jehmlich, N and von Bergen, M and Laczny, CC and May, P and Trenkwalder, C and Oertel, W and Mollenhauer, B and Wilmes, P},
title = {Correction: Integrated multi‑omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson's disease.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {230},
pmid = {41204381},
issn = {2049-2618},
}

@article {pmid41204312,
year = {2025},
author = {Sun, W and Liu, Q and Chen, H and Xie, X and Zhang, Z and Zeng, Y and Zhou, J and Zhou, X and Jiang, X and Liang, Z and Li, JF and Deng, Y},
title = {Rice phyllospheric Pantoea spp. suppress blast and bacterial blight diseases.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {137},
pmid = {41204312},
issn = {2524-6372},
support = {2022YFA1304402; 2023YFD1400200//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Rice is a major food crop in China as well as Asia, yet its production is threatened by microbial diseases including blast disease caused by fungal pathogen (Magnaporthe oryzae) and bacterial blight caused by several bacterial pathogens. To screen for bacterial microbiota associated with rice blast occurrence, and/or contributing to disease resistance, we performed microbiota analysis with rhizosphere soil, root, stem, and leaf samples of blast susceptible (CO39) and resistant (Y33R) rice grown in a blast disease nursery garden.

RESULTS: Our result showed no significant difference in microbiota of rhizosphere soil, root, or leaf between these two rice cultivars, but stem microbiota were significantly different. Pantoea spp. were enriched in stem of blast susceptible rice, suggesting that it may play a role after fungal infection. A total of 822 bacterial strains were isolated from the phyllospheric (including leaf and stem) samples of Y33R and CO39 rice. Based on 16S rRNA amplicon sequencing, and phylogenic analysis using 16S rRNA, gyrB, leuS, and rpoB gene sequences, the 3 isolated strains and 1 strain were identified as P. ananatis and P. dispersa, respectively. The strains A25-H1 and B10-A1 were selected for genome sequencing, and based on Average Nucleotide Identity (ANI) analysis, we confirmed that A25-H1 was P. ananatis and B10-A1 was P. dispersa. The P. ananatis consortium (A25-F1, A25-G1, and A25-H1 combination) A25-11 and P. dispersa strain B10-A1 displayed suppressive effect on blast disease when they were applied to the susceptible rice CO39. Although a P. ananatis strain SC7 has been reported to cause bacterial blight in rice, A25-11 or B10-A1 was non-pathogenic to rice under experimental conditions. Furthermore, they could also suppress bacterial blight caused by SC7 or Xanthomonas oryzae pv. oryzae strain Pxo99A. A25-11 and B10-A1 did not affect the growth of M. oryzae mycelia in confrontation culture analysis, but induced transcription of rice immunity genes and promoted ROS accumulation, suggesting that the biocontrol effect of A25-11 or B10-A1 may lie on immunity priming. We further showed that A25-11 and B10-A1 possessed growth promoting capacity including indole 3-acetic acid (IAA) production, phosphate solubilization, nitrogen fixation, and siderophore production. Under field condition, the consortium A25-11 and strain B10-A1 could effectively suppress leaf and panicle blast.

CONCLUSIONS: Overall, this study established a microbiome method for identifying the rice bacterial communities of agricultural significance, with capacity of rice disease management and/or growth promotion.},
}

@article {pmid41204050,
year = {2025},
author = {Li, J and Wang, S and Luo, P and Li, Z and Gopinath, D},
title = {Exploring the plausible genetic relationship of salivary and tongue microbiome with periodontitis: A mendelian randomization study.},
journal = {The Saudi dental journal},
volume = {37},
number = {10-12},
pages = {76},
pmid = {41204050},
issn = {1013-9052},
abstract = {Chronic periodontitis (CP) is associated with subgingival microbial dysbiosis and demonstrates specific microbial patterns, though definitive causal connections with microbiomes in distinct anatomical regions remain undetermined. Genome-wide association datasets for CP and oral microbial communities were sourced from a large European cohort and China National GeneBank DataBase (CNGBdb), respectively. Employing single-nucleotide polymorphisms (SNPs) as genetic instruments, Mendelian randomization (MR) analyses were conducted through the inverse-variance weighted (IVW) approach. Analysis methods were implemented through the 'TwoSampleMR' package (v0.6.4) in R software. Sensitivity analyses were performed to validate the robustness of the findings and mitigate the occurrence of horizontal pleiotropy. The MR analyses revealed three salivary bacterial taxa, Neisseria meningitidis (OR = 0.67, 95% CI, 0.49-0.98), Streptococcus vestibularis (OR = 0.74, 95% CI, 0.56-0.98), and Lancefieldella unclassified (OR = 0.68, 95% CI, 0.52-0.91) to be significantly associated with a reduced risk of CP (p < 0.05). In contrast, tongue microbial taxa Solobacterium unclassified (OR = 1.45, 95% CI, 1.04-2.04), Fusobacterium sp000235465 (OR = 1.40, 95% CI, 1.02-1.94), and Haemophilus parainfluenzae (OR = 1.56, 95% CI, 1.12-2.18) were associated with an increased CP risk (p < 0.05). No evidence of heterogeneity and directional pleiotropy was noted for these associations. This study highlights the association between specific salivary and tongue microbial taxa and CP, providing mechanistic linkages into the plausible relationship. It also suggests that some microbial taxa may be further explored as indicators for risk-stratified preventive measures and novel targets for precision prebiotics and therapies.},
}

@article {pmid41204024,
year = {2025},
author = {Mileng, K and Mani, S and Bezuidenhout, JJ and Mokgokong, PS and Ramatla, TA and Thekisoe, OMM and Lekota, KE},
title = {Bacterial Communities Harboured by Amblyomma Hebraeum Infesting Small Stock in Mahikeng city, South Africa.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {118},
pmid = {41204024},
issn = {1432-184X},
support = {GUN: CSUR23030681021//National Research Foundation/ ; },
mesh = {Animals ; South Africa ; *Bacteria/classification/genetics/isolation & purification ; Goats/parasitology/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sheep/parasitology ; *Amblyomma/microbiology ; *Tick Infestations/veterinary/parasitology/epidemiology ; *Goat Diseases/parasitology/microbiology/epidemiology ; Phylogeny ; *Sheep Diseases/parasitology/microbiology/epidemiology ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {Ticks are important vectors of pathogens affecting livestock productivity and public health, yet their bacterial communities remain poorly characterized in many parts of South Africa. This study investigated the bacterial diversity and potential pathogenic bacterial etiology associated with Amblyomma hebraeum ticks collected from sheep and goats in Mahikeng, North West province. A total of 168 adult ticks were sampled across four villages. Microbiome profiling was performed using high-throughput sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene on the Illumina MiSeq platform. High-throughput 16S rRNA sequencing revealed 16,193 ASVs in goat-derived ticks and 16,510 ASVs in those from sheep. Proteobacteria emerged as the dominant phylum across all samples, with ticks collected from goats showing a particularly high dominance of Rickettsia spp. (51.64% relative abundance), suggesting potential zoonotic risks. In contrast, ticks from sheep harboured significantly more diverse and evenly distributed bacterial communities, as indicated by Shannon (p = 0.0138) and Simpson (p = 0.0233) diversity indices, despite comparable species richness. A core microbiome comprising 1,374 ASVs (32.3%) was shared across all ticks, alongside 1,504 and 1,372 unique ASVs in goat- and sheep-derived ticks, respectively. Notably, several medically and veterinary-relevant genera, including Coxiella, Ehrlichia, Staphylococcus, Bacillus, Acinetobacter, Corynebacterium, and Streptococcus, were detected across both host groups. While total species richness was comparable between hosts, alpha diversity indices that account for evenness revealed host-based differences, and beta diversity patterns further showed clear separation of bacterial communities by host species. This study indicates that the host plays a crucial role as an ecological driver affecting the diversity of microbial communities associated with ticks. This study improves our understanding of the diversity, composition, and abundance of tick-associated microbiomes and pathogens in South African small ruminants. These insights support the development of microbiome-targeted strategies for detecting and controlling tick-borne diseases.},
}

Animals
South Africa
*Bacteria/classification/genetics/isolation & purification
Goats/parasitology/microbiology
*Microbiota
RNA, Ribosomal, 16S/genetics
Sheep/parasitology
*Amblyomma/microbiology
*Tick Infestations/veterinary/parasitology/epidemiology
*Goat Diseases/parasitology/microbiology/epidemiology
Phylogeny
*Sheep Diseases/parasitology/microbiology/epidemiology
DNA, Bacterial/genetics
High-Throughput Nucleotide Sequencing

@article {pmid41203821,
year = {2025},
author = {Young, JD and Pinnell, LJ and Wolfe, CA and Scott, MA and Lawrence, TE and Cavasin, JP and Ellis, JA and Langsten, KL and Richeson, JT and Morley, PS},
title = {Microbial communities and tight junction protein expression in the gastrointestinal tract of feedlot cattle.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39055},
pmid = {41203821},
issn = {2045-2322},
mesh = {Animals ; Cattle ; *Tight Junction Proteins/metabolism/genetics ; *Gastrointestinal Microbiome ; *Gastrointestinal Tract/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; Rumen/microbiology/metabolism ; Male ; Tight Junctions/metabolism ; Bacteria/genetics/classification ; },
abstract = {The gastrointestinal tract (GIT) of cattle plays a vital role in nutrient absorption, immune function, and microbial homeostasis. While the importance of the GIT microbiome and epithelial barrier integrity has been increasingly recognized, the typical composition of microbial communities and the expression of tight junction proteins (TJPs) in feedlot cattle remains poorly characterized. We investigated microbial community structure and TJP expression at three GIT sites: the rumen (RU), small intestine (SI), and large intestine (LI) in 21 finish-fed feedlot steers sourced from 21 commercial feedyards in the Texas Panhandle. Samples of luminal contents and GIT tissue were collected from each region, as well as feces and liver abscess material. Microbial communities were characterized using 16S rRNA gene sequencing. TJP gene expression was quantified by RT-qPCR using synthetic standards, and protein expression was evaluated by immunohistochemistry (IHC) with both computer-generated and pathologist-generated scoring. Microbial community structures varied primarily by GIT region rather than by individual animals raised at different locations. Nine bacterial families were identified as core microbiome members, with Lachnospiraceae being the most abundant across the GIT. TJP gene expression varied considerably by site, with RU having significantly lower Claudin 1, Claudin 2, and E-Cadherin expression than the SI and LI. IHC results paralleled qPCR findings, with region-specific patterns of protein localization and intensity. Computerized and pathologist-generated H-scores showed moderate agreement but differed notably between epithelial and lamina propria regions. This study provides a comprehensive baseline of microbial and host factors associated with gut health in a uniquely diverse population of feedlot cattle. The identification of regional microbial communities and distinct TJP expression patterns offers foundational insights into gastrointestinal physiology and barrier function. This work establishes baseline data to support future investigations into the relationships among microbial ecology, epithelial barrier function, and cattle health and productivity.},
}

Animals
Cattle
*Tight Junction Proteins/metabolism/genetics
*Gastrointestinal Microbiome
*Gastrointestinal Tract/microbiology/metabolism
RNA, Ribosomal, 16S/genetics
Rumen/microbiology/metabolism
Male
Tight Junctions/metabolism
Bacteria/genetics/classification

@article {pmid41203749,
year = {2025},
author = {Bowman, JP},
title = {Extensive fecal cast production and growth of Vibrionaceae in heat-stressed Atlantic salmon post-smolts.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39064},
pmid = {41203749},
issn = {2045-2322},
mesh = {Animals ; *Salmo salar/microbiology/physiology ; *Feces/microbiology ; Gastrointestinal Microbiome ; *Vibrionaceae/growth & development/genetics/isolation & purification ; *Heat-Shock Response ; RNA, Ribosomal, 16S/genetics ; Hot Temperature ; Female ; },
abstract = {Atlantic salmon (Salmo salar) are known to reduce or cease voluntary feeding and show altered digesta consistency under heat stress. This study was performed to determine what bacterial species occur and to characterize bacterial taxa and quantify changes in gut microbial abundance under heat stress. Atlantic salmon (all female, 1.5 kg average weight) in seawater tanks at 15 °C were fed for 2 to 4 weeks. Tank temperatures were increased to a 19 °C "warm phase" until voluntary feeding abated at which point tank temperatures were cooled to 15 °C for 4 weeks. At the end of each temperature phase the fish were stripped of feces and microbiome profiles were determined using 16 S rRNA V1-V3 metabarcoding. The tank experiment was repeated three times in successive years. Abundances of bacteria were determined using qPCR. Vibrionaceae comprised most reads after the warm phase completed. The prominent levels of Vibrionaceae were accompanied by a large predominance of cast (sloughed intestinal mucosa) containing fecal samples. Quantitative PCR (qPCR) estimated fecal Vibrionaceae cell populations increased 1.9-3.4 log units/g after the warm phase. This population then decreased by 0.3-1.1 log units/g by the end of the 15 °C recovery phase. The gut Vibrionaceae and non-Vibrionaceae compositions in the separate trials were different each time. The results indicated heat stress induced inappetence corresponds to increased cast production accompanied by predominance of Vibrionaceae. The predominance of different bacteria in each trial could be partly due to the different initial abundances of taxa in the inputted smolt. Vibrionaceae colonizing the Atlantic salmon gut should be the focus of studies on the microbiology of thermally induced inappetence and dysbiosis in Atlantic salmon.},
}

Animals
*Salmo salar/microbiology/physiology
*Feces/microbiology
Gastrointestinal Microbiome
*Vibrionaceae/growth & development/genetics/isolation & purification
*Heat-Shock Response
RNA, Ribosomal, 16S/genetics
Hot Temperature
Female

@article {pmid41203701,
year = {2025},
author = {Lee, Y and Seo, J and Di Camillo, B},
title = {SHAP-based binarization enhances metataxonomic machine learning with application to gut microbiota of inflammatory bowel disease.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39059},
pmid = {41203701},
issn = {2045-2322},
support = {IITP-2024-0044-1407//Korean Government [Ministry of Science and ICT (MSIT)]/ ; IITP-2024-0044-1407//Korean Government [Ministry of Science and ICT (MSIT)]/ ; DI_C_BIRD2020_01//Department of Information Engineering of the University of Padova/ ; },
mesh = {*Gastrointestinal Microbiome ; *Machine Learning ; Humans ; *Inflammatory Bowel Diseases/microbiology ; Biomarkers ; },
abstract = {Machine learning has been increasingly applied to microbiome data for biomarker discovery. However, microbiome datasets are typically high-dimensional, sparse, and correlated, which makes model training challenging and prone to overfitting. Previous studies have also reported that microbiome features exhibit binary-like characteristics, and that binarization does not necessarily reduce predictive performance. This observation motivated our work. Building on this idea, we propose a SHAP-based binarization pipeline. We first trained several machine learning models on raw continuous data and selected the best-performing model (random forest). Using SHAP values derived from the training set, we determined feature-specific thresholds that best separated positive and negative contributions. The dataset was then binarized using these thresholds and new models were trained on the transformed data. We evaluated this approach on gut microbiome abundance data (283 species, 220 genera, 1,569 individuals) to classify inflammatory bowel disease (IBD) versus healthy controls. The SHAP-based binarization consistently improved classification performance and interpretability compared with both continuous data and zero-threshold binarization. The best model's Matthews correlation coefficient increased from 0.884 to 0.928, with the largest improvements observed in non-tree-based models such as logistic regression and neural networks. SHAP summary plots also revealed clearer feature patterns, and biomarker rankings were more stable. In addition, the pipeline enabled us to identify a concise set of 17 microbial biomarkers associated with IBD. This study introduces a novel approach for microbiome data analysis by explicitly linking binarization thresholds to SHAP-derived feature contributions. Our approach was grounded in the observation of binary-like patterns revealed through SHAP values. Furthermore, although binarization inevitably raises concerns about information loss, our evaluation confirmed improvements not only in predictive performance but also in interpretability and biomarker stability, providing a broader validation of robustness. These findings highlight SHAP-based binarization as an effective strategy for high-dimensional microbiome data, with broad applicability and opportunities for future extension.},
}

*Gastrointestinal Microbiome
*Machine Learning
Humans
*Inflammatory Bowel Diseases/microbiology
Biomarkers

@article {pmid41203618,
year = {2025},
author = {Moriel, N and Jones, L and Harpenas, E and Rakow, N and Shmorak, S and Eventov Friedman, S and Ofek Shlomai, N and Yassour, M},
title = {Development of the preterm infant gut and gastric residuals microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9848},
pmid = {41203618},
issn = {2041-1723},
mesh = {Humans ; *Infant, Premature ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Female ; Male ; Intensive Care Units, Neonatal ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; *Stomach/microbiology ; Gestational Age ; Enteral Nutrition ; },
abstract = {Prematurity, defined as birth before 37 weeks of gestation, is the leading cause of mortality in children under five, affecting ~11% of live births worldwide (≈15 million annually). Despite advances in neonatal care, preterm infants remain at high risk of complications. In neonatal intensive care units, gastric residuals (GRs) are routinely monitored to guide enteral feeding, yet their microbial composition remains poorly understood. We performed metagenomic sequencing of 199 stool and 69 GR samples from 39 preterm infants during hospitalization to characterize stomach and gut microbiomes. To our knowledge, this is the first metagenomic sequencing of the GR in premature infants. We identified 11 GR microbial clusters, commonly dominated by Staphylococcus, Streptococcus, and Klebsiella, with microbial diversity correlating with aspiration frequency. Colonization was dynamic: early GR samples were enriched with Staphylococcus epidermidis and Bradyrhizobium, while later samples featured Escherichia coli, Staphylococcus hominis, and Streptococcus thermophilus. Stool samples formed eight microbial clusters, frequently enriched with Enterobacteriaceae. S. epidermidis was linked to higher gestational age and lower richness, whereas Bifidobacterium breve, a beneficial commensal, appeared later. Comparative analysis showed overlap between gut and gastric microbiota, with GR samples more dynamic and less subject-specific. Strain-level analysis revealed both individual-specific and widely shared taxa, including a pathogenic Klebsiella aerogenes strain associated with bacteremia, detectable a week before clinical isolation. These findings provide new insights into microbial colonization dynamics of preterm infants.},
}

Humans
*Infant, Premature
Infant, Newborn
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Female
Male
Intensive Care Units, Neonatal
Metagenomics
Bacteria/classification/genetics/isolation & purification
*Stomach/microbiology
Gestational Age
Enteral Nutrition

@article {pmid41203487,
year = {2025},
author = {Good, DA and Renwick, S and Caballero-Arias, H and O'Doherty, KC and Paulino, LC and Allen-Vercoe, E},
title = {Toward a Yanomami framework for ethical microbiome research.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.10.011},
pmid = {41203487},
issn = {1878-4380},
abstract = {This paper proposes an ethical framework for microbiome research with the Yanomami, an Indigenous Amazonian people, grounded in collaboration, reciprocity, and relational accountability. Key elements include dedicated funding for community-identified initiatives, sustained community-led ethical oversight, and meaningful benefit-sharing. This approach fosters trust and supports equitable, culturally aligned, and sustainable research collaboration.},
}

@article {pmid41203044,
year = {2025},
author = {Jagwani, S and Musumeci, L and Flores, L and Mackenzie, GG and Amiji, MM},
title = {Strategic modulation of the gastrointestinal microbiome to enhance pancreatic cancer immunotherapy.},
journal = {Drug discovery today},
volume = {},
number = {},
pages = {104528},
doi = {10.1016/j.drudis.2025.104528},
pmid = {41203044},
issn = {1878-5832},
abstract = {Pancreatic cancer (PC) remains one of the most lethal malignancies, characterized by aggressive progression, late detection, and limited response to current therapies. Recent research has revealed that the gastrointestinal and intratumoral microbiomes are key modulators of immune regulation, metabolism, and epigenetic pathways, influencing tumor progression and therapeutic efficacy. This review summarizes the complex microbiome-PC interplay, emphasizing microbial modulation of inflammation, immunity, and treatment resistance. We also highlight microbiome-targeted strategies, such as probiotics, prebiotics, postbiotics, and fecal microbiota transplantation, along with advanced drug-delivery platforms - including nanoparticles, engineered bacteria, and stimuli-responsive systems - for precise microbiome modulation. Integrating microbiome science with immunotherapy, nanotechnology, and epigenetic reprogramming offers promising opportunities to improve outcomes in PC.},
}

@article {pmid41203008,
year = {2025},
author = {Wang, Y and Hernandez, E and Junejo, MH and Damsky, W},
title = {Granuloma Annulare Patients Treated with JAK Inhibitors Show Cutibacterium acnes Expansion: A clue to the Mechanism Underlying Acneiform Eruptions Seen with JAK Inhibitors.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2025.10.600},
pmid = {41203008},
issn = {1523-1747},
}

@article {pmid41203007,
year = {2025},
author = {Li, H and Wang, X and Zhang, X and Mu, H and Hao, R and Li, Y and Liu, Q and Chi, R and Zhai, D},
title = {Disrupted Microbiome-Metabolome Networks Underlie Gut Barrier and Immune Imbalance in Severe Fever with Thrombocytopenia Syndrome.},
journal = {Microbes and infection},
volume = {},
number = {},
pages = {105586},
doi = {10.1016/j.micinf.2025.105586},
pmid = {41203007},
issn = {1769-714X},
abstract = {Severe fever with thrombocytopenia syndrome (SFTS) is a life-threatening tick-borne viral infection with a high mortality rate and limited treatment options. While gastrointestinal symptoms are common, the contribution of gut microbiome disruption to disease progression remains unclear. Previous studies have noted taxonomic shifts in SFTS-associated microbiota, but their functional and metabolic consequences have not been systematically characterized. We conducted an integrated metagenomic and metabolomic analysis of fecal samples from 20 SFTS patients and 20 healthy controls. At the time of admission, patients with SFTS exhibited acute-stage infection, characterized by symptoms such as fever, thrombocytopenia, and gastrointestinal disturbances. Metagenomic sequencing was used to assess the microbial gene content, taxonomic composition, and functional potential. Untargeted metabolomics analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed to profile fecal metabolites. The SFTS patients showed a significantly reduced microbial gene richness, alpha diversity, and compositional stability. Short-chain fatty acid (SCFA)-producing genera (e.g., Faecalibacterium and Roseburia) were depleted, while mucin-degrading and opportunistic taxa (e.g., Pseudomonas and Akkermansia) were enriched. Functionally, biosynthetic and homeostatic pathways were suppressed; while stress-adaptive, biofilm-forming, and virulence-associated pathways were elevated. Metabolomic profiling revealed depletion of anti-inflammatory metabolites (e.g., bile acids and curcumin sulfate) and enrichment of proinflammatory compounds (e.g., porphyrins and beta-tyvelose). Multi-omic correlation highlighted strong links between microbial disruption and altered metabolite production. In conclusion, SFTS is associated with significant alterations in the gut microbiome and its metabolic profile, which is characterized by the loss of beneficial microbial taxa and functions, alongside the emergence of virulence factors and stress-related signatures. These findings underscore the role of microbiome dysfunction in SFTS and suggest that microbiota-targeted strategies may offer supportive benefits, particularly in alleviating SFTS-associated gastrointestinal disturbances and secondary microbial imbalance.},
}

@article {pmid41202947,
year = {2025},
author = {Olsen, T and Elshorbagy, A and Johnson, JE and Nichenametla, SN and Dong, Z and Sambamurti, K and Richie, JP and Vinknes, KJ},
title = {Sulfur amino acids, metabolic health and beyond: Recent advances, translational implications, and future research considerations.},
journal = {Analytical biochemistry},
volume = {},
number = {},
pages = {116008},
doi = {10.1016/j.ab.2025.116008},
pmid = {41202947},
issn = {1096-0309},
abstract = {Dietary restriction of the sulfur amino acids methionine and cysteine (sulfur amino acid restriction [SAAR]) is a well-established paradigm for delaying disease onset and the aging process in several experimental models. In vivo, SAAR's anti-aging effects appear to be mediated by decreased growth hormone/insulin-like growth factor-1 (GH/IGF-1) signaling, along with improvement in insulin sensitivity and overall metabolic health. SAAR-fed animals also exhibit reduced regional and total adiposity, as well as oxidative stress and inflammation. Recent studies suggest that SAAR improves cognition, induces significant changes in gut microbiome composition, and that its benefits may depend on the age at which the intervention begins. In humans, observational studies have shown that higher plasma total cysteine levels are positively correlated with adiposity, insulin resistance, and an increased incidence of diabetes. Likewise, high dietary methionine and cysteine intake has been linked to increased risk of cardiovascular disease and diabetes-related mortality. Human dietary intervention studies have only been partly successful in translating the benefits of SAAR, and practical challenges for implementation remain to be addressed. This review summarizes recent advances in the SAAR field and discusses its translational potential for promoting metabolic health and reducing the risk of age-related diseases.},
}

@article {pmid41202881,
year = {2025},
author = {Hasan, MN and Wang, H and Luo, W and Du, Y and Xiong, L and Gu, L and Li, T},
title = {A Gly-β-muricholic acid and FGF15 combination therapy synergistically reduces "humanized" bile acid pool toxicity in cholestasis mice.},
journal = {Journal of lipid research},
volume = {},
number = {},
pages = {100936},
doi = {10.1016/j.jlr.2025.100936},
pmid = {41202881},
issn = {1539-7262},
abstract = {Hydrophobic bile acid-mediated hepatobiliary injury is a major driver of cholestasis progression. Most anti-cholestasis treatments being tested clinically are based on a single agent, which does not always sufficiently alleviate bile acid toxicity to slow disease progression. This study investigates a therapeutic strategy of combining glycine-conjugated β muricholic acid (Gly-βMCA) and fibroblast growth factor-15 (FGF15) to alleviate bile acid hepatobiliary toxicity in Cyp2c70 KO mice that lack endogenous muricholic acid (MCA) synthesis and have a "humanized" hydrophobic bile acid pool composition. The effects of the single and combination treatments on bile acid metabolism, liver injury, and gut microbiome were investigated in female Cyp2c70 KO mice with progressive cholangiopathy and portal fibrosis. While all three treatments significantly reduced biochemical and histologic features of liver injury, the Gly-βMCA and FGF15 combination achieved a remarkably higher reduction in both bile acid pool size and hydrophobicity than either single treatment. Mechanistically, this resulted from synergistically increased biliary hydrophilic MCA species derived from Gly-βMCA, inhibited intestine endogenous bile acid absorption by Gly-βMCA, and repressed cholesterol 7α-hydroxylase (CYP7A1) by FGF15, which counteracted the undesirable farnesoid x receptor (FXR) antagonism activity of Gly-βMCA. Furthermore, a hydrophobic bile acid pool in Cyp2c70 KO mice was associated with markedly reduced beneficial Lactobacillaceae family bacteria abundance, which was enriched by Gly-βMCA and the combination treatments. In conclusion, the Gly-βMCA and FGF15 combination shows enhanced efficacy in decreasing humanized bile acid pool size and hydrophobicity and holds potential as a therapeutic strategy to decrease bile acid burden in cholestasis.},
}

@article {pmid41202606,
year = {2025},
author = {Li, Y and Xiao, H and Liu, L and Jiang, F and Yu, E},
title = {Multi-omics reveals the mechanism of environmental concentration of microcystin-LR-induced muscle damage and nutrient loss and the role of gut-muscle axis in Nile tilapia.},
journal = {Ecotoxicology and environmental safety},
volume = {306},
number = {},
pages = {119352},
doi = {10.1016/j.ecoenv.2025.119352},
pmid = {41202606},
issn = {1090-2414},
abstract = {Microcystin-LR (MC-LR), a prevalent and highly potent cyanobacterial toxin, is generated during the outbreaks of these blooms. Despite its prevalence, there is a scarcity of information regarding the chronic effects and underlying molecular mechanisms of MC-LR at environmentally relevant concentrations on muscular toxicity in fish. Hence, we assessed the muscular toxicity of chronic MC-LR exposure via histological and biochemical analyses and delved into the underpinning mechanisms via holistic multi-omics approaches of gut microbiome, serum metabolome, muscle transcriptome and metabolome in Nile tilapia. After 60 days of MC-LR exposure, 30 μg/L MC-LR exposure significantly triggered muscular toxicity, as illustrated by decreased nutrient value, reduced myofiber diameter and sarcomere length, and diffuse dissolution of myofibrils. Transcriptomic and metabolomic analyses of muscle revealed that MC-LR exposure altered antioxidant status, protein turnover, amino acid metabolism, nucleotide synthesis and breakdown, and lipid metabolism regulation, leading to oxidative stress, inflammation response, apoptosis, decreased protein deposition and inhibited myofiber growth of Nile tilapia. Furthermore, MC-LR exposure perturbed the intestinal microbiota composition and compromised the integrity of the intestinal barrier, resulting in increased toxicity-related metabolites such as lipopolysaccharide (LPS), phenol and phenylacetic acid entering the muscle through the bloodstream, promoting muscle injury. These results provided new insight into the underlying biomolecular mechanisms and potential roles of the gut-muscle axis in MC-LR-induced muscular toxicity in aquatic animals.},
}

@article {pmid41202528,
year = {2025},
author = {Hu, X and Wu, M and Zhao, B and Xu, T and Jia, Z and Zhao, X},
title = {Construction of a succession model for the microbiome in water from submerged corpses based on single-molecule real-time sequencing.},
journal = {Forensic science international. Genetics},
volume = {81},
number = {},
pages = {103378},
doi = {10.1016/j.fsigen.2025.103378},
pmid = {41202528},
issn = {1878-0326},
abstract = {Decomposition of corpses in aquatic environments is regulated by multiple factors, and traditional methods for estimating the postmortem submerged interval (PMSI) have clear limitations. To explore the microbial succession patterns in the water of submerged corpses and their potential application in PMSI estimation, this study submerged rat carcasses in both river water and tap water, collecting water samples on days 0, 2, 6, 9, 14, 20, 27, 40, 54, and 70 postmortem. The microbial succession dynamics in the water were analyzed using single-molecule real-time sequencing. The results indicated that, although the response patterns to decomposition differed between the two water sources, key microorganisms common to various decomposition stages were identified, suggesting their important role in the process. This study characterized the microbial community succession trajectory at the species level and identified several species with potential for PMSI indication. Based on this, we constructed a simple random forest prediction model. During the 70-day decomposition period, the mean absolute errors (MAE) of the river water model and the tap water model were 5.8745 days and 4.8599 days, respectively. This research elucidates the microbial community succession patterns induced by corpse submersion in water, constructs a methodological framework for PMSI estimation based on water microbiomes, and provides crucial support for the development of more versatile PMSI inference models.},
}

@article {pmid41202150,
year = {2025},
author = {Champagne-Jorgensen, K and Gommerman, JL},
title = {Two of a kind, one with MS: Gut microbes tip the balance.},
journal = {Science immunology},
volume = {10},
number = {113},
pages = {eaed4910},
doi = {10.1126/sciimmunol.aed4910},
pmid = {41202150},
issn = {2470-9468},
mesh = {*Gastrointestinal Microbiome/immunology ; Humans ; Animals ; *Multiple Sclerosis/immunology/microbiology ; Mice ; Fecal Microbiota Transplantation ; },
abstract = {An MS twin study links ileal Lachnospiraceae to spontaneous CNS autoimmunity in mice receiving a human microbiome transplant.},
}

*Gastrointestinal Microbiome/immunology
Humans
Animals
*Multiple Sclerosis/immunology/microbiology
Mice
Fecal Microbiota Transplantation

@article {pmid41202107,
year = {2025},
author = {Pérez-Trejo, A and Aguirre-Macedo, ML and Banaszak, AT and García-Maldonado, JQ},
title = {Differentiation of the bacterial communities associated with Orbicella faveolata across different growth conditions and life-cycle stages.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0335445},
doi = {10.1371/journal.pone.0335445},
pmid = {41202107},
issn = {1932-6203},
mesh = {Animals ; *Microbiota/genetics ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; *Anthozoa/microbiology/growth & development ; *Life Cycle Stages ; Phylogeny ; High-Throughput Nucleotide Sequencing ; },
abstract = {The coral microbiome can strongly influence coral health, development, and resilience. While larval settlement is fundamental for coral restoration efforts using assisted larval propagation, post-settlement survival remains a major challenge. The study of lab-bred Orbicella faveolata settlers (LBOFS) microbiome has been proposed due to its potential role in coral adaptation processes. However, there is limited information about LBOFS bacterial communities and comparisons between different growth conditions and life-cycle stages have not been conducted. Using 16S rRNA high-throughput sequencing, we analyzed the structure and composition of LBOFS-associated bacteria and compared them to those from outplanted LBOFS and wild settlers. We also compared the microbiomes of settlers to adult colonies. The LBOFS bacterial community was composed of 4224 ASVs with the Orders Kiloniellales, Rhodobacterales, Cytophagales, Cyanobacteriales, and Flavobacteriales being the most abundant across the samples, with a rare biosphere consisting of 44.6% relative abundance. A Principal Coordinates Analysis and a PERMANOVA indicated significantly different bacterial community structures based on settler growth conditions and life-cycle stage. Linear discriminant analysis Effect Size analysis identified specific taxa whose differential abundances contributed to the observed differences. For settler growth conditions, the differences were mainly due to the Order Cyanobacteriales for LBOFS, SAR202 clade for outplanted settlers, and Microtrichales for wild samples. Statistical analysis of functional prediction showed significant differences only in nitrogen fixation for LBOFS. For life-cycle stage, LEfSe revealed that the Orders Cytophagales and Cyanobacteriales exhibited the highest differential abundances in adults and settlers, respectively. Functional prediction revealed that nitrogen fixation and oxygenic photoautotrophy were more enriched in settlers, whereas nitrate reduction and anaerobic chemoheterotrophy were more enriched in adults. This study highlighted the bacterial taxa and predicted metabolic processes that could potentially contribute to coral settler functioning, providing a valuable baseline for future research to enhance their survival rates using probiotics.},
}

Animals
*Microbiota/genetics
*Bacteria/genetics/classification
RNA, Ribosomal, 16S/genetics
*Anthozoa/microbiology/growth & development
*Life Cycle Stages
Phylogeny
High-Throughput Nucleotide Sequencing

@article {pmid41202104,
year = {2025},
author = {Huang, Y and Tang, T and Dai, X and Sun, F},
title = {Quantifying microbial interactions based on compositional data using an iterative approach for solving generalized Lotka-Volterra equations.},
journal = {PLoS computational biology},
volume = {21},
number = {11},
pages = {e1013691},
doi = {10.1371/journal.pcbi.1013691},
pmid = {41202104},
issn = {1553-7358},
abstract = {Understanding microbial interactions is fundamental for exploring population dynamics, particularly in microbial communities where interactions affect stability and host health. Generalized Lotka-Volterra (gLV) models have been widely used to investigate system dynamics but depend on absolute abundance data, which are often unavailable in microbiome studies. To address this limitation, we introduce an iterative Lotka-Volterra (iLV) model, a novel framework tailored for compositional data that leverages relative abundances and iterative refinements for parameter estimation. The iLV model features two key innovations: an adaptation of the gLV framework to compositional constraints and an iterative optimization strategy combining linear approximations with nonlinear refinements to enhance parameter estimation accuracy. Using simulations and real-world datasets, we demonstrate that iLV surpasses existing methodologies, such as the compositional LV (cLV) and the generalized LV (gLV) model, in recovering interaction coefficients and predicting species trajectories under varying noise levels and temporal resolutions. Applications to the lynx-hare predator-prey, Stylonychia pustula-P. caudatum mixed culture, and cheese microbial systems revealed consistency between predicted and observed relative abundances showcasing its accuracy and robustness. In summary, the iLV model bridges theoretical gLV models and practical compositional data analysis, offering a robust framework to infer microbial interactions and predict community dynamics using relative abundance data, with significant potential for advancing microbial research.},
}

@article {pmid41201920,
year = {2025},
author = {Soni, S and Mittal, P and Lo, JH and Yang, Y and Smbatyan, G and Lee, K and Wan, J and Kumagai, H and Yen, K and Mehta, HH and Miller, B and Torres-Gonzalez, L and Battaglin, F and Shah, UH and Bartolini, M and Zhang, W and Craig, DW and Millstein, J and Cohen, P and Lenz, HJ},
title = {Age-diet interactions significantly influence intratumoral gene expression, gut microbiome signature and tumor microenvironment in colorectal cancer.},
journal = {Neoplasia (New York, N.Y.)},
volume = {70},
number = {},
pages = {101245},
doi = {10.1016/j.neo.2025.101245},
pmid = {41201920},
issn = {1476-5586},
mesh = {*Colorectal Neoplasms/pathology/etiology/genetics/metabolism/microbiology ; Animals ; *Gastrointestinal Microbiome ; Mice ; *Tumor Microenvironment/genetics ; Humans ; *Diet ; *Gene Expression Regulation, Neoplastic ; Disease Models, Animal ; Age Factors ; Male ; *Aging ; },
abstract = {Colorectal Cancer (CRC) is the third most prevalent malignancy, leading to significant morbidity and mortality globally. Epidemiological studies suggest that chronological age and diet are among the major contributing factors correlated with the incidence of CRC. Our study aimed to provide insights into the association between age, diet, and gut microbiome in CRC using molecular techniques including RNA sequencing, cytokine analysis, and metagenomic analysis. We used syngeneic MC38 mice model divided into two age groups (old and young) and three diet groups (standard chow, calorie-restricted and high-fat). The major findings of this study are that age and diet impact intratumoral gene signaling (nuclear and mitochondrial), and hub genes we identified are associated with prognosis in CRC. Fecal microbiome analysis showed that old microbiomes have higher alpha diversity compared to young mice. Our results demonstrate that interactions between host (age) and external (diet) factors regulate tumor growth mediated by cytokines, mitochondrial derived proteins, and the gut microbiome. Collectively, our findings advance current understanding of the mechanisms by which aging, diet and gut microbiota impact CRC onset and progression though further investigation is warranted.},
}

*Colorectal Neoplasms/pathology/etiology/genetics/metabolism/microbiology
Animals
*Gastrointestinal Microbiome
Mice
*Tumor Microenvironment/genetics
Humans
*Diet
*Gene Expression Regulation, Neoplastic
Disease Models, Animal
Age Factors
Male
*Aging

@article {pmid41201910,
year = {2025},
author = {Kulal, R and Touseef Khan, M and Bhaskarrao Borse, B and Peddha, MS},
title = {Effect of encapsulated spice oleoresins on chronic unpredictable mild stress-induced depression and gut microbiome modulation in mice model.},
journal = {Nutritional neuroscience},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/1028415X.2025.2582520},
pmid = {41201910},
issn = {1476-8305},
abstract = {Depression affects millions globally, prompting the search for novel treatments. Natural compounds like spice oleoresins show promise due to their bioactive constituents. This study explores the use of Hydroxypropyl-beta-cyclodextrin (HPBCD) for nano-encapsulation to enhance the efficacy of pepper, turmeric, and chilli oleoresins in alleviating depression in a mice model. Chronic unpredictable mild stress (CUMS) was induced for 28 days, followed by administering nano-encapsulated oleoresins (25 mg/kg). Behavioural analyses revealed improved activity, while neurochemical studies showed increased serotonin and dopamine levels with reduced monoamine oxidase (MAO) activity. Western blot highlighted changes in BDNF, supported by histopathological evidence of neuroprotection. Biochemical assays indicated reduced oxidative stress, acetylcholinesterase activity, and enhanced catalase and superoxide dismutase levels. 16S rRNA sequencing revealed improved gut microbiota, with increased beneficial bacteria. Notably, nano-encapsulated chilli oleoresin exhibited the highest efficacy. These findings support the multi-targeted potential of nano-encapsulated spice oleoresins as complementary treatments for depression, addressing neurobiological and gut-related factors.},
}

@article {pmid41201906,
year = {2025},
author = {Gao, Y and Zhu, T and Zhang, Z and Hu, H and Wang, Q and Liu, H and Xiong, L},
title = {Characterization of a Cold-Active Xylanase from Paenibacillus sp. XP01, and Its Application in Hydrolyzing Alkali-Pretreated Corncob Residues.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c08788},
pmid = {41201906},
issn = {1520-5118},
abstract = {Xylan, a key hemicellulose in agricultural byproducts, is significantly underutilized in biorefineries. The human gut microbiome, with its diverse enzymes, holds great potential for biocatalyst discovery. In this study, Paenibacillus sp. XP01, a xylan-degrading strain, was isolated from human feces. Genomic analysis identified a GH11 endo-β-1,4-xylanase, designated Xyn157, which exhibited a cold-active property. It retained 47% residual activity at 0 °C and 72% at 4 °C. It also exhibited catalytic activity against insoluble xylan in corncob. Enzymatic profiling confirmed its endoacting mode, with xylotriose as the minimum substrate and branched chains impairing efficiency. Xyn157 hydrolyzed alkali-pretreated corncob residues (ACR) to produce xylo-oligosaccharide (XOS), with a yield of 6.4% (w/w). In vitro fermentation of Xyn157-treated ACR, which produced hydrolysis products of ACR (CRH), significantly promoted the growth of beneficial bacteria (e.g., Bifidobacterium, Ligilactobacillus), suppressed pathogens (e.g., Enterobacter and Klebsiella), and boosted short-chain fatty acid (SCFA) production compared to the ACR group. These findings highlight Xyn157's potential to convert insoluble xylan in ACR into functional prebiotics, expanding its applications in waste-to-prebiotic bioprocessing.},
}

@article {pmid41201826,
year = {2025},
author = {Sorger, Z and Sengupta, P and Beier-Heuchert, K and Bautor, J and Parker, JE and Kemen, E and Doehlemann, G},
title = {GH25 lysozyme mediates tripartite interkingdom interactions and microbial competition on the plant leaf surface.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {45},
pages = {e2510124122},
doi = {10.1073/pnas.2510124122},
pmid = {41201826},
issn = {1091-6490},
support = {390686111//Deutsche Forschungsgemeinschaft (DFG)/ ; DECRyPT//Deutsche Forschungsgemeinschaft (DFG)/ ; },
mesh = {*Arabidopsis/microbiology ; *Muramidase/metabolism/genetics ; *Plant Leaves/microbiology ; Plant Diseases/microbiology ; Microbiota ; Oomycetes ; },
abstract = {Microbial communities inhabiting plants have emerged as crucial factors in regulating plant health and defense against disease-causing pathogens. The yeast Moesziomyces bullatus ex. Albugo (MbA) on Arabidopsis produces a glycoside hydrolase 25 (GH25) protein that regulates the leaf microbiome by antagonizing the pathogenic oomycete Albugo laibachii. Applying MbA or GH25 rescued Arabidopsis thaliana shoot fresh weight under A. laibachii infection, highlighting their crop protection potential. Interaction assays revealed no antagonistic activity of GH25 against other plant pathogenic oomycetes or fungi besides A. laibachii. We identified a community of bacteria closely associated with A. laibachii. Three of these bacteria are inhibited by GH25 and one of them, Curtobacterium sp. could override the inhibition of A. laibachii by MbA. This points to a tripartite antagonism where Curtobacterium and A. laibachii protect each other from MbA. Moreover, Curtobacterium selectively inhibits other A. laibachii-associated bacteria not targeted by MbA but that themselves suppress A. laibachii. This study uncovers an interkingdom network where GH25 lysozyme shapes microbial interactions between yeast, oomycete, and associated bacteria.},
}

*Arabidopsis/microbiology
*Muramidase/metabolism/genetics
*Plant Leaves/microbiology
Plant Diseases/microbiology
Microbiota
Oomycetes

@article {pmid41201785,
year = {2025},
author = {Baker, SG and Morton, CO and Green, H},
title = {The impact of freezing temperatures on soft tissue and microbial decomposition using human and porcine remains: a pilot study.},
journal = {Forensic science, medicine, and pathology},
volume = {},
number = {},
pages = {},
pmid = {41201785},
issn = {1556-2891},
abstract = {Environmental factors such as temperature, vertebrate and invertebrate activity and microbial succession patterns are important variables driving the decomposition process. However, the effects of low temperatures, specifically freezing on how a body decomposes are less understood. This pilot project aimed to determine the taphonomic effects of freezing on morphological changes during decomposition and the microbiome in an Australian context. Two human donors (one frozen, one non-frozen) and two frozen and two non-frozen Sus scrofa (pig) carcasses (n = 4) were allowed to decompose on the surface of woodlands for 12-weeks during summer 2017. Visual morphological changes were recorded, and microbial swabs were collected at regular intervals and analysed via real-time PCR to assess differences in bacterial community structure. Results indicated clear differences in decomposition patterns between frozen and non-frozen remains. Frozen remains were slow to enter 'early' decomposition but first to skeletonise. Microbial results suggest that patterns in community structure between bacteria may indicate if a body has been frozen at or around the time of death. This research suggests that quantifying the microbiome present during the fresh and early stages of decomposition and noting observations of an outside-in decomposition pattern may be a useful tool in identifying if remains have experienced extreme cold temperatures at the time of death. This knowledge could improve approaches to PMI estimation, particularly if the remains have experienced a freeze-thaw event after death.},
}

@article {pmid41201733,
year = {2025},
author = {Saleh, RM and Hassan, OM},
title = {The infectome framework: linking polymicrobial ecology and biofilm dynamics to precision diagnostic approaches.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {41201733},
issn = {1439-0973},
abstract = {Chronic infections are a persistent global health problem and are frequently sustained by polymicrobial communities rather than by a single pathogen. This review brings together current evidence for the infectome concept, defined as the dynamic set of pathogenic or pathobiont taxa in the host, their shared functional capacities, and the interactions that connect them. We analyze how community-level processes promote persistence, cause diagnostic failure, and drive therapeutic resistance, with emphasis on multispecies biofilms, quorum sensing, horizontal gene transfer, metabolic cooperation, and immune modulation. We also highlight advances in multi-omics and computational integration that now permit high-resolution infectome profiling and reveal taxa and interspecies networks that are not captured by routine culture. Clinical examples such as periodontitis, bacterial vaginosis, chronic rhinosinusitis, device-associated infections, and recurrent urinary tract infections show the translational value of this shift. On the therapeutic side, we discuss infectome-informed options including antivirulence agents, biofilm-disrupting enzymes, bacteriophages and lysins, community-wide susceptibility-guided regimens, and microbiome-restoration strategies. Finally, we identify the main requirements for the field: standardized sampling and analytic workflows, reproducible infectome signatures linked to clinical outcomes, and trial designs able to capture ecological dynamics and meet regulatory expectations for community-targeted interventions. Adopting an infectome perspective can enable precision infectiology and reshape the management of chronic and recurrent infections.},
}

@article {pmid41201719,
year = {2025},
author = {Gautam, P and Vishwakarma, RK and Nath, M and Nath, G and Pathak, A},
title = {Microbiota Dysbiosis in Amyotrophic Lateral Sclerosis: A Systematic Review of Human Studies.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {10},
pmid = {41201719},
issn = {1559-1182},
mesh = {*Amyotrophic Lateral Sclerosis/microbiology/complications ; Humans ; *Dysbiosis/microbiology/complications ; *Gastrointestinal Microbiome/physiology ; },
abstract = {Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by progressive motor neuron degeneration. Despite intensive research, its pathogenesis remains poorly understood. Recent insights suggest a pivotal role of the gut microbiota in modulating neuroinflammation and neurodegeneration via the gut-brain axis. This systematic review aims to synthesize clinical evidence on gut microbiota dysbiosis in ALS, exploring microbial and metabolic alterations and their associations with disease progression and severity. A comprehensive literature search was conducted across PubMed, Embase, Scopus, Web of Science, and other databases up to May 10, 2024, adhering to PRISMA 2020 guidelines. Eighteen eligible human studies were selected based on predefined inclusion criteria. Data on microbial diversity, taxonomic shifts, metabolite profiles, and clinical correlations were extracted and assessed using a modified Newcastle-Ottawa Scale. Most studies reported altered microbial diversity, reduced butyrate-producing bacteria (e.g., Faecalibacterium, Roseburia), and increased pro-inflammatory taxa (e.g., Escherichia coli, Bacteroides) in ALS. Integrated microbiome-metabolome analyses revealed disruptions in SCFAs, bile acids, and lipid metabolism, some correlating with ALSFRS-R scores and cognitive impairment. Although some studies showed minimal or no differences, the overall evidence supports a link between dysbiosis and ALS pathophysiology. Probiotic trials demonstrated limited efficacy, highlighting the need for targeted, patient-specific interventions. Gut microbiota dysbiosis is increasingly recognized as a contributor to ALS progression. However, methodological variability, small sample sizes, and limited longitudinal data restrict definitive conclusions. Future research should employ standardized, multi-omics approaches and larger cohorts to clarify causal links and develop microbiome-informed diagnostics and therapies for ALS.},
}

*Amyotrophic Lateral Sclerosis/microbiology/complications
Humans
*Dysbiosis/microbiology/complications
*Gastrointestinal Microbiome/physiology

@article {pmid41201258,
year = {2025},
author = {Zhang, Y and Wang, M and Sun, Y and Gao, H and Su, X},
title = {Function inference of million-scale microbiomes using multi-GPU acceleration.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0207225},
doi = {10.1128/spectrum.02072-25},
pmid = {41201258},
issn = {2165-0497},
abstract = {Amplicon sequencing enables taxonomic profiling of microbial communities but offers limited insight into their functional potential. Existing tools such as Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) infer functions through phylogenetic placement and ancestral state reconstruction; however, these methods are computationally intensive and inefficient for large-scale data sets. To address these challenges, we introduce microbiome graphics processing unit (GPU)-based function inference (MGFunc), an ultra-high-throughput framework for microbiome functional inference leveraging multi-GPU acceleration. MGFunc transforms functional prediction for amplicons into standardized matrix multiplication using a pre-constructed genomic content network. It further integrates split data loading, matrix partition, and dynamic scheduling across multiple GPUs, enabling scalable, batch-wise analysis of millions of samples under limited GPU memory and system random access memory (RAM). Compared to PICRUSt2, MGFunc achieves speedups of up to several hundred thousand times, completing the functional interpretation of one million samples within one minute by four GPUs on a single server. This work provides a highly efficient and low-latency solution for ultra-large microbiome data sets functional inference, paving the way for global-scale microbiome studies. The MGFunc software is freely accessible at https://github.com/qdu-bioinfo/MGFunc.IMPORTANCEUnderstanding what microbes do-their functions-is essential for studying health, disease, agriculture, and the environment. While cost-effective sequencing methods like 16S rRNA gene analysis are widely used, they do not directly reveal microbial functions. Existing tools that predict these functions from 16S data are often too slow for today's large studies involving hundreds of thousands of samples. In this work, we developed microbiome graphics processing unit (GPU)-based function inference (MGFunc), a new method that predicts microbial functions quickly and accurately by using GPUs and a streamlined mathematical approach. MGFunc can analyze over one million samples in under a minute, making it one of the fastest tools available. This enables researchers to study the functional potential of microbial communities on a truly global and population scale.},
}

@article {pmid41201243,
year = {2025},
author = {Nash, J and Tremble, K and Schadt, C and Cregger, MA and Bryan, C and Vilgalys, R},
title = {Time-series RNA metabarcoding of the active Populus tremuloides root microbiome reveals hidden temporal dynamics and dormant core members.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0028525},
doi = {10.1128/msystems.00285-25},
pmid = {41201243},
issn = {2379-5077},
abstract = {UNLABELLED: The rhizosphere is a critical interface between plant roots and soil, harboring diverse microbial communities that are essential to plant and ecosystem health. Although these communities exhibit stark temporal dynamics, their dormancy/activity transitions remain poorly understood. Such transitions may enable microbes to rapidly adjust functional contributions faster than community turnover alone would allow. Here, we used RNA metabarcoding to characterize the active fraction of microbial communities on the roots of quaking aspen (Populus tremuloides) in a time-series study across a natural environmental gradient. We explore cryptic temporal microbial community dynamics of rhizosphere communities at the ecosystem scale. The active rhizosphere bacterial and fungal communities were more temporally dynamic than total communities, while total communities exhibited a stronger response to site-specific conditions. Notably, some core microbiome members were often inactive, yielding a smaller "active core" subset. The fungal endophyte Hyaloscypha finlandica was the only microbe that was both present and active in all plots across all timepoints. Soil temperature strongly influenced both total and active community composition, with the fungal class Eurotiomycetes showing a temperature-dependent seasonal decline in abundance. Together, these results reveal that modulation of microbial activity levels is a key mechanism by which the plant root holobiont responds to environmental variation, and that even dominant symbionts may frequently persist in dormancy within the rhizosphere.

IMPORTANCE: Members of the rhizosphere exhibit dynamic patterns of activity and dormancy. This study stresses the need to focus on active microbial communities to detect temporal changes in plant microbiomes. Additionally, the metabolic activity of microbes should be considered a key determinant of core microbiome membership. Parallel patterns in active community dynamics between fungal and bacterial communities provide a potentially generalizable rule of microbial community temporal dynamics in plant rhizospheres.},
}

@article {pmid41201238,
year = {2025},
author = {Rees, NP and Conway, J and Dugan, B and Amir, SS and Parker, A and Carding, SR and Duggal, NA},
title = {Defining Microbiota-Derived Metabolite Butyrate as a Senomorphic: Therapeutic Potential in the Age-Related T Cell Senescence.},
journal = {Aging cell},
volume = {},
number = {},
pages = {e70257},
doi = {10.1111/acel.70257},
pmid = {41201238},
issn = {1474-9726},
abstract = {Advancing age is accompanied by an accumulation of senescent T cells that secrete pro-inflammatory senescence-associated secretory phenotype (SASP) molecules. Gut-microbiota-derived signals are increasingly recognised as immunomodulators. In the current study, we demonstrated that ageing and the accumulation of senescent T cells are accompanied by a reduction in microbial-derived short-chain fatty acids (SCFAs). Culturing aged T cells in the presence of butyrate suppresses the induction of a senescence phenotype and inhibits the secretion of pro-inflammatory SASP factors, such as IL6 and IL8. Administration of faecal supernatants from young mice rich in butyrate prevented in vivo accumulation of senescent spleen cells in aged mice. The molecular pathways governing butyrate's senomorphic potential include a reduced expression of DNA damage markers, lower mitochondrial ROS accumulation, and downregulation of mTOR activation, which negatively regulates the transcription factor NFκB. Our findings establish butyrate as a potent senomorphic agent and provide the evidence base for future microbiome restitution intervention trials using butyrate supplements for combating T cell senescence, ultimately reducing inflammation and combating age-related pathologies to extend lifelong health.},
}

@article {pmid41201223,
year = {2025},
author = {Zha, Y and Xiang, M and Zuo, Y and Liu, D and Wang, Q},
title = {High-dose Dietary Fibre Supplementation Enhances the Gut Microbiome, Health, and Athletic Performance of College Basketball Players.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {5},
pages = {37069},
doi = {10.31083/IJVNR37069},
pmid = {41201223},
issn = {0300-9831},
support = {2019YFF0301702//National Key R&D Program of China/ ; XJ2022000601//Doctoral Research Fund/ ; },
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/drug effects ; *Basketball/physiology ; *Athletic Performance/physiology ; Young Adult ; *Dietary Fiber/administration & dosage ; Adolescent ; *Dietary Supplements ; Adult ; Body Composition ; Athletes ; Universities ; },
abstract = {BACKGROUND: Prolonged or intense exercise can disrupt gastrointestinal (GI) function and gut microbiota, impairing athletic performance. Dietary fibre supplementation may enhance gut microbiota diversity, improve body composition, and promote recovery in athletes. This study aimed to explore the effects of dietary fibre supplementation at two doses for 8 weeks on these aspects in college basketball players.

METHODS: Twenty male college basketball players (aged 17-25 years) were randomly assigned to a high-dose group (HDG; 10 participants; 6.84 g/day dietary fibre) or a low-dose group (LDG; 10 participants; 3.24 g/day dietary fibre). The participants consumed fibre-enriched meals daily while maintaining their regular training schedules. The outcome measures included gut microbiota diversity (metagenomic sequencing), body composition, fatigue recovery markers, glucose and lipid metabolism, and athletic performance. Statistical analyses included paired and independent t tests for within- and between-group comparisons and Spearman's correlation analysis to assess the relationships between gut microbiota and biochemical markers.

RESULTS: One participant in the high-dose group withdrew, and nineteen ultimately completed the study. Both groups showed significant within-group improvements (p < 0.05) in body weight (HDG: -2.77 ± 0.76 kg; LDG: -2.40 ± 0.67 kg), body fat percentage (HDG: -1.87 ± 0.69; LDG: -1.49 ± 0.45), cortisol (HDG: -6.79 ± 4.26 μg/dL; LDG: -4.5 ± 4.84 μg/dL), maximum power (HDG: 27.16 ± 9.77 W; LDG: 14.50 ± 9.43 W), maximal oxygen uptake (HDG: 8.78 ± 0.97; LDG: 6.90 ± 1.37), and half-court triangle run times (HDG: -0.48 ± 0.36 s; LDG: -0.25 ± 0.20 s). Meanwhile, fasting blood glucose significantly decreased (0.91 ± 0.55 mmol/L; p = 0.001), and the gut microbiome changes were more stable in the HDG, whereas the LDG presented greater shifts in microbial diversity. No significant between-group differences were observed.

CONCLUSIONS: Dietary fibre supplementation improved the gut microbiome composition, body composition, fatigue recovery, and athletic performance of college basketball players, regardless of dosage. Further studies are needed to evaluate higher doses and specific fibre types.},
}

Humans
Male
*Gastrointestinal Microbiome/drug effects
*Basketball/physiology
*Athletic Performance/physiology
Young Adult
*Dietary Fiber/administration & dosage
Adolescent
*Dietary Supplements
Adult
Body Composition
Athletes
Universities

@article {pmid41201222,
year = {2025},
author = {Zheng, Y and Gao, Z and Sun, L and Shi, J and Song, J and Ye, W},
title = {Calcium and Gastrointestinal Disorders: Mechanistic Insights and Therapeutic Interventions.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {5},
pages = {39241},
doi = {10.31083/IJVNR39241},
pmid = {41201222},
issn = {0300-9831},
support = {ZA CACM 2024002//Clinical Research Project of the China Association of ChineseMedicine/ ; 2020SJZDXK13//Health Commission of Zhejiang Chinese Medical University Hangzhou Hospital of Traditional Chinese Medical/ ; },
mesh = {Humans ; *Gastrointestinal Diseases/drug therapy/therapy/metabolism/microbiology ; *Calcium/metabolism ; Gastrointestinal Microbiome ; Receptors, Calcium-Sensing/metabolism ; Dietary Supplements ; *Calcium, Dietary/administration & dosage ; Hypocalcemia ; },
abstract = {Calcium plays a central role in gastrointestinal (GI) physiology through regulating smooth muscle contractility, acid secretion, epithelial barrier integrity, and immune signaling. The dysregulation of calcium homeostasis has been increasingly implicated in the pathogenesis of GI disorders, including colorectal cancer, inflammatory bowel disease, peptic ulcer, and pancreatitis. Specifically, aberrant calcium-sensing receptor (CaSR) signaling has emerged as a critical molecular mechanism in colorectal tumorigenesis; meanwhile, calcium-mediated pathways influence gastric acid production and intestinal motility. This review critically evaluated recent advances in calcium signaling within the GI tract, highlighting the crosstalk involved with the gut microbiota and the roles of downstream effectors, including transient receptor potential vanilloid type 6 and store-operated calcium entry. This review also examined the therapeutic implications of calcium supplementation across various GI conditions, including bioavailability challenges under different disease states and nutrient interactions involving vitamin D and phosphate. Our review further addresses the role of calcium in mucosal immunity, the clinical relevance of hypocalcemia in GI diseases, and the potential of microbiome-guided nutritional interventions. However, despite growing mechanistic insights, considerable gaps remain in understanding host-microbiota-calcium interactions, genotype-specific responses to calcium, and long-term clinical outcomes. Thus, future research should clarify the dose-response relationships, stratify patient populations by CaSR polymorphisms and microbiome profiles, and establish precision strategies for calcium-based interventions in digestive health.},
}

Humans
*Gastrointestinal Diseases/drug therapy/therapy/metabolism/microbiology
*Calcium/metabolism
Gastrointestinal Microbiome
Receptors, Calcium-Sensing/metabolism
Dietary Supplements
*Calcium, Dietary/administration & dosage
Hypocalcemia

@article {pmid41200858,
year = {2025},
author = {Huang, Z and Brot, L and Fatouh, R and Bredon, M and Creusot, L and Lefèvre, A and Lamazière, A and Lefevre, JH and Emond, P and Planchais, J and Roux, X and Sokol, H and Rolhion, N},
title = {Saccharomyces boulardii CNCM I-745 mitigates antibiotic-induced gut microbiome functional alterations independently of the host.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2575924},
doi = {10.1080/19490976.2025.2575924},
pmid = {41200858},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Saccharomyces boulardii/physiology ; *Probiotics/pharmacology/administration & dosage ; *Anti-Bacterial Agents/adverse effects/pharmacology ; Vancomycin/adverse effects ; Dysbiosis/chemically induced/microbiology ; Cytokines/metabolism ; Leukocytes, Mononuclear/drug effects/immunology ; Amoxicillin-Potassium Clavulanate Combination/adverse effects ; Intestinal Mucosa/microbiology/drug effects/immunology ; Bacteria/drug effects/genetics/classification/growth & development ; },
abstract = {The probiotic Saccharomyces boulardii CNCM I-745 (Sb) is widely prescribed to alleviate antibiotic-induced diarrhea, yet its mode of action, particularly its potential direct effects on the gut microbiome, remains incompletely defined. This study aimed to evaluate whether Sb can directly mitigate antibiotic-induced gut microbiota dysbiosis and influence downstream host immune response. Using both static (MiPro) and dynamic (SHIME[®]) in vitro gut microbiota models, we assessed the effects of Sb supplementation under antibiotic treatment with amoxicillin/clavulanic acid (AMC) or vancomycin (Van). Quantitative microbiome profiling integrated with targeted metabolomics showed that Sb helped stabilize bacterial biomass, partially preserved metabolic functions, and restored the production of immunoregulatory metabolites propionate and indole-3-propionic acid under AMC treatment. In addition, ex vivo exposure of primary human immune cells (PBMCs) and intestinal mucosal tissue to microbiota modulated by Sb led to a significant reduction in pro-inflammatory cytokine secretion compared to microbiota not supplemented with Sb. Collectively, these results support a beneficial role for S. boulardii CNCM I-745 in preserving directly gut microbiome function and supporting host immune homeostasis during antibiotic treatment, particularly under AMC exposure. Our findings advance the understanding of probiotic-antibiotic-gut microbiome interactions, thereby guiding future optimization of microbiome-targeted adjuvant therapies.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Saccharomyces boulardii/physiology
*Probiotics/pharmacology/administration & dosage
*Anti-Bacterial Agents/adverse effects/pharmacology
Vancomycin/adverse effects
Dysbiosis/chemically induced/microbiology
Cytokines/metabolism
Leukocytes, Mononuclear/drug effects/immunology
Amoxicillin-Potassium Clavulanate Combination/adverse effects
Intestinal Mucosa/microbiology/drug effects/immunology
Bacteria/drug effects/genetics/classification/growth & development

@article {pmid41200610,
year = {2025},
author = {Ur Rehman, M and Saeed, H and Omer, O and Tashfeen, S},
title = {Gut Microbiota-Directed Interventions in Type 2 Diabetes: A Systematic Review of Clinical Outcomes and Complication Risk.},
journal = {Cureus},
volume = {17},
number = {10},
pages = {e95045},
pmid = {41200610},
issn = {2168-8184},
abstract = {Type 2 diabetes mellitus is increasingly recognized as a disorder not only of glucose metabolism but also of gut microbial imbalance, with emerging evidence suggesting a bidirectional link between microbiome composition and metabolic dysfunction. Recent randomized controlled trials and dietary interventions highlight that specific microbial taxa, such as butyrate-producing bacteria and Akkermansia muciniphila, play crucial roles in regulating insulin sensitivity, lipid metabolism, and systemic inflammation. Modulation of the gut-metabolic axis through probiotics, prebiotics, dietary strategies, and pharmacological agents demonstrates promising effects on glycemic control, cardiometabolic risk reduction, and attenuation of diabetes-related complications, though results vary across populations and intervention types. The variability in outcomes underscores the importance of personalized approaches, where baseline microbiota signatures may dictate therapeutic response. Despite encouraging findings, many studies remain limited by short duration, small sample size, and heterogeneity in microbiome analysis methods. This review synthesizes current evidence, highlights mechanistic insights linking microbial shifts to metabolic benefits, and identifies gaps in the literature. By doing so, it emphasizes the potential of microbiome-directed therapies as adjunctive strategies in the prevention and management of type 2 diabetes and its complications.},
}

@article {pmid41200544,
year = {2025},
author = {Cheng, J and Gao, Y and Lv, H and Li, J and Sun, X and An, T and Liu, H and Wang, J and Zhang, H and Wang, H and Zou, S and Fan, Z and Chen, Y},
title = {LGG/LAC-MMT combination mitigates AFB1-induced liver and intestinal injury in mice based on intestinal microbiota modulation.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1654294},
pmid = {41200544},
issn = {2297-1769},
abstract = {AFB1 induces hepatotoxicity and enterotoxicity. Lactobacillus acidophilus (LAC) and Lactobacillus rhamnosus (LGG), both belonging to LAB, have strong binding affinity for AFB1. Montmorillonite (MMT) not only adsorbs AFB1 but also serves as a carrier for LAB, thereby enhancing their colonization ability and prolonging their survival. Despite the unclear effects of LGG/LAC-MMT combination on AFB1-induced tissue injury and intestinal microbiota disruption, this study aimed to determine whether it could effectively alleviate tissue damage from AFB1 exposure and enhance LAB colonization capacity in mouse intestines. Separately, LGG (2 × 10[9] cfu/mL) and LAC (2 × 10[9] cfu/mL) were combined with MMT (0.5 mg/kg), and the AFB1-intoxicated mice were gavaged with the mixtures for 4 weeks. Findings suggested that LGG, LAC, and MMT supplementation restored oxidative stress and inflammatory caused by AFB1 to some degree. Furthermore, they altered the intestinal microbiota structure, enhancing the colonization ability of LABs, thereby alleviating liver and intestinal injury. The combination of LGG/LAC-MMT was more effective, especially LAC-MMT. Overall, LGG/LAC-MMT exhibits a synergistic effect and can effectively ameliorate AFB1-induced tissue injury and intestinal microbiota disorder.},
}

@article {pmid41200416,
year = {2025},
author = {Shunmugavelu, K and Shakthi Chakravarthy, BG and Priya, S},
title = {Determination of Fusobacterium nucleatum levels in patients with periodontal disease and oral squamous cell carcinoma.},
journal = {GMS hygiene and infection control},
volume = {20},
number = {},
pages = {Doc60},
pmid = {41200416},
issn = {2196-5226},
abstract = {INTRODUCTION: Fusobacterium (F.) nucleatum, a Gram-negative anaerobic bacterium, has been implicated in both periodontal disease and oral squamous cell carcinoma (OSCC). This review aims to evaluate the levels of F. nucleatum in patients with periodontal disease and OSCC, exploring its potential role in the pathogenesis.

METHODS: A comprehensive literature search was conducted across multiple databases, identifying studies that measured F. nucleatum levels in periodontal disease and OSCC tissues.

RESULTS: A higher prevalence of F. nucleatum exists in both periodontal disease and OSCC tissues compared to healthy controls.

CONCLUSION: It appears that there is a link between infection with F. nucleatum and the development of these oral diseases. Further research is warranted to elucidate the mechanisms underlying this association and to explore potential therapeutic interventions targeting F. nucleatum.},
}

@article {pmid41200410,
year = {2025},
author = {Danjuma, FY and Dashen, MM and Ngene, AC and Egbere, OJ},
title = {Prevalence of bacterial vaginosis and its associated risk factors among women of reproductive age attending Jos University Teaching Hospital, Plateau State, Nigeria.},
journal = {GMS hygiene and infection control},
volume = {20},
number = {},
pages = {Doc51},
pmid = {41200410},
issn = {2196-5226},
abstract = {INTRODUCTION: Bacterial vaginosis (BV) remains the most common cause of abnormal vaginal discharge due to altered vaginal flora with decreased Lactobacillus spp. and increased anaerobic bacteria. The objectives of this study were to establish the prevalence of BV and its risk factors among women of reproductive age.

METHOD: This cross-sectional descriptive survey was conducted among 220 non-pregnant women of reproductive age attending Jos University Teaching Hospital (JUTH) in Plateau state, north central Nigeria, between August 2021 and January 2022, in which 110 women were asymptomatic, and 110 women were symptomatic. Self-administered questionnaires were used to identify the sociodemographic status and predisposing factors of the participants. Positive BV diagnosis was made using the Nugent scoring system and bacterial species were identified on selective media. A descriptive analysis was performed using the Chi-squared test at a 95% confidence interval to determine the prevalence of BV and its associated risk factors.

RESULTS: The overall BV prevalence was 33.6%. BV was higher in symptomatic women (39.1%) than in asymptomatic women (28.2%). No correlation was found between BV and demography, knowledge, or health behaviour, including age, education, marital status, number of children, occupation, income, alcohol, tobacco smoking, or sexual as well as hygienic behaviour (p≥0.05). A total of 328 bacterial isolates from 16 species were identified, with Enterococcus (E.) faecalis being the most prevalent species, accounting for 39.3% of the total isolates. Other species isolated include Staphylococcus (S.) saprophyticus (13.6%), S. epidermidis (13.0%), S. aureus (4.7%), Streptococcus (Sr.) agalactiae (5.9%), Klebsiella (K.) pneumoniae (4.1%), Proteus (P.) mirabilis (2.4%), and Pseudomonas (P.) aeruginosa (3.6%) in the symptomatic group. S. saprophyticus (10,7%), S. aureus (3.8%), K. pneumoniae (2.5%), and P. aeruginosa (1.9%) were isolated in the asymptomatic group. P. mirabilis was not detected. Lactobacillus spp. were present but not dominant, with an overall prevalence of 8.2%.

CONCLUSION: The observed diversity in vaginal microbiota, particularly the higher prevalence of E. faecalis in asymptomatic women, suggests the complexity of microbial interactions. The low prevalence of Lactobacillus spp. indicates a potential risk for infections, while the presence of potentially pathogenic bacteria such as S. saprophyticus and Streptococcus agalactiae underscores the need for further research. Overall, the understanding of the vaginal microbiome is crucial for developing effective healthcare interventions for managing BV.},
}

@article {pmid41200380,
year = {2025},
author = {Mojgani, N and Bagheri, M and Ashique, S and Hosseini, SH and Hussain, A and Moharrami, M and Zahmatkesh, A and Moradi, M},
title = {Probiotics and postbiotics: a promising prophylactic measure for American foulbrood and European foulbrood diseases of honey bees.},
journal = {Veterinary research forum : an international quarterly journal},
volume = {16},
number = {10},
pages = {545-555},
pmid = {41200380},
issn = {2008-8140},
abstract = {American foulbrood (AFB) and European foulbrood (EFB) diseases caused by Paenibacillus larvae and Meliscococcus plutonius are prevalent honeybee brood diseases that pose significant economic challenges to the apiculture industry globally. Antibiotic treatment has led to the emergence of antibiotic-resistant strains, encouraging the search for alternative and safe measures to effectively control these diseases. Honeybee gut microbiomes have proven effects on all spectra of honeybee health by enhancing resistance to several diseases via immune modulation and the production of different antimicrobial metabolites. The major part of the gut microbiota is identified as probiotic bacteria, which are live microorganisms that, when administered in adequate amounts, confer health benefits to the host. Probiotics have shown promising health benefits for honeybees. Honeybee gut probiotics provide protection via the production of different metabolites (postbiotics), such as hydrogen peroxide, vitamins, organic acids, free fatty acids, bacteriocins, neurotransmitters, secreted bio-surfactants, and reactive oxygen species. Vast numbers of these gut bacteria and their postbiotics have wide-spectrum antibacterial effects on AFB and EFB. This review highlights the significance of the honeybee gut microbial community, its probiotic potency, and the role of postbiotic metabolites as safe prophylactic measures for preventing AFB and EFB diseases in honeybees.},
}

@article {pmid41200350,
year = {2025},
author = {Mohammadzadeh, P and Samadi, N and Mohammadi, B},
title = {Revolutionizing oronasal fistula treatment in Felis silvestris: Integrating bioengineered solutions and microbiome insights for enhanced healing.},
journal = {Open veterinary journal},
volume = {15},
number = {9},
pages = {4775-4788},
pmid = {41200350},
issn = {2218-6050},
mesh = {Male ; Animals ; Cats ; Microbiota ; *Oral Fistula/veterinary/therapy ; Wound Healing ; Tissue Scaffolds ; Bioengineering ; Polyethylene Glycols ; },
abstract = {BACKGROUND: Oronasal fistulas (ONFs) present significant therapeutic challenges in veterinary medicine, particularly in patients with comorbidities, such as chronic kidney disease. This case report demonstrates an innovative bioengineered approach for ONF repair in Felis silvestris that combines autologous biomaterials with microbiome analysis.

CASE DESCRIPTION: A 15-year-old male European wildcat with a chronic traumatic ONF (11 × 8 mm) and concurrent International Renal Interest Society Stage 2 chronic kidney disease received a customized implant composed of autologous platelet-rich fibrin (PRF), bone marrow aspirate, and a 3D-printed polyethylene glycol diacrylate (PEGDA) scaffold. PEGDA was selected for its high biocompatibility and rapid photopolymerization. Healing was monitored via computed tomography imaging and 16S rRNA sequencing. The results demonstrated significant microbial dysbiosis post-injury (Shannon index: 5.2 ± 0.3 vs. 3.1 ± 0.4; p < 0.05), with opportunistic pathogen enrichment (Enterococcus faecalis: 0.5% → 12.8%). Antibiotics reduced the bacterial load by 99.9% (p < 0.001) but did not improve the closure rate (p = 0.89), underscoring the mechanical role of the scaffold.

CONCLUSION: The bioengineered implant facilitated complete mucosal integration and osteoconduction at the 10-month follow-up, demonstrating promise for complex ONF repair. However, the single-case design limits the generalizability.},
}

Male
Animals
Cats
Microbiota
*Oral Fistula/veterinary/therapy
Wound Healing
Tissue Scaffolds
Bioengineering
Polyethylene Glycols

@article {pmid41200191,
year = {2025},
author = {Qi, P and Gong, F and Leng, M and Wei, Z},
title = {Beneficial perspective on Staphylococcus epidermidis: a crucial species for skin homeostasis and pathogen defense.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1674392},
pmid = {41200191},
issn = {1664-3224},
mesh = {*Staphylococcus epidermidis/immunology/physiology ; Humans ; *Homeostasis ; *Skin/microbiology/immunology ; Biofilms/growth & development ; Animals ; Microbiota/immunology ; *Staphylococcal Infections/immunology/microbiology ; Host-Pathogen Interactions/immunology ; },
abstract = {Human skin harbors a diverse microbiome that shapes immune function, protects against pathogens, and sustains tissue homeostasis. Among its dominant members, Staphylococcus epidermidis-a coagulase-negative staphylococcus-was long considered primarily an opportunistic pathogen, especially in the context of biofilm formation and implant-associated infections. However, emerging evidence reframes S. epidermidis as an active commensal, capable of controlling inflammation, supporting antimicrobial defenses, and stabilizing the cutaneous barrier. These dual roles are largely determined by its extensive strain-level heterogeneity and dynamic colonization strategies. Here, we review current progress in understanding the ecological versatility of S. epidermidis, with particular focus on its potential benefits, its diversity and colonization dynamics, and the balance of costs and benefits associated with its presence on human skin.},
}

*Staphylococcus epidermidis/immunology/physiology
Humans
*Homeostasis
*Skin/microbiology/immunology
Biofilms/growth & development
Animals
Microbiota/immunology
*Staphylococcal Infections/immunology/microbiology
Host-Pathogen Interactions/immunology

@article {pmid41200143,
year = {2025},
author = {Toh, QY and Kang, YN and Chee, SY and Chiu, HH},
title = {Effects of probiotics on patients with Prader-Willi syndrome: a systematic review and meta-analysis of randomized controlled trials.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1583574},
pmid = {41200143},
issn = {2296-861X},
abstract = {BACKGROUND: Prader-Willi Syndrome (PWS) involves growth, obesity, and behavioral challenges; probiotics may improve symptoms through the gut-brain axis, aiding treatment. This meta-analysis aimed to assess the impact of probiotic supplementation on individuals with PWS in terms of probiotic abundance, psycho-social outcomes, behavioral issues, and adverse events.

METHODS: We systematically conducted searches across PubMed, the Cochrane Central Register of Controlled Trials, EMBASE, and the Web of Science. Our study included relevant randomized controlled trials (RCTs) published before February 2025. Two independent review authors evaluated study eligibility, extracted data, and assessed the risk of bias in the included studies. Data synthesis employed a random-effects model based on heterogeneity test results and was presented as the standardized mean difference (SMD) with a 95% confidence interval (CI).

RESULTS: A total of five RCTs were included. Probiotic supplementation led to a notable increase in the abundance of the Bifidobacterium genus (SMD 1.21; 95% CI, 0.02 to 2.39). Notably, 12 weeks of probiotics intake demonstrated a favorable trend on social engagement (SMD -0.68; 95% CI: -1.14 to -0.21; p = 0.004). In contrast, probiotics did not exhibit a significant influence on behavioural problems, and the safety of probiotics consumption was assured as there was no significant increase in gastrointestinal adverse events.

CONCLUSION: The validation of a probiotic treatment for PWS is currently an aspirational goal. Additional investigation is required to comprehensively comprehend the connection between PWS and the gut microbiome, as well as its potential ramifications for the disease phenotype.

PROSPERO, CRD42023416791.},
}

@article {pmid41199951,
year = {2025},
author = {Prasad, JS and Suman, A and Kumar, D and Sharma, P and Ramakrishnan, B and Aswini, K},
title = {Agroecology-based assembly and function of endophytic bacteria in seeds of Triticum aestivum.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1699093},
pmid = {41199951},
issn = {1664-302X},
abstract = {The seed, a vital plant organ for its continuation, contains microbial endophytes that develop as part of the early plant microbiome and assist growing seedlings in various ways. In this study, bacterial endophytes from seeds of wheat cultivars grown under different agro-ecological conditions were genotypically and functionally analyzed. Despite environmental differences and cultivars adapted to distinct agroclimatic zones, the endophytic bacterial count ranged from 2.79 to 5.19 Log CFU/g. The dominant seed bacteria belonged to the phylum Firmicutes, with diverse members of the genus Bacillus. There were core and niche-specific bacteria among the different agroclimatic zones. The seed endophytic bacteria exhibited hydrolytic enzyme activities, mainly amylase, cellulase, and xylanase. The nitrogen fixation capacity ranged from 0.81 to 32.06 nmol ethylene h[-1] mg[-1] protein, while phosphate solubilisation ranged from 147 to 440 μg mL[-1]. Some seed endophytes from the North Western Plains Zone (NWPZ) showed strong antagonism toward Fusarium graminearum (52%), Bipolaris sorokiniana (35.9%), and Tilletia indica (43.4%). The green fluorescent protein (GFP)-tagged endophytic bacteria, when reintroduced to wheat seeds, were observed to colonize and migrate within germinating seedlings, Confirm their potential for internal establishment and movement within the host. These seed endophytic bacteria may offer notable benefits by colonizing root tissues during germination, thereby enhancing plant growth and yield.},
}

@article {pmid41199950,
year = {2025},
author = {Sang, Z and Zhang, Y and Kao, E and Zhu, T and Yang, J and Xu, ZZ and Huang, S and Teng, F and Wang, W},
title = {Decoding oral leukoplakia: microbiome dysbiosis and inflammatory dynamics unveiled in a rat model.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1613165},
pmid = {41199950},
issn = {1664-302X},
abstract = {INTRODUCTION: Oral leukoplakia (OLK) is an oral precancerous lesion associated with oral microbiome dysbiosis and systemic inflammation. However, the longitudinal changes of the microbiome and its causal relationship with inflammation remain unclear, and traditional sequencing struggles to detect low-biomass samples.

METHODS: A 4-nitroquinoline-1-oxide (4-NQO)-induced rat OLK model was used. The oral microbiome was analyzed via 2bRAD-M sequencing; serum levels of tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) were measured. Additionally, functional pathway analysis of the microbiome and its correlation with inflammation were conducted.

RESULTS: In OLK, we observed significant shifts in the oral microbial diversity, marked by elevated abundances of Streptococcus, Glaesserella, and Pseudomonas aeruginosa. Moreover, shifts in the microbiota precede the manifestation of clinical symptoms of OLK. Functional pathway analysis highlighted enrichment in metabolism, quorum sensing, and cancer-associated microRNA pathways. Serum levels of inflammatory markers (TNF-α and IL-6) were significantly elevated in OLK and significantly correlated with specific bacterial taxa.

DISCUSSION: This study demonstrates the utility of 2bRAD-M sequencing in overcoming traditional metagenomic limitations, offering a high-resolution view of microbiome dynamics in low-biomass environments such as the oral mucosa. These findings establish the oral microbiota as candidate early biomarkers for OLK screening and prevention, opening avenues for precision diagnostics and targeted therapies to mitigate cancer risk associated with OLK.},
}

@article {pmid41199947,
year = {2025},
author = {Geng, Z and Yuan, L and See, D and Zhao, Y},
title = {Characterization of the integrated gut microbiota and metabolite profiles in osteoporosis patients with different traditional Chinese medicine syndromes.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1663716},
pmid = {41199947},
issn = {1664-302X},
abstract = {INTRODUCTION: This study aims to investigate whether the Traditional Chinese Medicine (TCM) classification of osteoporosis corresponds to specific gut microbial and metabolic profiles, thereby providing a microbiological basis for TCM syndrome differentiation.

METHODS: Body composition was assessed using dual-energy X-ray absorptiometry in healthy elderly controls and osteoporosis patients categorized by TCM subtype. Gut microbiota composition and metabolite profiles were analyzed via 16S rRNA gene sequencing and liquid chromatography-tandem mass spectrometry (LC-MS/MS), respectively.

RESULTS: The gut microbiota dysbiosis index was significantly elevated in osteoporosis patients compared to healthy controls, with the highest levels observed in the spleen-kidney Yang deficiency subtype. Distinct microbial signatures were identified: Intestinibacter and Phascolarctobacterium were significantly enriched in kidney Yang deficiency osteoporosis, while Olsenella was markedly increased in spleen-kidney Yang deficiency osteoporosis. Correlation analyses revealed significant associations between these microbial markers and clinical parameters: Intestinibacter and Phascolarctobacterium abundances negatively correlated with bone mineral density at multiple skeletal sites, whereas Olsenella levels were negatively associated with appendicular skeletal muscle index. Importantly, microbial metabolic pathways differed between TCM subtypes, with kidney Yang deficiency associated with vitamin D metabolism and spleen-kidney Yang deficiency linked to lipid metabolism.

CONCLUSION: TCM classification captures meaningful biological heterogeneity in osteoporosis, reflected in distinct microbiome and metabolic signatures. These findings provide a microbiological basis for TCM syndrome differentiation and may inform personalized approaches to osteoporosis diagnosis and treatment.},
}

@article {pmid41199945,
year = {2025},
author = {Busi, SB},
title = {Editorial: Monitoring, modeling, and mitigation in terrestrial ecosystems: microbial response to climate change.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1717735},
doi = {10.3389/fmicb.2025.1717735},
pmid = {41199945},
issn = {1664-302X},
}

@article {pmid41199864,
year = {2025},
author = {Wang, EM and Shremo Msdi, A and Quach, VN and Nguyen, SQ and Quach, E and Jo, J and Eubank, TA and Garey, KW and Rosario, N},
title = {Angiotensin converting enzyme inhibitors and angiotensin receptor blockers impact on the gut microbiome: a systematic review.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1685424},
pmid = {41199864},
issn = {1664-2392},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Animals ; *Angiotensin Receptor Antagonists/pharmacology ; Hypertension/drug therapy ; Blood Pressure/drug effects ; Renin-Angiotensin System/drug effects ; },
abstract = {BACKGROUND: Inhibition of the renin-angiotensin system (RAS) may influence gut microbial composition and blood pressure, yet current evidence remains limited. This review examines how angiotensin-converting enzyme inhibitors (ACEis) and angiotensin receptor blockers (ARBs) modify gut microbiome composition, function, and blood pressure regulation.

METHODS: We conducted a systematic search of MEDLINE and EMBASE from inception to September 2025 using terms including "human," "rat," "angiotensin converting enzyme inhibitor," "angiotensin receptor blocker," and "gut microbiome." Eligible studies were required to report changes in microbiome diversity, bacterial composition, or short-chain fatty acids (SCFAs) associated with ACEi/ARB treatment across animal or human models. Data extraction and risk of bias assessments were performed independently by multiple reviewers.

RESULTS: After deduplication, 642 retrieved articles were filtered and nine met inclusion criteria (eight in rodent models, one human study). ACEi/ARB administration in animals was associated with increased microbial diversity, restoration of intestinal oxygen balance, and enrichment of SCFA-producing anaerobic genera such as Bifidobacterium, Bacteroides, Blautia, and Akkermansia. In the human study, ACEi/ARB use did not significantly alter microbial diversity, but decreased populations of facultative aerobic pathogens including Staphylococcus and Enterobacterales. Functionally, prolonged RAS inhibition elevated levels of acetate, propionate, and butyrate, and enhanced gut barrier integrity while attenuating inflammatory signaling. The human study was found to have a moderate risk of bias.

CONCLUSIONS: ACEi and ARB therapies appear to reshape gut microbiome structure and metabolic function, promoting SCFA-producer expansion, improved gut barrier integrity, and modulation of microbial taxa linked to inflammation and hypertension. However, human data is limited, and further transitional research is needed to confirm these findings.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Angiotensin-Converting Enzyme Inhibitors/pharmacology
Animals
*Angiotensin Receptor Antagonists/pharmacology
Hypertension/drug therapy
Blood Pressure/drug effects
Renin-Angiotensin System/drug effects

@article {pmid41199641,
year = {2025},
author = {Postoeva, A and Krieger, E and Leontyeva, A and Kudryavtsev, AV and Galeeva, J and Fedorov, D and Kuzmichenko, P and Ilina, E and Govorun, V},
title = {Taxonomic diversity of fecal microbiota associated with different metabolic phenotypes in residents of Arkhangelsk, Northwestern Russia.},
journal = {Journal of biomedical research},
volume = {},
number = {},
pages = {1-17},
doi = {10.7555/JBR.39.20250258},
pmid = {41199641},
issn = {1674-8301},
abstract = {The study aimed to assess the taxonomic diversity and composition of gut microbiota in Arkhangelsk residents, Northwestern Russia, with varying metabolic statuses. A population-based cross-sectional "Know Your Heart" study (2015-2017, participants aged 35-69 years) included a health examination and gut microbiota analysis (n = 685). Participants were divided into four metabolic phenotypes: metabolically healthy non-obese (MHN), metabolically unhealthy non-obese (MUN), metabolically healthy obese (MHO), and metabolically unhealthy obese (MUO). Analyses were performed using RStudio software (v.4.2.0) with the vegan and phyloseq packages (v.1.42.0) for microbiota analysis. The sample was distributed across phenotypes as follows: MHN (47.6%), MUN (22.1%), MHO (10.4%), and MUO (19.9%). Beta-diversity analysis revealed significant differences in overall microbiome composition between MUO and MHN participants, while alpha-diversity did not differ significantly across phenotypes. The MHN group was characterized by a higher abundance of beneficial commensals such as Christensenellaceae R-7 group, Ruminococcaceae UCG-005, and Eubacterium xylanophilum group, which are taxa previously associated with metabolic health and longevity. In contrast, the MUO group showed an increased abundance of Streptococcus salivarius and Negativibacillus, taxa linked to gut dysbiosis and metabolic disorders. Blautia spp. emerged as a major hub in the microbiota of obese participants, consistent with its reported association with visceral fat. In conclusion, microbial composition was similar in obese participants despite metabolic dysfunction, whereas unidirectional taxonomic shifts were observed in those with metabolic dysfunction alone. The differences in the predominance of microbial taxa across metabolic phenotypes suggest that these taxa have a role in the development of metabolic disorders and obesity.},
}

@article {pmid41199396,
year = {2025},
author = {Liu, Q and Hu, D and Qiao, Y and Zai, X and Hao, X and Zong, Y and Zhang, D and Shi, X and Zhang, F and Li, P and Song, C},
title = {Phyllosphere microbes in foxtail millet primarily affect quality by modulating coloration and bitter compounds.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {229},
pmid = {41199396},
issn = {2049-2618},
support = {YDZJSX2022A041//The Development Fund of Central Government Guiding Local Science and Technology/ ; YDZJSX2024D046//The Development Fund of Central Government Guiding Local Science and Technology/ ; 2021YFD1900200//The National Key Research and Development Program of China/ ; },
mesh = {*Setaria Plant/microbiology/chemistry ; *Microbiota ; Taste ; Rhizosphere ; Pseudomonas/isolation & purification/metabolism/genetics/classification ; *Plant Leaves/microbiology ; Bacteria/classification/genetics/metabolism/isolation & purification ; },
abstract = {BACKGROUND: Crop quality is influenced by crop-related factors such as varieties and metabolites, as well as by environmental conditions. Recent studies have shown the important role of rhizosphere microbes in determining crop quality and flavor, but the effects of phyllosphere (aboveground) microbes and metabolites remain unclear. Here, we examined the interaction between phyllosphere metabolites and the microbiome in three foxtail millet varieties with differing eating qualities: two high-eating-quality varieties (Yugu1, Jingu21) and one low-eating-quality variety (Daobaqi) in the field.

RESULTS: Thirteen metabolites were found to be depleted in the high-eating-quality varieties, four of which were identified as bitter compounds. These depleted metabolites were negatively correlated with the abundance of two microbial genera, Curtobacterium and Pseudomonas, enriched in the high-eating-quality foxtail millet panicles. Further analyses revealed that the abundance of these microbes was significantly associated with reduced bitterness and improved viscosity in the panicles. Additionally, synthetic microbial community experiments validated that these microbes enhanced foxtail millet quality by increasing the yellow coloration and reducing levels of bitter compounds.

CONCLUSIONS: In summary, the higher abundance of Curtobacterium and Pseudomonas in the panicles correlated with reduced bitter compounds and enhanced foxtail millet quality. This work provides new insights into the role of phyllosphere metabolites and microbiomes in determining crop quality.},
}

*Setaria Plant/microbiology/chemistry
*Microbiota
Taste
Rhizosphere
Pseudomonas/isolation & purification/metabolism/genetics/classification
*Plant Leaves/microbiology
Bacteria/classification/genetics/metabolism/isolation & purification

@article {pmid41199352,
year = {2025},
author = {Rahbar Saadat, Y and Barzegari, A and Saadatian, Z and Montazersaheb, S and Zununi Vahed, S},
title = {Gut microbiota and kidney aging: insights into current research.},
journal = {Nutrition & metabolism},
volume = {22},
number = {1},
pages = {133},
pmid = {41199352},
issn = {1743-7075},
abstract = {Aging induces structural and functional alterations in the kidneys, including changes in renal morphology and progressive decline in renal function. During aging, the gut microbiota undergoes profound shifts in composition and activity, transitioning from predominantly commensal to more pathogenic communities. Renal dysfunction further exacerbates this process by reducing toxin clearance and promoting the accumulation of uremic metabolites, which disrupt gut microbial balance. In turn, gut dysbiosis impairs kidney function, creating a self-perpetuating cycle of microbial imbalance and renal damage. Hence, breaking this vicious cycle of dysbiosis and kidney damage is important. This review sheds light on the bidirectional relationship between gut microbiota and kidney aging. It also highlights the potential of microbiota-targeted interventions to restore microbial balance and delay the onset of age-related issues.},
}

@article {pmid41199348,
year = {2025},
author = {Ghozlane, A and Thirion, F and Plaza Oñate, F and Gauthier, F and Le Chatelier, E and Annamalé, A and Almeida, M and Ehrlich, SD and Pons, N},
title = {Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {227},
pmid = {41199348},
issn = {2049-2618},
support = {ANR-11-DPBS-0001//Metagenopolis/ ; },
mesh = {*Metagenomics/methods ; Animals ; Mice ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; *Software ; Computational Biology/methods ; },
abstract = {BACKGROUND: The characterization of complex microbial communities is a critical challenge in microbiome research, as it is essential for understanding the intricate relationships between microorganisms and their environments. Metagenomic profiling has advanced into a multifaceted approach, combining taxonomic, functional, and strain-level profiling (TFSP) of microbial communities. Here, we present Meteor2, a tool that leverages compact, environment-specific microbial gene catalogues to deliver comprehensive TFSP insights from metagenomic samples.

RESULTS: Meteor2 currently supports 10 ecosystems, gathering 63,494,365 microbial genes clustered into 11,653 metagenomic species pangenomes (MSPs). These genes are extensively annotated for KEGG orthology, carbohydrate-active enzymes (CAZymes) and antibiotic-resistant genes (ARGs). In benchmark tests, Meteor2 demonstrated strong performance in TFSP, particularly excelling in detecting low-abundance species. When applied to shallow-sequenced datasets, Meteor2 improved species detection sensitivity by at least 45% for both human and mouse gut microbiota simulations compared to MetaPhlAn4 or sylph. For functional profiling, Meteor2 improved abundance estimation accuracy by at least 35% compared to HUMAnN3 (based on Bray-Curtis dissimilarity). Additionally, Meteor2 tracked more strain pairs than StrainPhlAn, capturing an additional 9.8% on the human dataset and 19.4% on the mouse dataset. Furthermore, in its fast configuration, Meteor2 emerges as one of the fastest available tools for profiling, requiring only 2.3 min for taxonomic analysis and 10 min for strain-level analysis against the human microbial gene catalogue when processing 10 M paired reads - operating within a modest 5 GB RAM footprint. We further validated Meteor2 using a published faecal microbiota transplantation (FMT) dataset, demonstrating its ability to deliver an extensive and actionable metagenomic analysis. The unified database design also simplifies the integration of TFSP outputs, making it straightforward for researchers to interpret and compare results.

CONCLUSIONS: These results highlight Meteor2 as a robust and versatile tool for advancing microbiome research and applications. As an open-source, easy-to-install, and accurate analysis platform, Meteor2 is highly accessible to researchers, facilitating the exploration of complex microbial ecosystems.},
}

*Metagenomics/methods
Animals
Mice
Humans
*Microbiota/genetics
*Bacteria/genetics/classification
*Metagenome
*Gastrointestinal Microbiome/genetics
*Software
Computational Biology/methods

@article {pmid41199330,
year = {2025},
author = {Yin, L and Zhao, J and Zhou, Z and Zhang, J and Qu, X and Shi, J and Yin, F},
title = {Effects of prenatal bifidobacterium supplementation on the gut microbiome in preterm infants of preeclamptic mothers.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1237},
pmid = {41199330},
issn = {1479-5876},
mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Pregnancy ; *Bifidobacterium/physiology ; *Infant, Premature ; *Pre-Eclampsia/microbiology ; Infant, Newborn ; *Dietary Supplements ; Adult ; *Mothers ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Male ; },
abstract = {BACKGROUND: This study examined the relationship between maternal preeclampsia (PE) and gut microbiota colonization in preterm infants and analyzed the effects of prenatal Bifidobacterium supplementation.

METHODS: This observational study included 45 preterm infants categorized according to their mothers' exposure status during pregnancy. Group A (healthy controls, n = 15) included infants born to healthy mothers who received no supplementation; Group B (PE+Bifidobacterium, n = 15) included infants whose mothers had PE and received Bifidobacterium supplementation as part of routine clinical management; and Group C (PE only, n = 15) included infants born to mothers with PE who did not receive Bifidobacterium supplementation. All enrolled infants were followed from birth for subsequent analyses. The initial postnatal fecal samples of the infants were collected and analyzed using 16S rRNA gene sequencing. Microbial diversity within the intestinal microbiota was evaluated using alpha diversity (within-sample) and beta diversity (between-sample) analyses. To identify taxon-specific differences among groups, we performed linear discriminant analysis effect size and differential abundance analysis, with statistical significance set at p < 0.05. The functional potential of the gut microbiota was inferred based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways via the PICRUSt2 algorithm.

RESULTS: Alpha diversity analysis revealed significantly greater microbial diversity in the fecal microbiota of preterm infants born to healthy mothers (Group A) than in those delivered by mothers with PE, regardless of prenatal Bifidobacterium exposure. Taxonomic profiling revealed distinct microbial community structures across groups: Group A exhibited significant enrichment of Bacteroides at all taxonomic levels, along with an elevated abundance of Clostridium at the class and order levels. Group B showed a markedly greater relative abundance of Actinobacteria at the phylum level and Rothia at the genus level, whereas Group C was dominated by Proteobacteria (phylum level) and Streptococcus (genus level). All intergroup differences were statistically significant following Benjamini‒Hochberg correction (q < 0.05). A functional analysis of the gut microbiota revealed 53 KEGG pathways with significant overall group differences (p < 0.05), among which 23 pathways were significantly different in at least two groups (q < 0.05). Notably, the activity of the LPS biosynthesis pathway was significantly upregulated in Group C compared with Group A (q = 0.001). Although LPS biosynthesis activity was reduced in Group B relative to Group C (q = 0.018), it remained elevated compared to Group A (q = 0.001), suggesting incomplete mitigation of endotoxin risk. Additionally, glycolytic activity was significantly impaired in Group C relative to Group A (q = 0.003) but was partially restored in Group B compared to Group C (q = 0.022).

CONCLUSIONS: Maternal PE impaired early-life gut microbiota establishment in preterm infants, manifesting in reduced microbial diversity, enrichment of pathogenic Proteobacteria and Streptococcus, and consequent functional dysbiosis characterized by elevated endotoxin biosynthesis potential and compromised energy metabolism. Although prenatal supplementation with Bifidobacterium partially restored the microbial compositional balance, promoting beneficial bacteria, reducing LPS synthesis activity, and partially improving glycolytic function, it failed to fully reverse endotoxin-related risks, indicating the need to develop more effective microbiota-targeted strategies to comprehensively optimize metabolic and immune homeostasis.},
}

Humans
Female
*Gastrointestinal Microbiome
Pregnancy
*Bifidobacterium/physiology
*Infant, Premature
*Pre-Eclampsia/microbiology
Infant, Newborn
*Dietary Supplements
Adult
*Mothers
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Male

@article {pmid41199168,
year = {2025},
author = {Guo, L and Pei, X and Tan, J and Sun, H and Jiang, S and Wei, H and Peng, J},
title = {Unraveling the role of bacteria with heritable versus non-heritable relative abundance in the gut on boar semen quality.},
journal = {Genetics, selection, evolution : GSE},
volume = {57},
number = {1},
pages = {66},
pmid = {41199168},
issn = {1297-9686},
support = {2022BBA0056//Hubei Technological Innovation Special Fund/ ; 2662023DKPY002//Fundamental Research Funds for the Central Universities/ ; CARS-35//Agriculture Research System of China/ ; },
mesh = {Animals ; Male ; Swine/microbiology ; *Gastrointestinal Microbiome/genetics ; *Semen Analysis/veterinary ; *Bacteria/classification/genetics/metabolism ; Fatty Acids, Volatile/metabolism ; Semen ; },
abstract = {BACKGROUND: The relative abundance of some bacteria in the gut of pigs is heritable, suggesting that host genetics may recursively influence boar semen quality by affecting the composition and function of gut microbiota. Therefore, it is essential to elucidate the specific contributions of heritable versus non-heritable gut microbiota to semen quality traits.

RESULTS: Our study aimed to identify heritable and non-heritable bacterial taxa at the genus level in the boar gut and to predict their functions and respective contributions to semen quality traits. At the genus level, 39 heritable and 91 non-heritable bacterial taxa were identified. Functional analysis revealed that predicted microbial functions in both groups were primarily enriched in carbohydrate, nucleotide, and amino acid metabolism. We further analyzed the average microbiability of heritable and non-heritable bacteria on short-chain fatty acids (SCFAs) and semen quality traits. The relative abundance of heritable bacteria was found to contribute more to SCFAs levels and semen quality than non-heritable bacteria. Mediation analysis revealed that SCFAs could mediate the influence of the relative abundance of heritable bacteria on host phenotypes, identifying 99 significant genus-SCFAs-semen quality trait mediation links.

CONCLUSIONS: Our findings underscore the substantial role of the relative abundance of heritable gut bacteria in shaping porcine semen quality through SCFAs mediation. These results highlight the potential of targeted microbiome interventions to enhance reproductive traits in pigs.},
}

Animals
Male
Swine/microbiology
*Gastrointestinal Microbiome/genetics
*Semen Analysis/veterinary
*Bacteria/classification/genetics/metabolism
Fatty Acids, Volatile/metabolism
Semen

@article {pmid41199152,
year = {2025},
author = {Han, X and Huang, H and Yu, X and Cha, M and Jian, J and Hu, X and Wu, Q},
title = {Letter to the Editor: The Oral Microbiome and Depression: An Emerging Medical Hypothesis.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.70143},
pmid = {41199152},
issn = {1601-0825},
support = {ZR2021QH283//Youth Project of Shandong Provincial Natural Science Foundation/ ; 202201060948//Shandong Provincial Medical and Health Technology Development Plan/ ; },
}

@article {pmid41198950,
year = {2025},
author = {Guendouzi, S and Ortega-Villaizan, AG and King, E and Benmati, M and Vicente-Carbajosa, J},
title = {Transcriptomic profiling of Arabidopsis Thaliana responses to Stutzerimonas stutzeri, chlorella vulgaris, and mixed consortium inoculation under salt stress.},
journal = {Plant molecular biology},
volume = {115},
number = {6},
pages = {125},
pmid = {41198950},
issn = {1573-5028},
support = {TED2021-1299998-l00//MCIN/AEI (Ministerio de Ciencia e Innovación / Agencia Estatal de Investigación, Spain)/ ; },
mesh = {*Arabidopsis/genetics/microbiology/physiology ; *Salt Stress/genetics ; Gene Expression Regulation, Plant ; Gene Expression Profiling ; *Chlorella vulgaris/physiology ; *Transcriptome ; Arabidopsis Proteins/genetics/metabolism ; },
abstract = {Plants, constantly exposed to dynamic environmental conditions, encounter various abiotic stresses that significantly affect their growth and development. In response, plants initiate complex physiological and molecular adjustments, including altered gene expression. One of the most influential factors in mitigating stress impacts is the plant-microbe interaction. Among these, plant growth-promoting rhizobacteria (PGPR) are well-studied for their ability to enhance plant resilience. More recently, microalgae have emerged as potential members of the plant microbiome, although their roles remain comparatively underexplored. This study investigates the transcriptomic responses of Arabidopsis thaliana to inoculation with the PGPR strain Stutzerimonas stutzeri, the green microalgae Chlorella vulgaris, and a consortium of both microorganisms under salt stress conditions. Through RNA-seq analysis, we identified a set of core genes commonly regulated across all inoculation treatments, including SALT OVERLY SENSITIVE 3 (SOS3), the potassium channel AKT2, and CBL-INTERACTING PROTEIN KINASE 5 (CIPK5), suggesting a shared stress-mitigation mechanism. Additionally, we identified genes uniquely regulated in response to the S. stutzeri-C. vulgaris consortium. These included components of the ethylene signaling pathway (EIN3/EIL1), detoxification-associated genes such as β-GLUCOSIDASE (BGLU22), and transcription factors linked to stress response, notably NAC6 and MYB12. Together, these findings provide insight into the specific and overlapping transcriptomic changes induced by bacterial, algal, and combined inoculations, contributing to our understanding of plant-microbe interactions under salt stress.},
}

*Arabidopsis/genetics/microbiology/physiology
*Salt Stress/genetics
Gene Expression Regulation, Plant
Gene Expression Profiling
*Chlorella vulgaris/physiology
*Transcriptome
Arabidopsis Proteins/genetics/metabolism

@article {pmid41198897,
year = {2025},
author = {Wattanawongwan, W and Krasaesin, A and Khieota, T and Thongchotchat, V and Porntaveetus, T and Wiriyakijja, P},
title = {Effects of chlorhexidine and a polyherbal mouthwash on the oral microbiome and user satisfaction: a randomized controlled trial.},
journal = {Clinical oral investigations},
volume = {29},
number = {12},
pages = {555},
pmid = {41198897},
issn = {1436-3771},
mesh = {Humans ; *Mouthwashes/pharmacology/therapeutic use ; *Chlorhexidine/pharmacology/therapeutic use ; *Microbiota/drug effects ; Male ; Female ; Double-Blind Method ; Adult ; *Patient Satisfaction ; *Anti-Infective Agents, Local/pharmacology ; *Gingivitis/drug therapy/microbiology ; Middle Aged ; *Mouth/microbiology ; },
abstract = {OBJECTIVE: This study aimed to comparatively evaluate the effects of polyherbal, chlorhexidine (CHX), and normal saline (NCC) mouthwashes on oral microbiome composition, microbial metabolic pathways, and patient-reported outcomes, with the goal of assessing the potential of polyherbal mouthwash as a natural alternative to CHX for managing gingivitis, while aiming to minimize CHX-associated microbial dysbiosis.

METHODS: A randomized, double-blind trial was conducted among 27 patients with gingivitis, randomly assigned to polyherbal, CHX, or NCC mouthwash groups. Participants used the assigned mouthwash twice daily for 7 days. Saliva samples were analyzed via 16 S rRNA sequencing to assess microbial diversity (alpha and beta) and taxonomic composition. Differential taxa and pathways were identified using FDR-corrected Wilcoxon tests and log₂ fold-change analysis. Patient-reported outcomes were evaluated using numerical rating scales (NRS).

RESULTS: The polyherbal mouthwash demonstrated significantly higher patient acceptability than CHX and NCC, with superior scores in taste, smell, texture, moisture retention, overall satisfaction, and willingness for continued use (p < 0.05). While CHX exhibited strong antimicrobial activity, its alcohol-containing formulation markedly disrupted microbial diversity, increased potentially dysbiotic genera (Streptococcus, Porphyromonas), and altered 23 metabolic pathways associated with dysbiosis. In contrast, the polyherbal mouthwash-which also contained cetylpyridinium chloride (CPC)- selectively increased beneficial genera (Amnipila, Absconditabacteriales [SR1], Peptostreptococcus), preserved overall microbial diversity, and modulated only two pathways, notably upregulating L-isoleucine biosynthesis.

CONCLUSION: The polyherbal mouthwash represents a promising alternative to CHX, demonstrating selective microbial modulation, preservation of microbiome stability, and enhanced patient acceptability. These findings support its potential integration into routine oral healthcare as a microbiome-friendly and patient-acceptable solution. Further studies are warranted to evaluate CPC-free polyherbal formulations across larger and more diverse populations over extended durations.},
}

Humans
*Mouthwashes/pharmacology/therapeutic use
*Chlorhexidine/pharmacology/therapeutic use
*Microbiota/drug effects
Male
Female
Double-Blind Method
Adult
*Patient Satisfaction
*Anti-Infective Agents, Local/pharmacology
*Gingivitis/drug therapy/microbiology
Middle Aged
*Mouth/microbiology

@article {pmid41198867,
year = {2025},
author = {Boetto, C and Romero, VB and Henches, L and Frouin, A and Auvergne, A and Patin, E and Bredon, M and , and Kennedy, SP and Duffy, D and Quintana-Murci, L and Sokol, H and Aschard, H},
title = {The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1537},
pmid = {41198867},
issn = {2399-3642},
support = {ANR-20-CE15-0012-01//Agence Nationale de la Recherche (French National Research Agency)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Healthy Volunteers ; Young Adult ; *Environment ; },
abstract = {The gut microbiome is a complex ecosystem characterized not only by its marginal taxonomic composition but also by its emergent properties. Bacteria develop local interactions to form coherent functional communities, whose effects on health and diseases cannot be predicted from the behavior of individual members. Understanding the factors underlying variability in these communities may therefore provide critical insights on the biological links between the gut microbiome and human phenotypes. Here, we examined the effect of a range of host factors, including demographics, medical history, and dietary habits, on these communities in 938 healthy individuals using MANOCCA, a covariance-based approach developed to address existing limitations. Increased age and smoking were associated with a significant overall decrease in co-abundance, and conversely a higher body mass index was associated with increased co-abundance. At the taxon level, a core of 200 genera were systematically impacted in their co-abundance with other taxa, suggesting a central role in structuring the network. Finally, we demonstrate that our approach offers a powerful framework for prediction purposes, with taxa co-abundance being able to predict the age of participants with an accuracy three-fold higher than a model based on abundance only.},
}

Humans
*Gastrointestinal Microbiome
Male
Female
Middle Aged
Adult
*Bacteria/classification/genetics/isolation & purification
Aged
Healthy Volunteers
Young Adult
*Environment

@article {pmid41198833,
year = {2025},
author = {Erdenetsetseg, B and Arakawa, K and Galipon, J and Undrakhbold, S and Fukuda, S and Boldgiv, B},
title = {Rhizospheric microbiomes differ between dormant and active Potaninia mongolica in the Gobi desert of Mongolia.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38858},
pmid = {41198833},
issn = {2045-2322},
support = {ID No. R12205//Japan Society for the Promotion of Science/ ; },
mesh = {*Rhizosphere ; *Soil Microbiology ; *Microbiota ; Desert Climate ; Mongolia ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Soil/chemistry ; Fungi/genetics/classification ; Plant Roots/microbiology ; },
abstract = {Rhizospheric microbiomes differ between active and dormant plants due to changes in root activity and exudate production, especially under environmental stress. In arid regions, native plants such as Potaninia mongolica Maxim enter dormancy to survive harsh conditions. However, rhizospheric microbial and chemical differences between active and dormant states of plants remain poorly described. This study investigated rhizospheric microbial communities and soil chemical changes in the case of active and dormant P.mongolica plants. Rhizospheric soil samples were collected, and soil texture and chemical variables were analyzed. High-throughput sequencing targeting the 16S rRNA and ITS regions was conducted to profile bacterial and fungal communities, respectively. Results showed that the dominant fungal phyla were Ascomycota and Basidiomycota, while Proteobacteria and Actinobacteria were the dominant bacterial phyla in both plant states. Although bacterial diversity did not differ significantly between active and dormant plants (p > 0.05, Welch's t-test), fungal diversity was significantly different. Among soil chemical variables, total nitrogen was notably elevated in the rhizosphere of dormant plants (mean = 7.93; SD = 5.91). These findings reveal differences in fungal community structure and nitrogen levels in the rhizosphere between active and dormant plant states. Understanding these interactions contributes to our knowledge of desert plant microbiome dynamics and may inform the use of microbial indicators or amendments to support vegetation restoration in arid environments.},
}

*Rhizosphere
*Soil Microbiology
*Microbiota
Desert Climate
Mongolia
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
Soil/chemistry
Fungi/genetics/classification
Plant Roots/microbiology

@article {pmid41198730,
year = {2025},
author = {Garrigós, M and García-Ruiz, O and Enkvist, CR and García-López, MJ and Moreno-Indias, I and Ruiz-López, MJ and Veiga, J and Figuerola, J and Videvall, E and Martínez-de la Puente, J},
title = {Effects of avian Plasmodium exposure on the microbiota of Culex pipiens.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38898},
pmid = {41198730},
issn = {2045-2322},
support = {PRE2021-098544//Ministerio de Ciencia, Innovación y Universidades/ ; PU19/01925//Ministerio de Ciencia, Innovación y Universidades/ ; FJC2021-048057-I//Ministerio de Ciencia, Innovación y Universidades/ ; PID2020-118205GB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; PTA2022-021854-I//Agencia Estatal de Investigación/ ; PID2020-118921RJ-100/AEI/10.13039/501100011033//Agencia Estatal de Investigación/ ; CPII21/00013//Instituto de Salud Carlos III/ ; 2023-05026//Swedish Research Council/ ; },
mesh = {Animals ; *Culex/microbiology/parasitology ; *Plasmodium/physiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Sparrows/parasitology ; Mosquito Vectors/microbiology/parasitology ; *Malaria, Avian/parasitology/transmission ; },
abstract = {Malaria parasites (Plasmodium spp.) are mosquito-borne parasites that infect humans and wildlife. Several studies support the role of mosquito microbiota as a major driver of Plasmodium transmission, although studies on wildlife malaria are typically neglected. Here, we used a 16S rRNA metabarcoding approach to assess whether the exposure to avian Plasmodium parasites affects the microbiota of their natural vector, Culex pipiens. Mosquitoes, captured in the field as larvae and grown in the laboratory, were allowed to feed on house sparrows (Passer domesticus) naturally infected with Plasmodium relictum (lineage SGS1) and uninfected birds. We analyzed the microbiota composition of the abdomens of individual mosquitoes and found 2,006 Amplicon Sequence Variants (ASVs). Culex pipiens' microbiota was dominated by bacteria of the genus Wolbachia, followed by the genera Stenotrophomonas and Faecalibacterium. We observed no difference in alpha nor beta diversity between mosquitoes that fed on Plasmodium-infected birds (exposed mosquitoes) and those that fed on uninfected birds (unexposed mosquitoes). However, exposed mosquitoes had a higher relative abundance of bacteria of the family Bacteroidaceae and the genus Bacteroides than the unexposed mosquitoes. Excluding the intracellular endosymbiont Wolbachia from the analyses, we obtained similar results, and also found a higher relative abundance of bacteria of the family Rikenellaceae in exposed mosquitoes. A pathway enrichment analysis based on KEGG annotations revealed that the bacterial community in exposed mosquitoes was enriched in pathways mainly related to biosynthesis and metabolism. Our results suggest that Cx. pipiens exposed to avian Plasmodium have slightly different microbiota composition, although further research is needed to establish the causality of these effects.},
}

Animals
*Culex/microbiology/parasitology
*Plasmodium/physiology
RNA, Ribosomal, 16S/genetics
*Microbiota
Sparrows/parasitology
Mosquito Vectors/microbiology/parasitology
*Malaria, Avian/parasitology/transmission

@article {pmid41198444,
year = {2025},
author = {Goryachok, M and Fairbanks-Mahnke, A and Fulte, S and Tamkin, E and McCarty, A and Larson, ED and Planet, PJ and Clark, SE},
title = {Functional CFTR may be required for Prevotella melaninogenica regulation of epithelial cell defense against Staphylococcus aureus.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2025.11.002},
pmid = {41198444},
issn = {1873-5010},
abstract = {BACKGROUND: Prevotella melaninogenica is enriched in the lungs of people with cystic fibrosis (pwCF), yet its functional impact on respiratory tract homeostasis remains incompletely understood. Prior studies identified immune modulatory effects following lung exposure to Prevotella, but the relevance of these findings for CF infections is unknown.

METHODS: The impact of P. melaninogenica on infection with the CF pathogen Staphylococcus aureus was evaluated using a mouse lung infection model and by measuring S. aureus adherence to human respiratory tract cystic fibrosis transmembrane conductance regulator (CFTR) mutant and isogenic wild-type (WT)-corrected CFBE41o- epithelial cells. Epithelial cytokine/chemokine secretion and RNA-sequencing were performed to compare P. melaninogenica-induced signaling programs in WT-corrected versus CFTR mutant cells.

RESULTS: P. melaninogenica significantly reduced S. aureus lung infection, associated with elevated S. aureus killing by lung neutrophils and impaired S. aureus adherence to epithelial cells. Live or killed P. melaninogenica were sufficient to mediate these effects, which were dependent on TLR2. P. melaninogenica impairment of S. aureus adherence required functional CFTR, as this effect was lost in CFTR mutant cells but restored by CFTR modulators. RNA-sequencing identified several antibacterial defense pathways selectively upregulated by P. melaninogenica in WT corrected epithelial cells, correlating with higher IL-8 and IL-6 cytokine production.

CONCLUSIONS: P. melaninogenica enhanced neutrophil and epithelial defense against S. aureus, but the benefits of epithelial cell regulation by P. melaninogenica were lost with CFTR dysfunction. CFTR modulators rescued P. melaninogenica responsiveness in epithelial cells, highlighting the potential for synergistic effects of host-microbiome interactions and CFTR targeted therapies.},
}

@article {pmid41198406,
year = {2025},
author = {Adame, MD and Segal, LN and Dickson, RP},
title = {The ensemble approach: integrating microbiome therapeutics into our treatment of pneumonia.},
journal = {The European respiratory journal},
volume = {66},
number = {5},
pages = {},
doi = {10.1183/13993003.01701-2025},
pmid = {41198406},
issn = {1399-3003},
}

@article {pmid41198034,
year = {2025},
author = {Dieter, L and Bowie, K and Luhung, I and Healy, HG and Roberts, SC and Mathew, T and Peaper, D and Martinello, RA and Gerstein, MB and Peccia, J},
title = {Aerosol-based Exposure to Opportunistic Pathogens Originating from Hospital Sink Drains.},
journal = {American journal of infection control},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajic.2025.10.030},
pmid = {41198034},
issn = {1527-3296},
abstract = {BACKGROUND: Hospital room sink drains contain biofilms that harbor opportunistic pathogens. Exposures to these pathogens may occur from aerosolization and droplet dispersion into patient rooms during sink use. This study characterizes aerosolization and droplet generation of sink drain opportunistic pathogens into operational hospital rooms.

METHODS: Sink drains, sink surfaces, water droplets, aerosols generated during sink use, and settled aerosols were sampled in patient rooms and analyzed via culture-, spectrometry- and genome-based approaches. Opportunistic pathogens were compared across samples via whole-genome sequencing and single-nucleotide polymorphism analysis. Biofilms and settled aerosols underwent 16S ribosomal deoxyribonucleic acid sequencing to assess impacts of sink drain biofilms into room bioaerosols.

RESULTS: Analyses suggested sink drain biofilm bacteria dispersed into hospital rooms. Opportunistic pathogens were identified in sink drains, droplets near sinks, and room aerosols. Stenotrophomonas maltophilia isolates from sink drain biofilm and droplets matched at the single-nucleotide level and microbial community analysis suggested general transmission of bacteria from sink drains into hospital rooms.

DISCUSSION: Viable opportunistic pathogens from sink drains were present in water droplets and aerosols within patient range, suggesting a potential exposure route.

CONCLUSIONS: Hospital sink drain biofilms contributed to the microbiome of hospital room surfaces and air, with microbes generally transmitted from sink drain sources to the room.},
}

@article {pmid41198001,
year = {2025},
author = {Gong, F and Liu, N and Miao, J and Wang, C and Lin, M and Luan, B and Chen, J and Chen, Y and Chen, X and Ge, F and Chen, W},
title = {Vitamin D regulation of gut microbiota-derived butyrate as a potential inhibitor of breast cancer proliferation.},
journal = {Gene},
volume = {},
number = {},
pages = {149872},
doi = {10.1016/j.gene.2025.149872},
pmid = {41198001},
issn = {1879-0038},
abstract = {Vitamin D is a fat-soluble vitamin implicated in the etiology, progression, and prognosis of breast cancer, yet its precise mechanisms of action remain elusive. We have integrated the latest insights from both basic and clinical research to find that in the human body, vitamin D is activated by hydroxylase to form the active form 1,25(OH)2D. 1,25(OH)2D may stimulate the abundance of butyrate-producing bacteria by upregulating their abundance, and butyrate can regulate the intestinal microenvironment and modulate the immune system to inhibit the proliferation of breast cancer. Notably, our investigations reveal a novel role of vitamin D in modulating the gut microbiome, particularly in stimulating the production of butyrate and other metabolites, which exhibit potent anti-proliferative effects on breast cancer cells. These findings open promising avenues for innovative clinical approaches in breast cancer therapy. This review delves into the intricate interplay between vitamin D, butyrate, and breast cancer, aiming to propose novel therapeutic strategies.},
}

@article {pmid41197947,
year = {2025},
author = {Zhou, Y and Li, J and Wang, D and Peng, L and Chen, K},
title = {Multimodal relationships and multifactorial associations between oral microecological and neurodegenerative diseases.},
journal = {Neuropharmacology},
volume = {},
number = {},
pages = {110760},
doi = {10.1016/j.neuropharm.2025.110760},
pmid = {41197947},
issn = {1873-7064},
abstract = {Dysregulation of the oral microbiome can result in inflammation of the oral mucosa and is associated with the development and advancement of numerous local and systemic illnesses, including those triggered by viral infections. The review thoroughly examines how the IL-17/Th17 response contributes to both protective immunity and inflammation in the oral mucosa, as well as its role in the onset of neurodegenerative diseases. A theoretical structure is offered for the possible connections among immune cells and the bacteria in the mouth. Changes in the oral microbiome and its produced pro-inflammatory factors may serve as non-invasive biomarkers for the invasion of potential neurodegenerative pathogens, offering predictive and early warning value for the severity of neurodegenerative diseases. Studying the intricate connection between the oral microbiome and neurodegenerative diseases offers potential for innovative strategies in preventing and treating the advancement of such conditions. Additional investigation is needed to reveal the mechanisms behind this connection and offer important insights for upcoming clinical procedures.},
}

@article {pmid41197919,
year = {2025},
author = {Mohit, and Verma, S and Venkatesh, V and Nityanand, S},
title = {Immuno-Microbial Crosstalk in Aplastic Anemia: Role of Gut and Viral Triggers.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108158},
doi = {10.1016/j.micpath.2025.108158},
pmid = {41197919},
issn = {1096-1208},
abstract = {Aplastic anemia (AA) is a rare but life-threatening hematological disorder, manifested in bone marrow failure and pancytopenia, which occurs worldwide due to the preferential immune mediated destruction of hematopoietic stem and progenitor cells. Despite the autoimmune etiology of AA, recent findings emphasize the key role of microbial and viral factors in the pathogenesis of AA by driving the host immune dysregulation. We delve into the immune-microbial crosstalk that is relevant in AA pathogenesis to provide novel insights related to gut microbial ecology, microbial metabolites, viral infections mediated inflammation and cytotoxicity against bone marrow components. Additionally, providing the roadmap of current knowledge for immune-mediated bone marrow failure focusing on activated cytotoxic T cells, altered regulatory T cells and proinflammatory cytokines. Imbalanced immune activation via defects in gut barrier function which promotes pathogen-associated molecular patterns (PAMPs) signaling through Toll-like receptors (TLRs) and other innate sensors. Considering the role of viral trigger such as Parvovirus B19, Epstein-Barr and Hepatitis as inducers of dysregulated immunity and their ability to affect antigen presentation, T cell receptor repertoires, and interferon pathways. We also delineate the potential of targeting the gut-immune axis for personalized AA therapy, including potential microbiome-directed interventions, antiviral and anti-cytokine approaches, as promising complement lines for standard immunosuppression therapy in AA. This cited approach will provide the advanced and novel clinical paradigm for the interconnected immune-microbial signals in pathogenesis of AA which promotes the host immune surveillance and also lead to precision medicine in AA treatment.},
}

@article {pmid41197774,
year = {2025},
author = {Gholamipour-Shirazi, P and Gholamipour-Shirazi, A},
title = {Infant Gut Microbiota and Functional Foods: Opportunities for Early Health Intervention.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clnesp.2025.10.032},
pmid = {41197774},
issn = {2405-4577},
abstract = {BACKGROUND & AIMS: The infant gut microbiome, established at birth, plays a critical role in immune, metabolic, and neurological development. Early-life exposures, including delivery mode and feeding practices, significantly influence microbial colonization. This review aims to evaluate how functional foods, including probiotics, prebiotics, synbiotics, and human milk oligosaccharides (HMOs), modulate the infant gut microbiota during this critical developmental window and their implications for long-term health.

METHODS: We synthesized findings from clinical trials, systematic reviews, and mechanistic studies exploring the role of functional food components in shaping infant microbiota composition and functionality. The review integrates insights from microbiology, immunology, and nutrition science, with emphasis on interventions during infancy.

RESULTS: Breastfeeding and HMOs promote Bifidobacterium dominance, linked to reduced risks of allergies, obesity, and inflammatory bowel disease. HMO-supplemented formulas approximate the microbial profiles of breastfed infants, and probiotics, such as Lactobacillus rhamnosus GG, reduce the incidence of atopic dermatitis. Synbiotics enhance gut health in preterm infants, thereby reducing morbidity. Despite the demonstrated benefits, challenges persist in probiotic stability, host-specific responses, and regulatory harmonization.

CONCLUSIONS: Functional foods offer a promising, evidence-based strategy to harness early microbial plasticity and promote resilience against chronic disease. Standardized formulations, longitudinal studies, and personalized approaches are needed to optimize their implementation in diverse infant populations.},
}

@article {pmid41197755,
year = {2025},
author = {Wang, XX and Liang, JJ and Duan, X and Chen, G},
title = {Microbial Metabolites for Cancer Immunotherapy: Current Evidence and Future Directions.},
journal = {Seminars in cancer biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.semcancer.2025.10.005},
pmid = {41197755},
issn = {1096-3650},
abstract = {Immune checkpoint blockade (ICB) therapy has transformed cancer treatment by activating the body's immune defenses to combat malignancies, offering substantial therapeutic outcomes for patients with advanced cancers. However, its efficacy varies considerably across different tumor types and individual patients. Recent studies have identified the human microbiome as a pivotal regulator of host homeostasis and systemic immunity and also found that it is essential for regulating immunotherapy's efficacy. Beyond direct microbial-host interactions, microbiota-derived immunomodulatory products, including metabolites, extracellular vesicles, and polysaccharides, have been shown to profoundly influence tumorigenesis, disease progression, and therapeutic responses. These microbial-derived immunomodulatory products can reshape the tumor microenvironment (TME) and modulate tumor immunity. Notably, emerging therapeutic strategies targeting or utilizing microbial immunomodulators have demonstrated promising efficacy in both preclinical and clinical models. This review provides a comprehensive overview of current research on microbiota-derived immunomodulatory products in cancer immunotherapy, highlighting their mechanistic roles and potential as innovative adjuncts in future tumor treatment strategies.},
}

@article {pmid41197754,
year = {2025},
author = {Xia, F and Yi, Q and Xu, Z and Zhou, Z and Tang, H and Zhang, K and Yan, Y},
title = {Microbial Modulation as a Game Changer: Boosting Immunotherapy Efficacy in Breast Cancer.},
journal = {Seminars in cancer biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.semcancer.2025.10.006},
pmid = {41197754},
issn = {1096-3650},
abstract = {Breast cancer is generally regarded as an immunologically cold tumor, characterized by limited T cell infiltration and poor responsiveness to immune checkpoint inhibitors. Increasing evidence suggests that the human microbiome, including both gut and tumor-associated microbial communities, serves as a critical regulator of systemic and local antitumor immunity, with potential to convert inert tumors into immune-responsive states. Gut microbiota influence systemic immune homeostasis through metabolites such as lipids, lactic acid, and trimethylamine N-oxide, which modulate T lymphocytes, dendritic cells, leukocytes, and stromal components. Tumor-resident microbiota further shape the tumor immune microenvironment by regulating CD4[+] and CD8[+] T cells, NKT cells, Tregs, and macrophages, thereby impacting the efficacy of immune checkpoint blockade. Emerging strategies to sensitize cold breast tumors through microbiome modulation include dietary phytochemicals, bariatric surgery induced microbial shifts, probiotics and postbiotics, polyvalent microbial antigen vaccines, and nanotechnology-based platforms. Clinical challenges remain, particularly interindividual microbial heterogeneity, safety and regulatory considerations, and the need for reliable microbial and immune biomarkers. This review summarizes current advances in microbiota-immune interactions in breast cancer and discusses opportunities for microbiome-targeted strategies to enhance immunotherapy outcomes.},
}

@article {pmid41197738,
year = {2025},
author = {Acevedo-Fontanez, LA and Sánchez-Feliciano, A and Ershadi, S and Reichenberg, J and Eichenfield, LF and Barbieri, JS},
title = {Periorificial Dermatitis: Pathophysiology, Diagnosis, and Management.},
journal = {Journal of the American Academy of Dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaad.2025.10.138},
pmid = {41197738},
issn = {1097-6787},
abstract = {Periorificial dermatitis is a chronic papulopustular facial dermatitis. Despite being frequently encountered in clinical practice and associated with significant effects on quality of life, its etiology remains incompletely understood, and no therapies are specifically approved by the Food and Drug Administration for its treatment. In this review, the current mechanistic understandings of periorificial dermatitis pathogenesis are discussed including the role of inciting factors, skin barrier dysfunction, inflammation, and the microbiome. In addition, we review the diagnostic features of periorificial dermatitis and how to distinguish it from clinical mimickers. Finally, treatment is discussed including skincare, topical, and systemic therapies.},
}

@article {pmid41197619,
year = {2025},
author = {Forbes, M and Ng, DYK and Boggan, RM and Frick-Kretschmer, A and Durham, J and Lorenz, O and Dave, B and Lassalle, F and Scott, C and Wagner, J and Lignes, A and Noaves, F and Jackson, DK and Howe, K and Harrison, EM},
title = {Benchmarking of human read removal strategies for viral and microbial metagenomics.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101218},
doi = {10.1016/j.crmeth.2025.101218},
pmid = {41197619},
issn = {2667-2375},
abstract = {Human reads are a key contaminant in microbial metagenomics and enrichment-based studies, requiring removal for computational efficiency, biological analysis, and privacy protection. Various in silico methods exist, but their effectiveness depends on the parameters and reference genomes used. Here, we assess different methods, including the impact of the updated telomere-to-telomere (T2T)-CHM13 human genome versus GRCh38. Using a synthetic dataset of viral and human reads, we evaluated performance metrics for multiple approaches. We found that the usage of high-sensitivity configuration of Bowtie2 with the T2T-CHM13 reference assembly significantly improves human read removal with minimal loss of specificity, albeit at higher computational cost compared to other methods investigated. Applying this approach to a publicly available microbiome dataset, we effectively removed sex-determining SNPs with little impact on microbial assembly. Our results suggest that our high-sensitivity Bowtie2 approach with the T2T-CHM13 is the best method tested to minimize identifiability risks from residual human reads.},
}

@article {pmid41197616,
year = {2025},
author = {Gao, P and Yuan, H and Mei, Z and Yin, X and Zeng, Y and Liu, Z and Yang, X and Xue, J and Liu, Z and Jiang, Y and Ye, W and Lu, M and Suo, C and Chen, X},
title = {The comprehensive oral microbiome landscape unveils its interplay with poor oral health in esophageal squamous cell carcinoma risk.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102431},
doi = {10.1016/j.xcrm.2025.102431},
pmid = {41197616},
issn = {2666-3791},
abstract = {Growing evidence links poor oral health to an increased esophageal squamous cell carcinoma (ESCC) risk, with the oral microbiome recognized as a key contributor. However, human-based evidence remains limited. Here, we analyze salivary shotgun metagenomic data from 390 ESCC case-control pairs and 16S rRNA sequencing data from 206 incident esophageal cancer (EC) case-control pairs. We identify 50 bacterial species altered in ESCC (e.g., enriched Porphyromonas catoniae and depleted Campylobacter rectus) and disruptions in 54 biochemical pathways (e.g., inosine 5'-phosphate degradation). These features potentially mediate the association between poor oral health and ESCC. Notably, this association is stronger among individuals with lower Streptococcus mitis levels, implicating pathways related to thiamine salvage and energy metabolism. Consistent findings in the validation dataset further support the interplay between the oral microbiome and oral health in EC risk. Our results highlight the promise of precision-targeted microbial interventions to improve oral health for ESCC prevention and management.},
}

@article {pmid41197352,
year = {2025},
author = {Jhetam, S and Shynkaruk, T and Hamaoka, T and Crowe, TG and Jeffery, A and Rogers, MB and Van Kessel, AG and Schwean-Lardner, K},
title = {Feeding leghorn chicks during simulated transport as an early feeding strategy and the benefits of a single spray probiotic application.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {106024},
doi = {10.1016/j.psj.2025.106024},
pmid = {41197352},
issn = {1525-3171},
abstract = {This study examined early, interrupted, or no feeding, with (P) or without (N) a spray-on probiotic (Lactobacillus reuteri), on chick stress, growth, gastrointestinal tract (GIT) development, microbiota, and gene expression during and after simulated transport (ST; 24 Hz vibration, 25°C, uncontrolled humidity). Lohmann LSL-Lite chicks (n = 1520) underwent 24 h of ST (5 h post-hatch) with either 24, 16, 8, or 0 h of feed access (FA) during ST with P or N treatment (trt). Following ST, birds were housed in pens for 14 d (5 replications/trt). Body weight, blood chemistry and heterophil-to-lymphocyte (H/L) ratio, relative length, weight and histomorphology of the GIT, quantitative PCR for ileum expression of genes related to inflammation and gut-barrier function, and microbiome analysis were assessed. At d 7 and 14, P birds were heavier. On d 1 (post-ST), H/L ratios were higher in the P trt, possibly from immunostimulation. Blood pH was lowest, and ionized calcium was highest in the 8-h trt. Glucose was higher in the N trt, and more dehydration occurred in the 0- and 8-h trt. The 0-h trt had reduced small intestine length and weight, and jejunum weight was highest in the P trt on d1. On d 7, duodenum and ileum weight were lowest for 8 h and N, respectively. Histomorphology revealed interactions in the ileum and cecum, suggestive of P preventing delayed gut development with interrupted FA. On d 1, ileum IL-6 expression was greater for 0 compared to 24 h. The P trt had a lower microbiome diversity but may have improved gut development with interrupted FA and prevented dehydration in the 0- and 8-h trt. Interrupting FA after 8 h had more negative effects than 0-h FA. With 0-h FA during ST, GIT development was delayed and could have contributed to ileum inflammation. Early FA had a positive effect on leghorn chick health, gut development, and growth. One post-hatch spray application of P may improve chick well-being over long transport durations.},
}

@article {pmid41197206,
year = {2025},
author = {Li, Y and Gao, Y and Wang, L and Si, J},
title = {NK cell adaptation in the tumor microenvironment: Insights for NK cell-based immunotherapy.},
journal = {Cytokine & growth factor reviews},
volume = {86},
number = {},
pages = {181-198},
doi = {10.1016/j.cytogfr.2025.10.003},
pmid = {41197206},
issn = {1879-0305},
abstract = {Natural killer (NK) cells serve as critical first responders within the immune system, orchestrating antitumor responses by directly eliminating malignant cells and modulating broader immune functions. Their capacity to recognize stressed targets without MHC-restricted neoantigen presentation, together with a favorable safety profile, underpins growing enthusiasm for NK cell‑based therapeutics. Nonetheless, the clinical efficacy of NK-cell-based therapies in solid tumor has been hindered by tumor microenvironment (TME)-driven immunosuppression, metabolic competition, and cell-intrinsic exhaustion mechanisms. In this review, we outline the journey from the discovery of NK cells to their role as a breakthrough target in cancer immunotherapy. We then provide a comprehensive framework of NK cell biology, from homeostatic regulation to TME-driven epigenetic, transcriptional, and metabolic adaptations. Notably, we discuss recent investigations into NK cell subset heterogeneity and their interactions with tumor cells, immune cells and the gut microbiome. Finally, we critically evaluated clinical progress while highlighting the imperative for rationally designed, mechanism-based combinations that address tumor escape pathways. The review concludes with a forward-looking perspective on engineering solutions to unlock the full therapeutic potential of NK cells across solid tumors and hematologic malignancies.},
}

@article {pmid41196682,
year = {2025},
author = {Cao, L and Shi, X and Li, T and Zhu, H and Liu, Y and Pei, R and Chen, C and Xu, Q and Zhang, H and Raza, W and Logrieco, AF and Wang, G and Liu, D and Shen, Q},
title = {Fusaric acid detoxification mediates interspecies interactions for sustainable Fusarium wilt disease management.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116531},
doi = {10.1016/j.celrep.2025.116531},
pmid = {41196682},
issn = {2211-1247},
abstract = {Microbial biocontrol agents (BCAs) play a critical role in maintaining plant health by antagonizing pathogens. However, most research has focused on direct suppression mechanisms (e.g., antibiosis and competition), while the neutralization of mycotoxin for disease management remains unexplored. Here, we report that a fungal BCA, Trichoderma harzianum (Th), subverts Fusarium verticillioides (Fv) infection via a fusaric acid (FSA) detoxification process in maize. Salicylate hydroxylase was found to detoxify FSA into an almost non-toxic metabolite, 10OH-FSA. This mechanism not only neutralized the pathogenicity of Fv but also mediated interspecies interactions contributing to Fv suppression. Additionally, FSA detoxification exhibited broad applicability in controlling different Fusarium diseases in maize, tomato, and wheat. More profoundly, Th-induced FSA detoxification activity in the rhizosphere could stimulate the growth of other FSA detoxification-capable microbes, amplifying disease suppression through ecological cross-talk. These findings unveil an ecological tactic employed by BCAs to manage soil-borne Fusarium wilt disease.},
}

@article {pmid41196658,
year = {2025},
author = {Verna, G and De Santis, S and Islam, BN and Sommella, EM and Licastro, D and Zhang, L and De Almelda Celio, F and Miller, EN and Merciai, F and Caponigro, V and Xin, W and Campiglia, P and Pizarro, TT and Chieppa, M and Cominelli, F},
title = {A missense mutation in Muc2 promotes gut microbiome- and metabolome-dependent colitis-associated tumorigenesis.},
journal = {The Journal of clinical investigation},
volume = {},
number = {},
pages = {},
doi = {10.1172/JCI196712},
pmid = {41196658},
issn = {1558-8238},
abstract = {Colitis-associated cancer (CAC) arises from a complex interplay between host and environmental factors. In this report, we investigated the role of the gut microbiome using Winnie mice, a UC-like model with a missense mutation in the Muc2 gene. Upon rederivation from a conventional (CONV) to a specific-pathogen-free (SPF) facility, Winnie mice developed severe colitis and, notably, spontaneous CAC that progressively worsened over time. In contrast, CONV Winnie showed only mild colitis but no tumorigenesis. By comparison, when rederived into germ-free (GF) conditions, SPF Winnie mice were protected from colitis and colon tumors, indicating an essential role for the gut microbiome in the development of CAC in these mice. Using shotgun metagenomics, metabolomics, and lipidomics, we identified a distinct pro-inflammatory microbial and metabolic signature that potentially drives the transition from colitis to CAC. Fecal microbiota transplantation (FMT), using either SPF Winnie or WT (Bl/6) donors into GF Winnie recipients, demonstrated that while colitis developed regardless of the donor, only FMT from SPF Winnie donors resulted in CAC. Our studies present a relevant model of CAC, providing strong evidence that the microbiome plays a key role in its pathogenesis, thereby challenging the concept of colon cancer as a strictly non-transmissible disease.},
}

@article {pmid41196474,
year = {2025},
author = {Song, H and Hosain, MM and Park, T},
title = {DeepIMB: Imputation of non-biological zero counts in microbiome data.},
journal = {Genes & genomics},
volume = {},
number = {},
pages = {},
pmid = {41196474},
issn = {2092-9293},
support = {NRF-2022R1A2C1092497//National Research Foundation of Korea/ ; },
abstract = {BACKGROUND: The high prevalence of non-biological zero counts, arising from low sequencing depth and sampling variation, presents a significant challenge in microbiome data analysis. These zeros can distort taxon abundance distributions and hinder the identification of true biological signals, complicating downstream analyses.

OBJECTIVE: To address the challenges of non-biological zeros in microbiome datasets, we propose DeepIMB, a deep learning-based imputation method for microbiome data, specifically designed to accurately identify and impute non-biological zero counts while preserving biological integrity.

METHODS: DeepIMB operates in two main phases. First, it identifies non-biological zeros using a gamma-normal mixture model applied to the normalized, log-transformed taxon count matrix. Second, it imputes these zeros with a deep neural network model that integrates diverse sources of information, including taxon abundances, sample covariates, and phylogenetic distances, thereby learning complex, nonlinear relationships within microbiome data.

RESULTS: By leveraging integrated information from multiple data types, DeepIMB accurately imputes non-biological zeros while preserving true biological signals. In our two simulation studies, DeepIMB outperformed existing imputation methods in terms of mean squared error, Pearson correlation coefficient, and Wasserstein distance.

CONCLUSION: DeepIMB effectively addresses the challenges posed by non-biological zeros in microbiome data. By improving the quality of the data and the reliability of downstream analyses, DeepIMB represents a significant advancement in microbiome research methodologies.},
}

@article {pmid41196415,
year = {2025},
author = {He, Y and Yang, T and Mi, J and He, S and Yang, Z and Lu, S and Yue, K and Huang, Y and Song, L and Xiao, Y and Ren, Z},
title = {B.uniformis IM01-derived IAA alleviates asthma via AhR/NLRP3 pathways in mice.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {82},
number = {1},
pages = {388},
pmid = {41196415},
issn = {1420-9071},
support = {2023YFC0871200//the National Key R&D Program of China/ ; 33054//the National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/ ; 29172//the National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention/ ; },
mesh = {Animals ; *Receptors, Aryl Hydrocarbon/metabolism ; *Asthma/pathology/metabolism/immunology/drug therapy ; *NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; *Indoleacetic Acids/metabolism/pharmacology ; Mice ; *Signal Transduction/drug effects ; Disease Models, Animal ; NF-kappa B/metabolism ; Mice, Inbred BALB C ; T-Lymphocytes, Regulatory/immunology ; Female ; Lung/pathology ; Interleukin-22 ; Tryptophan/metabolism ; Th2 Cells/immunology ; Interleukins/metabolism ; *Basic Helix-Loop-Helix Transcription Factors/metabolism ; },
abstract = {Symbiotic flora exhibits a strong association with the pathogenesis of allergic disorders. Certain Bacteroides species have demonstrated potential in ameliorating allergic conditions. However, the specific role of Bacteroides uniformis in allergic asthma and its underlying mechanisms remain incompletely understood. This study demonstrates that oral administration of B.uniformis IM01 significantly enhanced the production of indole-3-acetic acid (IAA), suppressed airway inflammatory cell airway infiltration and aberrant T helper 2 (Th2) immune responses, and improved the epithelial barrier function in a murine model of asthma. Mechanistically, B.uniformis IM01 upregulated tryptophan metabolism, elevating IAA levels in both colon and serum, which activated the aryl hydrocarbon receptor (AhR) and induced interleukin-22 (IL-22) production. Activated AhR may inhibit NF-κB/NLRP3 signaling pathway and facilitate the splenic differentiation of Foxp3[+] regulatory T cells (Tregs), thus attenuating lung barrier dysfunction and improving allergic asthma symptoms. In summary, our results revealed that B.uniformis IM01 upregulated production of IAA to activate AhR leading to inhibited NF-κB/NLRP3-mediated immune responses, and ameliorated allergic asthma through the gut-lung axis.},
}

Animals
*Receptors, Aryl Hydrocarbon/metabolism
*Asthma/pathology/metabolism/immunology/drug therapy
*NLR Family, Pyrin Domain-Containing 3 Protein/metabolism
*Indoleacetic Acids/metabolism/pharmacology
Mice
*Signal Transduction/drug effects
Disease Models, Animal
NF-kappa B/metabolism
Mice, Inbred BALB C
T-Lymphocytes, Regulatory/immunology
Female
Lung/pathology
Interleukin-22
Tryptophan/metabolism
Th2 Cells/immunology
Interleukins/metabolism
*Basic Helix-Loop-Helix Transcription Factors/metabolism

@article {pmid41196286,
year = {2025},
author = {Ni, Z and Ye, D},
title = {The impact of gut microbiota modulation on responses to immune checkpoint inhibitors in cancer.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2025.02719},
pmid = {41196286},
issn = {1588-2640},
abstract = {The gut microbiota has emerged as a critical determinant of antitumor immunity and a potential modulator of responses to immune checkpoint inhibitors (ICIs). Although pre-clinical and clinical studies suggest that specific bacterial taxa may influence both efficacy and immune-related adverse events (irAEs). However, the magnitude and consistency of these associations remain unclear. A systematic search of PubMed, Embase, Web of Science, and the Cochrane Library was conducted through March 2025. Eligible studies evaluated baseline gut microbiota composition, fecal microbiota transplantation (FMT), probiotic/prebiotic interventions, or antibiotic exposure in cancer patients treated with ICIs. Pooled hazard ratios (HRs) for overall survival (OS) and progression-free survival (PFS), and odds ratios (ORs) for response rates and irAEs, were estimated using random-effects models. Across 38 studies involving 5,642 patients were included. Pooled analysis demonstrated that enrichment of Akkermansia muciniphila, Bifidobacterium longum and Faecalibacterium prausnitzii was significantly associated with improved OS (HR 0.62, 95% CI 0.51-0.76) and PFS (HR 0.69, 95% CI 0.55-0.83). Conversely, antibiotic exposure before or during ICI treatment was associated with worse OS (HR 1.84, 95% CI 1.45-2.34). Patients undergoing FMT from responders exhibited higher objective response rates (OR 2.91, 95% CI 1.48-5.73). Microbiota diversity indices were consistently higher in responders than in non-responders. Collectively, gut microbiota composition and its modulation significantly impact the therapeutic efficacy and toxicity profile of ICIs. These findings highlight the translational potential of microbiome-based biomarkers and interventions in optimizing immunotherapy.},
}

@article {pmid41196057,
year = {2025},
author = {Fait Kadlec, T and Ilett, EE and da Cunha-Bang, C and Sengeløv, H and Brieghel, C and Gulay, A and Rafiq, S and Ravn, HB and Zheng, C and Nielsen, RV and Sørensen, SS and Zargari Marandi, R and Niemann, CU},
title = {Explainable machine learning to identify chronic lymphocytic leukemia and medication use based on gut microbiome data.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0094425},
doi = {10.1128/spectrum.00944-25},
pmid = {41196057},
issn = {2165-0497},
abstract = {Medication, particularly antibiotics, significantly alters gut microbiome composition, often reducing microbial diversity and affecting host health. Given that the gut microbiome may influence cancer progression, we integrated clinical, shotgun metagenomic, and medication data to assess microbiome composition across diseased and healthy cohorts, as well as the impact of medication on microbiome variation. The study cohorts included patients with chronic lymphocytic leukemia (CLL, n = 85), acute myeloid leukemia (AML, n = 61), myeloid dysplastic syndrome (MDS), and other severe hematological malignancies (n = 104); patients scheduled for elective cardiac surgery (n = 89); and kidney donors (n = 9), all collected as part of a consecutive microbiome sampling effort at Copenhagen University Hospital, Denmark; and healthy individuals (N = 59). First, our analyses revealed similarities in both diversity and composition between microbiomes of patients with CLL and patients prior to elective cardiac surgery, whereas patients with AML and MDS exhibited the least diverse and most distinct microbiomes. Second, when we quantified sources of microbiome variation, the combination of medication, disease, age, and sex accounted for 4% of variation between all cohorts and 10.4% of variation between CLL and pre-cardiac surgery patients only; the two cohorts selected for comparison due to their similar microbiomes. Notably, this left 90%-95% of the variation unexplained, emphasizing the need for better identification of the parts of the microbiome variation impacting health and disease. Third, using a machine learning approach, we validated and further refined the CLL-associated microbiome pattern from our previous studies. Overall, our data provide a foundation for further investigation into disease-specific microbial signatures and the potential interactions between medication, underlying disease, and the microbiome, with the ultimate goal to improve our understanding and clinical management of CLL.IMPORTANCEThis study reveals how disease and medication influence the gut microbiome in patients with chronic lymphocytic leukemia (CLL) when compared to other more severe hematological malignancies, a cohort of patients scheduled for elective cardiac surgery representing a severely diseased nonhematological cohort, and a cohort of healthy individuals. We found that patients with CLL and those scheduled for cardiac surgery had the most similar microbiome diversity and composition. Similarities across very different disease contexts suggest that disease status alone has limited impact. Consistently, across all cohorts, medication, disease, age, and sex together explained only less of microbiome variation, leaving 90%-95% unexplained. This underscores the important need for better identification of factors shaping the microbiome. In addition, we validated a previously published, machine learning-based CLL-associated microbiome signature, demonstrating the robustness of our previous findings differentiating the microbiome signature for CLL as compared to healthy individuals. The findings expand knowledge on how disease states and medical treatments shape gut microbiome composition and diversity, potentially leading to new ways of managing CLL and improving patient outcomes through microbiome signatures.},
}