@article {pmid41325973,
year = {2025},
author = {Meng, D and He, S and Wei, M and Lv, Z and Yang, G and Wang, Z},
title = {Gut microbiota's causal effect on physical activity: Insights from two-sample Mendelian randomization analysis.},
journal = {Physiology & behavior},
volume = {},
number = {},
pages = {115190},
doi = {10.1016/j.physbeh.2025.115190},
pmid = {41325973},
issn = {1873-507X},
abstract = {INTRODUCTION: Gut microbiota has been implicated in influencing various health-related behaviors, including physical activity. This study aimed to investigate the causal relationship between gut microbiota and physical activity in individuals of European ancestry.

MATERIALS AND METHODS: We conducted a two-sample Mendelian randomization analysis using genome-wide association data from the MiBioGen consortium and the UK Biobank. Numerous gut microbiome taxa were assessed for their causal effect on physical activity measures, including moderate-to-vigorous physical activity, vigorous physical activity, accelerometer-based average acceleration, and higher acceleration levels. Sensitivity analyses evaluated heterogeneity, pleiotropy, and potential reverse causation.

RESULTS: The analysis identified significant causal links between specific gut microbiome genera and physical activity levels. Key taxa were associated with physiological conditions conducive to exercise and behavior related to physical exertion. Sensitivity analyses confirmed the robustness of these findings, with minimal evidence of heterogeneity or pleiotropy, and reverse causality was largely excluded.

CONCLUSION: Gut microbiota may play a causal role in influencing physical activity levels, offering potential for microbiome-targeted interventions to promote physical health.},
}

@article {pmid41325637,
year = {2025},
author = {Pieterse, CMJ},
title = {The Extended Plant Immune System.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {},
number = {},
pages = {},
doi = {10.1094/MPMI-10-25-0144-HH},
pmid = {41325637},
issn = {0894-0282},
abstract = {When disease resistance was still viewed as a vague physiological response rather than a genetically defined process, Flor laid the foundation for our modern understanding of plant immunity with his gene-for-gene concept. Initially developed for simple host-pathogen interactions, this idea evolved into a more complex framework in which plants engage in continuous dialogue with a diverse microbiome. Within this community, beneficial, commensal, and pathogenic microbes interact both directly and indirectly through the plant host, extending the boundaries of plant immunity beyond the individual organism. This broader perspective envisions an "extended plant immune system" that integrates the plant's microbial partners into a coordinated, community-level defense. Like early views of disease resistance, this concept was first described in broad physiological or ecological terms. As the field has matured with the advent of next-generation sequencing, it has become clear that the microbiome-mediated extension of the plant immune system is also grounded in genetically determined molecular processes. These range from host-driven recruitment of protective microbiota, to microbial traits that suppress pathogens, and to plant mechanisms that enable beneficial microbes to trigger induced systemic resistance. This review is a symphony composed of historical progression of research from molecular recognition to community-level defense, distilling the principles that connect classical plant immunity with emerging plant-microbiome concepts and framing microbiome-mediated disease protection as an extension of the plant's innate immune system. This integrated perspective not only reframes our understanding of plant immunity but also offers a conceptual foundation for harnessing the extended immune system in sustainable crop protection.},
}

@article {pmid41325498,
year = {2025},
author = {Laric, PP and Mortazavi, A and Węgrzyn, E and Simon, K and Rittel, PS and Trefz, FM and Sabass, B},
title = {A reliable in vitro rumen culture system and workflow for screening anti-methanogenic compounds.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0335844},
doi = {10.1371/journal.pone.0335844},
pmid = {41325498},
issn = {1932-6203},
mesh = {*Rumen/microbiology/metabolism/drug effects ; Animals ; *Methane/metabolism/biosynthesis ; Cattle ; Workflow ; },
abstract = {Arguably the biggest man-made challenge of the century is halting climate change. Livestock's methane (CH4) emissions, a greenhouse gas with a higher global warming potential than carbon dioxide (CO2), represent a prime target for reducing anthropogenic impact. While the reduction of enteric methane emissions through feed additives has been demonstrated, potent and affordable compounds inhibiting methanogenesis in ruminants are not yet well established. Reliable methods for reproducible cultivation of the rumen microbiome in the laboratory are an essential tool for the study of methanogenesis. We have developed a versatile setup that allows for the cultivation of the ruminal microbiome in a benchtop configuration and combines, miniaturizes, and improves existing systems. The design is based on standard laboratory equipment, including bottles, serological pipettes, tubing, and Luer-Lock valves. The apparatus enables long-term cultivation of primary cultures extracted from the rumen of slaughtered cattle. We describe rumen content acquisition, preparation, the cultivation procedure, and demonstrate the system's performance. The efficacy of the system is demonstrated through the administration of various concentrations of state-of-the-art methanogenesis inhibitors. These inhibitors include lyophilized Asparagopsis taxiformis (AT), bromoform (BF), iodoform (IF), 3-nitrooxypropanol (3-NOP), rapeseed oil, and BF dissolved in rapeseed oil, with maximum CH4 reductions of 96.29% (p = 5.00E-05, Cohen's d = 30.29), 98.22% (p = 2.88E-05, d = 23.07), 96.26% (p = 1.03E-05, d = 30.29), 74.63% (p = 8.88E-05, d = 13.32), 28.96% (p = 0.001, d = 3.99), and 98.51% (p = 4.18E-06, d = 39.94), respectively, in comparison to the negative control. The gas production dynamics in our setup align with previously published results, which supports the validity of the system. Compared to conventional methodologies, the described setup offers enhanced versatility and ease of use. Furthermore, Fourier-transform-infrared-spectroscopy is implemented in a novel and low-cost approach for quantifying CH4 and CO2 in the headspace gas. Together, these methodological advances provide an accessible and reproducible platform for long-term in vitro rumen cultivation for the screening of anti-methanogenic additives.},
}

*Rumen/microbiology/metabolism/drug effects
Animals
*Methane/metabolism/biosynthesis
Cattle
Workflow

@article {pmid41325459,
year = {2025},
author = {Paredes-Vázquez, A and Balsa-Canto, E and Banga, JR},
title = {Identification of dynamic models of microbial communities: A workflow addressing identifiability and modeling pitfalls.},
journal = {PLoS computational biology},
volume = {21},
number = {12},
pages = {e1013204},
doi = {10.1371/journal.pcbi.1013204},
pmid = {41325459},
issn = {1553-7358},
abstract = {Microbial communities, complex ecological networks crucial for human and planetary health, remain poorly understood in terms of the quantitative principles governing their composition, assembly, and function. Dynamic modeling using ordinary differential equations (ODEs) is a powerful framework for understanding and predicting microbiome behaviors. However, developing reliable ODE models is severely hampered by their nonlinear nature and the presence of significant challenges, particularly critical issues related to identifiability. Here, we address the identification problem in dynamic microbial community models by proposing an integrated methodology to tackle key challenges. Focusing on nonlinear ODE-based models, we examine four critical pitfalls: identifiability issues (structural and practical), unstable dynamics (potentially leading to numerical blow-up), underfitting (convergence to suboptimal solutions), and overfitting (fitting noise rather than signal). These pitfalls yield unreliable parameter estimates, unrealistic model behavior, and poor generalization. Our study presents a comprehensive workflow incorporating structural and practical identifiability analysis, robust global optimization for calibration, stability checks, and rigorous predictive power assessment. The methodology's effectiveness and versatility in mitigating these pitfalls are demonstrated through case studies of increasing complexity, paving the way for more reliable and mechanistically insightful models of microbial communities.},
}

@article {pmid41325413,
year = {2025},
author = {Piekielko-Witkowska, A and Elisei, R and Léger, J and Bendlova, B and Bulanová Pekova, B and Caron, P and Durante, C and Fassnacht, M and Feldt-Rasmussen, U and Filipsson Nyström, H and Jansen, H and Köhrle, J and Kus, A and Ludgate, M and Mertens, J and Oczko-Wojciechowska, M and Peters, C and Schoenmakers, N and Stoupa, A and van Santen, H and Trimboli, P and van Trotsenburg, P and Visser, WE},
title = {EndoCompass Project: Research Roadmap for Thyroid Endocrinology.},
journal = {Hormone research in paediatrics},
volume = {},
number = {},
pages = {1-14},
doi = {10.1159/000549075},
pmid = {41325413},
issn = {1663-2826},
abstract = {BACKGROUND: Endocrine science remains underrepresented in European Union research programs despite the fundamental role of hormone health in human well-being. Analysis of the CORDIS database reveals a persistent gap between the societal impact of endocrine disorders and their research prioritization. At national funding level, endocrine societies report limited or little attention of national research funding toward endocrinology. The EndoCompass project - a joint initiative between the European Society of Endocrinology and the European Society of Paediatric Endocrinology, aimed to identify and promote strategic research priorities in endocrine science to address critical hormone-related health challenges.

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

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

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

@article {pmid41325179,
year = {2025},
author = {Hertl, V and Lackner, S and Ramirez-Obermayer, A and Baranyi, A and Wagner-Skacel, J and Mörkl, S},
title = {The Use of Nutritional Psychiatry in the Treatment of a Patient With Treatment-resistant Depression: A Biopsychosocial Case Report.},
journal = {Journal of psychiatric practice},
volume = {31},
number = {6},
pages = {337-345},
pmid = {41325179},
issn = {1538-1145},
mesh = {Humans ; Adult ; *Depressive Disorder, Treatment-Resistant/therapy/diet therapy ; Electroconvulsive Therapy ; Male ; *Malnutrition/diet therapy ; *Nutrition Therapy/methods ; },
abstract = {This case study describes a 30-year-old patient with recurrent depressive disorder and pharmacological treatment resistance. After 2 courses of electroconvulsive therapy without significant improvement, the illness was classified as treatment-refractory. A comprehensive nutrient analysis and dietary history identified malnutrition, nutrient deficiencies, and gastrointestinal issues. By supplementing the treatment-as-usual approach with personalized nutritional and nutrient therapy, a significant reduction in depressive symptoms was achieved, and the pharmacological medication could be reduced. This case suggests that targeted nutritional and nutrient interventions may help enhance the effectiveness of pharmacological treatment and support mental health by promoting metabolic processes.},
}

Humans
Adult
*Depressive Disorder, Treatment-Resistant/therapy/diet therapy
Electroconvulsive Therapy
Male
*Malnutrition/diet therapy
*Nutrition Therapy/methods

@article {pmid41324840,
year = {2025},
author = {Wu, Y and Wang, C and Yu, J and Zhou, X and Wang, Y and Chen, ZJ and Du, Y},
title = {Akkermansia muciniphila PROBIO therapy promotes arginine biosynthesis and reverses reproductive impairments in polycystic ovary syndrome rats.},
journal = {Frontiers of medicine},
volume = {},
number = {},
pages = {},
pmid = {41324840},
issn = {2095-0225},
abstract = {Polycystic ovary syndrome (PCOS) is a prevalent chronic disorder characterized by reproductive, endocrine, and metabolic abnormalities in women worldwide. Increasing evidence has implicated the gut microbiota in the pathogenesis of PCOS, raising the possibility that probiotic interventions could offer therapeutic benefits. Akkermansia muciniphila (AKK), known for its metabolic and immunomodulatory properties, remains underexplored in the context of PCOS. In this study, we utilized a dehydroepiandrosterone (DHEA)-induced PCOS model in Sprague-Dawley (SD) rats to investigate the therapeutic potential of a novel AKK strain, PROBIO (referred to as AP). Treatment with AP significantly alleviated multiple PCOS-related phenotypes, including hyperandrogenism, elevated luteinizing hormone to follicle-stimulating hormone (LH/FSH) ratio, disrupted estrous cycle, abnormal ovarian morphology, and impaired glucose metabolism. Mechanistically, 16S rRNA gene sequencing and untargeted metabolomics revealed that AP partially exerted its beneficial effects by modulating DHEA-induced gut microbiota dysbiosis. Notably, metabolomic profiling indicated enhanced arginine biosynthesis and increased serum L-arginine levels in AP-treated rats. Consistently, in vivo supplementation with L-arginine reproduced the therapeutic effects of AP, ameliorating hyperandrogenism, LH/FSH imbalance, ovarian abnormalities, and estrous cycle irregularities in DHEA-induced PCOS rats. Taken together, these findings suggest that AP ameliorates PCOS phenotypes by restoring gut microbial composition, modulating host metabolism, and promoting L-arginine biosynthesis. This study highlights the potential of AP as a novel probiotic-based intervention for PCOS and underscores the therapeutic relevance of L-arginine in managing this disorder.},
}

@article {pmid41324703,
year = {2025},
author = {Uwimbabazi, A and Ramasamy, S and Mwamba, TM and Syampungani, S},
title = {Microbial communities in mine waste- contaminated soil of Sub-Saharan Africa: potential application for ecoremediation.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {1},
pages = {22},
pmid = {41324703},
issn = {1573-2983},
mesh = {Biodegradation, Environmental ; *Mining ; *Soil Pollutants/metabolism/analysis ; *Soil Microbiology ; Africa South of the Sahara ; *Microbiota ; Bacteria/metabolism/classification ; *Industrial Waste/analysis ; },
abstract = {In recent years, mining activities have increased significantly across SSA (Sub-Saharan Africa), leading to adverse environmental and health impacts. Our review examined diverse microbiota inhabiting various types of mine waste in SSA, emphasizing their natural adaptive mechanisms to withstand extreme conditions. We highlighted key gaps and directions for future studies to support the use of mine waste-resistant microorganisms in ecoremediation efforts. A comprehensive literature search was conducted using reputable online databases to cover studies published between January 2010 and 2024 for information synthesis. Our analysis has revealed microbial communities mainly comprising Proteobacteria (33%), Firmicutes (22%), Actinobacteria (12%), and Acidobacteria (4.1%) of all reported microbial phyla, along with other microbial phyla such as Nitrospirae, Bacteroidetes and Ascomycota distributed across different mine-impacted ecosystems in SSA. The mine wastes reported in this study primarily consist of metals and metalloids (66.7%), followed by oil and hydrocarbons (16%), coal (6.3%), salt (6.2%), and smaller portions of rare metals, and phosphate, each accounting for 1.6%. Microbial species within these phyla exhibit the ability to thrive in polluted environments due to their inherent capacity to metabolize, degrade, and transform toxic compounds, thereby facilitating natural attenuation. However, technical, scientific, operational, implementation, regulatory, and economic challenges hinder bioremediation practices in SSA. Despite these challenges, the region offers significant opportunities that can serve as the foundation for overcoming such constraints. To support scalable and sustainable bioremediation, it is essential to conduct pilot studies focusing on indigenous microbes, alongside systemic monitoring to assess progress and optimize outcomes over time in bioremediation efforts.},
}

Biodegradation, Environmental
*Mining
*Soil Pollutants/metabolism/analysis
*Soil Microbiology
Africa South of the Sahara
*Microbiota
Bacteria/metabolism/classification
*Industrial Waste/analysis

@article {pmid41324625,
year = {2025},
author = {Majhi, S and Sikdar, M},
title = {Isolation and characterization of root nodule-associated bacteria from chickpea (Cicer arietinum) for evaluating plant growth-promoting activities and heavy metal tolerance.},
journal = {Archives of microbiology},
volume = {208},
number = {1},
pages = {44},
pmid = {41324625},
issn = {1432-072X},
support = {F.16-6(DEC. 2016)/2017(NET)//University Grants Commission/ ; SR/FST/LSI-560/2013(c)//DST-FIST Programme of Department of Life Sciences, Presidency University, Kolkata/ ; BT/ INF/22/SP45088/2022//DBT-BUILDER Grant of Department of Life Sciences, Presidency University, Kolkata/ ; },
mesh = {*Cicer/microbiology/growth & development ; *Metals, Heavy/metabolism/toxicity ; Phylogeny ; Indoleacetic Acids/metabolism ; *Enterobacter/isolation & purification/genetics/metabolism/classification/drug effects ; *Root Nodules, Plant/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/isolation & purification/classification/genetics/metabolism ; Ammonia/metabolism ; Soil Microbiology ; Plant Growth Regulators/metabolism ; },
abstract = {Two bacterial strains were isolated from root nodules of the chickpea plant (Cicer arietinum) in West Bengal and characterized to assess their potential for heavy metal (HM) tolerance and plant growth-promoting (PGP) attributes. Phylogenetic analysis based on the 16 S rRNA gene identified these strains, SMAJ_63 and SMAJ_180, belonging to the genera Enterobacter sp. and Labrys sp, respectively. The two strains were screened for tolerance to multiple HMs, including arsenic (As), cadmium (Cd), cobalt (Co), chromium (Cr), and copper (Cu), with particular emphasis on chromium (Cr) due to its high environmental relevance and comparatively limited exploration in the literature. Two strains, SMAJ_63 and SMAJ_180, were evaluated for their tolerance to HMs, and their IC50 values were determined. PGP attributes, including phosphate solubilization, indole acetic acid (IAA), and ammonia production were determined. Strain SMAJ_63 exhibited IAA production of 23.29 µg/mL, whereas strain SMAJ_180 did not produce any detectable IAA. However, both strains were capable of producing ammonia, with strain SMAJ_63 and strain SMAJ_180 yielding 27.24 mM and 0.75 mM, respectively. Both strains demonstrated the ability to solubilize inorganic phosphate into soluble forms, indicating their potential contribution to enhanced phosphorus availability. Furthermore, strain SMAJ_63 exhibited exopolysaccharide (EPS) production, yielding 0.67 g/L, whereas strain SMAJ_180 did not produce any detectable EPS. In conclusion, these findings highlight the potential of the selected strains as effective PGP bacteria under heavy metal stress, indicating their applicability in enhancing crop productivity and contributing to sustainable agricultural practices.},
}

*Cicer/microbiology/growth & development
*Metals, Heavy/metabolism/toxicity
Phylogeny
Indoleacetic Acids/metabolism
*Enterobacter/isolation & purification/genetics/metabolism/classification/drug effects
*Root Nodules, Plant/microbiology
RNA, Ribosomal, 16S/genetics
*Bacteria/isolation & purification/classification/genetics/metabolism
Ammonia/metabolism
Soil Microbiology
Plant Growth Regulators/metabolism

@article {pmid41324463,
year = {2025},
author = {Furman, O and Sorek, G and Moraïs, S and Levin, L and Tovar-Herrera, OE and Winkler, S and Mizrahi, I},
title = {Persistent auxiliary microbiome of early novel colonizers in the developing rumen with lasting functional significance.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf252},
pmid = {41324463},
issn = {1751-7370},
abstract = {The early life assembly of the rumen microbiome is a critical process with lasting implications for host development and function. Using high-resolution longitudinal metagenomics in calves tracked from birth to three years (∼800 days) of age, we reconstructed 2873 high-quality metagenome-assembled genomes (MAGs), including 517 novel genomes primarily detected in early life. These novel genomes, spanning 274 genera and largely classified as non-core taxa, reveal a diverse and functionally distinct auxiliary microbiome. Unlike in other ecosystems, this early microbial community persists into adulthood, retaining ecological and functional relevance despite a decline in abundance. Temporal clustering revealed strong associations between auxiliary taxa and dietary transitions, with functional enrichments in environmental sensing, nutrient biosynthesis, and volatile fatty acid metabolism. Metabolic network analyses showed that auxiliary genomes complement non-auxiliary community members in key functions, with potential effects on the host. Our findings suggest that early colonizers act as ecosystem engineers, with the potential to shape the developmental trajectory of the rumen microbiome. This study thus positions the early microbiome not as a transient feature of colonization, but as a structured, functionally coherent auxiliary community that interacts with the mature rumen ecosystem.},
}

@article {pmid41324448,
year = {2025},
author = {Donald, K and Serapio-Palacios, A and Bozorgmehr, T and Tabusi, M and Finlay, BB},
title = {Milk IgA promotes symbionts and limits pathobionts in the early life gut.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf266},
pmid = {41324448},
issn = {1751-7370},
abstract = {Secretory Immunoglobulin A (SIgA) is the dominant mucosal antibody and a key regulator of the gut microbiota. In early life, infants rely on breastmilk as their primary source of SIgA, but the role of milk-derived SIgA in early life microbiota colonization dynamics remains incompletely understood. Here, we show that species-specific SIgA in milk is antigen-inducible and discriminates between closely related but immunologically diverging microbes in the neonatal gut. More specifically, milk species-specific SIgA promotes colonization by an anti-inflammatory Escherichia coli strain while restricting the expansion of pro-inflammatory Proteus mirabilis. These findings uncover a dual role of maternal milk SIgA in actively sculpting the early life gut microbiota with species-level precision.},
}

@article {pmid41324297,
year = {2025},
author = {Lirakis, M and Dolezal, M and Nolte, V and Schlötterer, C},
title = {Diet-induced transgenerational effects on Drosophila dormancy are not mediated by the microbiome.},
journal = {The Journal of experimental biology},
volume = {},
number = {},
pages = {},
doi = {10.1242/jeb.250069},
pmid = {41324297},
issn = {1477-9145},
support = {641456//H2020 Marie Skodowska-Curie Actions/ ; FWF, P27630, W1225//Austrian Science Fund/ ; },
abstract = {Environmental signals exert influences not only on the current generation, but also extend to subsequent generations, even when these signals no longer persist. These transgenerational effects can be mediated through several mechanisms, including epigenetic inheritance and composition of the gut microbiome. In this study we investigated the contribution of the microbiome to diet-induced transgenerational effects on reproductive dormancy. Multiple strains of Drosophila simulans were subjected to a shift from sugar-rich to sugar-poor diet and the impact of this diet switch on dormancy was determined over multiple generations. Consistent with significant transgenerational effects, we observed a gradual reduction in dormancy incidence with an increasing number of generations exposed to the new, sugar-poor diet. Despite the variation in dormancy induced by the dietary shift, the microbiome composition remained largely stable. Consequently, we conclude that these transgenerational effects are not determined by changes in the bacterial microbiome composition.},
}

@article {pmid41324262,
year = {2025},
author = {Kuar, KD and Sarker, AK and Nelson, I and Plett, JM and Stack, CM and Morton, CO and Moffitt, MC},
title = {Screening leaf-associated fungi from the critically endangered plant Rhodamnia rubescens suggests biocontrol potential against myrtle rust.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf293},
pmid = {41324262},
issn = {1365-2672},
abstract = {AIMS: Myrtle rust, caused by the obligate pathogen Austropuccinia psidii, is a significant disease of myrtaceous plants. Species in Australia, such as Rhodamnia rubescens, are now critically endangered as a result of this disease. This research aimed to evaluate the culturable fungal communities present on, and within, leaves of symptomatic and asymptomatic R. rubescens plants as inhibitors of myrtle rust disease. We hypothesised that microbes present in asymptomatic leaves may possess biocontrol activity, thereby providing a mechanism of resistance observed in the field.

METHODS AND RESULTS: Fungal communities were isolated on three types of media and were identified using ITS sequencing. Of the 143 isolates obtained from both leaf types, germinating spores from nine isolates from the genera Nemania, Corynespora, Cladosporium, Pestalotiopsis, Quambalaria, Kalmanozyma, and Coniothyrium were found to inhibit the germination of A. psidii spores in vitro. However, no link was found between biocontrol activity of the isolates recovered and the degree of disease found on R. rubescens leaves. Isolates were also screened for antifungal activity during active hyphal growth using an unrelated pathogenic fungus Stagonosporopsis cucurbitacearum to test for broader bioprotective activity.

CONCLUSIONS: Isolates with antagonistic activities could be further explored in conservation efforts to protect plants against A. psidii symptoms, either in isolation, as part of a synthetic microbial community, or in more agricultural contexts to improve food security.},
}

@article {pmid41324164,
year = {2025},
author = {Zhang, H and Huang, X and Wang, S and Lei, Z and Wang, Y and Pan, K and Sheng, J and He, Z and Wang, Z and Zhu, H and Zhao, X},
title = {Root-Exuded Metabolites Recruit Selenium-Transforming Microbiota to Enhance Plant Selenium Acquisition.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70307},
pmid = {41324164},
issn = {1365-3040},
support = {//This study was supported by the National Key Research and Development Program of China (2023YFD1900904), 2025 Science and Technology Project of Hubei Geological Bureau (Grant KJ2025-5), the joint support from the Hubei Provincial Natural Science Foundation and Hubei Geological Bureau of China (Grant 2023AFD215), Wuhan Academy of Agricultural Sciences Innovation Project (XKCX202526), special fund of Xinjiang Key Laboratory of Soil and Plant Ecological Processes (24XJTRZW13), the Funding for Scientific Research Projects from Wuhan Municipal Health Commission (WY22B04), the Science and Technology Research Project of Hubei Province (D20234501), the Foundation of Talent Introduction Project of Hubei Polytechnic University (23xjz05R)./ ; },
abstract = {Microbial fortification represents a promising approach for selenium biofortification in crops. Building on the previous discovery that Bacillus cereus SESY enhances selenium uptake in Brassica napus, this study employed an integrated multi-omics approach to investigate the mechanism by which B. cereus SESY enhances Se bioavailability in the Brassica napus rhizosphere. Inoculation with B. cereus SESY significantly increased selenium content in Brassica napus roots and shoots in calcareous soil by 42.9% and 21.5%, respectively, and increased the selenium content of shoots in yellow brown soil by 30.7%. B. cereus SESY promoted the transformation of residual Se into bioavailable forms and enriched bacterial taxa with high motility and Se-transforming capacity (e.g., Lysobacter, Rhodanobacter, Sphingomonas and Burkholderiaceae) in rhizosphere soil. Key genes of these bacteria involved in Se metabolism (e.g., trxA, narH, cysE, cysK, metB) and cell motility genes (e.g., FlgG, CheW, FliH) were up-regulated. Core rhizosphere metabolites such as N-formylmethionine and xanthine correlated strongly with enriched bacteria abundance and available Se. Joint application of these metabolites with enriched bacteria increased plant Se content by 144% and rhizosphere soil available Se by 13.4%. These results reveal a metabolite-mediated microbial network that enhances Se mobility and plant uptake, providing a novel strategy for microbiome-driven biofortification.},
}

@article {pmid41324109,
year = {2025},
author = {Butt, SA},
title = {Letter to Editor: Gut-Microbiome and Nutritional Analysis Reveals Food Intake as a Key Factor in the Incidence and Prevention of Colon Polyps: A Cross-Sectional Study.},
journal = {Health science reports},
volume = {8},
number = {12},
pages = {e71582},
pmid = {41324109},
issn = {2398-8835},
}

@article {pmid41323826,
year = {2025},
author = {Wang, J and Lu, X and Zhao, Y and Jiang, Z and Wang, J and Wang, Z and Zhang, X},
title = {Dietary Index for Gut Microbiota and Leisure Time Physical Activity: The Potential Combined Protective Impact on Hypertension Risk.},
journal = {Food science & nutrition},
volume = {13},
number = {12},
pages = {e71245},
pmid = {41323826},
issn = {2048-7177},
abstract = {Emerging evidence highlights the gut microbiome's role in hypertension via microbial metabolites and endothelial dysfunction, while the Dietary Index for Gut Microbiota (DI-GM) quantifies diet quality for microbiota health. In addition, leisure-time physical activity (LTPA) also reduces blood pressure, but their combined impact on population-level hypertension remains unclear. Therefore, this study explores the individual and joint effects of DI-GM and LTPA on hypertension risk. To address this objective, we conducted a cross-sectional study analysis of data from 27,643 adults in the National Health and Nutrition Examination Survey (NHANES 2007-2020). Excluding individuals with incomplete data, key variables included the DI-GM and LTPA pattern (categorized by intensity, frequency, and regularity; regularly active defined as > 2 days/week). Weighted logistic regression models and restricted cubic splines (RCS) evaluated independent, joint, and non-linear associations of DI-GM and LTPA with hypertension, adjusting for covariates. The results showed that higher DI-GM scores and greater weekly LTPA were inversely correlated with hypertension risk, exhibiting dose-dependent patterns (16% lower odds for DI-GM ≥ 6 vs. lowest groups; 16%-24% lower odds for LTPA (≥ 150 min/week) vs. lowest groups). RCS analysis showed a linear inverse dose-response relationship between DI-GM and hypertension. The regularly active LTPA pattern (> 2 days/week) was linked to a 24% lower risk of hypertension (OR = 0.76, 95% CI = 0.69-0.84), and there was also a significant association observed for the weekend warrior LTPA pattern (1-2 days/week) (OR = 0.80, 95% CI = 0.64-0.99). Notably, joint analysis demonstrated that individuals with DI-GM > 4 scores and LTPA ≥ 150 min/week or regularly LTPA pattern exhibited the lowest hypertension odds. In conclusion, both a high DI-GM score (≥ 6 points) and sufficient LTPA (≥ 150 min/week) were independently associated with reduced odds of hypertension, with their combined effect amplifying protective benefits. Prospective studies are warranted to confirm temporality and causal pathways.},
}

@article {pmid41323692,
year = {2025},
author = {Thompson, L and Goh, YE and Jamwal, M and Singh, BL and Brar, GK and Arnold, CD and Westcott, J and Long, JM and Krebs, NF and Zivkovic, A and Das, R and Duggal, M and McDonald, CM},
title = {The Effect of Quintuply-Fortified Salt on the Gut Microbiome of Young Children 1-5 y of Age in Punjab, India; A Substudy of a Randomized, Community-Based Trial.},
journal = {Current developments in nutrition},
volume = {9},
number = {11},
pages = {107580},
pmid = {41323692},
issn = {2475-2991},
abstract = {BACKGROUND: Young children in India often face multiple micronutrient deficiencies, yet interventions such as micronutrient powders have raised concerns about potential adverse effects on the gut microbiome. Large-scale food fortification is an effective strategy to improve micronutrient intake; however, its impact on the gut microbiome of children remains unclear.

OBJECTIVES: To determine whether intake of quintuply-fortified salt (QFS) for 12 mo adversely affects gut microbiome composition in children aged 1-5 y.

METHODS: In a double-blind, randomized, controlled trial in Punjab, India, children received: 1) QFS with iron as encapsulated ferrous fumarate [eFF], zinc, vitamin B12, folic acid, and iodine (eFF-QFS); 2) QFS with the same micronutrients, but iron as encapsulated ferric pyrophosphate [eFePP] plus ethylenediaminetetraacetic acid (eFePP-QFS); or 3) standard iodized salt for 12 mo. Stool samples were collected from 125 children (eFF-QFS, n = 43; eFePP-QFS, n = 45; iodized salt, n= 37) at baseline and 12 mo and analyzed via 16S rRNA gene sequencing. Changes in alpha diversity (Shannon, abundance-based estimator index) between groups were assessed with linear mixed models, beta diversity (Bray-Curtis dissimilarity) with linear regression and permutational multivariate analysis of variance, and relative abundance of Enterobacteriaceae, Lactobacillus, Bifidobacterium, Bacteroides, Prevotella, or Escherichia-Shigella with zero-inflated negative binomial mixed models.

RESULTS: Average discretionary salt utilization was estimated to be 3.5 g/child equivalent/d across groups. Abundance-based estimator index was higher in the iodized salt arm compared with eFePP-QFS, but similar to eFF-QFS. Permutational multivariate analysis of variance revealed no overall group differences; however, pairwise Bray-Curtis distances from baseline were modestly greater in eFF-QFS compared with the other groups. No significant changes in relative abundance were identified.

CONCLUSIONS: After 12 mo, QFS resulted no major changes in abundance of key taxa and minimal, inconsistent shifts in certain diversity metrics and relative to the iodized salt control, suggesting no adverse effects on microbiome composition among young children in this setting. Additional studies in settings with improved iron status are needed.This trial was registered at clinicaltrials.gov as NCT05166980 and at Clinical Trials Registry-India as CTRI/2022/02/040333.},
}

@article {pmid41323559,
year = {2025},
author = {Tian, S and Liu, Y and Yang, H and Chen, K and Li, J and Chen, L and Wu, T and Zhang, L},
title = {Multi-Omics Reveal That Gut Microbial Dysbiosis Drives Lipid Metabolic Disturbances and Inflammation in Gestational Hypertension.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {16411-16425},
pmid = {41323559},
issn = {1178-7031},
abstract = {BACKGROUND: Gestational hypertension (GH) is a common complication during pregnancy that poses serious health risks to both mother and fetus. Recent studies have underscored the potential roles of gut microbiota, lipid metabolism, and inflammatory response in GH's development and progression. However, the exact mechanisms behind these interactions are still unclear. Understanding how gut microbial composition impacts lipid metabolism and inflammation could offer valuable insights into GH's pathogenesis and may lead to new prevention and treatment methods.

METHODS: In this study, we conducted ELISA experiments to detect inflammatory cytokines in the serum of GH patients. Additionally, we performed 16S-rDNA sequencing analysis on the feces of GH patients to investigate the characteristics of their intestinal microbial communities; GH mouse model was constructed to assess the impact of intestinal flora on offspring. Furthermore, we utilized non-targeted lipid metabolomics to analyze lipid metabolic characteristics in the feces and blood of GH patients and established connections between the microbiome and lipidome through correlation analysis.

RESULTS: ELISA tests suggested the levels of inflammatory factors in the serum of GH patients increased significantly, including IL-6, IL-8, IL-17, IL-18, and IFN-γ. In comparison to the normal group, the GH group exhibited a marked reduction in microbial richness. LEfSe analysis found 16 distinct bacterial communities between the two groups. Animal models suggested that fecal microbiota transplantation from the GH group's intestinal flora resulted in a significant decrease in the birth weight of the offspring. Furthermore, comparative analysis of fecal and blood metabolic profiles suggested that TG (54:5/FA22:5) may serve as a key metabolite. Correlation analysis demonstrated that f-Oxalobacteraceae exhibited a significant negative correlation with the inflammatory factor IL-17 and TG (54:5/FA22:5) in the blood, while showing a significant positive correlation with g-Oxalobacter and s-formigenes.

CONCLUSION: Our results establish a connection between gut microbiota, lipid metabolism, and the inflammatory response in patients with GH. This understanding may enhance our comprehension of the underlying mechanisms associated with GH.},
}

@article {pmid41323349,
year = {2025},
author = {Garcia, I and Kilic, F and Bryan, CA and Castro-Vildosola, J and Jonnalagadda, SA and Kasturi, A and Tilly, J and Smith, J and Valentin, S and Moncayo, S and Hala, T and Klein, E and Corbett, BF},
title = {Social stress changes gut microbiome composition in male, female, and aggressor mice.},
journal = {Brain, behavior, & immunity - health},
volume = {50},
number = {},
pages = {101138},
pmid = {41323349},
issn = {2666-3546},
abstract = {Psychological stress causes gut dysbiosis, which is associated with adverse effects on physical and mental health in humans and mice. Identifying taxa of gut bacteria changed by stress, and whether stress differentially alters their relative abundance in males and females, has important implications for stress-related disorders. We modeled individual differences in resilience or susceptibility using the chronic social defeat stress (CSDS) paradigm. Here, C57BL/6 mice are exposed to a novel retired breeder CD-1 aggressor for 10 min per day for 10 days. In this paradigm, resilient and susceptible subpopulations can be identified using the social interaction paradigm following CSDS. Fecal samples were collected immediately following Day 1 and Day 10 of CSDS. 16S ribosomal RNA sequencing was used to identify the relative abundance of 200 bacteria species. We analyzed group differences in phyla, genera, and species in resilient, susceptible, and non-stressed control male and female C57/BL/6 intruders along with CD-1 aggressors. Stress reduced microbiome diversity and caused gut dysbiosis in all groups, including aggressors. These changes were not observed in non-stressed mice. CSDS altered the relative abundance of every gut bacteria phylum. CSDS reduced genera in the Firmicutes phylum whereas sex altered fewer genera. The relative abundance of an uncultured Ruminococcus species on Day 1 predicted social avoidance following CSDS, with a stronger correlation in stressed females compared to males. Together, our findings demonstrate that CSDS changes gut microbiome composition in male and female mice.},
}

@article {pmid41323231,
year = {2025},
author = {Wang, Z and Zhou, L and He, Y and Xv, X and Lv, M and Zhang, Z and Wang, F and Wang, S and Wang, Y},
title = {Preliminary analysis of gut microbiome characteristics in children with obstructive sleep apnea hypopnea syndrome.},
journal = {Frontiers in neurology},
volume = {16},
number = {},
pages = {1615891},
pmid = {41323231},
issn = {1664-2295},
abstract = {OBJECTIVE: To analyze the characteristic changes in the gut microbiome in children with obstructive sleep apnea-hypopnea syndrome (OSAHS) and to investigate the relationship between the gut microbiome and polysomnography (PSG) results.

METHODS: Children diagnosed with primary snoring and OSAHS by PSG were enrolled in the study group. Nonsnoring children undergoing elective surgery were selected as the control group. Stool, sleep monitoring data, and medical history data were collected. The clinical history data were analyzed by SPSS 25.0 software. 16S rRNA high-throughput sequencing technology was used to analyze the gut microbiome, and relevant biostatistical methods were used to analyze and describe the characteristics of the gut microbiome.

RESULTS: A total of 62 OSAHS patients (42 mild OSAHS and 20 moderate to severe OSAHS), 16 primary snoring patients and 46 controls were enrolled in this study. There were significant differences in the partial alpha diversity index (observed otus index, Chao1 index) and beta diversity under the Jaccard and unweighted UniFrac distance methods between the mild OSAHS group and the moderate to severe OSAHS group. There were differences in some gut microbiome at different levels of phylum, class, order, family, genus and species between the control group and OSAHS group. There was a significant difference in the abundance ratio between Firmicutes and Bacteroidetes (F/B), and the ratio gradually increased among the three groups. The predictive model for OSAHS diagnosis established by the receiver operating characteristic (ROC) curve showed that the area under the curve (AUC) of Firmicutes and the F/B were more than 50%. At the genus level, Akkermansia was positively correlated with sleep efficiency (SE), Dialister was positively correlated with mean oxygen saturation (SaO2mean) and lowest oxygen saturation (LSaO2), Escherichia-Shigella was negatively correlated with total sleep time (TST), and Faecalibacterium was negatively correlated with the obstructive apnea index (OAI).

CONCLUSION: The gut microbiome of children with OSAHS is slightly different at the phylum, class, order, family, genus and species levels. The F/B and Firmicutes abundance detection have limited predictive capability for the diagnosis of OSAHS. At the genus level, some gut microbiota were correlated with PSG indicators.},
}

@article {pmid41322988,
year = {2025},
author = {Chávez-Domínguez, RL and Torres, M and Acevedo-Domínguez, AA and Ibarra-Inocente, JA and Carranza, C},
title = {Reprogramming the host: Mycobacterium tuberculosis as a silent architect of the immuno-tumoral.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1697874},
pmid = {41322988},
issn = {2235-2988},
mesh = {Humans ; *Mycobacterium tuberculosis/pathogenicity/immunology ; *Host-Pathogen Interactions/immunology ; *Lung Neoplasms/immunology/microbiology/etiology ; *Tuberculosis, Pulmonary/complications/immunology/microbiology ; Tuberculosis/complications ; Tumor Microenvironment ; Virulence Factors/metabolism ; Animals ; },
abstract = {Pulmonary tuberculosis, caused by Mycobacterium tuberculosis (Mtb), remains one of the leading causes of infectious disease-related mortality worldwide. In parallel, lung cancer represents the most lethal neoplasm, with high mortality rates globally. Emerging studies suggest that chronic Mtb infection may contribute to the development of lung cancer, particularly adenocarcinoma. Several biological mechanisms support this hypothesis. Chronic inflammation from tuberculosis creates a microenvironment enriched in proinflammatory cytokines, reactive oxygen species (ROS), and growth factors that favor cell proliferation, genomic instability, angiogenesis, and immune evasion, which are considered classic hallmarks of cancer. Additionally, both protein and non-protein virulence factors of Mtb have been shown to interfere with critical cellular signaling pathways related to tumor cell survival and invasion. Clinically, multiple observational studies and meta-analyses report an increased incidence of lung cancer among individuals with a history of tuberculosis, especially when both conditions coexist in the same pulmonary regions. Specific mutations, including EGFR, have been identified in patients with prior tuberculosis, influencing both prognosis and therapeutic response. Nevertheless, key questions remain regarding the causal nature of this association, the role of Mtb strains, and the molecular factors such as epigenetic modifications or the lung microbiome. This review proposes that infection with Mtb could function as a carcinogenic agent. Further in vitro experiments, cellular models, and clinical investigations are urgently needed to support potential reclassification of this pathogen by international agencies such as the IARC.},
}

Humans
*Mycobacterium tuberculosis/pathogenicity/immunology
*Host-Pathogen Interactions/immunology
*Lung Neoplasms/immunology/microbiology/etiology
*Tuberculosis, Pulmonary/complications/immunology/microbiology
Tuberculosis/complications
Tumor Microenvironment
Virulence Factors/metabolism
Animals

@article {pmid41322953,
year = {2025},
author = {Krueger, Q and Shore, M and Reitzel, AM},
title = {Influence of Temperature and Saline Conditions on Bacteria Naturally Associated With the Cnidarian Host Nematostella vectensis.},
journal = {International journal of microbiology},
volume = {2025},
number = {},
pages = {4107949},
pmid = {41322953},
issn = {1687-918X},
abstract = {The associated microorganisms ("microbiome") of multicellular individuals ("host") are important for the physiology and survival of the host. Individual bacterial species vary in environmental tolerances that may limit their associations with hosts, especially when their range of survivable conditions is narrower. To elucidate the roles for different environmental niche spaces of bacteria that may compose the microbiome, we evaluated the survival and growth of individual and combinations of bacteria with and without an animal host, the sea anemone Nematostella vectensis (Cnidaria, Anthozoa). We assessed 62 environmental bacteria from seven genera (Alteromonas, Bacillus, Grimontia, Photobacterium, Pseudoalteromonas, Shewanella, and Vibrio) isolated from six estuaries and the host to determine their tolerance across a gradient of temperatures (30°-40°C) and salinities (5-30 ppt). Growth rates and plate counts revealed members of the Vibrio genus had the highest growth rate at higher salinities (15 and 30 ppt), while Bacillus and Alteromonas spp. exhibited consistent growth over a broader range of salinities and temperatures. Only 15% of isolates were capable of growth at the combination of highest temperature and lowest salinity (40°C, 5 ppt), suggesting that these environmentally relevant conditions may limit microbiome diversity. We further assessed three isolates (Bacillus velezensis, Pseudoalteromonas spiralis, and Vibrio diabolicus) for how bacterial growth changed when associated with N. vectensis. When anemones were exposed to environmentally relevant heat stress over 3 days, bacterial concentrations varied significantly. P. spiralis grew more under lower salinities and maintained stable concentrations. Conversely, V. diabolicus grew more with higher salinity and maintained these high concentrations in nearly all conditions. At sustained extreme temperatures for the anemones, the microbial composition exerted a small impact on survival. Together, these results support that environmental conditions are important drivers for the relative abundance of particular bacteria in the context of the host's microbiome.},
}

@article {pmid41322804,
year = {2025},
author = {Singh, P and Saini, P and Kalyankar, PP and Kailey, KR and Chauhan, R and Pannu, AK and Singh, N and Garg, K},
title = {Drug Management of Inflammatory Bowel Disease (IBD): A Narrative Review.},
journal = {Cureus},
volume = {17},
number = {10},
pages = {e95635},
pmid = {41322804},
issn = {2168-8184},
abstract = {The exact underlying etiopathogenesis of inflammatory bowel disease (IBD) remains unclear. Conventionally, autoimmune mechanisms have been linked with IBD, and thus various immunomodulatory or anti-inflammatory drugs have proven useful. The understanding of the complex gut mucosal immune system and the trafficking of leukocytes toward the intestine from lymphoid organs has allowed us to use molecular drugs that may target specific pathways, like the Janus kinase (JAK) pathway, phosphodiesterase, interleukins (IL)-12, 23, and adhesion molecules such as selectins. These agents have brought about a drastic change in the management strategy of IBD. Since many patients may not improve on conventional therapy, newer treatments are tried, which show better efficacy with fewer side effects. The present review highlights the concepts of newer therapeutic drugs, their interaction with host microbiome and gut-brain axis, and the new targets in the autoimmune phenomena, thereby providing a promising treatment for a better management of IBD in the present and future times.},
}

@article {pmid41322719,
year = {2025},
author = {Conway, J and January, GG and Muddiman, KJ and Dorrington, R and Howell, KL and Upton, M},
title = {Impact of growth conditions on the abundance and diversity of cultivable bacteria recovered from Pheronema carpenteri and investigation of their antimicrobial potential.},
journal = {FEMS microbes},
volume = {6},
number = {},
pages = {xtaf016},
pmid = {41322719},
issn = {2633-6685},
abstract = {The deep sea is a largely unexplored extreme environment supporting a diverse biological community adapted to low temperatures and high pressures. Such environments support microbial life that may be a source of novel antibiotics and other drugs. Whilst this is often the case, many species with bioactive capabilities may be missed with traditional culturing methods. In this study, a total of 16 different concentrations and types of media were employed, to culture 389 bacterial isolates using Dilution to Extinction methods and Actinobacteria Directed Cultivation techniques. This generated 72 (18.6%) isolates with narrow and broad-spectrum activity against ESKAPE pathogens including Escherichia coli (E. coli), methicillin-resistant Staphylococcus aureus, and vancomycin-resistant Enterococci. We also report that an early-stage 'One Strain Many Compounds' approach can reveal a greater number of bioactive isolates that otherwise would have been missed; 12 isolates initially deemed 'inactive' were seen to exhibit activity towards S. aureus and/or E. coli. We emphasize the importance of a thorough initial screening method to capture bioactive isolates and show how selecting only morphologically distinct isolates for screening may result in species with promising bioactivity being overlooked. Our findings justify on-going investigation of Pheronema sponges for bioactive microbiota.},
}

@article {pmid41322709,
year = {2025},
author = {Gaballah, K and Sekar, P and Abuzayed, D and Alowais, A and Shakir, A and Razouk, A and Mohammed, MM},
title = {Oral Microbial and Systemic Lipid Profiles in Patients With Asymptomatic Retained Partially Erupted Third Molars: A Preliminary Cross-Sectional Study.},
journal = {International journal of dentistry},
volume = {2025},
number = {},
pages = {4770383},
pmid = {41322709},
issn = {1687-8728},
abstract = {BACKGROUND: Partially erupted (PE) third molars are frequently retained in the oral cavity and may contribute to localized inflammation. Chronic subclinical inflammation at these sites has been suggested to influence systemic markers such as lipid profiles, potentially increasing cardiovascular risk. Additionally, microbial colonization, particularly by bacteria and Candida species, may exacerbate inflammatory responses.

OBJECTIVE: To investigate the lipid panel parameters and oral microbial burden in individuals with PE third molars compared to those with fully erupted (FE) third molars and to assess potential associations with systemic inflammation.

METHODS: A cross-sectional study was conducted on 64 participants aged 20-35 years, divided into two groups: group 1 with PE third molars and group 2 with FE third molars. Fasting lipid profiles were measured using the CardioChek PA Analyzer. Gingival crevicular fluid (GCF) samples were collected from under the operculum in group 1 and from the gingival sulcus in group 2. Quantitative PCR (qPCR) was used to assess Candida and bacterial load. Statistical analysis included unpaired t-tests and multivariate logistic regression, adjusting for confounders.

RESULTS: A higher prevalence of elevated total cholesterol (TC) was observed in group 1 (15.63%) compared to group 2, with an odds ratio (OR) of 7.215 (95% CI: 0.992-52.5; p=0.051). Candida presence was significantly greater in PE sites (p=0.0036), though load differences were not statistically significant except in triglyceride (TG)-associated samples. All samples were positive for bacteria; however, bacterial load was unexpectedly higher in FE sites (p=0.0066). Associations between lipid abnormalities and microbial presence were noted but not statistically conclusive.

CONCLUSION: PE third molars may be linked to elevated cholesterol levels and increased microbial colonization, particularly by Candida species. While no statistically significant associations were found, the trends suggest a potential inflammatory and metabolic role of third molar retention. Further longitudinal studies with larger sample sizes and detailed microbial profiling are needed to clarify these relationships.},
}

@article {pmid41322357,
year = {2026},
author = {Modeel, S and Siwach, S and Dolkar, P and Chaurasia, M and Yadav, P and Atri, A and Yadav, A and Negi, T and Negi, RK},
title = {Emerging risk factors and the role of gut microbiota in immunomodulation and therapeutic implications in colorectal cancer.},
journal = {Cancer pathogenesis and therapy},
volume = {4},
number = {1},
pages = {14-30},
pmid = {41322357},
issn = {2949-7132},
abstract = {The pathophysiology of many ailments, including neurological, gastrointestinal, and metabolic problems, is well known to be influenced by intestinal dysbiosis. Clinical research has provided evidence suggesting a strong correlation between dysbiosis of the gut microbiome and colorectal cancer (CRC) development. The active reprogramming of metabolic pathways to boost glycolysis, fatty acid production, lipogenesis, and glutaminolysis constitutes a major metabolic shift in cancer development, including CRC. The complex combination of different factors leads to CRC, making it an environmental disease. These factors include food and lifestyle choices, genetics and family history, age, underlying intestinal diseases, and dysbiosis of the gut microbiota. One of the primary risk factors for carcinoma development is diet, which impacts an individual's gut microbiome. In addition to impacting CRC formation, the gut microbiome also has immunomodulatory effects, including various immunological interactions and the underlying mechanisms governing them. Microbial interactions in CRC have been extensively studied, yet numerous unresolved queries exist on how gut bacteria can influence treatment. It is possible to perform microbiome-driven immunotherapies focusing on probiotics, prebiotics, and synbiotics. However, large-scale treatment utilization in CRC patients is limited by several issues, including variations in the microbial makeup of each patient's gut and a lack of established methods. The study highlights the impact of several risk factors, including dysbiosis of the gut microbiome and different approaches to halting and treating CRC progression with a focus on diet changes and modulation of the gut flora. Given the foregoing, we propose that if research gaps are addressed and immunotherapy is paired with microbial interventions, microbiota-based therapeutics could potentially impede the growth of tumors and treat CRC.},
}

@article {pmid41322272,
year = {2025},
author = {Kim, JM and Choi, BJ and Bayburt, H and Lee, JK and Jeon, CO},
title = {Identifying potential keystone bacterial species within the phycosphere of marine algae and unveiling their metabolic characteristics.},
journal = {Marine life science & technology},
volume = {7},
number = {4},
pages = {989-1007},
pmid = {41322272},
issn = {2662-1746},
abstract = {UNLABELLED: Metabolic interactions between microbiomes and algal hosts within the phycosphere of marine macroalgae are drawing increasing attention due to their roles in food webs, global nutrient cycles, industries, and their potential as food resources. However, these relations remain poorly understood. In this study, 43 marine macroalgae, including red, brown, and green algae, were collected from the coastal areas of Korea. We identified the bacterial communities within the loosely and tightly attached environments (LAEs and TAEs, respectively) of the phycosphere, along with those in the surrounding seawater, using 16S rRNA gene sequencing. β-Diversity analysis revealed significant differences between the bacterial communities among the three, with minimal variation related to sampling location or algal color. Indicator value analysis identified Pseudoalteromonas (in the LAE and TAE), Psychromonas (in the LAE), Marinomonas (in the LAE), and Litorimonas (in the TAE) as the dominant taxa in the phycosphere, in contrast to seawater. Network analysis suggested positive correlations among taxa within the same environments and negative correlations between those in the LAE and TAE, highlighting their distinct ecological conditions. Analysis using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States and Kyoto Encyclopedia of Genes and Genomes pathways revealed functional variations between the phycosphere- and seawater-residing microbes. The microbial taxa-function relationships were assessed through Spearman's rank-order correlation. Additionally, bacterial species belonging to the core taxa were isolated and their genomes sequenced. Their metabolic traits were analyzed via bioinformatics, recognizing key metabolic features essential for symbiotic interactions with algal hosts and survival within the phycosphere. The findings of this study advance our understanding of the marine algal phycosphere microbiome by detailing the metabolic characteristics of potential keystone species.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00325-6.},
}

@article {pmid41322104,
year = {2025},
author = {Khawaja, TW and Zhao, L and Siddiq, R and Ahmad, MU and Burns, CP and Parker, JM and Wakefield, MR and Fang, Y},
title = {Unmasking the microbiome: the hidden role of gut bacteria in the pathogenesis of colorectal cancer and its prevention strategies.},
journal = {Exploration of targeted anti-tumor therapy},
volume = {6},
number = {},
pages = {1002351},
pmid = {41322104},
issn = {2692-3114},
abstract = {Colorectal cancer (CRC) is a significant global health problem, ranking as the third most common cancer and the second leading cause of cancer deaths in the world. The highest incidence of CRC is found in developed regions, thus underlining its characterization as a Western disease. Major risk factors for CRC include an unhealthy diet, lack of physical exercise, and cigarette smoking. The gut microbiota refers to the complex community of microorganisms inhabiting the digestive tract and plays a crucial role in the maintenance of host health and modulation of immune responses. Gut dysbiosis can be caused by poor diet and alcohol consumption, increasing CRC risk. Specific bacteria, such as Fusobacterium nucleatum and Escherichia coli, may have a close relationship with CRC development, while the beneficial bacteria are frequently depleted in CRC patients. This paper will discuss the mechanisms of colorectal carcinogenesis, focusing on the effects of bacterial genotoxins, immune evasion, inflammation, and diet. Additionally, it reviews preventative strategies including short-chain fatty acids (SCFAs), prebiotics, probiotics, synbiotic supplements, and the method of fecal microbiota transplantation (FMT), showing their potential to improve overall gut health and reduce the risk for CRC. Understanding these mechanisms and implementing specific preventative strategies could significantly enhance clinical interventions and reduce the global burden of CRC.},
}

@article {pmid41322070,
year = {2025},
author = {Amirinia, F and Motamedi, M and Ardi, P and Jabrodini, A},
title = {Evaluating the Role of Candida albicans as a Potential Oral Carcinogen.},
journal = {Interdisciplinary perspectives on infectious diseases},
volume = {2025},
number = {},
pages = {4057977},
pmid = {41322070},
issn = {1687-708X},
abstract = {Oral cavity cancers, especially oral squamous cell carcinoma (OSCC), are a major subset of head and neck malignancies. Increasing evidence indicates that oral microbiota, particularly Candida albicans (C. albicans), plays a significant role in OSCC development and progression. While C. albicans is normally a commensal organism in the human microbiome, it can become pathogenic under certain conditions. The carcinogenic potential of C. albicans contributes to oral cancer by acting both as a co-factor and a direct pathogen. This involves complex interactions with the host immune system and the expression of multiple virulence factors. The dynamic relationship between C. albicans and its host influences disease outcomes and cancer progression. This review focuses on key virulence mechanisms of C. albicans, including adhesion to host cells, secretion of hydrolytic enzymes, production of carcinogenic metabolites, induction of chronic inflammation, and release of candidalysin, a cytolytic peptide toxin. Understanding these factors is essential to clarify how C. albicans promotes OSCC initiation and progression. Improved knowledge of C. albicans virulence may lead to targeted therapies, preventive strategies, and novel biomarkers for early detection, ultimately enhancing treatment outcomes and prognosis for patients with oral cavity cancers.},
}

@article {pmid41321998,
year = {2025},
author = {Aksornkitti, V and Visuthranukul, C and Leelahavanichkul, A and Joyjinda, Y and Sriswasdi, S},
title = {Gut microbiome enterotypes and temporal variations during a six-month inulin-supplemented weight loss randomized controlled trial in Thai children with obesity.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {5007-5019},
pmid = {41321998},
issn = {2001-0370},
abstract = {Gut microbiome profiles can reflect the host's health status and have the potential to predict the effectiveness of medical interventions. In this study, gut microbiome enterotypes of 143 Thai children with obesity who participated in a randomized controlled trial of inulin supplementation were analyzed to identify microbial markers for weight loss responses and healthier lifestyles. Two gut microbiome enterotypes, which encompass 25 % of the children with obesity, were exclusive to children with obesity, including a rarely described Megasphaera enterotype. Megasphaera enterotype was also positively associated with dietary fiber intake specifically in the inulin group. Prevotella and Bacteroides enterotypes are significantly associated with poor health status, including longer times spent on electronic devices and lower concentrations of butyrate, a beneficial short-chain fatty acid. Children with these enterotypes also exhibited some of the best weight loss outcomes after receiving only behavioral and dietary advice. Observed associations between enterotypes and clinical parameters are consistent with earlier research of different populations. Intervention-specific associations suggest potential criteria for a personalized selection of weight loss interventions.},
}

@article {pmid41321962,
year = {2025},
author = {Heneberg, P},
title = {Commensal, pathogen, or passenger? Rethinking the role of Blastocystis in human health.},
journal = {One health (Amsterdam, Netherlands)},
volume = {21},
number = {},
pages = {101272},
pmid = {41321962},
issn = {2352-7714},
abstract = {Blastocystis is one of the most prevalent intestinal protists, colonizing more than one billion people worldwide. Nevertheless, its role in health and disease remains blurred. Blastocystis was historically dismissed as a commensal. However, it can have pathogenic or protective effects. This review synthesizes molecular epidemiology, clinical research, microbiome studies, and experimental models through a One Health approach to reassess Blastocystis. Subtypes ST1-ST4 are dominant in humans, but their health outcomes vary. ST4 is associated with irritable bowel syndrome and inflammatory responses. However, it has also been shown to exert protective effects on murine colitis models. In contrast, ST3 is frequently detected in healthy individuals with a diverse gut microbiota. Blastocystis is also widespread in animals, untreated water, wastewater, and food, reflecting complex transmission dynamics and raising concerns in low- and middle-income countries where poverty-related exposures increase risks. Diagnostic advances have improved detection, although mixed infections and inconsistent clinical interpretations persist, and treatment guidelines remain absent. Rather than being a uniform pathogen or benign passenger, Blastocystis emerges as a context-dependent component of the gut ecosystem and environmental microbiota. Its ubiquity across humans, animals, and the environment requires integrated surveillance, subtype-informed research, and interdisciplinary health strategies. Recognizing the ecological complexity of Blastocystis is essential for equitable diagnostics, treatment, and public health responses within the One Health framework.},
}

@article {pmid41321951,
year = {2025},
author = {Gao, W and Wang, H and Jia, H and Zhang, J and Yan, Z and He, D and Zheng, C},
title = {Microbiome shifts during Fusarium oxysporum and F. solani (syn. Neocosmospora solani)-induced Ligusticum chuanxiong root rot: endophtic bacterial protective responses and fungal pathogenic tendencies.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20369},
pmid = {41321951},
issn = {2167-8359},
mesh = {*Plant Diseases/microbiology ; *Plant Roots/microbiology ; *Fusarium/pathogenicity ; *Microbiota ; *Ligusticum/microbiology ; Rhizosphere ; Soil Microbiology ; Rhizome/microbiology ; Endophytes ; Bacteria ; },
abstract = {Root rot disease is a globally significant threat to the health of diverse economically important crops. Understanding shifts in the plant microbiome during disease progression can aid in identifying beneficial microbes with disease-resistant potential and developing ecofriendly biocontrol strategies. However, microbiome changes during root rot progression in the medicinal plant Ligusticum chuanxiong remain poorly understood. This study aimed to investigate the response of host-associated microbiomes to pathogen stress (Fusarium oxysporum and F. solani syn. Neocosmospora solani) during L. chuanxiong root rot. The diversity, composition, function, and network interactions of bacterial and fungal communities were examined using high-throughput sequencing and network analysis in healthy rhizomes, healthy layers of diseased rhizomes, rotten layers of diseased rhizomes, and rhizosphere and non-rhizosphere soils. The bacterial diversity decreased as root rot progressed in end ophytic (from 0.72 to 0.38) and rhizosphere soils (from 0.80 to 0.68), whereas the fungal diversity showed no significant changes. The diseased samples were enriched with root rot pathogens and other potential pathogens, such as the soil bacterium Pectobacterium and the soil fungus Gibberella, whereas beneficial taxa, including endophytic Bacillus and Trichoderma, and soil-dwelling Candidatus_Solibacter and Beauveria, were significantly reduced. Notably, in the healthy layers of diseased rhizomes, which represent a "transitional phase", fungal communities resembled those in rotten tissues with increased pathogenic taxa (e.g., Ceratocystis and Plectosphaerella), whereas bacterial communities were more similar to healthy rhizomes and enriched in beneficial genera (e.g., Microbacterium and Variovorax). Functional prediction indicated suppressed bacterial activity and enhanced fungal saprotrophy in rotten rhizomes. The cross-kingdom network complexity decreased in both endophytic and soil microbial communities during root rot, while positive correlations within endophytic networks increased. Overall, as root rot progresses, the stability and competitive interactions within endophytic and soil microbiomes of L. chuanxiong weaken. Early in infection, endophytic bacterial and fungal communities exhibit divergent responses: bacteria likely contribute to disease resistance, whereas fungi may promote pathogenesis. This findings suggest that a more beneficial role for endophytic bacteria in controlling L. chuanxiong root rot. Restoring microbial community complexity may offer a viable biocontrol strategy. Our findings provide a theoretical foundation for future identification of specific beneficial microbes and the development of safe biocontrol approaches.},
}

*Plant Diseases/microbiology
*Plant Roots/microbiology
*Fusarium/pathogenicity
*Microbiota
*Ligusticum/microbiology
Rhizosphere
Soil Microbiology
Rhizome/microbiology
Endophytes
Bacteria

@article {pmid41321837,
year = {2025},
author = {Sundaray, JK and Mohapatra, M and Rasal, A and Udit, UK and Mohanty, S and Mohanty, D and Das, II and Sahoo, L and Sahoo, PK},
title = {Sex-specific gut microbiome dynamics in Labeo catla: links to reproductive hormones, metabolic dimorphism, and environmental factors.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1651975},
pmid = {41321837},
issn = {1664-302X},
abstract = {INTRODUCTION: Gut microbiota play a critical role in aquaculture by enhancing nutrient metabolism, digestion, immune response, and reproductive performance in fish. Labeo catla, one of the most commercially important Indian major carps, demands better reproductive management; however, insights into its gut microbiome composition and functional dynamics, particularly during the crucial pre-spawning phase, remain limited.

METHODS: In this study, we investigated the structural and functional attributes of gut microbial communities in male and female L. catla reared in ICAR-CIFA ponds using high-throughput Illumina MiSeq 16S rRNA gene sequencing and examined their associations with reproductive traits.

RESULTS AND DISCUSSION: Histological analysis confirmed active gametogenesis in both sexes, while hormonal assays showed higher estradiol levels in females compared to males. Microbiome profiling revealed Proteobacteria as the dominant phylum, followed by Fusobacteria, Bacteroidetes, and Firmicutes. Cetobacterium and Shewanella were the most prevalent genera, with sex-specific differences in microbial diversity and composition. Functional prediction analysis identified genes associated with reproduction, lipid metabolism, digestion, and immunity. Correlation studies revealed a negative association between Bacteroidetes and 11-KT, while Shewanella and Serratia showed positive correlations with estradiol, indicating a potential role of gut microbes in modulating reproductive readiness. Canonical Correspondence and variance partitioning analyses revealed that gut microbiome variation in male and female L. catla was predominantly influenced by biological factors (63.97%) compared to environmental factors (20.99%). Notably, despite their low abundance, Clostridium perfringens and Pseudomonas stutzeri were identified as keystone taxa significantly shaping microbial network structure and stability.

CONCLUSION: This study provides the first comprehensive insight into the sex-specific gut microbiome's dynamics in L. catla during the pre-spawning season and highlight their application in broodstock management and sustainable aquaculture practices.},
}

@article {pmid41321829,
year = {2025},
author = {de Bruyn, C and Scott, K and Panter, H and Bezombes, F and Ralebitso-Senior, K},
title = {Advancing time-since-interval estimation for clandestine graves: a forensic ecogenomics perspective into burial and translocation timelines using massively parallel sequencing.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1684366},
pmid = {41321829},
issn = {1664-302X},
abstract = {Forensic taphonomy and entomology has focused on estimating the post-mortem interval (PMI), particularly for surface depositions, using human cadavers and other mammalian models by considering morphological changes of the body and insect activity during decomposition. The PMI is crucial in forensic investigations as it provides key information regarding the victim's identity, the circumstances of their death and can confirm or refute a suspect's alibi. Gravesoil microbial communities are a potential tool that can complement traditional approaches to detect and confirm the presence of human remains in clandestine burials, aiding forensic investigations. The estimation of the time-since-burial (post-burial interval; PBI), and the time-since-translocation (post-translocation interval; PTI), a new concept, have potential to aid clandestine grave location but have received relatively little attention in forensic ecology research. Advances in massively parallel sequencing (MPS) provide a high-throughput means to estimate PBI and PTI by characterising soil microbial communities in graves with remains, from early to skeletal stages of decomposition, or where remains have been intentionally removed from crime scenes and relocated. This review presents a perspective on the use of the soil microbiome as an indicator for post-mortem time-since-interval estimations, with specific focus on the PBI and PTI. In addition, it provides a framework, supported within forensic ecogenomics, on how the PBI and PTI can be used as a forensic tool complemented by MPS. The review highlights the need for further research to validate microbial community analysis across diverse biogeographical regions to enhance its precision and reliability as a forensic investigative tool. Such validation could potentially enhance the accuracy of post-burial and post-translocation interval estimations, ultimately improving methods for clandestine grave identification.},
}

@article {pmid41321827,
year = {2025},
author = {Ji, H and Yang, Z and Hao, Y and Wang, Y and Cao, Z and Yang, H and Wang, W and Li, S},
title = {Alpha-linolenic acid reshapes the gastrointestinal ecology to enhance immune function in dairy cows: insights from microbiome and metabolome profiling.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1687786},
pmid = {41321827},
issn = {1664-302X},
abstract = {INTRODUCTION: Alpha-linolenic acid (ALA), an essential polyunsaturated fatty acid, modulates gastrointestinal microbiota and host immunity, yet its regulatory mechanisms in dairy cows remain unclear.

METHODS: This study investigated how dietary ALA influenced gut microbiota, metabolome, and immune function in lactating Holstein cows. Ten cows were randomly assigned to two groups (n = 5) receiving either a low-ALA (LALA, 5.02 ± 0.09% ALA of total fatty acids) or high-ALA diet (HALA, 32.04 ± 1.55% ALA of total fatty acids). Rumen fluid, feces, and blood samples were analyzed post-intervention.

RESULTS: The HALA group exhibited increased ruminal abundance of Eubacterium coprostanoligenes group and Ruminococcus (p < 0.05), alongside reduced proinflammatory metabolites including dodecanoic acid, myristic acid, and prostaglandin I2 in the rumen. Plasma leukotriene C4 levels were also decreased (p < 0.05). Metabolomic enrichment analysis revealed significant downregulation of arachidonic acid metabolism. Correlation analyses demonstrated that Eubacterium coprostanoligenes group negatively associated with suppressed prostaglandin I2 (rumen metabolite) and leukotriene C4 (plasma metabolite), but positively correlated with enriched fecal Clostridia UCG-014 and Ruminococcus.

DISCUSSION: These findings indicate that high dietary ALA reshapes gastrointestinal microbiota and attenuates inflammatory responses by inhibiting microbial-metabolite-driven arachidonic acid metabolism, thereby enhancing immune regulation in dairy cows.},
}

@article {pmid41321823,
year = {2025},
author = {Zheng, Z and Xie, D and Han, Y and Li, G and Wang, S and Zhang, X and Huang, T and Xu, W and Wu, G},
title = {Deciphering the urinary microbiome and urological cancers: from correlation to mechanisms and treatment.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1699308},
pmid = {41321823},
issn = {1664-302X},
abstract = {Given that the sterility of urine and the urinary tract has been questioned by research, urinary microbiome dysbiosis has been recognized as one of the potential cancer-promoting factors. The composition of the urinary microbial community in healthy individuals has a relatively high similarity at the phylum level, with factors like age and gender influencing the expression and distribution. In contrast, the urinary microbiome of patients with urologic cancers shows significant variability and diversity depending on the type of cancer. Most of the early studies focused on the distribution, aggregation, and expression of microbiota in urologic cancers, warranting advanced studies on the causal relationship between microbes and urologic cancers. Bladder and prostate cancer tumorigenesis and progression can be influenced by microbes through chronic inflammatory or immunomodulatory pathways making them cancer models strongly associated with the urinary microbiome. Here, we summarize the expression characteristics of the microbiomes associated with these cancers and analyze the pathophysiological mechanisms and signaling pathways of the microbiome in the tumor promotion or suppression. By examining the role played by the urinary microbiome in the pathogenesis of urologic cancers, we assess the potential of specific microbial groups as biomarkers for diagnosis and surveillance. Additionally, involving the microbiome or using adjunctive participation in tumor therapy is becoming an emerging cancer treatment option. Improving urinary microbial homeostasis in urinary cancers by direct treatment with microbial products, microbial co-immunotherapy, probiotic-assisted therapy, and fecal microbial transplantation may broaden the scope of therapy and enhance the efficacy of conventional medicines.},
}

@article {pmid41321819,
year = {2025},
author = {Jiang, J and Zhou, S and Song, J and Xia, C and Yang, X and Yang, K and Li, F},
title = {Diet-microbiome coevolution: the core mechanism for semi-aquatic adaptation and cross-habitat niche coexistence of the web-footed shrew (Nectogale elegans).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1711143},
pmid = {41321819},
issn = {1664-302X},
abstract = {The adaptation of mammals to semi-aquatic niches represents a pivotal ecological transition, in which the coevolution of dietary specialization and gut microbiome is regarded as playing a fundamental role. However, the general mechanisms that link these traits to survival across habitats remain insufficiently investigated, particularly in small mammals with high metabolic constraints. Using the web-footed shrew (Nectogale elegans), a rare small mammal with extreme semi-aquatic specialization, this study supplements the understanding of host-microbe symbiosis in the process of small mammals adapting to new ecosystem. To address how diet facilitates semi-aquatic adaptation, we integrated benthic community surveys and dietary DNA metabarcoding. Our results showed that the web-footed shrew primarily utilizes benthic macroinvertebrates (Diptera, Ephemeroptera, and Trichoptera), consistent with the composition of local benthic biomass, and supplemented by Cypriniformes fish. Comparative analysis of DNA metabarcoding with sympatric terrestrial rodents further revealed that semi-aquatic shrews achieve niche differentiation through two complementary mechanisms: habitat partitioning (aquatic vs. terrestrial) and trophic level differentiation (secondary consumers of invertebrates vs. consumers of plants). This discovery extends niche theory, demonstrating how habitat-specific resource utilization shapes trophic stratification. Compared to the terrestrial group, the gut microbiome of the semi-aquatic shrew exhibited significant differences in both microbiome composition and functional potential: dominance of Proteobacteria and Firmicutes, reduced abundances of carbohydrate-active enzymes (CAZymes), as well as selective enrichment of genes involved in fatty acid metabolism. These results reflect the high-fat, high-protein niche of semi-aquatic shrews. Additionally, the seasonal stability of the microbiome of the semi-aquatic shrew mirrors the consistency of benthic resources, and maintaining metabolic homeostasis is key to long-term adaptation to fluctuating environments. Overall, this study demonstrates a framework for semi-aquatic adaptation in small mammals: dietary specialization drives niche differentiation, which in turn selects for gut microbiome adaptation, optimizing habitat-specific resource utilization. This research underscores the role of diet-microbiome coevolution in enabling semi-aquatic adaptation, offering novel insights into ecological niche differentiation and specialization mechanisms in small mammals.},
}

@article {pmid41321665,
year = {2025},
author = {Lahtinen, E and Hugerth, LW and Edfeldt, G and Säfholm, A and Kornfält, S and Engstrand, L and Strevens, H and Schuppe-Koistinen, I},
title = {pHyph, a novel antibiotic-free treatment for bacterial vaginosis, promotes Lactobacillus growth and reduces the abundance of pathogens in the vagina.},
journal = {AJOG global reports},
volume = {5},
number = {4},
pages = {100566},
pmid = {41321665},
issn = {2666-5778},
abstract = {BACKGROUND: Bacterial vaginosis (BV) is the most common vaginal infection among women of reproductive age worldwide, caused by dysbiosis of the vaginal microbiome. Despite its prevalence, the underlying molecular mechanisms remain poorly understood, making diagnosis and treatment challenging. Although antibiotics are the standard therapy, recurrence rates are high, up to 50% within 1 year, and repeated treatments contribute to the rise of antimicrobial resistance. There is an urgent need for alternative, sustainable, and microbiome-friendly treatment options.

OBJECTIVE: To evaluate whether pHyph, a novel antibiotic-free treatment, promotes a shift in the vaginal microbiome toward a health-associated composition in women with clinically diagnosed BV.

STUDY DESIGN: In a randomized, double-blind, placebo-controlled trial, vaginal swabs were collected from 152 women diagnosed with BV. Microbiome composition was assessed before and after a 6-day treatment with pHyph or a placebo-like comparator, using qPCR targeting 25 bacterial, 2 viral, and 8 eukaryotic species.

RESULTS: pHyph significantly increased the abundance of Lactobacillus iners, Lactobacillus gasseri and Lactobacillus jensenii after treatment, while decreasing the abundance of BV-associated species, such as Gardnerella vaginalis, BVAB2, and Fannyhessea vaginae (Wilcoxon signed rank test, P<.05). The growth-promoting effect on Lactobacillus was more pronounced in women who had detectable levels at baseline. Notably, a substantial number of participants in the pHyph group (n=33) transitioned to a Lactobacillus-dominated community state type (CST), compared to none in the comparator group.

CONCLUSIONS: pHyph supports BV resolution by promoting a Lactobacillus-dominated vaginal microbiome and reducing BV-associated species, offering a promising antibiotic-free alternative.},
}

@article {pmid41321569,
year = {2025},
author = {Xie, J and Wang, C and Zhao, Y and Li, X and Ma, G and Yang, K},
title = {Metabolomic and microbial diversity perspectives on Aspergillus oryzae culture-induced modifications in ovine feed utilization and rumen ecosystem.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1658361},
pmid = {41321569},
issn = {2297-1769},
abstract = {INTRODUCTION: Aspergillus oryzae culture (AOC) is widely used as a feed additive to enhance ruminant productivity and rumen function. However, the underlying mechanisms at the microbiome-metabolome interface remain poorly understood. This study aimed to elucidate how dietary AOC supplementation influences sheep production performance, rumen fermentation, microbial communities, and metabolomic profiles.

METHODS: Twelve rumen-fistulated sheep were randomly assigned to a control group (basal diet) and a trial group (basal diet + 1% AOC). The experiment lasted 30 days, during which production performance, nutrient digestibility, ruminal pH, volatile fatty acids (VFA), ammonia nitrogen, microbial diversity (16S rDNA sequencing), and metabolomic profiles (LC-MS) were systematically assessed.

RESULTS: AOC supplementation significantly increased average daily gain (ADG) and neutral detergent fiber (NDF) digestibility by 7.00% (p < 0.05), and improved nitrogen retention. Total VFA and acetate concentrations were elevated, with a stable ruminal pH. Microbiome analysis revealed an increased relative abundance of Succiniclasticum and beneficial fiber-degrading taxa. Metabolomic profiling identified upregulation of antioxidant metabolites (e.g., ginsenoside Rg3, lipoamide) and activation of key pathways such as phenylalanine metabolism and the TCA cycle, alongside downregulation of inflammatory markers.

DISCUSSION: AOC enhances sheep productivity and rumen health by modulating fibrolytic microbiota, promoting VFA synthesis, and activating antioxidant and energy metabolism pathways. These findings provide a theoretical basis for the use of AOC as a sustainable feed additive to improve ruminant production efficiency and welfare.},
}

@article {pmid41321522,
year = {2025},
author = {Cai, W and Xu, Y and Cheng, W and Xu, J and Chen, X and Fei, H and Chen, X and Wang, C and Mao, H},
title = {Multi-omics reveal beneficial effects of chrysanthemum stalks on growth performance and immune function in Hu sheep.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {23},
number = {},
pages = {44-61},
pmid = {41321522},
issn = {2405-6383},
abstract = {Chrysanthemum stalks (CS), a plant by-product, often face underutilization and resource wastage. This study aimed to explore the effects of partially replacing peanut vines (PV) in the diet with CS on the growth performance, rumen fermentation performance and microbiota, as well as the plasma physiology, biochemistry, and metabolism of Hu sheep. Twenty-seven 6-month-old male Hu sheep (weighing 39.4 ± 0.5 kg; mean ± SD) were randomly assigned to three groups: 1) basal diet (CON); 2) CS replaced 7.88% of PV (low substitution [LS]); and 3) CS replaced 15.57% of PV (high substitution [HS]). The feeding trial lasted for 91 d. Replacement of peanut vines with chrysanthemum stalks significantly increased dry matter intake in both LS and HS groups as compared to the CON group (P = 0.021; linear effect, P = 0.050), while average daily weight gain only increased significantly in the LS group (P = 0.020; quadratic P = 0.042). The concentrations of volatile fatty acids (VFAs) and ammonia nitrogen (NH3-N) were the highest in rumen of LS group (P < 0.05; quadratic effect, P < 0.05). The LS group also had the highest relative abundance of Prevotella (P = 0.011; quadratic P = 0.001). The rumen metabolomic analysis showed elevated levels of flavonoids, terpenoids, and amino acids in the LS group (P < 0.05). Additionally, the LS group exhibited significantly higher levels of total antioxidant capacity, immunoglobulin A, and immunoglobulin M (P < 0.05; quadratic P < 0.05), while tumor necrosis factor-α and interferon-γ levels were lower (P < 0.05; quadratic P < 0.05). The plasma metabolomic analysis revealed increases in phospholipids, amino acids, and indole derivatives in the LS group (P < 0.05). In general, CS improved the growth performance of Hu sheep by increasing VFA concentrations and promoting beneficial bacteria like Prevotella in the rumen. Additionally, flavonoids and terpenoids in CS were positively associated with immune response and antioxidant capacity. These beneficial effects were more pronounced in the LS group compared to the HS group, highlighting the potential of CS as a roughage substitute for improving sheep growth performance and immune function.},
}

@article {pmid41321514,
year = {2025},
author = {Liu, Z and Jiang, A and Kong, Z and Lv, X and Zhang, J and Wu, J and Zhou, C and Tan, Z},
title = {Multi-omics analysis reveals the mechanism of rosemary extract supplementation in increasing milk production in Sanhe dairy cows via the "rumen-serum-milk" metabolic pathway.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {23},
number = {},
pages = {396-414},
pmid = {41321514},
issn = {2405-6383},
abstract = {Rosemary extract (RE) has shown potential as a plant-derived feed additive, but its effects on Sanhe dairy cows are still unknown. In this study, 30 multiparous Sanhe dairy cows (days in milk 171 ± 17 days) with similar body condition were randomly divided into two groups: the RE group (n = 15) was fed the basal diet plus 20 g RE/d, and the CON group (n = 15) was fed only the basal diet. The experiment lasted for 57 days, including a one-week adaptation period. Compared with the CON group, milk yield (P = 0.022) increased significantly with RE supplementation, while milk fat (P = 0.071) also tended to increase. Milk urea nitrogen (P = 0.003) and serum urea nitrogen (P = 0.013) contents were significantly reduced in the RE group compared with the CON group. In rumen fermentation, the content of butyric acid (P = 0.035) in RE group was significantly increased, while valeric acid (P = 0.080) content had an increasing trend. In addition, RE supplementation improved the antioxidant capacity of Sanhe dairy cows by significantly increasing the serum total antioxidant capacity (P < 0.001), superoxide dismutase activity (P = 0.001), immunoglobulin A content (P < 0.001), and immunoglobulin G content (P = 0.005), while decreasing serum malondialdehyde content (P < 0.001), to improve immunity and also affect the composition of serum free amino acids. Metabolomic results showed that a total of 13 co-differential metabolites were identified in rumen and serum, including ursolic acid, a major component of RE, which was higher in both rumen and serum. The milk metabolome analysis identified glycerides, glycerophospholipids, and sphingolipids as the three lipid types that exhibited higher identification intensity in RE. Rumen metagenomic results showed that RE supplementation affected the composition of rumen microorganisms, and differential microbial Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analyses revealed that the RE group was significantly enriched in the fatty acid biosynthesis pathway and the glycerophospholipid metabolism pathway; two pathways related to lipid synthesis. By associating the genus-level differential microorganisms in the rumen with the "rumen-serum-milk" metabolome and mapping the correlation network, it was found that g_Sharpea, g_Tistlia, and g_Acetobacter, which were more abundant in RE, correlated with more differential metabolites and clustered in the same module. Among the 10 microbial biomarkers screened in the rumen, g_Acetobacter and g_Prevotella were more abundant in the RE, and Mantel's analysis showed that they correlated with rumen fermentation parameters and oxidative and immunological indicators in serum. These results reveal the regulatory mechanism of RE supplementation feeding to enhance milk production and improve milk quality by improving oxidative stress capacity and immunity and reducing nitrogen loss in Sanhe dairy cows, suggesting that RE has the potential as a feed additive for dairy cows.},
}

@article {pmid41321512,
year = {2025},
author = {Li, Y and Ko, K and Liu, X and Kačániová, M and Lee, Y and Zhang, G},
title = {Effects of inulin on growth performance and intestinal health of broilers by modulating intestinal microbiota and metabolome.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {23},
number = {},
pages = {257-270},
pmid = {41321512},
issn = {2405-6383},
abstract = {Inulin, a natural dietary fiber, confers multiple physiological benefits. However, the effects of inulin on the liver and intestinal health of broilers remain unclear. The study investigated the effects and mechanisms of inulin supplementation on hepatic and intestinal health of broilers. A total of 192 male broilers (821.15 ± 14.99 g) at 21 d of age were randomly allocated to four treatment groups, comprising eight replicates per group with six broilers each. The dietary treatments included: a control group (CON) receiving a basal diet and three treatment groups fed the basal diet supplemented with 0.5, 1.0, or 2.0 g/kg inulin (designated as INU-0.5, INU-1.0, and INU-2.0, respectively). Results indicated that dietary inulin supplementation elicited a quadratic response in final body weight (FBW, P = 0.032). Inulin supplementation produced linear improvements in average daily gain (ADG, P = 0.044) alongside quadratic reductions in both average daily feed intake (ADFI) and feed-to-gain ratio (F/G ratio) (P < 0.001). Notably, inulin supplementation linearly decreased malondialdehyde (MDA) levels (P < 0.001) while significantly enhancing superoxide dismutase (SOD) activity (P < 0.001). Furthermore, inulin supplementation demonstrated dose-dependent effects on lipid metabolism, including a linear reduction in abdominal fat deposition (P < 0.001), decreased hepatic and serum concentrations of total cholesterol (TCHO, both P < 0.001) and triglycerides (TG, P < 0.001 and P = 0.001, respectively), and reduced serum levels of both high-density lipoprotein (HDL, P = 0.010) and low-density lipoprotein (LDL, P < 0.001) (P < 0.01). Parallel improvements in intestinal barrier function were observed, with linear increases in jejunal expression of tight junction proteins (claudin-5, occludin, and zonula occludens-1 [ZO-1]), mucin 2 (MUC2), and diamine oxidase (DAO) (P < 0.001). Additionally, inulin supplementation selectively increased the abundances of key microbes, including Bacteroides, Lactobacillus, and Akkermansia, while decreased the abundances of Alistipes, Odoribacte, Parabacteroides, Rikenella, and Erysipelatoclostridium (P < 0.001). These microbial shifts were associated with modulation of key metabolic pathways, including taurine and hypotaurine metabolism, purine metabolism, arginine and proline, and phenylalanine metabolism. Collectively, these findings demonstrate that inulin supplementation enhances broiler productivity while improving both intestinal and hepatic health (P < 0.05) through microbiota-mediated metabolic regulation. Therefore, dietary inulin supplementation would be a recommendable nutritional strategy to optimize production efficiency in commercial broiler industry.},
}

@article {pmid41321511,
year = {2025},
author = {Pi, Y and Mu, C and Gao, K and Liu, Z and Peng, Y and Yu, K and Su, Y and Zhu, W},
title = {Increasing carbohydrates or nitrogenous compounds by cecal infusion leads to an opposite influence on colonic microbiota and host metabolism in a pig model.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {23},
number = {},
pages = {62-77},
pmid = {41321511},
issn = {2405-6383},
abstract = {Gut microbes, particularly those in the hindgut, play an important role in fermenting undigested nutrients (carbohydrates and proteins) and in regulating host metabolism via the gut-liver metabolic axis. However, the effects of variations in the ratio of carbohydrates to proteins on host metabolism remain largely unknown. In this study, we investigated the response of large intestinal microbiota and host metabolism to changes in nutrient substrate availability by infusing corn starch or casein hydrolysate via cecal cannulas. Twenty-four growing pigs with cecal cannulas were randomly divided into three groups (n = 8): a control group infused with saline; a starch group infused with corn starch; and a casein group infused with casein hydrolysate (50 g/d) dissolved in saline. The infusion was performed daily for 19 d. Compared with the control, starch infusion significantly increased the relative abundances of Bifidobacterium, Bacteroidales S24-7 group and Megasphaera (P < 0.05), while decreasing Anaerovibrio, Campylobacter and Veillonella (P < 0.05). Conversely, casein hydrolysate infusion significantly increased Streptococcus, Desulfovibrio and Mogibacterium (P < 0.05), while decreasing Coprococcus and Ruminococcus at the genus level (P < 0.05). Starch infusion increased short-chain fatty acid (SCFA) concentrations (P = 0.001), whereas casein hydrolysate infusion reduced them (P = 0.001); these effects were observed in both colonic digesta and liver. Additionally, serum metabolomics and liver gene expression analysis revealed that host metabolic states were significantly altered in different ways following starch and casein hydrolysate infusion (P < 0.05). Starch infusion enhanced host energy metabolism, gluconeogenesis and lipid metabolism by increasing concentrations of tricarboxylic acid (TCA) cycle-related metabolites (e.g., succinic acid, oxaloacetic acid, and L-malic acid) and fatty acid (FA) synthesis (e.g., D-glyceric acid, stearic acid, and palmitic acid) (P < 0.05), alongside upregulation of FA synthase (FAS), stearoyl-CoA desaturase (SCD), acetyl-CoA carboxylase (ACC), phosphoenolpyruvate carboxykinase 1 (PCK1) and pyruvate kinase (PK) gene expression (P < 0.05). In contrast, casein hydrolysate infusion enhanced glycolysis and reduced FA synthesis by increasing glucose-6-phosphate, L-lactic acid, glycerol, glycolic acid, etc. (P < 0.05), in parallel with upregulation of acyl-CoA oxidase 1 (ACOX-1), peroxisome proliferator-activated receptors α (PPAR-α), carnitine palmitoyltransferase-1α (CPT-1α) and PK gene expressions in the liver (P < 0.05). Correlation result demonstrated a strong association between altered gut microbiota and several serum metabolites (P < 0.05). In summary, these results indicate that increasing carbohydrate or nitrogenous compound levels in the large intestine can distinctly alter microbiota composition, thereby influencing host metabolism. These findings provide novel insights into the crosstalk between the large intestinal microbiome and host metabolism.},
}

@article {pmid41321425,
year = {2026},
author = {Hartsgrove, CE and Walker, GS and Silva, KD and Nunez, K and Alejos, K and Joseph, M and Wright, JR and McMullen, B and Lamendella, R and Maeng, LY},
title = {Acute 17β-Estradiol Administration Enhances Fear Extinction Memory and Alters Gut Microbiota in Female Rats.},
journal = {Biological psychiatry global open science},
volume = {6},
number = {1},
pages = {100620},
pmid = {41321425},
issn = {2667-1743},
abstract = {BACKGROUND: Previous studies have shown that fear extinction memory and the gut microbiome are impacted by ovarian hormones. Elevated 17β-estradiol (E2) levels during fear extinction learning have been shown to enhance fear extinction recall 24 hours later. In this study, we concurrently examined the long-term maintenance of this facilitation and the role of the gut microbiome as a potential mediator.

METHODS: Naturally cycling adult female Sprague Dawley rats underwent an auditory-cued fear conditioning/extinction paradigm, during which the estrous cycle was tracked and fecal samples were collected. Habituation and conditioning took place when the rats were in estrus on day 1. On day 2, rats were administered either a sesame oil vehicle (n = 24) or E2 (15 μg/kg) (n = 25) before extinction training. Recent recall took place 24 hours after extinction training, and remote recall took place 1 to 2 weeks after extinction training (vehicle n = 13, E2 n = 12).

RESULTS: E2-treated rats showed significantly lower freezing behavior compared with vehicle-treated rats during recent recall, but not remote recall. Gut bacterial analysis using 16S ribosomal RNA sequencing revealed unique enrichment of estrogen-regulating and anxiety-related bacterial families during remote recall.

CONCLUSIONS: The current data suggest that E2-enhanced fear extinction consolidation may be linked to alterations in gut microbiome composition. These findings may reveal a novel potential target for anxiety and other fear-based psychiatric disorders.},
}

@article {pmid41321404,
year = {2025},
author = {Shalbaf, N and Sadeghi, S and Homaee, S and Saberian, F},
title = {Probiotics, prebiotics, synbiotics, and FMT for glycemic control: A systematic review of clinical efficacy and mechanistic readouts in type 2 diabetes and related dysglycemia.},
journal = {Metabolism open},
volume = {28},
number = {},
pages = {100419},
pmid = {41321404},
issn = {2589-9368},
abstract = {OBJECTIVE: To systematically evaluate the clinical efficacy of probiotics, prebiotics, synbiotics, and fecal microbiota transplantation (FMT) on glycemic control in adults with type 2 diabetes (T2D) and related dysglycemia, and to synthesize associated mechanistic changes in microbial metabolites and composition.

METHODS: A systematic review was conducted following PRISMA 2020 guidelines. PubMed/MEDLINE, Scopus, and Web of Science were searched from inception through August 2025 for randomized controlled trials (RCTs) in adults with T2D, prediabetes, or metabolic syndrome. Interventions included probiotics, prebiotics, synbiotics, or FMT compared to control. Outcomes were glycemic indices (e.g., HbA1c, HOMA-IR) and mechanistic biomarkers (e.g., SCFAs, bile acids). Risk of bias was assessed using the Cochrane RoB 2 tool. A narrative synthesis was performed.

RESULTS: Thirty studies were included. Multi-strain probiotics, prebiotics, and synbiotics yielded modest but significant improvements in HbA1c (≈-0.2 to -0.4 %), fasting glucose, and HOMA-IR, particularly with durations ≥12 weeks. These benefits were linked to mechanistic shifts, including increased circulating butyrate and ursodeoxycholate, enrichment of SCFA-producing taxa, and reduced endotoxemia. Efficacy was moderated by concomitant medications: metformin use was synergistic, while sulfonylureas attenuated effects. FMT consistently improved clamp-measured insulin sensitivity in insulin-resistant phenotypes, but its effects on HbA1c were less consistent and donor-dependent.

CONCLUSION: Microbiome-targeted interventions, especially multi-strain probiotics and substrate-matched synbiotics, are effective adjuncts for improving glycemic control, with effects mediated through microbial metabolite production. FMT primarily modulates insulin sensitivity. Clinical outcomes are context-dependent, influenced by intervention design, duration, and pharmacomicrobiomic interactions.},
}

@article {pmid41321285,
year = {2025},
author = {Blanton, MB and Napier, EG and Keen, KE and Stuart, EV and Cinco, IR and Hemati, H and Bruntz, RC and Khadka, R and Grant, KA and Messaoudi, I},
title = {Short-Term Alcohol Consumption Is Sufficient to Disrupt Microbial Communities and the Intestinal and Circulating Metabolites in a Non-Human Primate Model.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {23},
pages = {e71280},
doi = {10.1096/fj.202503336R},
pmid = {41321285},
issn = {1530-6860},
support = {1R01AA028735-01//HHS | NIH | National Institute on Alcohol Abuse and Alcoholism (NIAAA)/ ; U01AA013510//HHS | NIH | National Institute on Alcohol Abuse and Alcoholism (NIAAA)/ ; R24 AA019431/AA/NIAAA NIH HHS/United States ; F31AA031600-01A1//HHS | NIH | National Institute on Alcohol Abuse and Alcoholism (NIAAA)/ ; T32 AA027488/AA/NIAAA NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Macaca mulatta ; *Alcohol Drinking/adverse effects/metabolism ; Male ; *Dysbiosis/microbiology/metabolism ; *Intestines/microbiology ; *Ethanol ; Disease Models, Animal ; },
abstract = {The gut microbiome is a complex and dynamic community of microorganisms that play a crucial role in maintaining host health and facilitating inter-organ communication. The microbiome is altered by the exposome, a phenomenon known as dysbiosis. Alcohol misuse can disrupt the gut microbial community in a dose- and duration-dependent manner. Previous studies showed that chronic alcohol misuse can induce intestinal hyperpermeability and significantly shift microbial communities. However, these data were obtained primarily from cross-sectional clinical and rodent-based studies following long-term chronic alcohol consumption. Clinical studies often utilize samples from patients with alcoholic liver disease and are confounded by variability in factors that can modulate the microbiome and reliance on self-reported data. The intestinal cellular and microbial composition of rodent models differs significantly from that of humans, limiting the clinical translation of those findings. Therefore, the impact of alcohol misuse on the gut microbial communities and their metabolic implications remains poorly understood. Since rhesus macaques share significant genetic/physiological traits, as well as gut microbial communities, with humans, we assessed the impact of 6 months of voluntary daily alcohol consumption on the gut microbiome and its implications for the circulating and intestinal metabolomes. We report that short-term drinking induces dynamic changes in the abundance of short-chain fatty acid producers and increases microbes associated with the negative regulation of inflammation. Finally, altered fatty- and amino-acid metabolite signatures were observed. Taken together, these data enhance our understanding of the longitudinal implications of alcohol use.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Macaca mulatta
*Alcohol Drinking/adverse effects/metabolism
Male
*Dysbiosis/microbiology/metabolism
*Intestines/microbiology
*Ethanol
Disease Models, Animal

@article {pmid41321251,
year = {2025},
author = {Sharma, N and Roy, S},
title = {Dysbiosis and Dyslipidemia: Unraveling the Microbiome's Role in Lipid Metabolism and Therapeutic Potential.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {133},
number = {12},
pages = {e70100},
doi = {10.1111/apm.70100},
pmid = {41321251},
issn = {1600-0463},
mesh = {Humans ; *Dyslipidemias/microbiology/therapy/metabolism ; *Dysbiosis/microbiology/metabolism/therapy/complications ; *Gastrointestinal Microbiome ; *Lipid Metabolism ; Probiotics/therapeutic use ; Animals ; Prebiotics ; Cardiovascular Diseases ; },
abstract = {Dysbiosis, an imbalance in the gut microbiota, has emerged as a critical factor in the development of various metabolic diseases, including dyslipidemia. Dyslipidemia, a multifactorial disorder influenced by both genetic and environmental factors, is a significant risk factor for cardiovascular diseases (CVD), such as coronary artery disease (CAD) and stroke. The gut microbiota plays a pivotal role in maintaining lipid homeostasis, interacting with the host's immune, metabolic, and endocrine systems. Recent studies have highlighted the involvement of microbiota-derived metabolites, such as bile acids, lipopolysaccharides, and short-chain fatty acids (SCFAs), in modulating lipid levels and regulating hyperlipidemia. Understanding these complex microbiome-host interactions opens new avenues for therapeutic interventions aimed at correcting lipid imbalances and restoring microbial balance. Approaches such as probiotics, prebiotics, synbiotics, and dietary modifications hold promise in managing dyslipidemia and preventing associated cardiovascular diseases. As research continues to unravel these connections, the microbiome is increasingly recognized as a promising target for therapeutic strategies in dyslipidemia.},
}

Humans
*Dyslipidemias/microbiology/therapy/metabolism
*Dysbiosis/microbiology/metabolism/therapy/complications
*Gastrointestinal Microbiome
*Lipid Metabolism
Probiotics/therapeutic use
Animals
Prebiotics
Cardiovascular Diseases

@article {pmid41320950,
year = {2025},
author = {Reljic, D and Hermann, HJ and Dieterich, W and Neurath, MF and Zopf, Y},
title = {Exercise improves gut microbial metabolites in an intensity-dependent manner: a pooled analysis of randomized controlled trials.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2579354},
doi = {10.1080/19490976.2025.2579354},
pmid = {41320950},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Middle Aged ; Fatty Acids, Volatile/metabolism ; Female ; Feces/chemistry/microbiology ; *Metabolic Syndrome/microbiology/therapy/metabolism ; *Obesity/microbiology/therapy/metabolism ; Randomized Controlled Trials as Topic ; *Exercise/physiology ; Adult ; Bacteria/metabolism/classification/isolation & purification/genetics ; Resistance Training ; Cardiorespiratory Fitness ; },
abstract = {BACKGROUND: Obesity and the metabolic syndrome (MetS) are global health challenges. The gut microbiome, particularly its fermentation products, short-chain fatty acids (SCFAs), is increasingly recognized as a key modulator of cardiometabolic health. Growing evidence suggests that exercise may play a critical role in SCFA production. This study presents a pooled analysis of data from three randomized controlled trials to examine the effects of low-volume high-intensity (HIGH-EX) versus moderate-intensity (MOD-EX) interval training, each combined with single-set resistance training, on SCFAs and cardiometabolic health in obese MetS patients.

METHODS: Data from 113 patients allocated to 12 weeks of HIGH-EX, MOD-EX, or a control group (CON) were analyzed. Fecal SCFA concentrations, cardiorespiratory fitness (VO2max), muscle strength, inflammation (hsCRP), and MetS severity (MetS z-score) were assessed pre- and post-intervention. Exercise intensity was monitored via regular blood lactate measurements during interval training.

RESULTS: HIGH-EX and MOD-EX improved VO2max (+4.2 and +2.7 mL/kg/min), strength across major muscle groups (+19 to 29%), hsCRP (-2.2 and -1.3 mg/L), and MetS z-score (-1.1 and -0.5 units). Only HIGH-EX significantly increased total fecal SCFAs (+30%), including acetate (+27%), propionate (+28%), and butyrate (+43%). Mean blood lactate concentrations during training were strongly correlated with SCFA increases (r = 0.68, p < 0.001). No changes were observed in CON.

CONCLUSIONS: Low-volume combined interval and resistance training improved fitness and metabolic health at both moderate and higher intensities. However, only HIGH-EX enhanced SCFA production, potentially associated with lactate-mediated microbial adaptations. Exercise intensity may thus be a key determinant of gut-metabolic benefits.},
}

Humans
*Gastrointestinal Microbiome/physiology
Male
Middle Aged
Fatty Acids, Volatile/metabolism
Female
Feces/chemistry/microbiology
*Metabolic Syndrome/microbiology/therapy/metabolism
*Obesity/microbiology/therapy/metabolism
Randomized Controlled Trials as Topic
*Exercise/physiology
Adult
Bacteria/metabolism/classification/isolation & purification/genetics
Resistance Training
Cardiorespiratory Fitness

@article {pmid41320781,
year = {2025},
author = {Shapira, E and Voinsky, I and Klin, H and Gurwitz, D},
title = {Butyrate-Mediated Upregulation of Insulin Pathway Gene Expression Suggests Potential Antidiabetic Effects.},
journal = {Drug development research},
volume = {86},
number = {8},
pages = {e70203},
doi = {10.1002/ddr.70203},
pmid = {41320781},
issn = {1098-2299},
support = {//The authors received no specific funding for this work./ ; },
mesh = {Humans ; Up-Regulation/drug effects ; *Insulin/metabolism/genetics ; *Hypoglycemic Agents/pharmacology ; *Diabetes Mellitus, Type 2/drug therapy/genetics/metabolism ; Cell Line ; Insulin Resistance/genetics ; Signal Transduction/drug effects/genetics ; *Butyric Acid/pharmacology ; *Butyrates/pharmacology ; Adult ; },
abstract = {Type 2 diabetes (T2D) is a major cause of morbidity in developed countries and involves insulin resistance, a failure to correctly respond to insulin. Numerous studies in rodent T2D models suggested that the short-chain fatty acid butyrate, produced by gut microbiota species through fermentation of dietary fibers, improves T2D symptoms. Here, we explored the potential antidiabetic effects of butyrate by measuring the transcription of selected T2D-implicated genes in human B lymphocyte-derived lymphoblastoid cell lines (LCLs) from 17 unrelated adult healthy donors. Human LCLs were cultured with and without sodium butyrate (1 mM for 48 h), followed by RNA extraction and real-time PCR analysis of the selected T2D-related genes. Butyrate significantly upregulated the expression of MT2A, RRAGD, IGF1R, OXTR, and INSR, while no changes were observed in the expression of other selected genes implicated in insulin signaling. Our findings, which should be considered preliminary until demonstrated by in vivo T2D animal models, suggest that butyrate is a potential modulator of metabolic pathways relevant to insulin resistance. Future studies should explore the tentative therapeutic potential of butyrate and its upregulated genes using proteomics and metabolomics in relevant tissues of T2D animal models, possibly followed by controlled clinical trials.},
}

Humans
Up-Regulation/drug effects
*Insulin/metabolism/genetics
*Hypoglycemic Agents/pharmacology
*Diabetes Mellitus, Type 2/drug therapy/genetics/metabolism
Cell Line
Insulin Resistance/genetics
Signal Transduction/drug effects/genetics
*Butyric Acid/pharmacology
*Butyrates/pharmacology
Adult

@article {pmid41320718,
year = {2025},
author = {Liu, Y and Zhou, N and Liu, J and Li, G and Chen, R and Li, G and Li, Y},
title = {The Impact of Fluoride Varnish Application on the Supragingival Plaque Microbiome in Preschoolers: A Dynamic Study.},
journal = {Current microbiology},
volume = {83},
number = {1},
pages = {50},
pmid = {41320718},
issn = {1432-0991},
support = {202401AU070088//Science and Technology Support Program of Jiangsu Province/ ; XDYC-YLWS-2023-0047//Xingdian Talent Support Plan of Yunnan Province-Medical and Health Talents Special Project/ ; D2019-007//Academic Leader Project of Yunnan Province/ ; 2019-35//Famous Doc tor Special Project of Yunnan Province/ ; 202201AY070001-174//the Joint Fund of Yunnan Provincial Science and Technology Office and Kunming Medical University/ ; 202301AY070001-046//the Joint Fund of Yunnan Provincial Science and Technology Office and Kunming Medical University/ ; 202501AY070001-052//the Joint Fund of Yunnan Provincial Science and Technology Office and Kunming Medical University/ ; },
mesh = {Humans ; *Dental Plaque/microbiology ; Child, Preschool ; *Fluorides, Topical/administration & dosage/pharmacology ; *Microbiota/drug effects ; *Bacteria/classification/genetics/drug effects/isolation & purification ; Male ; Female ; Dental Caries/prevention & control/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Fluoride varnish application is used in many studies as a minimally invasive technique to prevent caries. Notably, oral microorganisms play a crucial role in the incidence and progression of tooth caries. However, the effect of fluoride varnish application on the dynamic microbial alterations that occur in dental plaques remains unclear. In this study, we investigated the impact of fluoride varnish application on the supragingival microbial composition and structure in preschoolers. We enrolled 27 preschoolers and collected supragingival plaque samples from the same sites at multiple time points: baseline (0 h, F0 group), 24 h (F1 group), 1 month (F2 group), 3 months (F3 group), and 6 months (F4 group). To unravel the changes in microbial composition and structure after fluoride varnish application, all specimens underwent high-throughput sequencing of the 16 S rRNA gene. The Shannon and Simpson indices showed no significant differences across groups (P > 0.05). Principal co-ordinates analysis (PCoA) revealed significant differences in microbial community structures across all time points (P < 0.001, R[2] = 0.44), with F0 and F1 groups showing similarity. Significant variations in bacterial composition were observed among eight strains, including Neisseria mucosa and Corynebacterium matruchotii (P < 0.05). This study found that Duraphat fluoride varnish application effectively modifies the composition and structural characteristics of supragingival plaque in preschoolers, enhancing anti-caries properties.},
}

Humans
*Dental Plaque/microbiology
Child, Preschool
*Fluorides, Topical/administration & dosage/pharmacology
*Microbiota/drug effects
*Bacteria/classification/genetics/drug effects/isolation & purification
Male
Female
Dental Caries/prevention & control/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid41320670,
year = {2025},
author = {Chen, H and Zhang, X and Li, S and Fang, Y and Han, Y and Jing, X},
title = {Multi-Omics Analysis Reveals OBSCN as a Key Modulator of Tumor Microenvironment, Microbial Signatures and Clinical Outcomes in Gastric Cancer.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70186},
doi = {10.1002/mbo3.70186},
pmid = {41320670},
issn = {2045-8827},
support = {//This work was supported by Scientific Research Project of Weifang Health Commission (No. WFWSJK-2023-268)./ ; },
mesh = {Humans ; *Stomach Neoplasms/genetics/microbiology/therapy/pathology ; *Tumor Microenvironment/genetics ; Mutation ; *Cytoskeletal Proteins/genetics/metabolism ; Immunotherapy ; MicroRNAs/genetics ; Biomarkers, Tumor/genetics ; Multiomics ; },
abstract = {Emerging evidence suggests that OBSCN, a giant cytoskeletal protein gene, plays multifaceted roles in cancer progression, yet its impact on gastric cancer (GC) remains poorly understood. Through integrative analysis of multi-omics datasets, we observe a close relationship between OBSCN expression and outcome of immunotherapy. Besides, elevated expression of OBSCN strongly associated with adverse disease free survival (DFS). Tumor-resident microbes, such as Fusobacterium, can impact the expression of microRNAs (miRNAs) targeting OBSCN. In terms of genomic alterations, mutational status of OBSCN is substantially associated with the alpha- and beta-diversity of intratumoral microbiome and patients with mutated OBSCN exhibit elevated higher tumor mutational burden (TMB) and better response to immunotherapy. Furthermore, machine learning models based on the OBSCN mutation-related gene signatures (OMRGS) achieve outstanding performance in prediction of response to immune checkpoint inhibitors. In summary, our findings position OBSCN as a novel molecular nexus linking genomic alterations, intratumoral microbiome dysbiosis, and immune infiltration in GC, providing a rationale for future biomarker-driven therapeutic strategies.},
}

Humans
*Stomach Neoplasms/genetics/microbiology/therapy/pathology
*Tumor Microenvironment/genetics
Mutation
*Cytoskeletal Proteins/genetics/metabolism
Immunotherapy
MicroRNAs/genetics
Biomarkers, Tumor/genetics
Multiomics

@article {pmid41320596,
year = {2025},
author = {Klironomos, J and Zhang, J and Wang, G},
title = {From feedbacks to functional teams in the rhizosphere.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.11.013},
pmid = {41320596},
issn = {1878-4380},
abstract = {Johnson and Marín's paper presents functional team selection (FTS) as a major conceptual advance in plant-microbiome ecology. FTS explains how limiting resources and/or stress selects cooperative microbial teams that promote plant adaptation, integrating ecological feedback and evolutionary selection to predict when and where resilient plant-microbiome partnerships will arise.},
}

@article {pmid41320400,
year = {2026},
author = {Karagöz, MF and Ünaldı, BÖ and Buhurcu, CA and Şen, N and Aydoğdu, GS and Demirci, KŞ and Gündüz, ZG and Güler, MS and Ağagündüz, D and Coreta-Gomes, F},
title = {Seaweed polysaccharides and their potential health effects via gut microbiota modulation.},
journal = {Carbohydrate polymers},
volume = {373},
number = {},
pages = {124621},
doi = {10.1016/j.carbpol.2025.124621},
pmid = {41320400},
issn = {1879-1344},
mesh = {*Seaweed/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Polysaccharides/pharmacology/chemistry ; Humans ; Fermentation ; Bacteroidetes/drug effects ; Carrageenan/chemistry/pharmacology ; Fatty Acids, Volatile/metabolism ; Molecular Weight ; Firmicutes/drug effects ; Alginates/chemistry/pharmacology ; },
abstract = {Macroalgae, commonly known as seaweeds, are a valuable source of polysaccharides known to modulate gut microbiota. In this work, the impact of polysaccharide structural features on gut microbiota was explored. The low molecular weight algae polysaccharides showed better degradation by gut bacteria. Moreover, the content of sulfate and carboxylic groups seem to promote high fermentation, triggering an increase in gut microbiota health. The effect of ramification degree of algae polysaccharides on fermentability is still unclear. Agar polysaccharides with low molecular weight and a higher degree of sulfation have been shown to produce higher amounts of SCFA, and decrease in Firmicutes/Bacteroidetes ratio. An increase of sulfation degree of porphyran showed to increase the total SCFA production and a decrease on the ratio of butyric to propionic acid. Carrageenan's molecular weight does not seem to affect SCFA production, and the effect of sulfation degree is not clear. The consumption of these polysaccharides was shown to decrease the Firmicutes/Bacteroidetes ratio. Fucoidans of low molecular weight seem to promote a lower Firmicutes/Bacteroidetes ratio. Alginate consumption both of high and low molecular weight has been shown to increase Bacteroidetes. Low molecular weight laminarans are highly fermented and significantly increase the production of SCFA. Ulvan and sulfated rhamnan polysaccharides have been shown to increase the production of SCFA, although microbiota modulation data are still undisclosed. Overall, seaweed polysaccharides have shown several health benefits, which have been related with gut microbiota modulation.},
}

*Seaweed/chemistry
*Gastrointestinal Microbiome/drug effects
*Polysaccharides/pharmacology/chemistry
Humans
Fermentation
Bacteroidetes/drug effects
Carrageenan/chemistry/pharmacology
Fatty Acids, Volatile/metabolism
Molecular Weight
Firmicutes/drug effects
Alginates/chemistry/pharmacology

@article {pmid41320393,
year = {2026},
author = {Wang, S and De Paepe, K and Onyango, SO and Zhang, B and Huang, Q and Wang, S and Van de Wiele, T},
title = {Starch-entrapped microspheres selectively promote propionate or butyrate production through individual-specific modulation of the human fecal microbiome.},
journal = {Carbohydrate polymers},
volume = {373},
number = {},
pages = {124614},
doi = {10.1016/j.carbpol.2025.124614},
pmid = {41320393},
issn = {1879-1344},
mesh = {Humans ; *Starch/chemistry/pharmacology ; *Feces/microbiology ; *Microspheres ; Prebiotics ; *Butyrates/metabolism ; *Propionates/metabolism ; *Gastrointestinal Microbiome/drug effects ; Adult ; Male ; Zea mays/chemistry ; Female ; Inulin/chemistry ; Fermentation ; Young Adult ; },
abstract = {Starch microspheres encapsulated with chitosan synergistically and beneficially modulate the microbiota composition and metabolic activity of a pooled fecal slurry compared to starch, suggesting a superior prebiotic potential. Interindividual differences in prebiotic potential are, however, unexplored. Therefore, we incubated starch-entrapped microspheres (MS), high amylose maize starch (HAMS) and the reference prebiotic inulin with the separate fecal microbiota derived from six healthy individuals. The variation in microbial community composition was largely driven by inter-individual variability (effect size of 71.7 %). Despite the inter-individual variability, the different prebiotic substrates significantly affected the microbiota composition (effect size of 9.5 %) and metabolic activity over the course of fermentation. MS delayed the fermentation and reduced the gas production and acidification in all donors compared to HAMS and inulin. Furthermore, compared to HAMS, MS more effectively promoted propionate or butyrate production in a donor-dependent manner. MS increased butyrate levels with 0.1 ± 0.72 mM per unit of starch across all donors. Additional, MS increased the propionate production with 0.52 ± 0.71 mM per unit of starch in donors 1, 2, 4, 6. The donor-specific propiogenic and butyrogenic effects of MS were linked to the enrichment of Bacteroides and Agathobacter species. Our findings confirm the superior prebiotic effect of MS and provide directions for the design and manufacture of starch-based functional foods to enhance gut health.},
}

Humans
*Starch/chemistry/pharmacology
*Feces/microbiology
*Microspheres
Prebiotics
*Butyrates/metabolism
*Propionates/metabolism
*Gastrointestinal Microbiome/drug effects
Adult
Male
Zea mays/chemistry
Female
Inulin/chemistry
Fermentation
Young Adult

@article {pmid41320368,
year = {2026},
author = {Li, S and Deng, R and Sang, J and Zhu, Y and Ma, C and Nan, W and Wang, T and Si, H and Li, Z},
title = {Integrated microbial and metabolic coordination orchestrates antler growth induced by guar gum and xylo-oligosaccharides.},
journal = {Carbohydrate polymers},
volume = {373},
number = {},
pages = {124586},
doi = {10.1016/j.carbpol.2025.124586},
pmid = {41320368},
issn = {1879-1344},
mesh = {Animals ; *Mannans/pharmacology/chemistry ; *Galactans/pharmacology/chemistry ; *Plant Gums/pharmacology/chemistry ; *Antlers/growth & development/drug effects/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Oligosaccharides/pharmacology/chemistry ; Osteogenesis/drug effects ; Bile Acids and Salts/metabolism ; Glucuronates ; },
abstract = {Antlers are a unique mammalian bone organ characterized by rapid growth, a process critically dependent on nutrient availability and the gastrointestinal tract microbiome. Polysaccharides and oligosaccharides shape microbiome output, but their roles in antler development remain unclear. Here, the strongest short-chain fatty acid effect was found with guar gum (GG) and xylo-oligosaccharides, which altered the rumen microbiome in vitro incubations with six polysaccharides and oligosaccharides. GG enriched Lachnospiraceae and Oscillospiraceae, and glycoside hydrolase families, enhancing butyrate biosynthesis and amino acid catabolism, while xylo-oligosaccharides selectively enriched Selenomonadaceae, supporting vitamin and fatty acid biosynthesis in vivo in the rumen. GG increased the fecal microbiome involved in bile acid deconjugation and dihydroxylation. Targeted metabolomics demonstrated that GG elevated the circulating levels of bile acids (chenodeoxycholic acid, deoxycholic acid, taurohyodeoxycholic acid) and osteogenic factors (IGF-1, BMP2, FGF2), and resulted in free fatty acid changes in the serum. Transcriptomics and RT-PCR revealed activation of angiogenic pathways in reserve mesenchyme and osteogenic signaling in mineralized cartilage of antlers. In vitro assays demonstrated that taurohyodeoxycholic acid significantly promoted osteogenic differentiation of mesenchymal cells. Our results revealed the distinct microbial adaptations of specific carbohydrates and elucidated a "GIT-antler" axis intervention for enhancing bone growth in mammals.},
}

Animals
*Mannans/pharmacology/chemistry
*Galactans/pharmacology/chemistry
*Plant Gums/pharmacology/chemistry
*Antlers/growth & development/drug effects/metabolism
*Gastrointestinal Microbiome/drug effects
*Oligosaccharides/pharmacology/chemistry
Osteogenesis/drug effects
Bile Acids and Salts/metabolism
Glucuronates

@article {pmid41320317,
year = {2025},
author = {Kushima, H and Ishii, H and Umeyama, T and Kinoshita, Y and Fujita, M and Tsunoda, T and Makimura, K and Miyazaki, Y},
title = {The Lung Mycobiome in Idiopathic Interstitial Pneumonia, Collagen Tissue Disease-related Interstitial Lung Disease, and Sarcoidosis.},
journal = {Medical mycology journal},
volume = {66},
number = {4},
pages = {177-184},
doi = {10.3314/mmj.25-00016},
pmid = {41320317},
issn = {2186-165X},
mesh = {Humans ; Male ; Female ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Mycobiome ; *Lung Diseases, Interstitial/microbiology ; *Lung/microbiology ; DNA, Fungal/genetics ; *Idiopathic Interstitial Pneumonias/microbiology ; Adult ; *Sarcoidosis/microbiology ; *Fungi/classification/genetics/isolation & purification ; DNA, Ribosomal Spacer/genetics/chemistry ; Sequence Analysis, DNA ; },
abstract = {Dysbiosis of the lung microbiome may be associated with the development and progression of respiratory diseases. As fungal spores invade the lungs more easily than bacteria, it seems likely that fungi colonizing the lungs are also involved in respiratory diseases. In this study, we investigated the relationship between fungal flora (mycobiome) and diffuse lung disease. Of the 185 patients who underwent bronchoalveolar lavage (BAL) during the diagnostic process, 42 with diffuse lung disease were selected for a mycobacterial analysis of BAL fluid. Twenty patients with idiopathic interstitial pneumonia (IIP), 8 with collagen tissue disease-related interstitial lung disease (CTD-ILD), 8 with sarcoidosis, and 6 with other diseases were included. Fungal DNA was extracted, and internal transcribed spacer 2 (ITS2) regions were sequenced. Of the 42 patients, 29 had polymerase chain reaction amplification products in the ITS2 region. Significant differences in alpha diversity (observed species, Shannon, and Simpson indices) were found between the CTD-ILD and sarcoidosis groups, and between the IIP and sarcoidosis groups. A comparison of the mycobiomes of individual patients (beta diversity) showed that the clustering patterns differed among the groups. In particular, BAL fluid samples from patients with sarcoidosis showed a clear clustering pattern of mycobacterial composition. Our results may lead to significant advances in our understanding of the etiology of these diseases.},
}

Humans
Male
Female
Middle Aged
Bronchoalveolar Lavage Fluid/microbiology
Aged
*Mycobiome
*Lung Diseases, Interstitial/microbiology
*Lung/microbiology
DNA, Fungal/genetics
*Idiopathic Interstitial Pneumonias/microbiology
Adult
*Sarcoidosis/microbiology
*Fungi/classification/genetics/isolation & purification
DNA, Ribosomal Spacer/genetics/chemistry
Sequence Analysis, DNA

@article {pmid41320171,
year = {2026},
author = {Ying, F and Shao, W and Li, L and Cao, X and Xu, X and Tao, Y},
title = {Banxia Xiexin Decoction Ameliorates Ulcerative Colitis via a Flora-Metabolite-Inflammation Axis Through Integrated Metabolomic and Microbiome Analysis.},
journal = {Biomedical chromatography : BMC},
volume = {40},
number = {1},
pages = {e70275},
doi = {10.1002/bmc.70275},
pmid = {41320171},
issn = {1099-0801},
support = {2023-4-282//Jinhua Science and Technology Project/ ; },
mesh = {Animals ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; *Colitis, Ulcerative/metabolism/drug therapy/microbiology ; *Gastrointestinal Microbiome/drug effects ; Mice ; Metabolomics/methods ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; *Metabolome/drug effects ; Cytokines/metabolism ; Inflammation/metabolism/drug therapy ; Colon/drug effects ; },
abstract = {Banxia Xiexin Decoction (BXD), a classic traditional Chinese medicine formula traditionally used for gastrointestinal disorders, has demonstrated considerable therapeutic potential in ulcerative colitis (UC). Yet, its mechanism of action remains incompletely elucidated. In this study, we applied an integrated strategy incorporating UPLC-Q-TOF/MS-based plasma metabolomics and gut microbiome analysis to explore the anti-UC effects of BXD. In a DSS-induced murine model of UC, BXD treatment mitigated colonic inflammation, as evidenced by reduced levels of pro-inflammatory cytokines (IL-1β, IL-6, and TNF-α), repaired intestinal barrier integrity, and restored metabolic homeostasis via regulation of tryptophan and nitrogen metabolism. Notably, BXD promoted the production of microbially derived tryptophan metabolites, including indole-3-propionic acid (IPA) and indole-3-carboxaldehyde (IAld). IAld acts as a ligand for the aryl hydrocarbon receptor (AhR), facilitating the differentiation and function of regulatory T cells (Tregs) and thereby helping to suppress excessive inflammation. Gut microbiota analysis further indicated that BXD enriched beneficial genera such as Akkermansia and Bifidobacterium, while reducing the abundance of pro-inflammatory bacteria belonging to the Lachnospiraceae family. These results demonstrate the role of BXD in modulating the flora-metabolite-inflammation axis, providing a scientific rationale for its use in UC and highlighting its multi-target actions involving anti-inflammatory effects, metabolic reprogramming, and microbiota restoration.},
}

Animals
*Drugs, Chinese Herbal/pharmacology/therapeutic use
*Colitis, Ulcerative/metabolism/drug therapy/microbiology
*Gastrointestinal Microbiome/drug effects
Mice
Metabolomics/methods
Male
Mice, Inbred C57BL
Disease Models, Animal
*Metabolome/drug effects
Cytokines/metabolism
Inflammation/metabolism/drug therapy
Colon/drug effects

@article {pmid41319485,
year = {2025},
author = {Liu, H and Ou, Y and Wang, X and Yang, L and Yan, L and Shang, M},
title = {Rhizosphere microbiome-driven acetochlor biodegradation in biofilters: Unveiling the mechanisms of process enhancement by wetland plants.},
journal = {Journal of hazardous materials},
volume = {502},
number = {},
pages = {140635},
doi = {10.1016/j.jhazmat.2025.140635},
pmid = {41319485},
issn = {1873-3336},
abstract = {Acetochlor (ACT), a selective herbicide from the chloroacetanilide class, is widely used in the black soil region of Northeast China. Due to its high solubility and persistence, it is frequently detected in both water and soil, posing potential threats to ecosystems and human health. This study established biofilters planted with Canna indica (CAN-BF) and Iris pseudacorus (CAL-BF), using a plant-free filter (CK) as a control. We systematically compared acetochlor removal efficiency, changes in physicochemical parameters, microbial community structure, and functional gene distribution, and explored the degradation pathways. The results showed that after 48 h of operation, the acetochlor removal rates in CAN-BF and CAL-BF increased by 19.31 ± 0.88 % and 15.80 ± 1.99 %, respectively, compared to CK. The greater performance of CAN-BF was attributed to its higher biomass, well-developed root system, and stronger radial oxygen loss. High-throughput sequencing identified Tolumonas, Dechloromonas, and Pseudomonas as key potential degraders of acetochlor, with these genera being significantly enriched in the planted biofilters. GC-MS and functional gene predictions indicated that ACT degradation involves multiple enzymatic steps, including de-ethoxymethylation, dechlorination, decarbonylation, hydroxylation, and nitration, resulting in the formation of products like 2-ethyl-6-methylphenol. Key functional genes (such as dhaA, fdhA, mxaJ, K01455, norB, and nemA) were significantly enriched in the planted filters. This study highlights how plants enhance ACT degradation by regulating microbial communities and metabolic enzymes in the rhizosphere, providing theoretical and technical support for ecological engineering strategies to address chloroacetanilide pesticide pollution.},
}

@article {pmid41319410,
year = {2025},
author = {Ajith Kumar, AP and Rajashekaraiah, PB and Chandraprakash, SCA and Beena Chandran, P and Malali, VA and Chandavarkar, V},
title = {Salivary biomarkers in forensic science: Bridging molecular biology and legal medicine.},
journal = {Journal of forensic and legal medicine},
volume = {117},
number = {},
pages = {103044},
doi = {10.1016/j.jflm.2025.103044},
pmid = {41319410},
issn = {1878-7487},
abstract = {Saliva has emerged as a versatile and non-invasive biological specimen in forensic science. It is a rich source of genomic, transcriptomic, proteomic, metabolic, and microbiomic factors, offering significant potential in forensic investigations. This review explores the multi-dimensional aspects of salivary biomarkers in forensic science, integrating molecular biology with legal medicine. It provides a comprehensive overview of the saliva composition, highlighting its biochemical constituents and the methodologies employed for its effective collection in forensic scenarios. From a molecular and analytical perspective, we delve into the diverse classes of salivary biomarkers, including genomic markers that enable individual and kinship profiling; transcriptomic and proteomic biomarkers that reveal gene expression and protein profiles that contribute in post-mortem interval estimation and physiological state evaluation; and metabolomic and microbiomic signatures which offer additional discriminatory power to infer health, lifestyle, and even geographic origins. The forensic applications of these biomarkers and their growing acceptance in judicial proceedings, where the admissibility and evidential value of saliva-derived data are critically assessed, are discussed. Supported by relevant case studies, this review highlights the real-world utility and impact of salivary biomarkers in forensic practice. The challenges and limitations of saliva in forensics are addressed. Additionally, insights into future prospects, such as salivaomics, lab-on-a-chip platforms, and AI-driven data interpretation, are provided. In conclusion, by mapping the intersection of molecular diagnostics and legal frameworks, this review underscores that saliva can be a revolutionary medium that advances the accuracy and accessibility of forensic identification by bridging its biological complexity with forensic applications.},
}

@article {pmid41319383,
year = {2025},
author = {Deng, H and Yang, J and Li, R and Li, K and Lu, H and Lin, B and Xu, X and Liao, J and Ye, C and Deng, J and Wu, B and Sun, L},
title = {ASSR-mediated sludge yield reduction couples deterministic enrichment of Nitrospira with metabolic resource partitioning.},
journal = {Water research},
volume = {290},
number = {},
pages = {125031},
doi = {10.1016/j.watres.2025.125031},
pmid = {41319383},
issn = {1879-2448},
abstract = {The anaerobic side-stream reactor (ASSR) process offers a microbiome-driven strategy for sustainable wastewater treatment, yet the ecological mechanisms governing its sludge yield reduction efficiency remain unresolved. Here, we demonstrate that a pilot-scale anaerobic-anoxic-oxic (AAO) system with integrated anaerobic side-stream reactor (ASSR) (designated AAO-ASSR/SR) reduced sludge production by 43.6 % compared to a conventional AAO system (designated AAO/CK), while maintaining effluent quality. Through integrated multi-omics and ecological modeling, we revealed the core microbiome-driven mechanism for ASSR-mediated sludge yield reduction. This mechanism is characterized by three key features: (1) enhanced microbial stability via cooperative networks, (2) deterministic assembly selecting slow-growing keystone taxa (e.g., Nitrospira, 18.6 % abundance in SR), and (3) metabolic resource partitioning from biomass synthesis to amino acid cross-feeding. Functional metagenomics revealed that Nitrospira (phylum Nitrospirota, comprising >99 % Nitrospira) and Novosphingobium (phylum Proteobacteria) mediated increased amino acid metabolism and reduced ATP biosynthesis in SR, contrasting with Bacteroidota-dominated biomass synthesis in CK through enhanced protein, nucleotide metabolism and ATP biosynthesis. By coupling deterministic microbial assembly with functional repartitioning, this work contributes to establish a design principle for targeted microbiome engineering in low-sludge systems, advancing sustainable wastewater management through ecological optimization of microbial resource allocation.},
}

@article {pmid41279300,
year = {2025},
author = {Yancey, CE and Brumfield, KD and Buss, J and Colwell, RR and Ettwiller, L},
title = {A Bait-and-Switch strategy links phenotypes to genes coding for Polymer-Degrading Enzymes in Intact Microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41279300},
issn = {2692-8205},
support = {R01 ES030317/ES/NIEHS NIH HHS/United States ; },
abstract = {Advances in next generation sequencing have made it possible to explore microbial community dynamics and regulation of functionally important genes through metagenomics and metatranscriptomics. However, the use of meta-omics to link enzyme function directly with complex, community-level phenotypes remain largely unexplored. To overcome this gap, we developed a novel framework that integrates ecological concepts by microbial community perturbation with association analysis to a targeted phenotype. Specifically, we introduce a hypothesis-free "bait and switch" strategy demonstrated through salt marsh soil microcosm pulse experiments to detect and characterize novel enzymes responsible for chitin degradation. Soil microbial communities were "baited" with shell compost, a chitin-rich substrate, to trigger community succession toward chitin degraders and gene upregulation of chitinases. A "switch" was then employed, by addition of glucose, inducing rapid downregulation of genes putatively responsible for chitin degradation. Results demonstrate the feasibility of this approach to identify functionally important enzymes, in this example, 48 hours after chitin addition. The bait and switch community perturbation provides a framework for discovery of polymer degrading enzymes present in complex microbial communities and serves as a proof of concept applicable for linking enzyme function with emergent community level phenotypes.},
}

@article {pmid41319282,
year = {2025},
author = {Han, JE and Lee, DS and Jeong, SW and Yun, JH and Kang, S and Jang, S and Lee, E and Baek, JH and Jeon, CO and Bae, JW},
title = {Pre-Administration of Akkermansia Muciniphila Prevents the Development of Severe Acute Graft-Versus-Host Disease in Systemic Organs.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e15982},
doi = {10.1002/advs.202415982},
pmid = {41319282},
issn = {2198-3844},
support = {NRF-2020R1A2C3012797//National Research Foundation of Korea/ ; RS-2023-00227274//National Research Foundation of Korea/ ; 22213MFDS537//Ministry of Food and Drug Safety/ ; },
abstract = {Acute graft-versus-host disease (aGvHD) remains a significant clinical challenge, with no optimal treatment despite advancements in medical science. This life-threatening condition, characterized by multi-organ involvement and high mortality, is increasingly linked to the gut microbiota. Therefore, this study investigates the protective effects of Akkermansia muciniphila on aGvHD, focusing on its capacity to modulate the gut microbiome and reduce disease symptoms. A. muciniphila is orally administered to mice prior to inducing aGvHD through allogeneic hematopoietic stem cell transplantation. The effects of A. muciniphila administration on the development of aGvHD are assessed through disease activity scoring, histological analysis, metabolite and immune profiling, and gut microbiota analyses. Pre-administration of A. muciniphila significantly reduces aGvHD severity, particularly in the gastrointestinal tract, alleviates gut dysbiosis, and increases the levels of metabolites such as tauroursodeoxycholic acid and short-chain fatty acids. These findings provide the basis for new therapeutic strategies for aGvHD and contribute to improving treatment outcomes for patients with intractable diseases.},
}

@article {pmid41319188,
year = {2025},
author = {Zhi, L and Song, L and Wang, G and You, B and Shang, Y and Jia, Y},
title = {Effects of fermented tea seed oil on the skin lipid barrier and microbiome of sensitive skin.},
journal = {International journal of cosmetic science},
volume = {},
number = {},
pages = {},
doi = {10.1111/ics.70054},
pmid = {41319188},
issn = {1468-2494},
support = {//PeiLai Group Co., Ltd./ ; hc202206//Beijing Technology and Business University/ ; },
abstract = {OBJECTIVE: Sensitive skin is typically characterized by dryness, reactivity and inflammation, often associated with a compromised skin barrier and an imbalanced microbiome. This study aims to investigate the effects and mechanisms of fermented tea seed oil in improving sensitive skin, particularly focusing on the skin lipid barrier and microbiome.

METHODS: Tea seed oil was fermented using biotechnology, and its lipid components were analysed both before and after fermentation. A double-blind, randomized, half-face controlled clinical trial was conducted on 25 Chinese young women with sensitive skin. Participants used a moisturizer containing 5% fermented tea seed oil or a base moisturizer for 4 weeks. Non-invasive methods were used to measure physiological parameters. Ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) and high-throughput gene sequencing technologies were employed to analyse skin lipids and the microbiome.

RESULTS: Fifty-three differential lipids were identified by comparing the lipid profiles of tea seed oil before and after fermentation. The most significant increase was observed in DHA-CoA, which has the potential to improve skin lipid metabolism and enhance the skin barrier. The participants showed significant improvements in skin hydration, redness reduction and facial wrinkles. Lipidomics analysis revealed notable changes in the skin lipid profile before and after treatment, with 41 and 15 differentially expressed lipids identified in the test and control groups, respectively. Microbiome results indicated no significant alterations in the diversity or abundance of skin microbiota after treatment. Nevertheless, the composition of the skin microbiota demonstrated a beneficial shift, with Propionibacterium acnes being suppressed while Streptococcus increased. These microbial changes are associated with skin barrier repair as well as sensitivity and inflammation.

CONCLUSION: Fermented tea seed oil demonstrates notable clinical benefits for sensitive skin. It effectively regulates lipid metabolism and the composition of skin microbiota, thereby strengthening the lipid barrier and reducing the risk of potential inflammation. The increased presence of DHA-CoA in the fermented tea seed oil may serve as a key molecular contributor to its improved reparative efficacy.},
}

@article {pmid41319143,
year = {2025},
author = {Lopes, IG and de Lima, NM and Ribeiro, T and Murta, D and Yong, JWH and Lalander, C},
title = {Olive Pomace Inclusion Alters the Microbial Community of Black Soldier Fly Larvae Frass While Maintaining Fertilizer Quality.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70180},
doi = {10.1002/mbo3.70180},
pmid = {41319143},
issn = {2045-8827},
support = {//This study was supported financially in part by Formas (grant number 2021-02001) and by the Carl Tryggers Stiftelse (grant number CTS21:1483)./ ; },
mesh = {Animals ; Larva/microbiology/growth & development ; *Olea/chemistry ; *Fertilizers/analysis ; *Microbiota ; *Simuliidae/growth & development/microbiology ; Bacteria/classification/isolation & purification/genetics ; Fungi/classification/isolation & purification/genetics ; Animal Feed/analysis ; *Diptera/microbiology/growth & development ; Portugal ; },
abstract = {Olive pomace (OP) is a sludge arising from the production of olive oil, generated in increasing amounts in Portugal. The management of this toxic waste stream is complex and the number of processing plants is limited. In this study, OP was incorporated as a feed component for rearing black soldier fly larvae (BSFL) under industrial conditions. Larvae were reared inside a climate-controlled room with regulated temperature and humidity. The rearing cycle lasted 13 days, after which larvae were harvested. In addition to assessing bioconversion efficiency and larval proximate composition, the resulting frass was examined for its fertilizer potential. Frass was analyzed for plant nutrient content and microbial profile in three forms: fresh, heat-treated (70°C for 1 h), and pelletized. The inclusion of OP in the diets reduced waste-to-biomass conversion efficiency (21.5%DM to approximately 13.3%DM) but did not affect the proximate composition of the larval biomass, which consistently contained around 43%DM crude protein and 20%DM crude fat. Neither the presence of OP nor the applied post-treatments altered the nutrient composition of frass, which contained on average 3.5% total N, 2.6% P2O5, and 5.9% K2O. However, at the highest inclusion level (84%), the abundance of bacterial and fungal groups was significantly reduced. The predominant phyla in the frass were Actinobacteria, Bacteroidota, Firmicutes, Proteobacteria, Ascomycota and Basidiomycota, and the dynamics of microbial communities were influenced by specific micronutrients. The presence of OP led to a significant reduction of potentially pathogenic bacteria and fungi in the frass, indicating a sanitizing effect attributable to this material.},
}

Animals
Larva/microbiology/growth & development
*Olea/chemistry
*Fertilizers/analysis
*Microbiota
*Simuliidae/growth & development/microbiology
Bacteria/classification/isolation & purification/genetics
Fungi/classification/isolation & purification/genetics
Animal Feed/analysis
*Diptera/microbiology/growth & development
Portugal

@article {pmid41318827,
year = {2025},
author = {He, Z and Zhu, W and Zeng, Y and Li, S and Ma, J and Yang, Z and Wang, H and Zhang, H and Liu, B and Wang, T},
title = {Integration of microbiome and transcriptome information in helping diagnosis of colorectal cancer.},
journal = {Discover oncology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12672-025-04036-3},
pmid = {41318827},
issn = {2730-6011},
support = {202401AY070001-038//Joint Special Project Grant on Applied Basic Research from Department of Science and Technology of Yunnan Province and Kunming Medical University/ ; 202401AY070001-038//Joint Special Project Grant on Applied Basic Research from Department of Science and Technology of Yunnan Province and Kunming Medical University/ ; 202401AY070001-038//Joint Special Project Grant on Applied Basic Research from Department of Science and Technology of Yunnan Province and Kunming Medical University/ ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is a major global public health issue, with over 1.8 million new cases and 881,000 deaths in 2018. This study aims to explore the application of integrating microbiome and transcriptome analysis in the diagnosis of colorectal adenocarcinoma (COAD), focusing on its potential in identifying cancer biomarkers and predicting disease progression.

METHODS: By utilizing COAD transcriptome and microbiome data from TCGA, diversity and differential expression analyses were conducted to identify microbiome composition differences between primary tumors (PT) and solid tissue normal (STN) samples, and the role of mRNA in prognosis. Mediation analysis was used to identify interactions between microbiome, transcriptome, in COAD tumors. The Multi-Omics Graph convolutional NET works (MOGONET) framework was employed to combine these data for COAD tumor prediction.

RESULTS: Significant changes in microbiome composition and specific mRNA expression patterns were closely related to COAD development. It was observed that the Simplex virus genus can mediate the abundance of the BRAF transcripts, thereby affecting the risk of COAD. The MOGONET model demonstrated high accuracy in predicting COAD tumors, achieving 0.977 accuracy, 0.988 F1 score, and 1.0 AUROC.

CONCLUSION: Integrating microbiome and transcriptome analysis shows significant potential in COAD diagnosis and prognostic assessment. These findings provide important insights for further clinical applications and cancer treatment strategies.},
}

@article {pmid41318814,
year = {2025},
author = {Li, J and Liu, L and Tao, M and Han, Z and Ma, M and Jiang, L and Liu, C and Liu, D and Zhang, P and Zhang, M and Xue, R and Gong, J and Zhang, X and Shen, L and Qi, C},
title = {Impact of concomitant medications on efficacy of CLDN18.2-specific CAR-T cell therapy in advanced gastric cancer.},
journal = {British journal of cancer},
volume = {},
number = {},
pages = {},
pmid = {41318814},
issn = {1532-1827},
abstract = {BACKGROUND: Claudin18.2 (CLDN18.2)-specific CAR-T cell therapy has demonstrated promise in advanced gastric cancer (GC). However, the impact of concomitant medications on the efficacy outcomes remains unclear.

METHODS: We retrospectively analyzed advanced GC patients receiving CLDN18.2-specific CAR-T cell therapy from a phase I trial. Concomitant medications were defined as any drugs administered within 30 days before and after CAR-T cell infusion, including corticosteroids, antibiotics, tocilizumab, granulocyte colony-stimulating factor (G-CSF), thrombopoietin (TPO), and erythropoietin. Metagenomic sequencing was employed to elucidate the differences in gut microbiome signatures between responders and non-responders.

RESULTS: Of 72 patients included in the study, 6 (8.3%) received corticosteroids, 49 (68.1%) received tocilizumab, and 22 (30.6%) received antibiotics, 15 (20.8%) received G-CSF, 5 (6.9%) received thrombopoietin, and no patient received erythropoietin. The median progression-free survival (PFS) (2.6 vs. 5.8 months; P < 0.001) and overall survival (OS) (3.9 vs. 9.5 months; P < 0.001) were significantly shorter for patients who received antibiotics for infection compared to those who did not. No significant differences were observed in objective response rate (ORR), PFS, and OS between patients who received corticosteroids, tocilizumab, antibiotics for prophylaxis, G-CSF, or TPO and those who did not. A higher abundance of Fusobacterium nucleatum, Lactobacillus mucosae, Prevotella pallens, and Streptococcus pseudopneumoniae in gut microbiome was associated with a superior treatment response.

CONCLUSIONS: The study indicates that the use of antibiotics for infection reduces the efficacy outcomes of CLDN18.2-specific CAR-T cell therapy for advanced GC, while other concomitant medications do not affect the outcomes. Further research is needed to clarify the optimal administration of these medications and the underlying mechanisms of the gut microbiome in impacting CAR-T treatment response.

TRIAL REGISTRATION: NCT03874897.},
}

@article {pmid41318735,
year = {2025},
author = {Shokri Garjan, H and Samadi Pakchin, P and Ferdousi, R},
title = {Computational prediction and conformation of relationships among microbes, drugs and diseases.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-29306-6},
pmid = {41318735},
issn = {2045-2322},
abstract = {Complex and diverse microbial communities are closely linked to human health, and their study plays a vital role in advancing medicine, particularly personalized healthcare. Identifying potential microbe-disease-drug relationships is useful for drug discovery and clinical treatment, and it also improves our understanding of microbial mechanisms. Due to the complexity and cost of biological experiments, computational methods provide a rapid and efficient way to predict potential interactions between microbes, drugs, and diseases. In this article, we predict relationships between microbes, drugs, and diseases using existing similarity and interaction data through Cytoscape software. Some of the potential relationships were confirmed by the available information, while the others require further clinical investigation. Due to the critical role of the microbiome in disease and medicine, more research and information are needed in this field. In the future, the various interactions between drugs, microbes, and diseases may improve the understanding of personalized medicine, promote early diagnosis, and provide potential treatments for a wide range of diseases.},
}

@article {pmid41318676,
year = {2025},
author = {Wu, S and Liu, S and Zhang, C and Yu, B and Tan, J and Liu, X},
title = {CD74[+]CCL5[+] effector CD8[+] T cells drive mucosal inflammation and predict biologics response in inflammatory bowel disease.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-025-07509-9},
pmid = {41318676},
issn = {1479-5876},
support = {TJYXZDXK-009A and TJYXZDXK-010A//Tianjin Key Laboratory of Indoor Air Environmental Quality Control, Tianjin University/ ; 21624317//Fundamental Research Funds for the Central Universities/ ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) exhibits heterogeneous mucosal inflammation and variable responses to biologics therapy. This study aimed to identify the immune cell subsets and molecular programs driving disease pathogenesis and to develop predictive biomarkers for therapeutic outcomes.

METHODS: We integrated single-cell RNA sequencing, bulk transcriptomic deconvolution, GWAS-based Mendelian randomization, and gut microbiome profiling across multiple IBD cohorts. Immune-microbial interactions were systematically characterized and linked with clinical phenotypes and treatment response. Immunohistochemistry was performed on colonic tissues from 12 IBD patients and 10 healthy controls to validate CCL5 and CD8 + T cell expression. Flow cytometric analysis of peripheral blood samples from 7 IBD patients and 12 healthy individuals was conducted to assess circulating CCL5 + CD8 + T cell proportions.

RESULTS: CCL5 + effector CD8 + T cells emerged as key mediators of colonic inflammation, displaying high IFN-γ/TNF activity and RUNX3/NF-κB-coordinated transcriptional programs. Immunohistochemical validation demonstrated profoundly elevated CCL5 expression (median 4.170% vs. 0.3450%, P < 0.0001) and CD8 + T cell infiltration (median 2.025% vs. 0.2150%, P < 0.0001) in IBD colonic tissues. Peripheral blood showed modest trends toward increased CCL5 + CD8 + T cells, though far less pronounced than tissue changes. Tissue-resident effector CD8 + T cell abundance correlated with disease severity and infliximab resistance. Six causally associated genes (DMAJCI, RMF167, SPRY1, ZFP96, FKBP11, SELPLG) formed a predictive signature for diagnosis and treatment response. Microbiome analyses revealed disrupted networks and immune-microbiome coupling.

CONCLUSION: CCL5 + CD8 + T cells are profoundly enriched in IBD colonic tissues and drive mucosal inflammation through pro-inflammatory pathways. A six-gene model, particularly involving FKBP11, demonstrated potential for disease stratification and infliximab response prediction. These findings highlight immune and microbial features of IBD that merit further functional and clinical validation.},
}

@article {pmid41318663,
year = {2025},
author = {Liu, S and Zhao, Z and Ji, Y and Zhu, H and Sun, Y and Li, M and Yu, Q},
title = {Synthetic bacterium-facilitated colonization of nitrogen-fixing bacteria for remodeling the rhizosphere microbiome and improving plant yield.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02189-5},
pmid = {41318663},
issn = {2049-2618},
support = {32170102//National Natural Science Foundation of China/ ; 2024YFD1701100//National Key R&D Program of China/ ; U23A20158//Joint Funds of the National Natural Science Foundation of China/ ; NCC2022-PY-09//Foundation of Nankai University-Cangzhou Bohai New Area Green Chemical Research Institute/ ; 63253191//Fundamental Research Funds for the Central Universities/ ; },
abstract = {BACKGROUND: Nitrogen-fixing bacteria (NFBs) play a critical role in biological nitrogen fixation for supplying essential nitrogen nutrients to plants in agriculture and natural ecosystems. Especially, these bacteria and Leguminosae plants form symbiosis to improve plant growth and soil fertility. Theoretically, the inoculation of NFBs into soils increases biological nitrogen fixation, but the efficiency of NFBs is frequently compromised by the low capacity of NFB root colonization. In this study, we introduced the synthetic bacterium EcCMC, which was genetically engineered to express the surface-displayed artificial polysaccharide (PS)-recognizing protein Cmc, to test if it can improve NFBs root colonization in representative Leguminosae plants, including Astragalus sinicus and Medicago sativa. Rhizosphere microbiomes, biochemical indicators, and plant yields were evaluated after 28 days in the three treatments, i.e., the control group without addition of any exogenous bacterium, the NFBs plus EcM (bacteria only expressing mCherry rather than Cmc) group, and the NFBs plus EcCMC group (n = 3).

RESULTS: Owing to its polysaccharide-binding capacity, EcCMC strongly bound to the surface of A. sinicus roots. This binding was followed by the increased recruitment of the exogenous NFBs, Sinorhizobium meliloti and Sphingomonas endophytica, on the roots. As revealed by amplicon sequencing of the 16S rRNA gene, a combined inoculation of EcCMC and the NFBs increased the relative abundance of both Rhizobiales and Sphingomonadales, two important bacterial groups involved in nitrogen fixation. Consistently, metabolomic analysis showed that the metabolites involved in nitrogen fixation remarkably accumulated in the rhizosphere soils inoculated with NFBs plus EcCMC. Moreover, inoculation of NFBs plus EcCMC increased the activity of nitrogenase from 10.8 ~ 11.3 to 16.2 nmol/min/g (significant difference, p < 0.05, t-test), together with the total soil nitrogen levels from 217 ~ 258 to 414 mg/kg (significant difference, p < 0.05), and the soil organic matter levels from 19.5 ~ 20.8 to 23.6 mg/kg (significant difference, p < 0.05). Consequently, the yield of A. sinicus was remarkably improved by the inoculation of NFBs plus EcCMC. Similar results were observed in the experiments using Medicago sativa.

CONCLUSIONS: This study sheds a novel light on a synthetic biology-assisted regulation of rhizosphere microbiomes for enhanced nitrogen fixation and soil fertility in Leguminous plants. The designed polysaccharide-binding protein may be used as a universal tool to promote plant growth and enhance crop resilience in the future. Video Abstract.},
}

@article {pmid41318640,
year = {2025},
author = {Foltz, AE and Herman, MA},
title = {Caenorhabditis elegans microbiome members have combinatorial effects on host survival and fitness.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-29741-5},
pmid = {41318640},
issn = {2045-2322},
abstract = {Microbiomes are a fundamental part of eukaryotic life and play a role in both host health and fitness. Although microbes are often associated with health and positive effects on the host, certain microbiome compositions are associated with disease. Some disease-associated microbiome compositions are correlated with a change in abundance of a member that is part of the healthy microbiome. We used Caenorhabditis elegans and its experimental microbiome, CeMbio, to explore the interactions that individual microbiome members have with the host, and how the entire microbiome community interacts with the host. We compared the effects of individual microbiome members on host survival to those of the standard C. elegans laboratory diet of E. coli OP50 as well as to the experimental microbiome. We found that while all microbiome members and the whole experimental microbiome are detrimental to C. elegans survival when compared to E. coli, the survival effects of the individual members show more variation when compared to the experimental microbiome. We also measured effects on host fitness by measuring fecundity and development time across the same comparisons. We found consistent effects on fecundity, but development time was more variable when compared to E. coli, but consistently slower when compared to the experimental microbiome. We found that comparisons of the individual microbiome members' effects on host survival and fitness to the effects of the experimental microbiome suggests that the members act in combination with one another. These combinatorial interactions result in specific effects of the microbiome that are different from those of the individual microbiome members that in some cases may be complementary. This further suggests there are potentially different mechanisms resulting in the observed differences in how host survival and fitness respond to individual microbiome members, as well as the whole microbiome. Elucidation of the mechanisms involved in these combinatorial microbe-microbe and host-microbe interactions will lead to greater understanding of the nature of the host-microbiome and host-microbe relationships.},
}

@article {pmid41318612,
year = {2025},
author = {Rivera, DS and Beltrán, V and Hoepfner, C and Del Pilar Fernández, M and Oliva, CA and Vera, MJ and Farías, C and Valenzuela, R and Pérez, I and Correa, LA and Urbina, F},
title = {Nutritional modulation of host physiology, behavior, and gut microbiome in the captive rodent Octodon degus.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-26991-1},
pmid = {41318612},
issn = {2045-2322},
support = {11190603//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; },
abstract = {Diet is a key determinant of health by affecting nutrient metabolism, energy balance, body weight regulation, and mental health. The gut-brain axis is a critical pathway through which dietary factors influence cognitive function and behavior via microbial metabolites. While this relationship has been extensively studied in traditional laboratory models, diet-microbiome-cognition interactions remain largely unexplored in Octodon degus, an emerging model for aging, neurodegeneration, and cognitive research. Here, we compared two widely used rodent diets-LabDiet and Champion-to evaluate their effects on digestive efficiency, behavior, and gut microbiome composition. We also examined the relationships between these variables using piecewise structural equation modeling (pSEM). Our results indicated that LabDiet-fed degus exhibited enhanced nutrient absorption, higher fecal acetic acid levels, and a higher abundance of Actinobacteria (particularly Bifidobacterium), likely driven by its vitamin C supplementation. These animals also showed improved working memory and social motivation, but they displayed increased anxiety-like behavior. In contrast, Champion-fed degus, which consumed a more fiber-diverse, plant-based diet, showed lower anxiety traits and significantly greater gut microbial richness, with higher abundance of Bacteroidota and Tenericutes. Innate behaviors, such as burrowing and nesting, remained unaffected by the diet. SEM analysis revealed that diet explained most of the variance in microbial activity and identified a positive association between acetic acid levels and cognitive performance. This emphasizes a strong relationship among diet, microbiome, and brain function. Overall, our results suggest that dietary composition is a key factor influencing experimental outcomes in degus, with important implications for physiology, cognition, and microbial ecology. Standardizing dietary inputs is essential to ensure reproducibility in behavioral and biomedical studies using this model. Additionally, our results reinforce the microbiome's role as a mediator of diet-driven brain function via SCFAs, underscoring degus as a powerful system for investigating diet-microbiome-neurobehavioral interactions relevant to aging and mental health.},
}

@article {pmid41318525,
year = {2025},
author = {Athari, SZ and Amoghli Tabrizi, B and Khakpour, M and Kianfar, N and Khani, E and Abbasi, A and Nourazar, MA},
title = {A 30% high-fiber diet mitigates oxidative stress and inflammation while modulating cecal microbiota in rats undergoing high-intensity exercise.},
journal = {BMC sports science, medicine & rehabilitation},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13102-025-01441-7},
pmid = {41318525},
issn = {2052-1847},
abstract = {High-intensity training (HIT) can induce inflammation and oxidative stress, posing challenges for athletes, while dietary fiber may offer protective benefits. This study examined the impact of a 30% increase in dietary fiber intake on oxidative stress, inflammation, hematological parameters, and gut microbiota in male Wistar rats subjected to HIT. Thirty-two rats (250 ± 20 g) were randomly assigned to four groups (n = 8 each): Control-NF (no training, normal diet), Control-Fib (no training, high-fiber diet), HIT-NF (HIT, normal diet), and HIT-Fib (HIT, high-fiber diet). HIT was performed at 90% VO2max, five days per week for eight weeks. The high-fiber diet was enriched with wheat bran, providing 37-52% total dietary fiber, predominantly insoluble fractions (cellulose, hemicellulose, and lignin) with minor soluble components (arabinoxylans and β-glucans). Antioxidant enzyme activities, inflammatory cytokines, hematological indices, and cecal bacterial profiles were evaluated using two-way ANOVA (diet×training) with Tukey's post-hoc test. HIT significantly reduced catalase, SOD, and GPx activities and elevated TGF-β, IFN-γ, IL-17, and hsCRP levels, whereas fiber supplementation reversed these effects, restored leukocyte balance, and improved phagocytic activity. HIT also disturbed microbial composition by reducing Lactobacillus spp. and increasing coliform counts, while fiber partially normalized these alterations. Collectively, the findings provide novel evidence that a 30% high-fiber diet intake can serve as a practical nutritional strategy to mitigate physiological stress, inflammation, and microbiota imbalance induced by high-intensity exercise.},
}

@article {pmid41318497,
year = {2025},
author = {Wang, Z and Xing, Y and Xu, M and Chen, C and Zhu, Q and Chen, H and Zhang, Y and Chen, W and Feng, J and Zhang, A and Ma, R and Liu, X and Li, S and Yan, Q and Xing, G and Yao, X and Kong, X},
title = {Altered gut mycobiome and cross-kingdom microbial interactions in systemic lupus erythematosus.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-025-07423-0},
pmid = {41318497},
issn = {1479-5876},
support = {LJ212410161043//Basic Research Project of Liaoning Provincial Department of Education for Universities/ ; 2025-BS-0684//Doctoral Start-up Foundation of Liaoning Province/ ; },
}

@article {pmid41318317,
year = {2025},
author = {Liu, WC and Kuo, HY and Tsai, HW and Lin, YJ and Ruan, JW and Lee, CC and Sun, HY and Wu, IC and Chang, TT},
title = {Intratumoral microbiome composition and its role in tumor recurrence in primary liver cancer.},
journal = {Journal of the Formosan Medical Association = Taiwan yi zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jfma.2025.11.031},
pmid = {41318317},
issn = {0929-6646},
abstract = {BACKGROUND: The human microbiome is increasingly recognized as a factor in cancer development, though its role in primary liver cancer (PLC) remains unclear. This retrospective cohort study examines tissue-specific microbiota differences between hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA), and explores their association with tumor recurrence in PLC.

METHODS: Clinical data from 116 patients (85 HCC and 31 age-matched CCA) were analyzed. Fresh frozen samples underwent RNAscope™ ISH assay for microbial RNA detection, while the MiSeq platform targeted 16 S ribosomal RNA. Microbiome functional pathways were explored with Tax4Fun2, and predictors of recurrence were identified through logistic regression analysis.

RESULTS: Microbial RNA was detected within liver sinusoids, the basal lamina of intrahepatic bile ducts, and hepatocyte cytosol. 16 S ribosomal RNA analysis revealed differences in microbiome composition, including a distinct Firmicutes/Bacteroidetes ratio between CCA and HCC patients. Specific functional pathways were differentially enriched between the two groups. LEfSe and logistic regression analyses identified Aquabacterium spp. as a potential marker for HCC recurrence (OR, 14.77; 95 % CI, 1.07-203.94; p = 0.044). Increased abundances of Brevundimonas spp. (OR, 3.1 E+17; 95 % CI, 4.3 E+3-2.2 E+31; p = 0.013), Novosphingobium spp. (OR, 3.5 E+20; 95 % CI, 4.4 E+5-2.8 E+35; p = 0.007), and Pelomonas spp. (OR, 3.3 E+21; 95 % CI, 3.0 E+8-3.5 E+34; p = 0.001), along with decreased Staphylococcus spp. (OR 0.00; 95 % CI, 0.00-0.06; p = 0.003), were independent predictors of CCA occurrence.

CONCLUSION: This study reveals that intratumoral microbiota help distinguish PLC subtypes and are associated with recurrence, identifying Aquabacterium as a potential marker for HCC recurrence and microbiome-based management.},
}

@article {pmid41318270,
year = {2025},
author = {Forton, C and DeVries, J and Lou, M and Brundin, S and Cave, T and Anis, E and Madaj, ZB and Isaguirre, C and Johnson, A and Sheldon, RD and Smart, L and Bohnert, KM and Kassien, J and Holzgen, O and Youssef, NA and Khan, T and Brundin, L},
title = {Corrigendum to "Gut microbiome-derived tryptophan metabolites predict relapse in alcohol use disorder".},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106193},
doi = {10.1016/j.bbi.2025.106193},
pmid = {41318270},
issn = {1090-2139},
}

@article {pmid39938913,
year = {2025},
author = {Tang, L and Li, S and Zhu, H and Ma, X and Wu, Y},
title = {Predictive Value of LncRNA TUG1 for Complications after Caesarean Section with Scarred Uterus.},
journal = {The Tohoku journal of experimental medicine},
volume = {267},
number = {3},
pages = {281-289},
doi = {10.1620/tjem.2025.J015},
pmid = {39938913},
issn = {1349-3329},
mesh = {Humans ; Female ; *Cesarean Section/adverse effects ; *RNA, Long Noncoding/genetics/blood ; *Cicatrix/genetics ; Adult ; *Uterus/pathology ; Pregnancy ; ROC Curve ; *Postoperative Complications/etiology ; Predictive Value of Tests ; },
abstract = {This study aims to investigate the predictive value of long non-coding RNA taurine-upregulated gene 1 (lncRNA TUG1) for complications following cesarean section in patients with scarred uterus. We first included 186 subjects with scarred uterus. The levels of TUG1 in the serum of these subjects were measured using RT-qPCR, and based on the expression levels of TUG1, they were divided into TUG1 high expression group (90 cases) and TUG1 low expression group (96 cases). The postpartum hemorrhage, postoperative site infections, pelvic floor muscle strength, and vaginal microbiota status were compared between the two groups. And the predictive value of TUG1 for complications following cesarean section in women with scarred uteri was assessed using the receiver operating characteristic (ROC) curve. The levels of TUG1 were found to be strongly positively correlated with the abdominal scar score of the pregnant women. Furthermore, TUG1 levels in women who experienced pelvic floor dysfunction (PFD), vaginal microbiome disorders, surgical site infections (SSI), and postpartum hemorrhage were significantly higher than those in women without these complications. The ROC curve indicated that TUG1 predicted PFD, vaginal microbiota disorders, SSI, and postpartum hemorrhage with areas under the curve (AUC) of 0.811, 0.832, 0.819, and 0.887, respectively. TUG1 was positively correlated with abdominal scar scores and demonstrated good predictive value for complications after cesarean section in women with scarred uteri. These findings suggest that TUG1 has the potential to serve as a clinical biomarker for these complications.},
}

Humans
Female
*Cesarean Section/adverse effects
*RNA, Long Noncoding/genetics/blood
*Cicatrix/genetics
Adult
*Uterus/pathology
Pregnancy
ROC Curve
*Postoperative Complications/etiology
Predictive Value of Tests

@article {pmid41317994,
year = {2025},
author = {Merrill, LC and Martínez, RL and Palacios, N and Dawson-Hughes, B and Noel, SE and Wang, Y and Tucker, KL and Mangano, KM},
title = {Gut microbes related to the Dietary Approaches to Stop Hypertension score are associated with bone quantity but not with bone quality in a cross-sectional study of older Puerto Rican adults.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {101129},
doi = {10.1016/j.ajcnut.2025.101129},
pmid = {41317994},
issn = {1938-3207},
abstract = {BACKGROUND: BMD explains fractures incompletely; studies relating lifestyle to bone quality are lacking.

OBJECTIVES: To examine associations of diet quality with bone measures (BMSi, TBS, BMD); evaluate moderation by inflammation; identify gut microbiome features linked to diet quality; and quantify diet-microbiome-bone relationships.

METHODS: This cross-sectional study included participants from the Boston Puerto Rican Osteoporosis Study. Diet was assessed with a culturally tailored FFQ, and diet quality with the Dietary Approaches to Stop Hypertension (DASH) score.. BMSi was measured using microindentation; BMD by dual-energy X-ray absorptiometry (DXA); TBS derived from DXA. Inflammation was assessed with a biomarker score (BMS) and tested as a moderator of diet-bone associations via interaction terms in linear regression. Gut microbiome composition (shotgun metagenomics) was analyzed with MaAsLin regression to assess diet associations. A machine learning algorithm determined dietary, microbial, and bone-related predictors of bone health; sample sizes varied by outcome: BMSi (n = 86); TBS (n = 204); BMD femoral neck (n = 220), total hip (n = 221), lumbar spine (n = 207).

RESULTS: DASH score was not associated with BMSi (β = -0.10; 95% CI: -0.46, 0.27; P = 0.60), TBS (β = 0.002; 95% CI: -0.002, 0.005, P = 0.36), BMD at the femoral neck (β = 0.002; 95% CI: -0.002, 0.005; P = 0.30), or lumbar spine (β = 0.002; 95% CI: -0.003, 0.006, P = 0.52 but was at total hip (β = 0.004; 95% CI: 0.003, 0.008; P = 0.03). The association was not moderated by inflammation (β = -0.0001, P = 0.89). Lachnospira eligens was one of 4 taxa positively associated with DASH score, and BMD. No microbial pathways were associated with the DASH score.

CONCLUSIONS: DASH score was associated with hip BMD, but not with BMSi or TBS. Select diet-related gut microbes, and an inflammation score were associated with BMD. Future studies should examine dietary inflammation in relation to bone quality.},
}

@article {pmid41317866,
year = {2025},
author = {Davido, B and Corcione, S},
title = {Re: 'Faecal microbiota transplantation for urinary tract infections' by Gardlik et al.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2025.11.028},
pmid = {41317866},
issn = {1469-0691},
}

@article {pmid41317857,
year = {2025},
author = {Rackerby, B and Kim, E and Bobe, G and Dallas, DC and Park, SH},
title = {Effects of whey protein isolate on the human gut microbiota and intestinal function in older adults.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27204},
pmid = {41317857},
issn = {1525-3198},
abstract = {Whey protein is commonly used to prevent sarcopenia in older adults due to its high digestibility and amino acid content. Its bioactive components may also influence the gut microbiota, which plays a growing role in healthy aging as microbial composition shifts with age. This study investigated whether daily supplementation with whey protein isolate (WPI) improves gut microbiota diversity and composition in older adults. Sixteen participants consumed 59 g of WPI (35 g of protein) daily for 3 wk. Whey protein isolate significantly increased Simpson diversity in individuals with low baseline diversity, with effects appearing by d 3 and persisting after intervention. Taxonomic analysis revealed increases in beneficial taxa (e.g., Ruminococcaceae, Faecalibacterium, and Christensenella) and reductions in potentially harmful groups (e.g., Proteobacteria, Streptococcaceae, and Colidextribacter), particularly in the low diversity group. ANCOM-BC analysis based on absolute abundance confirmed increases in probiotic genera including Lactobacillus, Lactococcus, and Christensenella. Despite these microbial shifts, no significant changes were observed in gastrointestinal symptoms or stool consistency. These findings highlight the potential of WPI supplementation as a dietary strategy to promote a healthier gut microbiome in older adults, particularly in those with low baseline diversity.},
}

@article {pmid41317787,
year = {2025},
author = {Zhu, Y and Augustijn, HE and Andreu, VP and Draisma, A and van Wezel, GP and Dodd, D and Fischbach, MA and Medema, MH},
title = {gutSMASH 2.0: extended identification of primary metabolic gene clusters from the human gut microbiota.},
journal = {Journal of molecular biology},
volume = {},
number = {},
pages = {169567},
doi = {10.1016/j.jmb.2025.169567},
pmid = {41317787},
issn = {1089-8638},
abstract = {Microbiota-derived metabolites serve as key messengers mediating host-microbe and microbe-microbe interactions, often through specialized primary metabolic pathways. gutSMASH was initially developed to systematically identify the metabolic gene clusters (MGCs) that encode these pathways in anaerobic gut microbial genomes. Here, we present gutSMASH 2.0, a major update that significantly expands its functionality. This version introduces 14 new detection rules covering 12 additional types of MGCs. The comparative genomics framework was enhanced with 26 experimentally validated MGCs and 15,024 gene clusters from the Cultivated Genome Reference 2 (CGR2) collection. Furthermore, gutSMASH 2.0 integrates transcription factor binding site prediction using LogoMotif's methodology, enabling investigation of MGC regulatory elements. Together, these improvements make gutSMASH a more powerful tool for automated discovery and analysis of niche-determining metabolic pathways in the gut microbiome. gutSMASH 2.0 is freely available at https://gutsmash.bioinformatics.nl/.},
}

@article {pmid41317335,
year = {2025},
author = {Liang, Y and Lu, C and Ma, D and He, X},
title = {Gut Microbiome Mediates the Effect of Inflammatory Bowel Disease on Sarcopenia: A Bidirectional Mendelian Randomization Study.},
journal = {Digestion},
volume = {},
number = {},
pages = {1-23},
doi = {10.1159/000549749},
pmid = {41317335},
issn = {1421-9867},
abstract = {BACKGROUND: Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), imposes a global health burden. Observational studies suggest links between IBD and sarcopenia as well as obesity, but establishing causality is challenging due to confounding factors.

METHOD: This study utilized two-sample Mendelian randomization (MR) analyses to explore bidirectional causality between obesity, sarcopenia, and IBD, using genetic instruments from summary-level data. The primary causal estimates were derived using the inverse-variance weighted (IVW) method. To ensure robustness, we performed a range of sensitivity analyses, including MR-Egger regression and the weighted median method to detect and adjust for horizontal pleiotropy, and MR-PRESSO to identify and remove potential outliers.

RESULT: MR analysis revealed significant associations between obesity, sarcopenia, and IBD, especially CD. Trunk fat percentage, body fat percentage and abdominal subcutaneous adipose tissue volume were positively associated with an increased risk of CD, whereas hand grip strength showed a negative association, highlighting the role of obesity and sarcopenia in CD risk. Conversely, CD was causally linked to lower abdominal fat, muscle mass, and strength. For UC, only visceral adipose tissue volume showed an association with disease risk. Mediation analysis indicated the gut microbiome might mediate the causal effect of CD on sarcopenia-related traits.

CONCLUSION: This MR study confirms bidirectional causality between sarcopenia, obesity, and IBD, particularly CD. It highlights the complex interplay between body composition and IBD pathogenesis. Moreover, the gut microbiome may mediate the relationship between CD and sarcopenia. These findings underscore the importance of managing obesity and sarcopenia in IBD treatment and suggest potential therapeutic targets related to the gut-muscle axis.},
}

@article {pmid41317299,
year = {2025},
author = {Khan, MH and Hochstedler-Kramer, B and Halverson, T and Nwachokor, J and Pham, TT and Wolfe, AJ and Acevedo-Alvarez, M},
title = {Longitudinal Impact of Methenamine Hippurate on the Urobiome of Postmenopausal Women With Recurrent UTIs.},
journal = {International urogynecology journal},
volume = {},
number = {},
pages = {},
pmid = {41317299},
issn = {1433-3023},
support = {LU 212575/AU/2020 RFC//Loyola University Chicago Stritch School of Medicine/ ; },
abstract = {INTRODUCTION AND HYPOTHESIS: Postmenopausal women with recurrent urinary tract infections (RUTI) are repeatedly exposed to antibiotics; therefore, they are at risk for colonization by multi-drug resistant organisms. Methenamine hippurate (MH), an antibiotic alternative, has shown clinical promise in preventing RUTI; its activity is traditionally attributed to formaldehyde production, though the precise mechanism of action remains uncertain. We hypothesize that MH administration alters the urobiomes of women with RUTI.

METHODS: We conducted a longitudinal study of postmenopausal women with a clinical history of RUTI, evaluating their urobiomes for 3 months. Expanded quantitative urine culture (EQUC) assessed diversity and urobiome composition of catheterized urine, voided urine, and peri-urethral swabs; 16S rRNA gene sequencing determined taxonomic classification, beta diversity, and differential abundance analysis of voided urine only.

RESULTS: No UTIs occurred for any participant. Instead, we observed improvement in symptoms. EQUC and 16S sequencing revealed predominance of Enterobacteriaceae, especially E. coli, and members of several Gram-positive genera, including emerging uropathogens. Following MH therapy initiation, diversity of catheterized urine specimens increased and voided urine microbiomes of most participants differed significantly during at least one post-treatment week relative to pre-treatment composition. Differential abundance analysis revealed many significantly different taxa; several were not among the most abundant.

CONCLUSIONS: MH treatment did not sterilize the bladder nor did it eliminate uropathogens. Instead, it uniquely altered each participant's voided urine microbiome. To understand the mechanism of action, researchers should look beyond suspected uropathogens and consider the participant and the rest of their urobiome.},
}

@article {pmid41317253,
year = {2025},
author = {Jeong, JS and Ko, JW and Yoo, SY and Jung, SC and Kim, JH and Lee, SH and Kim, KH and Kim, NY and Kwon, MJ and Kim, SK and Lee, SH and Kim, JS and Kim, TW},
title = {Lacticaseibacillus Casei KGC1201 Isolated from Panax Ginseng Mitigates Dextran Sulfate Sodium-Induced Colitis by Modulating the Gut Environment.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41317253},
issn = {1867-1314},
support = {RS-2023-00219213//Bio&Medical Technology Development Program of the National Research Foundation (NRF) funded by the Korean government (MSIT)/ ; 2021R1A6A1A03045495//Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education/ ; },
abstract = {Gut microbiota dysbiosis is closely linked to the pathogenesis of inflammatory bowel disease (IBD), highlighting the therapeutic potential of probiotics that affect the gut microbiome when ingested. In this study, we evaluated the effects of Lacticaseibacillus casei KGC1201, a strain isolated from Panax ginseng, on a mouse model of dextran sulfate sodium (DSS)-induced colitis. L. casei KGC1201 culture powder at doses of 206 and 412 mg/kg was administered orally once daily, one week before DSS administration until sacrifice. A 2% DSS solution was provided ad libitum in drinking water for 7 days, and the mice were sacrificed 3 days after DSS withdrawal. Body weight changes, stool condition, colon length, and the histopathology of the colon tissue were assessed. Additionally, fecal samples were analyzed by 16 S rRNA sequencing to evaluate the gut microbiota composition. Administration of L. casei KGC1201 alleviated colitis symptoms such as weight loss, diarrhea, and decreased colon length. It also modulated the gut microbiota composition and beneficial functional metabolic pathways, including promoting the growth of beneficial gut microbiota. Moreover, it promoted intestinal epithelial regeneration by activating Wnt3a/β-catenin signaling, a crucial pathway for epithelial self-renewal and repair. These findings suggest that the ginseng-derived L. casei KGC1201 is a promising probiotic candidate for mitigating colitis and supporting intestinal health in patients with IBD.},
}

@article {pmid41317234,
year = {2025},
author = {Hetta, HF and Alanazi, FE and Alqifari, SF and Ali, MAS and Albalwi, MA and Albalawi, AA and Ramadan, YN},
title = {The Gut-Brain Axis in Autism: Inflammatory Mechanisms, Molecular Insights, and Emerging Microbiome-Based Therapies.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {211},
pmid = {41317234},
issn = {1559-1182},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Brain/metabolism/pathology ; Animals ; *Inflammation/microbiology ; Fecal Microbiota Transplantation ; *Autism Spectrum Disorder/therapy/microbiology ; Dysbiosis ; Probiotics/therapeutic use ; *Brain-Gut Axis ; *Autistic Disorder/therapy/microbiology ; },
abstract = {Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with multifactorial etiology, including genetic, environmental, and microbial influences. Recent studies have highlighted the gut-brain axis as a crucial mediator in ASD pathophysiology, linking alterations in gut microbiota to neurodevelopmental and behavioral abnormalities. Individuals with ASD frequently exhibit dysbiosis, characterized by an imbalance in gut microbial composition, reduced microbial diversity, and increased intestinal permeability. These changes contribute to systemic inflammation, altered neurotransmitter synthesis, and metabolic dysfunctions, ultimately impacting brain function. Emerging therapeutic approaches targeting gut microbiome, such as probiotics, prebiotics, dietary modifications, and fecal microbiota transplantation (FMT), have shown potential in alleviating both gastrointestinal (GI) and ASD-related symptoms. This review explores the latest evidence on microbiome alterations in ASD, the mechanisms by which gut dysbiosis influences neurodevelopment, and the therapeutic potential of microbiome-based interventions. Understanding these connections may open new avenues for targeted treatments in ASD management.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Brain/metabolism/pathology
Animals
*Inflammation/microbiology
Fecal Microbiota Transplantation
*Autism Spectrum Disorder/therapy/microbiology
Dysbiosis
Probiotics/therapeutic use
*Brain-Gut Axis
*Autistic Disorder/therapy/microbiology

@article {pmid41317233,
year = {2025},
author = {Rafique, QT and Gogoi, V and Barah, P},
title = {Beyond the Gut: Integrating Oral Microbiota into the Microbiota-Brain Axis in Depression.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {207},
pmid = {41317233},
issn = {1559-1182},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Brain/microbiology ; *Depression/microbiology ; *Mouth/microbiology ; *Microbiota/physiology ; Dysbiosis ; Depressive Disorder, Major/microbiology ; Animals ; COVID-19 ; },
abstract = {Depression, a major contributor to years lived with disability (YLD), affects nearly 300 million people worldwide. In the aftermath of the COVID-19 pandemic, cases of major depressive disorder (MDD) or clinical depression have risen by 28% particularly among women and young adults. Characterized by persistent low mood, cognitive impairment, suicidal ideation, sleep disturbances, appetite changes, and fatigue, depression continues to impose a profound public health burden, compounded by the limited efficacy of current treatments and the lack of reliable diagnostic or predictive biomarkers. While the gut microbiota has been extensively implicated in depression's pathophysiology, emerging evidence indicates that the oral microbiome which ranks second only to the gut in microbial diversity also plays a significant role in neuropsychiatric health. Oral microbial dysbiosis may contribute to depression through immune, inflammatory, and neuroactive pathways, positioning the oral microbiome as both a potential non-invasive biomarker and a novel therapeutic target. Incorporating oral microbial profiling into clinical research could not only refine our understanding of depression's underlying mechanisms but also facilitate the development of microbiome-based strategies in precision psychiatry. This growing recognition highlights the importance of expanding research beyond the gut-brain axis to encompass the oral-brain axis as an integral component in the quest for effective diagnostics and interventions.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Brain/microbiology
*Depression/microbiology
*Mouth/microbiology
*Microbiota/physiology
Dysbiosis
Depressive Disorder, Major/microbiology
Animals
COVID-19

@article {pmid41317226,
year = {2025},
author = {Xie, Y and Xiong, W and Chen, H and Chen, W and Li, Q and Hou, S and Zhou, H and Zhu, H and Ye, B},
title = {Characteristics of the Esophageal Microbiota in Patients with Achalasia.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {41317226},
issn = {1573-2568},
support = {No. 82470565//the National Natural Science Foundation of China/ ; JSPH-MC-2023-18//Yong Scholars Fostering Fund of the First Affiliated Hospital of Nanjing Medical University/ ; CSTB2024NSCQ-MSX1197//Chongqing Natural Science Foundation General Project ./ ; },
abstract = {BACKGROUND: Achalasia (AC) is clinically characterized by chronic intraluminal food stasis and bacterial fermentation, which may contribute to esophageal dysbiosis. This research seeks to analyze the microbiome of individuals with AC, pinpoint significant biomarkers, and explore their relationships with clinical and electrophysiological factors to enhance our comprehension of the mechanisms underlying AC.

METHODS: This study, conducted at a single center, involved 16S rRNA sequencing of esophageal mucosal samples collected from individuals with achalasia and a control group. We assessed microbial diversity, identified distinct taxa using LEfSe, predicted functional capabilities through PICRUSt, and examined the relationship between microbiota and clinical parameters. Biomarkers were identified using a random forest algorithm and subsequently validated through qPCR.

RESULTS: Patients with achalasia displayed notable dysbiosis in their esophageal microbiome, marked by changes in community structure while showing no significant shifts in diversity. There was a marked increase in the opportunistic bacterium Fusobacterium, alongside a reduction in beneficial species such as Akkermansia and Ligilactobacillus. The presence of Pseudomonas and Ralstonia was linked to the Eckardt score. The rise in Fusobacterium was further validated through qPCR analysis. Functional predictions suggested an increase in acetyl-CoA biosynthesis among these patients. Notably, levels of Fusobacterium were positively associated with critical clinical indicators, including pressures in the lower and upper esophageal sphincters and the Eckardt score.

CONCLUSIONS: Esophageal dysbiosis is associated with esophageal hypomotility in achalasia patients.},
}

@article {pmid41317036,
year = {2025},
author = {Hillier, RA and Gibson, R and Maruthappu, T and Whelan, K and Prpa, EJ and Neill, HR and Phillips, CG and Hall, WL},
title = {Probiotics, Prebiotics, and Synbiotics as Oral Supplements for Skin Health, Function, and Disease Throughout the Life Course: A Scoping Review.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuaf205},
pmid = {41317036},
issn = {1753-4887},
support = {BB/X010821/1//Biotechnology and Biological Sciences Research Council through the Diet and Health Open Innovation Research Club (OIRC)/ ; //Yakult UK & Ireland Limited/ ; //Yakult UK & Ireland/ ; },
abstract = {In this review we sought to map the body of published literature on the role of oral probiotics, prebiotics, and synbiotics in maintaining and optimizing skin health and function and preventing and managing skin conditions throughout the life course. Globally, the burden of skin diseases is considerable. Diet is a modifiable risk factor for many dermatological conditions, and one mechanism by which nutrition influences skin health is through the gut microbiome. Oral probiotics, prebiotics, and synbiotics have the potential to improve skin health, delay skin aging, and successfully treat dermatological diseases. We developed a scoping review protocol in accordance with the Johanna Briggs Institute methodology. Six online databases were systematically searched for peer-reviewed literature, and non-peer-reviewed sources were also considered. All records were screened independently by 2 reviewers using predefined eligibility criteria. A total of 516 studies were included in the scoping review, comprising 73 systematic reviews. Most studies investigated probiotics (n = 401). Infants (0-12 months old) and adults (18-60 years old) were the age groups most frequently receiving supplementation with probiotics (42% [n = 114] and 41% [n = 112] of human studies, respectively), whereas only 15% of studies (n = 41) comprised adults participants older than 60 years. Of the skin diseases investigated, atopic dermatitis was the most extensively researched (n = 330 studies), followed by psoriasis (n = 24), and acne (n = 23). Skin health and function in healthy populations is a growing area of research; outcomes related to wrinkling, elasticity, aging, or UV irradiation response accounted for 54 studies. Consistencies in the evidence base found in our investigation underscore the need for an umbrella review on oral probiotics, prebiotics, and synbiotics and atopic dermatitis, as well as a systematic review on skin aging. Preliminary evidence for roles in managing rosacea, alopecia, and melasma suggests additional research avenues. Future studies should consider participant diets, probiotic strain and dose reporting, and inclusivity of populations and languages.},
}

@article {pmid41316932,
year = {2025},
author = {Moghoofei, M and Pajavand, H and Shahbazi, R and Rezaei, M and Taki, E},
title = {The Role of Viral and Bacterial Infections in the Etiology of Behçet's Disease.},
journal = {Journal of clinical laboratory analysis},
volume = {},
number = {},
pages = {e70133},
doi = {10.1002/jcla.70133},
pmid = {41316932},
issn = {1098-2825},
abstract = {BACKGROUND: Behçet's disease (BD) is a complex systemic vasculitis with a poorly understood etiology that involves genetic, environmental, and immunological factors. Increasing evidence suggests that viral and bacterial infections may trigger or exacerbate BD through immune-mediated pathways. This review aims to clarify how different infectious agents may contribute to BD pathogenesis.

METHODS: For this review, articles addressing microbial involvement in BD were collected from established databases such as PubMed, Scopus, and Web of Science. Priority was given to studies evaluating classical pathogens-including Herpes simplex virus and Streptococcus spp.-as well as more recent agents such as SARS-CoV-2, Borrelia burgdorferi, and Helicobacter pylori. Findings from immunological, molecular, and clinical research were integrated to highlight shared mechanisms related to host-pathogen interactions.

RESULTS: The reviewed literature shows that microbial infections may influence BD through multiple interconnected mechanisms. A central concept is the possible cross-reactivity between microbial and human heat shock proteins (HSPs), which may activate Th1/Th17 cytokine pathways and enhance neutrophil activity. The review also highlights the dual functions of TRIM proteins in antiviral responses and inflammatory dysregulation, as well as the involvement of inflammasome activation and pattern recognition receptors (PRRs). These combined processes may help explain how infections initiate or intensify immune responses in BD.

CONCLUSION: By synthesizing current microbial and immune evidence, this review provides an updated perspective on BD immunopathogenesis and outlines testable mechanisms for future research. Understanding these links may support the development of more targeted therapeutic strategies.},
}

@article {pmid41316850,
year = {2025},
author = {Shi, Y and Zhang, M and Miao, H and Feng, Y and He, H and Zhang, T and Zhang, H},
title = {Association between dietary index for gut microbiota and hypertension: a cross-sectional NHANES-based study.},
journal = {Journal of hypertension},
volume = {},
number = {},
pages = {},
doi = {10.1097/HJH.0000000000004209},
pmid = {41316850},
issn = {1473-5598},
abstract = {BACKGROUND: Gut microbiota is essential in hypertension pathogenesis, and dietary patterns modulate microbial diversity and metabolic function. Specific associations between dietary index for gut microbiota (DI-GM) and hypertension remains unclear.

OBJECTIVE: To explore associations between DI-GM and hypertension risk.

METHODS: We analyzed data from 11 429 participants in National Health and Nutrition Examination Survey (NHANES) 2005-2016. Weighted multivariate logistic regression and restricted cubic spline (RCS) models assessed DI-GM-hypertension relationship and nonlinearity. Subgroup analyses evaluated heterogeneity across populations.

RESULTS: After full covariate adjustment, DI-GM showed a significant inverse association with hypertension [odds ratio (OR) = 0.95, 95% CI: 0.91-0.99]. Compared to the lowest quartile of DI-GM, the highest quartile was associated with a significant 21% reduction in the risk of hypertension (OR = 0.79, 95% CI: 0.66-0.96). No nonlinear relationship was detected (P-nonlinear = 0.593). Subgroup analyses revealed stronger inverse associations in women, younger adults (20-44 years), college-educated individuals, unmarried/married/cohabiting participants, and never-smokers. Significant interactions were seen for marital status and smoking.

CONCLUSION: Higher DI-GM scores were significantly associated with a reduced risk of hypertension, with the most robust relationships observed among nonsmokers and individuals with partners. This suggests that future dietary interventions must fully account for population heterogeneity to achieve more precise hypertension prevention and management.},
}

@article {pmid41316726,
year = {2025},
author = {Nishijima, S and Fullam, A and Schmidt, TSB and Kuhn, M and Bork, P},
title = {VIRE: a metagenome-derived, planetary-scale virome resource with environmental context.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1225},
pmid = {41316726},
issn = {1362-4962},
support = {12/RC/2273-P2//Uehara Memorial Foundation/ ; //EMBL/ ; },
abstract = {Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a comprehensive resource comprising over 1.7 million high- and medium-quality viral genomes recovered from >100 000 publicly available metagenomes derived from samples that cover diverse ecosystems, including host-associated, aquatic, terrestrial, and anthropogenic environments. Using a unified and scalable pipeline, we systematically assembled viral genomes and provided detailed information on genome completeness, taxonomic classification, predicted lifestyle, and host assignment based on CRISPR spacer matches. VIRE contains >89 million predicted viral open reading frames, as well as detailed functional annotations derived from multiple databases. Importantly, VIRE is seamlessly integrated with related microbiome resources such as SPIRE (https://spire.embl.de) and Metalog (https://metalog.embl.de), enabling users to jointly explore viral genomes, metagenome-assembled genomes, and associated environmental or clinical metadata. Accessible at https://vire.embl.de, VIRE provides an open-access, scalable platform for investigating viral diversity, evolution, and ecology on a planetary scale.},
}

@article {pmid41316495,
year = {2025},
author = {Liu, Z and Yu, W and Sun, T and Li, M and Li, X and Qin, L and Liu, X and Bian, Y and Zhao, S and Zhao, Q and Zhao, H and Feng, Q},
title = {Ambient temperature affects the composition of the vaginal microbiome, and temperature-sensitive vaginal microbes influence assisted reproductive technology outcomes.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02212-9},
pmid = {41316495},
issn = {2049-2618},
support = {2021YFC2700400//National Key Research and Development Program of China/ ; 2021YFC2700400//National Key Research and Development Program of China/ ; 2021YFC2700400//National Key Research and Development Program of China/ ; 2021YFC2700400//National Key Research and Development Program of China/ ; 2021YFC2700400//National Key Research and Development Program of China/ ; 2021YFC2700400//National Key Research and Development Program of China/ ; 2021YFC2700400//National Key Research and Development Program of China/ ; 2021YFC2700400//National Key Research and Development Program of China/ ; 2021YFC2700400//National Key Research and Development Program of China/ ; 2021YFC2700400//National Key Research and Development Program of China/ ; 2021YFC2700400//National Key Research and Development Program of China/ ; 2021YFC2700400//National Key Research and Development Program of China/ ; 31988101//the Basic Science Center Program of NSFC/ ; 31988101//the Basic Science Center Program of NSFC/ ; 31988101//the Basic Science Center Program of NSFC/ ; 31988101//the Basic Science Center Program of NSFC/ ; 31988101//the Basic Science Center Program of NSFC/ ; 31988101//the Basic Science Center Program of NSFC/ ; 31988101//the Basic Science Center Program of NSFC/ ; 31988101//the Basic Science Center Program of NSFC/ ; 31988101//the Basic Science Center Program of NSFC/ ; 31988101//the Basic Science Center Program of NSFC/ ; 31988101//the Basic Science Center Program of NSFC/ ; 31988101//the Basic Science Center Program of NSFC/ ; 32370916//the National Natural Science Foundation of China/ ; 32370916//the National Natural Science Foundation of China/ ; 32370916//the National Natural Science Foundation of China/ ; 32370916//the National Natural Science Foundation of China/ ; 32370916//the National Natural Science Foundation of China/ ; 32370916//the National Natural Science Foundation of China/ ; 32370916//the National Natural Science Foundation of China/ ; 32370916//the National Natural Science Foundation of China/ ; 32370916//the National Natural Science Foundation of China/ ; 32370916//the National Natural Science Foundation of China/ ; 32370916//the National Natural Science Foundation of China/ ; 32370916//the National Natural Science Foundation of China/ ; ZR2023YQ061//the Natural Science Foundation of Shandong Province for Excellent Youth Scholars/ ; ZR2023YQ061//the Natural Science Foundation of Shandong Province for Excellent Youth Scholars/ ; ZR2023YQ061//the Natural Science Foundation of Shandong Province for Excellent Youth Scholars/ ; ZR2023YQ061//the Natural Science Foundation of Shandong Province for Excellent Youth Scholars/ ; ZR2023YQ061//the Natural Science Foundation of Shandong Province for Excellent Youth Scholars/ ; ZR2023YQ061//the Natural Science Foundation of Shandong Province for Excellent Youth Scholars/ ; ZR2023YQ061//the Natural Science Foundation of Shandong Province for Excellent Youth Scholars/ ; ZR2023YQ061//the Natural Science Foundation of Shandong Province for Excellent Youth Scholars/ ; ZR2023YQ061//the Natural Science Foundation of Shandong Province for Excellent Youth Scholars/ ; ZR2023YQ061//the Natural Science Foundation of Shandong Province for Excellent Youth Scholars/ ; ZR2023YQ061//the Natural Science Foundation of Shandong Province for Excellent Youth Scholars/ ; ZR2023YQ061//the Natural Science Foundation of Shandong Province for Excellent Youth Scholars/ ; 2021-I2M-5-001//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-5-001//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-5-001//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-5-001//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-5-001//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-5-001//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-5-001//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-5-001//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-5-001//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-5-001//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-5-001//CAMS Innovation Fund for Medical Sciences/ ; 2021-I2M-5-001//CAMS Innovation Fund for Medical Sciences/ ; 2020ZLYS02//Shandong Provincial Key Research and Development Program/ ; 2020ZLYS02//Shandong Provincial Key Research and Development Program/ ; 2020ZLYS02//Shandong Provincial Key Research and Development Program/ ; 2020ZLYS02//Shandong Provincial Key Research and Development Program/ ; 2020ZLYS02//Shandong Provincial Key Research and Development Program/ ; 2020ZLYS02//Shandong Provincial Key Research and Development Program/ ; 2020ZLYS02//Shandong Provincial Key Research and Development Program/ ; 2020ZLYS02//Shandong Provincial Key Research and Development Program/ ; 2020ZLYS02//Shandong Provincial Key Research and Development Program/ ; 2020ZLYS02//Shandong Provincial Key Research and Development Program/ ; 2020ZLYS02//Shandong Provincial Key Research and Development Program/ ; 2020ZLYS02//Shandong Provincial Key Research and Development Program/ ; Q2022144//the Program for Chang Jiang Scholars/ ; Q2022144//the Program for Chang Jiang Scholars/ ; Q2022144//the Program for Chang Jiang Scholars/ ; Q2022144//the Program for Chang Jiang Scholars/ ; Q2022144//the Program for Chang Jiang Scholars/ ; Q2022144//the Program for Chang Jiang Scholars/ ; Q2022144//the Program for Chang Jiang Scholars/ ; Q2022144//the Program for Chang Jiang Scholars/ ; Q2022144//the Program for Chang Jiang Scholars/ ; Q2022144//the Program for Chang Jiang Scholars/ ; Q2022144//the Program for Chang Jiang Scholars/ ; Q2022144//the Program for Chang Jiang Scholars/ ; ts20190988//the Taishan Scholars Program of Shandong Province/ ; ts20190988//the Taishan Scholars Program of Shandong Province/ ; ts20190988//the Taishan Scholars Program of Shandong Province/ ; ts20190988//the Taishan Scholars Program of Shandong Province/ ; ts20190988//the Taishan Scholars Program of Shandong Province/ ; ts20190988//the Taishan Scholars Program of Shandong Province/ ; ts20190988//the Taishan Scholars Program of Shandong Province/ ; ts20190988//the Taishan Scholars Program of Shandong Province/ ; ts20190988//the Taishan Scholars Program of Shandong Province/ ; ts20190988//the Taishan Scholars Program of Shandong Province/ ; ts20190988//the Taishan Scholars Program of Shandong Province/ ; ts20190988//the Taishan Scholars Program of Shandong Province/ ; 2023QNTD004//the Fundamental Research Funds of Shandong University/ ; 2023QNTD004//the Fundamental Research Funds of Shandong University/ ; 2023QNTD004//the Fundamental Research Funds of Shandong University/ ; 2023QNTD004//the Fundamental Research Funds of Shandong University/ ; 2023QNTD004//the Fundamental Research Funds of Shandong University/ ; 2023QNTD004//the Fundamental Research Funds of Shandong University/ ; 2023QNTD004//the Fundamental Research Funds of Shandong University/ ; 2023QNTD004//the Fundamental Research Funds of Shandong University/ ; 2023QNTD004//the Fundamental Research Funds of Shandong University/ ; 2023QNTD004//the Fundamental Research Funds of Shandong University/ ; 2023QNTD004//the Fundamental Research Funds of Shandong University/ ; 2023QNTD004//the Fundamental Research Funds of Shandong University/ ; },
abstract = {OBJECTIVE: To investigate the influence of environmental factors on the composition and structure of the vaginal microbiome and to explore the interaction among environmental factors, vaginal microbiome, and outcomes of assisted reproductive technology (ART).

METHODS: Adonis test was utilized to evaluate the impact of 33 host/environmental variables on vaginal microbiome. Distributed lag nonlinear model analysis (DLNM), Mfuzz analysis, and linear mixed effect model were employed to establish the correlations between ambient temperature and vaginal microbes.

RESULTS: Ambient temperature was one of the most important environmental factors associated with vaginal microbiome. As the temperature increased, succession of vaginal microbes showed four patterns of abundance variation. Furthermore, a group of vaginal microbes showed a preference for certain temperatures, and these microbes' varying interactions partly drove the shift of microbial networks at different temperatures. The community assembly process of vaginal microbiome deviated from neutral model and exposure to ambient temperature did not affect the role of stochastic processes in shaping vaginal microbial community. Notably, vaginal microbiome prior to embryo transfer was significantly associated with preterm birth. Preterm women exhibited higher abundance of Lactobacillus iners and lower abundance of Lactobacillus crispatus.

CONCLUSIONS: Ambient temperature change can affect the structure and composition of the vaginal microbiome and correlate with the abundance of certain vaginal microbes. Temperature-sensitive vaginal bacteria may affect the risk of future preterm births. Video Abstract.},
}

@article {pmid41316410,
year = {2025},
author = {Pawar, M and Pingale, S and Kadam, K and Jadhav, A and Kaul-Ghanekar, R},
title = {Artificial intelligence-driven screening, early diagnosis, and treatment strategies for cervical cancer: an overview.},
journal = {Infectious agents and cancer},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13027-025-00716-5},
pmid = {41316410},
issn = {1750-9378},
}

@article {pmid41316404,
year = {2025},
author = {Fieschi-Méric, L and Pasmans, F and Fernández Meléndez, E and De Bruyckere, S and Blomme, E and Verbrugghe, E and Martel, A},
title = {Bsal susceptibility depends on host origin but not on skin microbiota in captive Pleurodeles waltl.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {123},
pmid = {41316404},
issn = {2524-4671},
abstract = {BACKGROUND: Amidst the current biodiversity crisis, amphibians are particularly endangered by the emergence of infectious diseases. The skin disease chytridiomycosis is caused by the fungi Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), which may interact with bacterial symbionts present on the amphibian epidermis. Extensive research has explored the interactions between the amphibian microbiota and Bd; yet, little is known about its interactions with Bsal. In this paper, we used the ribbed newt (Pleurodeles waltl), a model species displaying pronounced among-individual variation in response to Bsal, to (1) determine whether susceptibility to Bsal and individual microbiota vary between source groups; (2) test whether susceptibility to Bsal can be predicted from skin microbiota before exposure and (3) quantify microbiota volatility over time to determine whether Bsal infection intensity and chytridiomycosis severity correlate with the magnitude of shifts in bacterial communities caused by Bsal exposure.

RESULTS: Our results demonstrate that newts of different origin harbor distinct microbiota even under uniform rearing conditions. We show that Bsal infection intensity and disease severity cannot be predicted from the diversity, structure, or composition of the skin microbiota of P. waltl. Instead, a strong relation between newts' source group and their response to Bsal suggests that other factors might underpin among-individual variation in Bsal susceptibility in this species. Moreover, our results indicate that the intensity of early Bsal infection and longer-term severity of chytridiomycosis do not correlate with the magnitude of microbiota change following Bsal exposure.

CONCLUSION: These results demonstrate a limited involvement of the microbiota in Bsal dynamics in P. waltl, suggesting that other mechanisms contribute to individual Bsal susceptibility. Further research on the relation between chytrid pathogens and their amphibian hosts will be instrumental to improve the conservation of the most endangered vertebrate class on earth.},
}

@article {pmid41316171,
year = {2025},
author = {Meldrum, OW and Tiew, PY and Xu, H and Low, DY and Ivan, FX and Narayana, JK and Jaggi, TK and Ching, J and Chotirmall, SH},
title = {Integrated multi-omics profiling for risk stratification in Asians with COPD.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-025-03440-1},
pmid = {41316171},
issn = {1465-993X},
support = {(#020458-00001//LKCMedicine-ICL Fellowship/ ; MOH-001636//National Research Foundation Singapore under its Open Fund-Large Collaborative Grant and administered by the Singapore Ministry of Health's National Medical Research Council/ ; MOH-001356//Singapore Ministry of Health's National Medical Research Council under its Clinician-Scientist Individual Research Grant/ ; MOH-001855//Singapore Ministry of Health's National Medical Research Council under its Clinician-Scientist Award (CSA) Investigator (INV) category/ ; RT1/22//Singapore Ministry of Education under its AcRF Tier 1 Grant/ ; },
}

@article {pmid41315930,
year = {2025},
author = {Chaussard, A and Bonnet, A and Le Corff, S and Sokol, H},
title = {TaxaPLN: a taxonomy-aware augmentation strategy for microbiome-trait classification including metadata.},
journal = {BMC bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12859-025-06312-z},
pmid = {41315930},
issn = {1471-2105},
abstract = {BACKGROUND: The gut microbiome plays a crucial role in human health, making it a cornerstone of modern biomedical research. To study its structure and dynamics, machine learning models are increasingly used to identify key microbial patterns associated with disease and environmental factors, but their performance is often limited by the intrinsic complexity of microbiome data and the small size of available cohorts. In this context, data augmentation has emerged as a promising strategy to overcome these challenges by generating artificial microbiome profiles.

RESULTS: We introduce TaxaPLN, a data augmentation method based on PLN-Tree generative models, which leverages the taxonomy and a data-driven sampler to generate realistic synthetic microbiome compositions. Additionally, we propose a conditional extension based on feature-wise linear modulation, enabling covariate-aware generation. Experiments on diverse curated microbiome datasets show that TaxaPLN preserves ecological properties and generally improves or maintains predictive performances, outperforming state-of-the-art baselines on most tasks. Furthermore, the conditional variant of TaxaPLN establishes a new benchmark for metadata-aware microbiome augmentation.

CONCLUSION: TaxaPLN provides a model-based framework for augmenting microbiome datasets while preserving their ecological and clinical relevance. By integrating taxonomic structure and host metadata, it enhances predictive modeling across diverse real-world settings. To facilitate reproducible and scalable microbiome analysis using our method, TaxaPLN is released as an open-source Python package available on PyPI (plntree), with MIT-licensed source code hosted at https://github.com/AlexandreChaussard/PLNTree-package.},
}

@article {pmid41315900,
year = {2025},
author = {Ardis, CK and Bui, TPN and Nieuwdorp, M},
title = {Gut microbiota in cancer cachexia: a new frontier for research and therapy.},
journal = {Genes & nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12263-025-00791-8},
pmid = {41315900},
issn = {1555-8932},
support = {09150182010020//European Union's Horizon Training Mobility Actions- Consortium Grant agreement MiCCrobioTAckle/ ; 09150182010020//NWO VICI grant 2020/ ; 101141346//ERC Advanced grant/ ; },
}

@article {pmid41315888,
year = {2025},
author = {van der Windt, N and Paix, B and Biesmeijer, JC and Ambo-Rappe, R and Huang, YM and Nirbadha, KGS and Sipkema, D and de Voogd, NJ},
title = {Host Evolutionary History Drives Prokaryotic Diversity in the Globally Distributed Sponge Family Petrosiidae.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70186},
doi = {10.1111/mec.70186},
pmid = {41315888},
issn = {1365-294X},
support = {101000392//Horizon 2020 Framework Programme/ ; 16.161.301//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; //European Regional Development Fund/ ; //Collectivité Territoriale de Martinique/ ; CRG-1-814 2012-BER-002//King Abdullah University of Science and Technology/ ; MOST 105-2621-B-346-002//Ministry of Science and Technology/ ; MNPH104403//Marine National Parks Headquarters/ ; },
abstract = {Sponge microbial communities play a crucial role in marine ecosystem functioning and serve as a rich source of bioactive compounds. While host identity is recognised as a major determinant of microbiome diversity, the underlying evolutionary mechanisms remain poorly understood. This study aimed to comprehensively assess phylosymbiosis patterns within the sponge family Petrosiidae. In total 21 sponge species, collected across a broad geographic scale, were examined to investigate how host phylogeny influences microbiome composition. Using 28S rRNA, 18S rRNA and COI gene barcoding to identify host sponges, combined with 16S rRNA gene amplicon sequencing to characterise prokaryotic communities, we provide evidence of phylosymbiosis through multiple analytical approaches, including distance-based metrics and topological congruence. Our results show that host phylogeny and identity play a significant role in structuring sponge microbiomes, even at finer taxonomic resolutions. However, we observed notable incongruencies, where closely related sponge species exhibit divergent microbial communities that appear to be associated with depth or geographical location. This study represents the first large-scale investigation of phylosymbiosis in sponges at the family level, providing valuable insights into the evolutionary and ecological drivers shaping sponge microbiomes, particularly in the sponge family Petrosiidae.},
}

@article {pmid41315812,
year = {2025},
author = {Porter, S and Holtappels, D and Montoya, A and Koskella, B},
title = {Causes and consequences of bacterial local adaptation via MGEs in the plant microbiome.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70766},
pmid = {41315812},
issn = {1469-8137},
support = {1943239//Division of Environmental Biology/ ; 1942881/2020-08319//National Institute of Food and Agriculture/ ; NE2335//Multistate HATCH funding/ ; },
abstract = {Adaptations that enable plant-associated bacteria to fill disparate niches comprise a critical component of microbial diversity. Genes that confer locally adaptive bacterial traits, ranging from heavy metal resistance to pathogen or symbiont infectivity, often reside within mobile genetic elements (MGEs) that can move between genomes. While MGEs may speed microbial adaptation, they also have selfish fitness interests and potentially separate evolutionary trajectories from their host genome. MGEs can also impose physiological burdens and be limited in the transmissibility of function across hosts, which likely constrains bacterial local adaptation. Given these constraints, the prevalence of adaptive loci on potentially exploitative MGEs poses a dilemma: how do fitness conflicts and alignments between MGEs and the main replicon shape bacterial local adaptation and impact plant hosts? We synthesize research on ways MGEs confer rapid, niche-specific fitness advantages to bacteria, identify factors that promote or constrain bacterial adaptation, and highlight MGE impacts on plants. We focus on large, self-transmissible MGEs (islands, plasmids, and prophages; though we expect relevance to other MGEs as well) to better understand how MGEs bolster yet constrain bacterial local adaptation. We specifically explore the role of MGEs in shaping bacteria that themselves play a role in expanding or contracting the plant niche.},
}

@article {pmid41315807,
year = {2025},
author = {Parween, S and Tabassum, N and Shekhawat, K and Gnannt, B and Alzayed, W and Jalal, R and Hirt, H},
title = {Host genome and bacterial taxa shape the Arabidopsis seed microbiome.},
journal = {EMBO reports},
volume = {},
number = {},
pages = {},
pmid = {41315807},
issn = {1469-3178},
support = {BAS/1/1062-01-01//King Abdullah University of Science and Technology (KAUST)/ ; RGC/3/5638-01-01//King Abdullah University of Science and Technology (KAUST)/ ; },
abstract = {Plant-microbiome interactions are crucial in shaping plant growth, stress resilience, and disease resistance. Among these, the seed microbiome plays a pivotal role in early plant development and ecological adaptation. However, little is known about the factors that determine the abundance and functions of the seed microbiome, as well as the role of the host genome in shaping the microbial diversity across different ecotypes. In this study, we investigated the diversity of the Arabidopsis seed microbiomes that originate from multiple geographical locations. High-throughput sequencing identified key bacterial taxa that govern Arabidopsis seed microbiota diversity. Distinct compositions of bacterial taxa were identified in Arabidopsis accessions sharing geographical location and similar soil features. Genome-wide association studies (GWAS) revealed that both the abundance of key taxa and common functional traits are associated with specific host genetic loci such as the RNA-binding protein RPB47B, mutants of which showed altered physiological properties related to soil properties and microbial diversity. Overall, our study establishes that geographical, soil and genetic host factors shape the Arabidopsis seed microbiome.},
}

@article {pmid41315750,
year = {2025},
author = {Heyman, E and Chodick, G and Fallach, N and Dubnov-Raz, G},
title = {The association between antibiotic use in infancy and overweight during childhood and adolescence: a historical cohort study.},
journal = {International journal of obesity (2005)},
volume = {},
number = {},
pages = {},
pmid = {41315750},
issn = {1476-5497},
abstract = {BACKGROUND AND OBJECTIVE: The role of the microbiome and gut flora alterations in childhood obesity has drawn increasing scientific attention. However, large-scale, long-term cohort studies with real-world data on exposure and outcomes are lacking. We aimed to examine the association between exposure to antibiotics during infancy and the development of overweight and obesity during childhood and adolescence.

METHODS: We conducted a historical cohort study using data from a large Israeli health provider (Maccabi Healthcare Services, MHS). Eligible patients born between 1998-2002 who received antibiotics before age 2 years were compared with unexposed infants. Valid body mass index (BMI) data were available for 76,840 eligible infants, including 65280 exposed to antibiotics (52.2% males) and 11,560 unexposed (46.1% males). Study outcomes were overweight and obesity during childhood/ adolescence.

RESULTS: Compared to unexposed, antibiotic-exposed infants had significantly higher mean ( ± SE) BMI percentiles in all age groups: childhood (57.8 ± 0.1 vs 55.0 ± 0.2), early adolescence (58.2 ± 0.1 vs. 55.1 ± 0.3), and late adolescence (57.4 ± 0.2 vs. 55.0 ± 0.4), all p < 0.001. The odds of overweight and obesity versus unexposed infants increased significantly (p < 0.001) with the number of dispensed narrow-spectrum antibiotic packs, from an odds ratio of 1.15 (95%CI: 1.02-1.29) for 1-2 packs, to 1.52 (95%CI: 1.13-2.05) among those exposed to 10 or more packs. No such association was found for broad-spectrum antibiotics.

CONCLUSIONS: Exposure to narrow spectrum antibiotics during infancy was associated with a higher BMI and an increased likelihood of overweight and obesity in childhood and adolescence.},
}