@article {pmid40957911,
year = {2025},
author = {Zhang, W and Lahry, K and Cipurko, D and Huang, S and Zbihley, O and Sevilleja, AM and Rudzka, D and Frietze, LR and Assari, M and Katanski, CD and Singh, M and Attina, A and Guillorit, H and Watkins, CP and Gourlain, D and Varlet, D and Falconi, J and Djiane, A and Hirtz, C and Chen, H and Macari, F and Johnson, K and Chevrier, N and David, A and Pan, T},
title = {Two microbiome metabolites compete for tRNA modification to impact mammalian cell proliferation and translation quality control.},
journal = {Nature cell biology},
volume = {},
number = {},
pages = {},
pmid = {40957911},
issn = {1476-4679},
support = {RM1HG008935//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R33CA272357//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; P30 DK42086//University of Chicago (UChicago)/ ; },
abstract = {The microbiome affects eukaryotic host cells via many metabolites, including the well-studied queuine as substrate for host tRNA queuosine modification. The microbial metabolite pre-queuosine 1 (preQ1) is produced in the bacterial tRNA queuosine biosynthesis pathway, with unknown effects on host cell biology. Here we show that preQ1 strongly represses cell proliferation in both human and mouse cells. Queuine reverses this effect by competing with preQ1 to modify the same tRNA. PreQ1 is detectable in the plasma and tissues of mice, and its injection suppresses tumour growth in a mouse cancer model. Mechanistically, preQ1 reduces cognate tRNA levels specifically, as well as codon-dependent translation of housekeeping genes. We identify the endoplasmic reticulum-localized inositol-requiring enzyme 1 (IRE1) ribonuclease as the enzyme responsible for the selective degradation of preQ1-modified tRNAs on translating ribosomes. Our results identify two microbial metabolites competing for host tRNA modification, which elicits translation quality control and impacts cell proliferation.},
}

@article {pmid40957908,
year = {2025},
author = {Iliev, ID and Blander, JM and Collins, N and Guo, CJ and Longman, RS and Sonnenberg, GF and Zeng, MY and Artis, D},
title = {Microbiota-mediated mechanisms of mucosal immunity across the lifespan.},
journal = {Nature immunology},
volume = {},
number = {},
pages = {},
pmid = {40957908},
issn = {1529-2916},
abstract = {The microbiota has a fundamental role in regulating homeostasis and inflammation across the barrier surfaces of the body. The gut is a unique bioreactor where the high concentration of microorganisms, microbial and dietary metabolites, microbial-derived molecular structures, immune cells, stroma and neurons form a complex, highly interactive and precisely regulated system. The mucosal immune system in the gut has profound local and systemic effects, influencing both health and disease. A critical period of immune imprinting occurs early in life, shaped by the neonatal microbiota and nutrition, to influence immune development and long-term disease susceptibility. Microbiota-derived metabolites have crucial roles in immune modulation, influencing epithelial integrity, oral tolerance and inflammatory responses. This Review explores the interactions between the microbiota and the mucosal immune system from infancy to adulthood, highlighting the impact on health and disease. We also discuss therapeutic interventions, including microbiota-derived molecules, dietary metabolites and emerging microbiome-based co-therapies.},
}

@article {pmid40957733,
year = {2025},
author = {You, G and Yu, S and Liu, M and Diao, L and Lian, R and Li, Y},
title = {Decoding the multifactorial etiology of chronic endometritis.},
journal = {Placenta},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.placenta.2025.09.007},
pmid = {40957733},
issn = {1532-3102},
abstract = {Chronic endometritis (CE) is a persistent inflammatory disorder of the endometrium, typically marked by abnormal plasma cell infiltration. It is closely associated with adverse pregnancy outcomes. The pathogenesis of CE involves a complex interplay of both infectious and non-infectious factors. Infectious etiologies include ascending infection pathways, pelvic infection pathways, sexually transmission, hematogenous infection pathways and special infections, while non-infectious factors encompass uterine structural pathology, autoimmune disorders and iatrogenic factors. Considering the multifactorial etiology of CE, adopting a personalized management approach that integrates both microbial and immune factors may enhance pregnancy outcomes for CE women.},
}

@article {pmid40957661,
year = {2025},
author = {Young, GR and Noor, N and Khirwadkar, A and Beck, LC and Sharip, MT and Whelan, K and Kennedy, NA and Satsangi, J and Marchesi, J and Jostins-Dean, L and Stewart, C and Lyons, PA and Parkes, M and Lamb, CA and , },
title = {Gut microbiome comparability between DNA extraction kits.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336648},
pmid = {40957661},
issn = {1468-3288},
}

@article {pmid40957466,
year = {2025},
author = {Xu, T and Han, M and Zeng, Y and Yang, R and Xiang, L and Tang, H and Liu, X and Chi, Y and Xu, Z and Zhang, S and Huo, D and Zhong, X},
title = {Top-down selection of pit mud local microbial conmmunity for efficient anaerobic digestion of distilled grain waste.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133339},
doi = {10.1016/j.biortech.2025.133339},
pmid = {40957466},
issn = {1873-2976},
abstract = {China's annual production of 12 million tons of distilled grain waste (DGW) from Baijiu manufacturing poses significant environmental challenges. Conventional anaerobic digestion (AD) using wastewater sludge exhibits poor compatibility with DGW's unique physicochemical properties, achieving suboptimal methane yields. This study pioneered a top-down domestication strategy employing indigenous pit mud (PM) microbiome as a specialized inoculum for enhanced DGW valorization. PM-based reactors demonstrated superior performance over anaerobic sludge (AS), achieving 73 % higher biogas yields (518.52 vs 298.99 mL/g VTS) and 95 % higher methane productivity (246.65 vs 126.81 mL/g VTS). Peak methane yields reached 432.59 mL/g VTS, establishing a new benchmark for DGW digestion. Comprehensive 16S rRNA sequencing revealed dynamic microbial succession during 91-day domestication, with Firmicutes becoming dominant (>90 %) under thermophilic conditions. Community assembly mechanisms shifted from deterministic homogeneous selection (76-88 %) to stochastic ecological drift (76 %), reflecting adaptive microbial restructuring. PICRUSt2 functional analysis unveiled strategic metabolic reprogramming: PM consortia upregulated glycolysis and ATP synthesis pathways while downregulating citrate cycles, optimizing carbon flux toward substrate-level energy generation. The domesticated PM microbiome exhibited remarkable resilience, rapidly recovering from operational perturbations while maintaining stable volatile fatty acid profiles. This work establishes the first successful application of substrate-adapted indigenous microbiota as specialized AD inoculum for DGW, offering a sustainable circular bioeconomy solution for China's massive DGW waste stream while advancing fundamental understanding of microbial community domestication mechanisms.},
}

@article {pmid40957411,
year = {2025},
author = {Franco, M and Buso, H and Carfora, F and Costanzo, GAML and Felice, C and Rattazzi, M and Cinetto, F and Milito, C and Firinu, D},
title = {Non-infectious pulmonary and gastrointestinal manifestations in primary antibody deficiencies: lessons for the clinic.},
journal = {Expert review of clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1080/1744666X.2025.2556435},
pmid = {40957411},
issn = {1744-8409},
abstract = {INTRODUCTION: Primary antibody deficiencies (PADs), especially common variable immunodeficiency (CVID), are clinically significant inborn errors of immunity due to complex phenotypes and long-term complications. This review provides an updated overview of pulmonary and gastrointestinal manifestations in PADs, focusing on CVID.

AREAS COVERED: We conducted a structured literature review of original articles, reviews, and guidelines from the last 10 years, using databases such as PubMed and Scopus. The focus was on immunopathogenesis, clinical features, and treatment of noninfectious pulmonary and gastrointestinal complications in CVID. Key shared immunological pathways include B- and T-cell dysregulation, cytokine-driven inflammation, and microbiota alterations.

EXPERT OPINION: Early recognition of noninfectious complications in CVID is vital to prevent organ damage and improve outcomes. A multidisciplinary, personalized approach involving genetic, immunologic, and microbiologic assessments and specialists including pathologists, pulmonologists, and gastroenterologists is essential, considering the pulmonary-gastrointestinal axis's role in mucosal immune dysfunction and systemic immune dysregulation.},
}

@article {pmid40957387,
year = {2025},
author = {Pan, X and Chen, X and Ma, Y and Zou, J and Lin, Y and Zhao, X and Wang, Y and Tang, Y and Gao, F},
title = {Chemotaxis-guided nanoplatform for non-alcoholic steatohepatitis therapy via macrophage reprogramming, hepatoprotection and gut microbiome modulation.},
journal = {Biomaterials},
volume = {326},
number = {},
pages = {123694},
doi = {10.1016/j.biomaterials.2025.123694},
pmid = {40957387},
issn = {1878-5905},
abstract = {Non-alcoholic steatohepatitis (NASH), characterized by hepatic steatosis, inflammation, and varying degrees of fibrosis, has become a growing global health burden. Obeticholic acid (OCA, a farnesoid X receptor agonist) has shown limited efficacy due to poor solubility, single-target mechanisms, and off-target side effects, notwithstanding the great promise of this agent in NASH clinical trials. Here, we designed M2 macrophage-derived membrane (M2M)-camouflaged poly (lactic-co-glycolic acid) (PLGA) nanoparticles (O@PLGA@M) to achieve targeted OCA delivery to the inflamed liver niche for recovering hepatic homeostasis in NASH. The M2M improved the inflamed liver-targeting of the nanoplatforms via chemotaxis and promoted M1-to-M2 macrophage repolarization, as evidenced by a 2.5-fold increase in CD206 expression and 45 % reduction in CD86 expression in the liver. In a methionine/choline-deficient (MCD) diet-induced murine NASH model, O@PLGA@M exhibited excellent biosafety and multifaceted anti-NASH efficacy, including anti-steatosis, anti-inflammatory, and anti-fibrotic effects. Mechanistically, O@PLGA@M reprogrammed macrophages by modulating macrophage polarization and inhibiting recruitment of immune cells to reduce the inflammatory cascade. They also exerted hepatoprotection effects by reducing steatosis and hepatocyte damage. Moreover, O@PLGA@M modulated the gut microbiome by redirecting it towards a beneficial state, which further relieved NASH through the gut-liver axis. These findings demonstrated that the biomimetic nanoplatforms could be employed as promising strategies that integrated targeted delivery and multimodal synergistic therapy for NASH management.},
}

@article {pmid40957299,
year = {2025},
author = {Li, H and Chen, J and Hou, J},
title = {Unraveling the gut-brain enigma: New frontiers in functional dyspepsia and gastroparesis.},
journal = {Pathology, research and practice},
volume = {275},
number = {},
pages = {156220},
doi = {10.1016/j.prp.2025.156220},
pmid = {40957299},
issn = {1618-0631},
abstract = {Functional Dyspepsia and Gastroparesis present significant challenges in gastroenterology due to their overlapping symptoms and complex pathophysiology. This review explores recent advances in understanding these disorders, focusing on shared mechanisms involving gut-brain interactions, microbiome dysregulation, and immunological factors. We discuss evolving diagnostic techniques, including gastric emptying scintigraphy and novel approaches like wireless motility capsules. Management strategies encompass dietary modifications, pharmacological interventions targeting neuromodulation and motility, and emerging therapies such as microbiome modulation. Advanced interventions, including gastric electrical stimulation and endoscopic techniques, are examined for refractory cases. The review also highlights the potential of Traditional Chinese Medicine in addressing multiple aspects of Functional Dyspepsia and Gastroparesis. Despite progress, differentiating between these conditions remains challenging due to symptom overlap and variable gastric emptying patterns. We emphasize the need for a personalized, multidisciplinary approach to patient care and identify critical areas for future research, including standardization of diagnostic criteria and exploration of integrated gastroduodenal pathophysiology.},
}

@article {pmid40956896,
year = {2025},
author = {Sharan, D and Nurek, A and Stemczynski, J and Turan, K and Little, AS and Coyne, MJ and McMillin, M and Sidebottom, AM and Comstock, LE and Light, SH},
title = {DNA-utilization loci enable exogenous DNA metabolism in gut Bacteroidales.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {38},
pages = {e2505388122},
doi = {10.1073/pnas.2505388122},
pmid = {40956896},
issn = {1091-6490},
support = {R35GM146969//HHS | National Institutes of Health (NIH)/ ; Searle Scholars Program//Kinship Foundation (The Kinship Foundation)/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; Mice ; *DNA/metabolism ; *DNA, Bacterial/metabolism/genetics ; *Bacteroides thetaiotaomicron/metabolism/genetics ; Humans ; Bacterial Proteins/genetics/metabolism ; *Bacteroidetes/metabolism/genetics ; Germ-Free Life ; Uracil/metabolism ; },
abstract = {The human gut microbiome plays a central role in nutrient metabolism, yet the fate of exogenous nucleic acids within this ecosystem remains poorly understood. Here, we show that multiple Bacteroidales species efficiently metabolize exogenous DNA, with Bacteroides thetaiotaomicron converting it into the deaminated nucleobases uracil and xanthine. Using genetic and biochemical approaches, we identify ddbABCDEF, a six-gene locus encoding secreted nucleases and an outer membrane transporter, essential for exogenous DNA metabolism in B. thetaiotaomicron. Colonization of gnotobiotic mice with ddbABCDEF mutants reveals that this pathway significantly alters nucleobase pools in a gnotobiotic mouse model. Comparative genomic analyses demonstrate that ddbABCDEF is evolutionarily related to a natural transformation system present in Bacteroidota and has diversified into four distinct subtypes, each linked to unique DNA-processing activities in closely related gut Bacteroidales strains. These findings thus expand our understanding of DNA metabolism in the gut microbiome and reveal a distinctive pathway for nucleobase production with implications for host-microbe interactions.},
}

*Gastrointestinal Microbiome/genetics
Animals
Mice
*DNA/metabolism
*DNA, Bacterial/metabolism/genetics
*Bacteroides thetaiotaomicron/metabolism/genetics
Humans
Bacterial Proteins/genetics/metabolism
*Bacteroidetes/metabolism/genetics
Germ-Free Life
Uracil/metabolism

@article {pmid40956701,
year = {2025},
author = {Natarajan, O and Gibboney, SL and Young, MN and Lim, SJ and Nguyen, F and Pluta, N and Atkinson, CGF and Liberti, A and Kees, ED and Leigh, BA and Breitbart, M and Gralnick, JA and Dishaw, LJ},
title = {Prophage regulation of Shewanella fidelis 3313 motility and biofilm formation with implications for gut colonization dynamics in Ciona robusta.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
doi = {10.7554/eLife.103107},
pmid = {40956701},
issn = {2050-084X},
support = {IOS-1456301//National Science Foundation/ ; MCB-1817308//National Science Foundation/ ; NSF IOS-2226050/51//National Science Foundation/ ; Graduate Research Fellowship Program//National Science Foundation/ ; },
mesh = {Animals ; *Biofilms/growth & development ; *Prophages/physiology/genetics ; *Shewanella/virology/physiology/genetics ; *Gastrointestinal Microbiome ; *Ciona/microbiology ; },
abstract = {Lysogens, bacteria with one or more viruses (prophages) integrated into their genomes, are abundant in the gut of animals. Prophages often influence bacterial traits; however, the influence of prophages on the gut microbiota-host immune axis in animals remains poorly understood. Here, we investigate the influence of the prophage SfPat on Shewanella fidelis 3313, a persistent member of the gut microbiome of the model marine tunicate, Ciona robusta. Establishment of a SfPat deletion mutant (ΔSfPat) reveals the influence of this prophage on bacterial physiology in vitro and during colonization of the Ciona gut. In vitro, deletion of SfPat reduces S. fidelis 3313 motility and swimming while increasing biofilm formation. To understand the in vivo impact of these prophage-induced changes in bacterial traits, we exposed metamorphic stage 4 Ciona juveniles to wildtype (WT) and ΔSfPat strains. During colonization, ΔSfPat localizes to overlapping and distinct areas of the gut compared to the WT strain. We examined the differential expression of various regulators of cyclic-di-GMP, a secondary signaling molecule that mediates biofilm formation and motility. The pdeB gene, which encodes a bacterial phosphodiesterase known to influence biofilm formation and motility by degrading cyclic-di-GMP, is upregulated in the WT strain but not in ΔSfPat when examined in vivo. Expression of the Ciona gut immune effector, VCBP-C, is enhanced during colonization by ΔSfPat compared to the WT strain; however, VCBP-C binding to the WT strain does not promote the excision of SfPat in an SOS-dependent pathway. Instead, VCBP-C binding significantly reduces the expression of a phage major capsid protein. Our findings suggest that SfPat influences host perception of this important colonizing commensal and highlights the significance of investigating tripartite dynamics between prophages, bacteria, and their animal hosts to better understand the gut microbiota-host immune axis.},
}

Animals
*Biofilms/growth & development
*Prophages/physiology/genetics
*Shewanella/virology/physiology/genetics
*Gastrointestinal Microbiome
*Ciona/microbiology

@article {pmid40956524,
year = {2025},
author = {Yu, J and Hosain, MM and Park, T},
title = {Identification of microbiome markers for ordered groups.},
journal = {Genes & genomics},
volume = {},
number = {},
pages = {},
pmid = {40956524},
issn = {2092-9293},
support = {NRF-2022R1A2C1092497//National Research Foundation of Korea/ ; },
abstract = {BACKGROUND: Identifying microbiome markers associated with ordered phenotypes, such as disease stages or severity levels, is crucial for understanding disease progression and advancing precision medicine. Despite this importance, most existing methods for differential abundance analysis are designed for binary group comparisons and do not incorporate ordinal information, limiting their ability to capture trends across ordered categories.

OBJECTIVE: To develop and evaluate statistical methods that explicitly account for ordinal phenotype structure in microbiome data, addressing challenges such as sparsity and zero inflation, and improving the detection of meaningful microbial associations.

METHODS: In this study, we propose and evaluate three novel approaches specifically tailored for microbiome association analysis with ordered groups: the binary optimal test, the linear trend test, and the proportional odds model-based permutation test (POMp). These methods explicitly account for the ordinal structure of phenotypes and address the sparsity and zero-inflation commonly observed in microbiome data through permutation-based inference. We applied the proposed methods to three publicly available gut microbiome datasets, including two related to obesity and one concerning colorectal cancer.

RESULTS: All three proposed methods successfully identified differentially abundant features (DAFs) that exhibited stronger ordinal associations compared to those identified by existing methods. In particular, POMp consistently outperformed other approaches in terms of correlation with phenotype order, demonstrating its potential to identify biologically relevant markers.

CONCLUSION: The findings of this study highlight the importance of incorporating ordinal information in microbiome studies and provide robust statistical tools for advancing microbial biomarker discovery in complex disease contexts.},
}

@article {pmid40956019,
year = {2025},
author = {Gao, Z and Danzhen, Z and Li, Y and Zhu, J and Chu, L and Yang, Z},
title = {Exploring Nasal Structural-Microbial Interactions in Multiple Sclerosis-Associated Olfactory Impairment.},
journal = {Annals of clinical and translational neurology},
volume = {},
number = {},
pages = {},
doi = {10.1002/acn3.70181},
pmid = {40956019},
issn = {2328-9503},
support = {gyfybsky-2022-45//Major and Refractory Disease Clinical Collaboration Pilot Project of Integrated Traditional Chinese and Western Medicine for Cerebral Infarction and the Doctoral Research Initiation Fund Project of the Affiliated Hospital of Guizhou Medical University/ ; 82371330//National Natural Science Foundation of China/ ; 82460251//National Natural Science Foundation of China/ ; Qiankehe Foundation-ZK [2023] General 393//Guizhou Provincial Department of Science and Technology, General Project,/ ; 2024GZYXKYJJXM0103//Science and Technology Fund Project of Guizhou Health Commission/ ; },
abstract = {BACKGROUND: Olfactory dysfunction is frequently observed in patients with multiple sclerosis (MS); however, its underlying mechanisms remain poorly understood. To date, no studies have directly examined the nasal mucosal microbiota in MS. This study aimed to explore potential relationships among olfactory function, nasal microbiota composition, and superior turbinate volume in MS.

METHODS: This single-center observational study included 42 patients with MS and 37 healthy controls (HC) in China. Olfactory function was evaluated using the University of Pennsylvania Smell Identification Test (UPSIT). Deep nasal microbiota profiles and MRI-based measurements of superior turbinate volume were analyzed.

RESULTS: A reduced relative abundance of Prevotella buccalis (P. buccalis) was observed in MS with lower UPSIT scores (p = 0.030). In HC, a positive correlation was found between UPSIT scores and the superior turbinate volume (Rp = 0.329, p = 0.041), whereas no such correlation was observed in MS (Rs = -0.022, p = 0.625), suggesting a dissociation between olfactory performance and turbinate morphology in MS. Additionally, in MS, superior turbinate volume showed negative correlations with several genera, including Cupriavidus, Methylobacterium-Methylorubrum, Ideonella, and Acinetobacter (all p < 0.05), indicating potential associations between mucosal structure and microbial composition.

DISCUSSION: These preliminary findings suggest that alterations in nasal microbiota may be linked to olfactory impairment and mucosal structural changes in MS. While P. buccalis emerged as a potential microbial correlate of olfactory dysfunction, its role remains unclear and may reflect secondary ecological shifts. Further mechanistic studies and larger cohorts are needed to determine causality and assess the diagnostic or therapeutic value of nasal microbiome features in MS.},
}

@article {pmid40955808,
year = {2025},
author = {Han, H and Zhang, L and Wu, Y and Ye, Q and Cai, X},
title = {Exploring the Causal Association Between Oral Microbiome Abundance and Asthma Risk Using Two-Sample Mendelian Randomization.},
journal = {Pediatric pulmonology},
volume = {60},
number = {9},
pages = {e71301},
doi = {10.1002/ppul.71301},
pmid = {40955808},
issn = {1099-0496},
support = {//This study was funded by the National Natural Science Foundation of China (Nos. 82160003 and 82360009)./ ; },
mesh = {Humans ; *Asthma/microbiology/genetics ; Mendelian Randomization Analysis ; *Microbiota/genetics ; Polymorphism, Single Nucleotide ; Genome-Wide Association Study ; *Saliva/microbiology ; *Mouth/microbiology ; Female ; Male ; Denmark ; Risk Factors ; Case-Control Studies ; },
abstract = {BACKGROUND: Asthma is influenced by genetic and environmental factors, and emerging evidence suggests that the oral microbiome may play a role in its pathogenesis. This study aimed to explore the causal association between oral microbiome abundance and asthma risk using a two-sample Mendelian randomization (MR) approach.

METHODS: We utilized genome-wide association studies (GWAS) data comprising 56,167 asthma cases and 408,442 controls of European ancestry, alongside 610 individuals from the Danish ADDITION-PRO cohort for oral microbiome analysis. We selected 267 single nucleotide polymorphisms (SNPs) linked to salivary microbiota as instrumental variables (IVs) with an F-statistic > 10. MR analyses were carried out using inverse variance weighted (IVW), MR-Egger, weighted median, and weighted mode methods, complemented by sensitivity analyses.

RESULTS: Our findings revealed a significant association between specific salivary microbiota and asthma risk. Notably, increased abundance of Genus Rothia was positively associated with asthma risk (IVW: OR = 1.03), while an unspecified Streptococcus species showed a negative correlation (IVW: OR = 0.97). Sensitivity analyses confirmed these results' robustness, with no signs of pleiotropy or significant heterogeneity.

CONCLUSION: The study suggests a causal relationship between specific oral microbiota and asthma risk, emphasizing the oral microbiome's potential significance in asthma pathogenesis.},
}

Humans
*Asthma/microbiology/genetics
Mendelian Randomization Analysis
*Microbiota/genetics
Polymorphism, Single Nucleotide
Genome-Wide Association Study
*Saliva/microbiology
*Mouth/microbiology
Female
Male
Denmark
Risk Factors
Case-Control Studies

@article {pmid40955665,
year = {2025},
author = {Li, J and Kuhn, KA},
title = {Microbial threads in the tapestry of rheumatoid arthritis.},
journal = {The Journal of clinical investigation},
volume = {135},
number = {18},
pages = {},
doi = {10.1172/JCI195374},
pmid = {40955665},
issn = {1558-8238},
mesh = {Humans ; *Arthritis, Rheumatoid/microbiology/immunology/pathology ; *Gastrointestinal Microbiome/immunology ; Animals ; Autoantibodies/immunology ; *Immunity, Mucosal ; *Bacteria/immunology ; },
abstract = {Rheumatoid arthritis (RA) has a preclinical period of 5-10 years preceding the appearance of joint pain and swelling characteristic of clinical RA. Preclinical RA has been characterized by circulating IgA and IgG classes of autoantibodies targeting citrullinated protein antigens (ACPAs) that are highly specific for future clinical RA, circulating IgA plasmablasts, and autoantibody production at mucosal sites, all of which point toward mucosal tissues as the origin of immune dysregulation. In individuals at risk for developing and with established RA, oral and gut microbial shifts correlate with immune activation. Specific bacterial taxa such as Segatella copri, Subdoligranulum didolesgii, Eggerthella lenta, and Streptococcal species have been shown to contribute to the development and/or perpetuation of RA through mechanisms that include molecular mimicry, antigen citrullination, and disruption of mucosal immunity. Furthermore, microbial metabolites, including short-chain fatty acids, bile acids, and tryptophan derivatives, regulate immune homeostasis and offer potential therapeutic avenues. The gut microbiome also influences therapeutic responses by modulating conventional disease-modifying antirheumatic drugs. This Review synthesizes current knowledge on the bacterial microbiome's role in RA pathogenesis and treatment responses, highlighting microbiome-targeted interventions as potential strategies for disease prevention and management.},
}

Humans
*Arthritis, Rheumatoid/microbiology/immunology/pathology
*Gastrointestinal Microbiome/immunology
Animals
Autoantibodies/immunology
*Immunity, Mucosal
*Bacteria/immunology

@article {pmid40955584,
year = {2025},
author = {Wang, J and Zhao, F and He, L and Xu, X and Zhou, Z and Ren, C and Zhou, G and Guo, Y and Wang, J and Zhou, S and Delgado-Baquerizo, M},
title = {Aboveground Productivity Shapes the Active Soil Microbiome Across China.},
journal = {Global change biology},
volume = {31},
number = {9},
pages = {e70497},
doi = {10.1111/gcb.70497},
pmid = {40955584},
issn = {1365-2486},
support = {42277284//National Natural Science Foundation of China/ ; 2024SF-YBXM-543//Shaanxi Province 2024 Key R&D Plan/ ; 2024K-31//Qinling Hundred Talents Project of Shaanxi Academy of Science/ ; 2025ZY007//2025 central government to guide local science and technology development in Qinghai Province/ ; 202306970056//China Scholarship Council/ ; },
mesh = {*Soil Microbiology ; China ; *Microbiota ; Climate Change ; Soil/chemistry ; Ecosystem ; Forests ; },
abstract = {Soil microbes are the planet's most abundant, diverse, and functionally vital organisms, yet only a small portion of these microbes actively drive soil processes. While resource availability is known to influence microbial physiological traits under multiple soil processes, how aboveground resource input structures the spatial distribution of the soil active microbiome remains virtually unknown. Here, we report the results from a continental standardized soil sampling at 601 sites across major biomes in China. We measured the proportion of the active microbiome (SAM%) using 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) staining by flow cytometry and simultaneously evaluated their main environmental drivers. On average, < 2% of all microbes constitute the active soil microbiome. Forests supported the most active soil microbiomes (> 2%), while cropland harbored the lowest (< 1%). Aboveground productivity, peaking in tropical warmer and wetter regions, was the major environmental factor explaining variation in the active soil microbiome. Our study suggests that a less productive planet may result in drastic reductions in the active soil microbiome with consequences for supporting ecosystem function and biogeochemical cycles under climate change.},
}

*Soil Microbiology
China
*Microbiota
Climate Change
Soil/chemistry
Ecosystem
Forests

@article {pmid40955358,
year = {2025},
author = {Tomar, A and Kumar, C and Parmar, K and Khan, N and Singh, R and Dwivedi, SK and Prasad, D},
title = {Innovative metabolic reprogramming in rice: unlocking drought resilience through microbial consortia interaction and sustainable agriculture.},
journal = {3 Biotech},
volume = {15},
number = {10},
pages = {343},
pmid = {40955358},
issn = {2190-572X},
abstract = {Rice is a global staple food facing climate change challenges, such as drought, salinity, alkalinity, and heat stress. Proteomics, genomics, gene expression, and metabolic changes use adaptation strategies, but translating them into field conditions remains a challenge. This review highlights the role of microbial consortia in drought adaptation, crop resilience, and food security through several drought mitigation strategies. Plants use a "cry for help" strategy to restructure their microbiome, alleviate stress, and improve health and nutrition. Understanding the complex feedback between microbes and plants is crucial for future crop drought resilience. Microbial consortia eliminate stress, such as drought stress, by acclimatizing plants to various tactics, enhancing water uptake. Techniques like UPLS/GC detect profiling and plant growth regulators influenced by microbial consortia under water scarcity. Metabolomics can identify secondary metabolites, chemical signaling, and governing systems in plant groups, contributing to drug development and drought tolerance in cereal crops, such as rice and wheat. Key microbial consortia candidates have been identified for nitrogen-fixing bacteria, phosphate-solubilizing bacteria, mycorrhizal fungi, phytohormones, siderophores, and biofortifying crops with nutrients, such as zinc. Future research is needed to understand molecular pathways and identify microbial species that improve drought tolerance. Key challenges include addressing drought effects on plants, understanding plant-microbial consortia functions, and advancing multiomics, synthetic communities (SynComs), and host-mediated microbiome engineering for drought-resilient agriculture.},
}

@article {pmid40955058,
year = {2025},
author = {Chatterjee, P and Spalinger, MR and Acevedo, C and Santos, AN and Gries, CM and Manz, SM and Canale, V and Shawki, A and Sayoc-Becerra, A and Lei, H and Crawford, MS and Eckmann, L and Borneman, J and McCole, DF},
title = {Intestinal epithelial PTPN2 limits pathobiont colonization by immune-directed antimicrobial responses.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2559029},
doi = {10.1080/19490976.2025.2559029},
pmid = {40955058},
issn = {1949-0984},
mesh = {Animals ; *Protein Tyrosine Phosphatase, Non-Receptor Type 2/genetics/metabolism/immunology ; *Intestinal Mucosa/microbiology/immunology ; Mice, Knockout ; Mice ; *Epithelial Cells/microbiology/immunology ; *Escherichia coli/immunology/growth & development ; *Escherichia coli Infections/immunology/microbiology/genetics ; Humans ; Cytokines/metabolism ; Mice, Inbred C57BL ; Gastrointestinal Microbiome ; Female ; Male ; },
abstract = {Loss of activity of the inflammatory bowel disease (IBD) susceptibility gene, protein tyrosine phosphatase non-receptor type 2 (PTPN2), is associated with altered microbiome composition in both human subjects and mice. Furthermore, expansion of the bacterial pathobiont, adherent-invasive E. coli (AIEC), is strongly linked to IBD pathogenesis. The mechanism by which intestinal epithelial cells (IEC) maintain equilibrium between commensal microbiota and immune cells to restrict invading pathobionts is poorly understood. Here, we investigated the role of IEC-specific PTPN2 in regulating AIEC colonization. Tamoxifen-inducible, intestinal epithelial cell-specific Ptpn2 knockout mice (Ptpn2[∆IEC]) and control Ptpn2[fl/fl] mice were infected with either noninvasive E. coli K12, or fluorescent-tagged mAIEC (mAIEC[red]) for four consecutive days or administered PBS. Subsequently, bacterial colonization in mouse tissues was quantified. mRNA and protein expression were assayed in intestinal epithelial cells (IECs) or whole tissue lysates by PCR and Western blot. Tissue cytokine expression was determined by ELISA. Intestinal barrier function was determined by in vivo administration of 4 kDa FITC-dextran (FD4) or 70kDa Rhodamine-B dextran (RD70) fluorescent probes. Confocal microscopy was used to determine the localization of tight-junction proteins. Ptpn2[∆IEC] mice exhibited increased mAIEC[red] - but not K12 - bacterial load in the distal colon compared to infected Ptpn2[fl/fl] mice. The higher susceptibility to mAIEC[red] infection was associated with altered levels of antimicrobial peptide (AMPs). Ileal RNA expression of the alpha-defensin AMPs, Defa5, and Defa6, as well as MMP7, was significantly lower in Ptpn2[∆IEC] vs. Ptpn2[fl/fl] mice, after mAIEC[red] but not K12 infection. Furthermore, we observed an increased tight junction-regulated permeability determined by elevated in vivo FD4 but not RD70 permeability in Ptpn2[∆IEC]-K12 mice compared to their respective controls. This effect was further exacerbated in Ptpn2[∆IEC] mAIEC-infected mice. Further, Ptpn2[∆IEC] mice displayed lower IL-22, IL-6, IL-17A cytokine expression post mAIEC infection compared to Ptpn2[fl/fl] controls. Recombinant IL-22 reversed the FD4 permeability defect and reduced bacterial burden in Ptpn2[∆IEC] mice post mAIEC challenge. Our findings highlight that the intestinal epithelial PTPN2 is crucial for mucosal immunity and gut homeostasis by promoting anti-bacterial defense mechanisms involving coordinated epithelial-immune responses to restrict pathobiont colonization.},
}

Animals
*Protein Tyrosine Phosphatase, Non-Receptor Type 2/genetics/metabolism/immunology
*Intestinal Mucosa/microbiology/immunology
Mice, Knockout
Mice
*Epithelial Cells/microbiology/immunology
*Escherichia coli/immunology/growth & development
*Escherichia coli Infections/immunology/microbiology/genetics
Humans
Cytokines/metabolism
Mice, Inbred C57BL
Gastrointestinal Microbiome
Female
Male

@article {pmid40954993,
year = {2025},
author = {Park, SL and Kim, MS and Kim, TH},
title = {Gut Microbiome and Estrogen.},
journal = {Journal of menopausal medicine},
volume = {31},
number = {2},
pages = {95-101},
doi = {10.6118/jmm.24024},
pmid = {40954993},
issn = {2288-6478},
support = {/SCH/Soonchunhyang University/Korea ; },
abstract = {Estrogens are steroid hormones that are involved in regulating the growth, development, and functioning of the human reproductive system as well as in controlling the neuroendocrine, skeletal, adipogenesis, and cardiovascular systems. Estrogen is released into the bloodstream in two different states: as a free hormone or in association with proteins such as sex hormone-binding globulin or albumin. Unbound estrogen, which is not bound to proteins, can freely pass through cell membranes without any regulatory constraints. The microbiome is a distinct microbial population that inhabits a well-defined environment characterized by specific physio-chemical properties. It engages in a symbiotic relationship with the host, assisting in internal equilibrium regulation and immune reaction modulation. Over the years, several research investigations have underscored the importance of the microbiome in promoting wellness and preventing illnesses. An alteration in the microbiome, also known as dysbiosis, can disrupt bodily processes and contribute to the onset of ailments such as cardiovascular disorders, cancers, and respiratory conditions. The microbiome plays a crucial role in maintaining human health. Several elements affect the balance of the intestinal microecological system such as dietary habits, medication usage, pathogens, and endocrine factors. Recent research has indicated a disparity between genders in the prevalence of certain diseases associated with the microbiome, with sex hormones playing a crucial role in affecting specific health conditions.},
}

@article {pmid40954473,
year = {2025},
author = {de Jong, YA and Seren, RM and Ramšak Marčeta, V and Checa, A and Petursdottír, DH and Badolati, I and Moeckel, C and Ahmed Osman, O and Hell, E and Huseby, DL and Hughes, D and Wheelock, CE and Garcia, SL and Udekwu, KI and Qazi, KR and Sverremark-Ekström, E},
title = {Impact of early-life human microbiota on the murine host metabolome: insights from a two-generation HMA mouse model and implications for allergic disease.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {575},
pmid = {40954473},
issn = {1471-2180},
abstract = {INTRODUCTION: Human microbiota-associated (HMA) models are used to allow in vivo studies of the human gut microbiome and its effects on host physiology. In particular, alterations in early life microbiota have been linked to allergy development during childhood. In this study, we investigated how pools of human microbiota collected from infants with different allergy risk, thrive in mice and their offspring, as well as how they influence the host metabolome.

METHOD: We used a two-generation HMA mouse model in which dams were colonized with human feces from three groups of infants (n = 19, samples collected during the first 8 weeks of life). In two of the groups, all infants had a strong hereditary risk for allergic disease (n = 12), but only 6 of them developed allergy before 2 years of age. In the third group, which was used as a control, none of the infants had allergic heredity or developed allergy (n = 7). Microbiota trajectories were followed from inoculation to mouse offspring, and metabolic profiles were monitored in several intestinal organs as well as in the serum of the murine offspring.

RESULTS: The human microbiota adapted to the murine host but still presented distinct compositional features, reflecting the original inoculated samples. These microbial differences were mirrored in the mouse offspring metabolome, with group-associated patterns in sphingolipids, acylcarnitines and tryptophan metabolites. Furthermore, the metabolic profiles of the mouse offspring aligned with those observed in fecal water preparations from the corresponding human infant fecal samples.

CONCLUSION: Our findings highlight the significant impact of early-life microbiota on the host metabolome and show that our two-generation HMA model is suitable for studying microbiota‒metabolome relationships relevant to humans. The differences in microbiota‒metabolome correlations between individuals who develop or do not develop allergic disease suggest that an allergic predisposition might be more multifaceted than previously believed.},
}

@article {pmid40954401,
year = {2025},
author = {Mousa, N and Elmetwalli, A and Abdel-Razik, A and Mousa, E and Abdelsalam, M and Elbaz, S and El-Wakeel, N and Eldars, W and Gad, E and Arafa, M and Abdelmaksoud, M and El-Bendary, M and Marei, O and El-Assmy, A and Mousa, A and El-Assmy, A and Shiha, G},
title = {Periodontitis and Metabolic Dysfunction-Associated Steatotic Liver Disease: emphasizing the clinical interplay between hepatologists and dentists.},
journal = {Odontology},
volume = {},
number = {},
pages = {},
pmid = {40954401},
issn = {1618-1255},
abstract = {This narrative review aims to elucidate the connection between periodontitis and Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD), which is currently the most prevalent liver disease. By raising awareness of this link, healthcare providers can enhance their knowledge of the relationship between oral health and liver disease, offering valuable guidance to patients seeking advice from medical and dental professionals. A comprehensive search strategy was implemented to gather relevant literature from various databases, including PubMed, Scopus, and Web of Science. Keywords and controlled vocabulary terms related to MASLD, periodontitis, and their potential connections were used. Emphasis was placed on recent publications to incorporate up-to-date research findings. Various types of studies, such as primary research, systematic reviews, meta-analyses, guidelines, consensus statements, and expert opinions, were considered. The selection of studies focused on understanding the association between MASLD and periodontitis, as well as the underlying mechanisms. Special attention was given to studies exploring the oral-gut-liver axis and the pathogenic links between MASLD and periodontitis. Recent research suggests a possible connection between MASLD and periodontitis, as both conditions share common risk factors such as obesity, insulin resistance, and inflammation. Chronic inflammation associated with periodontitis may contribute to the progression of MASLD by promoting insulin resistance and systemic inflammation. The oral microbiome, which plays a crucial role in periodontitis development, may also influence MASLD pathogenesis. Dysbiosis in the oral microbiome can lead to the translocation of oral bacteria into the bloodstream, triggering systemic inflammation and potentially worsening liver damage in individuals with MASLD. Improving periodontal health can impact the progression of MASLD/MAFLD and enhance patient outcomes. Collaborative care models that integrate dental and medical expertise are crucial for optimal health outcomes in individuals with both conditions.},
}

@article {pmid40954372,
year = {2025},
author = {Jauri, PV and Silva, C and Massa, AM},
title = {Early shifts in soil microbial community structure and functions upon application of a biofertilizer in a kaki (Diospyros kaki) orchard.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {40954372},
issn = {1874-9356},
abstract = {Biofertilizers are key tools for sustainable agriculture and soil health Maintenance, yet their specific effects on soil functions and microbiota remain unclear. In order to address this, we aimed to evaluate how a biofertilizer alters soil microbial communities, physicochemical properties, and functions after 18 months of periodical use in a kaki monoculture. We found that the biofertilizer indirectly reshaped microbial community structure-especially bacterial diversity-likely through interactions with the native microbiome. Functional changes included increased microbial biomass, nitrogen mineralization, and dehydrogenase activity, with reduced acid phosphatase activity. The composition of bacterial and fungal communities exhibited significant differences between biofertilizer-treated soils and control soils across most evaluated taxonomic levels. Biodiversity was altered with biofertilizer application in bacterial communities, while fungal communities were less affected. Microbial co-occurrence networks differed between the two soil treatments, although a few patterns were consistent among treated and control soils. A novel contribution of this work is the integration of co-occurrence network analysis with microbial functional traits, revealing that core microbial networks linked to nitrogen and phosphate cycling persist despite disturbance. These findings highlight the role of microbial biodiversity and community assembly in sustaining soil functions under biofertilizer application.},
}

@article {pmid40954302,
year = {2025},
author = {Li, Y and Ma, A and Johnson, E and Eng, C and De, S and Jiang, S and Li, Z and Spakowicz, D and Ma, Q},
title = {The new microbiome on the block: challenges and opportunities of using human tumor sequencing data to study microbes.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {40954302},
issn = {1548-7105},
support = {P01AI177687//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01GM152585//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R35GM149224//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01GM129066//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; P01CA250957//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; DP2AI171139//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; P01AI177687//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01AI149672//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01GM152585//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U24CA224331//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; K01AG070310//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01CA248741//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R21CA294050//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; INV-002704/GATES/Gates Foundation/United States ; 1046611//American Lung Association (Lung Association)/ ; RSG-23-1023205//American Cancer Society (American Cancer Society, Inc.)/ ; },
abstract = {Microbes within tumors have been recognized and experimentally related to oncogenesis, tumor growth, metastasis and therapeutic responsiveness. Studying the tumor microbiome presents difficulties, as early indications suggest that microbe populations are low in abundance, sparse and highly heterogeneous. Disparate results from computational profiling of the tumor microbiome have cast doubt on the premise of microbes in tumors. Yet decades of experimental evidence support the presence of tumor microbes, at least in a limited number of tumor types. In this Perspective, we discuss the importance of iteratively improving microbe-targeted sequencing techniques, established analytical pipelines, robust computational tools and solid validations to address current challenges and fill existing knowledge gaps. The vast amount of human tumor sequencing data available could greatly enhance systematic investigations of microbiome-tumor interactions with methods to quantify the composition of the tumor microbiome accurately.},
}

@article {pmid40954296,
year = {2025},
author = {Zhang, R and Mirdita, M and Söding, J},
title = {De novo discovery of conserved gene clusters in microbial genomes with Spacedust.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {40954296},
issn = {1548-7105},
support = {CompLifeSci project horizontal4meta//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; CompLifeSci project horizontal4meta//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; RS-2023- 00250470//National Research Foundation of Korea (NRF)/ ; },
abstract = {Metagenomics has revolutionized environmental and human-associated microbiome studies. However, the limited fraction of proteins with known biological processes and molecular functions presents a major bottleneck. In prokaryotes and viruses, evolution favors keeping genes participating in the same biological processes colocalized as conserved gene clusters. Conversely, conservation of gene neighborhood indicates functional association. Here we present Spacedust, a tool for systematic, de novo discovery of conserved gene clusters. To find homologous protein matches, Spacedust uses fast and sensitive structure comparison with Foldseek. Partially conserved clusters are detected using novel clustering and order conservation P values. We demonstrate Spacedust's sensitivity with an all-versus-all analysis of 1,308 bacterial genomes, identifying 72,843 conserved gene clusters containing 58% of the 4.2 million genes. It recovered 95% of antiviral defense system clusters annotated by the specialized tool PADLOC. Spacedust's high sensitivity and speed will facilitate the annotation of large numbers of sequenced bacterial, archaeal and viral genomes.},
}

@article {pmid40954286,
year = {2025},
author = {Jung, S and Bae, H and Song, WS and Chun, Y and Le, J and Alam, Y and Verlande, A and Chun, SK and Kim, J and Kelly, ME and Lopez, ML and Park, SH and Onofre, D and Baek, J and Jang, KH and Rubtsova, VI and Anica, A and Masri, S and Lee, G and Jang, C},
title = {Dietary fibre-adapted gut microbiome clears dietary fructose and reverses hepatic steatosis.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {40954286},
issn = {2522-5812},
support = {R01-AA029124//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R21-AA030358//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; T32GM008620//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; F31DK134173//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; K22-CA234399//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 2021R1A6A3A-14039681//National Research Foundation of Korea (NRF)/ ; 021R1A6A3A14039132//National Research Foundation of Korea (NRF)/ ; RS-2024-00411784//National Research Foundation of Korea (NRF)/ ; 11-23-PDF-03//American Diabetes Association (ADA)/ ; HI19C1352//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/ ; R01CA244519//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; R01CA259370//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; P30CA062203//UC | UC Irvine | Chao Family Comprehensive Cancer Center (CFCCC)/ ; },
abstract = {Excessive consumption of the simple sugar fructose, which induces excessive hepatic lipogenesis and gut dysbiosis, is a risk factor for cardiometabolic diseases. Here we show in male mice that the gut microbiome, when adapted to dietary fibre inulin, catabolizes dietary fructose and mitigates or reverses insulin resistance, hepatic steatosis and fibrosis. Specifically, inulin supplementation, without affecting the host's small intestinal fructose catabolism, promotes the small intestinal microbiome to break down incoming fructose, thereby decreasing hepatic lipogenesis and fructose spillover to the colonic microbiome. Inulin also activates hepatic de novo serine synthesis and cystine uptake, augmenting glutathione production and protecting the liver from fructose-induced lipid peroxidation. These multi-modal effects of inulin are transmittable by the gut microbiome, where Bacteroides acidifaciens acts as a key player. Thus, the gut microbiome, adapted to use inulin (a fructose polymer), efficiently catabolizes dietary monomeric fructose, thereby protecting the host. These findings provide a mechanism for how fibre can facilitate the gut microbiome to mitigate the host's exposure to harmful nutrients and disease progression.},
}

@article {pmid40954201,
year = {2025},
author = {Szabó, G and Eloe-Fadrosh, EA and Pett-Ridge, J and Woyke, T},
title = {A genomic view of Earth's biomes.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
pmid = {40954201},
issn = {1471-0064},
abstract = {Microorganisms are essential to all life on Earth through critical roles in key biological processes and diverse interactions with other organisms that shape ecosystems, drive biogeochemical cycles and influence both human health and environmental health. High-throughput sequencing from environmental samples has revolutionized the understanding of microbial diversity and functions. With vast amounts of genomes now available across Earth's biomes, these data provide a blueprint of microbial life that can be harnessed for a more holistic understanding of microbiome structure and function across the various ecosystems on Earth. Here we review the application of genome-centric approaches, including recent advances in single-cell sequencing and functional profiling, to survey microbial and viral diversity. We highlight some of the most impactful evolutionary and functional discoveries, explore the spatial diversity and temporal dynamics of microorganisms across diverse environments, and discuss genome-enabled insights into host-associated microorganisms.},
}

@article {pmid40954169,
year = {2025},
author = {Celikoglu, M and Raab, C and Vollert, H and Harder, J and Liu, X and Baines, JF and Fluhr, JW and Keck, CM and Infante, VHP and Meinke, MC},
title = {A pilot study on the cutaneous effects of ethanol in a moisturizing cream on non-lesional skin of patients with atopic dermatitis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {32536},
pmid = {40954169},
issn = {2045-2322},
abstract = {Ethanol is widely used in cosmetic formulations as a solvent, preservative, and penetration enhancer, yet its effects on atopic skin remain controversial. This study explores the impact of ethanol in skin care products on skin physiology, microbiome composition and subjective perception. A two-part investigation was conducted: (I) ex vivo analysis using porcine skin models exposed to varying ethanol concentrations, and (II) a double blinded, placebo controlled, randomized clinical pilot study on 9 patients with Atopic Dermatitis (AD) comparing creams with and without 12% ethanol. The ex vivo study revealed that ethanol concentrations above 15% negatively affected epidermal barrier integrity, increasing stratum corneum (SC) permeability and transepidermal water loss (TEWL). In the clinical trial, 12% ethanol demonstrated no significant adverse effects on SC hydration, erythema, pH, or TEWL over 30 days. Microbiome analysis revealed a localized increase in Xanthomonas species associated with ethanol use, while no significant community-wide changes were observed. The implications of increased Xanthomonas abundance in response to the application of a 12% ethanol cream for atopic dermatitis remain unclear. Subjective evaluations reported similar perceptions for both formulations, with no notable exacerbations in non-lesional AD skin. These findings indicate that ethanol in concentrations ≤ 12% is safe for atopic skin.},
}

@article {pmid40953868,
year = {2025},
author = {Thariat, J and Leconte, A and Lequesne, J and Vela, A and Carsuzaa, F and Dejean, C and Renard, S and Pereira, S and Lebars, S and Nadin, L and Plisson, L and Bastit, V and Woisard, V and Hervieu-Klisnick, Z and Lasne-Cardon, A and Clarisse, B},
title = {Flap sparing in postoperative radiotherapy versus standard flap-agnostic radiotherapy of oral cavity cancers (OPTIFLAP): protocol for a de-escalation, randomised, non-inferiority, phase III trial.},
journal = {BMJ open},
volume = {15},
number = {9},
pages = {e109094},
doi = {10.1136/bmjopen-2025-109094},
pmid = {40953868},
issn = {2044-6055},
abstract = {INTRODUCTION: The standard treatment of oral cavity cancers (OCC) relies on surgery and postoperative radiotherapy (poRT) for advanced stages or poor factors. In more than 75% of cases, reconstructive surgery with a flap aims to restore the function lost with tumour resection. Current poRT planning and delineation guidelines omit the presence of a flap. It may be assumed that poRT with flap sparing may allow for reducing radio-induced toxicities and improving functional outcomes, without impairing local primary control. The OPTIFLAP trial assesses non-inferior locoregional control using flap sparing compared with conventional flap-agnostic radiotherapy in patients with OCC, while reducing treatment-related toxicity and improving functional outcomes.

METHODS AND ANALYSIS: The OPTIFLAP study is a French, multicentre, 1:1 randomised, phase III, controlled trial. It will recruit 348 patients with OCC with a flap. Recruitment is active with the first enrolment on 2 July 2025 and is planned over 48 months. The primary outcome is non-inferior 2-year locoregional control rate using flap sparing compared with flap-agnostic radiotherapy (as per standard routine practice) in completely resected OCCs undergoing poRT. Key secondary outcomes include rates of toxicities, locoregional relapse-free survival, progression-free survival, overall survival, quality of life, functional outcomes (assessed by the Performance Status Scales for Head and Neck Cancer, the MD Anderson Dysphagia Inventory (self-questionnaire) and the Phonation Handicap Index (self-questionnaire)), flap doses and outcomes between arms depending on dosimetric parameters. The trial incorporates translational ancillary studies addressing individual radiosensitivity, salivary microbiome evolution, radiomics and dosiomics of flap changes, as well as medico-economic evaluation.

ETHICS AND DISSEMINATION: The study protocol has been approved by the Medical Ethics Committee East III (January 2025; Ref 24.05832.000442) and the French Agency for Medical and Health Products Safety (December 2024; ID-RCB: 2024-A01764-43) and was validated by review boards of all participating centres. Written informed consent will be obtained from all participants. Study results will be published in international peer-reviewed scientific journals and presented at relevant scientific conferences.

TRIAL REGISTRATION NUMBER: NCT06798922.},
}

@article {pmid40953729,
year = {2025},
author = {Yilmaz, N and Gürsoy, UK and Belstrøm, D and Polat, R and Gürsoy, M},
title = {Salivary microbiota in children with and without type 1 diabetes mellitus: A one-year follow-up study.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {106109},
doi = {10.1016/j.jdent.2025.106109},
pmid = {40953729},
issn = {1879-176X},
abstract = {OBJECTIVE: Longitudinal data on the composition of salivary microorganisms in type 1 diabetes mellitus (T1DM) patients are lacking. This study aimed to characterize and compare the salivary microbiota of children with and without T1DM in a longitudinal approach. We hypothesized that the bacterial composition in saliva differs between healthy and T1DM children in a 1-year period.

METHODS: Overall, 55 children (4-15 years old; 26 with T1DM, 29 healthy controls) completed the study. Oral examinations (plaque index, bleeding on probing, and Decayed, Missing, Filled Teeth index) and unstimulated saliva sampling were performed at baseline and after 1 year. Microbial composition was assessed via 16S rRNA gene sequencing (V1-V3 region) and referenced against the Human Oral Microbiome Database.

RESULTS: Beta diversity analysis (Principal coordinate analysis (PCoA)) showed greater separation between groups at baseline than at follow-up. Linear discriminant analysis effect size identified that T1DM was associated with Fusobacterium species, whereas Rothia species associated with health. Alpha diversity indexes (Chao 1, Shannon and Simpson) showed no significant differences between the groups (P>0.05).

CONCLUSION: Our results demonstrated that the salivary microbiota of T1DM children is significantly distinct from healthy controls during 1-year of follow-up. Future studies are needed to reveal whether improved T1DM management benefits microbial composition.

CLINICAL SIGNIFICANCE: The microbial shift in diabetic children may contribute to increased susceptibility to oral diseases, highlighting the importance of preventive dental care in this population.},
}

@article {pmid40953724,
year = {2025},
author = {Lan, T and Zhang, Y and Xie, R and Wu, Q and Wang, H and Du, J and Guo, W},
title = {Aromatic hydrocarbon exposure alters soil microbial communities and redox-driven carbon metabolism.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122845},
doi = {10.1016/j.envres.2025.122845},
pmid = {40953724},
issn = {1096-0953},
abstract = {The environmental behavior and toxicological impacts of benzene, toluene, ethylbenzene, and xylene (BTEX) have been widely studied. Yet their concentration-dependent effects on soil microbial structure, redox dynamics, and metabolism remain insufficiently understood, constraining predictions of ecosystem responses and the development of targeted bioremediation strategies. Here, we explored how exposure to different concentrations of BTEX reshaped microbial community structure and metabolic function by integrating phased amplicon sequencing, metagenomic analysis, and metabolite profiling. BTEX exposure did not significantly alter the overall microbial richness or diversity across treatment groups but substantially changed the taxonomic composition (Stress = 0.096, R = 0.2284, P = 0.0500). It reduced the dominance of Bacillus and enriched various Clostridium spp. closely associated with acetate and butyrate production. At higher BTEX concentrations, Sporolactobacillus was selectively enriched, directing carbon flow toward lactate production. Functionally, BTEX inhibited early reactions in the pentose phosphate pathway (PPP), while increasing the abundance of genes involved in downstream glycolysis and PPP, leading to rapid pyruvate and NADH accumulation. Meanwhile, inhibition of NADH: ubiquinone oxidoreductase indicated a reduced capacity for respiratory NADH turnover. At slight BTEX concentrations, the redox imbalance increased NADH availability, thereby enhancing alcohol synthesis by 38.03% (±29.18%) (P < 0.05). Conversely, high BTEX concentrations enhanced lactate biosynthesis, redirecting carbon and reducing equivalents away from alcohol and acid accumulation (P<0.05). These findings demonstrate that BTEX reshapes microbial redox dynamics and carbon allocation in a concentration-specific manner, providing mechanistic insights into soil microbiome responses to aromatic hydrocarbon pollution and a basis for designing and optimizing future bioremediation strategies.},
}

@article {pmid40953715,
year = {2025},
author = {Lee, K and Kim, H and Wang, JH},
title = {Clinical evidence linking osteoporosis and the gut microbiome in postmenopausal females: A systematic review.},
journal = {Bone},
volume = {},
number = {},
pages = {117644},
doi = {10.1016/j.bone.2025.117644},
pmid = {40953715},
issn = {1873-2763},
abstract = {BACKGROUND: Recent studies have highlighted the intricate relationship between gut microbiome (GM) and osteoporosis (OP), particularly in postmenopausal females. However, the precise mechanisms underlying this association remain unclear.

MATERIALS AND METHODS: This retrospective review and meta-analysis aimed to elucidate the role of GM in postmenopausal OP (PMO) by synthesizing clinical findings from recent literature. A systematic search of four databases (PubMed, Google Scholar, Cochrane Library, and Web of Science) identified 16 relevant clinical studies published between January 2000 and July 2025.

RESULTS: A total of 1520 postmenopausal females (mean age: 59.25 ± 6.63 years) were included, comprising 656 patients with PMO and 864 healthy controls (HC). A meta-analysis of gut microbial α diversity revealed a significant reduction (p = 0.04) in the abundance-based coverage estimator (ACE) index in patients with PMO, indicating a loss of microbial richness. At the same time, β-diversity findings were inconsistent across studies. Taxonomic analysis confirmed differences between patients and HC at the phylum and genus levels. PMO is characterized by a significant increase in primary bile acids and a reduction in tryptophan and daidzein metabolism at the metabolic level. Additionally, Patients with PMO exhibited markedly lower serum estradiol levels, higher levels of lipopolysaccharide and tumor necrosis factor-α, a higher proportion of Th17 cells, and a lower Treg cell population, indicating a pro-inflammatory state.

CONCLUSION: Overall, this review provides a comprehensive synthesis of current clinical evidence on the role of GM in PMO, emphasizing its potential impact on bone metabolism. Given these findings, targeting the composition of gut microbiota and its metabolites may offer a promising therapeutic strategy for mitigating OP in postmenopausal females.},
}

@article {pmid40953322,
year = {2025},
author = {Li, B and Yeganeh, M and Lee, D and Chusilp, S and Balsamo, F and Ganji, N and Wang, CY and Zito, A and Biouss, G and Pierro, A},
title = {Exploring the Complex Pathophysiology of Necrotizing Enterocolitis in Preterm Neonates.},
journal = {Annual review of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-pathmechdis-070224-014223},
pmid = {40953322},
issn = {1553-4014},
abstract = {Necrotizing enterocolitis (NEC) is the most common gastrointestinal emergency in preterm neonates, with a mortality rate of 30-50% in advanced cases. Despite decades of research, its multifactorial pathophysiology remains incompletely understood. This review summarizes recent advances in NEC research and proposes an integrative theoretical framework for its pathogenesis. We examine key contributing factors, including intestinal vascular development, mucosal immunity, intestinal regeneration, the enteric nervous system, and the gut microbiome, highlighting how prematurity disrupts these processes and predisposes neonates to NEC. Furthermore, we propose a sequential model of NEC pathogenesis, hypothesizing that impaired intestinal microcirculation in preterm neonates compromises blood flow in response to enteral feeding, leading to localized ischemia. This initiates epithelial barrier dysfunction, exacerbates inflammatory responses, impairs intestinal regeneration, and disrupts enteric nervous system function, collectively driving NEC progression. By integrating experimental and clinical findings, we provide a comprehensive perspective on NEC initiation in preterm neonates and identify potential avenues for future research and therapeutic interventions.},
}

@article {pmid40953197,
year = {2025},
author = {Ogarkov, O and Orlova, E and Suzdalnitsky, A and Mokrousov, I},
title = {Microbiota of the Lung Tuberculoma: Paucibacillary Bacterial Community.},
journal = {International journal of mycobacteriology},
volume = {14},
number = {3},
pages = {209-218},
pmid = {40953197},
issn = {2212-554X},
abstract = {Caseum, the central necrotic material of tuberculous lesions, is a reservoir of drug-resistant persisting Mycobacterium tuberculosis (MTB). However, tubercle bacilli are not the only bacterial inhabitants of this necrosis. We discuss the available data on metagenomic and amplicon sequencing of 16S rRNA of caseous necrosis from surgically excised tuberculosis (TB) foci. This approach facilitated the characterization of the biodiversity and the potential biochemical pathways of these bacterial communities. We postulate that in terms of MTB content relative to satellite anaerobic lipophilic bacteria, caseum may present two distinct terminal states. "True" TB necrosis, containing 99.9% tubercle bacilli, and a polymicrobial community wherein anaerobic lipophilic bacteria predominate over MTB. Isolation from caseum and genomic characterization of several Corynebacterium and Staphylococcus species support this concept.},
}

@article {pmid40953029,
year = {2025},
author = {Park, R and Chevalier, C and Kieser, S and Marizzoni, M and Paquis, A and Armand, S and Scheffler, M and Allali, G and Assal, F and Momjian, S and Frisoni, GB},
title = {Gut microbiome signatures in iNPH: Insights from a shotgun metagenomics study.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0330251},
doi = {10.1371/journal.pone.0330251},
pmid = {40953029},
issn = {1932-6203},
abstract = {Idiopathic normal pressure hydrocephalus (iNPH), a leading cause of reversible dementia in older adults, is marked by ventriculomegaly, gait disturbances, cognitive decline, and urinary incontinence. Emerging evidence suggests that gut dysbiosis (microbial imbalance) may influence neuroinflammation and cerebrospinal fluid dynamics, potentially contributing to glymphatic system dysfunction and ventricular enlargement. This study used shotgun metagenomics to analyze the gut microbiome in iNPH patients (n = 18) compared to healthy controls (n = 50), individuals with ventriculomegaly but no iNPH symptoms (n = 50), and Alzheimer's disease patients (n = 50). Microbiome analysis showed an enrichment of species previously linked to various disease states, such as Enterocloster bolteae and Ruminococcus gnavus, indicating general dysbiosis. In contrast, enrichment of specific taxa, including Evtepia gabavorous and Cuneatibacter sp., were specifically associated with iNPH clinical traits, pointing to possible disease-specific microbial markers. Functional analysis showed enrichment of pathways related to carbohydrate and amino acid metabolism, including the S-adenosyl-L-methionine superpathway, implicating inflammatory and immune processes. These findings suggest distinct gut microbiome signatures in iNPH, offering insights into potential gut-brain interactions that may contribute to the disorder's pathophysiology and highlighting possible targets for future therapeutic strategies.},
}

@article {pmid40952532,
year = {2025},
author = {Manjarrez-Rascón, DM and Muñoz-Ramirez, ZY and Carrillo-Campos, J and Ortiz-Aguirre, I and González-Escobedo, R},
title = {Spatial variation and composition of bacterial communities in a cave system from Northern Mexico.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {9},
pages = {326},
pmid = {40952532},
issn = {1573-0972},
abstract = {Caves are oligotrophic, light-deprived ecosystems that host highly specialized and diverse microbial communities playing critical roles in biogeochemical cycling and ecological stability. In this study, we present the first comprehensive characterization of bacterial communities within the Nombre de Dios Caves in Chihuahua, northern Mexico. Using full-length 16S rRNA gene sequencing with PacBio HiFi technology, we analyzed bacterial diversity across five cave chambers. A total of 36 bacterial phyla, including 822 genera, were identified, with Bacteroidota, Pseudomonadota, and Bacillota being the most dominant. At the genus level, JC017, Staphylococcus, Crocosphaera, and Enterobacter were among the most abundant taxa. Alpha diversity analyses revealed significant differences in Shannon diversity and evenness, suggesting that local chamber-specific factors may influence bacterial richness and community balance. Similarly, beta diversity analyses showed clear compositional differences between chambers, particularly in the palm tree and bathroom chambers, the latter being notably isolated from tourist access. This spatial variation highlights the influence of environmental heterogeneity and human presence on microbial community structure. The microbial assemblages included ecologically important genera such as Crocosphaera and Nodosilinea, known for nitrogen fixation, exopolysaccharide production, and biofilm development. Clinically relevant genera, including Escherichia, Klebsiella, Staphylococcus, and Enterococcus, were also detected, suggesting the possible introduction of allochthonous microbes through anthropogenic activity. These findings underscore the ecological and public health significance of cave microbiomes and offer valuable insights for microbial monitoring and conservation strategies in fragile karst environments.},
}

@article {pmid40952160,
year = {2025},
author = {Xu, Q and Zhang, Y and Tao, S},
title = {Functional dynamics reveal the response of the crabapple (Malus sp.) phyllosphere microbiome to Gymnosporangium yamadae infection.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0084325},
doi = {10.1128/msystems.00843-25},
pmid = {40952160},
issn = {2379-5077},
abstract = {The phyllosphere microbiome plays a vital role in plant defense against airborne pathogens. In this study, we investigated microbial dynamics of crabapple (Malus 'Kelsey') phyllosphere across six stages of Gymnosporangium yamadae infection using metatranscriptomic sequencing. Infected leaves exhibited increased transcriptional alpha diversity of fungi, bacteria, and viruses, with a notable negative correlation between fungal and bacterial diversity. Microbial taxa in diseased leaves exhibited heightened transcriptional activity compared with healthy counterparts, with fungi progressively dominating the microbial community. Functional co-occurrence networks revealed increased complexity in infected leaves, suggesting a potential reorganization of the microbial interactions in response to pathogen invasion. These structural shifts were accompanied by significant functional changes, as revealed by functional annotation and random forest modeling, which showed significantly enhanced microbial carbohydrate metabolism and upregulated plant cell wall-degrading enzymes (e.g., PL3, CE8, and CE5) in diseased leaves. Key transcripts associated with these functions, originating from Termitomyces sp. J132 and Alternaria alternata, were opportunistically expressed and significantly positively correlated with host flavonoid glycosides, which serve as markers of rust lesion development. Additionally, diseased leaves showed activation of microbial pathways related to aromatic compound degradation and ascorbate metabolism, potentially contributing to redox homeostasis under host defense stress. At later infection stages, we detected high expression of genes encoding cell wall-degrading enzymes in Saitozyma podzolica. Together, our findings underscore the dynamic, functional role of the phyllosphere microbiome in modulating plant-pathogen interactions and shaping disease progression, providing a foundation for microbiome-informed strategies to enhance plant disease resistance.IMPORTANCEOur study reveals stage-specific shifts in the transcriptional activity and functional capacity of the crabapple phyllosphere microbiome during Gymnosporangium yamadae infection. We identified key microbial taxa potentially involved in pathogen facilitation or antagonism and elucidated their roles in plant-pathogen interactions. These findings highlight the importance of the phyllosphere microbiome in regulating plant health and suggest new avenues for microbiome-based approaches to improving plant disease resilience.},
}

@article {pmid40952134,
year = {2025},
author = {Horinouchi, M},
title = {Identification of dehydrogenase, hydratase, and aldolase responsible for the propionyl residue removal in degradation of cholic acid C-17 side chain in Comamonas testosteroni TA441.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0030825},
doi = {10.1128/spectrum.00308-25},
pmid = {40952134},
issn = {2165-0497},
abstract = {Bacterial steroid degradation is gaining attention for its diverse roles, such as Mycobacterium tuberculosis's reliance on the degradation of the C17 side chain of cholesterol for survival in host environments. ORF40-44 of Comamonas testosteroni TA441, previously characterized for its A-, B-, C-, and D-ring cleavage pathways, were hypothesized to correspond to the igr operon of M. tuberculosis, encoding the dehydrogenase ChsE1E2, hydratase ChsH1H2MaoC, and aldolase Ltp2 ChsH2DUF35, responsible for propionyl residue removal in the degradation of the cholic acid C17 side chain. However, low amino acid identity between the corresponding enzymes precluded functional assignment without experimental evidence. In this study, we generated gene-disrupted mutants of ORF40-44 and demonstrated that ORF41/ORF44, ORF40/ORF42, and ORF43 encode the dehydrogenase, hydratase, and aldolase, respectively. ORF40 encodes a bifunctional protein comprising MaoC and DUF35 domains. The MaoC domain of ORF40 and the ORF42-encoded protein form the hydratase, while the DUF35 domain is essential for aldolase activity. A mutant expressing ORF40MaoC and ORF40DUF35 separately exhibited both hydratase and aldolase activities, suggesting these activities do not require a strictly formed complex of hydratase and aldolase. However, efficient propionyl residue removal appears to depend on the proper formation of each enzymatic complex, including ChsE1E2, ChsH1H2MaoC, and Ltp2ChsH2DUF35. Although (ChsE1-ChsE2)2 does not form a stable complex with (ChsH1-ChsH2MaoC)2-(Ltp2-ChsH2DUF35)2, some degree of interaction was suggested. AlphaFold-predicted three-dimensional structures of the TA441 enzymes and their complexes revealed striking similarities to those of M. tuberculosis, despite low amino acid identities. These findings shed light on the structural and functional conservation of bacterial steroid-degrading enzymes.IMPORTANCEResearch on bacterial steroid degradation began over 50 years ago, primarily to produce substrates for steroid drugs. Recently, the role of steroid-degrading bacteria in human health has garnered increasing attention. Comamonas testosteroni TA441 is a prominent model organism for studying aerobic steroid degradation, with its overall pathways for A-, B-, C-, and D-ring cleavage already elucidated. In this study, we identified the mechanism for removing the propionyl residue in the degradation of the cholic acid C17 side chain, a crucial step in degrading steroids with a C17 side chain, such as cholic acid, cholesterol, and other biologically significant compounds in animals and plants. The functions and structures of the identified enzymes show remarkable similarity to those in Mycobacterium tuberculosis. These findings suggest that insights gained from TA441 could provide valuable clues for understanding M. tuberculosis steroid metabolism and the broader ecological and health-related implications of bacterial steroid degradation.},
}

@article {pmid40952102,
year = {2025},
author = {Guillén Matus, DG and Donaghy, CM and Vijayan, N and Lane, ZT and Howell, M and Glavin, GG and Angeles-Boza, AM and Nyholm, SV and Balunas, MJ},
title = {Multi-omics analysis reveals important role for microbial-derived metabolites from Botryllus schlosseri in metal interactions.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0079325},
doi = {10.1128/msystems.00793-25},
pmid = {40952102},
issn = {2379-5077},
abstract = {Marine microbial communities govern many of the biological and chemical processes in the ocean, including element cycles, ecosystem health, and disease. Marine organisms are surrounded by microbes, with complex molecular interactions occurring between bacterial symbionts, eukaryotic hosts, and their pathogens or prey. Trace metals in the ocean can be either beneficial or detrimental to marine life depending on their concentrations and bioavailability. Multiple marine tunicate species are known to bioaccumulate trace metals in their mantel, and research suggests that tunicate microbiota plays an important role in this process. Botryllus schlosseri, a marine colonial tunicate, has become a model organism for cellular and developmental studies, yet its ecological interactions are still not well understood. Using an integrated multidisciplinary approach, we established a comprehensive baseline and explored correlations between members of the B. schlosseri microbiome, metabolome, and metallome to elucidate the ecological effects of trace metals in host-microbe-pathogen interactions. We identified significant correlations between metals, including manganese, nickel, cerium, zinc, and cobalt, with various metabolites and bacterial taxa. These findings offer insights into B. schlosseri's biological and chemical interactions with microorganisms and their environment, contributing to bridging the knowledge gap of host-microbiome-environment interactions and establishing a foundation for continuing research on the ecological effects of trace metals in these biological systems.IMPORTANCEGiven the importance of marine invertebrates and their microbial communities in marine ecosystems, we sought to characterize the largely unknown microbial associates, metal sequestration, and metabolite production of the marine colonial tunicate, Botryllus schlosseri, a model organism for cellular and developmental studies. Using an integrated multidisciplinary approach, we identified significant correlations between metals, metabolites, and bacterial taxa. B. schlosseri tissue was highly enriched in metals compared to seawater, and B. schlosseri microbiome beta-diversity was significantly different from seawater. We also introduced the concept of the pan-metabolome to classify metabolites based on their presence or absence across complex samples and found microbial metabolites in both the core and flexible metabolome. These findings offer insights into B. schlosseri's biological and chemical interactions with microorganisms and their environment, bridging the knowledge gap of host-microbiome-environment interactions and establishing a foundation for continuing research on the ecological effects of trace metals in these biological systems.},
}

@article {pmid40952003,
year = {2025},
author = {Sun, T and Zheng, Q and Huang, R and Yang, L and Liu, Z and Zhang, Z and Liu, X and Yang, H and Li, X and Tong, J and Zhu, L},
title = {Exploring cervicovaginal microbiome differences between single and multiple endometrial polyps: implications for non-invasive classification.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0002325},
doi = {10.1128/msystems.00023-25},
pmid = {40952003},
issn = {2379-5077},
abstract = {Single and multiple endometrial polyps (EP) are common gynecological conditions with differing recurrence rates, influencing clinical treatment decisions. This study aimed to characterize the reproductive tract microbiome in both subtypes to support the development of methods for the non-invasive categorization of EPs. Using metagenomic sequencing, we analyzed vaginal and cervical samples from 27 reproductive-aged patients with single EP and 22 with multiple EP. Compared with controls and multiple EP cases, single EP vaginal and cervical samples exhibited a lower percentage of community state types (CST) I and II. Sneathia amnii was identified as a characteristic species in both the vagina (P = 0.0051) and cervix (P = 0.0398) of single EP patients compared with controls. Mesorhizobium sp. (vaginal P = 0.0110, cervical P = 0.0210), Acinetobacter baumannii (vaginal P = 8.0 × 10[-5], cervical P = 0.0314), and Pasteurella multocida (vaginal P = 0.0173, cervical P = 0.0210) were enriched in single EP compared with multiple EP. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of vaginal microbiome revealed unique pathways in single EP, including aminoacyl-tRNA biosynthesis, pantothenate and coenzyme A (CoA) synthesis, pyrimidine metabolism, glycolysis/gluconeogenesis, and biosynthesis of phenylalanine, tyrosine, and tryptophan. Using a random forest model, we further selected microbiota and clinical parameters to differentiate single and multiple EPs, thus achieving an area under curve (AUC) of 0.861. Our findings characterized the composition of the cervicovaginal microbiota of single and multiple EPs and proposed biomarkers for their non-invasive classification based on a random forest model.IMPORTANCEThe prevalence rate of endometrial polyps (EPs), a common gynecological condition, varies between 7.8% and 34.9%. Multiple EPs are associated with higher recurrence rates and chronic endometritis than single EPs and thus require more aggressive clinical interventions. However, only laparoscopic surgery can accurately identify single and multiple polyps. Non-invasive adjunctive diagnostic methods can aid in altering surgical indications preoperatively. Using metagenomic sequencing, we thoroughly analyzed the vaginal and cervical samples of 27 single EP and 22 multiple EP patients of reproductive age. We then identified distinct microbial patterns in the single and multiple samples, which were crucial for understanding EP pathogenesis and its association with gynecological health. Using a random forest model, key bacterial taxa that differentiate single and multiple EPs were identified with high accuracy. These could potentially serve as non-invasive diagnostic biomarkers. This research delineates the cervicovaginal microbiome of the reproductive tract in EP patients, offering a basis for developing non-invasive diagnostic tools and personalized treatment strategies.},
}

@article {pmid40952002,
year = {2025},
author = {Guan, R and Garrido-Oter, R},
title = {Integrated diversity and network analyses reveal drivers of microbiome dynamics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0056425},
doi = {10.1128/msystems.00564-25},
pmid = {40952002},
issn = {2379-5077},
abstract = {UNLABELLED: Microbial communities are key components of ecosystems, where interactions among microbes drive biodiversity and productivity. An increased number of microbiome data sets are available, owing to advances in sequencing; however, standard analyses often focus on community composition, neglecting the complex interactions between co-occurring microbes. To address this, we developed a computational framework integrating compositional and co-occurrence network analyses. We applied this approach to extensive microbial amplicon data sets, focusing on plant microbiota, which typically exhibits high diversity and remains challenging to characterize due to the large number of low-abundance taxa. We show that identifying a subset of representative microbial taxa captures the overall community structure and increases the statistical power. From these taxa, we inferred a large-scale co-occurrence network and clustered microbes with co-varying abundances into units for diversity measurement. This approach not only reduces unexplained variance in diversity assessments but also captures the key microbe-microbe relationships that govern assembly patterns. Furthermore, we introduced a bootstrap- and permutation-based statistical approach to compare microbial networks from diverse conditions. Our method robustly distinguishes meaningful differences and pinpoints specific microbes and features driving those differences. These results highlight the importance of incorporating microbe-microbe interactions in microbiota studies, leading to more accurate and ecologically meaningful insights. Our framework, available as an R package ("mina"), enables researchers to identify condition-specific interactions via network comparison and gain a deeper understanding of community ecology. With broad applicability beyond plant systems, this package provides a valuable tool for leveraging microbiome data across disciplines, from agriculture to ecosystem resilience and human health.

IMPORTANCE: Understanding microbiome dynamics requires capturing not only changes in microbial composition but also interactions between community members. Traditional approaches frequently overlook microbe-microbe interactions, limiting their ecological interpretation. Here, we introduce a novel computational framework that integrates compositional data with network-based analyses, significantly improving the detection of biologically meaningful patterns in community variation. By applying this framework to a large data set from the plant microbiota, we identify representative groups of interacting microbes driving differences across microhabitats and environmental conditions. Our analysis framework, implemented in an R package "mina," provides robust tools allowing researchers to assess statistical differences between microbial networks and detect condition-specific interactions. Broadly applicable to microbiome data sets, our framework is aimed at enabling advances in our understanding of microbial interactions within complex communities.},
}

@article {pmid40952001,
year = {2025},
author = {Raich, SS and Majzoub, ME and Haifer, C and Paramsothy, S and Shamim, MMI and Borody, TJ and Leong, RW and Kaakoush, NO},
title = {Bacterial taxonomic and functional changes following oral lyophilized donor fecal microbiota transplantation in patients with ulcerative colitis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0099125},
doi = {10.1128/msystems.00991-25},
pmid = {40952001},
issn = {2379-5077},
abstract = {UNLABELLED: Oral lyophilized fecal microbiota transplantation (FMT) can induce remission in patients with active ulcerative colitis (UC); however, our understanding of how this form of FMT alters the patient microbiome remains limited. Here, we analyzed data from a recent randomized, double-blind, placebo-controlled clinical trial of FMT in UC to assess donor species colonization and factors responsible for efficacy using this form of therapy. The gut microbiome of donors and patients was profiled longitudinally using deep shotgun metagenomic sequencing, and microbiome diversity, species-genome bin presence, functional profiles, and the resistome were studied. The gut microbiome of patients treated with oral lyophilized FMT significantly increased in species-genome bin richness and shifted in composition toward the donor profiles; this was not observed in patients receiving placebo. While species-genome bin richness was not associated with clinical response in this trial, we identified donor- and patient-specific features associated with the induction of remission and maintenance of response. However, the presence of a Clostridium species-genome bin, as well as L-citrulline biosynthesis contributed by Alistipes spp., was seen in responders treated by either donor. Several of the above outcomes were found to be consistent when data were analyzed at the level of metagenome-assembled genomes. FMT was also found to deplete the resistome within patients treated with antibiotics to levels lower than the UC baseline. Single donor oral lyophilized FMT substantially modifies taxonomic diversity and composition as well as microbiome function and the resistome in patients with UC, with several features identified as strongly linked to response regardless of the donor used.

IMPORTANCE: There is a limited amount of work examining the effects of oral lyophilized fecal microbiota transplantation (FMT) on the microbiome of patients with ulcerative colitis (UC), and less so studies examining species-level dynamics and functional changes using this form of FMT. We performed deep shotgun metagenomic sequencing to provide an in-depth species-genome bin-level analysis of the microbiome of patients with UC receiving oral lyophilized FMT from a single donor. We identified key taxonomic and functional features that transferred into patients and were associated with clinical response. We also determined how FMT impacts the resistome of patients with UC. We believe these findings will be important in ongoing efforts to not only improve the efficacy of FMT in UC but also allow for the transition to defined microbial therapeutics, foregoing the need for FMT donors.},
}

@article {pmid40951971,
year = {2025},
author = {Freitas, AC and Li, G and Shawon, J and Qamar, H and Pell, LG and Kabir, M and Oduaran, OH and Puebla-Barragan, S and Bassani, DG and O'Callaghan, KM and Onuora, JC and Loutet, MG and Heasley, C and Starke, CWE and Mahmud, AA and Hamer, DH and Pullenayegum, E and Hossain, MI and Siddiqui, MM and Islam, MS and Sherman, PM and Shah, PS and Gaffar, SMA and Sultana, S and Morris, SK and Ahmed, T and Haque, R and Sarker, SA and Roth, DE},
title = {Abundance of Bifidobacterium species in the infant gut microbiota and associations with maternal-infant characteristics in Dhaka, Bangladesh.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0031425},
doi = {10.1128/msphere.00314-25},
pmid = {40951971},
issn = {2379-5042},
abstract = {The early infant gut microbiota is generally dominated by bifidobacteria, but there is substantial variation at the (sub)species level. Patterns of postnatal Bifidobacterium subspecies colonization in low- or middle-income countries have not been widely studied. We used (sub)species-specific qPCR to quantify B. infantis (n = 1132), B. longum (n = 364), and B. breve (n = 399) in stool samples from infants (0-6 months of age) in urban Dhaka, Bangladesh. B. infantis absolute abundance started low at birth but increased in the first two months, whereas B. longum and B. breve abundances remained comparatively low. B. infantis emerged earlier in infants delivered by C-section, but by ~2 months of age, infants delivered by C-section or vaginally had similar B. infantis absolute abundances. Infant antibiotic exposure (ever vs. never), human milk feeding patterns (exclusive, predominant, and partial), and detection of maternal stool B. infantis were not associated with infant B. infantis. In settings where B. infantis is widespread, its patterns of postnatal colonization can be used to inform the design of targeted microbiota-modifying interventions in infancy.IMPORTANCEBifidobacteria are considered to be an important member of the early infant gut microbiota, but several factors may influence the timing of their emergence and overall abundance. Moreover, bifidobacteria abundance varies considerably between different species and subspecies, underscoring the importance of techniques that enable sub-speciation. B. longum subspecies infantis (B. infantis) is thought to have several health-promoting properties, and despite growing interest in the use of B. infantis to promote health (e.g., probiotics), relatively few studies have explored its natural patterns of colonization, particularly in low- and middle-income countries. By applying (sub)species-specific qPCR, we precisely tracked the timing of emergence, longitudinal abundance patterns, and ecological dynamics of B. infantis, B. longum, and B. breve in the postnatal period, which provided new insights to inform the design of targeted microbiota-modifying interventions in early infancy.},
}

@article {pmid40951970,
year = {2025},
author = {Guan, Y and Berne, E and Hennessy, RC and Garbeva, P and Nicolaisen, MH and Bak, F},
title = {NRPS gene dynamics in the wheat rhizoplane show increased proportion of viscosin NRPS genes of importance for root colonization during drought.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0085224},
doi = {10.1128/msphere.00852-24},
pmid = {40951970},
issn = {2379-5042},
abstract = {Secondary metabolites are bioactive compounds, diverse in structure, with versatile ecological functions, including key roles in mediating interactions between microorganisms and plants. Importantly, these compounds can promote the colonization of plant surfaces, such as roots, or modulate root exudates to enhance microbial recruitment and establishment. However, owing to the vast diversity of secondary metabolites, their importance in plant root colonization-particularly under stress conditions, such as drought-remains unclear. To determine the involvement of some of these secondary metabolites in root colonization, we used amplicon sequencing targeting the adenylation domain of the non-ribosomal peptide synthases (NRPSs) and the 16S rRNA gene from the rhizoplane of wheat grown in soil under normal and drought stress conditions. Results showed that drought transiently affected the bacterial community composition and the NRPS composition in the rhizoplane. We observed that drought selected for distinct groups of siderophores from different taxonomical groups, enriching for Streptomyces and depleting Pseudomonas siderophores. In addition, drought enriched Pseudomonas-derived NRPS genes encoding viscosin, a cyclic lipopeptide with biosurfactant properties, indicating that compounds linked to motility and colonization provide a competitive advantage during rhizoplane colonization under drought stress conditions. This observation was experimentally confirmed using the viscosin-producing P. fluorescens SBW25 and its viscosin-deficient mutant. A higher abundance of SBW25 colonized the roots under drought stress conditions compared to the viscosin-deficient mutant. In summary, our work demonstrates the potential for amplicon sequencing of NRPS genes, coupled with in planta experiments, to elucidate the importance of secondary metabolites in root colonization.IMPORTANCETo harness beneficial plant-microbe interactions for improved plant resilience, we need to advance our understanding of key factors required for successful root colonization. Bacterial-produced secondary metabolites are important in plant-microbe interactions; thus, targeting these genes generates new knowledge that is essential for leveraging bacteria for sustainable agriculture. We used amplicon sequencing of the NRPS A domain on the rhizoplane of wheat exposed to drought stress to identify important secondary metabolites in plant-microbe interactions during drought. We show that the siderophores respond differently to drought stress depending on taxonomic affiliation and that the potential to synthesize viscosin increases root colonization. Importantly, this study demonstrates the potential of amplicon sequencing of NRPS genes to reveal specific secondary metabolites involved in root colonization, particularly in relation to drought stress, and highlights how the resolution provided by this approach can link specific compounds to a specific stress condition in a soil system.},
}

@article {pmid40951793,
year = {2025},
author = {Goetz, SL and Glen, AK and Glusman, G},
title = {MicrobiomeKG: bridging microbiome research and host health through knowledge graphs.},
journal = {Frontiers in systems biology},
volume = {5},
number = {},
pages = {1544432},
pmid = {40951793},
issn = {2674-0702},
abstract = {The microbiome represents a complex community of trillions of microorganisms residing in various body parts and plays critical roles in maintaining host health and wellbeing. Understanding the interactions between microbiota and their host offers valuable insights into potential strategies for promoting health, including microbiome-targeted interventions. We have created MicrobiomeKG, a knowledge graph for microbiome research, that bridges various taxa and microbial pathways with host health. This novel knowledge graph derives algorithmically generated knowledge assertions from the supplementary tables that support published microbiome papers. By identifying knowledge assertions from supplementary tables and expressing them as knowledge graphs, we are casting this valuable content into a format that is ideal for hypothesis generation. To address the high heterogeneity of study contexts, methodologies, and reporting standards, we leveraged neural networks to implement a standardized edge scoring system, which we use to perform centrality analyses. We present three example use cases: linking helminth infections with non-alcoholic fatty-liver disease via microbial taxa, exploring connections between the Alistipes genus and inflammation, and identifying the Bifidobacterium genus as the most central connection with attention deficit hyperactivity disorder. MicrobiomeKG is deployed for integrative analysis and hypothesis generation, both programmatically and via the Biomedical Data Translator ecosystem. By bridging data gaps and facilitating the discovery of new biological relationships, MicrobiomeKG will help advance personalized medicine through a deeper understanding of the microbial contributions to human health and disease mechanisms.},
}

@article {pmid40951757,
year = {2025},
author = {Gupta, S and Angrup, A and Rana, SS and Batra, G and Rana, N and Ramola, M and Vashist, T and Bisht, K and Monga, N and Jolly, SS and Singla, M and Sareen, S and Goyal, A and Duseja, RN},
title = {Microbial overlap in dental plaque and tumor tissue of esophageal cancer patients: A pilot study.},
journal = {Journal of Indian Society of Periodontology},
volume = {29},
number = {2},
pages = {153-163},
pmid = {40951757},
issn = {0972-124X},
abstract = {INTRODUCTION: Microbial dysbiosis has been shown to be involved in various types of gastrointestinal cancers, but there is a dearth of strong studies linking the oral microbiome imbalance with esophageal cancer (EC).

OBJECTIVES: The main objective of the study was to identify the link between oral microbiome and EC.

MATERIALS AND METHODS: Twelve suspected EC and two healthy control patients were recruited. After the histological confirmation of EC, four confirmed EC patient samples and two healthy control samples were subjected to 16S metagenomics study using the Oxford Nanopore Technology sequencing platform.

RESULTS: Species richness of microbial community was higher in the healthy controls followed by diseased plaque, tumor tissue and adjacent tissue. Bacillota, Pseudomonata, Fusobacteriota, Bacteroidota, and Campylobacterota were the major phyla identified in all the groups. Majorly prevalent genera (core microbiome analysis) in all the groups were Streptococcus, Salmonella, Bacillus, Enterococcus, Veillonella, Klebsiella, Clostridioides, Prevotella, Gemella, Selenomonas, Firmicutes, and Proteobacteria followed by Bacteroidetes and Fusobacteria.

CONCLUSION: Our study suggests an association between oral microbiome and EC. The prevalence of same microbial genus in the oral cavity (dental plaque) and tumor tissue depicts a possible link. Our study opens the plausible microbe-based biomarker screening of EC.},
}

@article {pmid40951721,
year = {2025},
author = {Passadakis, G and Neophytou, C and Davidopoulou, S and Papadimitriou, K},
title = {Effectiveness of Probiotics in Managing Oral Halitosis: A Systematic Review of Randomized Controlled Trials.},
journal = {Journal of International Society of Preventive & Community Dentistry},
volume = {15},
number = {4},
pages = {301-312},
pmid = {40951721},
issn = {2231-0762},
abstract = {AIM: Halitosis, characterized by volatile sulfur compound (VSC) production, is a prevalent oral health concern affecting 31.8% of the global population. Conventional treatments such as chlorhexidine-based mouthwashes offer temporary relief, but probiotics have emerged as a promising biological therapy by modulating oral microbiota. We aimed to systematically evaluate the efficacy of probiotic monotherapy in reducing halitosis-related VSC levels and organoleptic test (OLT) scores in randomized controlled trials (RCTs).

MATERIALS AND METHODS: A comprehensive database search (PubMed, Scopus, ClinicalTrials.gov, and gray literature) was conducted following PRISMA guidelines. The review protocol was prospectively registered with the Open Science Framework (OSF). Only RCTs comparing probiotics to placebo in systemically and periodontally healthy adults were included. Primary outcomes were changes in VSC levels and OLT scores, assessed using halimeters, Oral Chroma devices, or OLT evaluation. Risk of bias was assessed using the Cochrane RoB 2 tool.

RESULTS: Six RCTs (n = 360 participants) met the inclusion criteria. Five studies demonstrated significant VSC reduction after probiotic intervention (P < 0.05). Three studies reported OLT score improvements, particularly with Streptococcus salivarius K12 and Weissella cibaria. Four studies confirmed microbiome alterations, with the effects of probiotics persisting post-treatment. No serious adverse effects were reported.

CONCLUSION: Probiotics significantly reduce VSC levels, improve OLT scores, and modulate the growth of oral microbiota. However, the heterogeneity of studies and limited long-term follow-up hinder clinical translation. Larger, standardized trials are essential for establishing the clinical efficacy. Probiotics present a safe adjunct therapy for halitosis management. Future research should focus on longitudinal studies, specific strain efficacy, and microbiome-targeted interventions.},
}

@article {pmid40951341,
year = {2025},
author = {Liao, L and Zeng, M and Liu, D and He, Y and Du, W and Cao, Y},
title = {Focus on gut microbes: new direction in cancer treatment.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1505656},
pmid = {40951341},
issn = {2234-943X},
abstract = {Gut microbes are emerging as critical regulators in cancer therapy, influencing the efficacy and toxicity of radiotherapy, chemotherapy, immunotherapy, targeted therapy, Traditional Chinese Medicine, and rehabilitation interventions. Acting through metabolic reprogramming, immune modulation, DNA damage, and tumor microenvironment remodeling, specific microbial taxa and their metabolites can either enhance or hinder treatment outcomes. However, these interactions are highly context-dependent and shaped by individual factors such as diet, geography, and host immunity. While microbial interventions such as probiotics, fecal microbiota transplantation, and engineered bacteria show promise, their translation into precise and safe clinical applications remains limited by interindividual variability, regulatory hurdles, and incomplete mechanistic understanding. Future efforts should focus on defining high-evidence microbial signatures, clarifying causal mechanisms, and developing personalized microbiome-based therapeutic strategies, potentially integrated with nanotechnology. This review underscores the need for interdisciplinary approaches to harness gut microbiota as co-targets in cancer treatment.},
}

@article {pmid40951316,
year = {2025},
author = {Zhang, B and Sheng, Z and Bu, C and Wang, L and Lv, W and Wang, Y and Xu, Y and Yan, G and Gong, M and Liu, L and Hu, W},
title = {Whipworm infection remodels the gut microbiome ecosystem and compromises intestinal homeostasis in elderly patients revealed by multi-omics analyses.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1663666},
pmid = {40951316},
issn = {2235-2988},
abstract = {INTRODUCTION: Whipworm (Trichuris trichiura) coexists with symbiotic microbiota in the gastrointestinal ecosystem. There is a paucity of data on the association between whipworm infection and the gut microbiota composition in elderly individuals. This study was designed to investigate changes in gut microbiota and function and its metabolite profile in patients with whipworm infection.

METHODS: We used 16S rRNA gene sequencing to identify microbial signatures associated with whipworm infection. Subsequently, shotgun metagenomic sequencing revealed functional changes that highlighted disruptions in microbial gene expression and metabolic pathways influencing host health. Ultraperformance liquid chromatography-mass spectrometry metabolomics was used to characterize whipworm infectioninduced metabolic perturbations and elucidate metabolite dynamics linked to microbial activity. Collectively, this multi-omics approach deciphered structural, functional, and metabolic remodeling of the gut ecosystem that distinguished whipworm-infected patients from healthy controls.

RESULTS: Analyses of the gut microbiome in patients with whipworm infection revealed significantly increased observed species richness and ACE indices, along with an enrichment of Prevotella 9-driven enterotypes. Additionally, metagenomic and metabolomic analyses indicated enrichment in metabolic pathways related to amino acid, energy and carbohydrate metabolism. Metabolic network analysis further suggested that the upregulated Prevotella copri and Siphoviridae sp. were positively correlated with elevated levels of myristic acid and DL-dipalmitoylphosphatidylcholine.

CONCLUSION: These findings suggest that whipworm infection significantly remodels the gut microbiome ecosystem and compromises intestinal homeostasis.},
}

@article {pmid40951306,
year = {2025},
author = {Kosinska-Kaczynska, K and Zgliczynska, M and Krawczyk, D and Piatkowska, M and Balabas, A and Czarnowski, P and Goryca, K and Glinicki, P and Ostrowski, J and Zeber-Lubecka, N},
title = {Analysis of the microbiota of pregnant women in relation to weight gain during pregnancy - a pilot study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1655581},
pmid = {40951306},
issn = {2235-2988},
abstract = {INTRODUCTION: Excessive body weight was associated with changes in individual microbiota. However, limited research on the impact of excessive gestational weight gain (GWG) revealed that microbiota patterns related to GWG differed from those linked to pregestational overweight or obesity.

AIM: The aim was to compare differences in the microbiota of women in the third trimester of gestation who had excessive and non-excessive weight gain during pregnancy.

MATERIAL AND METHODS: Women with a singleton gestation at 34 + 0 weeks and normal pregestational body mass index were recruited to the study. Patients who were diagnosed with excessive weight gain formed the study group (n=11), while those with non-excessive weight gain formed the control group (n=10).

RESULTS: In cervico-vaginal samples, bacterial 16S rRNA gene sequencing demonstrated a decrease in alpha diversity, measured with the Shannon index, in the study group compared to the control group. While the difference was not statistically significant after correction for multiple testing, the Chao index showed a persistent trend toward reduced species richness in the study group. In stool samples, we identified 29 genera with differential representation between the groups, including nine overrepresented and ten underrepresented genera. The cervico-vaginal microbiota analysis detected 12 species distinguishing the study group from the controls, with four genera (Ralstonia, Pandoraea, Kocuria, and Rhodobacteraceae unclassified) being more prevalent in the study group. However, in both sites none difference was found to be statistically significant after p-value correction.

CONCLUSIONS: Despite small sample size, we demonstrated slight trends in microbiota composition between groups. These suggest potential differences in microbial diversity and composition associated with excessive GWG, which supports further investigation.},
}

@article {pmid40951210,
year = {2025},
author = {Kakde, SP and Qadeer, A and Khalil, M and Dhami, A and Rashid, Z and Zahir, D and Ahsan, SA and Dhillon, TA and Siddique, MU and Uzokwe, MC},
title = {Safety and Efficacy of Ketogenic Diet in the Management of Multiple Sclerosis: A Systematic Review.},
journal = {Cureus},
volume = {17},
number = {8},
pages = {e89965},
pmid = {40951210},
issn = {2168-8184},
abstract = {This systematic review examines the safety and efficacy of ketogenic diets (KD) in multiple sclerosis (MS) management. Following Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines, we systematically searched five major databases through April 2025, identifying six relevant studies published between 2017 and 2024. These studies, predominantly focusing on relapsing-remitting MS, demonstrate consistent benefits of ketogenic interventions across multiple domains. Findings suggest KD normalizes gut microbiome composition, reduces pro-inflammatory markers (ALOX5, COX1, COX2), improves body composition with favorable changes in adipokines (decreased leptin, increased adiponectin), and enhances clinical outcomes, including fatigue, depression, sleep quality, and quality of life measures. Objective neurological improvements were observed in Expanded Disability Status Scale (EDSS) scores, walking ability, and manual dexterity. Adherence rates were notably high, with benefits partially persisting after intervention completion. The metabolic shift induced by ketosis may provide alternative neuronal energy substrates, reduce oxidative stress, and attenuate neuroinflammation. Despite limitations including small sample sizes and study heterogeneity, these preliminary findings suggest KDs represent a promising adjunctive approach in MS management, addressing both inflammatory and neurodegenerative components of the disease. Larger, controlled trials with longer follow-up periods are warranted to establish long-term safety and efficacy profiles.},
}

@article {pmid40951136,
year = {2025},
author = {Al Harrasi, RJ and Al Balushi, AY and Al Kindi, FI and Al Kindi, NA and Kamel, AH},
title = {Potential Role of Oral Microbiota in Medication-Related Osteonecrosis of the Jaw in Cancer Patients: A Narrative Review.},
journal = {Cureus},
volume = {17},
number = {8},
pages = {e89943},
pmid = {40951136},
issn = {2168-8184},
abstract = {Medication-related osteonecrosis of the jaw (MRONJ) is a severe complication frequently observed in cancer patients undergoing antiresorptive therapies, such as bisphosphonates and denosumab. Emerging evidence suggests that dysbiosis of the oral microbiota plays a pivotal role in the pathogenesis of MRONJ. The complex interplay between microbial communities, host immune responses, and the effects of cancer treatments creates an environment conducive to pathogenic colonization, chronic inflammation, and impaired bone healing, which are the key hallmarks of MRONJ. Chemotherapy, radiotherapy, and antiresorptive agents significantly disrupt oral microbiota homeostasis, reducing microbial diversity and the overgrowth of opportunistic pathogens. These alterations exacerbate the inflammatory responses, accelerate bone resorption, and impede tissue repair. The identification of specific microbial biomarkers associated with MRONJ could facilitate early detection and targeted interventions, such as antimicrobial and probiotic therapies, to restore the microbial balance and mitigate the risk of MRONJ. Furthermore, the implementation of personalized preventive protocols, including rigorous oral hygiene and multidisciplinary collaboration among oncologists, dentists, and microbiologists, is critical for reducing the incidence and severity of MRONJ in high-risk populations. Future research should focus on elucidating the mechanisms by which microbial dysbiosis contributes to MRONJ, validating microbiome-based diagnostic tools, and optimizing therapeutic strategies to preserve oral and systemic health in patients with cancer. Integrating microbial ecology into the MRONJ management framework offers a promising avenue for addressing this challenging condition and improving the outcomes for vulnerable individuals.},
}

@article {pmid40951128,
year = {2025},
author = {Shende, S and Das, R and Joshi, S and Yanamandra, S and Taji, N and Karyakarte, RP},
title = {Human Papilloma Virus Infection and Vaginal Microbiome Profiles in Pre-menopausal Women: A Cross-Sectional Study.},
journal = {Cureus},
volume = {17},
number = {8},
pages = {e89872},
pmid = {40951128},
issn = {2168-8184},
abstract = {BACKGROUND: Cervical cancer is a common cancer among women worldwide, especially in low- and middle-income countries. Persistent infection with high-risk human papillomavirus (HR-HPV) largely drives the development of cervical cancer. While Lactobacillus-dominant communities are considered protective, dysbiosis, marked by reduced Lactobacilli and increased anaerobic diversity (community state type (CST)-IV), may promote viral persistence. This study aims to assess HR-HPV prevalence and compare vaginal microbiome profiles in women with suspected HPV infection and healthy controls.

MATERIAL AND METHODS: Vaginal swabs were collected from pre-menopausal women with clinically suspected HPV infection and healthy controls. Samples underwent HR-HPV detection using the Truenat® HPV-HR RT-PCR (real-time polymerase chain reaction) assay (Molbio Diagnostics Limited, Goa, India). Vaginal microbiome profiling was performed using 16S rRNA gene amplicon sequencing on the GridION platform (Oxford Nanopore Technologies plc, Oxford, United Kingdom). Taxonomic classification was carried out using the EPI2ME 16S workflow with Kraken2 (Johns Hopkins University, Baltimore, Maryland, United States), and CSTs were assigned using the VALENCIA (VAginaL community state typE Nearest CentroId clAssifier) algorithm. Statistical analyses and microbial community comparisons were performed using MicrobiomeAnalyst (Xia Lab, Sainte-Anne-de-Bellevue, Quebec, Canada).

RESULTS: A total of 86 clinically suspected HPV cases and 63 healthy pre-menopausal controls were enrolled. Overall, high-risk HPV (HPV 16/31 and HPV-18/45) was detected in 11.6% (10/86) of cases, with no positivity in the control group. Vaginal microbiome profiling revealed significantly higher alpha diversity in women with inflammatory cytology compared to healthy controls, and increased Shannon and Simpson diversity indices in HPV-positive and inflammatory groups. Beta diversity analysis showed distinct microbial clustering between all groups. Taxonomic analysis demonstrated a predominance of Lactobacillus spp. in healthy individuals, particularly Lactobacillus crispatus and Lactobacillus iners, whereas disease groups showed increased abundance of Pseudomonas, Rheinheimera, and Agrobacterium. CST-I was more common in healthy controls (7/17, 41.2%), while CST-IV-linked to dysbiosis-was predominant among suspected cases (9/21, 47.6%). Linear discriminant analysis effect size (LEfSe) analysis identified Lactobacillus, Anaerococcus, and Dialister as key genera in healthy individuals, whereas Pseudomonas, Rhizobium, and Rheinheimera were enriched in HPV-positive and inflammatory smear groups, highlighting potential microbial biomarkers of vaginal dysbiosis.

CONCLUSION: These findings underscore the importance of vaginal microbiome composition in cervical health and support further investigation into microbial biomarkers for early detection and targeted interventions in HPV-associated disease.},
}

@article {pmid40950593,
year = {2025},
author = {Silva, ACP and Migliaccio, F and Barosa, B and Gallucci, L and Yücel, M and Foustoukos, D and Le Bris, N and Bartlett, SJ and D'Alessandro, V and Vetriani, C and Giovannelli, D},
title = {Hydrodynamic flow and benthic boundary layer interactions shape the microbial community in Milos shallow water hydrothermal vents.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1649514},
pmid = {40950593},
issn = {1664-302X},
abstract = {In shallow-water hydrothermal vents, the dynamic interface between the discharged reduced hydrothermal fluids and the oxidized seawater allows the establishment of gradients capable of supporting diverse and complex microbial mats. Due to their shallow depths and proximity to land masses, shallow vents are heavily influenced by dynamic forcing, tidal fluctuations, and episodic events (e.g., storms, tides, etc.). Although several studies have investigated the microbial communities inhabiting shallow vents in the last decades, less is known about how microbial communities respond to episodic events and how the complex interplay of physical and chemical drivers shapes the establishment and structure of microbial biofilms in these systems. Here we present data combining the taxonomic and functional diversity of the white microbial mats commonly found in sulfide rich shallow-water hydrothermal vents in Paleochori Bay (Milos Island, Greece), using a combined approach of 16S rRNA transcript amplicon sequencing (from RNA) and shotgun metagenomic sequencing (from which 16S rRNA genes were retrieved). We show that the white microbial mats of Milos shallow-water hydrothermal vents are dominated by Epsilonproteobacteria, now classified as Campylobacterota, with metabolic functions associated with chemolithoautotrophic lifestyles and exposed to a diverse array of viral communities. Taxonomic names follow the classification available at the time of analysis (2012). We explore how dynamic forcing and storm events influence microbial community restructuring and turn-over, and provide evidence that dynamic interactions with the benthic boundary layer play a key role in controlling the spatial distribution of taxa. Overall, our results show diverse processes through which geodynamic events influence microbial taxonomic and functional diversity.},
}

@article {pmid40950589,
year = {2025},
author = {Li, YH and Yang, M and Wei, TS and Chen, HG and Gong, L and Wang, Y and Gao, ZM},
title = {Survival strategies for the microbiome in a vent-dwelling glass sponge from the middle Okinawa Trough.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1636046},
pmid = {40950589},
issn = {1664-302X},
abstract = {The adaptive mechanisms of sponge microbiomes to harsh deep-sea environments, including hydrothermal vents and cold seeps, remain unclear. Here, we used metagenomics to investigate the microbiome of an undescribed vent-dwelling glass sponge from the middle Okinawa Trough, probably representing a novel species within the family Bolosominae. Eleven high-quality prokaryotic metagenome-assembled genomes (MAGs) were retrieved, none assignable to known species, with two representing new genera. Dominant MAGs included sulfur-oxidizing bacteria (SOB) and ammonia-oxidizing archaea, followed by methane-oxidizing bacteria (MOB) and nitrite-oxidizing bacteria. Global distribution analysis suggested that most MAGs were sponge-specific symbionts. Comparative genomics revealed functional redundancy among SOB and early-stage genome reduction in a unique MOB lineage. Additionally, a total of 410 viral contigs were identified, most exhibiting a lytic lifestyle and forming distinct clades from known viruses. Our work expands understanding of the diversity and novelty of deep-sea sponge-associated prokaryotes and viromes, and suggests their niche adaptation to hydrothermal fluid environments.},
}

@article {pmid40950585,
year = {2025},
author = {Kardaras, FS and Siatravani, E and Tsilipounidaki, K and Petinaki, E and Hatzigeorgiou, AG and Miriagou, V},
title = {Identification of nasopharyngeal microbial dysbiosis in COVID-19 patients by 16S rRNA gene sequencing.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1631198},
pmid = {40950585},
issn = {1664-302X},
abstract = {BACKGROUND: The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has prompted extensive research into factors influencing the onset and severity of the disease. Among these factors, the role of the nasopharyngeal microbiome, a vital ecosystem critical for respiratory health and immune modulation, remains incompletely understood. This study aimed to elucidate the relationship between the composition of nasopharyngeal microbiota and the clinical presentation of COVID-19 during the initial phase of infection.

MATERIALS AND METHODS: A total of 81 nasopharyngeal swab samples were collected from individuals in Central Greece between January and February 2021. Following quality control, 77 samples were selected for microbiome analysis. This selection included SARS-CoV-2-negative controls (NE, n = 26) and SARS-CoV-2-positive patients classified as asymptomatic (AS, n = 19), mild (MI, n = 16), or severe (SE, n = 16) based on clinical criteria. All COVID-19-positive samples were collected within 2 days of symptom onset, and participants with recent hospitalization or antibiotic use were excluded. Microbiome profiling was performed using 16S rRNA gene-targeted metagenomic sequencing, followed by comprehensive bioinformatics and statistical analyses.

RESULTS: Significant differences were observed in both alpha and beta diversity measures, with alpha diversity decreasing as the severity of COVID-19 increased. Three of the four individual study groups, namely NE, MI, and SE, exhibited distinct microbial profiles, while the asymptomatic group showed greater heterogeneity. Significant variations in the abundance of specific phyla, families, and genera were identified between the different study groups. When comparing the NE and SE groups, we observed a significant increase in the abundance of the Proteobacteria phylum in the SE group, while the abundance of Fusobacteria was significantly lower in the SE group. In symptomatic COVID-19 patients, we observed a significant reduction in the abundance of key family constituents of the nasopharyngeal microbiota, such as Fusobacteriaceae, Prevotellaceae, and Streptococcaceae, suggesting a disruption in microbial homeostasis during the infection. Conversely, we found an increased prevalence of families associated with pathogenic or opportunistic pathogenic bacteria, including Enterobacteriaceae and Bacillaceae, in the SE group, suggesting a potential role of these taxa in the disease progression of COVID-19.

CONCLUSION: These findings shed light on specific genera that undergo significant changes during COVID-19 infection and contribute to our understanding of the dynamic nature of the nasopharyngeal microbiome in relation to disease progression and severity.},
}

@article {pmid40950551,
year = {2025},
author = {Zhao, S and Zhang, X and Miao, Y and Gao, X and Wan, Q and Qiu, W and Si, H and Han, Y and Du, X and Feng, Y and Liu, L and Chen, Y},
title = {Integrated analysis of metabolome and microbiome in a mouse model of sodium valproate-induced autism.},
journal = {Experimental biology and medicine (Maywood, N.J.)},
volume = {250},
number = {},
pages = {10452},
pmid = {40950551},
issn = {1535-3699},
abstract = {Sodium valproate (SV) has been shown to induce autism in animal models. In this study, the SV method was used to establish a mouse model of autism, and anxiety-like behaviours and learning memory performance were evaluated by behavioural tests. The effects of SV on metabolic profiles and gut microbiota were assessed by integrating gas chromatography-mass spectrometry and 16S ribosomal RNA gene sequencing. Correlations between metabolites and gut microbiota were determined using Spearman correlation coefficient. Behavioral tests, including the three-chambered social assay, repetitive behaviors, open field test, elevated plus-maze test, and novel object recognition test, demonstrated that SV treatment exacerbated anxiety-like behaviors and impeded spatial learning and memory in mice. SV disrupted metabolic pathways in hippocampus, cortex, intestine, and serum, affecting primarily valine, leucine and isoleucine biosynthesis, glycerophospholipid metabolism and glutathione metabolism and so on. SV also altered gut microbiota at the genus level, decreasing the abundances of Dubosiella, Faecalibaculum, Clostridia_UCG-014, Bifidobacterium, and Alloprevotella, while increase the abundances of Lactobacillus, Alistipes, and Lachnospiraceae in intestine. The results of correlation analysis showed that in hippocampus, Bifidobacterium was positively correlated with serine and glycine, while Alistipes was negatively correlated with them. These findings suggested that SV may contribute to the development of autism progression by altering the gut microbiota abundances and metabolite profiles. This may provide new direction for the management of autism.},
}

@article {pmid40950517,
year = {2025},
author = {Galviz-García, L and Romero-Romero, S and Herrera-Herrera, A and Mercado-Camargo, J and Díaz-Caballero, A and Plazas-Román, J and Ardila, CM},
title = {Nickel Bioaccumulation in Oral Biofilm, Gingival Tissue, and Saliva During Fixed Orthodontic Treatment: A 12-Month Prospective Cohort Study on Predictors and Salivary pH Correlation.},
journal = {Journal of clinical and experimental dentistry},
volume = {17},
number = {8},
pages = {e920-e928},
pmid = {40950517},
issn = {1989-5488},
abstract = {BACKGROUND: Nickel-based alloys in fixed orthodontic appliances are susceptible to electrochemical corrosion in the oral environment, releasing ions with cytotoxic and allergenic potential. While previous studies have documented initial nickel release patterns, the longitudinal dynamics of its accumulation across oral biospaces (saliva, biofilm, gingival tissue) and interactions with salivary pH remain poorly characterized. This study investigates nickel accumulation in saliva, oral biofilm, and gingival tissue over 12 months of orthodontic treatment and its association with salivary pH.

MATERIAL AND METHODS: This 12-month prospective cohort study enrolled 120 participants undergoing fixed orthodontic treatment. Nickel concentrations were quantified via graphite furnace atomic absorption spectrophotometry in three biospaces at baseline (T0), 6 months (T1), and 9-12 months (T2). Salivary pH was measured concurrently. Statistical analyses included non-parametric longitudinal comparisons, inter-biospace contrasts, Spearman correlations, and multivariate regression modeling to identify predictors of nickel accumulation.

RESULTS: Nickel exhibited distinct spatiotemporal patterns: progressive accumulation in biofilm (0.0008→21.5833 µg/L, p<0.001) versus biphasic kinetics in gingiva and saliva (peaking at T1 then declining). By T2, biofilm concentrations were 1000× higher than other biospaces (p<0.001). Treatment duration was the strongest predictor across all compartments (β=0.56-0.67, p<0.001), with biofilm accumulation additionally modulated by salivary pH (β=0.22, p=0.027) and age (β=-0.19, p=0.041). A time-dependent correlation emerged between salivary pH and biofilm nickel (T0: r=0.17, p=0.112; T2: r=0.41, p=0.008), suggesting pH-microbiome interactions.

CONCLUSIONS: Oral biofilm serves as the dominant long-term nickel reservoir during orthodontic treatment, with accumulation dynamics influenced by treatment duration, pH, and age. The pH-dependent biofilm-metal interaction highlights its potential as a biomarker for exposure monitoring and a target for preventive strategies. These findings support the development of pH-modulating oral care protocols and corrosion-resistant orthodontic materials to mitigate nickel exposure risks. Key words:Nickel, saliva, Spectrophotometry, Atomic, Orthodontic Appliances, Hydrogen-Ion Concentration.},
}

@article {pmid40950404,
year = {2025},
author = {Kyriakidis, NC and Echeverría, CE and Bautista, J and Rivera-Orellana, S and Ramos-Medina, MJ and Salazar-Santoliva, C and Izquierdo-Condoy, JS and Ortiz-Prado, E and Guerrero, S and López-Cortés, A},
title = {Reprogramming cancer immunity with next-generation combination therapies.},
journal = {Frontiers in cell and developmental biology},
volume = {13},
number = {},
pages = {1652047},
pmid = {40950404},
issn = {2296-634X},
abstract = {Cancer immunotherapy has fundamentally reshaped oncology by harnessing the immune system to eliminate malignant cells. Immune checkpoint inhibitors targeting CTLA-4 and PD-1/PD-L1 have achieved durable remissions in select cancers, yet most patients exhibit resistance due to tumor heterogeneity, immunometabolic rewiring, and the immunosuppressive tumor microenvironment. To address these limitations, next-generation immunotherapies have emerged, targeting multiple layers of immune regulation. These include co-inhibitory and co-stimulatory checkpoint modulators, bispecific antibodies, adoptive cell therapies, cancer vaccines, oncolytic viruses, cytokine-based strategies, and synthetic immunomodulators that activate innate sensors. Nanotechnology and in vivo immune engineering further enhance specificity, reduce toxicity, and broaden applicability. Combination immunotherapy has become central to overcoming resistance, with rational regimens integrating ICIs, cytokines, vaccines, and targeted agents. Biomarker-guided strategies, leveraging tumor mutational burden, immune cell infiltration, and multi-omic profiling, are enabling personalized approaches. However, immune-related adverse events and variability in therapeutic responses necessitate predictive biomarkers and improved patient stratification. Emerging frontiers include microbiome-targeted interventions, chronotherapy, and AI-driven modeling of tumor-immune dynamics. Equally critical is ensuring global equity through inclusive trial design, diverse biomarker validation, and expanded access to cutting-edge therapies. This review provides a comprehensive analysis of multimodal immunotherapeutic strategies, their mechanistic basis, and clinical integration. By unifying innovation in immunology, synthetic biology, and systems medicine, next-generation cancer immunotherapy is poised to transition from a transformative intervention to a curative paradigm across malignancies.},
}

@article {pmid40950274,
year = {2025},
author = {Wang, C and Kuang, B and Yang, K and Xiao, X and Wu, C and Li, A and Zeng, X and Wang, X and Ye, J},
title = {Chemotherapy-induced suppression of colorectal cancer-associated gut microbiota and modulation of host miRNA expression.},
journal = {American journal of translational research},
volume = {17},
number = {8},
pages = {6573-6586},
pmid = {40950274},
issn = {1943-8141},
abstract = {OBJECTIVES: To characterize gut microbiome alterations in colorectal cancer (CRC) patients following cancer chemotherapy (CCT) and to explore associations with bacterial translocation and host miRNA dynamics.

METHODS: Stool samples were prospectively collected from 20 CRC patients who had undergone radical surgery followed by adjuvant chemotherapy (CAPOX/mFOLFOX6). Stool samples were collected pre- and post-CCT. Microbial profiling was performed using 16S rRNA sequencing. Bacterial translocation was assessed by measuring serum anti-Lipopolysaccharides (LPS) IgA/IgG levels by ELISA. miRNA expression of miR-143 and miR-145 was quantified using qPCR.

RESULTS: Post-CCT samples showed significant increases in gut microbiome diversity (P<0.05), with higher relative abundances of Porphyromonas, Peptostreptococcus, and Parvimonas, and decreased abundances of Faecalibacterium and Ruminococcaceae (P<0.005). Network analysis identified Peptostreptococcus and Parvimonas as possible CRC-associated taxa. Serum anti-LPS IgA and IgG levels significantly declined post-CCT, indicating reduced bacterial translocation. Concurrently, miR-143 and miR-145 levels increased more than twofold post-CCT (P<0.01), positively correlating with microbial shifts.

CONCLUSION: CCT induces significant remodeling of CRC-associated gut microbiota, characterized by suppression of pathogenic genera and enrichment of pro-inflammatory taxa. These changes align with reduced bacterial translocation and increased expression of tumor-suppressive miRNAs, suggesting that CCT exerts dual therapeutic effects by simultaneously modulating microbial communities and host molecular pathways.},
}

@article {pmid40950221,
year = {2025},
author = {Suh, E and Huntley, N and van Warmerdam, T and Spychalla, JP and Nejat, N and Rasgon, JL},
title = {Hologenomic structure of bacterial and fungal community composition in the West Nile virus vector Culex tarsalis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.01.673577},
pmid = {40950221},
issn = {2692-8205},
abstract = {BACKGROUND: Microbiota play a crucial role in determining the ability for arthropod disease vectors to transmit pathogens. Microbial community structure can be heavily influenced by microbe-microbe interactions, host genetics and environmental factors. Here, we characterize the host population genetic structure, and bacterial and fungal communities in natural populations of the West Nile virus mosquito vector Culex tarsalis . Mosquitoes were collected and analyzed across the species range of the mosquito in the United States, where we used PoolRADSeq to quantify population genetic structure. Microbial community composition was characterized using bacterial 16S rRNA gene sequencing (V3-V4 region) and fungal ITS sequencing (ITS1 region).

RESULTS: PoolRADSeq identified four broad genetic clusters of mosquito populations, which corresponded to previous clusters identified by microsatellite analysis and RADSeq on individual mosquitoes. Microbiome diversity grouped mosquito populations into three broad clusters, with each cluster distinctively represented by diagnostic abundant bacteria (Ralstonia , Pseudomonas, or Zymobacter / Providencia , respectively). Clustering for fungal taxa was less pronounced. Geographic distance between populations was positively correlated with microbiome community dissimilarity, and multiple environmental factors were significantly correlated with microbial species richness and diversity.

CONCLUSIONS: These results suggest that bacterial and fungal communities are geographically structured in Cx . tarsalis , interact with important environmental factors, and are partially correlated with host genetic structure. As microbiota can affect the ability for mosquitoes to transmit pathogens, understanding the factors underpinning microbiome variation across space and time has important implications for the spread of vector-borne pathogens such as WNV.},
}

@article {pmid40950182,
year = {2025},
author = {Smith, C and Adair, K and Bohannan, BJM},
title = {Drivers of Variation of the Zebrafish Egg Microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.01.673521},
pmid = {40950182},
issn = {2692-8205},
abstract = {Microbiomes are integral to the fitness of many animals, yet little is known about early-life microbiome assembly. What is known largely comes from studies in non-model organisms, where it is difficult to distinguish host genetics from the environment as drivers of microbiome assembly. Here, we used a popular vertebrate model, zebrafish (Danio rerio), to address the major drivers of environmental assembly in 124 individuals. We surveyed the egg microbiome from fertilization to hatching using 16S rRNA gene sequencing and investigated development stage and parentage as potential drivers of microbiome variation. Phylogenetic diversity of the egg microbiome decreased during development, suggesting that environmental filtering may be a major driver of community assembly. Parentage also had an influence on microbiome assembly; eggs derived from the same clutch were often more similar in microbiome composition compared to eggs derived from different clutches. The effect of parentage on microbiome similarity decreased over development, suggesting that parents may be an initial source of egg microbiome members. The egg microbiome undergoes dramatic compositional shifts during development. Understanding the drivers of this variation is important to consider, especially given the role of the microbiome in health and development, and that early exposure to microbes may shape later animal development. Our findings suggest that parents may serve as an important source of microbial symbionts to their offspring, even in an animal that does not provide parental care, such as laboratory zebrafish, and that the developing egg may play an increasingly important role in driving microbiome variation across individuals.},
}

@article {pmid40950152,
year = {2025},
author = {Stoehr, MC and Martin, EM and Babalola, JT and Xue, J and Kern, MJ and Li, NY and Winters, MF and Bhagwagar, S and Smith, CJ},
title = {Effects of combined prenatal exposure to air pollution and maternal stress on social behavior and oxytocin and vasopressin systems in male and female mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40950152},
issn = {2692-8205},
abstract = {UNLABELLED: Prenatal exposures to air pollution and maternal psychosocial stress are each associated with increased risk of neurodevelopmental disorders, including autism spectrum disorder (ASD) and epidemiological work suggests that concurrent exposure to these risk factors may be particularly harmful. This is important given that the same populations often bear the brunt of both toxicant and psychosocial stress burdens. Social impairments are a defining symptom in ASD. Previous work modeling combined prenatal exposure to diesel exhaust particles (DEP) and maternal stress (MS) in rodents has found male-biased social deficits in offspring, as well as changes to neuroimmune processes and the gut microbiome. However, the precise neural circuits on which these exposures converge to impact social behavior is unclear. Oxytocin (OXT) and vasopressin (AVP) are neuropeptides critical to the regulation of social behavior across species, signaling primarily at the oxytocin receptor (Oxtr) and vasopressin V1a receptor (V1aR) in the brain. Here, we hypothesized that OXT and/or AVP expression would be reduced in the brain following DEP/MS exposure. Following prenatal exposure to DEP/MS or the vehicle/control condition (VEH/CON), we measured maternal and offspring outcomes during the perinatal period, social and anxiety-like behavior during adolescence, OXT and AVP cell/fiber density and Oxtr and Avpr1a mRNA expression in early adulthood in several brain regions in both males and females. We observed a decrease in interaction time in DEP/MS males as compared to VEH/CON in the sociability assay and a decrease in social novelty preference in DEP/MS females as compared to VEH/CON. No effects of sex or treatment were observed on OXT or AVP cell number or fiber density in the hypothalamic regions assessed. However, numerous sex differences were observed in Oxtr and Avpr1a mRNA. Moreover, Avpr1a mRNA was significantly increased following DEP/MS exposure in the nucleus accumbens in both sexes and tended to increase in the dorsal hippocampus. Conversely, Avpr1a mRNA tended to decrease in the amygdala in both sexes following DEP/MS exposure. Together, these findings suggest that DEP/MS exposure has a stronger impact on female social behavior than previously observed. Moreover, while DEP/MS exposure does not appear to impact OXT or AVP expression in the brain, V1aR expression is modulated by DEP/MS exposure in several brain regions.

HIGHLIGHTS: Prenatal DEP/MS reduces social novelty preference in femalesPrenatal DEP/MS does not alter OXT or AVP cell number in the PVNPrenatal DEP/MS does not alter OXT or AVP fiber density in the LH, AH, or MPOA Prenatal DEP/MS increases Avpr1a mRNA in the NAc Prenatal DEP/MS tends to decrease Avrp1a mRNA in the AMY and increase in dHipp.},
}

@article {pmid40950116,
year = {2025},
author = {Estrem, C and Dua, M and Fees, CP and Hoeprich, GJ and Au, M and Goode, BL and Deng, LL and Flavell, SW},
title = {Identification of bacterial signals that modulate enteric sensory neurons to influence behavior in C. elegans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.03.674032},
pmid = {40950116},
issn = {2692-8205},
abstract = {The bacterial microbiome influences many aspects of animal health and disease. Some bacteria have beneficial functions, for example providing nutrients, whereas others act as pathogens. These bacteria are sensed by host cells to induce adaptive changes in physiology and behavior. While immune and intestinal cells detect bacterial signals through well-characterized mechanisms, recent studies indicate that neurons can also directly sense bacterial signals. However, the bacterial sensory mechanisms in neurons are less well understood. In the nematode Caenorhabditis elegans , the enteric sensory neuron NSM innervates the pharyngeal lumen and is directly activated by bacterial food ingestion; in turn, NSM releases serotonin to induce feeding-related behaviors. However, the molecular identities of the bacterial signals that activate NSM are unknown. To identify these signals, we systematically probed bacterial macromolecules from nutritive bacteria using biochemical approaches and GC-MS identification. We find that polysaccharides from gram-positive and gram-negative bacteria are sufficient to activate NSM. We further identify peptidoglycan from gram-positive bacteria as a specific component capable of activating NSM. NSM responses to polysaccharides require the acid-sensing ion channels DEL-3 and DEL-7, which localize to its sensory dendrite in the pharyngeal lumen. Ingestion of bacterial polysaccharides enhances feeding rates and reduces locomotion, matching the known effects of NSM on behavior. We also examine bacterial signals from pathogenic bacteria that can infect and kill C. elegans . This approach identifies prodigiosin, a metabolite from pathogenic Serratia marcescens , as a bacterial cue that prevents NSM activation by nutritive bacterial signals. This study identifies molecular signals that underlie neuronal recognition of nutritive bacteria in the alimentary canal and competing signals from a pathogenic bacterial strain that mask this form of recognition.},
}

@article {pmid40950058,
year = {2025},
author = {Barrack, KE and Surve, SV and de Sousa Bezerra, AV and Murphy, CE and Soucy, SM and Aguilar Ramos, MA and Valls, RA and Ruff, RD and Balskus, EP and Sanville, JL and Madan, JC and O'Toole, GA},
title = {A genotoxin associated with colorectal cancer linked to gut dysbiosis in children with cystic fibrosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40950058},
issn = {2692-8205},
abstract = {Cystic fibrosis (CF) substantially alters the gastrointestinal microbiome from an early age, leading to significant changes in microbial composition and functionality. This study explores the physiological and microbiological factors contributing to dysbiosis in children with cystic fibrosis (cwCF), characterized by an increase in potentially pathogenic Escherichia coli and a decrease in beneficial anaerobes such as Bacteroides. In this study, we employed an in vitro medium representative of the nutritional environment of the CF colon to test the role of factors including mucin, fat, bile, pH, antibiotics and features associated with inflammation (e.g., nitrate, sulfate, formate, reactive oxygen species) on growth of clinical isolates of E. coli and Bacteroides spp. We further examined interactions between these two microbes under CF-like conditions to understand modulators of microbial competition, and identified glycerol, a surrogate of increased fat, as a significant driver of altered microbial competition. Finally, we investigated genetic determinants influencing these microbial interactions, with the focus on glycerol metabolism, by performing a transposon mutagenesis screen in E. coli. Results of this screen pointed to the role of colibactin production in mediating this microbial competition; colibactin is a DNA-damaging genotoxin associated with the increased risk of colorectal cancer (CRC) in CF populations. This work enhances our understanding of mechanisms of microbial competition in the CF gut, while potentially enhancing our understanding of colorectal cancer risk in persons with CF through the identification of early-life microbial biomarkers.},
}

@article {pmid40950012,
year = {2025},
author = {Evens, KC and Bakke, I and Bohannan, BJM},
title = {Aquaculture facility-specific microbiota shape the zebrafish gut microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40950012},
issn = {2692-8205},
abstract = {BACKGROUND: Environmental microbiomes, such as those in recirculating aquaculture systems (RAS), can play a key role in shaping host-associated microbial communities. In zebrafish (Danio rerio) research, these interactions can introduce uncontrolled sources of variation, potentially confounding experimental outcomes across multiple facilities. Despite widespread zebrafish use in microbiome studies, few have characterized the microbial composition of both tank water and fish across multiple independent facilities to evaluate the consequences of environmental microbiome variation on the host microbiome.

RESULTS: We compared water and zebrafish gut microbiomes across five aquaculture facilities-two in the United States and three in Norway-using a nested sampling design and 16S rRNA gene sequencing. Alpha diversity was consistently higher in tank water than in fish guts, and beta diversity metrics revealed distinct clustering by sample type, facility, and location. Differences in microbial community composition were significant across facilities, with both water and fish samples exhibiting facility-specific profiles. Similarity Percentage analysis identified taxonomic groups driving these differences, while Fast Expectation-Maximization for Microbial Source Tracking detected measurable contributions of tank water microbiota to zebrafish gut communities. Bray-Curtis dissimilarity values were lowest between fish and water from the same tank and increased with geographic and facility distance, indicating local microbial overlap. Relative abundance patterns and ordination plots further supported distinct and structured microbial assemblages across systems.

CONCLUSIONS: This study demonstrates that zebrafish aquaculture systems harbor unique microbial communities shaped by both environmental and geographic factors, with tank water acting as a potential source of gut-associated microbes. These findings underscore the importance of incorporating environmental microbiome assessments into zebrafish experimental design, particularly for studies focused on host-microbe interactions. Without such consideration, unaccounted variation in environmental microbiota may affect microbiome composition and reduce cross-study reproducibility. Moving forward, standardized reporting of environmental conditions and microbial composition across facilities will be critical for strengthening reproducibility and interpretation in zebrafish microbiome research.},
}

@article {pmid40950001,
year = {2025},
author = {Książek, M and Benedyk-Machaczka, M and Sochaj-Grzegorczyk, A and Mizgalska, D and Waligórska, I and Nowak, M and Kaczor, A and Potempa, B and Fuchs, A and Thøgersen, IB and Enghild, JJ and Scavenius, C and Mydel, P and Bagaitkar, J and Potempa, J},
title = {Innocent until proven guilty: Tannerella forsythia may attenuate the virulence of Porphyromonas gingivalis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.05.674453},
pmid = {40950001},
issn = {2692-8205},
abstract = {Periodontitis is caused by a dysbiotic microbiome beneath the gum line, primarily driven by the major pathobionts Porphyromonas gingivalis (Pg) and Tannerella forsythia (Tf). Their virulence depends on the excessive, uncontrolled activity of secreted proteases that sustain chronic inflammation, leading to the destruction of tissues supporting the tooth. Paradoxically, Tf also encodes multiple protease inhibitors, including miropin, a serpin with a broad range of targets. Here, we demonstrate that both native and recombinant miropin effectively inhibit lysine-specific gingipain (Kgp) and thiol protease (Tpr), impairing the growth of Pg in peptide-limited media and reducing its virulence in vivo . A rationally designed variant, RVK-miropin, also inhibited both lysine-specific and arginine-specific gingipains, fully suppressing Pg proliferation and virulence in a mouse infection model. Miropin is abundant on the surface of Tf and forms covalent inhibitory complexes with Pg proteases. In an oral gavage model of periodontitis, coinfection with wild-type Tf (but not a miropin-deficient mutant) and Pg significantly reduced alveolar bone loss caused by Pg alone. Miropin thus counteracts Pg virulence factors and host inflammatory responses, revealing an unexpected protective role for Tf . This challenges the traditional view of Tf as a primary periodontal pathogen, suggesting a context-dependent role as a microbial modulator within the dysbiotic biofilm. Beyond periodontal disease, the unique ability of miropin to inhibit structurally diverse proteases makes it a promising candidate for the development of new therapies that restore proteolytic balance in the periodontium.},
}

@article {pmid40949997,
year = {2025},
author = {O'Sullivan, B and Herbst, KW and Hogan, AH and Maltz-Matyschsyk, M and Radolf, JD and Lawrence, D and Lynes, MA and Salazar, JC and Graf, J and , },
title = {Comparison of a long-read amplicon sequencing approach to short-read amplicons for microbiome analysis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40949997},
issn = {2692-8205},
abstract = {Most microbiome studies to date rely on sequencing short amplicons of the 16S rRNA gene on Illumina's platforms. Because of the short read length, sequences often can be identified reliably only to the family or genus levels. Long read sequencing with whole-length 16S rRNA sequencing can improve taxonomic resolution, but often only to the species level. StrainID is an alternative approach that amplifies a large segment of the ribosomal operon, including the entire 16S rRNA gene, internal transcribed spacer, and a portion of the 23S rRNA gene. This longer amplicon is designed to allow ribotype-level classification. Although studies have demonstrated the utility of StrainID for several sample types, it has not yet been validated for saliva. Here, we compared the performance of StrainID to short read amplicons with saliva samples as well as a synthetic mock DNA community and human and mouse fecal samples. Short reads were amplified with primer pairs appropriate for the corresponding sample type, and were classified with two different taxonomic databases. For both saliva and fecal samples, we found that StrainID performed similarly to short reads overall and demonstrated a key benefit with phylogenetic-based beta diversity tests and taxonomic classification. Our results further build on establishing StrainID as a valid method and specifically validate its use with saliva samples.},
}

@article {pmid40949730,
year = {2025},
author = {Dip, D and Constant, P},
title = {The potential biofertilization effect of H2 is accompanied by a modest impact on the composition of microbial communities in the rhizosphere of common vetch.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20019},
pmid = {40949730},
issn = {2167-8359},
abstract = {BACKGROUND: N2-fixing nodules release molecular hydrogen (H2) in the rhizosphere of legumes. The process activates H2-oxidizing bacteria (HOB) in soil, leading to multiple effects on biogeochemical processes and a potential biofertilization effect. The legacy effect of the energy potential of H2 on the soil microbial community structure and the population density of HOB has received little attention. The aim of the current study is to evaluate how the legacy effect of HOB, previously activated in soil microcosms exposed to elevated H2 concentrations (eH2), affects biomass production yield of common vetch (Vicia sativa), the abundance of HOB, and the composition of the rhizosphere microbiome.

METHODS: Contrasting soil samples displaying more than 60% difference in H2 oxidation activity were used as growth substrate for vetch. Soil microbial community composition and diversity were examined by bacterial 16S rRNA polymerase chain reaction (PCR) amplicon sequencing, and dry weight (DW) of the above- and below-ground biomass of vetch was analyzed to assess the impact of HOB enrichment on plant growth. The population density of high-affinity HOB was estimated by using the droplet digital polymerase chain reaction (ddPCR) technique to target the hhyL gene, encoding for the large subunit of group 1H/5 [NiFe]-hydrogenase.

RESULTS: The abundance of HOB possessing group 1H/5 [NiFe]-hydrogenase was indistinguishable between the treatments, indicating that soil nutrient content (inorganic and organic carbon) and the energy potential of H2 were insufficient to support their growth. Aeromicrobium spp. and Ramlibacter spp. were favored by eH2 exposure at the activation stage, but their response was lost after vetch growth. The root biomass and the root/shoot ratio were reduced in soil conditioned with eH2 compared to control soil exposed to ambient H2, suggesting that the plant growth-promotion activity of HOB reduces root proliferation for nutrient prospection. These results provide new experimental evidence suggesting the biofertilization effect of H2 is not universal and requires specific conditions that are yet to be identified.},
}

@article {pmid40949573,
year = {2025},
author = {Deng, S and Huang, B and Zeng, B and Cao, S and Gong, B and Liao, W and Zhang, W and Luo, S and Yang, S},
title = {Soybean green manure intercropping improves citrus quality by improving soil quality and altering microbial communities.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1560550},
pmid = {40949573},
issn = {1664-462X},
abstract = {INTRODUCTION: Intercropping leguminous green manure in orchards represents a widely adopted agroecological practice that concurrently influences soil physicochemical properties, microbial communities, and crop performance. However, the temporal mechanisms by which different durations of soybean green manure (SGM) intercropping regulate soil-plant-microbe interactions remain insufficiently understood. This study elucidates the impact of SGM intercropping duration on ecosystem functionality in citrus orchards.

METHODS: A multi-year field experiment compared SGM intercropping durations (0-, 1-, and 2-year treatments). We assessed citrus fruit quality parameters (total soluble solids, TSS; sugar-acid ratio, TSS/TA) and soil properties (pH, available nitrogen, total nitrogen, available phosphorus, available potassium, and organic matter). Microbial community structure was analyzed via high-throughput sequencing. Spearman correlation analysis (|ρ| ≥ 0.8, p < 0.05) delineated networks among intercropping duration, soil parameters, keystone microbial taxa (e.g., Proteobacteria, Acidobacteriota, Ascomycota), and fruit quality indicators.

RESULTS: The two-year intercropping treatment (T2) significantly enhanced fruit quality: TSS increased by 11.66% and the sugar-acid ratio (TSS/TA) by 41.95% (p < 0.05). Soil properties improved markedly: pH rose by 0.42 units, while AN, TN, AP, AK, and OM increased by 41.80%, 9.15%, 16.78%, 100.50%, and 79.53%, respectively (p < 0.05). Microbial communities underwent structural reorganization, exhibiting increased α-diversity, enhanced network complexity, and selective enrichment of beneficial taxa including Actinobacteria, Mortierellales, and Ascomycota. Correlation networks revealed significant associations among intercropping duration, soil parameters, keystone microbes, and fruit quality.

DISCUSSION: This study demonstrates that SGM intercropping enhances fruit quality through dual mechanisms: (1) amelioration of soil properties (pH elevation and improved nutrient availability), and (2) functional restructuring of microbial communities. Notably, specific taxa such as Actinobacteria play pivotal roles in nutrient cycling. Our findings provide empirical evidence for microbiome-mediated optimization of soil functionality, offering a sustainable rehabilitation strategy for degraded orchards and reinforcing the scientific value of ecological intensification in perennial cropping systems.},
}

@article {pmid40949138,
year = {2025},
author = {Jeong, YH and Jung, Y and Li, W and Yang, HJ and Oh, YC and Bae, JS},
title = {Spirodelae Herba ethanol extract attenuates neurotoxicity in hippocampal cells and improves scopolamine-induced cognitive impairment in mice.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1638068},
pmid = {40949138},
issn = {1663-9812},
abstract = {BACKGROUND: Spirodelae Herba (SH) is an herb that has been used in traditional medicine in East Asia. Whereas its anti-inflammatory, anti-allergic, and antioxidant activities have recently been demonstrated, the effects of SH ethanol extract (SHE) on neurotoxicity in hippocampal neurons, neuroinflammation in microglia, and cognitive impairment in mice have not been studied.

METHODS: In this study, we explored the protective effect of SHE on neurotoxicity related to oxidative stress and the related molecular mechanisms in a hippocampal cell model. We also examined the inhibitory effect of SHE on neuroinflammation and its related mechanisms in endotoxin-stimulated microglia. We also explored the ameliorative effect of SHE on cognitive impairment in mice through behavioral tests and examined histopathological changes in the hippocampus and cortex using Nissl staining. In addition, we conducted a comprehensive analysis of the related mechanisms, including the microbiota-gut-brain axis.

RESULTS: SHE inhibited glutamate-induced neurotoxicity in HT22 cells and induced changes in related mechanisms. SHE effectively inhibited lipopolysaccharide-induced neuroinflammation in BV2 cells and regulated the activation of related mechanisms. In addition, SHE administration significantly alleviated scopolamine (SCO)-induced decreases in memory and learning ability in mice. SHE suppressed damage to hippocampal neurons in the mice's brain and significantly increased the expression of the brain-derived neurotrophic factor and its related pathway proteins in hippocampal tissue. Furthermore, microbiome analysis revealed that SHE administration normalized SCO-induced gut microbiota imbalance (dysbiosis). These findings indicate that the cognitive improvement effects of SHE may be mediated through the modulation of the gut microbiota composition and the microbiota-gut-brain axis.

CONCLUSION: The results of this study demonstrate the neuroprotective and anti-neuroinflammatory effects of SHE and its strong potential as a preventive and therapeutic agent for cognitive impairment.},
}

@article {pmid40948940,
year = {2025},
author = {Xu, W and Xu, Q and Luo, P and Qu, X and Guo, D and Xie, Z and Hang, N and Kuang, M and Chen, E and Wang, L and Yan, Z and Cai, S and Mao, W and Tang, B},
title = {Gut-Brain-Microbiome Axis in the Regulation of Cancer Immune Escape and Immunotherapy in Tumors.},
journal = {Research (Washington, D.C.)},
volume = {8},
number = {},
pages = {0885},
pmid = {40948940},
issn = {2639-5274},
abstract = {Accumulating evidence demonstrates crosstalk involving the intestine and the brain, with the gut microbiota serving as a critical mediator of this interaction. The gut microbiota, along with its derived metabolites and bioactive compounds, modulates the immune microenvironment of brain tumors via the gut-brain axis, thereby influencing tumor initiation, progression, invasion, and metastasis. This review systematically summarizes the pathophysiological mechanisms underlying gut-brain axis modulation of brain tumors and examines emerging therapeutic approaches, including advances in immunotherapy and targeted therapy, that hold promise for future brain tumor treatment strategies.},
}

@article {pmid40948860,
year = {2025},
author = {Meiners, F and Ortega-Matienzo, A and Fuellen, G and Barrantes, I},
title = {Gut microbiome-mediated health effects of fiber and polyphenol-rich dietary interventions.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1647740},
pmid = {40948860},
issn = {2296-861X},
abstract = {Dietary components substantially influence aging-related health outcomes through the interaction with the gut microbiome. In this narrative review, we compiled human dietary intervention trials with varying complexities: from simple modifications like the addition of herbs and spices, nuts and beans, to whole-diet patterns such as the calorie-restricted high-polyphenol Green-Mediterranean diet. We show that the addition of fiber- and polyphenol-rich foods consistently enrich short-chain fatty acid (SCFA) producing bacteria such as Faecalibacterium, Eubacterium, Roseburia, and Blautia, and modulate various plasma and fecal metabolites, including increased levels of propionic acid when combining nuts with caloric restriction, increased visceral fat loss mediated by urolithins, and enhanced anti-inflammatory effects, potentially due to synergistic action between SCFAs and polyphenol metabolites. Furthermore, we highlight that relatively simple dietary modifications can produce meaningful microbiome and metabolite shifts, particularly in elderly and metabolically compromised populations, where the microbiome may be more responsive to intervention, and intervention effects are more pronounced. When added to strategies like caloric restriction, these foods can help preserve microbial diversity, maintain beneficial taxa, and enhance anti-inflammatory effects. These insights can inform the development of microbiome-targeted dietary strategies for improving health in high-risk populations.},
}

@article {pmid40948781,
year = {2025},
author = {Zhu, H and Huang, Y and Wang, X and Xiang, W and Xie, Y},
title = {Trends and hotspots in research related to tumor immune escape: bibliometric analysis and future perspectives.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1604216},
pmid = {40948781},
issn = {1664-3224},
abstract = {BACKGROUND: Tumor immune escape, a defining hallmark of malignant tumors, enables cancer cells to thrive within the host by evading detection and attack by the immune system. While immune checkpoint inhibitors, such as PD-1/PD-L1 antibodies, have delivered significant clinical advances, their effectiveness is tempered by modest response rates and a growing challenge of drug resistance. In this study, we aimed to explore the development process and trend of tumor immune escape, analyze the current hot spots, and predict the future research directions.

METHODS: A bibliometric analysis was conducted in this study to retrieve and analyze 1839 publications from January 1, 2009 to February 14, 2025 related to tumor immune escape. Literature was obtained from Web of Science Core Collection (WoSCC) and data visualization and trend analysis were performed using VOSviewer, CiteSpace, Bibliometrix software package.

RESULTS: The bibliometric analysis indicates that research on tumor immune escape has primarily focused on China, the United States, and European countries. China ranks first in research output and impact, with notable contributions from institutions like the Sun Yat-sen University System and the University of Texas System. The journal with the most publications is Frontiers in Immunology, while the most cited article globally is Jiang P's 2018 publication in Nature Medicine, titled "Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response." Keyword co-occurrence and burst analysis indicate that the field has undergone a thematic evolution. Early research centered around classical immune checkpoint molecules and T cell exhaustion, while more recent trends have shifted toward the tumor microenvironment (TME), multi-target combination immunotherapies, and mechanisms of immune evasion involving metabolic reprogramming and the microbiome. The integration of artificial intelligence (AI) and machine learning (ML) in immunotherapy prediction and biomarker discovery has also gained momentum, highlighting a growing cross-disciplinary approach.

CONCLUSION: This bibliometric study provides a comprehensive overview of the intellectual landscape, research hotspots, and developmental trajectory of tumor immune escape research over the past 14 years. By mapping influential nation, authors, core journals, reference, and keyword bursts, this work not only summarizes major contributions in the field but also helps researchers better understand its evolution and emerging directions. Based on the observed patterns, we propose three key areas that warrant further exploration: (1) advancing interdisciplinary research at the intersection of the microbiome, metabolism, and immune regulation; (2) integrating artificial intelligence and multi-omics data to enhance predictive modeling and therapeutic precision; and (3) combining multi-modal therapeutic strategies to overcome immune escape more effectively.},
}

@article {pmid40948779,
year = {2025},
author = {Zhu, L and Huang, J and Luo, Z and Yan, H and Wu, X and Liao, R},
title = {Lactobacillus salivarius extracellular vesicles enhance gut and liver function in MAFLD.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1660131},
pmid = {40948779},
issn = {1664-3224},
abstract = {BACKGROUND: Metabolic dysfunction-associated fatty liver disease (MAFLD) is associated with an accumulation of fat in the liver, disruptions in lipid metabolism, and imbalances in the gut microbiome. Extracellular vesicles (EVs) derived from probiotics have emerged as potential mediators of host lipid metabolism effect. The precise mechanisms by which EVs derived from probiotics influence MAFLD are still not fully understood.

METHODS: We examined the therapeutic potential of EVs sourced from Lactobacillus salivarius SNK-6 (LsEVs) using a mouse model of MAFLD and fatty acids induced cells.

RESULTS: Oral LsEVs administration reduced weight gain, lower liver enzyme levels, and less liver fat in mice. Meanwhile, LsEVs increases the secretion of anti-inflammatory factor IL-4 in mice subjected to a high-fat diet, but inhibited the pro-inflammatory cytokine secretion in lipopolysaccharide induced gut cells. Mechanistically, LsEVs enhance liver cell mitophagy via Beclin-1 and PPAR related pathways. LsEVs also increased tight junction proteins in epithelial cells. Furthermore, LsEVs boost gut bacterial diversity in MAFLD -afflicted mice by promoting beneficial Bacteroidota and suppressing harmful Desulfovibrio.

CONCLUSIONS: Our research established a foundation for the future use of LsEVs in treating MAFLD and provided novel insights into the mechanisms of lipid metabolism influenced by EVs derived from probiotics in the context of MAFLD.},
}

@article {pmid40948777,
year = {2025},
author = {Tukaj, S},
title = {Hsp90 as a pathophysiological factor and emerging therapeutic target in atopic dermatitis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1658399},
pmid = {40948777},
issn = {1664-3224},
abstract = {Heat shock protein 90 (Hsp90) is a molecular chaperone that plays a critical role in stabilizing and regulating numerous client proteins involved in inflammation, immune activation, and skin barrier homeostasis. Emerging evidence suggests that Hsp90 contributes to the pathophysiology of atopic dermatitis (AD), a chronic inflammatory skin disorder characterized by immune dysregulation, epidermal barrier dysfunction, and microbial imbalance. Notably, elevated intracellular Hsp90 activity has been reported in peripheral blood leukocytes of AD patients, alongside increased extracellular Hsp90 and anti-Hsp90 IgE antibodies. Preclinical studies employing murine models of AD, including dinitrochlorobenzene (DNCB)- and calcipotriol (MC903)-induced dermatitis, have demonstrated that both topical and systemic inhibition of Hsp90 ameliorates disease severity. These improvements correlate with reduced epidermal hyperplasia, decreased expression of Th/Th2 cytokines, attenuation of keratinocyte-derived alarmins, and suppression of inflammation. Additionally, Hsp90 inhibition limits the infiltration or activation of immune cells such as T cells, neutrophils, eosinophiles, and mast cells in the skin. Mechanistic investigations reveal that Hsp90 blockade downregulates key signaling pathways implicated in AD pathogenesis, notably NF-κB and JAK-STAT. In vitro studies further corroborate that Hsp90 inhibition reduces proinflammatory responses in keratinocytes, CD4[+] T cells, and eosinophils. Beyond modulating skin inflammation, Hsp90 blockade partially restores gut microbiota dysbiosis and impairs Staphylococcus aureus biofilm formation, both relevant to AD pathogenesis. Although clinical data on Hsp90 inhibitors in AD are still lacking, early-phase trials in psoriasis and hidradenitis suppurativa suggest potential therapeutic benefit. Collectively, these findings underscore a multifaceted role for Hsp90 in AD and support its potential as a promising novel therapeutic target.},
}

@article {pmid40948759,
year = {2025},
author = {Deng, X and Huang, S},
title = {Microbiome-macrophage crosstalk in the tumor microenvironment: implications for oral squamous cell carcinoma progression and therapy.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1651837},
pmid = {40948759},
issn = {1664-3224},
abstract = {Oral squamous cell carcinoma (OSCC) remains a formidable malignancy with persistently poor clinical outcomes. Recent research has underscored the pivotal role of the innate immune system, particularly tumor-associated macrophages (TAMs), a key component of the myeloid lineage, in orchestrating the tumor microenvironment (TME) and shaping disease progression. As professional phagocytes of the innate immune system, macrophages not only mediate pathogen recognition and inflammatory responses but also undergo functional polarization in response to local cues. In OSCC, dysbiosis of the oral microbiota, marked by the overrepresentation of species such as Fusobacterium nucleatum and Porphyromonas gingivalis-acts as a chronic inflammatory trigger that promotes epithelial-mesenchymal transition (EMT), immune evasion, and tumor growth. These pathogenic bacteria actively engage innate immune signaling pathways such as TLRs and CSF-1R, skewing macrophages toward an immunosuppressive M2 phenotype. M2-like TAMs then contribute to tumor progression by secreting anti-inflammatory cytokines (IL-10, TGF-β), promoting angiogenesis, and expressing immune checkpoint ligands such as PD-L1. This review summarizes current knowledge on the bidirectional crosstalk between dysbiotic microbiota and innate immune macrophages in OSCC, highlighting key receptor-mediated pathways and their implications for immune suppression, metastasis, and therapy resistance. Targeting microbiota modulation or innate immune reprogramming represents a promising strategy for restoring anti-tumor immunity and enhancing therapeutic efficacy in OSCC.},
}

@article {pmid40948461,
year = {2025},
author = {Xu, Y and Wang, MC},
title = {The intratumoral microbiota in breast cancer: from basic research to clinical translation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2560695},
doi = {10.1080/19490976.2025.2560695},
pmid = {40948461},
issn = {1949-0984},
abstract = {Breast cancer remains a leading global malignancy among women, with increasing incidence and mortality. Recent advances in multi-omics technologies have revealed the presence of diverse microbial communities in the tumor microenvironment, comprising bacteria, viruses, and fungi. These microbes play complex roles within tumor initiation and progression, affecting local inflammation and modulating host metabolism, genomic stability, and immune responses. Emerging evidence indicates that the intratumoral microbiota holds diagnostic potential and represents a novel biomarker for molecular subtyping and prognosis. Furthermore, intratumoral microbiota offer new avenues for targeted interventions, such as engineered bacteria and phage therapy, which may overcome limitations of conventional treatments. This review summarizes current insights into the composition, colonization pathways, mechanisms, and clinical applications of intratumoral microbiota, underscoring their potential to advance precision medicine in breast cancer.},
}

@article {pmid40948444,
year = {2025},
author = {Bryson, S and Sisson, Z and Nelson, B and Grove, J and Reister, E and Liachko, I and Auch, B and Graiziger, C and Khoruts, A},
title = {Use of proximity ligation shotgun metagenomics to investigate the dynamics of plasmids and bacteriophages in the gut microbiome following fecal microbiota transplantation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2559019},
doi = {10.1080/19490976.2025.2559019},
pmid = {40948444},
issn = {1949-0984},
abstract = {Proximity ligation shotgun metagenomics facilitate the analysis of the relationships between mobile genetic elements, such as plasmids and bacteriophages, and their specific bacterial hosts. We applied this technique to investigate the changes in the fecal microbiome of patients receiving fecal microbiota transplantation (FMT) for recurrent Clostridioides difficile infections (rCDI). FMT was associated with successful engraftment of donor bacteria along with their associated bacteriophages. While fecal microbial diversity increased in all patients, the extent of specific bacterial taxa engraftment varied among individual patients. Interestingly, some donor bacteriophages remained closely linked to their original bacterial hosts, while others expanded their associations across different bacterial taxa. Notably, FMT partially reduced the content of vancomycin resistance and extended-spectrum beta-lactamase genes in the fecal microbiome of rCDI patients.},
}

@article {pmid40948418,
year = {2025},
author = {Stinson, LF and Norrish, I and Mhembere, F and Cheema, AS and Mullally, CA and Payne, MS and Geddes, DT},
title = {Seeding and feeding: nutrition and birth-associated exposures shape gut microbiome assembly in breastfed infants.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2557981},
doi = {10.1080/19490976.2025.2557981},
pmid = {40948418},
issn = {1949-0984},
abstract = {Gut microbiome establishment in early life is influenced by maternal, infant, and environmental factors, with disruptions linked to later disease risk. Although infant diet is a major determinant of microbial composition, longitudinal data in breastfed infants, particularly in the context of birth interventions, remain limited. We profiled 698 stool samples from 84 predominantly or exclusively breastfed infants in the BLOSOM cohort, spanning 10 time points from 1 week to 2 years of age using full-length 16S rRNA gene sequencing and targeted qPCR. After an initial volatile period, microbiome composition and diversity stabilized between months 2 and 5. Introduction of solid foods then triggered a marked ecological shift, with significant increases in diversity (p < 1 × 10[-11]) and broad compositional restructuring. In contrast, weaning had minimal impact on overall microbiota structure but was associated with lower abundances of several Bifidobacterium species, highlighting the sustained bifidogenic effect of human milk. Cesarean delivery was associated with transient reductions in Bacteroides abundance and prevalence, but did not affect Bifidobacterium, likely due to the bifidogenic effects of human milk. Reductions in Bacteroides, however, were not reflected in quantitative analyses, emphasizing the importance of absolute abundance measures. Our results offer novel insight into gut microbiome development under optimal feeding conditions, suggesting that breastfeeding may buffer early-life microbiome perturbations, while diet transitions exert major and lasting effects.},
}

@article {pmid40948329,
year = {2025},
author = {Huang, S and Li, S and Zhao, R and Yang, H and Liu, Y and Wang, X and Zhang, J and Shen, C and Li, F and Xu, H and Guo, C and Ni, X and Li, H and Cao, Q and Zhou, Z},
title = {Post-COVID-19 disruption of the respiratory microbiome modulates Mycoplasma pneumoniae: a multi-center retrospective investigation study.},
journal = {Emerging microbes & infections},
volume = {},
number = {},
pages = {2562053},
doi = {10.1080/22221751.2025.2562053},
pmid = {40948329},
issn = {2222-1751},
abstract = {Since the COVID-19 pandemic, there has been a notable resurgence of Mycoplasma pneumoniae pneumonia (MPP) in children, with a concerning rise in the severity of cases. Although changes in post-pandemic respiratory infection patterns have been documented, the reasons behind the increased severity of MPP, especially concerning shifts in the respiratory microbiota, are not well understood. This study aims to explore how pandemic-associated disruptions in respiratory microbiota contribute to MPP severity. Through analysis of multiple independent cohorts, we found that the depletion of protective respiratory microbiota exacerbates MPP severity by reducing colonization resistance against M. pneumoniae. We identified two antagonistic microbiota modules with distinct metabolic features and community structures that regulate pathogen colonization and disease severity. Using a Susceptible-Infected-Recovered (SIR) model, we simulated M. pneumoniae infection dynamics across different microbiota states. Additionally, a machine-learning model based on eight key microbes effectively distinguished between cases and controls and predicted infection severity, offering insights into post-pandemic respiratory infections. This study underscores the essential role of the respiratory microbiota in influencing the severity of M. pneumoniae infections. Our findings offer a framework for managing respiratory infections in the post-pandemic era, highlighting the significance of understanding microbial community dynamics in determining disease outcomes. These insights could guide the development of therapeutic strategies focused on restoring or enhancing the protective microbiota, which may offer an effective strategy for the management of MPP and other respiratory infections.},
}

@article {pmid40948029,
year = {2025},
author = {Peng, Y and Jiang, S and Song, Y and Luo, P and Li, J and Hu, D and Zhou, JG and Yu, G and Xu, T and Wang, S},
title = {ggalign: Bridging the Grammar of Graphics and Biological Multilayered Complexity.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e07799},
doi = {10.1002/advs.202507799},
pmid = {40948029},
issn = {2198-3844},
support = {82303953//National Natural Science Foundation of China/ ; 81802533//National Natural Science Foundation of China/ ; 82472912//National Natural Science Foundation of China/ ; 32270677//National Natural Science Foundation of China/ ; 82504050//National Natural Science Foundation of China/ ; 2025JJ40079//Hunan Provincial Natural Science Foundation of China/ ; 2024ZD0525700//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 2023ZD0502105//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 2022-4-4087//Capital's Funds for Health Improvement and Research of China/ ; 2018YFA0902802//National Key Research and Development Program of China/ ; Z191100006619010//Beijing Municipal Science & Technology Commission/ ; 24YJCZH462//Ministry of Education in China Liberal Arts and Social Sciences Foundation/ ; QJJ-2024-333//Youth Science and Technology Elite Talent Project of Guizhou Provincial Department of Education/ ; ZunshiKeheHZ(2023)142//Excellent Young Talent Cultivation Project of Zunyi City/ ; ZYSE2023-02//Future Science and Technology Elite Talent Cultivation Project of Zunyi Medical University/ ; 7//Key Program of the Education Sciences Planning of Guizhou Province/ ; //Central South University Startup Funding/ ; },
abstract = {Data visualization is essential for exploring and communicating complex biological datasets. As omics data grow in scale and complexity, there is an increasing demand for visualization tools that are both flexible and extensible. We present ggalign, an R package that extends the ggplot2 ecosystem by introducing an integrative framework for composable visualization. Designed to overcome limitations of existing tools, ggalign supports modular, data-aware layouts-including circular, stacked, and quadrant-based configurations-and enables the representation of diverse data relationships, such as one-to-many and many-to-one connections. Its ability to reorder and group observations using data-driven or domain-specific criteria enhances the interpretability of high-dimensional datasets. Moreover, ggalign introduces a novel linking mechanism for visualizing interconnections across heterogeneous data types, as demonstrated in genomic and microbiome case studies. Together, these features position ggalign as a versatile and reproducible solution for multi-omics research, supporting both exploratory data analysis and publication-ready presentation.},
}

@article {pmid40947719,
year = {2025},
author = {Wei, CR and Basharat, Z and Osama, M and Mah, K and Waheed, Y and Hassan, SS},
title = {An Overview of the Association of the Urinary Tract Microbiome with Various Diseases and Implications for Therapeutics.},
journal = {Mini reviews in medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113895575398906250825113635},
pmid = {40947719},
issn = {1875-5607},
abstract = {The urinary tract (UT) was once considered sterile, but now it is known to host a diverse community of microorganisms, known as the urinary microbiome. The collective microbiota is made up of bacteria, fungi, and viruses, necessary for maintaining UT health. This review aims to synthesize current knowledge on the urinary microbiome and clarify its emerging role as a key modulator in both health and a wide spectrum of UT disorders. Dysbiosis within this microbial community has been linked to conditions such as urinary tract infections (UTIs), interstitial cystitis/ bladder pain syndrome (IC/BPS), urinary incontinence, urolithiasis, benign prostatic hyperplasia (BPH), and even urinary tract malignancies. Advances in methodologies, such as expanded quantitative urine culture and metagenomics, have provided valuable insights into microbial variability influenced by factors like age, sex, and disease conditions. Additionally, this review explores the therapeutic potential of probiotics and bacteriophages, as well as the association of urinary microbiota with autoimmune and inflammatory conditions. Special emphasis is placed on translational relevance, including emerging microbiome-targeted therapies and personalized interventions for UTIs. Ethical considerations allied with UT microbiome research, such as data privacy, informed consent, and equitable access to emerging therapies, are also discussed. Despite substantial progress, challenges such as methodological heterogeneity, a lack of longitudinal data, and unresolved causal relationships persist. The study concludes by identifying key knowledge gaps and proposing future directions for multidisciplinary research to advance therapeutic innovation in urological health.},
}

@article {pmid40909751,
year = {2025},
author = {Balsamo, JM and Yan, Y and Thai, D and Cologna, SM and Bess, EN},
title = {Multiomic Analysis Reveals Molecular Pathways Associated with Intestinal Aggregation of α-Synuclein.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40909751},
issn = {2692-8205},
support = {R01 NS138879/NS/NINDS NIH HHS/United States ; },
abstract = {Aggregates of the protein α-synuclein may initially form in the gut before propagating to the brain in Parkinson's disease. Indeed, our prior work supports that enteroendocrine cells, specialized intestinal epithelial cells, could play a key role in the development of this disease. Enteroendocrine cells natively express α-synuclein and synapse with enteric neurons as well as the vagus nerve. Severing the vagus nerve reduces the load of α-synuclein aggregates in the brain, suggesting that this nerve is a conduit for gut-to-brain spread. Enteroendocrine cells line the gut lumen, as such, they are in constant contact with metabolites of the gut microbiota. We previously found that when enteroendocrine cells are exposed to nitrite-a potent oxidant produced by gut bacterial Enterobacteriaceae-a biochemical pathway is initiated that results in α-synuclein aggregation. Here, we determined that dopamine production is critical to this mechanism of nitrite-induced α-synuclein aggregation. Using enteroendocrine cells, we modulated dopamine biosynthesis and profiled the cellular proteome and lipidome. Proteomic signatures in dopamine-free cells were distinctly different than in enteroendocrine cells, highlighting pathways relevant to intestinal development of Parkinson's disease. Intriguingly, we observed that enteroendocrine cells maintain viability upon exposure to nitrite and in the presence of α-synuclein aggregates. This cellular robustness suggests that dopamine-producing enteroendocrine cells may be a reservoir of toxic α-synuclein aggregates, which can spread through a prion-like process. As a possible antidote, our findings show that benserazide-a chemical inhibitor of dopamine biosynthesis-limits formation of these aggregates in enteroendocrine cells. These studies lay a foundation for mechanistically informed therapeutic targets to prevent intestinal formation of α-synuclein aggregates before they spread to the brain.},
}

@article {pmid40947184,
year = {2025},
author = {Wang, C and Qin, S and Shi, J and Zhu, J and Ju, X and Wang, W and Yang, L},
title = {Ideal dietary fiber model: Personalized gut microbiota modulation based on structure-function relationships.},
journal = {Carbohydrate polymers},
volume = {368},
number = {Pt 2},
pages = {124097},
doi = {10.1016/j.carbpol.2025.124097},
pmid = {40947184},
issn = {1879-1344},
abstract = {Dietary fiber has emerged as a central modulator of gut microbiota composition and host physiology, garnering unprecedented scientific attention. Here, we propose the "Ideal Dietary Fiber Model"-a personalized, structure-guided framework designed to precisely shape gut microbial ecosystems and promote host health. Departing from traditional fiber classifications, this model emphasizes the construction of composite fiber formulations based on detailed structural parameters, including monosaccharide composition, glycosidic linkage types, and degree of polymerization. Particular focus is given to oligosaccharides, whose fine structural features confer high selectivity in modulating microbial communities and the production of key metabolites such as short-chain fatty acids, indoles, and neurotransmitter precursors. This review synthesizes recent advances in fiber-microbiota interactions across metabolic, inflammatory, and neurocognitive diseases, including obesity, type 2 diabetes, Non-Alcoholic Fatty Liver Disease, inflammatory bowel disease, colorectal cancer, depression, anxiety, and Alzheimer's disease. While mechanistic insights continue to expand, current evidence remains largely preclinical, highlighting the gap between experimental findings and clinical translation. We argue that integrating microbiome stratification with fiber structure-function databases will be essential for advancing precision nutrition. The Ideal Dietary Fiber Model offers a conceptual and practical foundation for microbiota-targeted dietary design, but its therapeutic potential requires rigorous clinical validation.},
}

@article {pmid40947138,
year = {2025},
author = {Wang, W and Yu, Y and Wang, R and Wang, Y and Ding, X and Lu, G and Lu, C and Liang, C and Zhang, S and Yi, B and Bai, J and Zhang, L and Li, P and Wen, Q and Cui, B and Zhang, F},
title = {Holdemanella biformis augments washed microbiota transplantation for the treatment of radiation enteritis.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-335230},
pmid = {40947138},
issn = {1468-3288},
abstract = {BACKGROUND: Current microbiome-based therapeutics face two prominent issues: the limited clinical efficacy of probiotics and the significant variability in the efficacy of microbiota transplantation across different diseases. Although washed microbiota transplantation (WMT) is a new faecal microbiota transplantation, a single therapeutic agent cannot be universally effective for multiple dysbiosis-related diseases.

OBJECTIVE: We introduced a new therapeutic concept, X-augmented WMT (X-auWMT), which combines a disease-specific beneficial microbe, 'X', with WMT to enhance its effectiveness. Our goal was to identify a candidate 'X' bacterium to augment WMT efficacy and examine the efficacy of X-auWMT in animal models of radiation enteritis (RE).

DESIGN: We conducted a prospective, non-randomised cohort study on a cohort of abdominal or pelvic cancer patients who developed RE after radiotherapy to identify a potential beneficial microbe. We used RE mouse models to evaluate the efficacy of X-auWMT compared with WMT. Multiomics analyses and experiments were undertaken to elucidate the underlying mechanisms.

RESULTS: WMT significantly alleviated multiple clinical symptoms in RE patients compared with routine treatments. We identified Holdemanella biformis as a candidate 'X' bacterium within the RE cohort and developed Hb-auWMT. Hb-auWMT significantly mitigated radiation-induced injury compared with WMT, exhibiting enhanced anti-apoptotic effects, improved maintenance of epithelial hypoxia, increased Treg cell levels and elevated butyrate and valerate levels in the RE mouse model. PPAR-γ is an essential pathway for the therapeutic efficacy of Hb-auWMT.

CONCLUSIONS: This study overcomes the aforementioned recognised limitations with probiotics and microbiota transplantation and provides a new research paradigm in the concept of microbiome-based therapeutics.},
}

@article {pmid40947007,
year = {2025},
author = {Ish-Horowicz, J and Filippi, S},
title = {Modelling phylogeny in 16S rRNA gene sequencing datasets using string-based kernels.},
journal = {Journal of theoretical biology},
volume = {},
number = {},
pages = {112249},
doi = {10.1016/j.jtbi.2025.112249},
pmid = {40947007},
issn = {1095-8541},
abstract = {The bacterial microbiome is increasingly being recognised as a key factor in human health, driven in large part by datasets collected using 16S rRNA (ribosomal ribonucleic acid) gene sequencing, which enable cost-effective quantification of the composition of an individual's bacterial community. One of the defining characteristics of 16S rRNA datasets is the evolutionary relationships that exist between taxa (phylogeny). Here, we demonstrate the utility of modelling these phylogenetic relationships in two statistical tasks (the two sample test and host trait prediction) and propose a novel family of kernels for analysing microbiome datasets by leveraging string kernels from the natural language processing literature. We show via simulation studies that a kernel two-sample test using the proposed kernel is sensitive to the phylogenetic scale of the difference between the two populations. In a second set of simulations we also show how Gaussian process modelling with string kernels can infer the distribution of bacterial-host effects across the phylogenetic tree and apply this approach to a real host-trait prediction task. The results in the paper can be reproduced by running the code at https://github.com/jonathanishhorowicz/modelling_phylogeny_in_16srrna_using_string_kernels.},
}

@article {pmid40946970,
year = {2025},
author = {van Walraven, N and FitzGerald, RJ and Danneel, HJ and Amigo-Benavent, M},
title = {Bioactive peptides in cosmetic formulations: Review of current in vitro and ex vivo evidence.},
journal = {Peptides},
volume = {},
number = {},
pages = {171440},
doi = {10.1016/j.peptides.2025.171440},
pmid = {40946970},
issn = {1873-5169},
abstract = {Bioactive peptides are increasingly employed in cosmetic products and these are generically known as cosmetic peptides. This review aims to provide an update on current information related to commercially available cosmetic peptides, and the in vitro and ex vivo evidence for their potential biological effects. A total of 102 commercially available cosmetic peptides were identified. The majority of these peptides are inspired by molecules already found in the human body, including sequences from extracellular matrix molecules, also known as matrikines. Cosmetic peptides are produced either through chemical synthesis or via biotechnological processes. Their claimed biological activities include signaling to increase collagen and hyaluronic acid production, modulation of pigmentation, maintenance of a healthy skin microbiome, antioxidant activity and cellular defense, immunomodulation, neurotransmitter inhibition, enzyme activity inhibition and trace mineral carriers. The primary structure and current scientific evidence for the bioactivities of these peptides are presented and discussed. The review highlights the diverse methodological approaches used and the outcomes measured in the assessment of cosmetic peptide efficacy. Overall, a large range of cosmetic peptides are commercially available whose efficacy is supported by divergent levels of in vitro and ex vivo data.},
}

@article {pmid40946892,
year = {2025},
author = {Cornu Hewitt, B and Odendaal, ML and de Rooij, MMT and Bossers, A and Chu, ML and van Kersen, W and Lotterman, A and van der Giessen, J and Bogaert, D and Smit, LAM},
title = {Occupational and environmental livestock exposures are associated with alterations in the upper respiratory tract microbiome.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122847},
doi = {10.1016/j.envres.2025.122847},
pmid = {40946892},
issn = {1096-0953},
abstract = {Livestock farm emissions have been linked to respiratory health, potentially mediated through alterations in the respiratory microbiota. We investigated the associations between occupational and environmental livestock farm exposures and changes in the upper respiratory tract (URT) microbiome. Nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected from goat farmers (91 NP and 96 OP samples) and rural residents (956 NP and 954 OP samples), and microbial community composition was characterised using 16S rRNA gene amplicon sequencing. First, we compared the respiratory microbiome of goat farmers and residents to assess the effects of occupational exposure. Next, we evaluated how varying levels of environmental livestock exposure influenced the microbiome of rural residents. Goat farmers exhibited higher NP microbial diversity but lower OP diversity compared to the residents. NP samples from farmers had higher relative abundances of the genera Sphingomonas, Pseudomonas and Jeotgalicoccus, and lower abundances of Corynebacterium, Lawsonella and Nocardioides. In the OP of goat farmers, Rothia was the most significantly increased genus. Residential exposure levels - assessed through livestock density (pigs, cattle, poultry, and goats) and modelled livestock-related microbial emissions - were not associated with overall microbiome diversity or composition. However, increasing livestock exposure was associated with subtle taxonomic shifts, particularly in the NP. Our findings highlight the pronounced influence of occupational exposure on the URT microbiome and the more subtle effects of environmental exposure, both of which may have implications for respiratory health.},
}

@article {pmid40946852,
year = {2025},
author = {Zheng, C and Song, J and Shan, M and Qiu, M and Cui, M and Huang, C and Chen, W and Wang, J and Zhang, L and Yu, Y and Fang, H},
title = {Nutrition cycling microbiomes drive the succession of antibiotic resistome in long-term manured soils.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.09.019},
pmid = {40946852},
issn = {2090-1224},
abstract = {INTRODUCTION: The spread of antibiotic resistance genes (ARGs) in the environment has received widespread attention. Nutrition cycling microbiomes specifically refer to microorganisms capable of mineralizing nitrogen and phosphorus, which dominate the microbial community in long-term manured soils. However, changes in nutrition cycling genes/microbiomes and the mechanisms by which these microbiomes mediate ARG transfer through vertical and horizontal gene transfer remain poorly understood.

OBJECTIVES: This study aimed to elucidate how nutrition cycling microbiomes mediate the dissemination and ecological risk of antibiotic resistance genes (ARGs) in long-term manure-amended soils.

METHODS: Here, we employed metagenomic assembly and binning to investigate the distribution of nutrition mineralization genes, nutrition cycling microbiomes, mobile genetic elements (MGEs), and ARGs in rapeseed cake, pig manure, duck manure and their corresponding long-term amended soils.

RESULTS: Long-term application of organic manures led to the dominance of nutrition cycling microbiomes associated with methanogenesis (pmoA and mmoX) and incomplete denitrification (norBC), thereby exacerbating soil nutrient loss. Nutrition cycling microbiomes, particularly Rhodanobacter and Pseudomonas, served as the primary host for ARGs and harbored multiple clinically relevant resistance genes, including MexF, ceoB, and mdtB. Notably, the abundance of ARGs in rapeseed cake and pig manure was 2.09-2.23-fold and 6.74-7.38-fold higher, respectively, than in duck manure, promoting the vertical transmission of ARGs via nutrition cycling microbiomes under long-term application. Furthermore, a significant positive correlation between nutrition mineralization genes and ARGs revealed a co-dispersal mechanism between nutrition cycling microbiomes and ARGs in long-term manured soils.

CONCLUSIONS: It is concluded that the nutrition cycling microbiome plays a more prominent role in shaping antibiotic resistome through vertical transfer in manured soils, compared to horizontal gene transfer mediated by MGEs.},
}

@article {pmid40946808,
year = {2025},
author = {Kuper, CF and Rennen, EAJ and Kaufmann, W},
title = {The nasal microbiome, inhalation exposure, and brain toxicity: A commentary.},
journal = {Neurotoxicology},
volume = {},
number = {},
pages = {103320},
doi = {10.1016/j.neuro.2025.103320},
pmid = {40946808},
issn = {1872-9711},
abstract = {The microbiome is increasingly discussed in diseases of the nervous system. The nasal microbiome is largely unexplored in neurotoxicity, while inhalation exposure to xenobiotics has been associated with neurodegenerative diseases linked to neurodegenerative diseases that are a growing health problem. The concept of a link between pathological changes of the nasal microbiome (dysbiosis) and brain neurotoxicity upon inhalation exposure is still in its early stages. In this commentary we argue that research into the nasal microbiome offers a great opportunity to obtain important information about the neurotoxicity of inhaled xenobiotics.},
}

@article {pmid40946805,
year = {2025},
author = {Sun, E and Zhu, X and Ness, R and Murff, HJ and Sun, S and Yu, C and Fan, L and Azcarate-Peril, MA and Shrubsole, MJ and Dai, Q},
title = {Magnesium Treatment Increases Gut Microbiome Synthesizing Vitamin D and Inhibiting Colorectal Cancer: Results from a Double-Blind Precision-based Randomized Placebo-Controlled Trial.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajcnut.2025.09.011},
pmid = {40946805},
issn = {1938-3207},
abstract = {BACKGROUND: Carnobacterium maltaromaticum and Faecalibacterium prausnitzii induce de novo gut synthesis of vitamin D to inhibit colorectal carcinogenesis in mice. Magnesium (Mg) treatment increases circulating vitamin D and Mg homeostasis is dependent on TRPM7 genotype.

OBJECTIVE: We hypothesize that Mg treatment increases gut C. maltaromaticum and F. prausnitzii and the effect differs by TRPM7 polymorphism.

METHODS: The Personalized Prevention of Colorectal Cancer Trial is a double-blind, precision-based randomized controlled trial with 240 participants randomized by both treatment and TRPM7 genotype. Stool, rectal swabs, and rectal mucosa were collected.

RESULTS: Of 239 participants that completed the trial, 226 with valid microbiome data were analyzed (treatment n=112, placebo n=114). The interaction between treatment and TRPM7 genotype was only significant for C. maltaromaticum (p=0.001) and F. prausnitzii (p=0.02) in rectal swabs. In a stratified analysis by TRPM7 genotype without the missense variant, Mg treatment compared to placebo significantly increased abundance of C. maltaromaticum (0.217±0.615 (23.01%) compared to -0.065±0.588 (-6.30%); P=0.006) and F. prausnitzii (0.105±0.817 (2.13%) compared to -0.095±0.856 (-1.92%); P =0.04) in rectal swabs. The effect on C. maltaromaticum remained after multiple comparisons (Q=0.05 for C. maltaromaticum across all sample types and genotypes). In those with the TRPM7 missense variant, Mg decreased C. maltaromaticum, but not F. prausnitzii, compared to placebo in rectal swabs (-0.065±0.511 (-6.54%) compared to 0.133±0.503 (13.30%); adjusted P=0.04). The effect did not remain after FDR correction. Mg treatment's effect on C. maltaromaticum in rectal swabs primarily appeared in females, and the treatment-genotype interaction remained significant.

CONCLUSION: In individuals with adequate TRPM7 function, Mg supplementation increases abundance of C. maltaromaticum and F. prausnitzii.

CLINICAL TRIAL REGISTRY: This trial was registered on ClinicalTrials.gov as NCT04229992 (https://clinicaltrials.gov/study/NCT04229992?term=NCT04229992&rank=1). The parent study is registered as NCT03265483, and another relevant study is registered as NCT01105169.},
}

@article {pmid40946701,
year = {2025},
author = {Iyengar, ARS and Dunkley, PR and Dickson, PW},
title = {Immunity in Parkinson's disease - the role of adaptive and auto-immune responses and gut-microbiome axis.},
journal = {Journal of neuroimmunology},
volume = {409},
number = {},
pages = {578755},
doi = {10.1016/j.jneuroim.2025.578755},
pmid = {40946701},
issn = {1872-8421},
abstract = {Parkinson's disease (PD) is the second most common neurodegenerative disorder. It is characterised by loss of dopaminergic neurons in the mid-brain and accumulation of α-synuclein aggregates referred to as Lewy bodies. PD is a progressive disease and the treatments available are aimed at addressing only its symptomatology. Immune dysregulation is one of the several mechanisms that are hypothesized to contribute towards PD pathogenesis. This review firstly addresses the interaction of innate and adaptive immune components and the role of adaptive immune responses, with a particular focus on T lymphocytes in PD. The review secondly examines the evidence for the involvement of the autoimmune system in PD, including the presence of autoantibodies and the association of autoimmunity with proteins linked with PD (α-synuclein and neuromelanin) and with infections. The review thirdly explores the connection between the gut microbiota the immune system and the impact of this relationship on the pathogenic processes of PD. Finally, this review discusses adaptive immunity based therapeutic strategies for PD, probable PD detection approaches based on autoimmunity, and the potential of gut-microbiome replenishment in PD treatment.},
}

@article {pmid40946672,
year = {2025},
author = {Farsadi, S and Sharifi, Y and Bagheri, M and Aghdashi, MA},
title = {Evaluating the gut microbiota alterations and their correlation with cytokine gene expression in patients with ankylosing spondylitis.},
journal = {International immunopharmacology},
volume = {165},
number = {},
pages = {115534},
doi = {10.1016/j.intimp.2025.115534},
pmid = {40946672},
issn = {1878-1705},
abstract = {PURPOSE: Ankylosing spondylitis (AS) is a common form of spondyloarthritis, recognized as a chronic autoimmune disorder with an unclear etiology. This study aimed to investigate changes in the intestinal microbiota, (Bifidobacterium sp., Bacteroides sp., Clostridium leptum, and Enterobacteriaceae) and to explore their relationship with cytokine gene expression in patients with AS attending a rheumatology clinic or admitted to the rheumatology ward of Imam Khomeini Hospital in Urmia, Iran.

METHODS: This investigation involved a cohort of twenty patients diagnosed with AS alongside a control group of twenty healthy individuals matched for age and sex. Fecal specimens were collected to extract DNA, which was subsequently analyzed for the characterization of the gut microbiome via PCR and quantitative real-time PCR. Furthermore, RNA obtained from peripheral blood mononuclear cells was analyzed to quantify the expression of pro-inflammatory cytokines as well as anti-inflammatory cytokines using qPCR.

RESULTS: The analysis revealed that the bacterial load of Enterobacteriaceae, Bacteroides and Bifidobacterium were markedly elevated in the patients than in the control group (P < 0.05). The relative amount of TNF-α, IL-17F, IL-17 A, and INF-γ were significantly increased in patients group compared to controls (P < 0.05). But, the relative amount of TGF-β was significantly reduced in AS patients compared with controls (P = 0.03).

CONCLUSION: To conclude, an imbalance was observed in the dominant intestinal microbiota in AS patients, leading to a shift in the microbiota towards the production and secretion of inflammatory cytokines, as well as a reduction in anti-inflammatory cytokines, thereby playing a critical role in the pathogenesis of AS disease.},
}

@article {pmid40946372,
year = {2025},
author = {Tokuno, M and Commey, KL and Yamamoto, A and Tokushige, M and Tsukigawa, K and Nishi, K and Otagiri, M and Ekino, K and Yamasaki, K},
title = {Insights into the renal protective effects of 7-phenylheptanoic acid in chronic kidney disease mice: Modulation of indoxyl sulfate production and gut microbiome homeostasis.},
journal = {Drug metabolism and disposition: the biological fate of chemicals},
volume = {53},
number = {10},
pages = {100149},
doi = {10.1016/j.dmd.2025.100149},
pmid = {40946372},
issn = {1521-009X},
abstract = {7-Phenylheptanoic acid (7-PH) has been reported to slow the progression of chronic kidney disease (CKD) in mice. Although the mechanism behind this renal protection remains unclear, it is strongly linked to reduced production of indoxyl sulfate (IS), a uremic toxin derived from dietary L-tryptophan through a multistep enzymatic process. It is also known that there is a strong association between CKD progression and gut microbiome dysbiosis. This study aimed to determine the involvement of each enzymatic step and identify the primary target enzymes through which 7-PH suppresses IS production, as well as investigate whether the protective effects of 7-PH involve microbiome modulation. First, we evaluated the effects of 7-PH on tryptophan indole-lyase (TIL), cytochrome P450 2E1 (CYP2E1), and sulfotransferase enzymes using in vitro enzyme kinetic studies. We then analyzed the impact of 7-PH on gut microbiome homeostasis in adenine-induced CKD mice using high-throughput 16S rRNA gene sequencing of fecal samples. Our findings indicate that 7-PH primarily targets the conversion of L-tryptophan to indole by acting as a competitive inhibitor of TIL (Ki = 92 μM). It also exhibits weak noncompetitive inhibition of CYP2E1 but does not affect sulfotransferase activity. Microbiome analysis revealed that 7-PH attenuates CKD-associated gut microbiota dysbiosis by selectively preserving beneficial bacterial taxa, such as Muribaculaceae and Alloprevotella, while inhibiting dysbiotic and opportunistic pathogenic groups, including Staphylococcus and Oligella. Therefore, the renal protective effects of 7-PH involve at least 2 interconnected mechanisms: the suppression of IS production through TIL inhibition and the modulation of the gut microbiome. SIGNIFICANCE STATEMENT: The mechanisms behind the renal protective effects of 7-phenylheptanoic acid (7-PH) in chronic kidney disease mice have been clarified. 7-PH reduces indoxyl sulfate production by primarily inhibiting tryptophan indole-lyase activity. Additionally, 7-PH modulates the gut microbiome by preserving beneficial bacterial taxa while selectively suppressing opportunistic pathogens, thereby attenuating chronic kidney disease-associated microbiome dysbiosis.},
}

@article {pmid40946313,
year = {2025},
author = {Zaković, S and Rivera, GE and Gomaid, R and Martinez, CG and Kappler, C and Marois, E and Levashina, EA},
title = {The major role of the REL2/NF-κB pathway in the regulation of midgut bacterial homeostasis in the malaria vector Anopheles gambiae.},
journal = {Cell reports},
volume = {44},
number = {9},
pages = {116282},
doi = {10.1016/j.celrep.2025.116282},
pmid = {40946313},
issn = {2211-1247},
abstract = {Multicellular organisms harbor diverse microbial communities that play essential roles in host physiology. While often beneficial, these interactions require tight regulation to prevent dysbiosis and disease. This study examines the tissue-specific immune responses of mosquitoes to blood feeding and Plasmodium falciparum infection in Anopheles females. We demonstrate that REL2 regulates the expression of antimicrobial peptide genes and shapes midgut bacterial composition post-blood meal. Loss of REL2 leads to midgut dysbiosis, characterized by the overgrowth of Serratia spp., and mosquito lethality after blood feeding. Interestingly, Serratia-induced dysbiosis also reduces P. falciparum prevalence in surviving mosquitoes. Our findings highlight the critical role of the immune system in maintaining midgut bacterial homeostasis and uncover complex interactions between mosquito immunity, gut microbiota, and malaria parasites.},
}

@article {pmid40946247,
year = {2025},
author = {Yuan, T and Xing, J and Liu, P},
title = {Decoding the gut microbiota metabolite-matrix metalloproteinase-3 axis in breast cancer: a multi-omics and network pharmacology study.},
journal = {Molecular diversity},
volume = {},
number = {},
pages = {},
pmid = {40946247},
issn = {1573-501X},
abstract = {Breast cancer is a malignant tumor originating from the breast epithelium, and emerging evidence suggests that the gut microbiota influences its development, progression, and treatment, although its role remains underexplored. In this study, we employed an integrative multi-omics framework that combined network pharmacology, machine learning, SHapley Additive exPlanations (SHAP), and single-cell RNA sequencing to systematically investigate key interactions between microbial metabolites and their targets. Core regulators were further validated using Mendelian randomization (MR), while molecular docking was applied to evaluate the binding affinity of candidate metabolites. Matrix metalloproteinase-3 (MMP3) emerged as a central molecule involved in multiple cancer-related signaling pathways, including PI3K-AKT, MAPK, and HIF-1, with promising druggable potential. Eight non-toxic gut microbial metabolites-such as indole-3-propionic acid, glycocholic acid, and 4-hydroxyphenylpyruvate-demonstrated strong binding affinity to MMP3 and favorable pharmacokinetic properties, highlighting a previously unappreciated microbiota-MMP3 axis as a promising avenue for therapeutic intervention in breast cancer. These findings provide a basis for subsequent in vitro and in vivo validation and underscore the translational potential of the identified microbial metabolites, thereby supporting the development of microbiome-derived therapeutic strategies for breast cancer.},
}

@article {pmid40945908,
year = {2025},
author = {Gao, H and Wang, H and Li, X and Zhang, F and Ba, Y and Zhao, J and He, C and Xin, S and Liu, X and Liang, G},
title = {From Theory to Practice: A Comprehensive Review of Pseudomyxoma peritonei Research and its Implications for Future Treatment.},
journal = {The American journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajpath.2025.08.005},
pmid = {40945908},
issn = {1525-2191},
abstract = {Pseudomyxoma peritonei (PMP) is a rare disease characterized by symptoms such as mucinous ascites and omental cake, typically arising from a perforated epithelial tumour of appendix. Due to its rarity, non-specific histological characteristics, and slow progression, its pathogenesis and optimal treatment remain subjects of debate. PMP is still a challenging and enigmatic condition. Increasing global attention is being directed toward understanding its pathogenesis and establishing standard treatment approaches. PMP and mucin are inextricably linked. This article highlighted the important role of mucin in the disease's pathogenesis. It also discussed several potential therapeutic strategies for eliminating mucin in PMP. Tumor development and metastasis involve a series of steps that include the interaction between the tumor and the host-derived stromal environment, which promotes angiogenesis and activation of inflammatory cells. Inflammatory cytokines and chemokines play a crucial role in the progression and development of PMP. The microbiome and specific microorganisms may directly influence tumor development, progression, and responses to certain therapies in PMP. Thus, the paper summarized the interactions among bacteria, the immune system, and mucin interact in PMP, focusing on the mechanisms that related to abnormal mucin and tumor growth. This review critically examined the existing literature on the clinical features, pathological processes, and treatment options in PMP, aiming to guide future research towards identifying novel therapeutic targets and gut-related disease biomarkers.},
}

@article {pmid40945867,
year = {2025},
author = {He, X and Dennis, KK and Jarrell, ZR and Ly, VT and Go, YM and Jones, DP},
title = {Vanadyl sulfate supplementation alters the intestinal microbiome and bile acid metabolism.},
journal = {Toxicology and applied pharmacology},
volume = {},
number = {},
pages = {117548},
doi = {10.1016/j.taap.2025.117548},
pmid = {40945867},
issn = {1096-0333},
abstract = {Less than 10 μg/kg body weight (BW) vanadium (V) is consumed daily by humans in their diet and drinking water. V in the form of vanadyl sulfate (V[+4]) is promoted as an over-the-counter supplement with anti-diabetic effects and is consumed by some individuals at up to 200 μg/kg BW per day in dietary supplements. The impact of long-term consumption of high-dose V supplements on intestinal microbial communities and intestinal metabolomics is not known. This project tested the hypothesis that long-term intake of high-dose supplemental vanadyl sulfate alters the intestinal microbiome and metabolome in mice. In this study, four-week-old C57BL/6 J female mice were fed standard mouse food and provided V[+4] (0.02, 0.2, 2 mg/L in drinking water) or control drinking water (0 μg V[+4]/d) for 6 months. Cecal contents were analyzed with 16S rRNA microbiome sequencing and liquid chromatography-high-resolution mass spectrometry. Biostatistics, bioinformatics, community detection, and metabolic pathway enrichment analysis were used to characterize vanadyl sulfate-dependent changes to the cecal microbiome and metabolome. Pathway analysis of metabolomics data identified alterations to bile acid metabolism, likely by altering reabsorption, and inflammatory pathways including arachidonic acid and linoleate metabolism. Bile acids including cholic acid, chenodeoxycholic acid/deoxycholic acid, and lithocholic acid were decreased in V[+4]-treated animals. In addition, altered arachidonic acid levels associated with inflammatory pathways were observed. Integrated microbiome-metabolome analysis identified unique communities with inflammation-related metabolites as well as metabolites and microbes linked to bile acid metabolism. In summary, chronic high-dose V[+4] exposure at levels similar to human dietary supplement use altered bile acid metabolism and inflammatory pathways and resulted in compositional changes to the microbiome.},
}

@article {pmid40945782,
year = {2025},
author = {Castillo-Lopez, E and Hartinger, T and Ricci, S and Xu, K and Schwartz-Zimmermann, HE and Berthiller, F and Reisinger, N and Zebeli, Q},
title = {Association between the severity of subacute ruminal acidosis and the microbiome of the rumen, and the metabolome of the rumen, blood, and milk in primiparous cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27008},
pmid = {40945782},
issn = {1525-3198},
abstract = {Cows have been shown to develop different severities of SARA when fed the same diet. In the present study, we used 24 Holstein dairy cows to investigate the association between SARA severity and the ruminal microbiome as well as the metabolomes of the rumen, blood, and milk from 21 d before parturition until 70 DIM. The dietary concentrate was increased from 32% to 60% (DM basis) during the first week of lactation. Based on the severity of SARA, 3 groups were compared: high, moderate, and low severity. Relative to parturition, the rumen microbiome and metabolome were analyzed on d -21, 14, 28, and 56; blood metabolome was analyzed on d -21, -7, 1, 3, 7, 10, 14, 21, 28, 42, 56, and 70, and milk metabolome was analyzed on d 1, 3, 7, 14, 21, 56, and 70. Statistical analysis of the metabolome was performed with MetaboAnalyst v. 6.0; and statistical analyses for microbial abundance data were conducted in R using Maaslin2 package. Rumen microbial abundance profile was not associated with the SARA severity, but several amylolytic acid tolerant genera (i.e., Acidobacteria and Lactobacillus) were found only within the high SARA group. In addition, the transition to the lactation diet decreased fibrolytic bacteria and increased amylolytic and proteolytic bacteria (P < 0.05). In the ruminal metabolome, High SARA was associated with greater levels of nucleotides, nitrogen compounds, and pyrimidine derivatives as well as enrichment of metabolic pathways for nitrogen and AA metabolism (P < 0.05). In the blood metabolome, High SARA was associated with greater levels of cholesterol esters, phosphatidylcholines, and enrichment of metabolic pathways for steroid and bile acid biosynthesis (P < 0.05). In the milk metabolome, moderate SARA was associated with greater levels of triglycerides as well as enrichment of metabolic pathways for fatty acid biosynthesis (P < 0.05). The change from pre- to postpartum increased ruminal triglycerides, amino acids, carbohydrates and their derivatives in the rumen, and increased sugars and lipid derivatives in the blood. Milk showed a decrease mainly in triglycerides with increased DIM compared with first day of lactation. Overall, findings from this study reveal differential metabolomic response of dairy cows when fed the same diet. The greatest differences in the cow metabolome among SARA severity groups were observed either around calving or at peak of lactation, likely due to increased nutrient metabolism. High severity of SARA was associated with enriched metabolic pathways for nitrogen and AA metabolism in the rumen, as well as greater steroid biosynthesis, cholesterol esters and phosphatidylcholines in blood. Moderate SARA severity was associated with enrichment of metabolic pathways for fatty acid biosynthesis and triglycerides in milk.},
}

@article {pmid40945509,
year = {2025},
author = {Louw, NL and Eagan, JL and Larlee, J and Kehler, M and Keller, NP and Wolfe, BE},
title = {Long-term monitoring of a North American cheese cave reveals mechanisms and consequences of fungal adaptation.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.08.053},
pmid = {40945509},
issn = {1879-0445},
abstract = {Previous comparative and experimental evolution studies have suggested how fungi may rapidly adapt to new environments, but direct observation of in situ selection in fungal populations is rare due to challenges with tracking populations over human time scales. We monitored a population of Penicillium solitum over eight years in a cheese cave and documented a phenotypic shift from predominantly green to white strains. Diverse mutations in the alb1 gene, which encodes the first protein in the dihydroxynaphthalene (DHN)-melanin biosynthesis pathway, explained the green-to-white shift. A similar phenotypic shift was recapitulated with an alb1 knockout and experimental evolution in laboratory populations. The most common genetic disruption of the alb1 genomic region was caused by putative transposable element insertions upstream of the gene. White strains had substantial downregulation in global transcription, with genetically distinct white strains possessing divergent shifts in the expression of different biological processes. White strains outcompeted green strains in co-culture, but this competitive advantage was only observed in the absence of light. Our results illustrate how fermented food production by humans provides opportunities for relaxed selection of key fungal traits over short time scales. The local adaptation we observed may be part of a domestication process that could provide opportunities to generate new strains for innovation in fermented food production.},
}

@article {pmid40945381,
year = {2025},
author = {Pathak, VA and Kshirsagar, SJ and Deokar, GS},
title = {Linking altered gut microbiome to polycystic ovarian syndrome through immune mediated pathway.},
journal = {Journal of reproductive immunology},
volume = {172},
number = {},
pages = {104648},
doi = {10.1016/j.jri.2025.104648},
pmid = {40945381},
issn = {1872-7603},
abstract = {Polycystic ovarian syndrome (PCOS) is an endocrine disorder characterized by hyperandrogenism, ovulatory dysfunction, and metabolic disturbances. A balanced gut microbiome plays an important role in managing homeostatic signalling pathways in the body. These pathways regulate normal bodily functions but can become dysregulated under dysbiotic conditions. Recent research has highlighted the role of gut microbiota in the pathogenesis of polycystic ovarian syndrome. Key Bacterial taxa such as Akkermansia, Prevotella, Lactobacillus, Escherichia coli, Bacteroides and Ruminococcaceae (family-level) whose abundance is correlated with disease severity. At dysbiotic conditions, the pathobionts bypass the tight gut junction, enters the systemic circulation and trigger an immunomodulatory response subsequently releasing proinflammatory cytokines. Initially, first line and second line defence mechanisms are generated through immune responses such as IgG-mediated mechanisms. The immunological responses and inflammation cause macrophage pyroptosis, hormonal imbalance, and polycystic ovaries, followed by insulin resistance and hyperinsulinemia. Also, neuroendocrine alterations including dysregulation of GnRH secretion is influenced by gut-derived metabolites. The current review aids in understanding the mechanism pathway between gut microbiota and polycystic ovaries. Understanding 'The Gut-PCOS axis' explores various ways for targeting gut microbiota through prebiotics, probiotics and synbiotics as a potential therapeutic approach for polycystic ovarian syndrome management.},
}