@article {pmid41249178,
year = {2025},
author = {Zhang, J and Yu, D and Zhang, L and Wang, T and Zhang, L and Yan, J},
title = {Quantifying the relative contributions of bacterial and fungal communities to carcass decomposition using a quantitative microbiome profiling approach.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {210},
pmid = {41249178},
issn = {2055-5008},
support = {82101977//the National Natural Science Foundation of China/ ; 82030058//the National Natural Science Foundation of China/ ; },
mesh = {*Bacteria/classification/metabolism/genetics/isolation & purification ; *Fungi/classification/metabolism/isolation & purification/genetics ; Soil Microbiology ; *Microbiota ; Animals ; Metabolomics/methods ; *Mycobiome ; Postmortem Changes ; },
abstract = {Carcass microbial decomposition plays a vital role in global elemental cycling. However, bacterial and fungal absolute abundance dynamics, as well as their contributions to carcass decomposition, remain unclear. Here, the questions were investigated through quantitative microbiome profiling (QMP) and metabolomics. Within the first 14 days postmortem, microbial copies in grave soil and tissue increased by several orders of magnitude. Comparison of QMP with relative microbiome profiling (RMP) revealed strikingly different, even opposing successional trends for major phyla. Bacteria drove more metabolite variation than fungi in the decomposition. Co-occurrence networks revealed that key bacterial and fungal decomposers formed two distinct modules that were highly interconnected and significantly associated with carcass-derived metabolites, suggesting a synergistic relationship in the breakdown of organic matter. Notably, using QMP did not substantially enhance the accuracy of postmortem interval estimation. Collectively, our findings provide critical insights into microbial ecological dynamics during carcass decomposition.},
}

*Bacteria/classification/metabolism/genetics/isolation & purification
*Fungi/classification/metabolism/isolation & purification/genetics
Soil Microbiology
*Microbiota
Animals
Metabolomics/methods
*Mycobiome
Postmortem Changes

@article {pmid41249177,
year = {2025},
author = {Zhang, D and Hu, Q and Zhou, Y and Yu, H and Cong, W and Cheng, M and Wang, J and Liu, X and Zou, K and Long, S and Zhao, C and Jiang, J and Zhang, Y},
title = {Multi-omic profiling reveals distinct gut microbial and metabolic landscapes in golden snub-nosed monkeys under contrasting conservation strategies.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {209},
pmid = {41249177},
issn = {2055-5008},
support = {2020BCA081//Key Research and Development Project of Hubei Province/ ; 2013BAD03B02//National Key Technology R&D Program of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology/chemistry ; Metagenomics/methods ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Conservation of Natural Resources/methods ; Metabolomics/methods ; Metabolome ; *Colobinae/microbiology ; Endangered Species ; Multiomics ; },
abstract = {Gut microbiota are crucial for the fitness of endangered wildlife, yet how different conservation strategies affect these microbial ecosystems and their metabolic activities remains insufficiently understood. This study employed integrated metagenomic and metabolomic analyses to compare the gut microbial communities and fecal metabolomes of endangered golden snub-nosed monkeys (Rhinopithecus roxellana) under three distinct conservation scenarios: natural wild, food provisioning, and captivity. We established a comprehensive species-specific gut microbial gene catalog and observed significant microbial and metabolic divergence associated with each conservation strategy. Monkeys in managed settings (captive and provisioned) exhibited larger gut microbial gene catalogs than wild individuals. While alpha diversity was highest in the provisioned group, both captive and provisioned groups showed notably altered microbial community structures and co-occurrence networks compared to the wild baseline. Captivity was linked to the most pronounced shifts, including a microbiome assembly more strongly governed by deterministic processes, reduced network stability, and an enrichment of habitat specialists, alongside an increased abundance of antibiotic resistance genes (ARGs) and virulence factors (VFs), and distinct alterations in microbiota-metabolite co-variation patterns, particularly concerning amino acid metabolism. These findings highlight that food provisioning, when managed to emulate natural conditions, is associated with a less disruptive microbial and metabolic profile than intensive captivity, offering crucial insights for developing microbiome-informed conservation practices to enhance the health and long-term viability of this endangered primate.},
}

Animals
*Gastrointestinal Microbiome/genetics
Feces/microbiology/chemistry
Metagenomics/methods
*Bacteria/classification/genetics/metabolism/isolation & purification
*Conservation of Natural Resources/methods
Metabolomics/methods
Metabolome
*Colobinae/microbiology
Endangered Species
Multiomics

@article {pmid41248758,
year = {2025},
author = {Habimana-Griffin, L and Prusa, J and Wang, B and Strong, L and Ning, J and Tovar, ESR and Toth, K and Butler, B and Reynoso, FJ and Markovina, S and Ciorba, MA and Dantas, G},
title = {A novel focal duodenal radiation injury model reveals dose-, time-, and spatially-dependent microbiome perturbations after radiation injury.},
journal = {International journal of radiation oncology, biology, physics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijrobp.2025.11.011},
pmid = {41248758},
issn = {1879-355X},
abstract = {PURPOSE: The duodenum is a key organ at risk during stereotactic ablative radiotherapy (SABR). Understanding mechanisms of radiation-induced intestinal injury (RIII) could reveal novel strategies to reduce SABR toxicities. The gut microbiome contributes to RIII, however existing preclinical models either require surgical manipulation or fail to recapitulate high-dose conformal treatment fields used during SABR, confounding microbiome studies. We developed a non-invasive focal bowel irradiation model to assess microbiome dynamics in both the duodenum and the stool after high-dose duodenal irradiation.

MATERIALS AND METHODS: C57BL/6J mice received sham treatment or focal irradiation (12 or 18 Gy) to the proximal duodenum using a small animal irradiator. Stool and duodenal tissue samples were collected at days 4, 14, and 91 post-treatment and processed for bacterial 16S rRNA gene V4 region amplicon sequencing (Illumina MiSeq platform). Microbiome diversity metrics were calculated and multivariable linear mixed modeling identified bacterial taxa associated with radiotherapy.

RESULTS: Oral iodine contrast enabled duodenum visualization and 100% of mice survived until sacrifice. Focal duodenal irradiation led to dose- and time-dependent changes in duodenal bacterial community composition that were not observed in stool. At days 4 and 14 post-treatment, 18 duodenal taxonomic groups were significantly perturbed, while only 2 taxa were significantly altered in the stool.

CONCLUSIONS: Our focal duodenal irradiation model is safe, well-tolerated, and easy to implement. It enables characterization of microbiome perturbations during both the acute and late phases of injury and serves as a platform for testing new RIII mitigation strategies. Our findings reveal that irradiation-induced changes in the duodenal microbiome are dose-, time-, and spatially-dependent and are not reflected in stool samples. These results underscore the imperative of directly assessing tissue-associated microbiota, as relying solely on stool samples risks overlooking critical, localized microbial dynamics that may drive injury and repair.},
}

@article {pmid41249173,
year = {2025},
author = {Cheng, Q and Lv, S and Yin, N and Wang, J},
title = {Microbial regulators of physiological and reproductive health in women of reproductive age: their local, proximal and distal regulatory roles.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {207},
pmid = {41249173},
issn = {2055-5008},
support = {2022YFA1304102//National Key Research and Development Program of China/ ; T2341010//National Natural Science Foundation of China/ ; },
mesh = {Female ; Humans ; *Reproductive Health ; Pregnancy ; *Gastrointestinal Microbiome ; Fertility ; *Microbiota ; Homeostasis ; Reproduction ; },
abstract = {The female microbiome is emerging as a key regulator of gynecological and reproductive health. This review summarizes how local and gut microbes affect gynecological outcomes, fertility, and pregnancy through metabolic, immune, and hormonal pathways. We highlight underlying mechanisms and intervention strategies, emphasizing the restoration of microbial homeostasis as a promising avenue for advancing understanding, prevention, and management of women's physiological and reproductive health conditions.},
}

Female
Humans
*Reproductive Health
Pregnancy
*Gastrointestinal Microbiome
Fertility
*Microbiota
Homeostasis
Reproduction

@article {pmid41248824,
year = {2025},
author = {Desouky, MA and Eldahshan, W and Atawia, RT},
title = {Exploring the gut-lung-brain axis: Focus on endothelial dysfunction, impaired bioenergetics and strategies to mitigate lung and cognitive disorders.},
journal = {Life sciences},
volume = {},
number = {},
pages = {124089},
doi = {10.1016/j.lfs.2025.124089},
pmid = {41248824},
issn = {1879-0631},
abstract = {Dysbiosis has emerged as a major determinant in the pathogenesis of many human disorders and is a continuously expanding area of research. Identification of several microbial populations and their derived products marks an important milestone in microbiome research. Interestingly, there is evidence that gut microbiota-derived products affect distant organs such as the brain and lungs. Although the effect of gut dysbiosis on several lung- and brain-related disorders has been demonstrated, our knowledge of the mechanisms and consequences of individual metabolites and products on specific cell types such as endothelial cells is still evolving. Endothelial dysfunction is a prominent feature in vascular dementia and several lung disorders. Specifically, alteration in endothelial bioenergetics is an emerging area of research. In this review, the evidence on the interconnection between dysbiosis in the gut and three lung disorders- asthma, COPD and ARDS is discussed. Additionally, the association between these respiratory disorders and cognitive impairment is examined with mechanistic insights. Moreover, data involving the direct impact of key microbial metabolites and products on endothelial cells is synthesized and potential therapeutic modalities are highlighted. We identify the impact of microbial metabolites on endothelial dysfunction and bioenergetics as a potential gap in knowledge and a plausible avenue for future research.},
}

@article {pmid41248397,
year = {2025},
author = {Korenblik, V and Korosi, A and Brul, S and Bockting, C and Nieuwdorp, M and Lok, A},
title = {Feasibility and acceptability of 8-week oral tributyrin supplementation as add on to antidepressant medication in patients with depression: a study protocol paper for a pilot, randomised controlled trial.},
journal = {BMJ open},
volume = {15},
number = {11},
pages = {e108423},
doi = {10.1136/bmjopen-2025-108423},
pmid = {41248397},
issn = {2044-6055},
mesh = {Humans ; *Antidepressive Agents/therapeutic use/administration & dosage ; Pilot Projects ; Adult ; Feasibility Studies ; Double-Blind Method ; *Depressive Disorder, Major/drug therapy ; *Triglycerides/administration & dosage/therapeutic use ; Middle Aged ; Male ; *Dietary Supplements ; Female ; Young Adult ; Adolescent ; Administration, Oral ; Drug Therapy, Combination ; Aged ; Randomized Controlled Trials as Topic ; Gastrointestinal Microbiome ; Treatment Outcome ; },
abstract = {BACKGROUND: Major depressive disorder (MDD) is a severe mental health condition that profoundly affects both psychological and physical well-being. Growing evidence indicates that targeting the gut-brain axis could present new therapeutic opportunities for MDD, given the role of gut microbiota and their metabolites in its pathophysiology. One promising approach involves supplementation with butyrate, a short-chain fatty acid that has demonstrated antidepressant potential in preclinical models of depression. However, clinical research exploring the effects of butyrate supplementation in individuals with MDD remains lacking.

METHODS: This study is a double-blind, parallel, 1:1 randomised placebo-controlled trial. The primary aim of this pilot study is to assess the feasibility and acceptability of an 8-week oral supplementation with tributyrin, a triglyceride form of butyrate (4 g/day), added to usual treatment with antidepressant medication in 24 patients with mild-to-severe MDD aged 18-65 years. Secondary outcomes include changes in depressive symptoms, assessed weekly throughout the supplementation period and at 16 weeks post-supplementation during follow-up, as well as changes in anhedonia and affect, measured multiple times per day via a smartphone application throughout the supplementation period. Additional outcomes include changes in gastrointestinal symptoms, changes in faecal microbiome, metabolites in blood and faeces, inflammation, epigenetic markers, stress and intestinal permeability.

ETHICS AND DISSEMINATION: The study has been approved by the Medical Research Ethics Committee of the Amsterdam University Medical Centre, the Netherlands.

DISCUSSION: Should the pilot demonstrate feasibility and acceptability, a larger-scale study will be warranted to evaluate the efficacy of tributyrin supplementation in alleviating depressive symptoms. This pilot will provide valuable insights to guide sample size calculations and refine study design for subsequent trials. Ultimately, this research could lead to novel adjunctive treatments for MDD targeting gut-brain signalling, offering new therapeutic avenues for patients with MDD.

TRIAL REGISTRATION NUMBER: This trial has been registered in the International Clinical Trials Registry Platform (registry number: NL-OMON57116).},
}

Humans
*Antidepressive Agents/therapeutic use/administration & dosage
Pilot Projects
Adult
Feasibility Studies
Double-Blind Method
*Depressive Disorder, Major/drug therapy
*Triglycerides/administration & dosage/therapeutic use
Middle Aged
Male
*Dietary Supplements
Female
Young Adult
Adolescent
Administration, Oral
Drug Therapy, Combination
Aged
Randomized Controlled Trials as Topic
Gastrointestinal Microbiome
Treatment Outcome

@article {pmid41248372,
year = {2025},
author = {Fernando, SM and Muscedere, J and Rochwerg, B and Johnstone, J and Daneman, N and Marshall, JC and Lauzier, F and Rudkowski, JC and Arabi, YM and Heels-Ansdell, D and Sligl, W and Kristof, AS and Duan, E and Dionne, JC and St-Arnaud, C and Reynolds, S and Khwaja, K and Cook, DJ and , },
title = {Frailty and the risk of ICU-acquired infections in a randomised trial: a protocol and statistical analysis plan.},
journal = {BMJ open},
volume = {15},
number = {11},
pages = {e105227},
doi = {10.1136/bmjopen-2025-105227},
pmid = {41248372},
issn = {2044-6055},
mesh = {Humans ; *Frailty/complications ; *Intensive Care Units ; *Pneumonia, Ventilator-Associated/epidemiology/prevention & control ; *Cross Infection/epidemiology ; Length of Stay/statistics & numerical data ; Randomized Controlled Trials as Topic ; Risk Factors ; Aged ; Proportional Hazards Models ; Male ; Respiration, Artificial/adverse effects ; Female ; Research Design ; },
abstract = {INTRODUCTION: Dysregulated immunity may account for an increased risk of infection and other adverse outcomes among frail hospitalised persons. The primary objective of this study is to examine whether baseline frailty is associated with the risk of developing ventilator-associated pneumonia (VAP) or other intensive care unit (ICU)-acquired infections among invasively ventilated adults. Additional objectives are to examine the relationship between frailty and hospital length of stay, discharge to a long-term care facility and vital status. We hypothesise that persons with frailty compared with others would have an increased risk of VAP and other infections, a longer hospital stay, higher probability of discharge to a long-term care facility and higher mortality.

METHODS AND ANALYSIS: This is a preplanned secondary analysis of the PROSPECT trial (Probiotics to Prevent Severe Pneumonia and Endotracheal Colonization Trial) which enrolled patients across 44 ICUs in three countries. We will use Cox proportional hazards regression analysis to assess the association of frailty with the clinical outcomes of interest, adjusting for other baseline variables. Baseline demographic and descriptive outcome data will be reported using descriptive statistics. Regression results will be presented as adjusted HRs or ORs with 95% CIs for the associations of each independent variable with the primary, secondary and tertiary outcomes.

ETHICS AND DISSEMINATION: Participating hospital research ethics board approved the PROSPECT trial and data collection. The protocol for this study was approved by the Hamilton Integrated Research Ethics Board on 20 August 2015 (Project ID:19128). This study will identify whether frailty is associated with risk of VAP and other healthcare-associated infections in invasively ventilated patients, adjusted for other baseline factors. Results may be useful to patients, their caregivers, clinicians and the design of future research. Findings will be disseminated to investigators at a meeting of the Canadian Critical Care Trials Group. We will present study results at an international conference in the fields of critical care and infectious diseases, to coincide with or precede open-access peer-review publication. To aid knowledge dissemination, we will use a variety of formats. For example, for traditional and social media, we will create two different visual abstracts and infographics of our results suitable to share on clinician-facing and public-facing platforms.

TRIAL REGISTRATION NUMBER: NCT02462590.},
}

Humans
*Frailty/complications
*Intensive Care Units
*Pneumonia, Ventilator-Associated/epidemiology/prevention & control
*Cross Infection/epidemiology
Length of Stay/statistics & numerical data
Randomized Controlled Trials as Topic
Risk Factors
Aged
Proportional Hazards Models
Male
Respiration, Artificial/adverse effects
Female
Research Design

@article {pmid41248126,
year = {2025},
author = {Jefferson, J and Reigate, C and Giacomini, A and Rivero, MJ and Hitchings, M and Webster, TU and Wells, K},
title = {Triadic relationships between pasture exposure, gastrointestinal parasites, and hindgut microbiomes in grazing lambs.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0337086},
doi = {10.1371/journal.pone.0337086},
pmid = {41248126},
issn = {1932-6203},
mesh = {Animals ; Sheep/microbiology/parasitology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology/parasitology ; Bacteria/genetics/classification ; *Sheep Diseases/parasitology/microbiology ; Lolium ; },
abstract = {Livestock grazing in confined pastures often means grazing on a less diverse diet than under more natural conditions and increased exposure to gastrointestinal parasites prevailing in these pastures. However, how sward composition influences gut microbiome (GM) diversity and its relationship with parasite burden remains poorly understood. In this study, we analysed the faecal GM of weaned lambs grazing on two distinct sward types (perennial ryegrass and a mixed-species sward) over three consecutive months using 16S rRNA sequencing, in order to assess how microbial diversity and composition are related to environmental conditions and the gastrointestinal nematode (GIN) burden in naturally infected lambs. Sward type and sampling time explained some of the variation in GM alpha diversity and community composition (beta diversity), whereas individual lamb identity accounted for considerably more variation in microbial assemblages. Shifts in the relative abundance of bacterial genera such as Saccharofermentans, Anaerosporobacter, Butyrivibrio in relation to sward type and sampling time suggest mostly adaptive fluctuations in response to diet and pasture condition. Abundance shifts of Negativibacillus, and Candidatus Saccharimonas were also associated with GIN burden, which, in turn, was higher in lambs grazing on mixed swards compared to ryegrass. Our findings add to the growing understanding of how sheep microbiomes vary with pasture management and changes in parasite burden. We highlight that individual identity may shape gut microbiota, and that potential triadic interactions among gastrointestinal parasites, sward exposure, and the gut microbiome underscore the importance of considering host, parasite, and environmental factors collectively when evaluating microbiome dynamics in grazing livestock.},
}

Animals
Sheep/microbiology/parasitology
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Feces/microbiology/parasitology
Bacteria/genetics/classification
*Sheep Diseases/parasitology/microbiology
Lolium

@article {pmid41247816,
year = {2025},
author = {Gao, Y and Wang, X and Wang, Q and Jiang, L and Wu, C and Guo, Y and Cui, N and Tang, H and Tang, L},
title = {Global impact of pelvic inflammatory diseases attributable to sexually transmitted infections in women of childbearing age: a comprehensive analysis based on GBD 2021 data and bibliometric analysis.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000004066},
pmid = {41247816},
issn = {1743-9159},
abstract = {BACKGROUND: Pelvic inflammatory disease (PID), often caused by sexually transmitted infections (STIs), poses significant health threat to women of childbearing age (WCBA). This study assessed the global prevalence trends and research landscape of STIs-related PID.

METHODS: This study integrated GBD 2021 data and bibliometric analysis. Joinpoint regression calculated Average annual percentage change (AAPC) for age-standardized prevalence rate (ASPR) from 1990 to 2021. Decomposition analyses assessed the contributions of population growth, aging, and epidemiological changes to the prevalence trends for last 32 years. The Bayesian age-period-cohort (BAPC) model projected ASPR from 2022 to 2040, and the Nordpred model conducted a sensitivity analysis of the prediction results, which validated the findings' reliability. 1726 related publications were retrieved from the WOS Core Collection database. Bibliometric information was extracted with VOSviewer software for visualization.

RESULTS: In 2021, an estimated 1,009,957.64 cases of PID due to STIs occurred among WCBA globally, with chlamydial infection accounting for approximately 23%, gonococcal infection (4.98%), and other STIs (72.03%). From 1990 to 2021, the global ASPR of STIs-related PID increased by AAPC of 0.13%, with the largest increase observed among women in the 20-24 years age group. Regionally, the highest ASPR was observed in low SDI regions in 2021, while the fastest increase occurred in middle SDI regions over the last 32 years. Decomposition analyses highlighted the population growth as a key driver of global prevalence rise, accounting for 78.5 %. The global ASPR of STIs-related PID is projected to continue rising from 2022 to 2040. Bibliometric analysis showed stable research on STIs and PID, with an increased citation rate. The United States was the leading contributor. Research focused on chlamydia trachomatis, with recent studies exploring the vaginal microbiome, resistance and protective immunity.

CONCLUSIONS: This study performed an epidemiological assessment and bibliometric analysis of the PID attributable to STIs burden globally, informing policy-making and research directions.},
}

@article {pmid41247642,
year = {2025},
author = {Li, J and Hu, J and Yang, Y and Zhang, H and Liu, Y and Fang, Y and Qu, L and Lin, A and Luo, P and Jiang, A and Wang, L},
title = {Drug resistance in cancer: molecular mechanisms and emerging treatment strategies.},
journal = {Molecular biomedicine},
volume = {6},
number = {1},
pages = {111},
pmid = {41247642},
issn = {2662-8651},
support = {81772740//National Natural Science Foundation of China/ ; 82173345//National Natural Science Foundation of China/ ; 81972333//National Natural Science Foundation of China/ ; 82372883//National Natural Science Foundation of China/ ; 2022YFB4700904//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Drug Resistance, Neoplasm/genetics ; *Neoplasms/drug therapy/genetics/metabolism/pathology/therapy ; Tumor Microenvironment/drug effects ; Animals ; Immunotherapy ; Antineoplastic Agents/therapeutic use/pharmacology ; Epigenesis, Genetic ; },
abstract = {Therapeutic resistance remains a defining challenge in oncology, limiting the durability of current therapies and contributing to disease relapse and poor patient outcomes. This review systematically integrates recent progress in understanding the molecular, cellular, and ecological foundations of drug resistance across chemotherapy, targeted therapy, and immunotherapy. We delineate how genetic alterations, epigenetic reprogramming, post-translational modifications, and non-coding RNA networks cooperate with metabolic reprogramming and tumor microenvironment remodeling to sustain resistant phenotypes. The influence of the microbiome is highlighted as an emerging determinant of therapeutic response through immune modulation and metabolic cross-talk. By summarizing key regulatory circuits, We establishe a unified framework linking clonal evolution, metabolic adaptability, and tumor ecological dynamics. We further synthesizes novel therapeutic strategies that convert resistance mechanisms into therapeutic vulnerabilities, including synthetic lethality approaches, metabolic targeting, and disruption of stem cell and stromal niches. Advances in single-cell and spatial omics, liquid biopsy, and artificial intelligence are emphasized as transformative tools for early detection and real-time prediction of resistance evolution. This review also identifies major translational gaps in preclinical modeling and proposes precision oncology frameworks guided by evolutionary principles. By bridging mechanistic understanding with adaptive clinical design, this work provides an integrated roadmap for overcoming therapeutic resistance and achieving sustained, long-term cancer control.},
}

Humans
*Drug Resistance, Neoplasm/genetics
*Neoplasms/drug therapy/genetics/metabolism/pathology/therapy
Tumor Microenvironment/drug effects
Animals
Immunotherapy
Antineoplastic Agents/therapeutic use/pharmacology
Epigenesis, Genetic

@article {pmid41247431,
year = {2025},
author = {Dhungana, P and Dam, A and Kiang, TKL},
title = {Clinical Pharmacokinetic-Pharmacodynamic Relationships of Pharmacological Strategies for Attenuating p-Cresyl Sulfate in Patients with Kidney Disease.},
journal = {Clinical pharmacokinetics},
volume = {},
number = {},
pages = {},
pmid = {41247431},
issn = {1179-1926},
abstract = {p-Cresyl sulfate (pCS) is a highly toxic uremic compound that is produced from tyrosine and phenylalanine in the gut and primarily excreted renally. In patients with kidney dysfunction, the accumulation of pCS can lead to the worsening of kidney disease and manifestation of organ toxicities. Various pharmacological strategies have been proposed to reduce pCS in patients with chronic kidney disease (CKD), but systematic pharmacokinetic-pharmacodynamic assessments have not been conducted to our knowledge. The objectives of this scoping review were to comprehensively and critically summarize the available literature using a newly devised, pharmacokinetic-pharmacodynamic assessment method. We searched PubMed, Embase, and Scopus for primary research articles in patients with CKD and devised the following novel approach to systematically evaluate each study: (i) positive reduction or null reduction of pCS; (ii) dose dependency; (iii) time dependency; (iv) effects on free versus total pCS; and (v) relationships to diet regimens (e.g., protein intake), microbiome composition, blood biochemistry, and clinical outcomes (i.e., progression of renal disease measured by initiation of dialysis or renal transplant; cardiovascular outcomes such as incidence of myocardial infarction, heart failure, cardiovascular death; and changes in qualityof- life instruments). Fifty-nine studies were identified with a total of 2593 study participants (pre-dialysis CKD: n = 1060; CKD on dialysis: n = 1499; and post-transplant CKD: n = 34). The studies included AST-120 (n = 3), sevelamer (n = 9), sucroferric Noxyhydroxide (n = 1 [+ 1 overlapping with sevelamer]), prebiotics (n = 15), probiotics (n = 9), synbiotics (n = 13), antibiotics (n = 3), ketoanalogs (n=3), and curcumin (n = 3). Only AST-120 and synbiotics consistently demonstrated significant pCS reductions, and the percentage (%) reductions by AST-120 were 40.9-75.6% for free and 28.8-42.8% for total pCS; whereas the percentage reduction by synbiotics were 6.4-78.1% for total and 16.7% for free pCS, the latter only evident in a subgroup with antibiotic-free regimen. Although sevelamer was also associated with a pCS reduction, the percentage reduction was modest and only based on the total concentration. In contrast, the majority of sucroferric oxyhydroxide, prebiotics, probiotics, ketoanalogs, and curcumin studies did not demonstrate consistent pCS reductions. Furthermore, dose dependency was not established in the majority of studies, and although some temporal relationships were evident, the data were very limited. Only a few of the analyzed studies measured both bound and unbound forms of pCS, and inconsistencies have been reported in a few studies. In Ngeneral, it was also difficult to establish associations with outcomes in most studies because of limitations in experimental design, and in instances where potential pharmacokinetic-pharmacodynamic relationships were observed, they were generally weak and only with surrogate markers of commonly measured biochemistry, oxidative stress, lipid profiles, and inflammatory markers, with only a handful of studies capturing clinical outcomes. In conclusion, we have identified potential pharmacological interventions that may be further developed for the purpose of reducing pCS in patients with CKD.},
}

@article {pmid41247319,
year = {2025},
author = {Wang, Z and Guo, X and Zhang, H and Zheng, T and Liu, Y and Dai, L and Xie, Y and Shang, X and Zhang, L and Yang, L and Yuan, L and Hou, X},
title = {Rotation-driven changes in physicochemical properties modulate soil microbial diversity and community complexity in tobacco-woad soils.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0301624},
doi = {10.1128/spectrum.03016-24},
pmid = {41247319},
issn = {2165-0497},
abstract = {Continuous tobacco monocropping leads to soil degradation and yield reduction. To address this, we evaluated the effects of tobacco (Nicotiana tabacum L.)-woad (Isatis tinctoria L.) rotation (A2, A4) compared to tobacco monoculture (A1) and woad monoculture (A3) on soil health and crop quality over a multi-year period. Methods involved comparative analysis of soil nutrients, enzyme activities, microbial community structure, and crop chemical composition and economic value. Key results demonstrated that tobacco-woad rotation significantly improved soil fertility. The tobacco-woad rotation could increase the content of organic matter, alkaline available nitrogen, available phosphorus, and available potassium in the soil, which were increased by 1.44%, 17.96%, 4.61%, and 16.20%, respectively, compared to tobacco monoculture. Soil urease and catalase activities, particularly urease (increased by 2.31 times), were significantly enhanced during the tobacco pre-growth period under rotation. Soil microbial communities were significantly restructured under tobacco-woad rotation versus monocropping. Bacterial phyla Acidobacteria, Gemmatimonadota, and Methylomirabilota were enriched in tobacco-woad rotation (A2) relative to tobacco monoculture (A1), while Chloroflexi, Methylomirabilota, and Verrucomicrobiota increased in woad-tobacco rotation (A4) versus woad monoculture (A3). Fungal shifts featured decreased Ascomycota and Basidiomycota with increased Mortierellomycota in both rotations, alongside reduced Chytridiomycota in A4. Rotation enriched key bacterial genera (MND1, Nitrospira, Subgroup-10, and RB41) and fungal taxa (Mortierella, Saccharomyces, and Saitozyma). Crucially, rotation harmoniously improved the chemical composition of both tobacco and woad leaves, increasing reducing sugars, total sugars, nicotine, potassium, and the sugar ratio in tobacco. The proportion of high-quality tobacco leaves post-curing increased by 10.24% (A2), contributing to a significantly higher total crop production value. In conclusion, tobacco-woad rotation effectively alleviates soil degradation associated with continuous tobacco cropping by enhancing soil nutrient availability, boosting key enzyme activities, and optimizing the structure and interactions of the soil microbial community. These soil improvements collectively drive superior crop quality and economic returns, supporting their adoption as a sustainable agricultural practice.IMPORTANCE(i) The effects of rotation of tobacco with woad on the quality of tobacco production were clarified using physiological and biochemical analyses. (ii) The effects of rotating tobacco with woad on soil microorganisms were revealed by microbiome sequencing of tobacco soils. Tobacco-woad rotation significantly improved the relative abundance of soil-dominant bacteria and decreased the relative abundance of harmful fungi. (iii) An efficient cultivation model of tobacco and woad suitable for Shandong was established by combining soil microbiomics with tobacco plant growth and development. Rotation of tobacco to woad gave the best results.},
}

@article {pmid41247142,
year = {2025},
author = {Wang, Y and Hou, Q and Wei, F and Liu, B and Feng, Q},
title = {MNetClass: a control-free microbial network clustering framework for identifying central subcommunities across ecological niches.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0098925},
doi = {10.1128/msystems.00989-25},
pmid = {41247142},
issn = {2379-5077},
abstract = {Investigating microbiome subnetworks and identifying central microbes in specific ecological niches is a critical issue in human microbiome studies. Traditional methods typically require control samples, limiting the ability to study microbiomes at distinct body sites without matched controls. Moreover, some clustering methods are not well-suited for microbial data and fail to identify central subcommunities across ecological niches after clustering. In this study, we present MNetClass, a novel microbial network clustering analysis framework. It utilizes a random walk algorithm and a rank-sum ratio-entropy weight evaluation model to classify key subnetworks and identify central microbes at any body site, without the need for control samples. We demonstrate its capabilities on both simulated and real microbiome data sets. Simulation results indicate that MNetClass outperforms current unsupervised microbial clustering methods. In applied case studies, the analysis of microbiome data from five distinct oral sites revealed site-specific microbial communities. Furthermore, MNetClass demonstrated superior predictive performance on cross-cohort Autism Spectrum Disorder data and identified age-related microbial communities across different oral sites, underscoring its broad applicability in microbiome research.IMPORTANCEMNetClass provides a valuable tool for microbiome network analysis, enabling the identification of key microbial subcommunities across diverse ecological niches. Implemented as an R package (https://github.com/YihuaWWW/MNetClass), it offers broad accessibility for researchers. Here, we systematically benchmarked MNetClass against existing microbial clustering methods on synthetic data using various performance metrics, demonstrating its superior efficacy. Notably, MNetClass operates without the need for control groups and effectively identifies central microbes, highlighting its potential as a robust framework for advancing microbiome research.},
}

@article {pmid41247019,
year = {2025},
author = {Du, H and Jiang, X and Liu, Y and Hou, J and Li, C and Wu, R and Li, SC and Dai, W},
title = {One-year restoration of vaginal health: synergistic dynamics of microbiome and metabolome following the elimination of high-grade cervical intraepithelial neoplasia.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0119025},
doi = {10.1128/msystems.01190-25},
pmid = {41247019},
issn = {2379-5077},
abstract = {Therapeutic elimination of high-grade cervical intraepithelial neoplasia (CIN) is widely implemented for cervical cancer prevention. Despite the demonstrated dysbiosis of vaginal microenvironment in high-grade CIN, its post-therapy restorations remain to be poorly understood, especially in functional aspects. This study aimed to characterize temporal changes in both vaginal microbiota (VM) and metabolome (VMeta) following therapeutic elimination of high-grade CIN. We conducted a longitudinal study of 32 HPV-positive women with high-grade CIN who underwent therapeutic procedures. Vaginal swabs were collected at baseline (pre-therapy) and at 6- and 12-month follow-up visits for integrated VM and VMeta analysis. We observed a gradual restoration of Lactobacillus crispatus levels from baseline to 12 months (P < 0.05). Concurrently, we detected significant decreases in dysbiosis-associated bacteria, including Prevotella bivia, Ureaplasma parvum, and Peptoniphilus sp. 6 months post-therapy compared to the baseline. VMeta analysis revealed distinct metabolic shifts across the follow-up periods. The early post-therapy phase (baseline to 6 months) was characterized by enrichment of glycerophospholipids and depletion of nucleotide metabolites, while the later phase (6-12 months) showed increases in flavonoids, lysophospholipids, bioactive amides, and amino acid metabolism. Integration of correlation and dynamic Bayesian network analysis indicated potential regulatory relationships and time-lag effects involving HPV infection, L. crispatus, Bifidobacterium sp., Streptococcus anginosus, Megasphaera sp., U. parvum, and those metabolites. This study enhances our understanding of a sequential restoration process post-therapy in the vaginal microenvironment.IMPORTANCETherapeutic elimination of high-grade CIN is routine, yet functional recovery of the vaginal ecosystem is poorly defined. In a 12-month longitudinal multi-omics study of 32 women, we show stepwise restoration: progressive L. crispatus dominance with sustained decreases in dysbiosis-associated taxa (P. bivia, U. parvum, Peptoniphilus). Metabolically, an early rise in glycerophospholipids and fall in nucleotide metabolites is followed by later enrichment of flavonoids, lysophospholipids, bioactive amides, and amino acid derivatives. Correlation and dynamic Bayesian network analyses reveal putative regulatory links, time-lag effects, and downstream impacts of HPV clearance. These findings deliver a functional roadmap of post-therapy recovery, nominate measurable microbial-metabolite milestones and candidate biomarkers for monitoring, and suggest targets for adjunct interventions to accelerate re-establishment of protective states. This work informs precision follow-up in cervical cancer prevention programs.},
}

@article {pmid41247018,
year = {2025},
author = {Xiong, M and Kuang, W and Liu, Z and Tong, R and Deng, X and Wang, N and Wan, X and Feng, M and Luo, Y and Zhang, B and Zhang, Z and Zheng, F},
title = {Quercetin alleviates ulcerative colitis via regulating gut microbiota and tryptophan metabolism.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0070325},
doi = {10.1128/msystems.00703-25},
pmid = {41247018},
issn = {2379-5077},
abstract = {UNLABELLED: Quercetin, a natural flavonoid in traditional Chinese medicinal plants, has shown promise in alleviating ulcerative colitis symptoms despite uncertainties about its exact mode of action. This study explored how quercetin influences tryptophan breakdown and gut bacterial populations in mice with chemically induced colitis. The treatment demonstrated measurable improvements-normalizing body weight, reducing spleen enlargement, lowering clinical severity scores, preserving colon structure, and healing tissue damage. Through advanced microbiome profiling and metabolic analysis, researchers observed increased populations of helpful gut microbes alongside higher concentrations of tryptophan byproducts. These biochemical shifts stimulated the aryl hydrocarbon receptor system, which plays a key role in restoring gut lining integrity. The collective evidence points to quercetin's therapeutic potential through its dual action on microbial ecology and tryptophan-derived signaling pathways.

IMPORTANCE: Ulcerative colitis is a chronic inflammatory disease with limited effective therapeutic options. In this study, quercetin-a flavonoid commonly found in traditional Chinese medicinal herbs-was shown to relieve colitis symptoms by reshaping gut microbiota and restoring tryptophan metabolism. Notably, the increase in indolelactic acid, a key microbial metabolite, led to activation of the aryl hydrocarbon receptor, which supports intestinal barrier integrity and dampens inflammation. These findings reveal a gut microbiota-derived metabolite-host signaling axis as a central mechanism of action, highlighting the potential of quercetin as a microbiota-targeted therapeutic approach for UC.},
}

@article {pmid41247017,
year = {2025},
author = {Carpentier, J and Derocles, SA and Chéreau, S and Marquer, B and Linglin, J and Lebreton, L and Legeai, F and Vannier, N and Cortesero, A and Mougel, C},
title = {Contrasting glucosinolate profiles in rapeseed genotypes shape the rhizosphere-insect continuum and microbial detoxification potential in a root herbivore.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0126925},
doi = {10.1128/msystems.01269-25},
pmid = {41247017},
issn = {2379-5077},
abstract = {Plant secondary metabolites are key mediators of plant-insect-microbiome interactions, yet their role in structuring functionally relevant insect-associated microbial communities remains poorly understood. Here, we combined a factorial experiment using Brassica napus genotypes differing in glucosinolate (GLS) content with distinct succession to investigate the eco-evolutionary dynamics of the microbiota of the root herbivore Delia radicum. Amplicon sequencing and microbial culturing revealed that both rhizospheric and gut microbial communities are shaped by plant genotype and soil legacy, with a subset of bacterial taxa shared across compartments. Notably, Pseudomonas brassicacearum, harboring the isothiocyanates (ITC) detoxifying gene saxA, was consistently recovered from both plant and insect habitats. Functional assays confirmed its capacity to degrade 2-phenylethyl isothiocyanate (PEITC), a major toxic GLS hydrolysis product. Other gut-derived microbial isolates exhibited heterogeneous responses to PEITC, ranging from growth inhibition, promotion, or growth recovery after a prolonged lag phase. Despite the toxicity of ITC, insect fitness proxies were enhanced on GLS +plants, suggesting microbiota-mediated adaptation to host chemical defenses. Our findings reveal a plant genotype-specific filtering of environmentally acquired microbes and highlight the role of detoxifying symbionts in Delia radicum performance.IMPORTANCEUnderstanding how herbivorous insects adapt to plant chemical defenses is important in the context of new agricultural practices. This study highlights that the host plant genotype shapes not only rhizospheric and gut microbial communities but also promotes the acquisition of symbiotic bacteria capable of detoxifying harmful isothiocyanates. These findings reveal a functional microbial pathway for insect adaptation to plant defenses, with potential implications for pest management strategies. By uncovering the role of plant-associated microbiota, the acquisition of beneficial microbes, and their functional contributions to host fitness, this work provides a foundation for innovative agroecological approaches that leverage plant-microbe-insect interactions.},
}

@article {pmid41247016,
year = {2025},
author = {Beilinson, V and Chen, GY and Hargadon, AC and Ruby, EG and McFall-Ngai, MJ},
title = {Strain matters: host responses reflect symbiont origin in the squid-vibrio symbiosis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0049825},
doi = {10.1128/msystems.00498-25},
pmid = {41247016},
issn = {2379-5077},
abstract = {UNLABELLED: Understanding the cause and consequences of bacterial strain variation remains a challenge in the study of symbioses. While the diverse reactions of the host immune system to strain variants have been well studied in pathogenesis, much less is known about how strain variation influences beneficial associations. From the complex vertebrate gut microbiome to the more tractable invertebrate models of symbiosis, the host's cellular and molecular responses to this diversity remain largely a mystery. Here, we explore strain diversity in Vibrio fischeri, the bioluminescent bacterial symbiont of the Hawaiian bobtail squid, Euprymna scolopes. Phylogenetic analyses of the genomes of 62 V. fischeri strains, including 50 light organ-associated and 12 planktonic isolates, revealed several genes that were absent in planktonic strains, but uniformly present in symbiotic ones. To better understand the consequences of this diversity to the host, we selected five light-organ associated strains: three from E. scolopes but having different combinations of colonization factors, one from a congeneric squid host, and one from a marine fish. We colonized juvenile E. scolopes with these strains and, using RNAseq, found that (i) the most similar host transcriptomic responses occurred among the native E. scolopes strains, (ii) intermediate was the strain from the related squid, and (iii) least similar was the fish strain. Importantly, native strains downregulated immune-related genes more than non-native ones. Finally, host development was atypical or delayed when colonized by non-native strains. These experiments point the way to more targeted studies of the mechanisms underlying host responses to symbiont strain diversity.

IMPORTANCE: Variation among strains of a bacterial species is a powerful factor underlying the intensity of host responses during pathogenic infections. Less is known about the cellular and molecular responses of host tissues to differences between the strains present in an animal's normal microbiome. We use a natural, species-specific, symbiosis to explore the influence of strain-level differences on host gene expression and morphogenesis. Analysis of symbiotic strains from squids and fishes, as well as free-living strains, shows that the carriage of colonization determinants, while critical to competitive success among strains of a species, has a minimal effect on the transcriptional response of the host. We provide evidence that a more important driver of normal gene expression during the development of symbiosis is the history of a strain's co-diversification with its host species. Such studies, using simple invertebrate models, allow the recognition of otherwise obscured interactions underlying the more complex microbiomes of vertebrates.},
}

@article {pmid41246976,
year = {2025},
author = {Hoefle, D and Ramakrishnan, DK and Holländer, MA and Kiplimo, D and Konzag, W and Schena, L and Malacrinò, A and Tack, AJM and Abdelfattah, A},
title = {Fruit function beyond dispersal: effect of fruit decomposition on the plant microbiome assembly.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70698},
pmid = {41246976},
issn = {1469-8137},
abstract = {The evolutionary role of fruits has primarily been linked to seed dispersal. However, their influence on the soil and plant microbiomes subsequent to their decomposition has received no attention. We hypothesized that fruit decomposition alters the soil microbiome, and consequently the plant microbiome and performance. We used amplicon sequencing to analyze the bacterial communities in the soil, rhizosphere, and phyllosphere of tomato and chili plants grown with and without their fruit. Fruit decomposition affected soil chemistry, increased bacterial diversity and influenced bacterial community composition. Blrii41 and Sandaracinaceae and functions related to methanol oxidation and nitrification, mammalian and human gut metabolism were enriched. It also decreased germination rates and affected shoot but not root length. Fruit decomposition decreased phyllosphere microbial diversity and strongly shifted the rhizosphere and phyllosphere community composition. The plant microbiome showed increased functions related to ligninolysis, methanol oxidation, methylotrophy, and xylanolysis, among others. These results provide evidence that fruits exert a postdispersal influence on the seedling environment and the early plant microbiome assembly. This study expands the classical ecological view of fruit function and opens new directions for understanding microbial inheritance and leveraging fruit-derived microbiomes.},
}

@article {pmid41246908,
year = {2025},
author = {Miyake, K and Watanabe, D and Otawa, S and Kushima, M and Yui, H and Shinohara, R and Sakurai, D and Yamagata, Z},
title = {Gut Microbiome Alterations by Allergen Sensitisation and Symptom Severity in Paediatric Allergic Rhinitis.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70163},
pmid = {41246908},
issn = {1398-9995},
support = {20H03928//Scientific Research conferred by the Japanese Ministry of Education, Culture, Sports, Science, and Technology/ ; 24K13437//Scientific Research conferred by the Japanese Ministry of Education, Culture, Sports, Science, and Technology/ ; 23-iii5024//TERUMO LIFE SCIENCE FOUNDATION/ ; },
}

@article {pmid41246810,
year = {2025},
author = {Tan, H and Chen, M and Yao, H and Li, S and Nie, S},
title = {Dominant Gut Commensals Enriched by Pectin with Low Esterification Degree Orchestrate the Amelioration of Acute Ulcerative Colitis.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c09097},
pmid = {41246810},
issn = {1520-5118},
abstract = {Dietary fiber's health benefits are increasingly recognized as microbiota-dependent, with effects influenced by fiber structure. We previously observed that low-esterified pectin provides superior protection against DSS-induced colitis compared to its high-esterified form, but the mechanism was unknown. This study investigated the microbiota-dependent pathway underlying low-esterified pectin's anticolitic effect using FMT. By evaluating three pectin-induced bacteria (Bifidobacterium longum NSP002, Bacteroides xylanisolvens NSP003, Enterococcus faecium NSP004) individually and in a consortium, we found that the consortium exerted a significantly stronger protective effect, suggesting synergistic interactions and highlighting its potential as an FMT alternative. Mechanistically, this protection may involve three axes: (1) Gut microbiome remodeling (reduced Akkermansia, increased Bacteroides, elevated propionic acid). (2) Intestinal homeostasis modulation (reduced mme/calprotectin expression, activated PI3K/calcium signaling). and (3) Systemic metabolic reprogramming (increased serum phenylethylamine, enriched phenylalanine metabolism). These findings support the clinical potential of pectin for optimizing enteral nutrition and using pectin-enriched microbiota consortia to target IBD pathogenesis.},
}

@article {pmid41246777,
year = {2025},
author = {Wang, Z and Xu, J and Xu, G and Sha, Y and Wang, K and Chen, G},
title = {Decoding Hypercarotenemia: Integrating Pathophysiology, Clinical Recognition, and Precision Management.},
journal = {Cureus},
volume = {17},
number = {10},
pages = {e94519},
doi = {10.7759/cureus.94519},
pmid = {41246777},
issn = {2168-8184},
abstract = {Hypercarotenemia represents a complex metabolic phenotype characterized by supraphysiological circulating carotenoid concentrations exceeding 300 μg/dL for β-carotene, manifesting as distinctive cutaneous xanthochromia with preserved scleral clarity - a critical differentiating feature from hepatobiliary dysfunction. The contemporary surge in detection rates, which has increased over the past decade, correlates with global dietary paradigm shifts, including the growth in plant-based diet adoption and the concurrent rise in metabolic dysfunction. This comprehensive review synthesizes current understanding of hypercarotenemia pathophysiology through systematic literature analysis encompassing molecular mechanisms, epidemiological trends, clinical phenotypes, and therapeutic interventions, with particular emphasis on genetic discoveries and precision management approaches. Hypercarotenemia pathogenesis involves sophisticated interactions among three key mechanistic pathways: (1) intestinal absorption via SR-B1 receptors, (2) enzymatic conversion through β-carotene oxygenase 1 and 2 (Beta-carotene oxygenase 1 (BCO1)/BCO2) systems, and (3) genetic susceptibility primarily mediated by BCO1 variants (rs6564851, rs12934922, rs7501331). The condition demonstrates remarkable clinical heterogeneity influenced by individual metabolic capacity, intestinal microbiome composition, and concurrent endocrinopathies, particularly thyroid dysfunction and diabetes mellitus. The management paradigms have evolved from simple dietary restriction to precision nutrition approaches, integrating genetic profiling with individualized tolerance thresholds while preserving established health benefits of carotenoid-rich diets. Standard diagnostic criteria incorporate both biochemical thresholds and functional assessments, including the retinol:β-carotene molar ratio as a functional measure of BCO1 activity. Although traditionally considered benign, hypercarotenemia serves as a valuable biomarker for underlying metabolic dysfunction and genetic variants affecting fat-soluble vitamin homeostasis, warranting clinical attention for risk stratification and personalized dietary counseling.},
}

@article {pmid41246705,
year = {2025},
author = {Chohan, PK and Brunhammer, E},
title = {Self-Directed Recovery of Gu Syndrome: Reversal of Multisystem Dysfunction via Microbiome Restoration and Subconscious-Guided Protocols.},
journal = {Cureus},
volume = {17},
number = {10},
pages = {e94595},
doi = {10.7759/cureus.94595},
pmid = {41246705},
issn = {2168-8184},
abstract = {This case report documents a self-directed recovery from a complex, chronic multisystem condition consistent with Gu syndrome, involving Candida overgrowth, dysbiotic flora consistent with small intestinal bacterial overgrowth (SIBO), mold toxicity, intestinal hyperpermeability (leaky gut), and significant microbiome disruption. A 38-year-old male developed multiple symptoms after a trip to a developing country. His initial symptoms included excessive fatigue and weight gain, followed by multisystem involvement. Laboratory testing was positive for Candida albicans, dysbiotic flora consistent with SIBO, leaky gut, and mold toxicity. Management included dietary interventions, targeted supplementation, and intuitive subconscious guidance. The patient had a marked improvement in the clinical symptoms, physical and metabolic performance markers through a phased terrain-based recovery protocol and minimal pharmaceutical intervention. This case illustrates a novel integration of intuitive recovery and functional medicine with application for microbiome-centered therapeutic models.},
}

@article {pmid41246557,
year = {2026},
author = {Zhou, X and An, R and Li, X},
title = {Cervical cancer immune microenvironment: Mechanisms of HPV-mediated immune evasion and advances in immunotherapy (Review).},
journal = {Oncology letters},
volume = {31},
number = {1},
pages = {22},
doi = {10.3892/ol.2025.15375},
pmid = {41246557},
issn = {1792-1082},
abstract = {Cervical cancer, strongly associated with persistent infection by high-risk human papillomaviruses 16/18 (HPV 16/18), remains a major global health burden. The tumor immune microenvironment (TIME) of cervical cancer plays a decisive role in tumor progression and therapeutic outcomes, where HPV oncoproteins E5, E6 and E7 disrupt antigen presentation, interfere with interferon signaling, activate immune checkpoints and induce metabolic reprogramming, thereby establishing an immunosuppressive TIME. Therapeutic advances, including immune checkpoint inhibitors (e.g., pembrolizumab in KEYNOTE-826, nivolumab in CheckMate 358), therapeutic vaccines and adoptive cell therapies, have shown promise but face challenges such as low response rates, resistance, stromal barriers and microbiome-related influences. The aim of the present review is to summarize the current understanding of the cervical cancer TIME, elucidate HPV-mediated immune evasion mechanisms, and to highlight recent advances and ongoing challenges in immunotherapy. Future directions include combination strategies, novel immune targets, and precision approaches integrating spatial multi-omics and microbiota modulation, which may improve immunotherapy efficacy and support personalized treatments for cervical cancer.},
}

@article {pmid41246320,
year = {2025},
author = {Dey, P},
title = {Genes, guts, and microbes: decoding host-driven microbial regulation using intestine-specific conditional knockouts.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1674913},
doi = {10.3389/fimmu.2025.1674913},
pmid = {41246320},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology/genetics ; Humans ; Dysbiosis ; Mice, Knockout ; *Intestines/microbiology/immunology ; *Intestinal Mucosa/metabolism/microbiology/immunology ; *Host Microbial Interactions/genetics ; Mice ; },
abstract = {This narrative review underscores the influence of host genetics in actively regulating gut microbiota composition and function, highlighting the distinctive advantages of intestine-specific conditional knockout (cKO) models in gut microbiome research. In contrast to whole-body knockouts or germ-free animals, these precision models, enabled by Cre-loxP technology, eliminate confounding systemic effects to elucidate how localized host genes within intestinal cells regulate the gut microbial ecology. The review identifies three fundamental host-driven regulatory mechanisms through the analysis of specific gene deletions: (1) barrier integrity (e.g., mucus and junction proteins), (2) immune defenses (e.g., antimicrobial peptides and glycan synthesis), and (3) metabolic signaling (e.g., bile acid receptors and glucose transporter). These pathways jointly impose microbial symbiosis, and their disruption leads to dysbiosis characterized by increased abundance of pathobionts (e.g., Escherichia, Proteobacteria), directly connecting host genetics to inflammatory and metabolic disorders. This host-centric viewpoint emphasizes the gut as an active regulator, rather than a passive microenvironment for the microbiota, providing significant insights for creating tailored therapeutics that focus on host pathways to restore microbial balance in disorders such as inflammatory bowel diseases.},
}

Animals
*Gastrointestinal Microbiome/immunology/genetics
Humans
Dysbiosis
Mice, Knockout
*Intestines/microbiology/immunology
*Intestinal Mucosa/metabolism/microbiology/immunology
*Host Microbial Interactions/genetics
Mice

@article {pmid41246313,
year = {2025},
author = {Xiong, J and Li, J and Xu, H and Li, Y and Lu, L and Yang, S},
title = {Microbiome and metabolomics analyses of the effect of heat-sensitive moxibustion on allergic rhinitis in rats.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1656060},
doi = {10.3389/fimmu.2025.1656060},
pmid = {41246313},
issn = {1664-3224},
mesh = {Animals ; *Moxibustion/methods ; *Rhinitis, Allergic/therapy/metabolism/microbiology/immunology ; Rats ; Rats, Sprague-Dawley ; *Metabolomics/methods ; *Gastrointestinal Microbiome ; Male ; Disease Models, Animal ; Hot Temperature ; Acupuncture Points ; },
abstract = {BACKGROUND: The original concept of acupoint sensitization theory was put forward in Huangdi Neijing, which believed that acupoints, as the reflecting parts of the body surface, are personalized, changeable, and sensitive. Heat-sensitive moxibustion has a good therapeutic effect on allergic rhinitis, but the mechanism is still unclear. Notably, acupoint sensitization in allergic rhinitis (AR) rats was accompanied by a distal thermal effect, with an increase in tail temperature (TTI) after 40 min of moxibustion.

OBJECTIVE: The objective was to utilize multi-omics techniques and correlation analysis to explore the unique mechanisms of heat-sensitive moxibustion in intervening in AR compared with traditional moxibustion from the perspectives of gut microbiota and metabolites.

METHODS: Thirty-six Sprague-Dawley (SD) rats were randomly divided into two groups: the ovalbumin (OVA) group (n = 27) and the control group (Con) (n = 9). The rat model of AR induced by standardized OVA was established through intranasal infusion after intraperitoneal OVA injection. Through behavioral scoring, nasal symptoms were evaluated, including nasal scratching, runny nose, and sneezing, to ensure the success of the modeling. The OVA group was randomly divided into the moxibustion group (n = 17) and the AR group (n = 8). Then, through suspended moxibustion for 40 min, they were divided into TTI, namely, the heat-sensitive moxibustion group (HM) (n = 8) and the non-TTI group (OM) (n = 8), and one subject was excluded. The levels of serum IL-4 and IgE were quantified by enzyme-linked immunosorbent assay (ELISA), and the histological characteristics of nasal tissues were evaluated by hematoxylin and eosin (H&E) staining to determine the reliability of the AR rat model and the effectiveness of thermal sensitization. The V3 and V4 regions of the 16S ribosomal DNA (rDNA) gene were analyzed from rat feces using 16S rDNA sequencing technology. In addition, non-targeted metabolomics was used to identify the differential metabolites in rat urine. Finally, through the comparison and correlation analysis of different bacterial microbiota and metabolites, we aimed to clarify the unique material basis of heat-sensitive moxibustion in the context of AR.

RESULTS: After the OVA modeling was completed, through behavioral score evaluation, we found that there were differences between the OVA group and the control group. After the intervention treatment, it was found that the levels of IgE and IL-4 in the AR group were significantly higher than those in the control group. Staining showed that moxibustion relieved nasal symptoms, and the thermal sensitization effect was satisfactory. We noticed that significant changes occurred in the flora under heat-sensitive moxibustion treatment. We investigated the mechanism of HM in treating AR using an integrated 16S rRNA sequencing technology and untargeted metabolomics. Our results showed that HM treatment ameliorated AR in rats. The high-throughput sequencing results indicate that HM significantly increased the relative abundance of species, such as Patescibacteria, Saccharimonadaceae, UCG-010, Butyrivibrio, Turicibacter, Lactobacillus murinus, and Adlercreutzia, while decreasing the relative abundance of Prevotellaceae. This shift in microbial composition is conducive to improving the gut microbiota of AR rats. Untargeted metabolomics results showed that HM treatment regulated the metabolites such as 1-methylhistidine, xi-3-hydroxy-5-phenylpentanoic acid O-beta-d-glucopyranoside, cladosporin, cuminaldehyde, daidzein, Pe(18:0/15:0), N-nervonoyl asparagine, edulitine, N-arachidonoyl glycine, 9alpha-(3-methyl-2E-pentenoyloxy)-4S-hydroxy-10(14)-oplopen-3-one, quisqualic acid, ethyl glucuronide, zileuton O-glucuronide, trichloroethanol glucuronide, Asp Leu Ser Glu, quinolinic acid, and norvaline. We finally identified six crossing pathways by pin-to-pair comparison of three groups: glutamatergic synapse, dopaminergic synapse, Kaposi sarcoma-associated herpesvirus infection, cocaine addiction, melanin production, alcoholism, and histidine metabolism. Subsequently, we focused on studying the histidine metabolism. To clarify the changes in the activity of this pathway, we measured the histamine content using an enzyme-linked immunosorbent assay. Compared with the OM group, we found that HM had a trend toward superior efficacy in reducing tissue histamine compared to OM. The histamine content in the HM group was significantly lower than that in the OM group. This finding suggests that HM is more effective in reducing histamine, and its effect may be related to a more efficient regulation of the histidine metabolic pathway.

CONCLUSIONS: This study demonstrates that heat-sensitive moxibustion alleviates allergic rhinitis through a multi-targeted mechanism involving both the modulation of specific gut microbiota (notably L. murinus, Patescibacteria, Butyrivibrio, and Turicibacter)-which is closely associated with alterations in key metabolites (cuminaldehyde and 1-methylhistidine)-and the regulation of histidine metabolism. To our knowledge, this represents the first investigation to establish comprehensive correlations between gut microbiota and urinary metabolomics profiles in an AR model. Our findings confirm the therapeutic role of heat-sensitive moxibustion in AR recovery and provide mechanistic insights supporting its clinical application, thereby proposing a novel strategic approach for AR treatment.},
}

Animals
*Moxibustion/methods
*Rhinitis, Allergic/therapy/metabolism/microbiology/immunology
Rats
Rats, Sprague-Dawley
*Metabolomics/methods
*Gastrointestinal Microbiome
Male
Disease Models, Animal
Hot Temperature
Acupuncture Points

@article {pmid41246300,
year = {2025},
author = {Liu, J and Fu, R and Su, Y and Li, Z and Huang, X and Wang, Q and Shi, Z and Wei, S},
title = {Applications of artificial intelligence in cancer immunotherapy: a frontier review on enhancing treatment efficacy and safety.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1676112},
doi = {10.3389/fimmu.2025.1676112},
pmid = {41246300},
issn = {1664-3224},
mesh = {Humans ; *Artificial Intelligence ; *Neoplasms/therapy/immunology ; *Immunotherapy/methods/adverse effects ; Immune Checkpoint Inhibitors/therapeutic use/adverse effects ; Animals ; Treatment Outcome ; },
abstract = {Cancer immunotherapy represents a major breakthrough in oncology, particularly with immune checkpoint inhibitors (ICIs) and CAR-T cell therapies. Despite improved outcomes, challenges such as immune-related adverse events (irAEs) and treatment resistance limit clinical use. Artificial intelligence (AI) offers new opportunities to address these barriers, including target identification, efficacy prediction, toxicity monitoring, and personalized treatment design. This review highlights recent advances in AI applications for biomarker discovery, safety evaluation, gene editing, nanotechnology, and microbiome modulation, integrating evidence from clinical and preclinical studies. We also discuss future directions and challenges in applying AI to cancer immunotherapy, aiming to support further research and clinical translation.},
}

Humans
*Artificial Intelligence
*Neoplasms/therapy/immunology
*Immunotherapy/methods/adverse effects
Immune Checkpoint Inhibitors/therapeutic use/adverse effects
Animals
Treatment Outcome

@article {pmid41246295,
year = {2025},
author = {Yartey, SN and Awere-Duodu, A and Asantewaa, AA and Donkor, ES},
title = {Antibiotic impact on human microecology in low- and middle-income countries: a systematic age-stratified review of gut and respiratory microbiome and resistome.},
journal = {Therapeutic advances in infectious disease},
volume = {12},
number = {},
pages = {20499361251389738},
doi = {10.1177/20499361251389738},
pmid = {41246295},
issn = {2049-9361},
abstract = {BACKGROUND: Antibiotic exposure disrupts microbial communities in the gut and respiratory tract, causing functional changes that may have lasting health impacts and contribute to the spread of antibiotic resistance genes (ARGs) throughout life. However, age-stratified evidence of these effects, particularly in low- and middle-income countries (LMICs), remains limited.

OBJECTIVE: This systematic review assessed the impact of antibiotics on gut and respiratory microbiomes and resistomes in LMICs, with separate analyses for adults and children.

DATA SOURCES: PubMed, Scopus, Web of Science, & ScienceDirect.

METHODS: A comprehensive literature search was conducted using a predefined search strategy and eligibility criteria to identify relevant studies from LMICs. Twenty-five studies met the inclusion criteria: 23 examined the gut microbiome, and 2 focused on the respiratory microbiome. Key outcomes included microbial diversity (alpha/beta/gamma), taxonomic shifts, resistome profiles, functional changes, and recovery potentials, stratified by age group and body site.

RESULTS: Antibiotic exposure was generally associated with reductions in microbial diversity and altered taxonomic composition, with children showing more pronounced and prolonged disruptions than adults. Analysis of resistome changes revealed a critical finding: while antibiotics consistently selected for ARGs matching the drug class administered, a substantial reservoir of non-matching, background ARGs, conferring resistance to beta-lactams, aminoglycosides, vancomycin, tetracyclines, was also highly prevalent across studies. This indicates a silent pre-existing resistome that is enriched by antibiotic pressure. ARGs were more abundant in adult resistomes, though functional changes occurred across age groups. Microbiome recovery was observed over time, but resistome recovery was limited.

CONCLUSION: Antibiotic use significantly disturbs the gut and respiratory microbiomes and promotes ARG enrichment, especially in children, who demonstrate greater susceptibility and lower recovery potential. These findings emphasise the need for targeted antibiotic stewardship, improved microbiome recovery research, and enhanced resistome monitoring in LMICs.

TRAIL REGISTRATION: International Prospective Register of Systematic Reviews (PROSPERO), ID: CRD420250641394.},
}

@article {pmid41246285,
year = {2025},
author = {Ahmed, N and Gaur, V and Kamle, M and Chauhan, A and Chauhan, R and Kumar, P and Singh, NA},
title = {Microbiome-based therapeutics for metabolic disorders: harnessing microbial intrusions for treatment.},
journal = {Frontiers in medical technology},
volume = {7},
number = {},
pages = {1695329},
doi = {10.3389/fmedt.2025.1695329},
pmid = {41246285},
issn = {2673-3129},
abstract = {The rising global rates of metabolic disorders, such as obesity, type 2 diabetes, non-alcoholic fatty liver disease, and metabolic syndrome, call for new treatment methods beyond traditional drugs. The human gut microbiota, made up of trillions of microorganisms that plays a crucial role in maintaining metabolic balance through complex biochemical processes and interactions between hosts and microbes. Dysbiosis, which involves changes in microbial composition and a decrease in diversity, has become a major factor in metabolic problems. This disruption impacts the production of short-chain fatty acid, increase in permeability of intestine, and causes enduring low-grade inflammation. This review features into the potential of treatments based on microbiome for metabolic syndromes, focusing on probiotics, prebiotics, synbiotics, and postbiotics. It also encompasses innovative methods such as engineered microbial consortium, fecal microbiota transplantation (FMT), and vaginal microbiota transplantation (VMT). Probiotics show significant promise in improving blood sugar control and enhancing lipid levels. Prebiotics help bring about positive changes in microbial composition and the production of beneficial metabolites. Synbiotic combinations provide added benefits by helping good microbes thrive while supplying nutrients they can ferment. Postbiotics have recent research focus because they are safer, more stable, easier to store, and less likely to contribute to antibiotic resistance comparative to live probiotics. Even now there are substantial complications in translating microbiome research into standardized therapeutics despite of promising pre-clinical outcomes and some initial clinical data. These comprises individual variances, strain-specificity, dosage problems, regulation issues, and the necessity for personalised treatment strategies. Future success will depend upon personalized medicine, technological developments, and the incorporation of multi-omics strategy to generate metabolic health therapeutics depending on targeted microbiomes.},
}

@article {pmid41246281,
year = {2025},
author = {Jeong, M and Park, S and Jeong, S and Park, S and Yeo, S and Ryu, B and Shin, JH and Lee, S},
title = {Multi-omics insights into plant-microbe dysbiosis caused by cyanobacterial bloom-affected water.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100500},
doi = {10.1016/j.crmicr.2025.100500},
pmid = {41246281},
issn = {2666-5174},
abstract = {The use of untreated, cyanobacterial bloom-affected river water as a readily available source for crop production is a realistic scenario in many regions, yet its systemic impact on crop health remains poorly defined. Here, we investigate the multifaceted effects of this practice by cultivating lettuce (Lactuca sativa) with bloom-season water from the eutrophic Nakdong River and comparing it to lettuce grown in a nutrient-optimized hydroponic solution. We found that exposure to bloom-affected water severely inhibited plant growth and led to the accumulation of microcystins in edible tissues, with estimated daily intakes exceeding WHO safety thresholds. Multi-omics analyses revealed that this phenotype was driven by a synergistic failure of internal and external support systems: key mitochondrial genes for energy production were downregulated, protective antioxidant flavonoids were depleted, and the aquatic microbiome shifted to a dysbiotic state that favored stress-tolerant taxa while reducing beneficial ones. Together, these results establish how bloom-affected water initiates a vicious cycle of physiological stress and microbial dysbiosis that undermines crop health. This study provides an integrative framework for assessing risks in real-world hydroponic systems and for guiding future investigations into more complex soil-based agriculture.},
}

@article {pmid41246271,
year = {2025},
author = {Liu, M and Wen, X and Feng, M and Sun, Y and Feng, X and Jin, T and Liu, B and Muhammad, S and Liu, K and Cheng, J and Li, J},
title = {Evaluation of Lactiplantibacillus plantarum CRS 33 to therapeutic effects on a murine model of Escherichia coli-induced endometritis.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1608791},
doi = {10.3389/fvets.2025.1608791},
pmid = {41246271},
issn = {2297-1769},
abstract = {INTRODUCTION: Bovine endometritis is a common postpartum uterine disease in dairy cows that is traditionally treated with antibiotics. However, excessive antibiotic use can lead to antimicrobial resistance and treatment failure. Lactiplantibacillus plantarum CRS33, a novel probiotic strain isolated from the uterus of a healthy cow, exhibits strong antibacterial potential. This study aimed to investigate the probiotic characteristics of Lactiplantibacillus plantarum CRS33 through whole-genome sequencing and to evaluate its anti-inflammatory effects in a mouse model of Escherichia coli-induced endometritis.

METHODS: Whole-genome sequencing was performed to identify genes related to antibacterial, anti-inflammatory, and immune-regulatory activities, and to confirm the absence of antibiotic resistance and virulence genes. Female mice were induced with Escherichia coli endometritis and treated with Lactiplantibacillus plantarum CRS33 at a dose of 1 × 10[⁹] CFU/mL. Uterine morphology, wet weight index, inflammatory cell infiltration, cytokine levels (IL-6, IL-1β, IL-8, TNF-α), and uterine microbiota composition were analyzed.

RESULTS: Genomic analysis revealed that Lactiplantibacillus plantarum CRS33 contains multiple functional genes related to antimicrobial, anti-inflammatory, and immune-modulatory pathways and lacks antibiotic resistance or pathogenic determinants. Treatment with Lactiplantibacillus plantarum CRS33 significantly alleviated uterine inflammation, reduced the wet weight index (p < 0.05), and improved histopathological lesions. It also decreased pro-inflammatory cytokine levels and inflammatory cell infiltration, while enhancing microbial diversity and increasing the abundance of beneficial bacterial taxa.

DISCUSSION: Lactiplantibacillus plantarum CRS33 demonstrates strong anti-inflammatory and microbiota-regulating properties in Escherichia coli-induced endometritis, highlighting its potential as a safe and effective probiotic alternative to antibiotics. Further validation in dairy cows is warranted to confirm its therapeutic potential under practical conditions.},
}

@article {pmid41246144,
year = {2025},
author = {Kayashima, A and Fukuhara, S and Miyamoto, K and Iwasaki, E and Kato, M and Sujino, T},
title = {Biliary stents reshape the bile microbiome in the absence of cholangitis.},
journal = {Endoscopy international open},
volume = {13},
number = {},
pages = {a27333468},
doi = {10.1055/a-2733-3468},
pmid = {41246144},
issn = {2364-3722},
abstract = {BACKGROUND AND STUDY AIMS: Biliary stents are widely used in endoscopic retrograde cholangiopancreatography (ERCP), yet their impact on the native bile microbiome under non-infectious conditions remains unclear. We aimed to characterize stent-associated alterations in the biliary microbiome using 16S rRNA gene sequencing.

PATIENTS AND METHODS: We analyzed bile samples collected during ERCP from 35 patients without clinical or laboratory evidence of acute cholangitis. Patients were categorized into a control group (n = 25; naïve papillae) and an endoscopic biliary stenting (EBS) group (n = 10; previously stented). Microbial composition was assessed using high-throughput 16S rRNA sequencing after propensity score matching to balance background characteristics.

RESULTS: Beta diversity differed significantly between groups (PERMANOVA, P < 0.01), despite no significant differences in alpha diversity. The EBS group demonstrated increased relative abundance of Firmicutes and Fusobacteriota , and depletion of Proteobacteria . Notably, Enterococcus was significantly enriched in the EBS group (log fold change 6.74; q < 0.01), whereas Sphingomonas was reduced.

CONCLUSIONS: Endoscopic biliary stenting is associated with distinct bile microbiome alterations, characterized by enrichment of Enterococcus species in clinically stable patients. These findings suggest that stents may predispose to opportunistic colonization, providing a potential mechanistic link to future cholangitis. Recognizing such preclinical dysbiosis may inform tailored antimicrobial strategies and future stent design.},
}

@article {pmid41246092,
year = {2025},
author = {Jia, B and Wu, X and He, G and Wang, Q and Guan, L and Ren, J and Li, G and Zheng, X and Yang, S},
title = {Oral microbiome dysbiosis is associated with chronic respiratory diseases: evidence from a population-based study and a hospital cohort.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1696041},
doi = {10.3389/fpubh.2025.1696041},
pmid = {41246092},
issn = {2296-2565},
mesh = {Humans ; Male ; Female ; Middle Aged ; *Microbiota ; *Dysbiosis/microbiology/epidemiology ; Adult ; *Mouth/microbiology ; RNA, Ribosomal, 16S ; Aged ; Cohort Studies ; Nutrition Surveys ; Chronic Disease ; *Respiratory Tract Diseases/microbiology/epidemiology ; },
abstract = {BACKGROUND: The oral microbiome has been increasingly recognized for its role in systemic health through the oral-lung axis. However, population-level evidence linking oral microbial diversity and composition with chronic respiratory diseases (CRD) remains limited.

METHODS: We analyzed data from 4,384 adults in the 2009-2012 National Health and Nutrition Examination Survey (NHANES), defining CRD by self-reported chronic obstructive pulmonary disease (COPD), asthma, emphysema, or chronic bronchitis. Oral rinse samples underwent 16S ribosomal RNA (16S rRNA) V1-V3 sequencing. Alpha diversity, including observed amplicon sequence variants (ASVs), Faith's phylogenetic diversity (Faith's PD), Shannon-Weiner index, and Simpson index, and beta diversity, including Bray-Curtis, weighted UniFrac, and unweighted UniFrac distances, were assessed. Associations with CRD were examined using weighted logistic regression and restricted cubic splines (RCS). Differential genus abundance was identified by Wilcoxon tests with false discovery rate correction. A random forest model integrated microbial and clinical features. An independent hospital cohort was additionally profiled by 16S rRNA sequencing, and genus-level differences were assessed with linear discriminant analysis effect size (LEfSe) to validate NHANES findings.

RESULTS: Higher alpha diversity was inversely associated with CRD risk; each standard deviation increase in observed ASVs and Faith's PD reduced CRD odds by 19 and 17%, respectively (p < 0.05). Beta diversity showed significant community-level separation by CRD status (p = 0.01). Several genera, including Rothia and Veillonella, were enriched in CRD, whereas Prevotella, Haemophilus, and Neisseria were more abundant in non-CRD individuals. The random forest model achieved an area under the curve (AUC) of 0.65. In the hospital cohort, compositional shifts were consistent with NHANES findings, and LEfSe confirmed the depletion of Alloprevotella and Peptostreptococcus in CRD patients.

CONCLUSION: Oral microbial diversity and composition were significantly associated with CRD across both a representative U. S. population and a hospital cohort. Select genera and diversity indices may serve as non-invasive biomarkers for respiratory health, warranting further validation in longitudinal and mechanistic studies.},
}

Humans
Male
Female
Middle Aged
*Microbiota
*Dysbiosis/microbiology/epidemiology
Adult
*Mouth/microbiology
RNA, Ribosomal, 16S
Aged
Cohort Studies
Nutrition Surveys
Chronic Disease
*Respiratory Tract Diseases/microbiology/epidemiology

@article {pmid41245977,
year = {2025},
author = {Humińska-Lisowska, K and Łabaj, PP and Zielińska, K},
title = {Unique Athletic Gut Microbiomes and Their Role in Sports Performance: A Narrative Review.},
journal = {Journal of human kinetics},
volume = {99},
number = {},
pages = {79-97},
doi = {10.5114/jhk/202642},
pmid = {41245977},
issn = {1640-5544},
abstract = {The human gut microbiome, a diverse community of microorganisms, plays a crucial role in digestion, metabolism, immune function, and brain health. Key metabolites produced by the gut microbiota, such as short-chain fatty acids (SCFAs) and bile acids, are essential for energy production, metabolic regulation, and immune system modulation. The gut microbiome's composition is influenced by factors including diet, exercise, sleep, and age, and disruptions are linked to various health conditions. Elite athletes exhibit unique gut microbiota profiles that contribute to their exceptional performance and recovery. Their microbiomes are not only richer, but also possess unique microorganisms and functional capabilities, alongside distinct genetic landscapes that support their high-level physiological demands. This review focuses specifically on the athletic gut microbiome, exploring how it differs from that of an active or a sedentary individual, adapts to different training phases, extreme conditions like heat and hypoxia, and prolonged exertion. It highlights the dual role of the gut microbiome in both enhancing athletic performance and potentially contributing to disease development, particularly due to the prolonged exertion and stress associated with years of intense competition. The review also explores the implications of microbiome changes following periods of intense physical activity and their impact on the athlete's overall health. Finally, it evaluates athlete-specific interventions, including prebiotics, probiotics, and synbiotics, aimed at mitigating negative effects on the gut microbiome while supporting health and optimizing performance.},
}

@article {pmid41245891,
year = {2025},
author = {Yang, Q and Cai, Y and Guan, Y and Wang, Z and Guo, S and Qiu, S and Zhang, A},
title = {Metabolic phenotypes: Molecular bridges between health homeostasis and disease imbalance.},
journal = {Computational and structural biotechnology journal},
volume = {27},
number = {},
pages = {4710-4719},
doi = {10.1016/j.csbj.2025.10.057},
pmid = {41245891},
issn = {2001-0370},
abstract = {Metabolic phenotypes represent the overall characterization of an individual's metabolites at a specific point in time. They precisely reflect the complex interactions among genetic background, environmental factors, lifestyle, and gut microbiome, thereby serving as a key molecular link between healthy homeostasis and disease-related metabolic disruption. In recent years, high-throughput metabolomics strategies have enabled the systematic analysis of small molecule metabolites in physiological and pathological processes. These metabolites not only serve as biomarkers for disease diagnosis, prognosis assessment, and treatment response prediction, but also elucidate novel mechanistic pathways in disease progression. The high-coverage, high-sensitivity detection of metabolites afforded by mass spectrometry and NMR-based metabolomics enables advances in precision medicine, facilitating biomarker discovery, pharmacokinetic studies, and the assessment of nutritional interventions. This review uses several common metabolic diseases, such as obesity, diabetes, cardiovascular diseases, and cancer, to explore the key role of metabolic phenotypes in disease risk stratification and precise prediction. Future phenotypic research will shift toward integrating artificial intelligence, big data mining, and multi-omics with the goal of revealing the complete network through which metabolic phenotypes regulate diseases. This research is expected to advance early diagnosis, precise prevention, and targeted treatment, contributing to a medical paradigm shift from disease treatment to health maintenance.},
}

@article {pmid41245847,
year = {2025},
author = {Sopirala, MM and Weber, D and Sood, G and Yassin, M and Palmieri, TL and Narasimhan, S and Sheckter, C and Caffrey, J and Mandell, S and Pisney, L and Kandiah, S and Somani, J and Mackow, N and Brust, K and Karaba, S and Doll, M and Chen, D and Abbo, L and Bischoff, W},
title = {A research agenda for burn infection prevention: identifying knowledge gaps and prioritizing future directions.},
journal = {Antimicrobial stewardship & healthcare epidemiology : ASHE},
volume = {5},
number = {1},
pages = {e293},
doi = {10.1017/ash.2025.10213},
pmid = {41245847},
issn = {2732-494X},
abstract = {OBJECTIVE: Burn injuries result in loss of skin barrier and altered immune responses that in turn make patients especially vulnerable to healthcare-associated infections. Despite prolonged exposures of these patients to hospital environments, burn-specific infection prevention strategies are understudied. We present a research agenda identifying key research gaps and organizing them into priority areas to guide future investigations in this high-risk population.

DESIGN: Members of the Society for Healthcare Epidemiology of America (SHEA) Burn Infection Prevention and Control Special Interest Group and the American Burn Association (ABA) collaborated to develop this research agenda, combining expertise in infection prevention, antimicrobial stewardship, and burn care.

RESULTS: We identified five priority areas: (1) improving surveillance and epidemiologic data on burn infections; (2) better understanding of microbiology, including biofilms and the microbiome; (3) evaluating wound healing strategies; (4) refining infection prevention and control practices unique to burn units; and (5) building burn patient specific risk assessment and predictive models. The agenda highlights the need for standardized definitions and shared data platforms. It calls for evaluation of practical strategies for infection prevention, stewardship, and environmental control.

CONCLUSIONS: This research agenda intends to help guide future studies aimed at furthering knowledge and improving outcomes in burn care.},
}

@article {pmid41245833,
year = {2025},
author = {Ilie, OD and Văcărean-Trandafir, IC and Amărandi, RM and Nita, IB and Dobrin, PR and Doroftei, M and Ivanov, IC and Savuta, G and Kirov, B and Doroftei, B},
title = {Exploring gut microbiota alterations in Parkinson's disease: insights from a 16S amplicon sequencing Eastern European pilot study.},
journal = {Frontiers in neuroscience},
volume = {19},
number = {},
pages = {1654995},
doi = {10.3389/fnins.2025.1654995},
pmid = {41245833},
issn = {1662-4548},
abstract = {INTRODUCTION: Parkinson's disease (PD) is a neurodegenerative disorder increasingly associated with alterations in gut microbiota through the gut-brain axis (GBA). Despite growing global interest, studies examining microbiota composition in Eastern European populations remain limited.

METHODS: We profiled the gut microbiota of 59 Romanian individuals using 16S rRNA gene sequencing targeting the V3-V4 region. After quality filtering, 39 subjects (19 PD patients and 20 healthy controls [HC]) were retained for downstream analysis. Clinical metadata were collected to assess potential confounders, including age, sex, metabolic parameters, lifestyle, and comorbidities.

RESULTS: PD patients differed significantly from HCs in glycemia (p = 0.02), cholesterol (p = 0.027), and LDL levels (p = 0.047), and more frequently presented with restrictive diets and comorbidities such as cardiovascular disease and diabetes. While α-diversity metrics did not differ significantly between groups, principal coordinate analysis (PCoA) based on Aitchison distance showed moderate compositional separation. Permutational multivariate analysis of variance (PERMANOVA) confirmed that disease status was a significant driver of gut microbiota composition (R [2] = 5.3%, p = 0.002), independent of clinical and lifestyle covariates. Sparse partial least square linear discriminant (sPLS-DA) identified several genera distinguishing PD from HC, with Mogibacterium and RikenellaceaeRC9 gut group enriched in PD, and several known short-chain fatty acid (SCFA)-producing genera (Fusicatenibacter, Lachnospiraceae UCG-001, Butyricicoccus, Anaerostipes) enriched in HCs. Linear discriminant analysis (LDA) Effect Size (LEfSe) corroborated these findings, confirming the differential abundance of several SCFA-producing genera in the HC group.

DISCUSSION: Our results reveal distinct microbial signatures associated with PD in this Romanian cohort, marked by a consistent depletion of SCFA-producing bacteria in patients. These findings support the role of gut microbiota in PD pathophysiology and underscore the need for further studies in Eastern European populations.},
}

@article {pmid41245385,
year = {2025},
author = {Lee, C and Feuerstadt, P and Louie, T and Bancke, L and Guthmueller, B and Harvey, A and Hoeyer, F and Orenstein, R and Dubberke, ER and Khanna, S},
title = {Integrated analysis of the safety of fecal microbiota, live-jslm in adults with recurrent Clostridioides difficile infection from five prospective clinical trials: an update.},
journal = {Therapeutic advances in gastroenterology},
volume = {18},
number = {},
pages = {17562848251395566},
doi = {10.1177/17562848251395566},
pmid = {41245385},
issn = {1756-283X},
abstract = {BACKGROUND: Fecal microbiota, live-jslm (RBL) is approved in the United States and Canada for prevention of recurrent Clostridioides difficile infection (rCDI) in adults following standard-of-care (SOC) antibiotic treatment.

OBJECTIVES: Provide an updated integrated safety analysis, incorporating final safety data from Punch CD3-OLS.

DESIGN: Safety data were combined from five RBL trials: three phase II and two phase III trials.

METHODS: Adult participants had documented rCDI and completed SOC therapy before receiving one or two doses of RBL or placebo, rectally administered as one treatment course. Treatment-emergent adverse events (TEAEs) were recorded for ⩽6 months.

RESULTS: TEAEs were reported in 70.9% (845/1192) of RBL recipients; most TEAEs were mild to moderate and gastrointestinal in nature. Most serious TEAEs were related to preexisting conditions or CDI. There was no clustering of serious TEAEs. Most TEAEs leading to death were related to preexisting conditions.

CONCLUSION: Overall, data demonstrate RBL has a favorable 6-month safety profile.

TRIAL REGISTRATION: ClinicalTrials.gov: NCT01925417; NCT02299570; NCT02589847; NCT03244644; NCT03931941.},
}

@article {pmid41245267,
year = {2025},
author = {Makkar, SK and Bishnupuri, KS},
title = {The gut microbiome and gastrointestinal cancers: mechanisms, biomarkers and therapeutic opportunities.},
journal = {Frontiers in physiology},
volume = {16},
number = {},
pages = {1676796},
doi = {10.3389/fphys.2025.1676796},
pmid = {41245267},
issn = {1664-042X},
abstract = {Gastrointestinal (GI) cancers remain a leading global cause of cancer-related mortality, significantly impacting public health and healthcare systems worldwide. Emerging evidence underscores the critical role of gut microbiome dysbiosis-characterized by disrupted microbial diversity and function-in GI carcinogenesis. Utilizing recent advancements in multi-omics technologies and sophisticated computational biology, researchers have elucidated distinct microbial signatures associated with colorectal, gastric, hepatobiliary, pancreatic, and esophageal cancers. This review comprehensively analyzes the primary mechanisms through which gut microbes contribute to cancer development and progression, encompassing genotoxicity, chronic inflammation, metabolic dysregulation, epigenetic modifications, and immunomodulation. Moreover, we explore innovative microbiome-derived biomarkers for potential clinical applications, including early diagnosis, prognosis assessment, and therapeutic response prediction. The intricate interactions between microbiota and standard cancer therapies-chemotherapy, immunotherapy, and radiation therapy-are discussed, highlighting microbiome influences on therapeutic efficacy and adverse effect profiles. We also critically assess the impact of modifiable factors such as diet, medications, lifestyle, and environmental exposures on microbiome composition and cancer risk. The review evaluates emerging therapeutic interventions, including dietary modifications, probiotics, prebiotics, fecal microbiota transplantation (FMT), and engineered live biotherapeutics. Despite notable advancements, significant hurdles remain, including clarifying causality, methodological standardization, and equitable global research representation. Addressing these challenges, we propose a strategic research agenda aimed at harnessing microbiome insights to advance precision oncology and improve GI cancer outcomes globally.},
}

@article {pmid41245018,
year = {2025},
author = {Sun, T and Kenyon, V and Valitutti, F and Fasano, A and Martin, V and Leonard, MM},
title = {Rates of parent-reported allergic conditions in children at-risk of celiac disease.},
journal = {JPGN reports},
volume = {6},
number = {4},
pages = {480-484},
doi = {10.1002/jpr3.70079},
pmid = {41245018},
issn = {2691-171X},
abstract = {Allergies and other chronic immune mediated conditions are becoming increasingly common. Here we utilized a prospective birth cohort called the Celiac Disease Genomic Environmental Microbiome and Metabolomic (CDGEMM) study to examine the frequency of parent reported allergic conditions and their association with celiac disease (CeD). We examined 271 children at-risk of CeD from the United States and found a high frequency of allergic conditions. In our overall cohort, 19.8% reported food protein-induced allergic proctocolitis (FPIAP), 12.5% reported IgE-mediated food allergy, and 14.7% reported atopic dermatitis. Among the 23 children with CeD, 21.74% had FPIAP, 8.7% had an IgE-mediated food allergy, and 21.74% had atopic dermatitis. No significant association between allergic conditions and CeD was found (p > 0.35 for all). These results highlight the widespread occurrence of parent-reported allergic conditions in children but do not suggest an association between allergic conditions and CeD development.},
}

@article {pmid41244711,
year = {2025},
author = {Andac-Aktas, AB and Calibasi-Kocal, G},
title = {Immunological landscape of colorectal cancer: tumor microenvironment, cellular players and immunotherapeutic opportunities.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1687556},
doi = {10.3389/fmolb.2025.1687556},
pmid = {41244711},
issn = {2296-889X},
abstract = {Colorectal cancer (CRC) remains one of the most lethal malignancies worldwide, with outcomes shaped not only by genetic alterations but also by the complexity of the tumor microenvironment (TME). The TME encompasses stromal and endothelial cells, extracellular matrix components, gut microbiota, and a diverse array of immune cells that dynamically interact to influence tumor initiation, progression, and therapeutic response. This review delineates the immunological landscape of CRC, highlighting the dual functions of innate immune cells-including tumor-associated macrophages, natural killer cells, dendritic cells, neutrophils, and mast cells-and adaptive immune players such as cytotoxic T lymphocytes, helper T-cell subsets, and B/plasma cells. These cellular interactions contribute to the heterogeneity between immunologically "hot" microsatellite instability-high (MSI-H) tumors, which are highly responsive to immunotherapy, and "cold" microsatellite-stable (MSS) tumors, which remain resistant. Key mechanisms of immune evasion, such as cancer immunoediting, checkpoint signaling, and exosome-mediated communication, are examined alongside prognostic tools like the Immunoscore that serve as biomarkers of immune infiltration. Emerging immunotherapeutic strategies, including checkpoint blockade, macrophage reprogramming, natural killer cell agonists, and microbiome modulation, are discussed with emphasis on both their promise and limitations in CRC management. By integrating current insights into immune-tumor interactions, the review underscores opportunities for developing personalized, TME-targeted interventions to improve CRC outcomes.},
}

@article {pmid41244696,
year = {2025},
author = {Belanche, A and Belzecki, G and Hernandez-Sanabria, E and Martínez-Fernandez, G and Ramos-Morales, E and de la Fuente, G},
title = {Editorial: Unravelling the unknown of the rumen microbiome: implications for animal health, productivity, and beyond.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1720795},
doi = {10.3389/fmicb.2025.1720795},
pmid = {41244696},
issn = {1664-302X},
}

@article {pmid41244691,
year = {2025},
author = {Popowski, W and Domanowska, D and Koseski, D and Ostrowski, R and Zalewska, M and Małecka-Giełdowska, M and Łasica, A and Popowska, M},
title = {Analysis of the oral microbiome composition of healthy individuals and the in vitro antibacterial activity of platelet-rich fibrin from these individuals against oral pathogenic bacteria.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1691046},
doi = {10.3389/fmicb.2025.1691046},
pmid = {41244691},
issn = {1664-302X},
abstract = {Platelet-rich fibrin (PRF) is a platelet concentrate widely applied in various medical fields and is considered a valuable adjunct in tissue regeneration during surgical procedures. However, infections caused by biofilm-forming bacteria at surgical sites, combined with increasing antibiotic resistance, present a major clinical concern. Current research is focused on identifying alternative therapeutic strategies to improve infection control and promote wound healing. This study aimed to characterize the oral microbiome of healthy individuals and evaluate the in vitro antimicrobial properties of two PRF formulations. The antibacterial activity, along with its temporal dynamics at different initial bacterial concentrations, was assessed against Gram-negative bacteria (Escherichia coli, Porphyromonas gingivalis) and Gram-positive bacteria exhibiting diverse morphologies (Bacillus subtilis, Micrococcus luteus, Staphylococcus lentus, Enterococcus casseliflavus, Streptococcus mutans). Our results fill gaps in knowledge concerning the spectrum of PRF's antimicrobial activity, demonstrating efficacy against a range of opportunistic and pathogenic bacteria. Key findings include the absence of significant differences in oral microbiome composition between male and female participants, a lack of inhibitory effect of A-PRF against S. mutans, and a transient inhibitory effect against P. gingivalis observed only at low initial OD600 and within 24 h. These findings indicate that A-PRF therapy alone may not provide a sufficiently effective antibacterial effect in patients with oral infections, and that alternative or adjunctive therapeutic approaches should be considered in such cases.},
}

@article {pmid41244672,
year = {2025},
author = {Dubois, B and Delitte, M and Bragard, C and Legrève, A and Chandelier, A and Debode, F},
title = {Improving the profiling of wheat bacterial and fungal endophytic communities-a PCR clamping approach.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1690976},
doi = {10.3389/fmicb.2025.1690976},
pmid = {41244672},
issn = {1664-302X},
abstract = {BACKGROUND: Plant-associated endophytic microbial communities are an important source of biological diversity. To study them, efficient, robust, and standardized characterization methods are necessary. These communities are usually profiled using amplicon high-throughput sequencing (metabarcoding), but the large amount of host DNA often leads to substantial co-amplification of organellar sequences, thereby hampering accurate characterization. A promising solution is the use of PCR clamps, modified oligomers that block non-target DNA amplification. However, no practical guidelines are currently available to support their development, and no sets of clamps enabling comprehensive characterization of endophytic bacterial and fungal communities associated with wheat (Triticum aestivum ssp. aestivum) have been reported.

RESULTS: We developed PCR clamps to block wheat DNA co-amplification while targeting bacterial or fungal populations. For bacteria, two clamping strategies [blocking primers and peptide nucleic acid (PNA)] were evaluated on the 16S V5V7 region. The PNA exhibited superior efficiency (99.8% bacterial reads), whereas blocking primers still performed well (67-98%) and offered a cheaper alternative. The PNA approach was retained for subsequent designs due to its higher efficiency, and two additional PNAs targeting the 16S V4 region were designed to block chloroplast and mitochondrial DNA, respectively. The best results were achieved using both PNAs simultaneously, with 80% of reads being of bacterial origin. For fungi, two PNA clamps were designed targeting ITS1 and ITS2, leading to a substantial reduction in wheat DNA co-amplification, with up to 94 and 75% fungal reads obtained using the ITS1- and ITS2-targeting PNA, respectively. The results also highlighted that profiling endophytic communities without clamps risks significantly underestimating microbial diversity. Furthermore, four bacterial and fungal mock communities were created as tools for standardization and internal control, confirming that our clamps do not inhibit microbial DNA amplification.

CONCLUSION: Whereas amplifications without clamps yielded almost exclusively plant reads, the clamps developed here significantly increased the proportion of microbial reads. This in turn enhanced microbial diversity recovery and the reliability of conclusions drawn from endophytic community analyses. The methodology described provides a framework for clamp development that can be reproduced and adapted to any other host species.},
}

@article {pmid41244669,
year = {2025},
author = {Yuan, T and Chen, J and Yang, J and Li, L and Lu, S and Pu, J and Sun, Y and Lin, W and Lu, Y and Zhu, Z and Zheng, H and Xu, J},
title = {Species-level enterosignatures predict clinical phenotypes in chronic hepatitis B and causal triangulation of gut-metabolite-CHB interactions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1683451},
doi = {10.3389/fmicb.2025.1683451},
pmid = {41244669},
issn = {1664-302X},
abstract = {Chronic hepatitis B (CHB) remains a significant global health challenge, with research indicating the gut microbiota's influence on disease progression, although investigations have primarily been limited to the genus level. This study conducted species-level research using the Human Gut Microbiome Analysis Database (HGMAD) to examine differences in gut microbiota between CHB patients and healthy controls (HC), to investigate enterotype associations with CHB, to assess the predictive capacity of enterosignatures for CHB phenotypes, and to determine causal relationships among gut microbiota, metabolites, and CHB. The cross-sectional investigation included 129 CHB patients and 58 HC, with fecal samples analyzed by 16S rRNA gene sequencing of the V3-V4 region. Significant differences in α-diversity and β-diversity (P < 0.05) were observed between the CHB and HC groups. Taxonomic analysis revealed that the high prevalent bacteria group was lower in CHB patients (61.15%) than in HC (98.05%), indicating increased gut microbiota heterogeneity in CHB. Among known bacterial species, pathogens showed higher prevalence in CHB patients (22.80% vs. 11.49%), with several potential enteropathogenic bacteria (e.g., Bacteroides fragilis and Haemophilus parainfluenzae) enriched in CHB. Dimensionality reduction and clustering analysis of gut microbiota in CHB patients revealed two distinct enterotypes: ET-P dominated by Prevotella and ET-B dominated by Bacteroides. ET-P demonstrated a correlation with elevated levels of hepatitis B virus (HBV) DNA, hepatitis B surface antigen (HBsAg), hepatitis B e antigen (HBeAg), CD4[+]T-cell count and CD8[+]T-cell count, and alpha-fetoprotein (AFP). The enterosignatures of ET-P and ET-B effectively predicted key clinical indicators: the area under the curve (AUC) was 0.78 (95% confidence interval [CI]: 0.69-0.86) for HBeAg levels, 0.86 (95% CI: 0.79-0.93) for HBV DNA levels, 0.75 (95% CI: 0.65-0.84) for AFP status, and 0.85 (95% CI: 0.77-0.92) for CD4[+]T-cell count status. Mendelian randomization (MR) analysis, integrating two gut-microbiota databases, provided genetic evidence for causal relationships between 16 species-level gut microbes and CHB. An elevated abundance of Prevotella copri was associated with an increased risk of CHB (OR = 1.42, 95% CI: 1.01-2.00, P = 0.045). Additionally, mediation MR analyses revealed potential metabolite-mediated mechanisms underlying the role of gut microbiota in CHB. Two enterotypes were identified in CHB patients, ET-P demonstrated positive associations with HBV activity and viral load. The enterosignatures derived from both enterotypes effectively predicted key CHB clinical indicators, establishing causal links and potential underlying mechanisms between gut microbiota and CHB. These findings indicate that the gut microbiota maintains close connections to HBV infection, correlating with viral load, host immune status, and disease prognosis in hepatitis B.},
}

@article {pmid41244617,
year = {2025},
author = {Ma, ZS},
title = {Microbial Biomarkers of Breast Tumor and Mastitis: Deciphering the Delicate Balance between Potentially "Evil" and "Benign" Alliances in Mammary Microbiomes.},
journal = {Breast care (Basel, Switzerland)},
volume = {},
number = {},
pages = {},
doi = {10.1159/000548037},
pmid = {41244617},
issn = {1661-3791},
abstract = {INTRODUCTION: Breast cancer and mastitis significantly impact women's health and their infants' wellbeing. The advent of metagenomic sequencing technology has opened new avenues to explore the relationships between mammary microbiomes and these diseases. Despite recent extensive studies, detailed understanding of the mammary microbiome-disease relationships remains incomplete.

METHODS AND RESULTS: Here, we apply the Specificity and Specificity Diversity framework (Ma 2024, BMC Biology) to identify unique/enriched species (US/ES) associated with mastitis, breast cancer, or their healthy controls. The US/ES lists contain potential biomarkers and offer fresh insights into the intricacies of mastitis etiology and the relationship between breast tissue microbiomes and breast cancer.

CONCLUSIONS: (i) The dynamic balance between coexisting alliances of beneficial microbes and harmful microbes (including opportunistic pathogens) holds key to understanding mastitis etiology. (ii) Intra-tumor microbes may serve multiple roles - as oncogenic microbes, neutral bystanders, or tumor suppressors, and their dynamic balance can influence breast cancer onset and progression. (iii) Significant challenges remain in developing effective probiotics, prebiotics and infant formulas due to complex entanglements between beneficial and harmful microbes. This complexity suggests that broad-spectrum or one-size-fits-all probiotic approaches may prove inadequate, pointing instead to the need for personalized prebiotic/probiotic/infant-formula solutions to restore and maintain healthy mammary microbiomes.},
}

@article {pmid41244152,
year = {2025},
author = {Mizuno, M and Ogata, Y and Nishihara, Y and Nishio, M and Katano, H and Sekiya, I},
title = {Microbiome-based profiles of airborne bacteria to support microbial risk assessment in cleanroom environments.},
journal = {Regenerative therapy},
volume = {30},
number = {},
pages = {991-998},
doi = {10.1016/j.reth.2025.10.019},
pmid = {41244152},
issn = {2352-3204},
abstract = {INTRODUCTION: Maintaining aseptic conditions is essential for cell product processing, as sterilization cannot be applied to living cells. Conventional environmental monitoring relies on particle counts and culture-based colony-forming unit measurements. These indicators fail to capture much of the diversity and provenance of airborne microbes because many taxa are nonculturable or require growth conditions not supported by standard culture media. Therefore, comprehensive DNA-based microbiome analysis is critical for evaluating microbial risks that conventional methods may overlook; however, such studies remain limited in cleanroom settings. This study aimed to comprehensively visualize the structure of airborne microbial communities in cleanroom environments and clarify microbial risks that cannot be fully captured by particle counts or culture-based methods.

METHODS: We collected airborne bacterial DNA from cleanrooms with environmental Grades B, C, and D using a high-volume air sampler. The DNA was extracted and analyzed via 16S rRNA gene amplicon sequencing targeting the V3-V4 regions. Bioinformatic analysis was performed using the QIIME2 pipeline, and microbial diversity was assessed using alpha and beta diversity indices. Abundant taxa were categorized based on their likely origin (environment- or skin-derived), and their distributions were examined in relation to facility management practices.

RESULTS: Analysis revealed the consistent detection of skin-associated bacteria, such as Cutibacterium and Corynebacterium, and environmental bacteria, including Bacillus and Paracoccus, across all cleanroom grades. Alpha- and beta-diversities exhibited no significant differences among the grades. However, temporary and irregular increases in skin-derived bacteria indicated operator-related non-persistent contamination. This interpretation was supported by skewness and kurtosis analyses, which indicated occasional but noticeable shifts in microbial abundance, particularly in high-grade cleanroom environments.

CONCLUSIONS: This study demonstrates the limitations of conventional culture-based monitoring and underscores the value of DNA-based approaches for characterizing airborne microbial communities in cleanrooms. The detection of temporary increases in skin-associated bacteria indicates that operator-related contamination can occur even under stringent environmental conditions. These findings support the development of integrated monitoring strategies that can capture both the composition and temporal fluctuations of airborne microbiota to enhance microbial risk assessment.},
}

@article {pmid41243980,
year = {2025},
author = {Aguilar, C and Fontove-Herrera, F and Pashkov, A and García-Estrada, DA and Contreras-Peruyero, H and Guerrero-Flores, S and Ramírez-Sánchez, O and Sélem-Mojica, N},
title = {MicroAgroBiome: a toolkit for exploring specialized metabolism and ecological interactions in rhizosphere microbiomes of cultivated crops.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1083},
pmid = {41243980},
issn = {1362-4962},
support = {320237//Secretaría de Ciencia, Innovación, Tecnología e Innovación (SECIHTI)/ ; //Secretaría de Ciencia, Innovación, Tecnología e Innovación (SECIHTI) Postdoctoral Fellowship 2025/ ; IN114323//Universidad Nacional Autónoma de México/ ; },
abstract = {The microbiome is crucial to agroecosystems, as it influences plant nutrition, resilience, and overall health. Recent advances in metagenomics have expanded our understanding of plant-microbe interactions, yet curated, high-resolution data capturing the global diversity of crop-associated microbiomes remain scarce. To fill this gap, we developed MicroAgroBiome, a publicly accessible platform that offers standardized taxonomic and functional data, mainly from the rhizosphere microbiomes of agriculturally important crops. The platform integrates 554 metagenomes from 28 crops and soil sample health, advancing microbiome-informed agricultural strategies. It also underscores Latin America's growing leadership in agricultural microbiome research. MicroAgroBiome is available at https://agrobiom.matmor.unam.mx.},
}

@article {pmid41243859,
year = {2025},
author = {Nami, Y and Barghi, A and Sadeghi, M and Farhadi, T and Babaei, S and Haghshenas, B},
title = {Probiotics in Women's Health: Mechanisms, Benefits, and Potential Applications for Preventing Bacterial Vaginosis and Sexually Transmitted Diseases in Sexual Health Products.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {133},
number = {11},
pages = {e70086},
doi = {10.1111/apm.70086},
pmid = {41243859},
issn = {1600-0463},
support = {50004407//Kermanshah University of Medical Sciences/ ; },
mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; Female ; *Vaginosis, Bacterial/prevention & control/microbiology ; *Sexually Transmitted Diseases/prevention & control/microbiology ; *Women's Health ; Vagina/microbiology ; Lactobacillus/physiology ; Microbiota ; },
abstract = {This review summarizes key clinical findings on probiotics in addressing bacterial vaginosis (BV) and sexually transmitted diseases (STDs) in women. Lactobacillus bacteria play a critical role in maintaining a balanced vaginal microbiome by supporting an acidic environment and helping combat conditions like BV, AIDS, maternal group B Streptococcus (GBS), and candidiasis. Probiotics, either alone or combined with antibiotics, have shown promise in promoting microbiome recovery and potentially reducing recovery time. However, their efficacy depends on the strains used and specific conditions, emphasizing the need for further research. Additionally, probiotics can mitigate risks associated with excessive antibiotic use, including antibiotic resistance. The increasing interest in probiotics for women's sexual health has led to the development of specialized products, though identifying superior strains and optimal dosages remains an ongoing challenge. In conclusion, probiotics offer a non-invasive and cost-effective approach to supporting women's health by promoting microbiota balance and enhancing immune function. They offer a promising strategy for managing BV and potentially reducing STD risks. However, further research is necessary to standardize strains, dosages, and application methods in order to achieve consistent and effective outcomes.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
Female
*Vaginosis, Bacterial/prevention & control/microbiology
*Sexually Transmitted Diseases/prevention & control/microbiology
*Women's Health
Vagina/microbiology
Lactobacillus/physiology
Microbiota

@article {pmid41243640,
year = {2025},
author = {Zhang, M and Zhang, Y and Feng, G and Gao, W and Chen, Z and Lei, S and Wang, L and Li, S and Xiao, X and Long, Q},
title = {Neuroprotective Effects of Xanthoceras sorbifolia Bunge Oil on Tic Disorders Through Regulation of the Serotonergic Synaptic Pathway and the Gut Microbiome.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70317},
doi = {10.1002/mnfr.70317},
pmid = {41243640},
issn = {1613-4133},
support = {20254092//Research Project of Chinese Medicine in TCM Bureau of Guangdong Province/ ; 20244046//Research Project of Chinese Medicine in TCM Bureau of Guangdong Province/ ; KF2025A005//Open Funding Project of Jiyuan Neurohealth Industry Research Institute of Guangdong Pharmaceutical University/ ; A2024378//Research Foundation of Medical Science and Technology of Guangdong Province/ ; 2018B030322012//Guangdong Provincial Key laboratory of Chinese Medicine for Prevention and Treatment of Refractory Chronic Diseases/ ; 2025KTSCX056//Characteristic Innovation Projects of Regular Higher Education Institutions in Guangdong Province/ ; },
abstract = {Xanthoceras sorbifolia Bunge Oil (XSBO), a type of edible oil derived from a Chinese oilseed crop, is rich in a variety of bioactive compounds and has been recognized for its neuroprotective properties. Tic disorders (TD), a common and complex neurological disorder, are characterized by a multifaceted etiology and a lack of effective therapeutic interventions. Our research pioneers the exploration of XSBO's ability to ameliorate both behavioral symptoms and pathological changes associated with TD. We found that XSBO can activate the BDNF/TrkB signaling pathway, protect dopaminergic neurons, and thereby exert neuroprotective effects. In addition, XSBO has demonstrated potent antioxidant and anti-inflammatory properties that contribute to the attenuation of neuroinflammatory processes. In addition, XSBO has been shown to modulate the balance of the gut microbiome, correcting dysbiosis and, in turn, influencing the serotonergic synaptic pathway, which is critical for the amelioration and management of TD. In essence, XSBO presents a therapeutic profile for TD through a multi-pronged approach that includes neuroprotection, anti-inflammatory activity, and modulation of the brain-gut axis. This study not only delineates the mechanisms by which XSBO exerts its effects in the treatment of TD but also provides critical evidence to further refine its clinical use.},
}

@article {pmid41243448,
year = {2025},
author = {Vliex, LMM and Barnett, D and Monzel, E and Nauta, A and Oudhuis, GJ and Fassarella, M and Holst, JJ and Zoetendal, EG and Penders, J and Blaak, EE},
title = {2'-Fucosyllactose supplementation results in a transient improvement in gut microbial resilience after vancomycin use in adults with overweight or obesity: a randomized, double-blind, placebo-controlled intervention.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2580693},
doi = {10.1080/19490976.2025.2580693},
pmid = {41243448},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Double-Blind Method ; Male ; *Vancomycin/adverse effects/therapeutic use/administration & dosage ; Female ; Adult ; *Trisaccharides/administration & dosage ; Middle Aged ; *Anti-Bacterial Agents/adverse effects/therapeutic use/administration & dosage ; Feces/chemistry/microbiology ; *Obesity/microbiology/drug therapy ; *Overweight/drug therapy/microbiology ; Bacteria/classification/genetics/isolation & purification/drug effects ; Dietary Supplements ; Fatty Acids, Volatile/analysis/metabolism ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Antibiotic-induced perturbations of the gut microbiome can be long-lasting and potentially affect host metabolic health. Strategies supporting microbial resilience are needed to mitigate the negative impact of antibiotics. We investigated the potential of 2'-fucosyllactose (2'-FL) supplementation after vancomycin use in a double-blind placebo-controlled randomized intervention among adults with overweight/obesity. Participants received oral vancomycin for seven days followed by 2'-FL or placebo for eight weeks. At baseline, after vancomycin use and after supplementation, glucose tolerance, insulin sensitivity, plasma lipids, glucagon-like peptide 1, inflammatory cytokines, fecal short-chain fatty acids (SCFAs) and branched-chain fatty acids were analyzed. Gut microbial diversity, composition and resilience were analyzed using 16S rRNA gene sequencing. Vancomycin use decreased gut microbial richness and diversity and disrupted microbiota composition and fecal SCFA concentrations. 2'-FL improved gut microbial resilience compared to placebo (pTreatment*Time = 0.043) after two weeks of supplementation, but differences were no longer observed at the end of the intervention. Two-week 2'-FL supplementation also differentially impacted specific bacterial taxa. Eight-week 2'-FL supplementation decreased fasting plasma interleukin-6 (IL-6) concentrations (pTreatment*Time = 0.041). 2'-FL intake led to transient improvements in gut microbial resilience after vancomycin use, indicating its beneficial potential to limit antibiotic-induced perturbations. Subsequent effects on metabolic health were limited and require further study.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Double-Blind Method
Male
*Vancomycin/adverse effects/therapeutic use/administration & dosage
Female
Adult
*Trisaccharides/administration & dosage
Middle Aged
*Anti-Bacterial Agents/adverse effects/therapeutic use/administration & dosage
Feces/chemistry/microbiology
*Obesity/microbiology/drug therapy
*Overweight/drug therapy/microbiology
Bacteria/classification/genetics/isolation & purification/drug effects
Dietary Supplements
Fatty Acids, Volatile/analysis/metabolism
RNA, Ribosomal, 16S/genetics

@article {pmid41243094,
year = {2025},
author = {Andreani-Gerard, CM and Jiménez, NE and Palma, R and Muller, C and Hamon-Giraud, P and Le Cunff, Y and Cambiazo, V and González, M and Siegel, A and Frioux, C and Maass, A},
title = {Modeling the emergent metabolic potential of soil microbiomes in Atacama landscapes.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {142},
pmid = {41243094},
issn = {2524-6372},
support = {Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; Associated Team "SymBioDiversity"//Institut national de recherche en informatique et en automatique (INRIA)/ ; FB210005//Centro de Modelamiento Matemático, Facultad de Ciencias Físicas y Matemáticas/ ; FB210005//Centro de Modelamiento Matemático, Facultad de Ciencias Físicas y Matemáticas/ ; FB210005//Centro de Modelamiento Matemático, Facultad de Ciencias Físicas y Matemáticas/ ; FB210005//Centro de Modelamiento Matemático, Facultad de Ciencias Físicas y Matemáticas/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; ANID-MILENIO-ICN2021_044//Millennium Institute Center for Genome Regulation/ ; Exploración 13220002//Agencia Nacional de Investigación y Desarrollo/ ; Exploración 13220002//Agencia Nacional de Investigación y Desarrollo/ ; Exploración 13220002//Agencia Nacional de Investigación y Desarrollo/ ; Exploración 13220002//Agencia Nacional de Investigación y Desarrollo/ ; ANR-22-PEAE-0011//Agence Nationale de la Recherche/ ; ANR-22-PEAE-0011//Agence Nationale de la Recherche/ ; },
abstract = {BACKGROUND: Soil microbiomes harbor complex communities from which diverse ecological roles unfold, shaped by syntrophic interactions. Unraveling the mechanisms and consequences of such interactions and the underlying biochemical transformations remains challenging due to niche multidimensionality. The Atacama Desert is an extreme environment that includes unique combinations of stressful abiotic factors affecting microbial life. In particular, the Talabre Lejía transect is a natural laboratory for understanding microbiome composition, functioning, and adaptation.

RESULTS: We propose a computational framework for the simulation of the metabolic potential of microbiomes, as a proxy of how communities are prepared to respond to the environment. Through the coupling of taxonomic and functional profiling, community-wide and genome-resolved metabolic modeling, and regression analyses, we identify key metabolites and species from six contrasting soil samples across the Talabre Lejía transect. We highlight the functional redundancy of whole metagenomes, which act as a gene reservoir, from which site-specific adaptations emerge at the species level. We also link the physicochemistry from the puna and the lagoon samples to metabolic machineries that are likely crucial for sustaining microbial life in these unique environmental conditions. We further provide an abstraction of community composition and structure for each site that allowed us to describe microbiomes as resilient or sensitive to environmental shifts, through putative cooperation events.

CONCLUSION: Our results show that the study of multi-scale metabolic potential, together with targeted modeling, contributes to elucidating the role of metabolism in the adaptation of microbial communities. Our framework was designed to handle non-model microorganisms, making it suitable for any (meta)genomic dataset that includes high-quality environmental data for enough samples.},
}

@article {pmid41243049,
year = {2025},
author = {Elghannam, MT and Hassanien, MH and Ameen, YAR and Turky, EA and ELattar, GM and ELRay, AA and ELTalkawy, MD},
title = {New insights into the effects of microbiome and its derived metabolites on targeted immunotherapy.},
journal = {Journal of the Egyptian National Cancer Institute},
volume = {37},
number = {1},
pages = {74},
pmid = {41243049},
issn = {2589-0409},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; *Neoplasms/immunology/therapy/microbiology/metabolism/drug therapy ; *Immunotherapy/methods ; Tumor Microenvironment/immunology/drug effects ; Molecular Targeted Therapy/methods ; Bile Acids and Salts/metabolism ; Fatty Acids, Volatile/metabolism ; Methylamines/metabolism ; Indoles/metabolism ; },
abstract = {The significance of gut bacteria and their byproducts is gaining greater recognition, especially in the realm of immunotherapy. An imbalance in gut bacteria or their byproducts is intricately linked to the onset, progression, and treatment of cancer. Metabolites derived from gut microbiota, including short-chain fatty acids (SCFAs), secondary bile acids (SBAs), indole derivatives, and trimethylamine oxide (TMAO), engage with cellular targets to initiate intracellular signaling pathways. These signals are conveyed to the cell, influencing its growth. Targeted therapies encompass a complex and ever-evolving area that is crucial in cancer management. Nonetheless, it is vital to recognize that targeted therapy encounters a multitude of challenges. Factors influencing the success of targeted therapy include drug resistance resulting from prolonged use, side effects, and variations in genetic mutations, tumor diversity, and the complex nature of the tumor microenvironment. Recently, we have deepened our understanding of the relationship between the gut microbiome and anticancer targeted therapies. This is one face of the molecular pathologic epidemiology. This prompts us to investigate promising treatment strategies linked to these gut bacteria and their metabolites, thereby unlocking new possibilities for targeted anticancer therapies.},
}

Humans
*Gastrointestinal Microbiome/immunology/drug effects
*Neoplasms/immunology/therapy/microbiology/metabolism/drug therapy
*Immunotherapy/methods
Tumor Microenvironment/immunology/drug effects
Molecular Targeted Therapy/methods
Bile Acids and Salts/metabolism
Fatty Acids, Volatile/metabolism
Methylamines/metabolism
Indoles/metabolism

@article {pmid41242989,
year = {2025},
author = {Mullish, BH and Roberts, LA and Williams, HRT},
title = {Microbiota transplants: the concept of 'microbiome mismatching' explored.},
journal = {Signal transduction and targeted therapy},
volume = {10},
number = {1},
pages = {374},
pmid = {41242989},
issn = {2059-3635},
support = {MR/Z504002/1//RCUK | Medical Research Council (MRC)/ ; IS-BRC-1215-20013//DH | National Institute for Health Research (NIHR)/ ; IS-BRC-1215-20013//DH | National Institute for Health Research (NIHR)/ ; IS-BRC-1215-20013//DH | National Institute for Health Research (NIHR)/ ; },
}

@article {pmid41242981,
year = {2025},
author = {Andonotopo, W and Bachnas, MA and Dewantiningrum, J and Adi Pramono, MB and Bernolian, N and Yeni, CM and Putra Wiradnyana, AAG and Hariyasa Sanjaya, IN and Akbar, MIA and Darmawan, E and Sulistyowati, S and Stanojevic, M and Kurjak, A},
title = {The fetal exposome and Preterm Birth: a systematic synthesis of environmental exposures and multi-omics evidence.},
journal = {Journal of perinatal medicine},
volume = {},
number = {},
pages = {},
pmid = {41242981},
issn = {1619-3997},
abstract = {OBJECTIVES: Preterm birth (PTB), defined as delivery before 37 weeks of gestation, is a leading cause of neonatal mortality and long-term developmental impairment. Its complex etiology, spanning environmental, genetic, psychosocial, and socio-economic domains, limits effective prediction and prevention. We systematically synthesized evidence on how environmental exposures influence PTB risk through multi-omic disruptions within a fetal exposome framework.

METHODS: A comprehensive literature search was conducted in major biomedical databases, following PRISMA guidelines. Ninety-five human studies published through May 2025 were included, encompassing exposures such as ambient air pollution, endocrine-disrupting chemicals, maternal stress, nutrition, occupational hazards, climate variability, and microbiome alterations. Two reviewers independently extracted data (exposure type, omics platform, biospecimen, PTB subtype) with inter-rater reliability assessment, and study quality was evaluated using the Newcastle-Ottawa Scale. Findings were narratively stratified by exposure category, study design, and spontaneous vs. indicated PTB.

RESULTS: Environmental exposures were consistently associated with disruptions in oxidative stress, inflammation, immune regulation, hormonal signaling, placental aging, and microbial ecology, mediated by multi-omic signatures in maternal, placental, and fetal tissues. Candidate biomarkers show promise for early risk stratification but lack validation and population-level predictive performance due to heterogeneous exposure assessment and study design.

CONCLUSIONS: Integrating fetal exposome concepts with multi-omics enhances mechanistic insight into PTB risk and may support biomarker discovery and precision-guided prenatal interventions. Clinical translation requires standardized exposure measurement, biomarker validation, and equity-focused implementation.},
}

@article {pmid41242603,
year = {2025},
author = {Nouri, M and Chalmeh, A and Pourjafar, M and Pirbornatan, A and Amirian, A},
title = {Dose-dependent effects of a multicomponent toxin binder on the gut-liver-mammary axis and metabolic resilience in early-lactation dairy cows.},
journal = {Veterinary journal (London, England : 1997)},
volume = {},
number = {},
pages = {106489},
doi = {10.1016/j.tvjl.2025.106489},
pmid = {41242603},
issn = {1532-2971},
abstract = {The transition period in dairy cows' entails coordinated endocrine, metabolic, and immunological reprogramming that increases susceptibility to physiological endotoxemia, oxidative stress, hepatic strain, and insulin resistance. We conducted a randomized, blocked, four-arm longitudinal trial to evaluate dose-dependent effects of a multicomponent yeast-clay-probiotic toxin binder (Magnotox®) on systemic endotoxin load, redox balance, hepatic-lipid metabolism, insulin sensitivity, and performance in multiparous Holstein cows (n = 20) from -21 to +80 days in milk (DIM). Cows received a basal diet (Ctrl) or basal diet supplemented with 50g·d[-][1] (TB-Low), 75g·d[-][1] (TB-Med), or 100g·d[-][1] (TB-High) Magnotox. Blood and milk were sampled at six time points for lipopolysaccharide (LPS), malondialdehyde (MDA), total antioxidant capacity (TAC), fibrinogen, biochemical liver and lipid indices, and insulin-resistance metrics (HOMA-IR, QUICKI, RQUICKI). Linear mixed-effects and Bayesian hierarchical models were applied. TB-High elicited a sustained within-group post-calving decline in serum LPS (≈ 0.4 loge pg·mL[-][1] from immediate postpartum to ≈ Day +50), whereas the time-averaged between-group difference versus Ctrl was small (estimated EMM Δ TB-High - Ctrl ≈ -0.05 loge pg·mL[-][1]). Milk LPS did not differ among groups on the time-averaged scale (p = 0.48). TB-High showed higher HDL (+8.13mg·dL[-][1], p = 0.004) and increased total protein (+0.59g·dL[-][1], p < 0.0001) and albumin (+0.23g·dL[-][1], p = 0.0128) compared with Ctrl, with no significant changes in NEFA, glucose, or LDL. Oxidative stress was attenuated across binder groups (e.g., MDA reduction in TB-High = -0.241 ± 0.060, p < 0.001); TAC was better preserved over time in TB-High (Time × Group p = 0.034) with a similar trend in TB-Med (p = 0.059). Fibrinogen showed a non-significant downward trend in TB-High. Body condition score exhibited an overall group effect (p = 0.002), with the largest increases observed in TB-High and TB-Low; milk yield and component percentages were numerically higher in TB-High and TB-Med but did not differ significantly among groups. In summary, high-dose (100g·d[-][1]) multicomponent binder supplementation modulated the gut-liver-mammary axis during the transition period by mitigating endotoxemia and oxidative stress and supporting hepatic protein indices and body-reserve preservation, without adverse shifts in key energy metabolites. Larger, multi-herd trials with integrated rumen-intestinal microbiome profiling and mechanistic omics are warranted to confirm efficacy, refine dosing, and assess long-term productive and reproductive outcomes.},
}

@article {pmid41242569,
year = {2025},
author = {Yang, XL and Li, XH and Dong, BB and Zheng, PG and Liu, Q},
title = {Oral Microbiota Dysbiosis Contributes to Occurrence of Pneumonia in Patients Admitted to Intensive Care Unit with Spontaneous Intracerebral Hemorrhage.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108166},
doi = {10.1016/j.micpath.2025.108166},
pmid = {41242569},
issn = {1096-1208},
abstract = {Post-stroke pneumonia (PSP) is a major contributor to the high mortality rate among patients with spontaneous intracerebral hemorrhage. Dysbiosis of oral microbiota contributes to various pulmonary diseases through the oral-lung axis. This study aimed to explore the association between PSP and microbiota dysbiosis and to construct an early prediction model for PSP. A total of 139 patients admitted to the emergency intensive care unit between October 2022 and April 2024 were enrolled; 82 developed PSP. Oral microecological characteristics were analyzed to establish a PSP prediction model incorporating clinical characteristics. The relative abundance of oral microbiome was higher in patients with PSP according to abundance-based coverage estimator (z= -2.08, P=0.03707) and Chao index (z= -2.09, P=0.03673). A predictive model for PSP was built based on eight microbiomes and four clinical characteristics with an area under the curve of 0.837 (confidence interval: 0.757-0.917). The model was verified with area under the curve of 0.786 (95% confidence interval: 0.643-0.929). Porphyromonas were the oral bacteria with the greatest difference in relative abundance between the two groups, and were therefore selected as the exposed bacterial species. Sprague-Dawley rats exposed to Porphyromonas gingivalis exhibited oral microbiota dysbiosis and developed pneumonia, which could be eliminated by metronidazole, confirming its causative role. In conclusion, oral microbiota dysbiosis contributes to PSP occurrence, representing a novel pathogenic mechanism that has promoted the establishment of an early prediction model for PSP, facilitated early diagnosis, and provided new insights into preventing PSP.},
}

@article {pmid41242566,
year = {2025},
author = {Yousefi-Hashemabad, MJ and Hosseini Kakroudi, M and Pourashory, M and Forouzan, K and Yazdanpanah, N and Saleki, K and Rezaei, N},
title = {Intratumoral Bacterial Microbiota in Gastrointestinal Adenocarcinoma: From Computational Insights to Clinical Practice.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108174},
doi = {10.1016/j.micpath.2025.108174},
pmid = {41242566},
issn = {1096-1208},
abstract = {Intratumoral microbiota refers to bacteria and other organisms residing within the tumor microenvironment and are intriguingly found throughout the TME, including in cancer cells, immune cells, and stromal components. Among these microbiota, bacteria have gained attention due to their emerging roles in tumor biology. Recent research has uncovered new pathophysiological and therapeutic roles for targeting intratumoral bacterial microbiota. Emerging evidence pointed out that certain taxa, including Fusobacterium nucleatum and Porphyromonas gingivalis, can drive tumorigenic activity, whereas taxa such as Lactobacillus spp. may act as a protective agent. Overall, bacteria can influence cancer progression through mechanisms including immune modulation, metabolic reprogramming, and genomic instability. Furthermore, advances in artificial intelligence (AI) and microbiome profiling have identified prognostic microbial signatures and markers of treatment response. In addition, the mediation of the tumor microbiota via probiotics, antibiotics, engineered microbes, and fecal transplants exhibits novel approaches in targeted cancer therapy. The present review captures the role of intratumoral bacterial microbiota in adenocarcinomas and their significance in cancer development and progression as evidenced by experimental and clinical research.},
}

@article {pmid41242446,
year = {2025},
author = {Hu, X and Meng, P and Han, P and Li, L and Sun, B and Zhang, X and Song, X},
title = {Targeted blockade of IL-23 receptor by engineered IgY antibody attenuates bacterial enteritis via reprogramming gut microbiota-immune axis in grass carp (Ctenopharyngodon idella).},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {148967},
doi = {10.1016/j.ijbiomac.2025.148967},
pmid = {41242446},
issn = {1879-0003},
abstract = {Grass carp (Ctenopharyngodon idella), a key aquaculture species in China, is severely impacted by bacterial and viral infections, particularly A. hydrophila-induced enteritis, gill necrosis, and septicemia, necessitating sustainable alternatives to antibiotic-dependent disease management. In this study, an orally delivered anti-IL-23R IgY antibody (IgYIL-23R) was developed to attenuate bacterial enteritis in grass carp through dual modulation of gut immunity and microbiota. Microencapsulated IgYIL-23R (>1:8000 titer) was produced by immunizing hens with recombinant grass carp IL-23R and incorporated into fish diets (0.1-0.6 %). Optimal growth performance was observed in the 0.3 % IgYIL-23R group, with a 28.7 % increase in final weight and a 1.8-fold elevation in specific growth rate (P < 0.01). Concurrently, key pro-inflammatory genes (IL23R, IL-17, TNF-α) were suppressed by 60-75 %, and intestinal histoarchitecture was restored. IgYIL-23R administration significantly altered gut microbiota composition, reducing pathogenic Proteobacteria (68 %) and Aeromonas (82 %) while enriching beneficial Bacteroidetes (3.2-fold) and Akkermansia (4.1-fold) (P < 0.001). Upon challenge with A. hydrophila, fish fed 0.3 % IgYIL-23R exhibited a 55 % higher survival rate, minimal tissue damage, and enhanced metabolic functions, including antibiotic biosynthesis and α-linolenic acid metabolism. These findings demonstrate that targeted IL-23R blockade via oral IgY reprograms the microbiota-immune axis, providing a sustainable, antibiotic-free strategy for controlling enteritis in aquaculture.},
}

@article {pmid41242238,
year = {2025},
author = {Li, Y and Hou, J and Liu, M and Du, Z and Chen, H and Liu, G and Wang, Y and Yao, Y and Sun, P and Zhao, L and An, Y},
title = {Multiomics and machine learning unveil root exudate-microbiota interactions for cadmium control in rice.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127960},
doi = {10.1016/j.jenvman.2025.127960},
pmid = {41242238},
issn = {1095-8630},
abstract = {Human health and the safety of rice are threatened by cadmium (Cd) contamination in paddy soils. Although root exudates affect Cd bioavailability, the impact of complex mixtures of exudates and their interactions with rhizosphere bacteria on Cd speciation remain poorly understood. This study pioneers the "metabolome - microbiome - Cd speciation" coupling mechanism using a machine learning-assisted multi-omics analysis. Specifically, we characterized root-exudate composition, microbiome, and Cd speciation in rhizosphere soils of seven rice genotypes spanning low-to high-Cd accumulation. Of the 2659 root exudates identified, XGBoost-SHAP pinpointed ten key exudates that significantly influenced acid-extractable Cd (ACD-Cd; R[2] = 0.72 with grain Cd). Mantel testing revealed strong relationships (P < 0.01) between these key exudates and specific microbial taxa, including Candidatus Sulfobium mesophilum, Geotalea uraniireducens, and Hypericibacter terrae. Key exudates exhibited direct detrimental effects on ACD-Cd (λ = -0.727 to -0.486) and indirect effects through microbial recruitment (e.g., λ = -0.282 for hydroxysuberic acid via Candidatus Sulfobium mesophilum), as determined by partial least squares-structural equation modeling (PLS-SEM) quantification of interaction pathways. Overall regulation was primarily influenced by direct effects, primarily through chelation or precipitation with Cd ions, thereby reducing their bioavailability. Additionally, certain exudates such as L-theanine and Pimelic acid attracted Candidatus Sulfobium mesophilum, which participates in the sulfur cycle and forms insoluble metal sulfide precipitates, reducing the solubility and bioavailability of Cd in soils. This insight offers new targets for rhizosphere engineering to reduce Cd accumulation in rice grains.},
}

@article {pmid41242205,
year = {2025},
author = {Li, X and Gao, X and Yu, S and Du, F and Liu, J and Kan, X and Liu, X and Yao, D},
title = {Rhizosphere microbiota diversity and salt stress-alleviating functional genes in coastal wild salt-tolerant plants.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128397},
doi = {10.1016/j.micres.2025.128397},
pmid = {41242205},
issn = {1618-0623},
abstract = {Saline-alkali land significantly threatens global food security and ecological safety, and root-associated microorganisms help plants survive salt-alkali stress. However, the ecological functions and factors that influence the rhizosphere microbiomes of salt-tolerant plants remain poorly understood. In this study, we used high-throughput sequencing and metagenomics to reveal the microbial communities and functional traits of bulk and rhizosphere soil from salt-tolerant species (Suaeda glauca, Phragmites australis, and Spartina alterniflora) growing in saline soil. Bacterial and fungal taxa were significantly enriched in the rhizosphere soil compared to the non-rhizosphere soil. Metagenomic analyses revealed that metabolic pathways, including glycolysis and ABC transporters, were highly enriched in the rhizosphere. Functional profiling indicated that salt stress-related pathways were more abundant in the core genera Pseudomonas and Woeseia. The abundance of functional genes related to plant growth-promoting traits, including phosphate solubilization and salt adaptation pathways, was higher in the rhizosphere soil than in the non-rhizosphere soil, which was mainly driven by soil salinity, total nitrogen content, and total carbon content. Additionally, P. aeruginosa obtained from the rhizosphere of S. alterniflora exhibited high phosphorus solubilization efficiency (908.38 μg/mL), nitrogen fixation activity (2.84 μg/mL) and salt tolerance (≦ 5 % NaCl). These findings demonstrate that salt-tolerant plants shape microbial activities by controlling the rhizosphere microenvironment, mitigating salt stress, providing a scientific and practical foundation for the development of targeted microbial inoculants for saline-alkali land reclamation.},
}

@article {pmid41241915,
year = {2025},
author = {Preetham, K and Chatterjee, J},
title = {Research trend on the emerging role of the microbiome in idiopathic male infertility.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {12},
pages = {193},
pmid = {41241915},
issn = {1572-9699},
mesh = {Male ; Humans ; *Infertility, Male/microbiology/etiology ; *Microbiota ; Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Oxidative Stress ; },
abstract = {Idiopathic male infertility remains a major challenge in reproductive medicine despite extensive diagnostic workups, prompting research into novel etiologies and interventions. Emerging evidence highlights the microbiome's role in modulating male reproductive health. This study analyzes global research trends on idiopathic male infertility and associated microbial health over the past two decades using a structured bibliometric approach. Data extracted from Scopus were examined through Biblioshiny and VOSviewer. The analysis reveals a clear transition from traditional genetic and oxidative stress-based studies to microbiome-centered and multi-omics investigations. Increased Research output and citation rates in recent years, underscoring the growing relevance of microbiome studies. Key contributors like Agarwal A, Wang X, Zhang H, and Lundy SD advanced understanding from genetic and oxidative causes to gut-testis and semen microbiome interactions. Leading contributors and countries, particularly China and the USA dominate collaborative networks. Key themes link microbial dysbiosis, oxidative stress, inflammation, and hormonal imbalance with impaired spermatogenesis. Environmental and lifestyle factors, including diet, alcohol, antibiotics, endocrine disruptors, and microplastics, were increasingly recognized as influencing microbiome-mediated fertility. Mechanistic insights into the gut-testis axis, endotoxemia, immune modulation, and nutrient metabolism suggest avenues for diagnostics and microbiome-based interventions, including probiotics, nutritional modulation, and fecal microbiota transplantation.},
}

Male
Humans
*Infertility, Male/microbiology/etiology
*Microbiota
Dysbiosis/microbiology
*Gastrointestinal Microbiome
Oxidative Stress

@article {pmid41040223,
year = {2025},
author = {Keller, A and Adeniyi, A and Akkaya-Colak, KB and Festing, M and Schwieters, A and Kumar, R and Sledziona, J and Gupta, K and Stevens, P and Pietrzak, M and Coppola, V and Ranganathan, P and Ahmer, B and Forero, A and Knoblaugh, SE and Mihaylova, MM},
title = {Gasdermin C links nutrient and immune signaling to protist-induced type 2 immunity and intestinal repair.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41040223},
issn = {2692-8205},
support = {T32 CA229110/CA/NCI NIH HHS/United States ; T32 CA229114/CA/NCI NIH HHS/United States ; R00 AG054760/AG/NIA NIH HHS/United States ; P30 CA016058/CA/NCI NIH HHS/United States ; T32 GM141955/GM/NIGMS NIH HHS/United States ; },
abstract = {The Gasdermin family of proteins has recently been implicated in tissue repair and homeostasis through their effector function in type 2 immunity and pyroptosis. Yet the role of Gasdermin C proteins has not been fully characterized in the mammalian intestine, where environmental factors can influence epithelial regeneration and repair. Here we report that Gsdmc2-4 genes are regulated in a nutrient-dependent manner and are suppressed with aging. We uncover that commensal protists in the gut regulate Gsdmc2-4 expression through activation of type 2 immune responses. In intestinal organoid experiments, we find that STAT6 is necessary for Gsdmc2-4 induction in response to type 2 cytokines; however, basal expression of Gsdmc2-4 in vivo is only partially diminished in Stat6 knockout animals. Finally, in protist-colonized animals, loss of Gsdmc1-4 exacerbated mucosal erosion and inflammation in response to Dextran sodium sulfate (DSS) exposure, implicating these proteins in coordinating epithelial responses to injury.},
}

@article {pmid41241730,
year = {2025},
author = {Hrala, M and Deissová, T and Andrla, P and Radová, L and Zahornacká, S and Bohošová, J and Macháčková, T and Křen, L and Hrunka, M and Pinkasová, T and Ambrozová, M and Bosák, J and Slabý, O and Šmajs, D and Jabandžiev, P},
title = {Tissue and stool microbiome in pediatric inflammatory bowel disease patients: diversity differs in patients with relapsing and non-relapsing Crohn's disease.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {90},
doi = {10.1186/s13099-025-00766-5},
pmid = {41241730},
issn = {1757-4749},
support = {LX22NPO5103//NextGenerationEU/ ; LX22NPO5103//NextGenerationEU/ ; LX22NPO5103//NextGenerationEU/ ; LX22NPO5103//NextGenerationEU/ ; LX22NPO5103//NextGenerationEU/ ; NU21-07-00285//Ministry of Health of the Czech Republic/ ; NU21-07-00285//Ministry of Health of the Czech Republic/ ; NU21-07-00285//Ministry of Health of the Czech Republic/ ; NU21-07-00285//Ministry of Health of the Czech Republic/ ; NU21-07-00285//Ministry of Health of the Czech Republic/ ; NU21-07-00285//Ministry of Health of the Czech Republic/ ; NU21-07-00285//Ministry of Health of the Czech Republic/ ; NU21-07-00285//Ministry of Health of the Czech Republic/ ; NU21-07-00285//Ministry of Health of the Czech Republic/ ; NU21-07-00285//Ministry of Health of the Czech Republic/ ; },
abstract = {BACKGROUND: Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), are chronic conditions characterized by periods of clinical remission and relapse. Pediatric cases (pIBD) often have a more complicated disease course, where approximately 30% will develop a relapse within a year of diagnosis. Identifying prognostic markers for pIBD is important to optimize treatment and improve long-term outcomes. Our aim was to analyze the tissue microbiome, identify microbial prognostic markers, and validate their predictive power in non-invasive fecal samples.

RESULTS: Tissue and fecal microbiome were characterized from a prospective cohort comprising 33 therapeutically naïve pCD and 23 pUC patients, and 26 non-IBD pediatric controls, using amplicon 16S rRNA gene sequencing. Disease relapse was monitored for one year. At diagnosis, relapsing pCD patients exhibited a significantly decreased alpha diversity and altered beta diversity in tissue compared to non-relapsing pCD patients. Specific taxa were differentially abundant in relapsing pCD, with Barnesiella being the most depleted genus in tissue samples. Receiver Operating Characteristic (ROC) analysis identified Barnesiella (AUC = 0.818), Butyricimonas, and Collinsella as individual microbial tissue markers discriminating pCD relapse. Combining Barnesiella with the weighted Pediatric Crohn's Disease Activity Index (wPCDAI) further enhanced the specificity and sensitivity of the ROC analysis (AUC = 0.872 in tissue, 0.852 in feces), suggesting potential for non-invasive prognostic markers from stool.

CONCLUSIONS: Tissue and fecal microbial markers can predict relapse in pCD patients with high prognostic power, providing a basis for precision medicine and personalized treatment strategies in pIBD.},
}

@article {pmid41241723,
year = {2025},
author = {Carolin, E and Kathrin, T and Benoît, Q and Jean-Yves, G},
title = {Veterinary medicine in reintroduction and reinforcement of the European pond turtle Emys orbicularis: a review.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {668},
pmid = {41241723},
issn = {1746-6148},
mesh = {Animals ; *Turtles/physiology/microbiology ; *Conservation of Natural Resources/methods ; *Endangered Species ; *Veterinary Medicine ; Europe ; },
abstract = {The European pond turtle Emys orbicularis is among the most endangered reptile species in Europe, facing severe population decline due to habitat loss and environmental degradation. Conservation efforts increasingly rely on translocation-based strategies, including species reintroduction and reinforcement. Veterinary medicine plays a crucial role in ensuring the health and survival of captive-bred and translocated individuals, yet standardized health assessment protocols remain scarce. This review based on 418 publications synthesizes current veterinary practices related to freshwater turtle conservation, focusing on health monitoring before, during, and after translocation. We evaluate key medical concerns across different life stages, including prevention of zootechnical issues, pathogen screening, microbiome health, and adaptation challenges in captive and wild populations. Additionally, we propose standardized health assessment guidelines to improve diagnostic accuracy and long-term monitoring, and provide a global overview of the common health issues as well as normal blood reference values. By fostering transdisciplinary collaboration between veterinarians, researchers and conservationists, this study aims to refine best practices and ensure sustainable, evidence-based conservation efforts for E. orbicularis and other freshwater turtle species.},
}

Animals
*Turtles/physiology/microbiology
*Conservation of Natural Resources/methods
*Endangered Species
*Veterinary Medicine
Europe

@article {pmid41241720,
year = {2025},
author = {Patavoukas, E and Tong, B and Guðnadóttir, U and Charalampous, K and Brusselaers, N and Schuppe-Koistinen, I and Engstrand, L and Fransson, E and Wiberg-Itzel, E and Hugerth, L},
title = {Differences in the faecal microbiome of obese and non-obese pregnant women: a matched cohort study in Sweden.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {750},
pmid = {41241720},
issn = {1471-2180},
}

@article {pmid41241418,
year = {2026},
author = {Mustafa, SS and Schmale, I and Man, LX},
title = {Pathophysiology of Chronic Rhinitis and Chronic Sinusitis With and Without Nasal Polyposis.},
journal = {Immunology and allergy clinics of North America},
volume = {46},
number = {1},
pages = {1-11},
doi = {10.1016/j.iac.2025.09.001},
pmid = {41241418},
issn = {1557-8607},
mesh = {Humans ; *Sinusitis/etiology/immunology/physiopathology ; *Nasal Polyps/immunology/etiology ; Chronic Disease ; *Rhinitis/etiology/physiopathology/immunology ; Microbiota ; },
abstract = {This article covers the pathophysiology of chronic rhinitis and chronic rhinosinusitis (CRS), focusing on both phenotypic and endotypic distinctions. It highlights how genetic and environmental factors contribute to disease development, emphasizing the roles of epithelial barrier dysfunction and microbiome disruption. The article categorizes CRS into forms with and without nasal polyps, each involving unique immune responses and inflammation types. Specific endotypes are also discussed, highlighting the complexity and heterogeneity of these conditions.},
}

Humans
*Sinusitis/etiology/immunology/physiopathology
*Nasal Polyps/immunology/etiology
Chronic Disease
*Rhinitis/etiology/physiopathology/immunology
Microbiota

@article {pmid41241240,
year = {2025},
author = {Wang, J and Song, T and Gao, Q and Zhou, Y and Yang, Y and Gao, X and Ma, R and Li, G and Jiang, T and Chang, J and Yuan, J},
title = {Overlooked closed reactor thermal steam discharge: steering ARGs fate and microbiome evolution in kitchen waste-livestock manure composting.},
journal = {Bioresource technology},
volume = {441},
number = {},
pages = {133651},
doi = {10.1016/j.biortech.2025.133651},
pmid = {41241240},
issn = {1873-2976},
abstract = {Steam condensation and reflux in closed conditions impairs composting efficiency, which can be effectively addressed by a negative pressure condensation system. However, microecological dynamics driving microbial succession and antibiotic resistance genes (ARGs) fate during steam discharge-induced rapid maturation remain unclear. This study investigates the effect of real-time steam emission on the removal of ARGs in a closed composting system. Results show that steam discharge significantly expedites the temperature elevation and boosts the high-temperature removal efficiency of ARGs. Compared with the initial level, the total abundance removal rate of target ARGs reached 98 %. However, it promotes the spread and enrichment of specific ARGs (tetX, aadA, strB, ermF, and sul2) during the maturity stage by stimulating bacterial community dynamics, thereby reducing the removal rate to 68 %. The main mechanisms affecting ARGs changes are as follows: steam discharge relieves the environmental stress on bacteria, shifts community assembly toward non-dominant stochastic processes (|βNTI| < 2), thereby enhancing biodiversity (Shannon index) and the stability of bacterial communities. Meanwhile, these highly active bacteria exhibit strong network connectivity, facilitating horizontal gene transfer (HGT) mediated by intl1 and intl2 during the maturation stage. This study shows steam emission improves ARGs removal but exacerbates specific ARGs spread via microbial redistribution.},
}

@article {pmid41241214,
year = {2025},
author = {Ma, B and Hu, H and Lin, Y and Wang, Z and Song, Q},
title = {Technology-Enabled Integration of Single-Cell Transcriptomics and Microbiome Data Identifies RNA-Targetable Host-Microbiota Networks in Colorectal Adenoma.},
journal = {SLAS technology},
volume = {},
number = {},
pages = {100365},
doi = {10.1016/j.slast.2025.100365},
pmid = {41241214},
issn = {2472-6311},
abstract = {Although mechanism-to-intervention processes are becoming possible because to the convergence of single-cell technologies with RNA treatment methods, combined host-microbiome analysis with systematic target identification for colorectal adenoma is still fragmented. Here, we created a repeatable computational pipeline that combines MaAsLin2 for host-microbiome association modeling, QIIME2/DADA2 for microbiome processing, and Seurat/Harmony for single-cell analysis. Under strict statistical control (FDR < 0.05), three single-cell RNA sequencing datasets (GSE117875, GSE178341, and GSE144735; totaling 426,425 cells) were combined with parallel microbiome datasets (PRJNA397906, PRJNA541510, and PRJNA672605; 975 samples). In adenoma-associated microbiomes, we measured a 26.8% decrease in Shannon diversity (4.21→3.08), with a notable enrichment of Fusobacterium nucleatum and a depletion of Faecalibacterium prausnitzii. Immune activation patterns, goblet cell malfunction (MUC2 2.4-fold drop), and stem cell expansion (LGR5 3.2-fold increase) were all identified by single-cell analysis. 847 significant host-microbiome interactions were found by integration analysis, and F. nucleatum showed a substantial correlation with markers of inflammatory signaling (NFKB1: β=0.64, FDR<0.001) and stem cell proliferation (LGR5: β=0.72, FDR<0.001). 25 RNA-targetable candidates were identified by systematic prioritizing, including mRNA restoration targets (MUC2, FOXP3) and ASO/siRNA suppression targets (NFKB1, IL1B). By converting host-microbiome interaction networks into systematic RNA therapeutic options, this technology framework creates a template for the translation of transcriptomics into therapeutics and offers a repeatable pipeline for the creation of precision interventions in colorectal disease.},
}

@article {pmid41241180,
year = {2025},
author = {Han, H and Park, J and Zhang, R and Subramaniyam, N and Das, S and Ge, X and Babu Komakula, SS and Wang, C and Desert, R and Chen, W and Song, Z and Athavale, D and Anwar, A and Lantvit, D and Guzman, G and Frutos, MD and Ramos-Molina, B and Nieto, N},
title = {INTESTINAL EPITHELIAL CELL-DERIVED OSTEOPONTIN PROTECTS AGAINST METABOLIC DYSFUNCTION-ASSOCIATED STEATOHEPATITIS BY MODULATING BILE ACID COMPOSITION AND THE GUT MICROBIOME.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {},
number = {},
pages = {101678},
doi = {10.1016/j.jcmgh.2025.101678},
pmid = {41241180},
issn = {2352-345X},
abstract = {BACKGROUND & AIMS: The gut-liver axis plays a critical role in metabolic dysfunction‒associated steatohepatitis (MASH). Osteopontin (OPN, encoded by SPP1) is implicated in chronic liver disease; however, its expression in intestinal epithelial cells (IECs) and role in MASH remain unclear.

METHODS: We evaluated intestinal OPN expression during MASH progression in patients. To determine the function of IEC-derived OPN, we generated Spp1 knock-in (Spp1[KI IEC]) and knock-out (Spp1[ΔIEC]) mice and fed them a high-fat, high-fructose, high-cholesterol diet to induce MASH.

RESULTS: IEC OPN expression decreased with MASH progression and was inversely associated with liver injury. Loss of Spp1 in IECs exacerbated MASH, whereas overexpression or oral OPN administration was protective. Spp1[ΔIEC] mice exhibited increased hepatic inflammation, disrupted IEC morphology, elevated IEC apoptosis, reduced epithelial cell turnover, and heightened intestinal permeability. They also showed hepatic 16s rRNA presence and elevated conjugated bile acids (BAs), particularly taurocholic acid (TCA) and taurodeoxycholic acid (TDCA), in portal serum. These BAs promoted hepatocyte injury and activated liver macrophages, enhancing inflammation both in vitro and in vivo. Fecal microbiome analysis revealed reduced abundance of bile salt hydrolase (BSH)-expressing bacteria. Fecal microbiota transplantation from Spp1[ΔIEC] mice or treatment with a BSH inhibitor further worsened MASH.

CONCLUSION: IEC-derived OPN protects against MASH by modulating BA composition and shaping the gut microbiome.},
}

@article {pmid41241145,
year = {2025},
author = {Celis-Preciado, CA and Hamou Kuijpers, EB and Ramakrishnan, S and Howell, I and Wechsler, ME and Akuthota, P and Couillard, S},
title = {Applying precision medicine to the heterogeneity of asthma attacks.},
journal = {Chest},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chest.2025.11.013},
pmid = {41241145},
issn = {1931-3543},
abstract = {TOPIC IMPORTANCE: The standard of care for management of asthma attacks has remained unchanged for 70 years, relying on a symptom-based, severity-stratified approach. Severe asthma attacks are defined by a worsening of asthma requiring oral corticosteroids (OCS) for unresolved symptoms for at least 48 hours and/or decreased lung function. . The "one-size-fits-all" strategy with OCS overlooks the biological mechanisms driving attacks and may lead to suboptimal outcomes. Importantly, OCS-related toxicities lead to significant morbidity, and cumulative OCS use has been associated with increased mortality. Antibiotics, often used indiscriminately, also increase adverse events and antimicrobial resistance.

REVIEW FINDINGS: Recent studies have highlighted the heterogeneity of asthma attacks across clinical, etiological, and therapeutic dimensions. Biomarker-informed assessments using blood eosinophils, exhaled nitric oxide (FeNO), and point-of-care microbial molecular testing have improved the evaluation of attacks. Observational studies and trials have explored biomarker-guided management to reduce OCS and antibiotic use, potentially improving outcomes. Distinct inflammatory and OCS-response profiles were identified in patients on biologics, emphasizing the complexity of attacks and the importance of residual (untreated) type-2 inflammatory pathways. Studies on the airway microbiome revealed that microbial dysbiosis is associated with clinical and inflammatory clusters.},
}

@article {pmid41241019,
year = {2025},
author = {Sun, J and Xu, F and Yao, X and Niu, X and Shen, Y and Sun, H and Chen, B and Feng, J},
title = {Tectorigenin alleviates diabetic lung injury by restoring gut microbiota and metabolic homeostasis.},
journal = {Biochemical pharmacology},
volume = {},
number = {},
pages = {117545},
doi = {10.1016/j.bcp.2025.117545},
pmid = {41241019},
issn = {1873-2968},
abstract = {Diabetes mellitus (DM) significantly increases susceptibility to lung injury, and the lung is increasingly recognized as a target organ in diabetes. Given the critical role of gut dysbiosis in metabolic diseases, this study investigated whether Tectorigenin (TG) could alleviate streptozotocin (STZ)-induced diabetic lung injury through restoration of gut microbial and metabolic homeostasis. We comprehensively assessed lung histopathology, systemic inflammation, gut microbiome, and microbe-associated metabolites. TG treatment significantly reduced lung histopathological damage and suppressed inflammatory infiltration, as shown by decreased TNF-α, IL-1β and IL-6 levels. TG also restored expression of lung tight junction proteins (ZO-1/Occludin). Crucially, TG effectively corrected gut dysbiosis by restoring the Firmicutes/Bacteroidetes ratio, enriching beneficial bacteria including Lactobacillus and Limosilactobacillus (short-chain fatty acid, SCFA producers), while suppressing pathogens such as Enterobacteriaceae and Helicobacter. Metabolomics revealed that TG restored major disrupted microbial metabolic pathways including energy, amino acid and lipid metabolism. TG treatment suppressed pro-inflammatory signaling and reduced cytotoxic metabolites including prostaglandin E2 (PGE2) and 15-hydroxyeicosatetraenoic acid (15-HETE). Consequently, TG effectively inhibited pulmonary oxidative stress through reduced reactive oxygen species (ROS) and elevated Nrf2/GPX1 expression, suppressed macrophage M1 polarization (lower CD86/CD206 ratio), and ameliorated mitochondrial dysfunction (higher PGC-1α and SIRT-1) and ferroptosis. Integrated correlation analysis linked gut microbiota abundance with metabolite profiles and lung injury markers, revealing that TG reversed diabetes-induced Anaerostipes expansion and associated metabolic disturbances. We demonstrate that TG mitigates diabetic lung injury by targeting the gut-lung axis and maintaining metabolic homeostasis, providing a novel intervention strategy for diabetic pulmonary complications.},
}

@article {pmid41240781,
year = {2025},
author = {Chen, L and Deng, N and Lin, H and Zhong, J and Zhang, L},
title = {Trophic strategy drives the diversity and community composition of arsenic methylating prokaryotes in intestines of coral reef fish.},
journal = {Marine environmental research},
volume = {213},
number = {},
pages = {107706},
doi = {10.1016/j.marenvres.2025.107706},
pmid = {41240781},
issn = {1879-0291},
abstract = {Arsenic methylation by gut microbiota is the primary detoxification pathway for arsenic in marine fish. Furthermore, the composition and function of the gut microbiome are closely linked to host diet, which differs considerably among the diverse trophic guilds of coral reef fish. However, it remains unexplored whether and how the trophic strategy of the host fish fundamentally shapes the diversity and community composition of arsenic methylating prokaryotes within this complex intestinal environment. In this study, taxonomic databases based on arsenite methylating gene (arsM) for arsenic methylating archaea (AMA) and bacteria (AMB) with respective 143 and 105 non-redundant sequences were established and used for analyzing the diversity and community composition of AMA and AMB in the intestines of coral reef fish. The diversity of AMA and AMB was the highest in the intestines of omnivorous fish, while the highest abundances of AMA and AMB were detected in carnivorous fish. Haloarculaceae and Streptomycetaceae were the most abundant families of AMA and AMB, respectively. A significant difference in community composition was found only in the intestinal AMA of coral reef fish across different trophic strategies. This study demonstrates that trophic strategy is a key driver shaping the gut arsenic methylating prokaryotes in coral reef fish, offering novel insights into the mechanistic links between host ecology, gut microbiome assembly, and arsenic detoxification capacity in coral reef ecosystem.},
}

@article {pmid41240735,
year = {2025},
author = {Iturbe-Espinoza, P and Elsgaard, L and Sapkota, R and Ellegaard-Jensen, L and Winding, A},
title = {Eight-year effect of biochar amendment on soil properties, extracellular enzyme activity, N-cycling genes and microbiome structure in two Danish fallow soils.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128398},
doi = {10.1016/j.micres.2025.128398},
pmid = {41240735},
issn = {1618-0623},
abstract = {Biochar improves agricultural soil properties and short-term microbial diversity. However, biochar's long-term effects on microbiomes and soil health remain poorly understood. This study assessed the effects of 8-year field-aged biochar on microbiomes from two contrasting soils: a sandy clay soil and a coarse sandy soil, under temperate climate conditions. We hypothesize that even after 8 years, biochar amendment persistently alters soil physicochemical properties, stimulates extracellular enzyme activity, increases the abundance of N-cycling genes, and shifts the prokaryotic and fungal community structures. In June 2015, the topsoil in field lysimeters was amended with 2 % w/w straw biochar, and by August 2023, this biochar amendment resulted in a significant increased activity of five key extracellular enzymes (α-glucosidase, β-galactosidase, cellobiosidase, phosphomonoesterase, and arylsulfatase) involved in C, P, and S cycling in both soils. In the coarse sandy soil, biochar boosted the abundance of prokaryotes (16S rRNA gene), key nitrification genes (AOA-amoA and AOB-amoA), and the denitrification gene nosZ Clade I. In both soils, biochar caused an increase in the abundance of the nitrite reductase (nirS) gene, indicating a sustained impact on the N cycle, and an enrichment of an ammonia-oxidizing archaeon of the family Nitrosophaeraceae. Finally, a persistent shift in prokaryotic community structure was observed in both soils. The study clearly demonstrates that the effects of biochar persist after eight years, providing insights into the long-term impact of biochar on soil health.},
}

@article {pmid41239203,
year = {2025},
author = {Wen, S and Sun, J and Zeng, W and Xiang, H and Zhao, M and Xiang, D},
title = {Effects of different arbuscular mycorrhizal fungi on tobacco seedling growth and their rhizosphere microecological mechanisms.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1578},
pmid = {41239203},
issn = {1471-2229},
abstract = {BACKGROUND: Numerous studies have demonstrated significant variations in the plant growth-promoting effects among different species of arbuscular mycorrhizal fungi (AMF). However, the underlying mechanisms remain incompletely understood, particularly regarding how distinct AMF species regulate the rhizosphere microbiome.

RESULTS: Five AMF species (Funneliformis mosseae, Diversispora versiformis, Clariodeoglous etunicatum, Rhizophagus intraradices, and Acaulospora delicate) were inoculated to investigate their effects on tobacco seedling growth and rhizosphere microecological regulation. The results showed that all AMF inoculations significantly increased shoot and root biomass, N/P/K uptake, morphological traits (height, stem diameter, leaf area), chlorophyll content (SPAD), and root architecture (length, surface area, volume, diameter) of tobacco seedlings. Among them, the treatment inoculated with R. intraradices showed the most outstanding growth-promoting effect in all growth indicators. Metagenomic analysis indicated that AMF inoculation significantly altered the diversity and community structure of rhizosphere substrate microorganisms. Among them, R. intraradices inoculation yielded the highest microbial diversity, with an associated network exhibiting enhanced complexity. KEGG functional annotation revealed metabolic pathways (IAA biosynthesis, iron-siderophore transport regulation, exopolysaccharide production, and nutrient cycling) consistently associated with tobacco growth promotion in all AMF inoculations. However, species-specific mechanisms were observed: F. mosseae promotes tobacco seedling growth by enhancing IAA synthesis through the recruitment of beneficial microorganisms such as Nostoc, Flavisolibacter, Frateuria, and Sphingomonas. D. versiformis enhanced carbon fixation via the hydroxypropionate-hydroxybutyrate cycle, driven by the proliferation of Glaciecola, Pedococcus, Phycicoccus, and Hephaestia. C. etunicatum facilitated phosphorus/iron accumulation through organic phosphorus mineralization, phosphate transport, and iron acquisition accompanied by the recruitment of, Hartmannibacter, Lysobacter, Moheibacter, and Pseudolabrys. R. intraradices improved nitrogen assimilation through augmented nitrogen transport and assimilatory nitrate reduction (ANRA), correlated with the recruitment of Azospirillum, Sphingobium, Mesorhizobium, Paracoccus, and Parafilimonas. A. delicate stimulated plant growth via polyphosphate degradation and exopolysaccharide biosynthesis, associated with the enrichment of Segetibacter, Ferruginibacter, Hyphomicrobium and Pseudomonas. Notably, this study revealed that functional divergence in rhizosphere microbiomes associated with the five tested fungal species was primarily reflected in the abundance rather than the composition of functional genes.

CONCLUSION: In summary, AMF inoculation significantly enhanced tobacco seedling biomass and agronomic traits by improving mineral nutrient assimilation efficiency and restructuring the rhizosphere microbial community. Different AMF species exhibited distinct microecological regulation patterns. This study elucidated the growth-promoting mechanisms of AMF from a microbial interaction perspective, providing a theoretical basis for establishing a sustainable tobacco cultivation system.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-07600-9.},
}

@article {pmid41240715,
year = {2025},
author = {Zheng, Z and Wang, X and Su, Z and Li, S and Qin, J and Ren, N and He, L and Zhang, W},
title = {Melatonin alleviates intestinal damage in neonate mice following Salmonella Typhimurium and LPS challenges involving gut microbiota remodeling.},
journal = {International immunopharmacology},
volume = {168},
number = {Pt 1},
pages = {115761},
doi = {10.1016/j.intimp.2025.115761},
pmid = {41240715},
issn = {1878-1705},
abstract = {Neonates exhibit heightened susceptibility to intestinal barrier disruption induced by Salmonella Typhimurium (ST) and its virulence factor lipopolysaccharide (LPS), while antibiotic-independent interventions remain scarce. Here, we demonstrate that melatonin, administered via discrete perinatal and postnatal regimens, ameliorates ST- and LPS-induced intestinal injury in neonatal mice through gut microbiota remodeling. In perinatal studies, maternal melatonin supplementation in drinking water (100 μg/mL; gestational day 13 to postnatal day 21) enhanced intestinal maturation in healthy neonates, upregulated tight junction proteins (Claudin-3, ZO-1), and enriched beneficial taxa (e.g., Candidatus Arthromitus, Lachnospiraceae NK4A136). In infection models, postnatal intraperitoneal melatonin administration (10 mg/kg; 7 days) attenuated ST- and LPS-induced pathology: suppressing pathogens (Salmonella enterica, Escherichia-Shigella), elevating commensals (Ligilactobacillus), restoring villus architecture, and balancing inflammatory mediators (decreased TNF-α, increased IL-10). Collectively, these findings identify melatonin as a microbiota-targeted therapy for neonatal enteropathies, supporting its therapeutic potential against Salmonella-induced intestinal injury.},
}

@article {pmid41240707,
year = {2025},
author = {Fonseca, A and Kenney, S and Boney, J and Ganda, E},
title = {Mycobiome temporal and functional dynamics in broilers: Ecological perspective on bacterial-fungal correlations and the effect of feed additives.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {106092},
doi = {10.1016/j.psj.2025.106092},
pmid = {41240707},
issn = {1525-3171},
abstract = {The gut mycobiome (the fungal component of the microbiome) of chickens, though less abundant than bacterial populations, plays a vital role in gut ecology, yet remains underexplored. This study investigated the temporal, dietary, and ecological factors shaping the broiler chicken excreta-associated fungal communities and their correlation with bacterial microbiota. A total of 320 Cobb 500 (1-day-old) chicks were raised for 21 days in 32 randomly allocated cages. Treatments consisted of four experimental diets: a Basal Diet, a Basal Diet with an Antibiotic (bacitracin methylene disalicylate), an Essential oils blend (oregano oil, rosemary, and red pepper), or a Probiotic (Bacillus subtilis). Shotgun metagenomic sequencing was performed on excreta samples collected at days 1, 10, and 21 to evaluate fungal diversity, composition, cross-kingdom correlation and functional profiling. The fungal community was dominated by Ascomycota and Basidiomycota across all treatments and time points. While alpha diversity metrics did not differ significantly between treatments (P > 0.05), fungal richness and evenness increased significantly over time (P < 0.05), indicating age-driven ecological succession. Beta diversity analysis revealed distinct age-related clustering patterns, with early dominance by Candida albicans and later shifts toward genera such as Fusarium and Malassezia. Feed additives exerted limited influence on fungal composition or diversity metrics, although clustering patterns suggested subtle treatment-specific effects over time. Cross-kingdom correlation analysis identified co-occurring temporal dynamics between the two microbial communities. Candida was positively correlated with Streptococcus and Escherichia/Shigella but negatively associated with beneficial genera like Bifidobacterium and Faecalibacterium. Additionally, microbial functional characteristics were observed in each treatment exhibiting metabolic features. Overall, this study demonstrates that excreta fungal succession in the broiler gut is primarily driven by host age and highlights the temporal plasticity of concurrent changes in fungal and bacteria communities. The findings underscore the importance of multi-kingdom ecological approaches to better understand gut health in poultry production.},
}

@article {pmid41240551,
year = {2025},
author = {Cecil, A and Gentschev, I and Prehn, C and Hauck, S and Witting, M and Petrov, I and Ye, M and Othman, EM and Szalay, AA},
title = {Endogenous gut microbiome and implanted intranasal E. coli-Nissle modulate cancer tissues metabolism in 4T1 syngeneic tumor bearing mice.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {193},
number = {},
pages = {118750},
doi = {10.1016/j.biopha.2025.118750},
pmid = {41240551},
issn = {1950-6007},
abstract = {Despite recent progress in the diagnosis and treatment of advanced cancers, the overall patient treatment outcome did not substantially improve over the last years. Therefore, developing novel therapies, which may also work synergistically in combination with the conventional therapies is crucial. One promising new therapeutic approach is bacterium-mediated cancer therapy. In the current work, we describe the influence of the gut microbiome and intranasal E. coli Nissle applications on the metabolism in cancer tissues of 4T1 syngeneic tumor bearing mice. Here we found that after gut microbiome depletion and/or E. coli Nissle treatment the ratios of ADMA/Arginine, Putrescine/Ornithine and Kynurenine/Tryptophan as well as the total concentration of Carnosine, Kynurenine and H1 (synonymus for all sugars detectable) are significantly altered in tumor tissues of as the result of treatment. In conclusion, our current data show that E. coli Nissle bacteria facilitating metabolic modulation of tumors, a finding could be important for improved cancer therapy in patients.},
}

@article {pmid41240439,
year = {2025},
author = {Thoniyot, S and Balakrishnan, V},
title = {Integrating multi-omics data for personalized nutrition using knowledge graphs and graph neural networks: A comprehensive review.},
journal = {Computational biology and chemistry},
volume = {120},
number = {Pt 1},
pages = {108772},
doi = {10.1016/j.compbiolchem.2025.108772},
pmid = {41240439},
issn = {1476-928X},
abstract = {This comprehensive review focuses on the use of knowledge graphs and Graph Neural Networks (GNNs) to integrate multi-omics data in the field of personalized nutrition. It investigates how different biological datasets-like genomics, proteomics, metabolomics, and gut microbiome profiles-can be combined to create customized dietary plans. By reviewing scientific literature from 2015 to 2025, the study highlights how knowledge graphs help map complex biological interactions and how GNNs effectively analyze and interpret graph-based multi-omics information. The review demonstrates that knowledge graphs provide an elastic and scalable model for representing multi-relational biological information; however, GNNs enable the identification of complex non-local relationships between omics layers that cannot be detected using conventional statistics. The most significant benefits include improved forecast accuracy of individual responses to diet, enhanced biomarker discovery, and the potential for the development of customized nutritional therapy based on detailed characterization of the individual through comprehensive biological profiling. Nevertheless, several issues require further attention, including the quality and standardization of data across omics platforms, scalability uncertainty in computational models, interpretability shortcomings of models, and the ethical challenges associated with the use of personal genetic information. In this review, case studies are provided for comparing the graph-based approach with traditional methods and demonstrating how these methods outperform in terms of their capability to capture biological complexity. Future directions emphasize the importance of international cooperation, the utilization of technology in computational processes with potential for scalability, the development of models that are easier to interpret, and adherence to acceptable ethical standards: knowledge graphs and GNNs. KG and GNNs can couple multi-omics data, providing a paradigm shift towards precision nutrition by enabling unprecedented capabilities to optimize personal health outcomes through scientifically augmented, customized dietary interventions.},
}

@article {pmid41240269,
year = {2025},
author = {Israr, G and Qiao, Q and An, Y and Liu, F and Li, Z},
title = {From Mycobiome Remodeling to Therapeutic Candidate: Aspergillus ruber and 3-methyldioxyindole, Acknowledged as a Novel Modulator Via BPIS Treatment and Alleviating MASLD.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41240269},
issn = {1867-1314},
support = {nos.2022ZDYF121//The Key Research and Development (R&D) Program of Shanxi Province/ ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a leading significant public health concern, affecting 25-30% of the population globally. Recent advances in gut microbiome research are increasingly recognized. Studies exploring the gut-liver axis have mostly focused on bacteriomes. There are limited studies about commensal fungi. Our earlier research on the anti-inflammatory properties of bound polyphenols of the inner shell (BPIS) extracted from Foxtail millet in the mouse colitis model revealed that BPIS significantly increased the abundance of Aspergillus ruber (A. ruber) and remodeled the gut mycobiome. The present study demonstrated that BPIS mitigated MASLD caused by a high-fat diet (HFD), significantly enhancing A. ruber fungi in the gut microbiome. Further investigation exhibited that the administration of A. ruber and its metabolite 3-methyldioxyindole alleviated disordered lipid metabolism, abnormal weight gain, oxidative stress, low ATP synthesis, and histological complications in HFD-fed mice. A. ruber and 3-methyldioxyindole also improved HFD-induced breakage of the intestinal barrier by enhancing the expression of tight junction proteins (Occludin, ZO-1, and claudin) in the colon. The study suggests that the metabolite 3-methyldioxyindole demonstrates more promising effects in lipid metabolism homeostasis. A. ruber or 3-methyldioxyindole has great potential to be developed as an effective probiotic agent for treating MASLD.},
}

@article {pmid41240244,
year = {2025},
author = {Jayathilaka, NS and Weththasinghe, AV and Amarasekara, CI and Amasha, EADH and Wijekoon, KJ and Firdous, SM},
title = {Targeting the Gut-Brain Axis Through Insulin-like Growth Factors: Therapeutic Implications and Future Directions.},
journal = {Journal of molecular neuroscience : MN},
volume = {75},
number = {4},
pages = {150},
pmid = {41240244},
issn = {1559-1166},
mesh = {Humans ; Animals ; *Brain/metabolism ; Gastrointestinal Microbiome ; *Somatomedins/metabolism ; *Neurodegenerative Diseases/metabolism/drug therapy/therapy ; *Insulin-Like Growth Factor I/metabolism ; *Brain-Gut Axis ; *Gastrointestinal Tract/metabolism ; Insulin-Like Peptides ; },
abstract = {The gut-brain axis represents a sophisticated bidirectional communication network connecting the gastrointestinal tract and central nervous system through neural, endocrine, and immune pathways. Insulin-like growth factors (IGFs), particularly IGF-1 and IGF-2, function as pivotal mediators within this communication framework. These polypeptide growth factors regulate intestinal barrier integrity, microbiota homeostasis, neurogenesis, and synaptic plasticity mechanisms. Clinical evidence from 1989 to 2024 demonstrates that gut microbiota-derived short-chain fatty acids enhance IGF-1 production through novel molecular mechanisms. This narrative review examines IGF roles in gut-brain communication and evaluates therapeutic potential for neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, and depression, as well as inflammatory bowel disorders. Current clinical trials investigating IGF-based interventions show preliminary promising results, though studies remain limited in scope and patient numbers. Key therapeutic challenges include delivery mechanisms across biological barriers, oncogenic safety concerns related to cell proliferation, and substantial individual variability in treatment responses. Future directions emphasize development of tissue-specific IGF modulators, microbiome-targeted interventions, and precision medicine approaches utilizing advanced biomarkers. Understanding IGF-mediated gut-brain communication presents therapeutic opportunities for complex pathological conditions simultaneously affecting gastrointestinal and neurological systems.},
}

Humans
Animals
*Brain/metabolism
Gastrointestinal Microbiome
*Somatomedins/metabolism
*Neurodegenerative Diseases/metabolism/drug therapy/therapy
*Insulin-Like Growth Factor I/metabolism
*Brain-Gut Axis
*Gastrointestinal Tract/metabolism
Insulin-Like Peptides

@article {pmid41240124,
year = {2025},
author = {Jiao, Y and Xu, Y and Liu, Y and Li, X and Li, X and Liu, S and Liu, Y and Hou, Y and Guo, L},
title = {Microbial changes in different parts of the oral cavity during the early stage of clear aligner treatment: a preliminary study.},
journal = {Clinical oral investigations},
volume = {29},
number = {12},
pages = {569},
pmid = {41240124},
issn = {1436-3771},
mesh = {Humans ; Male ; Female ; *Dental Plaque/microbiology ; *Microbiota ; *Mouth Mucosa/microbiology ; *Orthodontic Appliances, Removable ; *Mouth/microbiology ; Adult ; Adolescent ; },
abstract = {OBJECTIVES: More and more patients choose clear aligners to improve their appearance and masticatory function. However, there is no study on whether clear aligner treatment affects the microecology of oral mucosal plaque. Therefore, we analyzed flora changes in different parts of patients' mucosa at various time points during the early stage of clear aligner treatment.

METHODS: Plaque samples were collected from the buccal, palatal, and dorsal lingual mucosa of 10 subjects before and 1, 3, 6, and 12 months post clear orthodontic treatment. Microbial community changes were analyzed by 16 S rRNA gene sequencing.

RESULTS: At 6 months, buccal plaque showed a significant decrease in alpha diversity and distinct microbial separation. By 12 months, diversity had recovered, and the community structure had returned to baseline levels. Genus-level changes varied by site: the periodontal pathogen Fusobacterium increased at 6 months and declined at 12 months; the periodontally relevant Prevotella showed a temporary increase at 3 months (palatal) and 1 month (dorsal lingual).

CONCLUSIONS: The clear aligner altered the microbial community of buccal mucosal plaque by 6 months, and the microbial community returned to the basal composition by 12 months.

CLINICAL RELEVANCE: This study highlights that clear aligner treatment transiently disrupts the oral mucosal microbiome, with a significant but reversible shift toward periodontal pathogen-associated flora within 6 months, suggesting the need for enhanced oral hygiene monitoring during early orthodontic therapy to mitigate potential periodontal risks.},
}

Humans
Male
Female
*Dental Plaque/microbiology
*Microbiota
*Mouth Mucosa/microbiology
*Orthodontic Appliances, Removable
*Mouth/microbiology
Adult
Adolescent

@article {pmid41240073,
year = {2025},
author = {Berkhout, MD and de Ram, C and Boeren, S and Plugge, CM and Belzer, C},
title = {Probiotic Engraftment of Akkermansia muciniphila in an In Vitro Synthetic Microbial Community.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {123},
pmid = {41240073},
issn = {1432-184X},
support = {0.24.002.002//Ministerie van Onderwijs, Cultuur en Wetenschap/ ; },
mesh = {*Probiotics ; *Gastrointestinal Microbiome ; Humans ; Mucins/metabolism ; *Verrucomicrobia/physiology ; Akkermansia ; Polysaccharides/metabolism ; Bacteroides thetaiotaomicron ; },
abstract = {Akkermansia muciniphila is a specialist mucin glycan-degrader that is common in the human gut. A. muciniphila is associated with host health and therefore proposed as a next-generation probiotic. However, it is unknown if consumption of live and active A. muciniphila will be effective in terms of survival and engraftment in the gut microbiome. Furthermore, it is of interest whether introduction of A. muciniphila would influence the resident mucosal microbiota. To this end, we investigate the addition of live A. muciniphila to a stable in vitro microbial mucin glycan-degrading synthetic community. A. muciniphila engrafted in this synthetic community and actively degraded mucin using essential mucin glycan-degrading enzymes. Addition of A. muciniphila did not induce major compositional changes, except that Bacteroides thetaiotaomicron increased in relative abundance at the expense of Bacteroides caccae. At the metaproteomic level, community function was not significantly affected, as peptidase, fucosidase, galactosidase and sulfatase expression remained stable. However, sialidase was significantly enriched after A. muciniphila addition, which can be explained by the relative increase of generalist glycan-degrader B. thetaiotaomicron. Overall, we show that a community without A. muciniphila still harbours a niche for this bacterium, but that A. muciniphila did not induce major changes in the in vitro mucosal synthetic community. This suggests that A. muciniphila applied as a probiotic can engraft and exert its beneficial effects on the host, without major impact on the human gut mucosal microbiota composition and function and warrants further research into A. muciniphila engraftment in vivo.},
}

*Probiotics
*Gastrointestinal Microbiome
Humans
Mucins/metabolism
*Verrucomicrobia/physiology
Akkermansia
Polysaccharides/metabolism
Bacteroides thetaiotaomicron

@article {pmid41239974,
year = {2025},
author = {Reichart, NJ and Bell, S and Garayburu-Caruso, VA and Sadler, N and Zhao, S and Hofmockel, KS},
title = {Impact of Moisture on Microbial Decomposition Phenotypes and Enzyme Dynamics.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf250},
pmid = {41239974},
issn = {1751-7370},
abstract = {Soil organic matter decomposition is a complex process reflecting microbial composition and environmental conditions. Moisture can modulate the connectivity and interactions of microbes. Due to heterogeneity, a deeper understanding of the influence of soil moisture on the dynamics of organic matter decomposition and resultant phenotypes remains a challenge. Soils from a long-term field experiment exposed to high and low moisture treatments were incubated in the laboratory to investigate organic matter decomposition using chitin as a model substrate. By combining enzymatic assays, biomass measurements, and microbial enrichment via activity-based probes, we determined the microbial functional response to chitin amendments and field moisture treatments at both the community and cell scales. Chitinolytic activities showed significant responses to the amendment of chitin, independent of differences in field moisture treatments. However, for other measurements of carbon metabolism and cellular functions, soils from high moisture field treatments had greater potential enzyme activity than soils from low moisture field treatments. A cell tagging approach was used to enrich and quantify bacterial taxa that are actively producing chitin-degrading enzymes. By integrating organism, community, and soil core measurements we show that 1) a small subset of taxa compose the majority (>50%) of chitinase production despite broad functional redundancy, 2) the identity of key chitin degraders varies with moisture level, and 3) extracellular enzymes that are not cell-associated account for most potential chitinase activity measured in field soil.},
}

@article {pmid41239968,
year = {2025},
author = {Kim, MS and Bisanz, JE},
title = {Design and application of synthetic human gut microbial communities.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2575923},
doi = {10.1080/19490976.2025.2575923},
pmid = {41239968},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation/methods ; Dysbiosis/therapy/microbiology ; Inflammatory Bowel Diseases/therapy/microbiology ; Host Microbial Interactions ; Bacteria/genetics/classification ; Animals ; },
abstract = {The gut microbiome shapes host health through a complex network driven by both host‒microbe and microbe‒microbe interactions. Disruption of these interactions, often referred to as dysbiosis, is associated with a range of infectious and chronic diseases. Owing to the success of fecal microbiota transplantation (FMT) for the treatment of recurrent Clostridioides difficile infection, FMT has been explored as a therapeutic option for a range of microbiota-associated conditions, including inflammatory bowel disease and obesity. However, the microbial diversity that is the greatest strength of FMT is also its greatest liability. Concerns relating to reliance on human donors, potential for transmission of multidrug-resistant organisms or undesirable phenotypes demonstrate a need for alternate approaches, including the generation of synthetic alternatives to FMT, which can be built in the laboratory from individual strains. Furthermore, these communities are powerful tools for conducting mechanistic research allowing for the generation of 'knockout' communities, which are not possible when working with undefined fecal transplants. This review examines strategies for designing synthetic microbial communities that represent a new generation of microbiome-derived therapies. We highlight how synthetic microbial communities are being used to answer mechanistic questions about host-microbiome interactions relevant to health and disease. Finally, we examine the current clinical translation of these communities as live biotherapeutic products (LBPs). While the regulatory frameworks for LBPs continue to evolve, early clinical successes illuminate the potential for synthetic microbial communities to treat complex human diseases through targeted manipulation and restoration of the gut microbiome.},
}

Humans
*Gastrointestinal Microbiome
Fecal Microbiota Transplantation/methods
Dysbiosis/therapy/microbiology
Inflammatory Bowel Diseases/therapy/microbiology
Host Microbial Interactions
Bacteria/genetics/classification
Animals

@article {pmid41239524,
year = {2025},
author = {Hashem, HR and Yehia, T and Azab, M and Abdellah, A and Amin, IA and Salah, M and Ramadan, M},
title = {Gut microbiome dysbiosis in hepatocellular carcinoma patients with persistent HCV viremia versus viral clearance: a cross-sectional study.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {88},
pmid = {41239524},
issn = {1757-4749},
abstract = {BACKGROUND: Hepatocellular carcinoma (HCC) remains a lethal complication of chronic hepatitis C virus (HCV) infection, even after successful direct-acting antiviral (DAA) therapy. The gut microbiome influences hepatocarcinogenesis through the gut‒liver axis; however, the microbial signatures associated with HCC in DAA-treated patients are poorly defined. This study aimed to elucidate the patterns of microbiomes in HCV-treated patients who developed HCC, with a focus on bacterial diversity, differentially represented taxa, and their associations with clinical markers (FIB-4) and metabolic profiles as potential biomarkers.

RESULTS: A total of 138 participants were enrolled: 46 HCC patients with persistent HCV viremia (RHCC), 46 HCC patients with HCV eradication (THCC), and 46 healthy controls. RHCC patients exhibited pronounced dysbiosis, characterized by reduced alpha diversity (Kruskal-Wallis; H = 14.37, p = 0.00076) and an elevated Firmicutes/Bacteroidetes (F/B) ratio (1.55 vs. 1.05 in controls; Mann-Whitney U test, U = 87.32, padj = 0.00079). At the genus level, Asteroleplasma was significantly enriched in RHCC (log₂FC = + 2.8, padj = 0.008), whereas the butyrate-producing genus Faecalibacterium was depleted (log₂FC = - 2.1, padj = 0.006). Machine learning identified Asteroleplasma, Moryella, Lachnoclostridium, Fournierella, Eubacterium xylanophilum, Succinivibrio, and Faecalibacterium as the top classifiers of RHCC (AUC = 0.81). Functional profiling revealed a 58% reduction in butyrate synthesis (padj = 0.0032) and increased lipopolysaccharide biosynthesis (log₂FC = + 3.2, padj = 0.002) in RHCC, both of which correlated with clinical deterioration (FIB-4 scores, r = 0.62).

CONCLUSIONS: Distinct gut microbial signatures distinguish HCC patients with persistent HCV viremia from those who achieve viral clearance, with implications for risk stratification and therapeutic targeting. The F/B ratio, abundance of Asteroleplasma, and functional pathway disruption (butyrate depletion) could serve as potential biomarkers for HCC progression. These findings underscore the influential role of the gut microbiome in hepatocarcinogenesis and its potential utility in personalized HCC management.},
}

@article {pmid41239321,
year = {2025},
author = {Alkuwaiti, SH and Skrabulyte-Barbulescu, J and Yassin, LK and Almazrouei, S and Aldhaheri, D and Alderei, M and BaniYas, S and Alshamsi, SH and Alnuaimi, A and Saeed, S and Alawadhi, M and Rutkowska-Gauvry, P and Ismail, FY and Hamad, MIK},
title = {Harnessing the microbiota-gut-brain axis to prevent and treat pediatric neurodevelopmental disorders: translational insights and strategies.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1286},
pmid = {41239321},
issn = {1479-5876},
}

@article {pmid41239215,
year = {2025},
author = {Soliman, S and Rezk, A and Rocha, FI and Rodriguez-Ramos, JC and Manoharan, B and Wang, Y and Han, Z and Hale, L and El-Kereamy, A},
title = {Strigolactone GR24 modulates citrus root architecture and rhizosphere microbiome under nitrogen and phosphorus deficiency.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1569},
pmid = {41239215},
issn = {1471-2229},
mesh = {*Rhizosphere ; *Phosphorus/deficiency/metabolism ; *Plant Roots/drug effects/growth & development/microbiology/anatomy & histology ; *Nitrogen/deficiency/metabolism ; *Microbiota/drug effects ; *Lactones/pharmacology ; *Citrus/microbiology/drug effects/growth & development/metabolism/anatomy & histology ; *Heterocyclic Compounds, 3-Ring/pharmacology ; Soil Microbiology ; *Plant Growth Regulators/pharmacology ; Soil/chemistry ; },
abstract = {Nutrient deficiencies, especially nitrogen (N) and phosphorus (P) deficiencies, are among the most critical challenges for sustainable crop production. Excessive use of chemical fertilizers contributes to environmental degradation and climate change, highlighting the need for alternative strategies to improve nutrient uptake. Strigolactones (SLs), a class of plant hormones, have emerged as key regulators of root development and plant-microbe interactions under nutrient-limited conditions. In this study, we investigated the effects of the SL analog GR24 on citrus rootstock C-32 under full nutrition, nitrogen deficiency, and phosphorus deficiency conditions. Plants were treated with five GR24 concentrations (0, 1, 2.5, 5, and 10 µM) and evaluated for changes in root architecture, biomass, soil nutrient content, and rhizosphere microbiomes. The results showed that SL application had a concentration-dependent effect on root morphology. The 2.5 µM SL treatment enhanced fine root initiation, proliferation, and lateral branching under nutrient deficiency, whereas higher concentrations (5 and 10 µM) generally had inhibitory effects. Root surface area and volume were modulated differently across diameter classes, depending on nutrient status and SL dose. Soil nutrient analyses indicated minor alleviating effects of SL on N and P starvation; however, SL significantly affected Cu and Mn. Microbiome analysis revealed that SL reduced bacterial ASV richness but increased dispersion in community structure, particularly under N and P deficiency. Functional annotation indicated changes in denitrification and methanotrophy pathways. Overall, SLs modulated both the root architecture and rhizosphere microbiome composition of citrus plants under nutrient stress. These findings suggest a dual role for SLs in enhancing root plasticity and microbial recruitment, with potential applications in sustainable crop nutrition and soil health.},
}

*Rhizosphere
*Phosphorus/deficiency/metabolism
*Plant Roots/drug effects/growth & development/microbiology/anatomy & histology
*Nitrogen/deficiency/metabolism
*Microbiota/drug effects
*Lactones/pharmacology
*Citrus/microbiology/drug effects/growth & development/metabolism/anatomy & histology
*Heterocyclic Compounds, 3-Ring/pharmacology
Soil Microbiology
*Plant Growth Regulators/pharmacology
Soil/chemistry

@article {pmid41239210,
year = {2025},
author = {Bódis, KB and Florea, DI and Goh, S and Kramser, N and Wienemann, T and Binsch, C and Stern, M and Pfeffer, K and Kelm, M and Roden, M and Wagner, R and Busch, L and Wischmann, P and , },
title = {PTA-DFS study: design of a randomised controlled trial assessing the effects of early percutaneous transluminal angioplasty on the healing of diabetic foot ulcers in persons with type 2 diabetes.},
journal = {BMC cardiovascular disorders},
volume = {25},
number = {1},
pages = {811},
pmid = {41239210},
issn = {1471-2261},
mesh = {Humans ; *Diabetic Foot/therapy/diagnosis/etiology/microbiology/physiopathology ; *Wound Healing ; *Diabetes Mellitus, Type 2/diagnosis/complications ; Time Factors ; Treatment Outcome ; Randomized Controlled Trials as Topic ; Male ; Amputation, Surgical ; *Peripheral Arterial Disease/therapy/physiopathology/diagnosis/diagnostic imaging ; Female ; *Angioplasty/adverse effects ; Risk Factors ; Aged ; Middle Aged ; },
abstract = {BACKGROUND: Peripheral arterial disease (PAD) and local infections increase the risk of non-healing diabetic foot ulcers (DFU) and limb amputations but are treatable by percutaneous transluminal angioplasty (PTA), local wound care and antibiotic therapy. The exact time to treat chronic leg artery stenosis (LAS) and the role of microbiome composition in DFU remain unclear. This study aims to assess whether an early PTA within 48 h after diagnosing a LAS offers advantages over standard care.

METHODS: The PTA-DFS Study is a randomised controlled monocentric trial including individuals with T2D and DFU, aged > 18 years with haemodynamically relevant chronic LAS. The primary study endpoint is to investigate the impact of the early PTA within 48 h on wound-healing assessed by wound area changes after PTA using a 3D-camera with artificial intelligence (AI)-based wound-analysis-system. The secondary endpoint is the effect of early PTA on the combined occurrence of major adverse limb (MALE) and safety-related cardiac events (MACE) over 12 month post-angioplasty using time-to-event analysis. Additional secondary outcomes are time to complete wound healing, major amputation rate and the need for new revascularization. Explanatory variables for wound healing are wound microbiome changes using whole-genome sequencing and oxygen saturation of the wound environment measured using near-infrared spectroscopy. Data will be collected at baseline, 24 h, 1, 2, 3, 6, and 12 months after PTA. Diabetic kidney disease, distal symmetric polyneuropathy, retinopathy, cardiomyopathy, LAS will be assessed by laboratory analyses, clinical scores, AI-based fundus photography, echocardiography, duplex sonography, and pulse oscillography.

DISCUSSION: The PTA-DFS aims to improve diagnostic and therapeutic algorithms, risk assessment and enable tailored therapies for persons with T2D and ischemic DFU.

TRIAL REGISTRATION: Trial Registration Number: NCT06124586 (Registration Date: 2023-08-2).},
}

Humans
*Diabetic Foot/therapy/diagnosis/etiology/microbiology/physiopathology
*Wound Healing
*Diabetes Mellitus, Type 2/diagnosis/complications
Time Factors
Treatment Outcome
Randomized Controlled Trials as Topic
Male
Amputation, Surgical
*Peripheral Arterial Disease/therapy/physiopathology/diagnosis/diagnostic imaging
Female
*Angioplasty/adverse effects
Risk Factors
Aged
Middle Aged

@article {pmid41239201,
year = {2025},
author = {Akanmu, AM and Lawal, IB and Ibrahim, SL and Marle-Köster, EV and Hassen, A},
title = {Metagenomic data from the rumen of South African Mutton Merino sheep supplemented with crude or encapsulated Acacia tannin extracts.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {86},
pmid = {41239201},
issn = {2730-6844},
support = {SRUG2204254606//National Research Foundation/ ; },
mesh = {Animals ; *Rumen/microbiology ; *Tannins/pharmacology/administration & dosage ; *Acacia/chemistry ; Sheep/microbiology ; *Metagenomics ; Gastrointestinal Microbiome ; *Plant Extracts/pharmacology ; Animal Feed ; Dietary Supplements ; },
abstract = {OBJECTIVES: This dataset was generated as part of a study investigating the impact of crude and encapsulated Acacia mearnsii tannin extracts on the rumen microbiota of South African Mutton Merino sheep. The aim was to provide high-quality metagenomic data to support methane mitigation strategies through dietary interventions targeting rumen microbial communities.

DATA DESCRIPTION: Rumen fluid was collected from 24 rams (six per treatment) fed a total mixed ration (TMR) supplemented with either distilled water (control), monensin (positive control), crude tannin, or microencapsulated tannin. However, one sample did not yield sufficient sequencing depth, resulting in 23 usable datasets. DNA was extracted and subjected to shotgun metagenomic sequencing on the Illumina NovaSeq 6000 platform. The dataset comprises paired-end reads deposited in the NCBI SRA under accession SRP480487. Taxonomic profiling reveals dominant phyla such as Bacteroidetes and Firmicutes, and the presence of archaeal genera such as Methanobrevibacter. This dataset provides insights into the structural and functional composition of the rumen microbiome and may be useful for comparative studies and biotechnology applications.},
}

Animals
*Rumen/microbiology
*Tannins/pharmacology/administration & dosage
*Acacia/chemistry
Sheep/microbiology
*Metagenomics
Gastrointestinal Microbiome
*Plant Extracts/pharmacology
Animal Feed
Dietary Supplements

@article {pmid41239036,
year = {2025},
author = {Casanova-Hernández, D and Pinacho-Pinacho, CD and Calixto-Rojas, M and Rubio-Godoy, M and Hernández-Velázquez, IM and Guevara-Avendaño, E and Méndez, O and Velázquez-Velázquez, E and Zamora-Briseño, JA},
title = {Challenging the paradigm: the Asian fish tapeworm (Schyzocotyle acheilognathi, Yamaguti 1934) lacks an intrinsic symbiotic bacterial community.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41239036},
issn = {1618-1905},
abstract = {Schyzocotyle acheilognathi is an invasive generalist cestode with a high capacity for adaptation to multiple hosts and freshwater environments. Recent reports suggest that this parasite possesses an intrinsic symbiotic microbiota distinct from that of its fish hosts, and its presence induces gut dysbiosis in the host. In this study, we reassessed these ideas. For this, we collected naturally parasitized fish specimens from different locations in Mexico, encompassing different host species, including Cyprinus carpio, Pseudoxiphophorus bimaculatus, Tlaloc hildebrandi, and Vieja hartwegi. We also tested whether this parasite induces a dysbiotic process in the gut bacterial community of Tlaloc hildebrandi. Parasites were identified based on morphological and molecular criteria, and their bacterial communities were characterized using metataxonomy. Our results revealed that S. acheilognathi does not harbor a consistent microbial community among the different host species surveyed. We also did not detect any dysbiotic effect on the gut microbiota of Tlaloc hildebrandi. These findings contradict previous data and provide evidence of the loose relationship between this parasite and bacteria, which we propose could be a part of its successful generalist strategy. The results presented herein offer a novel perspective on the quest for understanding the microbial ecology in generalist cestodes of freshwater fish.},
}

@article {pmid41238775,
year = {2025},
author = {Gigi, E and Gavert, N and Raijman-Nagar, L and Zwang, Y and Zemach, H and Livyatan, I and Levy-Barda, A and Laviv, Y and Kanner, AA and Amiel, A and Siegal, T and Leibovici, A and Selezen, I and Badran, O and Zohar, Y and Safadi, E and Prather, LL and Helfer, CR and Castro, P and Barshack, I and Dadosh, T and Levin-Zaidman, S and Goliand, I and Golani, O and Horn, S and Mandel, JJ and Shental, N and Shai, A and Yust-Katz, S and Straussman, R},
title = {Characterization of the tumor microbiome of brain metastases and glioblastoma reveals tumor-type-specific and location-specific microbial signatures.},
journal = {Nature cancer},
volume = {},
number = {},
pages = {},
pmid = {41238775},
issn = {2662-1347},
support = {22-109-PG//Israel Cancer Research Fund (Israel Cancer Research Fund, Inc.)/ ; 2927/21//Israel Science Foundation (ISF)/ ; 818086//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
abstract = {Brain tumors, including glioblastoma multiforme (GBM) and brain metastases, present a notable clinical challenge. Recent research highlights the presence of intratumor bacteria across many tumor types, yet the microbiome of brain tumors remains largely underexplored. Here we show that the microbiome of 322 brain tumors differs markedly by tumor type and location. Using multiple approaches to visualize, culture and sequence bacterial communities, we found that brain metastases harbor higher bacterial richness and diversity than GBM, with distinct microbial compositions. Moreover, metastases in posterior brain regions exhibited greater diversity than those in anterior regions. Pathway analysis revealed enrichment of bacterial metabolic pathways associated with tumor spread and metastasis in brain metastases while GBM was enriched with pathways supporting alternative phosphorus use. These findings provide valuable insights into the microbial landscape of brain tumors, highlighting tumor-type-specific and location-specific variation and suggesting potential roles for bacteria in brain tumor biology.},
}

@article {pmid41238755,
year = {2025},
author = {Griffiths, JA and Nirmalkar, K and Wu, WL and Krajmalnik-Brown, R and Mazmanian, SK},
title = {The gut microbiome shapes social behaviour across animal species.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41238755},
issn = {1740-1534},
abstract = {The gut microbiome has profound influences on brain activity and complex behaviours. Research across diverse animal species, in both natural environments and laboratory settings, has identified biological mechanisms that underlie gut-brain interactions. An emerging central theme is that the gut microbiome is shaped by, and actively contributes to, sociability throughout the lifespan. In this Review, we highlight recent literature revealing the effects of the microbiome on early neurodevelopment, immune modulation, stress responses and microorganism-mediated metabolism that affect social behaviour. Studies investigating the cellular and molecular pathways that underlie microbial influences on social behaviour have implicated brain regions and circuits that mediate critical aspects of animal behaviours, including bonding, mating, defence, aggression and social learning. Gut microbiome-brain research using animal models of social deficits and ecological studies in the wild, as well as investigations of human conditions comorbid with impaired social behaviour, could offer new and natural avenues for improved quality of life in individuals and social groups.},
}

@article {pmid41238743,
year = {2025},
author = {Zhang, L and Tan, X and Guo, Z and Liang, L and Yi, B and Liu, X and Li, F and Wang, Y and Wang, Y},
title = {Effects of gestational diabetes mellitus on the intestinal microbiota of the offspring.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39934},
pmid = {41238743},
issn = {2045-2322},
support = {24JRRA938//Gansu Provincial Science and Technology Project/ ; NCRCCHD-2022-GP-17//General Project of Clinical Medical Research of National Center for Clinical Medical Research on Child Health and Diseases/ ; },
mesh = {Humans ; Female ; *Diabetes, Gestational/microbiology ; Pregnancy ; *Gastrointestinal Microbiome ; Infant, Newborn ; Adult ; Meconium/microbiology ; Dysbiosis/microbiology ; Case-Control Studies ; Male ; },
abstract = {Gestational diabetes mellitus (GDM) significantly impacts maternal and neonatal health, yet its influence on the neonatal intestinal microbiota remains poorly characterized. This study investigated the effects of maternal GDM on offspring microbiota by analyzing meconium samples from newborns of GDM-affected mothers (n = 16) and healthy controls (n = 16). Microbiome analysis revealed distinct composition alterations in the intestinal microbiota of GDM-exposed neonates. Significant differences in microbial abundance were observed between groups: at the phylum level, the GDM group exhibited a significant increase in Bacteroidetes but significant reductions in Actinobacteria and Proteobacteria. At the genus level, opportunistic pathogens including Bacteroides and Escherichia-Shigella were significantly enriched in the GDM group. These findings demonstrate that maternal GDM perturbs the initial colonization of the neonatal intestinal microbiota. Interventions targeting maternal glycemic control during gestation may mitigate offspring microbiota dysbiosis and its potential clinical implications.},
}

Humans
Female
*Diabetes, Gestational/microbiology
Pregnancy
*Gastrointestinal Microbiome
Infant, Newborn
Adult
Meconium/microbiology
Dysbiosis/microbiology
Case-Control Studies
Male

@article {pmid41238729,
year = {2025},
author = {Lee, KY and Shin, SH and Park, G and Kang, SH and Kang, HJ and Kim, J and Lee, JJ and Son, GH and Hong, JY},
title = {Shotgun metagenomics of the vaginal microbiome in cervical shortening and preterm birth risk.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39988},
pmid = {41238729},
issn = {2045-2322},
support = {HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; RS-2023-00252948//Korea government (the Ministry of Science and ICT, the Ministry of Trade, Industry and Energy, the Ministry of Health & Welfare, the Ministry of Food and Drug Safety)/ ; },
mesh = {Female ; Humans ; *Vagina/microbiology ; *Premature Birth/microbiology ; *Microbiota/genetics ; Pregnancy ; *Metagenomics/methods ; Adult ; *Cervix Uteri/microbiology/pathology ; Risk Factors ; },
abstract = {Preterm birth (PTB), a leading cause of neonatal morbidity and mortality, is frequently associated with premature cervical remodeling and vaginal microbiome dysbiosis. Cervical shortening in mid-pregnancy is a well-established risk factor for spontaneous PTB (sPTB), yet the microbial signatures underlying this condition remain underexplored, especially in Asian populations. In this study, we conducted shotgun metagenomic analysis of vaginal samples from 35 East Asian pregnant women with a short cervix and 12 with normal cervical length. Species-level taxonomic profiling and functional pathway analysis revealed reduced Lactobacillus dominance, increased microbial diversity, and enrichment of non-optimal CST IV species, such as Fannyhessea vaginae, Bifidobacterium breve, and Mycobacterium canetti in the short cervix group. Functional profiling showed group differences in pathways related to folate biosynthesis, carbohydrate metabolism, and epithelial barrier regulation. Among women with a short cervix, those who delivered preterm had vaginal microbiomes enriched in opportunistic pathogens, including Peptoniphilus equinus, Treponema spp., and Staphylococcus hominis. Conversely, B. breve, Lactobacillus gasseri, and Lactobacillus paragasseri were associated with full-term delivery. Functions related to glycosylation, structural stability, and degradation of cervical mucin were enriched in the sPTB group. Network analysis identified distinct microbial interactions between Lactobacillus-dominated clusters and CST IV-associated taxa, providing ecological insights that may reflect competitive dynamics and potential influences on cervicovaginal barrier integrity. These findings enhance our understanding of the taxonomic and functional profiles of the vaginal microbiome linked to cervical shortening and sPTB, contributing to improved risk stratification and management strategies for PTB, particularly in women with cervical shortening.},
}

Female
Humans
*Vagina/microbiology
*Premature Birth/microbiology
*Microbiota/genetics
Pregnancy
*Metagenomics/methods
Adult
*Cervix Uteri/microbiology/pathology
Risk Factors

@article {pmid41238692,
year = {2025},
author = {Singhal, R and Qaissi, Z and Zheng, H and Hua, Y and Hardesty, JE and Rouchka, EC and Merchant, ML and Kong, M and Wahlang, B},
title = {Sex-dependent modulation of PCB-mediated toxicity from a proteomic and microbiome perspective.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39903},
pmid = {41238692},
issn = {2045-2322},
support = {P20GM113226, P20GM103436/GM/NIGMS NIH HHS/United States ; K01ES033289, P42ES023716, P30ES030283/ES/NIEHS NIH HHS/United States ; HT94252310949//U.S. Department of Defense/ ; },
mesh = {Animals ; *Polychlorinated Biphenyls/toxicity ; Male ; Female ; *Gastrointestinal Microbiome/drug effects ; Mice ; Proteomics/methods ; *Liver/drug effects/metabolism ; Mice, Inbred C57BL ; *Proteome/drug effects/metabolism ; Receptors, Aryl Hydrocarbon/metabolism ; Sex Factors ; Sex Characteristics ; Liver X Receptors/metabolism ; },
abstract = {Polychlorinated biphenyls (PCBs) have been associated with sex-dependent liver disease outcomes. Current mechanisms only partially explain these sex differences and alternative mechanisms including gut-liver toxicity warrant investigation. This study aims to identify PCB-induced changes in the hepatic proteome and gut microbiome and determine their contributions to sex-specific PCB toxicity. Male and female C57BL/6J mice were exposed to Aroclor1260 (20 mg/kg) and PCB126 (20 μg/kg) via oral gavage. After two weeks, hepatic and intestinal tissues were collected for peptide measurements (LC/MS) and 16S sequencing respectively. Proteomic analysis revealed that biological sex largely drove differences seen in the hepatic proteome and dictated PCB liver responses. PCB-exposed females manifested higher abundance of aryl hydrocarbon receptor (AHR) targets including CD36 vs. PCB-exposed males. Computational analysis also demonstrated enhanced AHR and liver-X-receptor (LXR) activation (higher z-scores) in PCB-exposed females vs. males. With regards to gut microbiome, both exposure and sex impacted the composition of microbial communities. Intriguingly, only PCB-exposed males exhibited increased Dehalobacterium abundance, and decreased mRNA levels for genes encoding gut barrier and antimicrobial proteins (Ocln, Reg3g). Overall, PCB-exposed females exhibited an altered proteome relevant to AHR and LXR responses, while PCB-exposed males exhibited more distinct changes in gut microbiota coupled with altered ileal gene expression. The findings suggest that, in addition to biological sex, organ-organ interactions should be considered when predicting toxicity outcomes, particularly for persistent compounds such as PCBs that can impact multiple organs simultaneously yet have tissue-specific toxic effects.},
}

Animals
*Polychlorinated Biphenyls/toxicity
Male
Female
*Gastrointestinal Microbiome/drug effects
Mice
Proteomics/methods
*Liver/drug effects/metabolism
Mice, Inbred C57BL
*Proteome/drug effects/metabolism
Receptors, Aryl Hydrocarbon/metabolism
Sex Factors
Sex Characteristics
Liver X Receptors/metabolism

@article {pmid41238653,
year = {2025},
author = {Wielkopolan, B and Szabelska-Beręsewicz, A and Obrępalska-Stęplowska, A},
title = {Bacteria associated with the cereal leaf beetle act as the insect's allies in adapting to protease inhibitors, but impair its development in laboratory condition.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39944},
pmid = {41238653},
issn = {2045-2322},
support = {UMO-2020/37/N/NZ9/02577//Narodowe Centrum Nauki/ ; },
mesh = {Animals ; *Coleoptera/microbiology/growth & development/drug effects ; Larva/microbiology/growth & development/drug effects ; *Protease Inhibitors/pharmacology ; *Bacteria ; Microbiota ; *Adaptation, Physiological ; Edible Grain/parasitology ; },
abstract = {Oulema melanopus [L.] (cereal leaf beetle, CLB) is one of the most serious cereal pests. Plant protease inhibitors (PIs) are known for their insecticidal properties. The role of CLB-associated bacteria in insect adaptation to PIs is not yet known. We investigated the role of CLB-associated bacteria in adaptation to PIs, and whether the reduction of bacteria will affect the CLB development. We found a decrease in proteases activity in insects with a diminished bacterial community compared to those with an intact bacterial community. Thus, the study showed that the CLB-associated bacteria participate in the adaptation of CLB larvae to PIs. On the other hand, regardless of the type of PI used, ultimately a higher survival rates were recorded for larvae with a reduced bacterial community compared to insects with a natural microbiome in laboratory conditions. In such conditions, higher larval survival rates and a higher percentage of larvae reaching the pupal and imago stages were recorded in insects whose bacterial community was reduced. Since the CLB bacterial microbiome showed a negative impact on the development of the insect's host and its survival in response to PIs in laboratory conditions, it can be concluded that CLB-associated bacteria can be an ally of its insect host, but also an adversary when conditions are not optimal for symbiosis.},
}

Animals
*Coleoptera/microbiology/growth & development/drug effects
Larva/microbiology/growth & development/drug effects
*Protease Inhibitors/pharmacology
*Bacteria
Microbiota
*Adaptation, Physiological
Edible Grain/parasitology

@article {pmid41238551,
year = {2025},
author = {Chen, M and Qi, C and Qing, W and Zhou, Z and Zhang, Y and Chen, R and Hou, Y and Ou, J and , and He, Y and Zhou, H},
title = {Vaginal microbiome and sexually-transmitted pathogens in Chinese reproductive-age women: a multicentre cross-sectional and longitudinal cohort study.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10002},
pmid = {41238551},
issn = {2041-1723},
support = {82002201//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82302610//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82205157//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81925026//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Female ; Humans ; *Vagina/microbiology ; Longitudinal Studies ; *Microbiota/genetics ; Adult ; Cross-Sectional Studies ; China/epidemiology ; RNA, Ribosomal, 16S/genetics ; *Sexually Transmitted Diseases/microbiology/epidemiology/virology ; Young Adult ; Dysbiosis/microbiology ; Coinfection/microbiology ; Middle Aged ; Papillomavirus Infections/microbiology ; Adolescent ; East Asian People ; },
abstract = {Sexually transmitted infections (STIs) are associated with vaginal dysbiosis, and co-infections are common but understudied. In this study, 6217 reproductive-age women are recruited from 38 study centres across China at baseline and 2738 participants are followed up at 6 months. We profile the vaginal microbiota by 16S rRNA gene sequencing in conjunction with measurement of nine common STIs. The primary outcome of this study is STI status, and secondary outcome is the risk of cervical lesions. Mycoplasmas hominis (MH) far exceeds other STIs in the association with vaginal microbiota, whereases previously reported associations between Human papillomavirus (HPV) and vaginal dysbiosis might be confounded by the co-infected MH in this study. Both MH infection and increased bacterial diversity are independently associated with increased risk of cervical lesion in HPV-negative women (Shannon, OR (odds ratio) = 1.71, 95% CI (confidence interval) = 1.23-2.36; MH, OR = 2.42 95% CI = 1.36-4.30). These associations are also identified in longitudinal analyses (Shannon, HR (hazard ratio) = 1.72, 95% CI = 1.04-2.86; MH, HR = 2.37, 95% CI = 0.98-5.72). Our findings highlight the importance of considering MH status when studying vaginal microbiota in cervical lesions, and suggest the need for further investigation of microbiota-associated mechanisms in HPV-negative cervical lesions. (ClinicalTrials.gov. NCT04694495).},
}

Female
Humans
*Vagina/microbiology
Longitudinal Studies
*Microbiota/genetics
Adult
Cross-Sectional Studies
China/epidemiology
RNA, Ribosomal, 16S/genetics
*Sexually Transmitted Diseases/microbiology/epidemiology/virology
Young Adult
Dysbiosis/microbiology
Coinfection/microbiology
Middle Aged
Papillomavirus Infections/microbiology
Adolescent
East Asian People

@article {pmid41238500,
year = {2025},
author = {Choi, HS and Park, EJ and Pang, EK},
title = {Comparative analysis of the microbial profiles in supragingival and subgingival plaques obtained from different dental prostheses.},
journal = {The Journal of prosthetic dentistry},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.prosdent.2025.10.021},
pmid = {41238500},
issn = {1097-6841},
abstract = {STATEMENT OF PROBLEM: The oral microbial ecosystem significantly influences periodontal and peri-implant health. Although various studies have investigated the microbial influence of specific dental restorative materials, studies that directly compared the microbial diversity across different restoration types within the same oral cavity are sparse, limiting the identification of consistent, material-specific microbial profiles.

PURPOSE: The purpose of this clinical study was to analyze and compare the supragingival and subgingival microbial diversity and composition associated with an unrestored natural tooth, a gold crown-restored tooth, a zirconia crown-restored tooth, and an implant-supported restoration within the same participant. A secondary objective was to evaluate whether specific restorative materials induced reproducible microbial profiles across individuals.

MATERIAL AND METHODS: Thirty participants possessing all 4 types of restorations (unrestored natural tooth, gold crown, zirconia crown, and implant) in their oral cavity were enrolled. Supra- and subgingival biofilm samples were collected by using sterile swabs. Deoxyribonucleic acid (DNA) was extracted, and microbial identification was conducted via 16S rRNA sequencing targeting the V3-V4 regions. Alpha diversity was quantified by using Shannon, npShannon, and Simpson indices; beta diversity was assessed by using Bray-Curtis and UniFrac distances. Taxonomic classification and biomarker identification were performed by using the EzBioCloud software program (CJ Bioscience) and linear discriminant analysis effect size (LEfSe). Statistical significance was determined with Kruskal-Wallis and permutational multivariate analysis of variance tests (α=.05). Sample collection was standardized and conducted by a single calibrated examiner. DNA extraction, sequencing, and bioinformatics analyses were completed at a single laboratory facility to ensure methodological consistency.

RESULTS: Gold crown- and zirconia crown-restored teeth exhibited significantly higher alpha diversity than unrestored natural teeth orimplant-supported restorations (Shannon: Gold, 4.3 ±0.6; Zirconia, 4.1 ±0.5; Natural tooth, 3.5  ±0.4; Implant, 3.0 ±0.6, P<.05). The lowest microbial diversity was noted in implant-supported restorations, predominantly characterized by anaerobic taxa, including Clostridiales. Beta diversity analysis revealed distinct and significant microbial clustering based on restorative types (PERMANOVA, pseudo-F=2.8, R²=.04, P<.01). LEfSe analysis identified Actinomyces spp. predominance in unrestored teeth, Prevotella and Spirochaetes in gold crowns, Porphyromonas and Atopobium in zirconia crowns, and Clostridiales in implants. These microbial signatures remained consistent within individuals and across the study population.

CONCLUSIONS: Restorative materials significantly influenced the supragingival and subgingival microbiome composition within the same oral environment. Implant-supported restorations displayed lower microbial diversity and a higher prevalence of pathogenic taxa. Thus, restorative material selection may critically impact long-term periodontal and peri-implant health outcomes.},
}

@article {pmid41238428,
year = {2025},
author = {Elkourashy, SA and Abu-El-Ruz, R and Askar, MZ and Hamdan, A and Zughaier, SM},
title = {The microbiome-lymphoma Axis: A systematic review and Meta-analysis of gut Dysbiosis pattern in diffuse large B-cell lymphoma.},
journal = {Blood reviews},
volume = {},
number = {},
pages = {101341},
doi = {10.1016/j.blre.2025.101341},
pmid = {41238428},
issn = {1532-1681},
abstract = {BACKGROUND: Gut microbiota has emerged as a critical mediator of immune homeostasis and cancer biology. Increasing evidence suggests that gut dysbiosis may play a significant role in the pathogenesis of diffuse large B-cell lymphoma (DLBCL), the most common and aggressive subtype of non-Hodgkin lymphoma (NHL). However, a comprehensive synthesis of the microbial alterations associated with DLBCL remains poorly defined.

METHODS: We systematically reviewed and meta-analyzed thirteen studies (n = 4087 cases) to assess gut microbiota alterations in DLBCL. Both observational and Mendelian randomization designs were included. Pooled odds ratios (OR) were calculated for mendelian randomization studies using random-effects models, and microbial shifts were analyzed at the species level to contextualize biological relevance. Observational studies were used for qualitative assessment.

RESULTS: Meta analysis was done for the mendelian randomization studies (n = 3737 cases). The overall pooled OR was 0.96 (95 % CI: 0.93-1.00), suggested a slight shift towards depletion, with considerable heterogeneity (I[2] = 78.7 %). Species-level analysis revealed significant enrichment of pro-inflammatory or potentially oncogenic taxa in DLBCL, including Bilophila (OR = 1.78), Desulfovibrionaceae (OR = 1.58), and Coprobacter (OR = 1.37). Conversely, beneficial commensals with anti-inflammatory and metabolic regulatory roles such as Eubacterium coprostanoligenes group (OR = 0.19), Alistipes (OR = 0.57), Ruminococcaceae UCG011 (OR = 0.75) were significantly depleted.

CONCLUSIONS: This first comprehensive synthesis demonstrates a reproducible species-level microbial signature in DLBCL, characterized by depletion of protective commensals and enrichment of pro-tumorigenic taxa. Mechanistically, these shifts may promote lymphomagenesis via inflammatory, metabolic, and immune-modulatory pathways. Our findings highlight the gut microbiota as a latent biomarker source and therapeutic target, supporting microbiota-modulating strategies in precision lymphoma care.},
}

@article {pmid41238281,
year = {2025},
author = {Masthan, A and Strople, J and Runde, J},
title = {Dietary Therapy in the Management of Inflammatory Bowel Disease: A Lasting Legacy and a New Frontier.},
journal = {Gastroenterology clinics of North America},
volume = {54},
number = {4},
pages = {875-889},
doi = {10.1016/j.gtc.2025.07.004},
pmid = {41238281},
issn = {1558-1942},
mesh = {Humans ; *Inflammatory Bowel Diseases/diet therapy ; Gastrointestinal Microbiome ; Enteral Nutrition ; Child ; Diet, Gluten-Free ; *Diet ; },
abstract = {This article highlights the evolving role of dietary strategies in the management of pediatric inflammatory bowel disease (IBD). Advances in understanding diet's influence on IBD pathogenesis and disease progression have renewed interest in the role of diet in the treatment of IBD. Exclusive enteral nutrition remains the gold standard, but whole food diets that mimic the composition of EEN or eliminate foods that negatively impact the intestinal microbiome and immune response have shown promise. Additional research that includes larger patient populations and objective data is needed to expand applicability and develop patient-centered recommendations.},
}

Humans
*Inflammatory Bowel Diseases/diet therapy
Gastrointestinal Microbiome
Enteral Nutrition
Child
Diet, Gluten-Free
*Diet