@article {pmid41075498,
year = {2025},
author = {Dias, MF and Nogueira, YJA and de Albuquerque, GS and Romano-Silva, MA and de Miranda, DM},
title = {A systematic review on the associations between Attention-Deficit/Hyperactivity Disorder and gut microbiome.},
journal = {Journal of psychiatric research},
volume = {191},
number = {},
pages = {597-603},
doi = {10.1016/j.jpsychires.2025.10.008},
pmid = {41075498},
issn = {1879-1379},
abstract = {Attention-Deficit/Hyperactivity Disorder (ADHD) is a prevalent neurodevelopmental condition in childhood, and growing evidence suggests a potential link between gut microbiome (GM) and ADHD symptoms via the microbiota-gut-brain axis. This systematic review aimed to evaluate current evidence on the associations between human GM and ADHD, addressing microbial composition, diversity measures, and potential pathways through which microbiota could be associated with the symptoms. A systematic search was conducted in PubMed, Embase, and Scopus databases. Fourteen studies met the eligibility criteria, which focused on original research assessing GM characteristics in individuals with ADHD. Selected articles comprised a total of 1319 participants, 67 % male, from Europe (53 %) and East Asia (47 %), mostly with children and adolescents aged 4-18 years. Alterations in microbial composition were observed among ADHD patients; including higher relative abundance of Agathobacter and Ruminococcus gnavus and decreased Faecalibacterium, identified in different studies. Results regarding alpha- and beta-diversity were inconclusive. There was also evidence of links between GM and inflammatory markers and neurotransmitter-related pathways. Despite current limitations, emerging data suggest that GM may play a role in ADHD pathophysiology, supporting its potential as a target for personalized therapeutic strategies.},
}

@article {pmid41075387,
year = {2025},
author = {Godefroy, E and Altare, F},
title = {Deciphering and harnessing gut microbiota-associated immune regulation in acute graft-versus-host disease.},
journal = {Current opinion in immunology},
volume = {97},
number = {},
pages = {102676},
doi = {10.1016/j.coi.2025.102676},
pmid = {41075387},
issn = {1879-0372},
abstract = {Allogeneic hematopoietic stem cell transplantation represents a curative treatment of choice for numerous severe hematological malignancies. While donor-derived transplanted T cells can limit disease relapse (GvT/GvL effect), they also induce, in 30-50% of the patients, acute graft-versus-host disease (aGvHD), a severe condition with elevated mortality and comorbidity rates. Gut microbiota composition has been associated with aGvHD outcome. This observation created a substantial research interest, and individual gut microbiota commensals have been acknowledged for their ability to promote immune regulation, both locally and systemically, and thus limit aGvHD-related inflammation. The mechanisms by which commensals support immune homeostasis are being decrypted at a remarkable rate. However, the trillions of micro-organisms comprising the gut microbiome interact, both directly and indirectly, with local immune cells, which is all the more critical in the context of heavy conditioning regimens these patients undergo, themselves damaging mucosal tissues and prompting inflammation. Commensals can help preserve the gut barrier integrity by actively limiting deleterious inflammation processes. Mechanistically deciphering the intricate crosstalk between gut microbes and gut immune cells, both at the species level and globally, represents a colossal challenge, but holds great promise in predicting and harnessing numerous pathological processes, including aGvHD. This review aims to examine the acquired knowledge concerning immunoregulatory responses driven by gut microbiota in the context of aGvHD. Recent preclinical and clinical studies harnessing such pathways proved to be encouraging, while substantial hurdles subsist regarding how to successfully harness this complex host/microbiota interplay to constrain aGvHD.},
}

@article {pmid41075335,
year = {2025},
author = {Ghaffar, A and Liljebjelke, K and Checkley, SL and Farooq, M and Abdul-Careem, MF},
title = {Exploring the indoor airborne microbiome and resistome in layer barns across Alberta, Canada.},
journal = {Research in veterinary science},
volume = {196},
number = {},
pages = {105930},
doi = {10.1016/j.rvsc.2025.105930},
pmid = {41075335},
issn = {1532-2661},
abstract = {The air in poultry barns carries a diverse range of microbial communities including potential opportunistic pathogens, which are important for both animal and human health. Bacteria carrying antimicrobial resistance genes (ARGs) can become airborne within poultry barns and be transmitted to animals and poultry workers, presenting a serious One Health concern. This study was aimed at characterizing the microbiome and resistome of bioaerosols sampled from layer chicken barns across Alberta. In total, 15 barns (9 cage housed and 6 floor housed) were sampled in this study using a microbial air sampler to characterize the microbiome and resistome using a shotgun metagenomic sequencing approach. The most abundant bacterial phyla found in the air of both housing systems for pullets were Bacilliota, Actinomycetota, and Bacteroidota. The respiratory pathogens such as Gallibacterium anatis, Ornithobacterium rhinotracheale, and Pasteurella multocida were relatively more abundant in the air of cage-housed barns, whereas Escherichia coli and Avibacterium paragallinarum were more prevalent in floor-housed barns. In total, 113 unique ARGs subtypes from 19 classes of antimicrobials were identified in this study. ARGs were significantly more abundant in the air of cage-housed barns compared to floor-housed barns. In particular, genes associated with resistance to tetracyclines, lincosamides, and macrolides were more frequently detected in cage-housed environments. Overall, both microbial and resistance gene levels were higher in the bioaerosols of cage-housed barns than in those from floor-housed pullet barns. The study results demonstrate the potential for air as a reservoir of ARGs and highlights microbial differences within cage and floor housing.},
}

@article {pmid41075060,
year = {2025},
author = {Fernández-Lucas, J},
title = {From tradition to innovation: the ongoing evolution of AMB express.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {147},
doi = {10.1186/s13568-025-01970-x},
pmid = {41075060},
issn = {2191-0855},
abstract = {Since its foundation in 2011, AMB Express has grown from a journal focused on classical applied microbiology and industrial biotechnology into a multidisciplinary platform covering microbiome research, antimicrobials, biocatalysis, and synthetic biology. In this Editorial, an overview of our journal's evolution is provided, along with an outline of the directions in which it should develop to maintain its status as a reference journal of applied microbiology and biotechnology.},
}

@article {pmid41075036,
year = {2025},
author = {Hatami, F and Aghelan, Z and Pouya, MR and Moulaeian, M and Rastegari, A and Abtahi, SH and Hoseini, S},
title = {Gut microbiota reconstitution and control of α-synucleinopathy with β-glucans: a promising approach for individuals with parkinson's disease.},
journal = {Metabolic brain disease},
volume = {40},
number = {7},
pages = {287},
pmid = {41075036},
issn = {1573-7365},
mesh = {*Gastrointestinal Microbiome/drug effects/physiology ; Humans ; *Parkinson Disease/drug therapy/metabolism/microbiology ; *alpha-Synuclein/metabolism ; *beta-Glucans/therapeutic use/pharmacology ; Animals ; *Synucleinopathies/drug therapy/metabolism ; Dysbiosis/drug therapy/metabolism ; },
abstract = {Parkinson's disease (PD) ranks as the second most prevalent neurodegenerative condition affecting individuals in their middle age and beyond. Its hallmark features include the abnormal accumulation of α-synuclein protein and the progressive loss of dopaminergic neurons. A substantial body of evidence supports the notion that an imbalance in the gut microbiome, known as dysbiosis, contributes to the misfolding and accumulation of α-synuclein, a key pathological feature of PD. This finding raises the possibility that restoring the gut microbiome, particularly the bacteria associated with α-synuclein, could serve as a promising therapeutic approach for PD. There is evidence that β-glucan can play an important role in the reconstitution of gut microbiome. In this regard, this study reviews the evidence showing the role of β-glucan in reducing α-synuclein accumulation and mitigating the progression of PD. This scooping review study presents promising prospects for advancing novel therapeutic approaches to benefit individuals with PD.},
}

*Gastrointestinal Microbiome/drug effects/physiology
Humans
*Parkinson Disease/drug therapy/metabolism/microbiology
*alpha-Synuclein/metabolism
*beta-Glucans/therapeutic use/pharmacology
Animals
*Synucleinopathies/drug therapy/metabolism
Dysbiosis/drug therapy/metabolism

@article {pmid41074949,
year = {2025},
author = {Malik, MZ and Nizam, R and Jacob, S and Al Alqaderi, H and Al-Mulla, F and Alqaderi, H},
title = {Microbial dysbiosis in oral cavity determines obesity status in adolescents.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {82},
number = {1},
pages = {354},
pmid = {41074949},
issn = {1420-9071},
support = {Institutional Funding//Kuwait Foundation for the Advancement of Sciences/ ; },
mesh = {Humans ; Adolescent ; *Dysbiosis/microbiology ; Female ; Male ; *Mouth/microbiology ; *Obesity/microbiology ; Microbiota/genetics ; Saliva/microbiology ; Body Mass Index ; Kuwait ; },
abstract = {The prevalence of obesity is rapidly increasing among adolescents in Kuwait. The ecological and dynamic changes within the oral microbiota during this developmental stage remain elusive. This study aimed to investigate the impact of body mass index (BMI) on salivary microbiome diversity and composition in Kuwaiti adolescents by utilizing next-generation sequencing technologies. DNA was extracted from saliva samples of 62 Kuwaiti adolescents enrolled in the nationwide Kuwait Healthy Lifestyle Study, categorized as underweight, normal weight, overweight, and obese based on their BMI percentiles. The 16 S metagenomic profiling was performed to identify the key oral lineages and genera associated with obesity through comprehensive analysis involving taxonomic composition, co-occurrence networks, and key metabolic profiles. Our study reveals an inverse relationship between oral bacterial diversity and obesity status in Kuwaiti adolescents. The obese and overweight groups showed comparatively low microbial taxa compared to those of normal weight. We identified three potential microbial biomarkers linked to obesity and overweight: Prevotella melaninogenica, Veillonella dispar, and Veillonella parvula. The abundance of Neisseria subflava and Rothia mucilaginosa in normal weight adolescents indicates their role in weight homeostasis. In- silico analysis of differentially expressed microbiota revealed increased activity of major metabolic enzymes such as glucose- 6- phosphate dehydrogenase, pyruvate oxidase, and glycogen phosphorylase, along with oxidative stress- related enzymes including superoxide reductase and glutathione peroxidase in obese and over-weight adolescents. Conversely, normal weight adolescents exhibited heightened activity of pyruvate synthase and tRNA- methyltransferase, which are linked to antioxidative pathways and balanced energy metabolism. Our study highlights taxonomic and functional shifts in the oral microbiota of Kuwaiti adolescents across varying BMI categories, signifying key microbial markers that could pave the way for future research focused on microbiome- targeted interventions in obesity management.},
}

Humans
Adolescent
*Dysbiosis/microbiology
Female
Male
*Mouth/microbiology
*Obesity/microbiology
Microbiota/genetics
Saliva/microbiology
Body Mass Index
Kuwait

@article {pmid41074715,
year = {2025},
author = {Ajith, TA and Sreejith, JK},
title = {Microbiota-gut-brain axis and probiotics: potential therapeutic strategies for treating Alzheimer's disease.},
journal = {Nutritional neuroscience},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/1028415X.2025.2567429},
pmid = {41074715},
issn = {1476-8305},
abstract = {The gut-brain axis explains that changes in the intestinal microbiota influence Alzheimer's disease (AD). Short-chain fatty acids produced by the gut microbiome regulate the permeability of the gut and blood-brain barrier. Furthermore, they upregulate brain-derived neurotrophic factor, promote angiogenesis and neurogenesis, and control tau and Aβ proteins, microglial activity, apoptosis, oxidative damage, M1/M2 polarization of microglia, and neuroinflammation, which eventually improves cognitive impairment. This effect is mediated by modification of serotonin, dopamine, and γ-aminobutyric acid levels. Compared to healthy controls, mild cognitive impairment and AD were associated with low levels of Firmicutes and Bifidobacterium and high levels of Proteobacteria and Bacteroidetes. Lactobacillus and Bifidobacterium species were effective in improving cognitive function. More longitudinal research is needed to investigate precision medicine in patients with dysbiosis in the preclinical stages of the disease. This review describes the role of the gut microbiome and probiotics in AD.},
}

@article {pmid41074693,
year = {2025},
author = {Perez-Garcia, J and Bozack, AK and Rifas-Shiman, SL and Zhou, Y and Sordillo, J and Coull, B and Luttmann-Gibson, H and Schwartz, J and Hivert, MF and Oken, E and Gold, DR and Cardenas, A},
title = {The Nasal Microbiome and Associations With Environmental Exposures and Respiratory Health.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70089},
pmid = {41074693},
issn = {1398-9995},
support = {/ES/NIEHS NIH HHS/United States ; /NH/NIH HHS/United States ; R01ES031259//United States National Institutes of Health (NIH)/ ; R01HD034568//United States National Institutes of Health (NIH)/ ; R24ES030894//United States National Institutes of Health (NIH)/ ; P30-ES000002//United States National Institutes of Health (NIH)/ ; },
abstract = {BACKGROUND: The nasal microbiome is directly in contact with the external environment and may play a role in respiratory health. This study aimed to evaluate the association of the nasal microbiome with air pollutants, meteorological conditions, and respiratory health in adolescents.

METHODS: We analyzed the nasal microbiome in 416 adolescents from the Project Viva cohort (mean age 13 years and 52% female). We tested for the association of alpha diversity, nasotypes, and bacterial genera abundance with environmental exposures from the past 2 days to the past year (PM2.5, NO2, O3, temperature, humidity, residential greenness) and respiratory outcomes (asthma, hay fever, wheezing, IgE, aeroallergen sensitization, FeNO, lung function) through regression models adjusted for confounders and corrected using a false discovery rate (FDR) < 5%.

RESULTS: Bacterial diversity was positively associated with hay fever and short-term exposure to NO2, while it was negatively correlated with temperature (FDR < 0.05). Adolescents whose nasal microbiome was dominated by Moraxella were exposed in the past week to lower O3 levels (ORs: 0.73-0.76) and higher temperature and humidity (ORs: 1.19-1.26). Staphylococcus dominance was positively associated with aeroallergen sensitization compared to Propionibacterium dominance (OR: 4.48, FDR = 0.03). Thirteen and eight bacterial genera abundance were associated with short-to-medium-term exposures (PM2.5, NO2, temperature) and respiratory outcomes (hay fever, wheezing, IgE, FeNO, lung function) (FDR < 0.05). Staphylococcus, Corynebacterium, Pelomonas, Lactococcus, Lachnospiraceae (unclassified), and Faecalibacterium abundance were associated with both environmental exposures and respiratory traits.

CONCLUSIONS: Nasal microbiome diversity was associated with hay fever, NO2, and temperature exposure. Multiple short-to-medium-term environmental exposures and respiratory outcomes were associated with nasotypes and bacterial genera abundance in adolescents.},
}

@article {pmid41074392,
year = {2025},
author = {Al-Mufti, SM and Abdulkareem, AA and Chasib, NH and Milward, M and Cooper, PR},
title = {Long Noncoding RNA Malat1 and Neat1 Associated With Dysbiotic Microbiome and Epithelial-Mesenchymal Transition in Periodontitis.},
journal = {Molecular oral microbiology},
volume = {},
number = {},
pages = {e70010},
doi = {10.1111/omi.70010},
pmid = {41074392},
issn = {2041-1014},
abstract = {INTRODUCTION: The regulatory mechanisms of epithelial-mesenchymal transition (EMT) involved in periodontitis pathogenesis are poorly understood. Consequently, this study aimed to investigate the association of the long noncoding (lnc) RNAs, NEAT1 and MALAT1, with EMT in periodontitis.

METHODS: Gingival tissue samples (n = 57) were obtained from periodontitis patients indicated for surgical treatment and healthy control individuals. Full mouth periodontal charting was recorded for all patients together with collection of subgingival biofilm samples to determine bacterial load for key-periodontal pathogens. Histopathological analysis was used to assess inflammatory cell infiltration, and RT-qPCR analysis was performed to quantify the expression of the key EMT biomarkers of E-cadherin, β-catenin, Snail1 and vimentin, and the lncRNAs of Neat1 and Malat1.

RESULTS: The clinical parameters and percentage of inflammatory cell infiltration were significantly higher in the periodontitis group compared with healthy controls. In periodontitis, expressions of Malat1 and E-cadherin were significantly downregulated, whereas Neat1, Snail1 and vimentin were significantly upregulated in comparison to controls. Receiver-operating characteristic (ROC) analyses demonstrated moderate-to-good diagnostic accuracy of Neat1, Malat1, Snail1, E-cadherin and vimentin (area under the curve [AUC]: 70.3%, 67.5%, 78.7%, 89.9% and 74.3%, respectively) to discriminate periodontal health from disease.

CONCLUSION: Probing pocket depth, bleeding scores, expression of Neat1, red complex bacteria (Porphyromonas gingivalis and Treponema denticola) and downregulation of Malat1 and E-cadherin were strongly associated with EMT. Data also highlighted an association between Neat1 and Malat1 with the induction of the EMT phenotype in periodontitis, and these lncRNAs may therefore provide novel diagnostic biomarkers.},
}

@article {pmid41074292,
year = {2025},
author = {Wang, Z and Wang, S and Chen, Y and Liang, L and Yang, L and Zeng, L},
title = {Ultrasound-assisted betaine-based natural deep eutectic solvents for green extraction of total phenols and flavonoids from Lithocarpus litseifolius: Mechanistic insights and anti-hyperuricemic applications.},
journal = {Food research international (Ottawa, Ont.)},
volume = {220},
number = {},
pages = {117048},
doi = {10.1016/j.foodres.2025.117048},
pmid = {41074292},
issn = {1873-7145},
mesh = {Animals ; *Flavonoids/isolation & purification/pharmacology ; Mice ; *Hyperuricemia/drug therapy ; *Betaine/chemistry ; *Plant Extracts/pharmacology/chemistry ; *Phenols/isolation & purification/pharmacology ; Male ; *Deep Eutectic Solvents/chemistry ; Polyphenols/isolation & purification ; Gastrointestinal Microbiome/drug effects ; },
abstract = {To develop an ecologically suitable and efficient method for the simultaneous extraction of total polyphenols (TP) and total flavonoids (TF) from Lithocarpus litseifolius (L. litseifolius), this study employed natural deep eutectic solvents (NADES) combined with ultrasound-assisted extraction. Betaine-acetic acid (1:2) was identified as the most effective NADES for extracting the target components. The extraction conditions were optimized using a Box-Behnken design. Under the optimized conditions, the extraction yields were 6.682 % for TP and 9.230 % for TF, closely matching the predicted yields of TP (6.697 %) and TF (9.241 %). These yields were 1.78-4.77 times and 1.73-7.82 times higher than those achieved using traditional solvents, demonstrating their favorable efficiency. HPLC results indicated that phloridzin (38.68 mg/g) and trilobatin (26.36 mg/g) were the primary components of the L.litseifolius extract. The kinetic and thermodynamic models were fitted to the extraction process, and the synergistic effect was verified via SEM, FT-IR, [1]H NMR, and IGMH. Experimental results from both in vivo and in vitro studies demonstrated that the extract exhibited a significant uric acid-lowering effect. It significantly reduced serum uric acid, creatinine, and blood urea nitrogen levels, inhibited liver and serum xanthine oxidase activity, and alleviated hepatorenal pathological damage in hyperuricemic mice. Furthermore, microbiome analysis indicated that the extract restored intestinal homeostasis by modulating beneficial bacterial abundance and improving gut microbiota composition. Spearman correlation analysis revealed strong associations between altered gut microbiota and hyperuricemia-related physiological indicators. This study provides a green and efficient extraction method for TP and TF from L.litseifolius and reveals the anti-hyperuricemic potential of its extract.},
}

Animals
*Flavonoids/isolation & purification/pharmacology
Mice
*Hyperuricemia/drug therapy
*Betaine/chemistry
*Plant Extracts/pharmacology/chemistry
*Phenols/isolation & purification/pharmacology
Male
*Deep Eutectic Solvents/chemistry
Polyphenols/isolation & purification
Gastrointestinal Microbiome/drug effects

@article {pmid41074291,
year = {2025},
author = {Huang, X and Wu, L and Zhang, Y and Huang, J and Luo, Y and Liao, H and Cai, Y and Gao, L and Xia, X},
title = {Guide the design of lactic acid bacteria synthesis community through computational metabolic interaction experimental pipeline.},
journal = {Food research international (Ottawa, Ont.)},
volume = {220},
number = {},
pages = {117046},
doi = {10.1016/j.foodres.2025.117046},
pmid = {41074291},
issn = {1873-7145},
mesh = {*Lactobacillales/metabolism/genetics ; *Food Microbiology/methods ; Fermentation ; *Fermented Foods/microbiology ; Amino Acids/metabolism ; Lactic Acid/metabolism ; *Microbial Consortia ; },
abstract = {Understanding whether ecological assembly principles can inform synthetic microbial community construction remains a critical challenge in fermented food research, hindered by the complexity of natural ecosystems. Here, we integrate top-down metabolic modeling with bottom-up experimental validation to establish a generalizable framework for food microbial community engineering. Genome-scale metabolic modeling of 507 spontaneously assembled lactic acid bacterial (LAB) communities revealed a significant enrichment of cooperative interactions in naturally fermented ecosystems compared to randomly assembled consortia. This cooperative propensity was driven by amino acid auxotrophies shaped by biosynthetic cost trade-offs, which structured cross-feeding networks across phylogenetically distant strains. Leveraging these ecological patterns, we developed a computational model that quantifies metabolic interaction costs to predict optimal strain combinations. We characterized 15 functional lactic acid bacterial species isolated from fermented foods based on their auxotrophic profiles and interaction capacities. Synthetic communities (2-6 members) engineered via this framework exhibited superior stress resilience (e.g., resistance to osmotic pressure and lactate accumulation) and accelerated substrate utilization compared to non-cooperative communities. Resource conversion efficiency increased by 18 %-37 % in cooperative communities, driven by complementary amino acid exchange. These findings establish metabolic interdependencies as a key driver of community assembly in both natural and synthetic contexts. Our approach provides actionable insights for designing robust starter cultures tailored to industrial fermentation challenges, advancing precision control in food microbiome engineering.},
}

*Lactobacillales/metabolism/genetics
*Food Microbiology/methods
Fermentation
*Fermented Foods/microbiology
Amino Acids/metabolism
Lactic Acid/metabolism
*Microbial Consortia

@article {pmid41074189,
year = {2025},
author = {Devoy, C and McLaughlin, RA and Cronin, C and Clarke, R and Connolly, RM and Crowley, E and Raigal, L and Collins, D and Bird, B and Hennessy, BT and Tangney, M},
title = {Operational determinants of recruitment and biospecimen collection in translational observational studies: a multi-site comparative analysis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1075},
pmid = {41074189},
issn = {1479-5876},
support = {18/SP/3522//Research Ireland/ ; 18/SP/3522//Breakthrough Cancer Research/ ; 18/SP/3522//Precision Oncology Ireland/ ; },
mesh = {Humans ; *Translational Research, Biomedical ; *Specimen Handling/methods ; *Patient Selection ; *Observational Studies as Topic ; },
abstract = {BACKGROUND: Biospecimen collection from study participants is essential for translational research, but operational challenges in study setup and conduct often impede successful delivery. This study uses a comparative approach to explore key logistical and staffing factors influencing setup duration, recruitment efficiency, sample acquisition, and data completeness across three investigator-led microbiome-wide association studies (MWAS) conducted at cancer centres in Ireland.

METHODS: Three academic observational MWAS enrolling participants with cancers of the breast, gastrointestinal tract, lung, biliary system, kidney, and skin were compared. Data from three cancer centres were analysed. Key variables included study team composition, administrative infrastructure, and full-time equivalent (FTE) research staffing. Metrics assessed included setup duration, recruitment rates, sample acquisition, and data completeness. Descriptive statistics, correlation analyses, and regression models were used to examine relationships between staffing and study performance.

RESULTS: Setup duration ranged from 30 days (Site B, with a pre-established trials unit) to 390 days (Site A, with no dedicated setup personnel). At Site C, the addition of an Academic Clinical Trials Coordinator reduced the remaining setup timeline from 274 to 185 days. Recruitment rates ranged from 1.1 to 1.3 participants/month, with the highest rates at sites with dedicated research nurses (RN +). Sample acquisition was 100% at RN + sites and 70.5% at the RN- site. Site C achieved full data completeness, defined as comprehensive documentation of screening, exclusions, and follow-up outcomes. Statistical modelling suggested that dedicated staffing (both administrative and clinical) was associated with improvements across all metrics, although small sample size limited statistical significance.

CONCLUSIONS: Dedicated administrative and clinical trial personnel significantly may enhance study efficiency, participant recruitment, and biospecimen collection in academic translational research. This study provides practical insights for improving study design and infrastructure planning in future observational studies. To our knowledge, this is the first multi-site comparative evaluation of operational determinants in academic MWAS.},
}

Humans
*Translational Research, Biomedical
*Specimen Handling/methods
*Patient Selection
*Observational Studies as Topic

@article {pmid41074142,
year = {2025},
author = {Han, X and Du, L and Dou, Y and Wang, H and Lv, M and Wang, L and Xiao, J and Yin, J and Wu, J},
title = {Orally ingested nanosilica causes liver-specific accumulation and induces liver senescence and fibrosis via the microbiota-gut-liver axis.},
journal = {Journal of nanobiotechnology},
volume = {23},
number = {1},
pages = {645},
pmid = {41074142},
issn = {1477-3155},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Silicon Dioxide/administration & dosage/toxicity ; Mice ; *Liver/drug effects/metabolism/pathology ; Mice, Inbred C57BL ; Administration, Oral ; Male ; Probiotics/pharmacology ; *Liver Cirrhosis/chemically induced ; *Nanoparticles/toxicity/administration & dosage ; Dysbiosis/chemically induced ; },
abstract = {BACKGROUND: The increased use of nanosilica (SiO2 NPs) poses a safety risk to public health. Current research on the tissue distribution and microbiota-gut-liver crosstalk toxicity of orally ingested SiO2 NPs remains poorly understood. In this study, we examined the distribution of SiO2 NPs by gavage in major organs as well as liver senescence and fibrotic injury induced by microbiota-gut-liver crosstalk following the sub-chronic oral ingestion thereof. In addition, probiotics were administered to investigate their protective potential against SiO2 NPs-induced hepatotoxicity.

RESULTS: Our results showed that C57BL/6J mice that received orally administered SiO2 NPs for 12 w exhibited gut dysbiosis, imbalance of metabolites (short-chain fatty acids and lactate), intestinal barrier damage, and disruption of gut homeostasis. Furthermore, ICP-OES revealed the silicon accumulation in the Liver, with 165% increase compared to the control, higher than that in other tissue. Liver exhibited functional abnormalities and underwent Lipid deposition, autophagy, senescence and fibrosis. 16S rRNA sequencing analysis demonstrated that SiO2 NPs reduced the abundance of probiotic Muribaculum and Ligilactobacillus, while increasing that of pathogenic Helicobacter. Notably, supplementation with probiotics remodelled the gut microbiome, particularly corrected the microbial communities disrupted by SiO2 NPs, increased the proliferation of other probiotics, and reduced harmful bacteria. Moreover, the results of Masson staining, Nile red staining, and immunofluorescence showed that probiotic supplementation ameliorated liver lipid deposition, senescence, and fibrosis induced by the oral ingestion of SiO2 NPs. Mechanistically, the TLR4/NF-κB and caspase-3-cytochrome C pathways may be involved in SiO2 NPs-induced hepatotoxicity and probiotic regulation.

CONCLUSIONS: Continuous oral ingestion of SiO2 NPs induced liver-specific accumulation, and caused abnormal deposition of liver lipids, senescence and fibrosis via microbiota-gut-liver crosstalk. Microbial therapy involving probiotic supplementation mitigated SiO2 NPs-induced hepatotoxicity and exerted protective effects. This study provides a scientific reference for the rational application, risk management, and prevention of the harmful effects caused by SiO2 NPs.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Silicon Dioxide/administration & dosage/toxicity
Mice
*Liver/drug effects/metabolism/pathology
Mice, Inbred C57BL
Administration, Oral
Male
Probiotics/pharmacology
*Liver Cirrhosis/chemically induced
*Nanoparticles/toxicity/administration & dosage
Dysbiosis/chemically induced

@article {pmid41073888,
year = {2025},
author = {Michel, A and Leoz, M and Nesi, N and Petat, H and Ar Gouilh, M and Charbonnier Le Clezio, C and Marguet, C and Hassel, C and Plantier, JC},
title = {Impact of RNA extraction on respiratory microbiome analysis using third-generation sequencing.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {908},
pmid = {41073888},
issn = {1471-2164},
}

@article {pmid41073886,
year = {2025},
author = {Mao, K and Lu, G and Qiu, Q and Zang, Y and Ouyang, K and Zhao, X and Song, X and Xu, L and Liang, H and Qu, M and Li, Y},
title = {Influence of creatine pyruvate on newly received cattle: insights from metagenomics and metabolomics.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {658},
pmid = {41073886},
issn = {1471-2180},
support = {CARS-37//the China Agriculture Research System of MOF and MARA/ ; CARS-37//the China Agriculture Research System of MOF and MARA/ ; 20232BCJ23016//the Young Talents Training Program for Academic and Technical Leaders of Major Disciplines in Jiangxi Province/ ; },
mesh = {Animals ; Cattle/growth & development/microbiology ; Rumen/microbiology/metabolism ; *Creatine/pharmacology/administration & dosage ; Metabolomics ; Metagenomics ; Gastrointestinal Microbiome/drug effects ; Metabolome/drug effects ; Animal Feed/analysis ; *Pyruvic Acid/pharmacology ; Bacteria/genetics/classification/metabolism ; },
abstract = {Transport stress is a critical factor affecting the health and growth performance of beef cattle, potentially leading to oxidative stress, inflammation, and metabolic disorders. Creatine pyruvate (CrPyr), as a potential stress alleviator, has unclear mechanisms of action. We monitored the growth of 17 Simmental calves (control, n = 8; CrPyr, n = 9) over 30 days post-transportation, collecting rumen and blood samples on days 1/4, and 30. This study aims to investigate the effects of CrPyr on the growth performance, rumen microbiome, and metabolome of calves subjected to transport stress. Results showed that CrPyr increased average daily gain and antioxidant capacity, while reducing the level of stress hormones and inflammation. In the 4 days post-transport, CrPyr mainly increases Ruminococcus abundance to boost ruminal nitrogen metabolism, providing substrates for microbial protein synthesis. CrPyr also provides energy for the proliferation of Ruminococcus by regulating ATP synthesis genes (ATPVC) and enriching purine metabolism products. Meanwhile, it strengthens the host's amino acid metabolism, especially aspartate, to enhance antioxidative capacity. By day 30, CrPyr primarily boosts Prevotella abundance to regulate VFA synthesis, supplying host energy. It regulates the ATP synthesis gene ATPF0A and enriches purine metabolism products, supporting Prevotella growth. Increased citric acid and ATP levels further aid host growth. The findings distinctly demonstrate that the mechanisms by which CrPyr alleviates transport stress through the regulation of the rumen microbiome and metabolome, and confirms that its effects are time-dependent. These findings provide a theoretical basis for the development of stress-alleviation strategies based on CrPyr and hold significant implications for enhancing the health and production performance of beef cattle.},
}

Animals
Cattle/growth & development/microbiology
Rumen/microbiology/metabolism
*Creatine/pharmacology/administration & dosage
Metabolomics
Metagenomics
Gastrointestinal Microbiome/drug effects
Metabolome/drug effects
Animal Feed/analysis
*Pyruvic Acid/pharmacology
Bacteria/genetics/classification/metabolism

@article {pmid41073868,
year = {2026},
author = {Leoni, C and Marzano, M and Filomena, E and D'Erchia, AM},
title = {Digital Droplet PCR (ddPCR) for Absolute Quantification of 16S rRNA Copy Number in Metagenomic Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2969},
number = {},
pages = {235-247},
pmid = {41073868},
issn = {1940-6029},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Polymerase Chain Reaction/methods ; *Gene Dosage ; DNA Copy Number Variations ; Fluorescent Dyes/chemistry ; },
abstract = {Digital Droplet PCR (ddPCR) is a quantitative PCR method that offers high sensitivity and accuracy in measuring the amount of nucleic acid in a sample, without the need of a standard curve. In ddPCR, a single sample is partitioned into up to 20,000 droplets, using the water-oil emulsion technology, and the amplification reaction occurs within each droplet using a fluorescent hydrolysis probe (Taqman) or a DNA-binding fluorescent dye. Following PCR, the emitted signals are individually measured in each droplet. Here, we describe a ddPCR optimized protocol for accurately quantifying the total copy number of the 16S rRNA gene in a metagenomic DNA sample. The protocol utilizes a primer pair, targeting the 16S V5-V6 hypervariable regions, in combination with a double-strand DNA-binding fluorescent dye.},
}

*RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
*Polymerase Chain Reaction/methods
*Gene Dosage
DNA Copy Number Variations
Fluorescent Dyes/chemistry

@article {pmid41073842,
year = {2025},
author = {Yao, J and Yuan, M and Fan, L and Xu, X and Wu, C and Zhang, F and Liu, Z and Yao, Y},
title = {Effect of long term-consecutive monoculture on fungal community structure and function in the rhizosphere of Chinese yam.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {11},
pages = {169},
pmid = {41073842},
issn = {1572-9699},
support = {JXSNKYJCRC202206//Basic Research and Talent Training Program of Jiangxi Academy of Agricultural Sciences/ ; JXXTCX202108//Agricultural Collaborative Innovation Project of Jiangxi Province/ ; },
mesh = {*Rhizosphere ; *Dioscorea/microbiology/growth & development ; *Soil Microbiology ; *Fungi/classification/genetics/isolation & purification ; China ; *Mycobiome ; Soil/chemistry ; Phosphorus/analysis ; },
abstract = {Continuous cropping obstacle from Chinese yam (Dioscorea spp.) is widespread in China, and it seriously reduced the yield and quality. Rhizosphere soil microbiome is rich and associated with continuous cropping obstacle. However, the effect of long-term consecutive monoculture (LTCM) of Chinese yam on rhizosphere soil fungal community is still limited. In this study, fields that were consecutively cropped with Chinese yam for 1, 10 and 20 years were subjected to rhizosphere soil fungal analysis. High-throughput sequencing was used to characterize rhizosphere soil fungal community structure and function, and to determine the effect of long-term consecutive monoculture (LTCM). Results indicated that LTCM induced soil acidification, increased concentration of soil available potassium (AK) and available phosphorus (AP), increased the richness but decreased the evenness of fungal community. However, the Shannon index in YF_10Y fungal community showed the lowest value. Increasing years of monoculture resulted in significant differentiation in community composition, marked by a reduction of biocontrol fungi and an increase of pathogens. Additionally, consecutive monoculture decreased the rate of carbohydrate and amino acid degradation. The comprehensive analysis conducted in this study provides insight into rhizosphere fungal structure and function in response to LTCM of Chinese yam. Information obtained in this study could be used for the development of new microbial fertilizers for Chinese yam, which would mitigate the problems associated with continuous monoculture.},
}

*Rhizosphere
*Dioscorea/microbiology/growth & development
*Soil Microbiology
*Fungi/classification/genetics/isolation & purification
China
*Mycobiome
Soil/chemistry
Phosphorus/analysis

@article {pmid41073839,
year = {2025},
author = {Xiang, Q and Yang, K and Cui, L and Sun, AQ and Lu, CY and Gao, JQ and Hao, YL and Ma, B and Hu, HW and Singh, BK and Chen, QL and Zhu, YG},
title = {Global exploration of drought-tolerant bacteria in the wheat rhizosphere reveals microbiota shifts and functional taxa enhancing plant resilience.},
journal = {Nature food},
volume = {},
number = {},
pages = {},
pmid = {41073839},
issn = {2662-1355},
support = {2023J02029//Natural Science Foundation of Fujian Province (Fujian Provincial Natural Science Foundation)/ ; 42207143//National Natural Science Foundation of China (National Science Foundation of China)/ ; BX2021293//China Postdoctoral Science Foundation/ ; },
abstract = {Drought stress impacts plant-microbe interactions, reshaping microbial community composition and biogeochemical cycling, thereby reducing crop productivity and threatening food security. However, the specific microbial responses and roles of plant-derived metabolites remain underexplored. Here we reveal that drought stress shifts the composition of wheat-associated microbiota across the phyllosphere, rhizosphere and root endosphere by favouring Actinobacteria and Ascomycota while depleting Proteobacteria and Basidiomycota. Targeted single-cell sorting and sequencing identified 21 active drought-tolerant bacteria (DTB) enriched in genes related to plant fitness and nutrient cycling. These DTB showed significant positive correlations with drought-enriched plant phytochemicals such as jasmonic acid and pipecolic acid. Moreover, the inoculation of synthetic community including four identified drought-tolerant taxa significantly stimulates the wheat growth under drought stress. A global exploration confirmed the widespread distribution of DTB, underscoring their promising potential to enhance crop resilience. This study provides new insights into drought-induced microbiome shifts and highlights microbial candidates for improving crop resilience in a changing climate.},
}

@article {pmid41073663,
year = {2025},
author = {Yoo, JS and Jung, DJ and Goh, B and Heo, K and Zheng, W and Lee, CC and Seo, JI and Geva-Zatorsky, N and Wu, M and Park, SB and Kasper, DL and Oh, SF},
title = {Human gut bacteria produce structurally related monoglycolipids with contrasting immune functions.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41073663},
issn = {2058-5276},
support = {K01-DK102771//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R01-AT010268//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01-AI165987//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2021R1A6A3A14044113//National Research Foundation of Korea (NRF)/ ; RS-2024-00411992//National Research Foundation of Korea (NRF)/ ; RS-2024-00348702//National Research Foundation of Korea (NRF)/ ; 2021R1A6A3A14039202//National Research Foundation of Korea (NRF)/ ; RS-2023-00217123//National Research Foundation of Korea (NRF)/ ; 2014R1A3A2030423//National Research Foundation of Korea (NRF)/ ; 2012M3A9C4048780//National Research Foundation of Korea (NRF)/ ; },
abstract = {Gut symbiont Bacteroides fragilis can produce α-galactosylceramides (BfaGCs), sphingolipids with immunomodulatory functions that regulate colonic natural killer T (NKT) cells. However, their synthesis pathway and whether other human gut bacteria can produce them are unclear. Here, using genetic and metabolomic approaches, we mapped the sphingolipid biosynthesis pathway of B. fragilis and determined that α-galactosyltransferase (agcT) is essential and sufficient for colonic NKT cell regulation in mice. The distribution of agcT is restricted to only a few species among Bacteroidales. However, structural homologues of AgcT, such as BgsB, are widely distributed in gut microbiota and produce α-glycosyldiacylglycerols (aGDGs), particularly in Enterococcus. Analysis of infant gut metagenomes revealed that B. fragilis predominantly accounts for agcT abundance regardless of the cohort, but bgsB-encoding bacteria were taxonomically diverse and showed dynamic changes with host age. In addition, aGDGs from bgsB-encoding species act as antagonistic ligands for BfaGC-mediated NKT cell activation in vitro and in vivo. Our findings highlight the distinct natures of immunoactive glycolipid-producing symbionts and their relevance in the human gut microbiome, particularly in early life.},
}

@article {pmid41073374,
year = {2025},
author = {Mons, E and Henderickx, JGE and Sanders, IMJG and Rader, AG and Perkins, CE and Stel, FM and van Groesen, E and Smits, WK and Theriot, CM and Martin, NI},
title = {Experimental glycopeptide antibiotic EVG7 prevents recurrent Clostridioides difficile infection by sparing members of the Lachnospiraceae family.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9017},
pmid = {41073374},
issn = {2041-1723},
support = {NACTAR 18504//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; NACTAR 20813//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; },
mesh = {Animals ; *Clostridioides difficile/drug effects ; *Clostridium Infections/prevention & control/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Mice ; Male ; *Glycopeptides/pharmacology/therapeutic use ; Gastrointestinal Microbiome/drug effects ; Vancomycin/pharmacology/therapeutic use ; Microbial Sensitivity Tests ; Humans ; Disease Models, Animal ; Recurrence ; Mice, Inbred C57BL ; },
abstract = {Oral vancomycin has a long history as the first-line treatment for Clostridioides difficile infection (CDI), but its use is associated with high relapse rates. Antibiotics that more selectively target C. difficile while sparing protective commensal gut bacteria, have the potential to prevent recurrent CDI (rCDI). Here, we investigate the experimental glycopeptide antibiotic, EVG7, in the context of rCDI. In vitro susceptibility assays reveal that clinical C. difficile isolates are up to 16-times more sensitive to EVG7 (MIC = 0.063-0.25 mg/L) compared to vancomycin (MIC = 0.5-2 mg/L). In a validated mouse model of rCDI in male mice, low dose oral EVG7 (0.04 mg/mL in drinking water) more effectively treats primary CDI and prevents recurrence, outperforming a 10-fold higher dose of vancomycin. Subsequent microbiome analysis and in vitro susceptibility testing reveal that EVG7 preserves Lachnospiraceae, a family of commensal bacteria associated with protection against C. difficile colonization.},
}

Animals
*Clostridioides difficile/drug effects
*Clostridium Infections/prevention & control/microbiology/drug therapy
*Anti-Bacterial Agents/pharmacology/therapeutic use
Mice
Male
*Glycopeptides/pharmacology/therapeutic use
Gastrointestinal Microbiome/drug effects
Vancomycin/pharmacology/therapeutic use
Microbial Sensitivity Tests
Humans
Disease Models, Animal
Recurrence
Mice, Inbred C57BL

@article {pmid41073263,
year = {2025},
author = {Whiteside, SA and McGinniss, JE and Deek, RA and Merenstein, C and Britton, N and Simon-Soro, A and Oyster, M and Kalman, L and Brown, MC and Graham-Wooten, J and McDyer, JF and Shah, P and D'Alessio, F and Cantu, E and Clausen, ES and Li, H and Diamond, JM and Bushman, FD and Christie, JD and Collman, RG},
title = {Lung transplant for CF: Low lung bacterial burden and immune mediators in year one associate with clad development.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2025.10.002},
pmid = {41073263},
issn = {1873-5010},
abstract = {BACKGROUND: Lung transplantation is commonly required for advanced lung disease in cystic fibrosis (CF). Long-term lung allograft survival is limited primarily by chronic lung allograft dysfunction (CLAD), and microbial factors have been implicated in CLAD development. However studies have not specifically investigated CF patients despite the unique microbe-rich nature of the CF respiratory tract. We investigated whether early post-transplantation lung microbiome features associate with CLAD development.

METHODS: We investigated a longitudinal cohort of 23 CF patients undergoing lung transplantation. Lung lavage was collected from donor lungs, and from recipient allografts serially during the first year post-transplantation. Patients were followed for a median of 4.9 years. This was complemented by a case-control study of 8 CF patients sampled at incident CLAD along with non-CLAD CF transplant controls. Lung bacteria were enumerated by 16S rRNA gene sequencing and quantified by qPCR, and immune mediators investigated by multiplex assay.

RESULTS: Cohort patients who developed CLAD had lower lung bacterial burden, lower relative abundances of classic CF lung microbiota, and lower mediator levels during the first-year post-transplantation than those remaining CLAD-free. In contrast, incident CLAD showed elevated lung immune mediators but no microbiome differences.

CONCLUSIONS: Low lung bacterial content and immune mediators during the first year post-transplantation for CF associate CLAD, whereas CLAD onset is characterized by elevated immune mediators but no lung microbiome differences. Whether airway bacteria early after transplantation for CF may protect against CLAD or serve as a biomarker merits further study.},
}

@article {pmid41072892,
year = {2025},
author = {Yao, H and Su, Q and Dai, Q and Li, L and Li, D},
title = {Thallium exposure disturbs gut microbiota composition, metabolic function, and host gut energy metabolism in aged mice.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {},
number = {},
pages = {115793},
doi = {10.1016/j.fct.2025.115793},
pmid = {41072892},
issn = {1873-6351},
abstract = {Gut microbiota regulates the development of environmental exposure-induced diseases. Although previous studies have reported the effect of thallium exposure on the gut microbiota of adult male mice, its effects on the aging gut microbiome, particularly in females, remain largely unexplored. Here, we showed that thallium exposure for 4 weeks altered fecal microbial β diversity in aged female and male mice, whereas a 2-week exposure did not. Combined LEfSe and indicator analyses revealed that in aged female mice, thallium exposure for 2 weeks increased Oscillibacter abundance, while exposure for 4 weeks increased the abundance of Lactobacillus, Limosilactobacillus, Adlercreutzia, and Priestia. In aged male mice, thallium exposure for 2 weeks increased the abundance of Rikenella, Bifidobacterium, Proteus, Enterococcus, and Chryseobacterium, while exposure for 4 weeks increased the abundance of Incertae_Sedis, Bifidobacterium, Clostridium, Christensenellaceae_R-7_group, and UCG-009. PICRUSt2 functional prediction analysis showed that thallium exposure may also affect energy metabolism-related pathways in gut bacteria. Thallium exposure significantly decreased C16:1 abundance in the colon, but not in the cecum, of aged male mice. Protein levels revealed that thallium exposure enhanced glycolysis in the cecum and colon of aged mice. Collectively, our findings reveal significant thallium-induced perturbations in the gut ecosystem and host metabolism in both the aged male and female cohorts, which may contribute to understanding thallium-induced health risks in the elderly.},
}

@article {pmid41072887,
year = {2025},
author = {Farzizadeh, N and Najmi, Z and Rosenbaum, AJ and Amoozgar, M and Hariri, A and Aminbeidokhti, M and Khosravi, A and Zarrabi, A},
title = {Decoding Preterm Birth: Non-Invasive Biomarkers and Personalized Multi-Omics Strategies.},
journal = {Developmental biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ydbio.2025.10.006},
pmid = {41072887},
issn = {1095-564X},
abstract = {A birth that occurs prior to 37 weeks of gestation is referred to as preterm birth (PTB). PTB is a health concern globally with significant outcomes including neonatal morbidity and mortality. Advancements in multi-omics have revolutionized the understanding of PTB pathogenesis, offering new opportunities for early prediction and risk categorization. This review highlights emerging liquid biomarkers derived from proteomic, metabolomic, genomic, transcriptomic, and epigenomic studies, emphasizing the integrative power of multi-omics approaches. Proteomic analyses have revealed key proteins in maternal and fetal compartments associated with inflammatory and extracellular matrix pathways, while metabolomics have identified lipid and metabolite profiles linked to energy metabolism and fetal development. Genomic and epigenomic studies have uncovered genetic variations and microRNAs involved in uterine contractility and immune modulation, providing novel insights into PTB's molecular underpinnings. Transcriptomic research further underscores the act of long non-coding RNAs (ncRNAs) in regulating gene expression and inflammatory responses. Multi-omics integration, coupled with machine learning models, has demonstrated superior predictive accuracy by synthesizing data across these domains, revealing intricate molecular interactions underlying PTB. Future research should prioritize longitudinal multi-omics studies to capture dynamic biological changes during pregnancy, expanding diverse population cohorts to enhance generalizability. Translating multi-omics insights into clinical practice necessitates collaborative efforts to develop cost-effective, accessible biomarker panels and establish standardized guidelines for implementation. These advancements hold the potential to transform prenatal care through personalized risk assessment and targeted preventive strategies, reducing the global burden of PTB.},
}

@article {pmid41072704,
year = {2025},
author = {Chalif, J and Morton, M and Haight, P and Mehra, Y and O'Malley, D and Spakowicz, D and Chambers, L},
title = {Assessment of Probiotic and Prebiotic Use in Gynecologic Cancer Patients: A Systematic Review.},
journal = {American journal of obstetrics and gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajog.2025.09.042},
pmid = {41072704},
issn = {1097-6868},
abstract = {OBJECTIVE: To evaluate evidence on the impact of probiotics and prebiotics on clinical outcomes, treatment efficacy, quality of life, safety, and translational endpoints in patients with gynecologic cancers.

DATA SOURCES: A systematic search of PubMed, Embase, and Scopus was conducted in March 2023 and updated through September 2025. Grey literature sources (ClinicalTrials.gov, reference lists) were also reviewed.

STUDY ELIGIBILITY CRITERIA: Eligible studies included randomized controlled trials (RCTs) and prospective interventional studies in women with gynecologic cancers (cervical, endometrial, ovarian, uterine, vulvar) undergoing treatment. Interventions were probiotic, prebiotic, or dietary fiber supplementation. Eligible outcomes included treatment toxicity, stool consistency, quality of life, postoperative outcomes, oncologic outcomes, safety, and microbiome endpoints. Exclusions were retrospective studies, case reports, reviews, conference abstracts, and studies without cancer-related outcomes.

Three independent reviewers screened studies using Covidence, with disagreements resolved by consensus or adjudication. Risk of bias was assessed with the Cochrane RoB 2.0 tool. Due to heterogeneity in strains, dosing, and outcomes, structured narrative synthesis was conducted rather than meta-analysis.

RESULTS: From 2,308 screened records, nine RCTs involving 663 patients were included. Seven studies evaluated probiotics and two assessed prebiotics/fiber. Most focused on radiation-induced toxicity in cervical (n=415) and endometrial cancer (n=170) patients. Probiotics significantly reduced incidence and severity of radiation-induced diarrhea, improved stool consistency, and decreased anti-diarrheal use (p<0.05). Prebiotics alone showed minimal benefit. One perioperative study found probiotics accelerated bowel recovery and reduced postoperative complications. Three translational studies showed probiotics reduced gut permeability but did not alter microbial composition. No trials examined chemotherapy or immunotherapy outcomes, progression-free survival, or overall survival. Adverse events were infrequent and no major safety concerns were identified.

CONCLUSIONS: Probiotic supplementation demonstrates consistent benefit in reducing radiation-induced gastrointestinal toxicity in gynecologic cancer patients, while prebiotics alone show limited efficacy. Evidence gaps include effects on chemotherapy, immunotherapy, oncologic outcomes, and survival. Heterogeneity in formulations limits clinical applicability, and standardized strain-specific trials are needed. Future research should evaluate long-term oncologic outcomes, optimize microbiome-directed interventions, and establish safety in immunocompromised populations.},
}

@article {pmid41072671,
year = {2025},
author = {Hu, Z and Lei, Y and Li, T and Zhang, T and Yang, Q and Yang, J and Huang, G and Guan, D and Zou, J},
title = {Strategic intercropping with mulberry (Morus alba L.) predictably modulates rhizosphere microbiome assembly and enriches pathways for secondary metabolite production.},
journal = {Genomics},
volume = {},
number = {},
pages = {111129},
doi = {10.1016/j.ygeno.2025.111129},
pmid = {41072671},
issn = {1089-8646},
abstract = {Intercropping is a key strategy for sustainable agriculture, but its effects on the rhizosphere microbiome remain poorly understood. Here, we investigated how intercropping mulberry (Morus alba L.) with functionally distinct partners-a nitrogen-fixing legume (Pisum sativum), a saprotrophic fungus (Morchella esculenta), and a medicinal plant (Polygonatum sibiricum)-shapes its rhizosphere bacterial community. Compared to monoculture, all intercropping systems significantly increased bacterial diversity and established unique community structures and functional signatures. Legume intercropping specifically enriched nitrogen-cycling bacteria like Bradyrhizobium and enhanced nitrogen metabolism pathways, whereas fungal intercropping fostered anaerobic decomposers. Crucially, all systems enriched pathways for secondary metabolite biosynthesis, suggesting a potential to enhance mulberry's economic value. Our findings establish that strategic partner selection is a powerful microbiome design tool, enabling predictable modulation of rhizosphere function for sustainable mulberry cultivation.},
}

@article {pmid41072644,
year = {2025},
author = {Zhou, X and Gao, B and Cui, H and Huang, FY and Rensing, C and Zhao, Y and Guo, H},
title = {Antibiotic resistome, potential pathogenic bacteria and associated health risk in geogenic chromium groundwater.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123016},
doi = {10.1016/j.envres.2025.123016},
pmid = {41072644},
issn = {1096-0953},
abstract = {Geogenic chromium (Cr) contamination in groundwater poses a global environmental challenge. However, with antibiotic resistance remaining a public health threat, the occurrence and associated health risks of antibiotic resistomes in Cr contaminated groundwater and their linkages to geogenic Cr are poorly understood. Here, we assessed the groundwater microbiome, potential pathogenic bacteria, and antibiotic resistomes with associated health risks in geogenic Cr impacted groundwater across shallow (< 100 m) and deep (> 100 m) aquifers in a plateau from Northwestern China. A total of 174 antibiotic resistance genes (ARGs) were detected with absolute abundances reaching 1.28×10[8] copies/L. Shallow and deep groundwater harbored distinct ARG profiles with significantly higher abundance and associated health risks presented in shallow groundwater (p < 0.01). A total of 332 potential pathogenic bacteria were identified, abundances of which 53.9% were strongly correlated to the prevalent ARGs. Toxic Cr(VI) as a potential co-selective agent was positively associated with elevated ARG-linked potential pathogenic bacteria and mobile genetic elements (MGEs). Our findings collectively revealed the geogenic Cr contaminated groundwater as a significant reservoir of ARGs and potential pathogens, highlighting the dual risks of geogenic Cr as both a toxicant and promoter for accelerating ARGs within aquifers.},
}

@article {pmid41072600,
year = {2025},
author = {Wang, Y and Wang, X and Gan, B and Jia, T and Xu, T and Xu, H},
title = {The "Butterfly Effect" of Heart Failure: Induced by the Combination of Polylactic Acid Nanoplastics and Copper from the Perspective of Gut Microbiome.},
journal = {Chemico-biological interactions},
volume = {},
number = {},
pages = {111769},
doi = {10.1016/j.cbi.2025.111769},
pmid = {41072600},
issn = {1872-7786},
abstract = {Plastic and heavy metal pollution have received extensive attention, but there is relatively little research on the damage to the gut-heart axis induced by the co-exposure to plastics and heavy metals. This study investigated the impact of the co-exposure of Polylactic acid nanoplastics (PLA-NPs) and copper (Cu) on heart failure (HF) in mice and explored the role of the gut microbiota in mediating this adverse outcome. Male C57BL/6J mice were divided into four groups: the Control group, the PLA-NPs group, the Cu group, and the Co-exposure group (PLA-NPs+Cu group). A 28-day exposure experiment was conducted. The research results indicate that, compared with the Single-exposure groups (PLA-NPs and Cu groups), the mice of Co-exposure group exhibited more severe toxic effects, including more pronounced myocardial hypertrophy and more severe myocardial fibrosis. These damages might be caused by increasing the heart's sensitivity to ferroptosis. Additionally, the co-exposure caused significant damage to the gut barrier and remarkable dysbiosis in the gut microbiota, such as a reduction in the abundances of beneficial bacteria like Lactobacillus. The fecal Microbiota Transplantation experiment confirmed that the alterations in gut microbiota play a pivotal role in the synergistic toxicity induced by PLA-NPs and Cu. This study for the first time reveals the mechanism of the combined effect of PLA-NPs and Cu on cardiac damage and emphasizes the crucial role of gut microbiota in this process.},
}

@article {pmid41072563,
year = {2025},
author = {Dedeepya, SD and Goel, V and Desai, NN},
title = {Comment on "Beyond beauty: Neurocosmetics, the skin-brain axis, and the future of emotionally intelligent skincare".},
journal = {Clinics in dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clindermatol.2025.10.001},
pmid = {41072563},
issn = {1879-1131},
}

@article {pmid41072405,
year = {2025},
author = {Li, W and Zheng, S and Xu, X and He, J and Jiao, X and Wang, M and Hu, W and Li, S and Jiang, X and Lim, B and Shao, F and Gao, X},
title = {A conserved adaptor orchestrates co-secretion of synergistic type VI effectors in gut Bacteroidota.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.09.012},
pmid = {41072405},
issn = {1934-6069},
abstract = {Interbacterial competition is crucial for shaping microbial communities and is often mediated by type VI secretion systems (T6SSs) that inject effectors into competing bacteria. T6SS effectors are released via structural proteins such as VgrG, but the secretion timing and coordination are unclear. Here, we report two effectors, BtpeA (Bacteroides T6SS phosphatase effector A) and BtaeB (Bacteroides T6SS amidase effector B), within the Bacteroidota T6SS that exert distinct cell-wall destructive activities critical for interspecies competition but whose secretion is interdependent. BtpeA and BtaeB co-secretion requires an adaptor protein, BtapC (Bacteroides T6SS adaptor protein C), that mediates the sequential assembly of the pre-firing complex, VgrG-BtpeA-BtaeB-BtapC. Structural analyses of this quaternary complex elucidate multi-cargo loading mechanisms with a conserved loop in BtaeB serving as a "checkpoint" to ensure BtpeA co-secretion. During mouse colonization, the combined activities of BtpeA and BtaeB significantly exceed the sum of the individual effectors. These findings unveil a T6SS-mediated co-delivery mechanism that ensures functional synergism of effectors, highlighting potential applications in modulating gut microbiota.},
}

@article {pmid41072356,
year = {2025},
author = {Cheng, M and Pan, C and Peng, J and Dong, T and Di, X and Chen, Q and Liu, Z},
title = {Gut microbiome and serum metabolome changes in gestational diabetes mellitus after diet-exercise intervention.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {268},
number = {},
pages = {117172},
doi = {10.1016/j.jpba.2025.117172},
pmid = {41072356},
issn = {1873-264X},
abstract = {Gestational diabetes mellitus (GDM) poses risks to both the mother and fetus. Diet and exercise interventions (DEI) improve blood glucose control and pregnancy outcomes, but the underlying mechanisms, especially those involving the gut microbiota and serum metabolites, are unclear. In this study, we conducted a comparative analysis of pre- and post-DEI outcomes by assessing HbA1c, fasting glucose, the diversity and functional pathways of the gut microbiota, and serum metabolomics. Post-DEI, the women maintained normal glycemic levels without delivery complications or adverse neonatal outcomes. The gut microbiota alpha/beta diversity remained stable, although the abundances of specific species (e.g., Faecalibacterium sp. and Prevotellamassilia sp.) and functional pathways (e.g., flavonoid biosynthesis and bacterial chemotaxis) were altered. Metabolomics identified 132 differentially regulated metabolites (83 upregulated and 49 downregulated) enriched glycerophospholipids, steroids and steroid derivatives, fatty acyls, and carboxylic acids and derivatives. In conclusion, while DEI did not significantly alter the gut microbial community structure, it potentially exerted targeted modulatory effects on specific microbial functions in women with GDM. Furthermore, DEI also induced alterations in serum metabolites and associated metabolic functions.},
}

@article {pmid41072219,
year = {2025},
author = {Wang, T and Yang, Y and Hou, J and Yin, L},
title = {Lotus leaf extract (LLE) alleviates obesity through gut flora and its metabolites.},
journal = {Food chemistry},
volume = {495},
number = {Pt 3},
pages = {146433},
doi = {10.1016/j.foodchem.2025.146433},
pmid = {41072219},
issn = {1873-7072},
abstract = {In this study, we investigated the effects of lotus leaf extract (LLE) on HFD (high-fat diet)-induced obese mice and the metabolic functions of the gut microbiome on LLE. We found that LLE alleviates obesity partly through interactions with the gut microbiota. Oral LLE modulates gut microbiota structure and counteracts HFD-induced dysbiosis. Furthermore, we observed a significant increase in serum levels of O-Nornuciferine in LLE-treated mice, suggesting that the gut microbiota may play a potential role in metabolising LLE components to enhance the production of this metabolite. O-Nornuciferine was associated with improvements in dyslipidemia and hepatic steatosis. Molecular docking analysis indicated that O-Nornuciferine may bind to PGC-1α (peroxisome proliferator-activated receptor γ coactivator-1α) in the liver and influence the expression of genes related to lipid metabolism. These results highlight the potential interplay between LLE and gut microbiota, and suggest that microbiota-derived O-Nornuciferine may contribute to the modulation of hepatic lipid metabolism.},
}

@article {pmid41072215,
year = {2025},
author = {Wang, Q and Gao, F and Zhu, D and Ren, H and Xu, Y and Lou, M and Fei, C and Xu, X and Yu, Z and Ren, Z},
title = {Alterations in the oral microbiome detected during long-term follow-up of COVID-19 recovered patients.},
journal = {Journal of infection and public health},
volume = {18},
number = {12},
pages = {102983},
doi = {10.1016/j.jiph.2025.102983},
pmid = {41072215},
issn = {1876-035X},
abstract = {BACKGROUND: The oral biome was significantly altered in COVID-19 patients, but there is still a gap in long-term follow-up studies of the oral microbiota of recovering patients.

METHODS: We recruited 62 patients with a confirmed COVID-19 diagnosis and collected tongue moss samples at three time points: 1 month (RP1), 3 months (RP3) and 5 months (RP5) of rehabilitation. We then sequenced the tongue samples for 16S rRNA amplicons.

RESULTS: The results showed that there was no significant difference in the oral microbial composition of patients who had been rehabilitated for 3 months compared to those who had been rehabilitated for 1 month, whereas patients who had been rehabilitated for 5 months showed a significant increase in the diversity of the oral microbiome compared to those who had been rehabilitated for 1 month. In addition, we characterized the dynamics of the oral microbiome of COVID-19 patients during their rehabilitation.

CONCLUSION: As patients recover, the diversity of their oral microbiome gradually returns to normal, providing microbiological evidence for the clinical diagnosis and treatment strategies of COVID-19.},
}

@article {pmid41072201,
year = {2025},
author = {Murawska-Wlodarczyk, K and Kushwaha, P and Stokes, O and Rasmussen, C and Neilson, JW and Maier, RM and Babst-Kostecka, A},
title = {Depth-dependent heterogeneity in topsoil stockpiles influences plant-microbe interactions and revegetation success in arid mine reclamation.},
journal = {The Science of the total environment},
volume = {1003},
number = {},
pages = {180673},
doi = {10.1016/j.scitotenv.2025.180673},
pmid = {41072201},
issn = {1879-1026},
abstract = {Covering mine tailings with uncontaminated soil is a common strategy to mitigate environmental impacts and promote ecosystem recovery during post-mining land reclamation. Topsoil is often stockpiled for future use as a capping layer, but prolonged storage alters its physical, chemical, and microbial properties, often hindering revegetation. This study evaluated soil health parameters within the 28-meter depth profile of a 14-year-old copper mine topsoil stockpile to identify key indicators of revegetation success in semi-arid ecosystem. Using non-invasive root phenotyping in rhizoboxes, filled with soils collected from different depth layers, we monitored plant growth and assessed how biochemical variability in stockpile materials affects germination and early establishment. Machine learning models integrating soil properties, plant responses, and sequenced soil bacterial/archaeal and fungal DNA, identified key indicators influencing plant performance. Results revealed significant heterogeneity in soil quality across depths, with distinct biochemical and microbial profiles shaping vegetation establishment. The upper 10 m exhibited greater potential for supporting growth, with seedling survival reaching 95 %, whereas deeper layers showed drastically reduced survival, sometimes as low as 0 %, due to microbial shifts to anoxic conditions and elevated Fe and Mn toxicity. Fungal communities played a dominant role in germination, while archaea were more influential during later plant establishment. Soil parameter comparisons before and after the experiment indicated recovery processes initiated by plant-soil feedback, including fungal community renewal. These findings highlight the role of stockpile formation in preserving soil health attributes critical for ecological recovery and provide practical insights for optimizing land reclamation in semi-arid ecosystems.},
}

@article {pmid41072166,
year = {2025},
author = {Garg, V and Armstrong, E and Celeste, A and Wang, C and Shukla, A and Tesfu, A and Odujoko, O and Madariaga, A and Lee, YC and Wang, L and Alqaisi, H and Soberanis, P and Grant, B and Braik, D and Chawla, T and Shlomovitz, E and Veneziani, A and Dhani, N and Grant, R and Jivraj, N and Bowering, V and Oza, AM and Allard, JP and Coburn, B and Lheureux, S},
title = {Multidisciplinary ambulatory management of malignant bowel obstruction (MAMBO) program in patients with advanced gynecological cancers: A prospective study.},
journal = {Gynecologic oncology},
volume = {202},
number = {},
pages = {110-117},
doi = {10.1016/j.ygyno.2025.09.012},
pmid = {41072166},
issn = {1095-6859},
abstract = {OBJECTIVES: This prospective study aimed to assess the feasibility of a risk-stratified, multidisciplinary ambulatory approach for managing malignant bowel obstruction (MBO) in patients with advanced gynecological cancer.

METHODS: A clinical risk-based MBO triage system was implemented by incorporating bowel function assessments, management regimes, and educational tools. An interdisciplinary team (IDT) guided treatment decisions. At risk patients received proactive management through nursing phone calls for up to 4 weeks, while patients with MBO continued proactive management for up to 8 weeks based on symptom resolution. The primary endpoint was the ratio of days alive and out of the hospital to days in the hospital within 60 days post-MBO diagnosis.

RESULTS: 92 patients (median age 62 years [range 31-83]) were enrolled. At enrollment, 49 % (n = 45) had MBO, and 51 % (n = 47) were at risk of MBO development. 7 % (n = 3) at-risk patients progressed to MBO in 4 weeks, while 93 % had symptom resolution with proactive outpatient management. Overall, 62 % (n = 57) of patients developed MBO during study period. Among these, 93 % (n = 53) needed inpatient care, with a median stay of 12.5 days (range 0-57) in the first 60 days. Median OS after MBO was 5.7 months (95 % CI, 3.6-8.4). The median of hospital-to-home ratio was 0.3 (range 0-19) within 60 days. MBO resolved in 42 % (n = 24) of the patients. Microbiome analysis showed lower Shannon diversity and species richness for MBO patients compared to those at risk.

CONCLUSION: This study confirms the feasibility of ambulatory management for MBO patients, using a risk-based MBO triage system guided by IDT.},
}

@article {pmid41072064,
year = {2025},
author = {Rezaie Pouya, M and Aghelan, Z and Hoseini, S and Rastegari, A and Khazaie, H},
title = {Associations of serum α-synuclein and 1,3-β-D-glucan levels with sleep architecture alterations in chronic insomnia disorder.},
journal = {Behavioural brain research},
volume = {496},
number = {},
pages = {115869},
doi = {10.1016/j.bbr.2025.115869},
pmid = {41072064},
issn = {1872-7549},
abstract = {BACKGROUND: Chronic insomnia disorder (CID) is a widespread sleep disorder linked to increased risks of various chronic diseases and often precedes neurodegenerative conditions such as Parkinson's and Alzheimer's disease. Emerging evidence suggests that gut microbiome disturbances contribute to CID through the gut-brain axis, involving microbial metabolites and neuroactive proteins.

OBJECTIVES: This study explored the relationships between serum 1,3-β-D-glucan (a marker of intestinal permeability and microbial translocation), alpha-synuclein (αSyn, a neuronal protein implicated in neurodegeneration), and sleep architecture in chronic insomnia individuals compared to healthy controls.

METHODS: Blood samples were taken from 15 people who had been diagnosed with CID, based on their results from the Pittsburgh Sleep Quality Index (PSQI) and video-polysomnography tests. For comparison, blood was also collected from 15 healthy volunteers, whose sleep quality was assessed using the PSQI. Serum concentrations of 1,3-β-D-glucan and αSyn protein were measured using enzyme-linked immunosorbent assay (ELISA).

RESULTS: The findings showed significantly elevated serum 1,3-β-D-glucan (p < 0.0001) and αSyn (p < 0.001) levels in the CID group, with a strong positive correlation between these markers (r = 0.964, p < 0.01). Moreover, increased αSyn levels were associated with alterations in sleep stages, particularly prolonged rapid eye movement (REM) sleep duration (r = 0.560, p < 0.05).

CONCLUSIONS: These findings support a mechanistic link between gut microbiota disruption, αSyn pathology, and altered sleep architecture in CID, highlighting novel pathways for understanding the neuroimmune mechanisms underlying sleep disturbances. Serum 1,3-β-D-glucan and αSyn may serve as potential biomarkers for identifying insomniac individuals at risk of synucleinopathies and offer novel targets for therapeutic intervention aimed at restoring gut health and improving sleep quality.},
}

@article {pmid41071924,
year = {2025},
author = {de Kroon, RR and Kreulen, IAM and Davids, M and van Thiel, IAM and Admiraal, I and Verdoes, X and van Weissenbruch, MM and Niemarkt, H and de Jonge, WJ and de Meij, T and , },
title = {The gut as a source of infection for fungal pathogens: increased fecal Candida albicans precedes onset of Candida late-onset sepsis in very preterm infants.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf524},
pmid = {41071924},
issn = {1537-6613},
abstract = {BACKGROUND: The skin-to-blood route is traditionally considered the main pathway in Candida late-onset sepsis (LOS) development in preterm infants. However, emerging evidence suggests that the gut also serves as a source of infection. We aimed to characterize fecal mycobiota and microbiota profiles preceding onset of Candida LOS to assess the role of the preterm gut microbiome in disease development.

METHODS: In this multicenter, case-control study, very preterm infants (<30 weeks of gestation) with Candida LOS were included. Each case was matched to non-affected controls by gestational and postnatal age, hospital site, and/or cumulative antibiotic exposure prior to day of LOS onset (t=0). Fecal samples collected at t=0 and the five preceding days were analyzed using ITS1 and 16S RNA sequencing. Microbial amplicon yields, composition, and inter-kingdom correlations were assessed.

RESULTS: Of 2,397 screened infants, fecal samples were available for 8/19 infants with Candida LOS. In these 8 cases, the ITS/16S amplicon yield ratio was increased (p<0.001) and the relative abundance of fecal Candida albicans correlated positively with fungal amplicon yield (ρ=0.71, padj=0.005), suggesting increased absolute abundance up to five days before onset. Additionally, bacterial yields were significantly lower (p=0.02) and α-diversity was significantly decreased (p=0.012), compared to the controls.

CONCLUSIONS: Increased fecal C. albicans preceded Candida LOS onset, implicating the preterm gut as a potential source of infection. Reduced bacterial yields and diversity suggest ecological alterations that may facilitate Candida pathogenicity in the preterm gut. These findings support further research into gut-derived Candida LOS and potential for microbiota-targeted prevention strategies.},
}

@article {pmid41071776,
year = {2025},
author = {Zhang, CR and Wang, M and Wang, L and Liu, L and Shen, YD and Chen, RF and Ren, S and Jin, WZ and Tang, HC and Wu, QG},
title = {Differential composition of the pulmonary microbiome in HIV-positive versus HIV-negative patients with Pneumocystis jirovecii.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0334220},
doi = {10.1371/journal.pone.0334220},
pmid = {41071776},
issn = {1932-6203},
mesh = {Humans ; *Pneumocystis carinii/isolation & purification ; Male ; Female ; Middle Aged ; *Microbiota ; *Pneumonia, Pneumocystis/microbiology/complications ; *HIV Infections/microbiology/complications ; Adult ; Bronchoalveolar Lavage Fluid/microbiology ; *Lung/microbiology/virology ; Coinfection/microbiology ; High-Throughput Nucleotide Sequencing ; Aged ; },
abstract = {Pneumocystis jirovecii is frequently detected in HIV patients and individuals with compromised immune function. The clinical outcomes of these two groups differ significantly, yet the underlying reasons remain unclear, with limited studies addressing this issue. This study investigates the alterations in the pulmonary microbiota of HIV-positive and non-HIV patients following pneumocystis jirovecii infection.Collect bronchoalveolar lavage fluid from patients with HIV and non HIV infected Pneumocystis jirovecii, and compare the differences in pulmonary microbiota between the two groups.In total, 77 patients with pulmonary infection that had next generation sequencing performed on their bronchoalveolar lavage fluid and confirmed pneumocystis jirovecii infection were recruited in our study. Of the 77 patients with pneumocystis jirovecii infection, 52 were infected with HIV, and 25 were uninfected.Our findings indicate that HIV-positive patients exhibit a more diverse microbiota, predominantly characterized by viral co-infections. Specifically, 88.5% of HIV-positive patients experienced viral co-infections, primarily involving herpes viruses, followed by bacterial (61.5%) and fungal (40.4%) co-infections. In contrast, non-HIV patients predominantly exhibited bacterial co-infections (72%), followed by viral (52%) and fungal (36%) co-infections. By analyzing the next generation sequencing data of both groups, we identified statistically significant differences in viral infections (p < 0.001), while no significant differences were observed for bacterial or fungal infections. Furthermore, among the background bacteria detected via next generation sequencing in both patient groups, 22 microbial species were commonly present. Notably, Leptospiral virus, Rosette fungus, and Actinomycetes were detected at higher frequencies in HIV-infected pneumocystis jirovecii patients, with statistically significant differences.Through comparing the pulmonary microbiota profiles of HIV-positive and non-HIV patients post-pneumocystis jirovecii infection, we uncovered distinct differences between the two groups, which may hold implications for guiding subsequent treatment strategies and improving clinical outcomes.},
}

Humans
*Pneumocystis carinii/isolation & purification
Male
Female
Middle Aged
*Microbiota
*Pneumonia, Pneumocystis/microbiology/complications
*HIV Infections/microbiology/complications
Adult
Bronchoalveolar Lavage Fluid/microbiology
*Lung/microbiology/virology
Coinfection/microbiology
High-Throughput Nucleotide Sequencing
Aged

@article {pmid41071577,
year = {2025},
author = {Anderer, S},
title = {Sugary Drinks May Influence Depression Through Gut Microbiome.},
journal = {JAMA},
volume = {},
number = {},
pages = {},
doi = {10.1001/jama.2025.17494},
pmid = {41071577},
issn = {1538-3598},
}

@article {pmid41071558,
year = {2025},
author = {Anderer, S},
title = {Oral Microbiome Composition Linked to Pancreatic Cancer Risk.},
journal = {JAMA},
volume = {},
number = {},
pages = {},
doi = {10.1001/jama.2025.19069},
pmid = {41071558},
issn = {1538-3598},
}

@article {pmid41071528,
year = {2025},
author = {Amani, A and Koroupi, K and Langarizadeh, MA and Aghilinasab, A and Ranjbar Tavakoli, M and Afshari, A and Forootanfar, H},
title = {Exploring the Therapeutic Potential of Diverse Bacterial Strains for Management of Periodontal Diseases.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41071528},
issn = {1867-1314},
abstract = {Periodontal diseases, including gingivitis and periodontitis, are among the most prevalent oral health problems worldwide and are associated with chronic inflammation and tooth loss. Increasing attention has been directed toward the role of the human microbiota, particularly the oral microbiota, in influencing periodontal health and disease. This manuscript presents a narrative review that synthesizes and critically evaluates the available evidence on the therapeutic potential of diverse bacterial strains, with special emphasis on probiotics, as adjunctive agents in the management of periodontal disease. Literature was identified through searches of PubMed and Google Scholar, with priority given to more recent studies. The review discusses host-microbiota interactions, oral microbiome characteristics, immunomodulatory effects of probiotics, and strain-specific outcomes related to periodontal indices. While a number of bacterial strains, including Lactobacillus reuteri, Lactobacillus rhamnosus, Bifidobacterium, and selected Streptococcus species, demonstrate potential benefits in reducing plaque accumulation, inflammation, and clinical attachment loss, the findings across studies remain heterogeneous. Overall, probiotics and related microbial strategies represent a promising adjunct to conventional periodontal therapies; however, more standardized and long-term clinical trials are required before firm conclusions can be drawn.},
}

@article {pmid41071393,
year = {2025},
author = {Wasim, R},
title = {The gut immune axis in ulcerative colitis: insights from microbiome research.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {1006},
pmid = {41071393},
issn = {1573-4978},
mesh = {Humans ; *Colitis, Ulcerative/microbiology/immunology/therapy ; *Gastrointestinal Microbiome/immunology ; Fecal Microbiota Transplantation/methods ; Dysbiosis/microbiology/immunology ; Probiotics/therapeutic use ; Intestinal Mucosa/immunology/microbiology ; Prebiotics ; Animals ; },
abstract = {Ulcerative colitis (UC) is a chronic, recurrent inflammatory bowel disease (IBD) marked by inflammation of the colonic mucosa. While its precise aetiology remains unclear, emerging evidence underscores the pivotal role of gut microbiota in UC pathogenesis. In healthy individuals, the gut microbiota contributes to immune modulation, nutrient absorption, and maintenance of intestinal barrier integrity. In contrast, individuals with UC exhibit gut dysbiosis-characterized by a reduction in beneficial bacteria such as Faecalibacterium prausnitzii and Bifidobacterium, and an increase in potentially pathogenic microbes like Escherichia coli. This microbial imbalance disrupts mucosal homeostasis, promotes persistent inflammation, and impairs epithelial healing. Contributing factors include genetic predisposition, antibiotic exposure, diet, and environmental influences. Novel microbiota-targeted interventions-such as probiotics, prebiotics, dietary modifications, and faecal microbiota transplantation (FMT)-are being actively explored, with promising preliminary outcomes in symptom relief and microbiome restoration. However, challenges persist in defining a "healthy" microbiome and standardizing therapeutic protocols. This study highlights the potential of microbiome modulation as a transformative approach in UC management and calls for further research into host-microbe interactions to advance precision-based, microbiota-oriented therapies.},
}

Humans
*Colitis, Ulcerative/microbiology/immunology/therapy
*Gastrointestinal Microbiome/immunology
Fecal Microbiota Transplantation/methods
Dysbiosis/microbiology/immunology
Probiotics/therapeutic use
Intestinal Mucosa/immunology/microbiology
Prebiotics
Animals

@article {pmid41071238,
year = {2025},
author = {Ikarashi, N and Kon, R and Sakai, H and Hosoe, T},
title = {Role of the gut microbiota in the pharmacological effects of traditional Kampo medicine and natural products.},
journal = {Journal of natural medicines},
volume = {},
number = {},
pages = {},
pmid = {41071238},
issn = {1861-0293},
abstract = {The human gastrointestinal tract harbors over a thousand coexisting bacterial species that together constitute a highly complex intestinal microbiome. Dysbiosis of this microbial ecosystem has been implicated in the pathogenesis of disorders such as ulcerative colitis and obesity and has driven the development of microbiota-targeted prevention and treatment strategies. Traditional Kampo medicines are used with the aim of restoring the balance of the whole body, having been developed and established uniquely in Japan based on traditional Chinese medicine with a history of over two millennia. Recent evidence has revealed that the gut microbiota plays critical roles in the pharmacological effects of traditional Kampo medicines. For example, the anti-obesity activity of Bofutsushosan has been linked to an increase in Akkermansia muciniphila. The laxative effect of Daiokanzoto is related to rheinanthrone, which is produced from sennoside A through the gut microbiota, and drugs and foods that can alter the gut microbiota change the laxative activity of Daiokanzoto. In recent years, clinical trials have been conducted to examine the relationship between changes in the gut microbiota and the pharmacological effects of Kampo medicines, and this relationship has come to the forefront. This review discusses the findings of basic and clinical research on the role of the gut microbiota in the pharmacological action of traditional Kampo medicines, focusing on Bofutsushosan, Daiokanzoto, Daikenchuto, and Hangeshashinto, and discusses future issues and prospects for research into these interactions.},
}

@article {pmid41071209,
year = {2025},
author = {Bautista, J and Ojeda-Mosquera, S and Altamirano-Colina, A and Hidalgo-Tinoco, C and Di Capua Delgado, M and López-Cortés, A},
title = {Bidirectional interactions between circadian rhythms and the gut microbiome.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {218},
pmid = {41071209},
issn = {1432-0614},
mesh = {*Gastrointestinal Microbiome/physiology ; *Circadian Rhythm/physiology ; Humans ; Animals ; Circadian Clocks/physiology ; Gastrointestinal Tract/microbiology ; Dysbiosis ; },
abstract = {Circadian rhythms are endogenous, near-24-h cycles that synchronize physiological and behavioral functions with environmental cues such as light/dark cycles and food intake. While the central pacemaker in the suprachiasmatic nucleus orchestrates these rhythms, peripheral clocks distributed across organs, including the gastrointestinal tract, exhibit autonomous oscillations that are crucial for local homeostasis. Concurrently, the gut microbiota undergoes diurnal fluctuations in composition and metabolic activity that are tightly coupled to host circadian mechanisms. Recent discoveries reveal a bidirectional relationship: host clocks influence microbial dynamics through feeding behavior, immune signaling, and epithelial renewal, whereas microbial metabolites such as short-chain fatty acids (SCFAs) and bile acids modulate circadian gene expression in peripheral tissues. Disruptions in circadian alignment, whether due to genetic mutations, lifestyle factors like shift work and irregular eating, or environmental perturbations, lead to microbial dysbiosis, metabolic dysfunction, inflammation, and heightened disease susceptibility. Conversely, altered microbiota rhythms can feed back into host systems, impairing metabolic control, immune responses, and neuroendocrine signaling. This reciprocal regulation extends to disease contexts, where circadian-microbiota misalignment contributes to obesity, type 2 diabetes, inflammatory bowel disease, and even neuropsychiatric disorders. This review synthesizes current insights into the molecular and physiological cross-talk between host circadian clocks and the gut microbiota. We discuss how temporal dynamics at the cellular, systemic, and microbial levels are integrated and how their disruption underlies pathogenesis. We further explore the potential of chronobiotics and chrononutrition, including time-restricted feeding (TRF) and bioactive dietary compounds, as emerging strategies to restore circadian-microbial synchrony and improve metabolic health. Understanding this intricate dialogue between host and microbiome may pave the way for personalized, time-based interventions to enhance healthspan and prevent disease occurrence or progression. KEY POINTS: • Circadian rhythms and microbiota form a bidirectional regulatory feedback loop. • Disruption of circadian-microbial synchrony drives metabolic and inflammatory disease. • Chrononutrition offers novel strategies to restore health via circadian-microbiota alignment.},
}

*Gastrointestinal Microbiome/physiology
*Circadian Rhythm/physiology
Humans
Animals
Circadian Clocks/physiology
Gastrointestinal Tract/microbiology
Dysbiosis

@article {pmid41070991,
year = {2025},
author = {Brennan, C and Shaffer, JP and Belda-Ferre, P and Mohanty, I and Weng, Y and Cantrell, K and Ackermann, G and Allaband, C and Bryant, M and Farmer, S and González, A and McDonald, D and Martino, C and Meehan, MJ and Rahman, G and Salido, RA and Schwartz, T and Song, SJ and Tribelhorn, C and Tubb, HM and Dorrestein, PC and Knight, R},
title = {Streamlined extraction of nucleic acids and metabolites from low- and high-biomass samples using isopropanol and matrix tubes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0191225},
doi = {10.1128/spectrum.01912-25},
pmid = {41070991},
issn = {2165-0497},
abstract = {UNLABELLED: An essential aspect of population-based research is collecting samples outside of a clinical setting. This is crucial because microbial populations are highly dynamic, varying significantly across hosts, environments, and time points, a variability that clinical sample collection alone cannot fully capture. At-home sample collection enables the inclusion of a larger and more diverse group of participants, accounting for differences in ethnicity, age, and other factors. However, managing large studies is challenging due to the complexities involved in sample acquisition, processing, and analysis. Building on our previous work demonstrating the effectiveness of single 1 mL barcoded, racked Matrix Tubes in reducing sample processing time and well-to-well contamination for paired DNA and metabolite extraction, we further validate this method against a previously benchmarked plate-based approach using the same extraction reagents. This validation focuses on samples from the built environment, human skin, human saliva, and feces from mice and humans. Importantly, we explore the impact of using a mix of bead sizes during bead-beating for cell lysis, demonstrating that it enhances taxonomic recovery compared to a single bead size. Finally, we assess the potential of 95% isopropanol for room-temperature sample preservation. Our results show that isopropanol performs comparably to 95% ethanol in many cases, suggesting it is viable as an alternative when ethanol is unavailable. Beyond minimizing contamination, halving processing time, eliminating human error during sample plating, and streamlining metadata curation, the Matrix tube approach produces metabolomic, 16S, and shotgun metagenomic data consistent with the Plate-based Method for both high- and low-biomass samples.

IMPORTANCE: Numerous studies have linked the microbiome to human and environmental health, yet many fundamental questions remain unanswered. Large-scale studies with robust statistical power are required to identify important covariates against a background of confounding factors. Cross-contamination, limited throughput, and human error have been identified as major setbacks when processing large numbers of samples. We present a streamlined method for sample accession and extraction of metabolites and DNA for both high- and low-biomass samples. This approach, previously shown to significantly reduce cross-contamination, employs an automation-friendly, single barcoded tube per sample. Additionally, we demonstrate that 95% isopropanol serves as an effective ambient-temperature storage solution for many sample types, providing an alternative in regions where ethanol is unavailable or restricted. This method has significant implications for the field, enabling large-scale studies to generate accurate insights with greater efficiency and expanded accessibility in situations in which ethanol is more costly or otherwise not available.},
}

@article {pmid41070965,
year = {2025},
author = {Rocha, GR and Benoit, DSW and Meyer, AS},
title = {Reproducible 3D bioprinting of Streptococcus mutans to create model oral biofilms.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0093525},
doi = {10.1128/spectrum.00935-25},
pmid = {41070965},
issn = {2165-0497},
abstract = {Novel approaches are needed to study relationships between oral biofilm strains, enable three-dimensional oral biofilm deposition, and hasten the rigor and pace of basic and translational biofilm studies. Previously, 3D-bioprinters were leveraged to deposit spatially patterned biofilms onto sugar-rich agar surfaces to study how the underlying spatial organization of various microbes impacts biofilm persistence and virulence. Herein, we have developed a new method to adapt this process from limited, soft agar surfaces to biomimetic solid substrates submerged in aqueous solutions for studying oral biofilms in vitro. Streptococcus mutans UA159 was used to compare standard in vitro biofilm development with our new 3D-printed bio-ink hydrogels on hydroxyapatite disks, which mimic tooth surfaces. Biofilms formed using the bio-ink methodology showed minimal quantitative differences in virulence factors, including environmental pH, biomass, and cell density, compared to biofilms formed using the standard in vitro methodology. The bio-ink technique resulted in higher exopolysaccharide deposition, a key virulence factor for biofilm cohesion and protection, as well as more homogeneous spatial distribution of bacterial microcolonies. Our newly developed technique produces 3D-printable model biofilms that match the virulence benchmarks of the standard method, opening possibilities to print biofilms onto any substrate and a new way to study multidimensional biofilm dynamics.IMPORTANCEDental caries is the most common oral disease caused by biofilms in humans with cost limitations. Changes in the human diet have increased the exposure to sugar-rich processed food, increasing the incidence and severity of dental caries and creating greater rationale for understanding biofilm deposition, microbial interactions, and maintenance of quiescence of the oral microbiota. Recent 3D-printing techniques have been leveraged to develop the first model biofilms, providing spatial control over microbe deposition and enabling unprecedented investigation of the impact of cell-cell interactions and spatial organizationupon biofilm persistence, sensitivity to drugs, and virulence. Here, we have developed new methods to extend bioprinting to oral biofilms using cariogenic Streptococcus mutans. Our technique is an attempt to establish an alternative method for oral biofilm formation in vitro that uses 3D-printing tools, preserving the virulence of standard in vitro biofilms while amplifying the availability and versatility of methods for understanding the microbiome.},
}

@article {pmid41070562,
year = {2025},
author = {Grodzka, O and Domitrz, I},
title = {Gut microbiota, probiotics, and migraine: a clinical review and meta-analysis.},
journal = {Journal of oral & facial pain and headache},
volume = {39},
number = {3},
pages = {13-26},
doi = {10.22514/jofph.2025.043},
pmid = {41070562},
issn = {2333-0376},
mesh = {Humans ; *Migraine Disorders/prevention & control/microbiology ; *Probiotics/therapeutic use ; *Gastrointestinal Microbiome/physiology ; },
abstract = {Migraine is a primary headache disorder affecting about 14% of the global population. The knowledge about migraine pathophysiology is increasing constantly; however, there are still many unknowns and uncertainties. Intestinal microbiota builds the gut environment together with metabolites and the immune system. Its connections with disorders outside the digestive system have been described, mainly neuropsychiatric diseases, due to the existence of the microbiota-gut-brain axis. Therefore, it is suggested that migraine is also correlated with changes in the microbiome. The review aimed to summarize the available literature related to the topic. We performed an electronic article search through the Embase Database and PubMed Database, and included 14 articles after analysis under the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) 2020 guidelines. Subsequently, a meta-analysis of randomized controlled clinical trials summarizing probiotics' effect on migraine prevention was conducted based on the same guidelines and resulted in including 2 adequate trials. Microbiome alterations have been observed in migraine patients with an influence on clinical presentation. Preclinical studies suggested a direct connection between migraine and microbiome changes. The meta-analysis has shown the influence of probiotics on migraine frequency (p = 0.003; Hedges' g = 1.22; standard error (SE) = 0.41), and no impact on migraine severity (p = 0.069; Hedges' g = 1.10; SE = 0.61) and attacks' duration (p = 0.149; Hedges' g = 0.18; SE = 0.15). However, the former was close to the statistical significance. The following work demonstrates a correlation between migraine and microbiome, which has a putative positive impact on migraine management. Moreover, probiotic supplementation can alleviate migraine symptoms. However, the main limitation is the limited number of studies, together with high heterogeneity and limited methodological consistency in the meta-analysis.},
}

Humans
*Migraine Disorders/prevention & control/microbiology
*Probiotics/therapeutic use
*Gastrointestinal Microbiome/physiology

@article {pmid41070134,
year = {2025},
author = {Li, Q and Liu, F and Zhong, J and Fang, X and Zhang, X and Xiong, H and Li, G and Chen, H},
title = {Multi-cohort metagenomics reveals strain functional heterogeneity and demonstrates fecal microbial load correction improves colorectal cancer diagnostic models.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1656016},
pmid = {41070134},
issn = {1664-302X},
abstract = {INTRODUCTION: Colorectal cancer (CRC) is strongly associated with alterations in the gut microbiome. While numerous studies have examined this association, most focus on genus- or species-level taxonomic classifications, overlooking functional heterogeneity at the strain level.

METHODS: We integrated 1,123 metagenomic samples from seven global CRC cohorts to conduct multi-level metagenome-wide association studies (MWAS). Fecal microbial load (FML) correction was applied to mitigate technical confounding. We evaluated the performance of taxonomic models at various resolutions strain, species, and genus levels in classifying CRC status both within and across cohorts.

RESULTS: Strain-level analysis revealed conspecific strains with divergent associations to CRC. For instance, distinct strains of Bacteroides thetaiotaomicron exhibited both protective and risk-increasing effects across different cohorts. Genomic functional annotation suggested potential mechanistic bases for these opposing roles. Correction for FML reduced confounding and significantly improved the performance of within-cohort and cross-cohort CRC classification models. Interestingly, genus- and species-level models demonstrated superior predictive robustness compared to strain-level models, likely due to higher microbial abundance and greater cross-population conservation at these taxonomic ranks.

CONCLUSION: Our study underscores the biological relevance of strain level analysis in elucidating functional diversity within the microbiome. However, higher taxonomic levels provide more robust and clinically translatable diagnostic markers for CRC. Integrating FML correction with multi-level taxonomic profiling enhances both mechanistic insight into microbiom CRC interactions and the generalizability of diagnostic models across diverse populations.},
}

@article {pmid41070130,
year = {2025},
author = {Wang, A and Chen, T and Zhang, H and Yang, Y and Cheng, X and Chen, D and Ling, B},
title = {Mechanistic study of Jiawei Zicao Plaster in atopic dermatitis via IL-17 signaling pathway and skin microbiome modulation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1668089},
pmid = {41070130},
issn = {1664-302X},
abstract = {BACKGROUND: Atopic dermatitis (AD) is a prevalent and difficult-to-cure chronic inflammatory skin condition. The mechanism of Jiawei Zicao Plaster (JZP), a clinically used Traditional Chinese Medicine (TCM) for AD, remains incompletely understood.

METHODS: Following successful model induction, JZP was topically applied to the dorsal skin of mice. Therapeutic efficacy was evaluated through histopathological examination of skin sections and quantification of inflammatory biomarkers using ELISA. To investigate the underlying mechanisms, we performed qRT-PCR to analyze gene expression in related signal pathway, along with 16S rRNA sequencing to characterize skin microbiota composition.

RESULTS: Network pharmacological analysis revealed that JZP may exert therapeutic effects by targeting antibacterial and anti-inflammatory pathways. Subsequent in vivo experiments demonstrated that JZP effectively ameliorates biochemical markers of AD by activating the IL-17 pathway. Analysis of skin microbiota indicated that JZP treatment led to an increase in Chryseobacterium abundance and a decrease in Staphylococcus abundance.

CONCLUSION: This study seeks to validate the efficacy of JPZ as a treatment for AD. Initial findings suggest that JPZ attains its therapeutic efficacy through the synergistic actions of IL-17 and antibacterial properties, providing a theoretical basis for the future development and application of this traditional Chinese medicine formula.},
}

@article {pmid41070121,
year = {2025},
author = {Long, C and Fu, X and Wu, Q and Wang, S and Zhou, X and Mao, J and Guo, L and Shi, W and Yang, H and Yang, T and Du, Y and Yue, J and Wu, D and Liu, H},
title = {Poncirus trifoliata vs. Citrus junos rootstocks: reshaping lemon rhizosphere microecology through microbial and metabolic reprogramming.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1650631},
pmid = {41070121},
issn = {1664-302X},
abstract = {INTRODUCTION: Trifoliate orange (Poncirus trifoliataL. Raf) and "Ziyang Xiangcheng" (Citrus junos Sieb. ex Tanaka) are the predominant rootstocks for lemon production in China, exhibiting distinct adaptations to soil pH and differential impacts on plant resilience. As pivotal mediators of scion-soil interactions, rootstocks have emerged as key research targets for their regulatory potential in rhizosphere microbial communities and metabolites.

METHODS: Pot-cultured systems were established with lemon (Citrus × limon "Eureka") saplings grafted onto trifoliate orange (PTL) and "Ziyang Xiangcheng" (CJL) rootstocks. Integrated metagenomic and GC-MS metabolomic approaches were employed to analyze rhizosphere microbial communities and metabolites.

RESULTS: The results demonstrated no significant difference in rhizospheric microbial α-diversity (richness) between PTL and CJL, although PTL exhibited higher evenness. β-Diversity and LEfSe analysis revealed significant structural divergence in communities. A total of 15 differentially enriched genera across three phyla were identified, among which Pseudomonas, Cupriavidus, and Burkholderia in CJL, along with Sphingobium in PTL, exhibited strong effects. Random forest modeling identified 15 key differential metabolites, with 4 significantly upregulated in CJL and 11 in PTL. Microbial-metabolite correlation and GSEA analysis uncovered 10 core pathways involving genetic information processing, energy metabolism, environmental adaptation, and disease resistance mechanisms. Soil analysis showed CJL significantly surpassed PTL in organic matter content, catalase activity and plant height, whereas PTL exhibited superior cellulase, sucrase and urease activities. Mechanistically, PTL appears to recruit Pseudomonas mediterranea via 1-Monostearin secretion to activate glycerolipid metabolism, enhancing drought tolerance. Its caffeate and salicyl alcohol-β-glucoside secretions potentially mobilize Sphingobium and Ensifer adhaerens to regulate amino sugar metabolism, promoting carbon sequestration and root defense. Conversely, CJL likely employs L-alanine exudation to recruit Pseudomonas putida, triggering exopolysaccharide biosynthesis through arginine-proline metabolism as a key tolerance mechanism (such as drought tolerance and alkali tolerance).

DISCUSSION: The findings elucidate rootstock-specific modulation of rhizosphere microecosystems, highlighting distinct microbial-metabolite interactions and tolerance mechanisms. These results provide theoretical support for precision rootstock selection and microbiome engineering to advance sustainable citrus production.},
}

@article {pmid41070119,
year = {2025},
author = {Li, F and Kong, X and Khan, MZ and Wei, L and Wei, J and Zhu, M and Liu, G and Huang, B and Wang, C and Zhang, Z},
title = {Gut microbiome regulation in equine animals: current understanding and future perspectives.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1602258},
pmid = {41070119},
issn = {1664-302X},
abstract = {The equine intestinal microbiome represents a complex and dynamic ecosystem that fundamentally influences host health and physiological function. This microbial community exhibits distinct compositional and functional variations across different anatomical segments of the intestinal tract, with diversity and abundance patterns shaped by host genetics, dietary inputs, and environmental conditions. The resident microbiota performs essential functions in feed fermentation, nutrient metabolism, pathogen exclusion, and immunological programming. This review synthesizes current knowledge regarding the core taxonomic and functional attributes of the equine intestinal microbiome, examining interspecies variation and conservation patterns. We evaluate key determinants of microbial community assembly and regulation, while examining mechanistic links between microbiota composition and host health outcomes. Through critical analysis of existing literature, this work provides an integrated framework for understanding the equine gut microbiome, with implications for clinical intervention strategies and evidence-based approaches to promote intestinal health in equine.},
}

@article {pmid41070060,
year = {2025},
author = {Liu, Y and Li, Y and Li, J},
title = {Integrative analysis of serum microorganisms and serum metabolomics in osteoporosis patients based on 16S rDNA sequencing and UHPLC/MS-based metabolomics.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1664359},
pmid = {41070060},
issn = {2296-858X},
abstract = {INTRODUCTION: Although significant progress has been made in the treatment and research of osteoporosis patients in recent years, the genetic mechanism of osteoporosis has not yet been fully elucidated.

METHODS: We conducted a comprehensive analysis using 16S sequencing and UHPLC-MS/MS metabolomics data to characterize the microbial composition and metabolic composition in the serum of osteoporosis patients.

RESULTS: At the phylum level, Proteobacteria are mainly present in Osteoporosis; In Normal, it is mainly Bacteroidota. At the genus level, Cupriavidus is the main species in Osteoporosis; In Normal, the main ones are Blautia, Bacteroides, Alcaligenes and Pseudomonas. Serum metabolomics revealed different metabolites (230 significantly differentially expressed metabolites) and lipid metabolism pathways (such as Glycerophospholipid metabolism) among the two groups. The combined serum microbiota and serum metabolomics datasets demonstrate a correlation reflecting the impact of microbiota on metabolic activity (p < 0.05).

DISCUSSION: Our research findings indicate that microbiota and metabolomics analysis provide important candidate biomarkers. The correlation between these serum microbiota and host metabolism is of great significance for optimizing early diagnosis and developing personalized treatment strategies. This study elucidates the relationship between serum microbiota and metabolites in osteoporosis.},
}

@article {pmid41070021,
year = {2025},
author = {Jia, D and Xue, S},
title = {Mediterranean diet research trajectories in China (2006-2025): a scoping review and scientometric analysis to localize global nutrition models.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1661835},
pmid = {41070021},
issn = {2296-861X},
abstract = {BACKGROUND: Mediterranean-diet (MedDiet) principles are increasingly invoked to counter China's nutrition-transition-driven epidemic of cardiometabolic disease, yet no field-wide synthesis of this scholarship exists. A bibliometric assessment can expose thematic evolution, knowledge gaps and localization pathways.

METHODS: We systematically searched Web of Science Core Collection and CNKI for Chinese-affiliated MedDiet human-health articles published between 2006 and 2 February 2025. After PRISMA-ScR screening we retained 384 records. VOSviewer and COOC mapped co-authorship, citations and keywords; latent-Dirichlet allocation detected topic drift; compound annual growth rate (CAGR) and field-weighted citation impact (FWCI) indexed performance. All data and scripts are openly archived.

RESULTS: Annual output climbed from one article in 2006 to 76 in 2022 (CAGR = 23%); FWCI = 1.34. Seven keyword clusters now pivot on gut-microbiome science, digital adherence and sustainability rather than early cardiometabolic replication. Temporal segmentation revealed three phases: replication (2006-2013), public-health expansion (2014-2019) and cross-disciplinary innovation (2020-2025). Bibliographic coupling resolved five citation schools; Jiangnan-diet localization has migrated into the leading clinical cluster. Lexical drift highlights ingredient substitution (rapeseed-oil phenolics) and late adoption of carbon-footprint terminology.

CONCLUSION: Chinese MedDiet scholarship is recalibrating toward a culturally adapted, digitally enabled and climate-aligned paradigm. Longer m-health-supported trials, life-course epidemiology and multi-omics Jiangnan cohorts are warranted to translate current bibliometric momentum into population-level health and sustainability gains.},
}

@article {pmid41069861,
year = {2025},
author = {George, C and Dharan, HM and Drescher, L and Lee, J and Qi, Y and Wang, Y and Chang, Y and Teo, SLM and Wainwright, BJ and Yung, C and Lauro, FM and Hazen, TC and Pointing, SB},
title = {Tropical intertidal microbiome response to the 2024 Marine Honour oil spill.},
journal = {Environmental science and ecotechnology},
volume = {28},
number = {},
pages = {100623},
pmid = {41069861},
issn = {2666-4984},
abstract = {Marine fuel oil (MFO) spills in tropical coastal environments are under-characterized despite increasing risk from maritime activities. Microbial and geochemical responses to the June 2024 Marine Honour MFO spill on Singapore's intertidal sediments were analyzed in real time over 185 days. Using metagenomics and hydrocarbon profiling, microbial community shifts and hydrocarbon degradation were quantified across visibly oiled (high-impact) and clean (low-impact) sites. Microbiomes at all sites adapted rapidly to the spill through increased diversity and abundance of genes encoding alkane and aromatic compound degradation, detoxification, and biosurfactant production. The dominant hydrocarbon-degrading bacteria differed markedly from those reported in other crude oil spills and in regions with different climates. Oil deposition intensity strongly influenced microbial succession and hydrocarbon-degrading gene profiles, and this reflected early toxicity constraints in heavily oiled areas. The persistence of hydrocarbon degradation genes beyond hydrocarbon detection in sediments suggested long-term functional priming may occur. The study provides novel genome-resolved insight into the microbial response to MFO pollution, advances understanding of marine environmental biodegradation, and provides urgently needed baseline data for oil spill response strategies in Southeast Asia and beyond.},
}

@article {pmid41069856,
year = {2025},
author = {Tian, C and Chang, X and Wu, J and Xiao, L and Du, J and Hu, Q and Yang, Y},
title = {Research progress of intestinal microbiota on cognitive dysfunction after spinal cord injury.},
journal = {iScience},
volume = {28},
number = {10},
pages = {113554},
pmid = {41069856},
issn = {2589-0042},
abstract = {Alterations in the gut microbiota are among the most common phenomena following spinal cord injury, often accompanied by cognitive impairment. Numerous studies have reported intrinsic links among these three aspects. However, the molecular mechanisms by which the gut microbiota influence cognitive function after spinal cord injury, as well as strategies for modulating the gut microbiota to treat cognitive deficits, remain inadequately summarized. Therefore, this review provides a comprehensive summary of the key mechanisms by which gut dysbiosis contributes to cognitive impairment and discusses therapeutic strategies targeting the gut microbiota. These insights may offer a theoretical basis for further research and microbiota-based drug development for cognitive dysfunction following spinal cord injury.},
}

@article {pmid41069710,
year = {2025},
author = {Burakova, I and Smirnova, Y and Gryaznova, M and Morozova, P and Kotarev, V and Lyadova, L and Ivanova, N and Denisenko, L and Syromyatnikov, M},
title = {Effect of interferon on broilers' fecal microbiome composition.},
journal = {Journal of advanced veterinary and animal research},
volume = {12},
number = {2},
pages = {487-496},
pmid = {41069710},
issn = {2311-7710},
abstract = {OBJECTIVE: The purpose of our study was to investigate the effect of chicken interferon on the intestinal microbiota of broiler chickens.

MATERIALS AND METHODS: The study used next-generation sequencing on the Ion Torrent pragmatic general multicast platform to target the V3 16S ribosomal ribonucleic acid hypervariable region gene, allowing us to analyze in detail changes in the composition of the broiler chicken microbiome.

RESULTS: Forty-one bacterial genera were identified in the studied groups of broilers. The highest abundance in both groups was observed for Lactobacillus, which was 31.08% ± 6.52 in the control group and 36.08% ± 7.25 in the interferon group. There was no clustering between the microbiome communities of the groups studied. We found a decrease or complete absence of Escherichia-Shigella, Eubacterium fissicatena group, Lachnospiraceae CHKCI001, and Pediococcus in the interferon-treated broiler group compared to the control group and an increase in the number of genera Ruminococcaceae CAG-352 and Turicibacter in the interferon group.

CONCLUSION: A decrease in E.-Shigella may indicate normalization of the intestinal microbiota of broilers, and it can also be concluded that the introduction of interferon helps to suppress opportunistic bacteria. In the interferon group, a sharp increase in the number of Turicibacter was observed. Representatives of this genus are among the most common members in the intestines of broilers.},
}

@article {pmid41069703,
year = {2025},
author = {Cai, Y and Wu, L and Brandt, BW and Buijs, MJ and Wei, X and Liu, H and Deng, D},
title = {Streptococcus cristatus reduces cariogenicity of saliva-derived microcosms under pH-dependent conditions.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2565450},
pmid = {41069703},
issn = {2000-2297},
abstract = {BACKGROUND: The study aims to investigate Streptococcus cristatus, an oral commensal bacterium, as a probiotic for dental caries prevention by modulating the oral microbiome.

METHODS: Saliva from four healthy donors was used to establish 24-h microcosm biofilms in an in vitro 96-well peg model. The preformed biofilms were then exposed to biofilm medium containing 0.2% sucrose (BM), with or without S. cristatus. They were grown for 48 h under two conditions: a constant pH-neutral regime (BM supplemented with 76 mM K2HPO4 and 15 mM KH2PO4, pH 7.0) or cariogenic pH-cycling regime (8 h pH-neutral and 16 h in BM containing 100 mM acetic acid, pH 5.5). Phosphate and acetate buffers were used to control pH. After 72 h, the biofilms were analyzed for biomass, lactic acid production, hydrogen peroxide (HP) concentrations, and microbial composition via 16S rRNA gene sequencing.

RESULTS: S. cristatus successfully integrated into 24-h preformed microcosm biofilms derived from individual saliva. Under pH-neutral conditions, it reduced biofilm biomass and lactate production while increasing hydrogen peroxide (HP) generation in a donor-dependent manner. Conversely, under cariogenic pH-cycling conditions, these inhibitory effects on biomass and lactate production were consistent across all donors, although HP was undetectable. Microbiome analysis revealed that S. cristatus increased species richness and mitigated the compositional shifts caused by pH-cycling. This was achieved by inhibiting Streptococcus salivarius/vestibularis across all donors, while promoting Streptococcus mitis group and Streptococcus anginosus in a donor-dependent manner.

CONCLUSIONS: S. cristatus represents a promising microbiome modulator with the potential to substantially mitigate the cariogenicity of oral microcosms.},
}

@article {pmid41069588,
year = {2025},
author = {Li, K and Liu, T and Zhong, X and Liu, J and Chen, P and Lin, B and Zhong, X},
title = {High-risk Sexual Behavior for HIV Acquisition is Associated with Gut Microbial Community in Men Who Have Sex with Men.},
journal = {Open forum infectious diseases},
volume = {12},
number = {10},
pages = {ofaf581},
pmid = {41069588},
issn = {2328-8957},
abstract = {BACKGROUND: Gut dysbiosis is observed in men who have sex with men compared with men who have sex with women. However, the association between risk of HIV acquisition and gut microbiota in HIV sero-negative men who have sex with men remains unclear.

METHODS: We conducted a cross-sectional study in HIV sero-negative men who have sex with men to explore the links between gut microbiota and risk of HIV acquisition. HIV sero-negative men who have sex with men were recruited. Fecal samples were collected for gut microbiota analysis using 16S rRNA gene sequencing. HIV risk assessment tool was used to estimate the risk of HIV acquisition. Latent class analysis was performed to categorize participants into different risk levels. Gut microbiota diversity was analyzed using the R package vegan. Linear discriminant analysis was used to analyze differential taxa between groups.

RESULTS: Two independent subgroups were identified. High-risk participants had >2 male partners and mostly engaged in receptive anal intercourse. The high-risk group exhibited significantly higher Shannon index and lower Simpson index, indicating increased gut microbiota diversity. Beta diversity analysis showed significant differences between the high-risk and low-risk groups (F = 2.0245, P = .0369). Linear discriminant analysis revealed differences in the relative abundance of multiple microbial taxa between the 2 groups, with Barnesiella significantly increased in the low-risk group and Roseburia higher in the high-risk group.

CONCLUSIONS: Risk of HIV acquisition in men who have sex with men is associated with gut dysbiosis, suggesting that gut microbiota may be a potential target for HIV prevention strategies.},
}

@article {pmid41069575,
year = {2026},
author = {Zhao, T and Sun, N and Ding, J and Peng, Z and Han, F and Qi, X},
title = {The specific hallmarks, emerging roles, key mechanisms, and clinical applications of intra-tumoral microbiota in human cancers.},
journal = {Genes & diseases},
volume = {13},
number = {1},
pages = {101733},
pmid = {41069575},
issn = {2352-3042},
abstract = {Intra-tumoral microbes have been revealed to exist in many cancer types, attracting widespread attention. The significance of intra-tumoral microbes is becoming increasingly apparent in various aspects of human cancers, encompassing cancer initiation, progression, metastasis, diagnostic approaches, prognostic evaluations, and therapeutic interventions. Despite the considerable focus dedicated to this topic by numerous scholars, a comprehensive analysis of intra-tumoral microbiota is still lacking in human cancers. Especially, identifying specific microbial hallmarks in the occurrence and development of cancer and different cancers remains the central task for investigators. This review focuses on the identification and analysis of distinct attributes and noteworthy characteristics exhibited by intra-tumoral microbiota across various types of cancer. The potential mechanisms of intra-tumoral microbiota action, as well as the significance of the microbiome in the diagnosis and prognosis of cancer, are systematically summarized. The capacity of intra-tumoral microbes to regulate cancer treatment with a focus on the relevant microbial species, and the possibility of targeting the microbiota to improve treatment effectiveness while preventing toxicity, are specifically highlighted. Lastly, the challenges, limitations, and prospects of intra-tumoral microbes in further study and clinical application, including prognostic, diagnostic, and therapeutic applications, are discussed in cancers. This review provides a systematic summary of the specific characteristics, molecular mechanisms, therapeutic effects, and diagnostic and prognostic values of intra-tumoral microbiota in different cancers, which will help improve the diagnosis, treatment, and prognosis of tumor patients and offer new ideas for achieving precise treatment of cancer with intra-tumoral microbiota.},
}

@article {pmid41069527,
year = {2025},
author = {Jiang, W and Gu, S},
title = {Editorial: The oral microbiome and its impact on systemic health: from disease development to biomaterials development.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1697069},
pmid = {41069527},
issn = {2235-2988},
}

@article {pmid41069464,
year = {2025},
author = {Sun, G and Li, Z and Wang, G and Cai, H and Yu, J and Li, Z and Chen, B and Xiao, G},
title = {Infestation by potato tuber moth restructures microbial communities in flue-cured tobacco rhizosphere and non-rhizosphere soils.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1670207},
pmid = {41069464},
issn = {1664-462X},
abstract = {INTRODUCTION: The rhizosphere microbiota is associated with the plant response to phytophagous pest infestation through the plant-rhizosphere microbe axis. However, the responses of microbial community characteristics of flue-cured tobacco rhizosphere and non-rhizosphere soil to potato tuber moth (PTM) Phthorimaea operculella larval feeding is unclear.

METHODS: In this study, the microbial structural composition was analysed in the rhizosphere and non-rhizosphere soil of healthy and PTM infested flue-cured tobacco plants at the vigorous growth stage collected from the field (with four replicates per group) using Illumina MiSeq sequencing. The featured microbes, co-occurrence networks, and potential functions of tobacco rhizosphere and non-rhizosphere soil microbial communities were analysed.

RESULTS: Amplicon data analyses showed that PTM infestation altered the microbial community composition in tobacco rhizosphere and non-rhizosphere and this alteration was similar between these two soil types. PTM infested plants showed enrichment of distinct microbial genera. For instance, the rhizosphere soil showed increased abundances of Gemmatimonas (bacteria) and Humicola (fungi), while the non-rhizosphere soil was enriched with Streptomyces (bacteria) and Penicillium (fungi). In contrast, the rhizosphere of healthy plants were characterized by enrichment of Gaiella (bacteria) and Trichoderma, Talaromyces (fungi), along with the non-rhizosphere soil dominated by Sphingomonas (bacteria) and Cordana (fungi). Furthermore, PTM infestation altered the potential functions of flue-cured tobacco rhizosphere and non-rhizosphere soils, and reduced the complexity of rhizosphere bacterial and fungal communities, as well as the non-rhizosphere fungal community. Notable changes were observed in bacterial metabolic pathways and significantly up-regulated the function of symbiotroph of fungi (Lichenized) (P < 0.05).

DISCUSSION: Together, these results enhance our understanding of how the underground microbiome of flue-cured tobacco responds to aboveground phytophagous insect (PTM) infestation, providing valuable insights that could facilitate translation into more effective PTM management practices.},
}

@article {pmid41069462,
year = {2025},
author = {Bziuk, N and Wassermann, B and Bickel, S and Omidvar, R and Manica, A and Berg, G},
title = {Aureobasidium pullulans: a microbiome-based perspective from global biomes to edible plant tissues.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1652366},
pmid = {41069462},
issn = {1664-462X},
abstract = {Aureobasidium pullulans is a globally distributed fungus commonly found in plant-associated and anthropogenic environments. Known for its antagonistic activity against plant pathogens, it is widely used as a biocontrol agent in sustainable agriculture. Despite its prevalence in edible plant tissues and frequent environmental exposure, its broader role within microbiomes and potential relevance for human health remain underexplored. In this perspective article, we highlight the global distribution of A. pullulans based on publicly available sequencing data and examine its ecological function from a microbiome-based viewpoint. Our synthesis supports the view of A. pullulans as a safe, plant-beneficial symbiont with high value for sustainable crop protection and potential relevance for the One Health framework. Future microbiome research should further explore its functional roles within plant and human-associated microbiomes to better harness its benefits while ensuring biosafety across ecosystems.},
}

@article {pmid41069328,
year = {2025},
author = {Tettevi, EJ and Simpong, DL and Maina, M and Adjei, S and Asuming-Brempong, E and Osei-Atweneboana, MY and Ocloo, A},
title = {Antibiotic-Induced Gut Dysbiosis Modulates Alzheimer's Disease-Associated Gene Expression and Protein Aggregation in 3xTg-AD Mice via the Gut-Brain Axis.},
journal = {Brain and behavior},
volume = {15},
number = {10},
pages = {e70946},
doi = {10.1002/brb3.70946},
pmid = {41069328},
issn = {2162-3279},
support = {//Council for Scientific and Industrial Research - Water Research Institute/ ; },
mesh = {Animals ; *Dysbiosis/chemically induced/metabolism ; *Alzheimer Disease/metabolism/genetics/microbiology ; Mice ; *Gastrointestinal Microbiome/drug effects/physiology ; *Anti-Bacterial Agents/pharmacology/adverse effects ; Female ; *Brain/metabolism ; Mice, Transgenic ; Disease Models, Animal ; *Brain-Gut Axis/drug effects/physiology ; Amyloid beta-Peptides/metabolism ; Gene Expression/drug effects ; tau Proteins/metabolism ; Anxiety/metabolism ; },
abstract = {INTRODUCTION: Alzheimer's disease (AD) is a progressive neurodegenerative disorder that poses a major global health challenge due to its increasing prevalence and lack of effective treatments. Emerging evidence suggests the gut-brain axis may play a pivotal role in AD pathogenesis. However, causal links between dysbiosis and late-stage AD pathology remain unclear.

METHODS: This study evaluated the effects of antibiotic-induced gut dysbiosis in aged 3xTg-AD mice (46-48 weeks). Female mice were randomly assigned to control or treatment groups and administered a broad-spectrum antibiotic cocktail (ampicillin, vancomycin, and neomycin) for 14 days. Behavioral tests (Y-maze, elevated plus maze) were performed to assess cognitive and anxiety-like behaviors. Gut microbiota composition was assessed via 16S rRNA qPCR. Gene expression of Acetylcholinesterase (AChE), Butyrylcholinesterase (BChE), and Tumor Necrosis Factor-Alpha (TNF-α) was analyzed via qRT-PCR, and cerebral amyloid-β1-42 and tau protein levels were quantified by ELISA.

RESULTS: Antibiotic treatment induced significant dysbiosis, with > 90% reduction in Firmicutes and Bacteroidetes. Dysbiotic mice displayed impaired spatial working memory, heightened anxiety-like behavior, and reduced locomotor activity. Molecular analyses revealed region-specific dysregulation of cholinergic genes: AChE was upregulated in the hippocampus but downregulated in the cortex, while BChE showed the opposite trend. TNF-α was significantly elevated in both regions, indicating neuroinflammation. Dysbiosis also led to increased brain levels of amyloid-β1-42 and tau.

CONCLUSION: Gut microbiome disruption exacerbates late-stage AD pathology, driving cognitive deficits, neuroinflammation, and hallmark protein aggregation. These findings support the gut-brain axis as a critical modulator of AD and highlight the microbiome as a potential therapeutic target.},
}

Animals
*Dysbiosis/chemically induced/metabolism
*Alzheimer Disease/metabolism/genetics/microbiology
Mice
*Gastrointestinal Microbiome/drug effects/physiology
*Anti-Bacterial Agents/pharmacology/adverse effects
Female
*Brain/metabolism
Mice, Transgenic
Disease Models, Animal
*Brain-Gut Axis/drug effects/physiology
Amyloid beta-Peptides/metabolism
Gene Expression/drug effects
tau Proteins/metabolism
Anxiety/metabolism

@article {pmid41069234,
year = {2025},
author = {de Campos Costa, MA and Zhao, X and Komura, D and Carbonero, ER and Choque-Delgado, GT and Tunçil, YE and Cipriani, T and Román-Ochoa, Y and Hamaker, BR and Cantu-Jungles, TM},
title = {New high-specificity fibers with strong and consistent responses across individuals.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo02728d},
pmid = {41069234},
issn = {2042-650X},
abstract = {Individual variability in gut microbiota responses limits the consistency of health benefits from prebiotic fiber interventions. Building on our concept of fiber hierarchical specificity, defined as the selective alignment and use of fibers by a narrow subset of gut microbes, we evaluated new putative high-specificity fibers for their ability to promote predictable and intense microbial shifts across individuals. Here, six candidate fibers (Acacia gum, Fucogalactan, Gellan gum, Guar gum, Locust bean gum, and Xylooligosaccharides) were tested in vitro using fecal microbiota from ten donors and compared to low-specificity (Fructooligosaccharides) and high-specificity (an insoluble glucan) reference fibers. SCFA analysis showed that Fucogalactan and Guar were strongly propiogenic, while Acacia and Locust promoted balanced SCFA production. Gellan exhibited minimal fermentability. Acacia, Fucogalactan, Guar, and Locust consistently enriched putative beneficial genera (Eisenbergiella, Hungatella, Anaerotruncus, and Parabacteroides, respectively), with strong and consistent responses across individuals, features characteristic of high-specificity fibers. In contrast, Fructooligosaccharides and Xylooligosaccharides produced more variable, and less intense responses. Our findings support Acacia, Fucogalactan, Guar, and Locust as high-specificity fibers that induce consistent, taxon-targeted shifts in the gut microbiome. These expand the repertoire of high-specificity fibers-a promising prebiotic approach for predictable microbiota modulation and related health outcomes.},
}

@article {pmid41069145,
year = {2025},
author = {Mohamed Mojahed Eladly, MAE and Morsy, HE and Elnabrawy, IMS and Hendawy, LMA and Abd ElHady, AMM},
title = {Gut microbiome Lactobacillus acidophilus and its relationship with thyroid nodules and thyroid hormonal profile.},
journal = {Endokrynologia Polska},
volume = {76},
number = {5},
pages = {499-506},
doi = {10.5603/ep.105734},
pmid = {41069145},
issn = {2299-8306},
mesh = {Humans ; *Lactobacillus acidophilus/isolation & purification ; Female ; Male ; Case-Control Studies ; *Gastrointestinal Microbiome ; Adult ; Prospective Studies ; *Thyroid Nodule/microbiology/blood ; Middle Aged ; *Thyroid Hormones/blood ; Feces/microbiology ; },
abstract = {INTRODUCTION: Thyroid diseases are often associated with the amounts and functioning of thyroid hormones, which may have an impact on the makeup of gut microbiomes. Multiple studies have shown a correlation between gut microbiota and both Graves' disease and Hashimoto's thyroiditis. However, there is no proven link between the gut microbiota and thyroid nodules. Researchers will examine the correlation between Lactobacillus acidophilus and thyroid nodules and hormones.

MATERIALS AND METHODS: This work is a prospective case-control investigation undertaken from 2021 to 2022 at endocrine clinics situated at Ain Shams University in Cairo. A total of 90 participants, 30 as a control group (group C), 30 patients with benign thyroid nodules (group A), and 30 patients with malignant thyroid nodules (group B) participated in the study. Measurements of hormonal profile, serum selenium, zinc, thyroglobulin, thyroid peroxidase antibody (anti-TPO), and stool polymerase chain reaction (PCR) for Lactobacillus acidophilus levels were made in all groups.

RESULTS: The cycle threshold (CT) at which lactobacilli PCR was expressed in group A was 32.340 ± 5.025 while in group B it was 34.957 ± 5.834 and in group C it was 27.530 ± 5.834, p < 0.001. There was highly significant variation between the studied groups.

CONCLUSION: The stool count of Lactobacillus acidophilus PCR showed a significant difference across the groups under study.},
}

Humans
*Lactobacillus acidophilus/isolation & purification
Female
Male
Case-Control Studies
*Gastrointestinal Microbiome
Adult
Prospective Studies
*Thyroid Nodule/microbiology/blood
Middle Aged
*Thyroid Hormones/blood
Feces/microbiology

@article {pmid41069041,
year = {2025},
author = {Koketsu, A and Fukase, S and Tamahara, T and Saito, T and Ito, A and Higashi, Y and Kajita, T and Kurobane, T and Miyakoshi, M and Iikubo, M and Kumada, K and Li, B and Shimada, M and Shimizu, R and Takahashi, T and Yamauchi, K and Sugiura, T},
title = {Bacterial Involvement in Oral Squamous Cell Carcinoma and Potentially Malignant Oral Disorders.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.70115},
pmid = {41069041},
issn = {1601-0825},
abstract = {OBJECTIVE: To clarify the relationship between oral squamous cell carcinoma (OSCC), potentially malignant oral disease (OPMD), and bacterial flora using metagenomic analysis.

METHODS: This cross-sectional observational study included 50 patients in the control group and 77 patients with OPMDs, 41 with early OSCCs, and 20 with advanced OSCCs. Patient saliva samples were subjected to high-throughput sequencing of 16S rRNA gene amplicons to evaluate the composition and diversity of the oral microbiome.

RESULTS: No significant differences were observed in patient backgrounds, other than sex. Patients with advanced OSCCs had greater oral bacterial diversity than those with early OSCC or OPMD. The advanced OSCC group formed a distinct cluster separate from the other groups. Sixteen and 275 species were identified at the phylum and genus levels, respectively. Compared with the control group, Actinomycetia and Streptococcus were significantly elevated in the early OSCC and OPMD groups. Peptostreptococcus and Fusobacterium were significantly higher in the advanced OSCC group than in the control, OPMD, and early OSCC groups.

CONCLUSIONS: The composition and diversity of oral microbiota may be associated with OPMD development and progression to OSCC. Consequently, the salivary microbiome may serve as a biomarker for oral cancer and help predict cancer progression.},
}

@article {pmid41068938,
year = {2025},
author = {Xu, J and Chen, X and Ren, J and Xu, J and Zhang, L and Yan, F and Liu, T and Zhang, G and Huws, SA and Yao, J and Wu, S},
title = {Multi-omics insights into microbiome-rumen epithelium interaction mechanisms underlying subacute rumen acidosis tolerance in dairy goats.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {345},
pmid = {41068938},
issn = {1474-760X},
support = {32272829//National Natural Science Foundation of China/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024-KFKT-031//National Center of Technology Innovation for Dairy/ ; },
mesh = {Animals ; *Goats/microbiology ; *Rumen/microbiology/metabolism ; *Acidosis/veterinary/microbiology/metabolism ; *Gastrointestinal Microbiome ; Epithelium/metabolism/microbiology ; Fatty Acids, Volatile/metabolism ; Female ; *Goat Diseases/microbiology ; Hydrogen-Ion Concentration ; *Microbiota ; Transcriptome ; Multiomics ; },
abstract = {BACKGROUND: To address rising demand for dairy products, dairy goats are often fed high-concentrate diets, which lead to subacute rumen acidosis (SARA). The mechanisms behind individual variation in SARA tolerance are not well understood. This study aims to elucidate roles of rumen microbiome-host interactions in SARA-susceptibility and tolerance.

RESULTS: Goats susceptible or tolerant to SARA were selected by feeding diets with different levels of rumen degradable starch. SARA-susceptible goats present prolonged periods of rumen pH below 5.8 and volatile fatty acids (VFAs) accumulation. Metagenomic analysis reveals a decrease in cellulose- and hemicellulose-utilizing bacteria and enzymes, along with increased lysozymes, suggesting disrupted rumen homeostasis. Transcriptomic and single-nucleus transcriptome analyses reveal upregulated Th17 cells, IL-17 signalling, and inflammatory pathways in SARA-susceptible goats. In contrast, SARA-tolerant goats maintain stable pH levels and enhance VFAs absorption. Bifidobacterium adolescentis and other beneficial bacteria are enriched in the rumen of SARA-tolerant goats. These microbes are positively correlated with 3-methyl pyruvic acid, a key metabolite involved in branched-chain amino acid synthesis and epithelial cell proliferation. Both microbiome transplantation and B. adolescentis direct feeding experiments confirm the protective effects of SARA-tolerant microbiota including B. adolescentis, promoting rumen epithelial VFAs absorption and reducing ruminal inflammation.

CONCLUSIONS: This study highlights the importance of Th17-mediated immune responses in ruminal inflammation and the role of B. adolescentis in regulating rumen epithelial VFAs absorption. Modulating VFAs absorption in the rumen epithelium represents a promising strategy for improving animal health and enhancing rumen fermentation efficiency.},
}

Animals
*Goats/microbiology
*Rumen/microbiology/metabolism
*Acidosis/veterinary/microbiology/metabolism
*Gastrointestinal Microbiome
Epithelium/metabolism/microbiology
Fatty Acids, Volatile/metabolism
Female
*Goat Diseases/microbiology
Hydrogen-Ion Concentration
*Microbiota
Transcriptome
Multiomics

@article {pmid41068935,
year = {2025},
author = {Shtossel, O and Louzoun, Y},
title = {GIMIC: smoothed graph-image representation of microbiome samples induce an optimal distance.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {350},
pmid = {41068935},
issn = {1474-760X},
support = {870/20//ISF grant/ ; 870/20//ISF grant/ ; },
mesh = {*Microbiota ; Humans ; Machine Learning ; *Image Processing, Computer-Assisted/methods ; Algorithms ; },
abstract = {An essential tool in microbiome is the distance between samples. This serves to detect groups of similar samples. We have recently shown that combining the cladogram with the abundance of each microbe into a sorted normalized abundance tree can improve the accuracy of machine learning and differential analysis. We show that smoothing these tree-based images to produce GIMIC (Smoothed Graph IMages of the MICrobiome) leads to an interpretable visualization of microbiome sets and that the difference between the smoothed tree-based images is a better metric than the current state-of-the-art in a wide array of tasks.},
}

*Microbiota
Humans
Machine Learning
*Image Processing, Computer-Assisted/methods
Algorithms

@article {pmid41068306,
year = {2025},
author = {Shin, AS and Xing, Y and Waseem, MR and Siwiec, R and James-Stevenson, T and Rogers, N and Bohm, M and Wo, J and Lockett, C and Gupta, A and Kadariya, J and Toh, E and Anderson, R and Dong, A and Xu, H and Gao, X},
title = {Microbiota and short chain fatty acid relationships underlie clinical heterogeneity and identify key microbial targets in irritable bowel syndrome (IBS).},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35375},
pmid = {41068306},
issn = {2045-2322},
support = {K23DK122015/DK/NIDDK NIH HHS/United States ; R03DK132446/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology/metabolism ; Female ; *Gastrointestinal Microbiome ; Male ; *Fatty Acids, Volatile/metabolism ; Feces/microbiology/chemistry ; Adult ; Middle Aged ; Bile Acids and Salts/metabolism ; Constipation/microbiology ; Metagenome ; Diarrhea/microbiology ; Bacteria/classification/genetics/metabolism ; },
abstract = {Short chain fatty acids (SCFA) are key microbial metabolites that modulate intestinal homeostasis and may influence irritable bowel syndrome (IBS) pathophysiology. We aimed to assess microbial features associated with SCFA and determine if features varied across IBS subtypes and endophenotypes. We analyzed stool microbial metagenomes, stool SCFA, and measurable IBS traits (stool bile acids, colonic transit, stool form) in 41 patients with IBS (IBS with constipation [IBS-C] IBS with diarrhea [IBS-D]) and 17 healthy controls. We used partial canonical correspondence analyses (pCCA), conditioned on transit, to quantify microbe-SCFA associations across groups. We further compared gut microbiome-encoded potential for substrate utilization across groups and within a subset of participants selected by their stool characteristics as well as stool microbiomes of patients with and without clinical bile acid malabsorption (BAM). Microbe-SCFA associations differed across groups and revealed key taxa including Dorea sp. CAG:317 and Bifidobacterium pseudocatenulatum in IBS-D and Akkermansia muciniphila and Prevotella copri in IBS-C that that could underlie subtype-specific microbially-mediated mechanisms. The greatest number of microbe-SCFA associations were observed in IBS-D. Several SCFA-producing species demonstrated inverse correlations with SCFA. Fewer bacterial taxa were associated with acetate to butyrate ratios in IBS compared to health. In participants selected by stool form, we demonstrated differential abundances of microbial genes/pathways for SCFA metabolism and degradation of carbohydrates and mucin across groups. SCFA-producing taxa were reduced in IBS-D patients with BAM. Keystone taxa responsible for SCFA production differ by IBS subtype and traits. IBS microbiomes appear exhibit reduced functional redundancy. Differences in substrate preferences are also linked to bowel functions. Focusing on taxa that drive SCFA profiles and stool form may be a rational strategy for identifying relevant microbial targets in IBS.},
}

Humans
*Irritable Bowel Syndrome/microbiology/metabolism
Female
*Gastrointestinal Microbiome
Male
*Fatty Acids, Volatile/metabolism
Feces/microbiology/chemistry
Adult
Middle Aged
Bile Acids and Salts/metabolism
Constipation/microbiology
Metagenome
Diarrhea/microbiology
Bacteria/classification/genetics/metabolism

@article {pmid41068182,
year = {2025},
author = {Gabrilska, RA and Omeir, K and Ancira, J and Miller, C and Tipton, CD and Rumbaugh, KP and Wolcott, J and Noe, A and Subasinghe, K and Rowe, M and Phillips, N and Phillips, CD},
title = {Functionally enriched human polymorphisms associate to species in the chronic wound microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {194},
pmid = {41068182},
issn = {2055-5008},
support = {R15GM141973-01/NH/NIH HHS/United States ; R15GM141973-01/NH/NIH HHS/United States ; },
mesh = {Humans ; *Microbiota/genetics ; Genome-Wide Association Study ; *Bacteria/classification/genetics/isolation & purification ; Wound Healing/genetics ; Polymorphism, Single Nucleotide ; Chronic Disease ; Female ; Male ; *Wounds and Injuries/microbiology ; *Wound Infection/microbiology ; Middle Aged ; },
abstract = {Chronic wounds are a burden to millions of patients worldwide and impaired wound closure has been shown to be associated with wound microbiota. Recent evidence suggests human genetics may shape differences in composition of wound microbiomes. Here, a microbiome genome-wide association study was used to test effects of human genetics on the relative abundances of bacterial species in chronic wounds. Sixteen species were associated with 193 genetic loci distributed across 25 non-overlapping genomic regions, with per-species heritability estimates ranging up to 20%. Functional analyses on genomic regions and species resulted in overrepresentation of pathways relevant to microbial infection and wound healing. Species associated with host genetics exhibited co-occurrence relationships with common wound pathogens including Staphylococcus aureus. Moreover, the genetic distance among patients was significantly related to differences in their overall wound microbiome composition. Identification of genetic biomarkers reveals predictive risk factors and new mechanistic insight for chronic wounds.},
}

Humans
*Microbiota/genetics
Genome-Wide Association Study
*Bacteria/classification/genetics/isolation & purification
Wound Healing/genetics
Polymorphism, Single Nucleotide
Chronic Disease
Female
Male
*Wounds and Injuries/microbiology
*Wound Infection/microbiology
Middle Aged

@article {pmid41068162,
year = {2025},
author = {Taubenheim, J and Kadibalban, AS and Zimmermann, J and Taubenheim, C and Tran, F and Schreiber, S and Rosenstiel, P and Aden, K and Kaleta, C},
title = {Author Correction: Metabolic modeling reveals a multi-level deregulation of host-microbiome metabolic networks in IBD.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8978},
doi = {10.1038/s41467-025-64877-y},
pmid = {41068162},
issn = {2041-1723},
}

@article {pmid41068119,
year = {2025},
author = {Liu, S and Feng, B and Zhang, Z and Miao, J and Lai, X and Zhao, W and Xie, Q and Ye, X and Cao, C and Yu, P and Sun, J and Guo, J and Wang, Z and Wang, Q and Zhang, Z and Pan, Y},
title = {UPGG: expanding the taxonomic and functional diversity of the pig gut microbiome with an enhanced genome catalog.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {196},
pmid = {41068119},
issn = {2055-5008},
support = {LZ23C170003//Zhejiang Provincial Natural Science Foundation of China/ ; LZ23C170003//Zhejiang Provincial Natural Science Foundation of China/ ; 2021YFD1200802,2023YFF1001100//National Key Research and Development Program of China/ ; 2021YFD1200802,2023YFF1001100//National Key Research and Development Program of China/ ; 32272832//National Natural Science Foundation of China/ ; 32272832//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Swine/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Archaea/genetics/classification/isolation & purification ; Metagenome ; *Genome, Bacterial ; Interspersed Repetitive Sequences ; Phylogeny ; Metagenomics ; },
abstract = {The porcine gut microbiome is crucial for pig health and key to its production performance. However, genome-level analysis across multiple kingdoms remains limited. Here, we reconstructed the unified pig gastrointestinal genome (UPGG), including bacterial, archaeal, and annotated over 78 million non-redundant protein-coding genes using 5784 metagenome samples. We identified antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and the distribution of 72,056 metabolic gene clusters within existing populations. We have constructed pan-genomes of 436 high-quality microbial species and, using these as references, discovered intraspecies genomic variations that revealed 23,350,975 single-nucleotide variants (SNVs). Finally, through comparative analysis of gut microbiome genomes conducted in this study, we observed that pigs may serve as a more suitable model than other animals for investigating human gut microbiota composition and functional patterns. In summary, we constructed a comprehensive reference catalog of the porcine gut microbiome and enhanced the understanding of the host-microbe coevolution.},
}

Animals
*Gastrointestinal Microbiome/genetics
Swine/microbiology
*Bacteria/genetics/classification/isolation & purification
*Archaea/genetics/classification/isolation & purification
Metagenome
*Genome, Bacterial
Interspersed Repetitive Sequences
Phylogeny
Metagenomics

@article {pmid41067969,
year = {2025},
author = {Tito, RY and Obregon-Tito, AJ and Meza-Sánchez, G and Vela-Collantes, D and Lewis, CM and Raes, J},
title = {Navigating trust and science: microbiome research in the Amazon.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.08.007},
pmid = {41067969},
issn = {1878-4380},
abstract = {Including Indigenous Peoples in microbiome research is both a scientific imperative and an ethical responsibility. Our long-standing partnership with the Matsés Peoples from the Peruvian Amazon provided scientific insights in microbial profiles that have coevolved with humans, studies only possible via trust-based ethical partnerships. Community-based participatory research (CBPR) is essential to navigate mistrust rooted in historical injustices. We present our experience implementing culturally informed protocols and equitable benefit-sharing as cornerstones of respectful, inclusive microbiome research with Peruvian Indigenous Peoples. This approach fosters sustainable research partnerships grounded in reciprocal trust and mutual benefit.},
}

@article {pmid41067712,
year = {2025},
author = {Garg, PM and Konnikova, L and Kallapur, SG and Shenberger, JS},
title = {Does the duration of empiric antibiotic treatment influence NEC incidence and severity relative to placental pathology?.},
journal = {Journal of neonatal-perinatal medicine},
volume = {},
number = {},
pages = {19345798251387332},
doi = {10.1177/19345798251387332},
pmid = {41067712},
issn = {1878-4429},
abstract = {Necrotizing enterocolitis (NEC) remains a leading cause of mortality in preterm infants. Studies show that exposure to chorioamnionitis is associated with increased rate of NEC. The influence of the early antibiotic exposure provides contrasting findings, with a few studies demonstrating an increased risk of NEC with prenatal and postnatal antibiotic treatment, and others showing a decreased NEC risk. Far fewer reports delineate the impact of the duration of early antibiotics or the potential confounding of antibiotics by placental pathology on incidence of NEC. The provision of antibiotics following birth is associated with increased risk of NEC secondary to changes in the gut microbiome, intestinal epithelium maturation, and the intestinal barrier function. This report presents current evidence about the clinical impact of intrauterine environment and postnatal antibiotic exposure on the intestinal injury in preterm infants. We present information from our own research in conjunction with information collected from an extensive search in the databases PubMed, EMBASE, and Scopus. Both translational and prospective clinical studies are needed to fully understand the combined impact of placental pathology and postnatal antibiotic exposure on the neonatal morbidities and mortality.},
}

@article {pmid41067705,
year = {2025},
author = {Mahesh, S and Rajesh, V and Shetty, V and Mutreja, A and Hegde, A and Kamath, VG and Kunder, MA and Aroor, S and Ramamurthy, T and Pai, SR and Ballal, M},
title = {Temporal Burden of WHO Critical-Priority Enterobacteriaceae in the Infant Gut During Early Life influenced by Maternal Postpartum Antibiotic Exposure.},
journal = {Indian journal of medical microbiology},
volume = {},
number = {},
pages = {100999},
doi = {10.1016/j.ijmmb.2025.100999},
pmid = {41067705},
issn = {1998-3646},
abstract = {PURPOSE: Antimicrobial resistance (AMR) in the gut microbiome progressively evolves during infancy. This study aimed to evaluate the prevalence of WHO Critical Priority Enterobacteriaceae in infants' gut commensals and investigate the factors associated with the development of AMR.

METHODS: Stool samples were collected from 67 infants at birth, 6-weeks and 14-weeks. E. coli, Klebsiella pneumoniae and Enterobacter species were isolated and tested for susceptibility to 22 antibiotics and screened for extended-spectrum beta-lactamase (ESBL) production. Chi-square test and logistic regression tests were performed to evaluate the influence of clinical and demographic factors on the carriage of drug-resistant Enterobacteriaceae.

RESULTS: Of the 67 infants, stool samples from 38 infants (58.4%) yielded 200 isolates of Enterobacteriaceae isolates across three-timepoints. E.coli was predominant at 6-weeks (53%) and 14-weeks (63%). Cephalosporins resistance peaked at 6-weeks, with E.coli showing the highest resistance to 3[rd] (43%) and 4[th] (38%) generation cephalosporins. ESBL production was highest at 6-weeks, with 40% of E.coli producing ESBL, and 34% of infants carrying ESBL-producing strains. Maternal postpartum cephalosporin use significantly increased the likelihood of infants carrying cephalosporin-resistant Enterobacteriaceae (p-value = 0.001; OR: 10.4; 95% CI: 2.31-46.83), ESBL-producers (p-value = 0.009), and multidrug-resistant isolates (p-value = 0.027).

CONCLUSION: These findings highlight that cephalosporin-resistant Enterobacteriaceae colonize the infant gut as early as 6-weeks, with maternal postpartum antibiotic exposure playing a significant role. Understanding these early-life drivers of AMR could help inform strategies to mitigate AMR spread in vulnerable populations.},
}

@article {pmid41067393,
year = {2025},
author = {Xu, Z and Zhao, D and Guo, R and Yang, L and Zhang, X and Wang, R and Zhang, Y and Zhang, L},
title = {Bacteroides caecimuris reduces Candida albicans virulence and enhances host antifungal immunity under heat-humidity and high-fat-high-sugar stress.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108090},
doi = {10.1016/j.micpath.2025.108090},
pmid = {41067393},
issn = {1096-1208},
abstract = {Prolonged exposure to damp-heat environments coupled with high-fat-high-sugar (HFHS) diets disrupts gut microbiota homeostasis and compromises immunity, elevating risks of enteritis, diabetes, and fungal infections. In this study, We established a murine intestinal infection model by simulating damp-heat conditions (35(±2) C, 90% humidity), administering an HFHS diet, and challenging with Candida albicans (C.albicans). Mice were treated with Compound Agrimony Enteritis Capsules (FuFangXianHeCao,FFXHC), a traditional Chinese herbal formulation. Gut microbiota profiling (16S rRNA sequencing) and mechanistic studies (in vivo and in vitro) were performed. 16S rRNA analysis revealed that FFXHC treatment enhanced the abundance of the intestinal flora, with a notable increase in the abundance of Bacteroides caecimuris (B.caecimuris)(Compared with 0.11% in the model group, it increased to 2.9% after FFXHC treatment). Consequently, B.caecimuris was identified as the dominant flora, and its in-vivo and in-vitro effects on C.albicans were investigated. It was determined that FFXHC treatment could stimulate the proliferation of B.caecimuris. In addition, In vitro qPCR and optical density data and in vivo data show that although B.caecimuris could not inhibit the growth of C.albicans, it could improve the survival status and liver function of infected mice, reduce intestinal inflammation, and reduce the colonization of C.albicans by inhibiting the formation of C.albicans hyphae and reducing its virulence. The B.caecimuris contributed to the differentiation of immune cells and the secretion of immune factors in infected mice, thereby enhancing the immune response and fortifying the host defense. Our study supports a role for B. caecimuris in mediating FFXHC anti-Candida effects, bridging traditional medicine with microbiome-based therapeutics. This study provides mechanistic insights into targeting gut microbiota to combat fungal infections under metabolic stress.},
}

@article {pmid41067230,
year = {2025},
author = {Xu, JY and Chen, H and Yu, YY and Chen, TY and Wang, YQ and Xue, W and Zheng, JH and Liu, JY and Zhai, W},
title = {Intestinal Lachnospiraceae bacterium-derived propionate inhibits the progression of clear cell renal cell carcinoma.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102410},
doi = {10.1016/j.xcrm.2025.102410},
pmid = {41067230},
issn = {2666-3791},
abstract = {Gut microbiota has been reported to be associated with the development of various diseases; however, its interaction with clear cell renal cell carcinoma (ccRCC) remains unknown. To investigate the potential relationship between gut microbiota alterations and ccRCC development, we analyze feces from healthy volunteers and ccRCC patients. We realize that ccRCC patients have a lower abundance of Lachnospiraceae bacterium (L. bacterium). Further experiments reveal that L. bacterium and its metabolite, propionate, exert the antitumor effects. Mechanistically, L. bacterium-derived propionate inhibits tumor cell proliferation and migration by downregulating the expression of homeobox D10 (HOXD10) and its downstream interferon-induced transmembrane protein 1 (IFITM1) and then activating JAK1-STAT1/2 pathway. Furthermore, we design a biofilm-coated L. bacterium as a potential probiotic to improve oral delivery and therapeutic efficacy. Finally, the expanded validation cohort confirms that measuring and targeting L. bacterium and its associated pathways will provide valuable insights into clinical management and improve the prognosis of patients with ccRCC.},
}

@article {pmid41067214,
year = {2025},
author = {Alon, M and Finkel, OM},
title = {Carving out the microbiota of Earth's largest biomass reservoir.},
journal = {Cell host & microbe},
volume = {33},
number = {10},
pages = {1643-1644},
doi = {10.1016/j.chom.2025.09.008},
pmid = {41067214},
issn = {1934-6069},
mesh = {*Microbiota ; *Wood/microbiology ; *Biomass ; *Fungi/classification/isolation & purification/genetics ; *Bacteria/classification/isolation & purification/genetics ; Ecosystem ; Earth, Planet ; },
abstract = {Despite being an essential part of terrestrial ecosystems for ∼400 million years, the microbiome of wood is surprisingly underexplored. In a recent issue of Nature, Arnold et al. make a long overdue dive into the unique and surprisingly diverse prokaryotic and fungal communities of heartwood and sapwood.},
}

*Microbiota
*Wood/microbiology
*Biomass
*Fungi/classification/isolation & purification/genetics
*Bacteria/classification/isolation & purification/genetics
Ecosystem
Earth, Planet

@article {pmid41067159,
year = {2025},
author = {Wang, T and Liu, C and Ma, R and Pan, X and Yang, T and Zhan, J and Tian, Y},
title = {Digestive and fermentation characteristics of esterified starches based on digestion kinetics, microbiome and metabolomics analysis.},
journal = {Food chemistry},
volume = {496},
number = {Pt 1},
pages = {146673},
doi = {10.1016/j.foodchem.2025.146673},
pmid = {41067159},
issn = {1873-7072},
abstract = {Esterified starch (ES) is one of the most common forms of resistant starch employed in the food industry. In this study, the digestive and fermentation properties of ES with different substitution groups were investigated by digestion kinetics, microbiome and metabolomics. The introduction of esterification groups slows down the digestion rate of starch and alters the crystal structure and molecular weight distribution. Following in vitro fermentation, ES significantly reduced the relative abundance of opportunistic pathogens. Furthermore, predicted analysis indicated that ES enhances the microbiota's capabilities in terms of pyruvate metabolism, and [EC: 1.2.4.1] and [EC: 2.3.1.12] were found to be over-expressed. The intervention of ES mainly regulates the levels of metabolites related to the metabolism and synthesis pathways of amino acids. Structural equation modeling indicates that, the molecular weight distribution of ES can significantly induce changes in the composition of the gut microbiota, and further affect metabolic enzymes and metabolites.},
}

@article {pmid41066946,
year = {2025},
author = {Moon, Y and Thiruppathi, G},
title = {The soil nematode exposome: Unraveling the impacts of particulate plastics from agroecosystems to one health.},
journal = {The Science of the total environment},
volume = {1003},
number = {},
pages = {180649},
doi = {10.1016/j.scitotenv.2025.180649},
pmid = {41066946},
issn = {1879-1026},
abstract = {The escalating accumulation of particulate plastics in terrestrial ecosystems demands innovative, biologically informed approaches to evaluate their ecological and human health impacts. Soil nematodes are gaining recognition as sensitive and ecologically relevant bioindicators for assessing the effects of plastic pollution in soils. Their widespread distribution, trophic adaptability, and close association with soil particles make them ideal sentinels for detecting subtle yet significant biological responses to micro- and nanoplastics. Plastic contamination can disrupt soil structure, microbiome composition, and nutrient cycling, which in turn affects nematode abundance, diversity, and community dynamics. Recent advancements in soil nematode-based bioassays, bolstered by molecular and omics technologies, offer novel insights into the nematode exposome, capturing direct particle interactions, microbial shifts, and trophic transfer processes. We propose a tiered assessment framework that leverages conserved molecular pathways in nematodes to predict both environmental and human health outcomes associated with plastic exposure. By integrating nematode ecological indices with mechanistic biomarkers, this framework transforms risk assessment into a more holistic, efficient, and cost-effective model. Incorporating nematodes into plastic pollution studies not only enhances our capacity to monitor soil ecosystem health but also plays a crucial role in safeguarding agricultural sustainability and public health in an increasingly plastic-laden food chain.},
}

@article {pmid41066555,
year = {2025},
author = {Macadangdang, BR and Wang, Y and Woodward, CL and Revilla, JI and Shaw, BM and Sasaninia, K and Varnum, GE and Makanani, SK and Berruto, C and Ahuja, U and Miller, JF},
title = {Targeted protein evolution in the gut microbiome by diversity-generating retroelements.},
journal = {Science (New York, N.Y.)},
volume = {390},
number = {6769},
pages = {eadv2111},
doi = {10.1126/science.adv2111},
pmid = {41066555},
issn = {1095-9203},
mesh = {*Gastrointestinal Microbiome/genetics ; *Retroelements/genetics ; Animals ; *Bacteroides/genetics/classification ; Mice ; Humans ; Female ; *Evolution, Molecular ; Germ-Free Life ; Gene Transfer, Horizontal ; *Bacterial Proteins/genetics ; Genetic Variation ; *Fimbriae Proteins/genetics ; },
abstract = {Diversity-generating retroelements (DGRs) accelerate evolution by rapidly diversifying variable proteins. The human gastrointestinal microbiota harbors the greatest density of DGRs known in nature, suggesting that they play adaptive roles in this environment. We identified >1100 distinct DGRs among human-associated Bacteroides species and discovered a subset that diversify adhesive components of type V pili and related proteins. We show that Bacteroides DGRs are horizontally transferred across species, display activity levels ranging from high to low, and preferentially alter the functional characteristics of ligand-binding residues on adhesive organelles. Specific variable protein sequences are enriched when Bacteroides strains compete with other commensal bacteria in gnotobiotic mice. Analysis of >2700 DGRs from diverse phyla in mother-infant pairs shows that Bacteroides DGRs are disproportionately transferred to vaginally delivered infants where they actively diversify. Our observations provide a foundation for understanding the potential roles of targeted genome plasticity in shaping host-associated microbial communities.},
}

*Gastrointestinal Microbiome/genetics
*Retroelements/genetics
Animals
*Bacteroides/genetics/classification
Mice
Humans
Female
*Evolution, Molecular
Germ-Free Life
Gene Transfer, Horizontal
*Bacterial Proteins/genetics
Genetic Variation
*Fimbriae Proteins/genetics

@article {pmid41066515,
year = {2025},
author = {Castelló-Sanjuán, M and González, R and Romoli, O and Blanc, H and Nigg, JC and Saleh, MC},
title = {Persistent viral infections impact key biological traits in Drosophila melanogaster.},
journal = {PLoS biology},
volume = {23},
number = {10},
pages = {e3003437},
doi = {10.1371/journal.pbio.3003437},
pmid = {41066515},
issn = {1545-7885},
abstract = {Persistent viral infections have been assumed to impose minimal fitness costs for insects. We established persistent mono-infections of Drosophila melanogaster with four different enteric RNA viruses: Drosophila A virus (DAV), Drosophila C virus (DCV), Bloomfield virus, and Nora virus. We observed that these infections significantly reduce fly survival, alter the number of viable offspring per female, modulate microbiome composition, impact locomotor abilities, and change activity patterns. These results demonstrate the significant impact of persistent viral infections on key biological traits and expand our understanding of the fitness costs of persistent viral infections for the host. In addition, the four viruses displayed different accumulation kinetics and elicited unique transcriptional profiles with no common core responses. The transcriptional changes triggered by DCV infection persisted even after viral clearance. This comprehensive comparative dataset represents a valuable resource for researchers studying host-pathogen interactions, providing detailed transcriptional profiles, and behavioral measurements across different viral infections and time points. Our findings reveal that persistent viral infections modulate critical aspects of insect biology, affecting host physiology and behavior.},
}

@article {pmid41066421,
year = {2025},
author = {Jensen, R and McKenney, EA and Beasley, JC and Cloete, CC and Melton, M and Lafferty, DJR},
title = {Interspecific variation in gut microbiome diversity across the Etosha National Park herbivore community.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0333639},
doi = {10.1371/journal.pone.0333639},
pmid = {41066421},
issn = {1932-6203},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Male ; *Herbivory ; Female ; Namibia ; RNA, Ribosomal, 16S/genetics ; Parks, Recreational ; Feces/microbiology ; Biodiversity ; *Bacteria/genetics/classification ; },
abstract = {The community of microbes in the gastrointestinal tract of mammals, known as the gut microbiome (GMB), plays a critical role in host ecology and evolution. GMB variation is modulated by both host physiology and environmental conditions experienced by the host. Here we characterized the GMBs of 11 free-ranging large herbivore species inhabiting Etosha National Park, Namibia. We examined how intrinsic (i.e., sex, gut morphology, feeding guild) and extrinsic (i.e., geographic zone, waterhole site) factors influenced GMB diversity and community structure within and across herbivore species. We extracted DNA from herbivore fecal samples (n = 312) and amplified the 16s rRNA gene region to identify bacterial taxa. We defined core bacterial taxa as those present at ≥1% relative abundance in ≥50% of the samples from each species. Within bovid species, the core phylum Verrucomicrobiota and the core genera RF39, Alistipes, Christensenellaceae_R-7 group, and NK4A214 were significantly different in abundance across geographic zones. Microbial richness was significantly greater in female than male eland, and we detected sex-specific differences in Christensenellaceae_R-7 group across all herbivores and P-251-O5 within gemsbok. Mean Bulla evenness was higher in ruminants than nonruminants and differed significantly between giraffes and impala. Elephants also showed a significant correlation between unweighted UniFrac distance and geographic distance between sample locations. By identifying baseline core microbial abundance and occurrence data for this herbivore community, wildlife managers can incorporate long-term GMB monitoring to track microbial shifts in host species over time.},
}

Animals
*Gastrointestinal Microbiome/genetics
Male
*Herbivory
Female
Namibia
RNA, Ribosomal, 16S/genetics
Parks, Recreational
Feces/microbiology
Biodiversity
*Bacteria/genetics/classification

@article {pmid41066365,
year = {2025},
author = {Bi, Z and Wang, F and Wang, S and Fang, Z},
title = {Immune repertoire profiling and T cell dysregulation in Peripheral Blood Mononuclear Cells of Type 2 diabetic patients.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0332736},
doi = {10.1371/journal.pone.0332736},
pmid = {41066365},
issn = {1932-6203},
mesh = {Humans ; *Diabetes Mellitus, Type 2/immunology/genetics/microbiology ; *Leukocytes, Mononuclear/immunology/metabolism ; Male ; Female ; *T-Lymphocytes/immunology/metabolism ; Middle Aged ; *Receptors, Antigen, T-Cell/genetics/immunology ; Aged ; Microbiota/immunology ; Gene Expression Profiling ; },
abstract = {OBJECTIVE: The prevalence of diabetes mellitus (DM) is escalating globally, presenting a significant public health challenge. The immune system, particularly T cells, plays a crucial role in the pathogenesis of diabetes. This study aims to elucidate the characteristics of T cell receptors (TCRs) and immune dysregulation within peripheral blood mononuclear cells (PBMCs) of diabetic patients, with exploratory analysis of microbial profiles.

METHODS: We employed high-throughput RNA-seq to analyze the protein-coding genes expression, and function enrichment with different expression, BCR/TCR repertoires and microbial communities in PBMC samples collected from both diabetic patients and healthy controls. Comparative analysis was conducted to identify distinct TCR signatures associated with diabetes. Microbial communities were secondarily assessed via unmapped RNA-seq reads.

RESULTS: Overall, we found different patterns of gene expression, gene function, immune cell proportion, immune repertoire and microbiome between the different DM and control groups. 1145 upregulated 400 down-regulated genes were identified, and immune response function terms were enriched, such as, cell-cell adhesion via plasma-membrane adhesion molecules, and homophilic cell adhesion via plasma membrane adhesion molecules (BP); as well as in the T cell receptor complex, plasma membrane signaling receptor complex, alpha-beta T cell receptor complex (CC), and in antigen binding and immunoglobulin receptor binding (MF). Furthermore, reactome pathway enrichment analysis revealed enrichment of these DEGs in Viral mRNA Translation, Influenza Viral RNA Transcription and Replication, SARS-CoV-1 modulates host translation machinery, Interleukin-6 family signaling, etc. DM PBMC showed significantly lower chao1 index of TCR (including TCRA and TCRB) and reduced expression of TRAV/TRBV genes compared to controls. Enriched pathways included T cell receptor complex, antigen binding, and interleukin-6 signaling. Exploratory analysis of microbial reads revealed decreased alpha diversity (chao1/ACE) in DM and 123 altered taxa, though microbial abundance was low.

CONCLUSION: Our study provides novel insights into T cell receptor dysregulation in diabetes. The role of PBMC-associated microbiota requires further validation.},
}

Humans
*Diabetes Mellitus, Type 2/immunology/genetics/microbiology
*Leukocytes, Mononuclear/immunology/metabolism
Male
Female
*T-Lymphocytes/immunology/metabolism
Middle Aged
*Receptors, Antigen, T-Cell/genetics/immunology
Aged
Microbiota/immunology
Gene Expression Profiling

@article {pmid41066278,
year = {2025},
author = {Tourab, H and Lopez-Perez, L and Arroyo-Gallego, P and Georga, E and Rujas, M and Ponziani, FR and Torrego-Ellacuria, M and Merino-Barbancho, B and Niccolo, N and Ciuti, G and Fotiadis, D and Antonio, G and Cabrera, MF and Arredondo, MT and Fico, G},
title = {The Use of Machine Learning and Explainable Artificial Intelligence in Gut Microbiome Research: A Scoping Review.},
journal = {IEEE journal of biomedical and health informatics},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/JBHI.2025.3593198},
pmid = {41066278},
issn = {2168-2208},
abstract = {Gut microbiome research has made tremendous progress, especially with the integration of machine learning and artificial intelligence that can provide new insights from complex microbiome data and its impact on human health. The use of explainable artificial intelligence is becoming critical in medicine and adopting it in precision medicine-models leveraging gut microbiome data is appealing for providing more transparency and trustworthiness in clinical research. This scoping review evaluates the use of machine learning and explainable artificial intelligence techniques and identifies existing gaps in knowledge in this research area to suggest future research directions. Online databases (PubMed and Scopus) were searched to retrieve papers published between 2018-2024, and from which we selected 76 publications. Different clinical applications of machine learning and artificial intelligence techniques in gut microbiome studies were explored in the reviewed articles. We observed a high prevalence in the use of black box models in the field, with Random Forest being the most used algorithm. The explainability remains somewhat limited in the field, but it appears to be improving. Researchers showed interest in SHAP applications as an explainable technique. Finally, not enough attention was paid to the reproducibility of the research work published. This review highlights opportunities for advancing research on explainable artificial intelligence models in the field of microbiome, supporting future applications of microbiome-based precision medicine.},
}

@article {pmid41066275,
year = {2025},
author = {Mutafcilar Velioglu, E and Arslan, U and Kayis, SA and Maçin, S and Kamada, N and Hakki, S},
title = {Correlation in the change of gut microbiota with clinical periodontal parameters in grade C periodontitis patients after non-surgical periodontal therapy.},
journal = {Journal of medical microbiology},
volume = {74},
number = {10},
pages = {},
doi = {10.1099/jmm.0.002065},
pmid = {41066275},
issn = {1473-5644},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *Periodontitis/therapy/microbiology ; Middle Aged ; Adult ; Saliva/microbiology ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; Dysbiosis/microbiology ; },
abstract = {Introduction. Intestinal dysbiosis is associated with systemic health, and approaches targeting the microbiome can influence the host. Oral and intestinal microbiota are interrelated; therefore, we aimed to determine whether non-surgical periodontal treatment (NSPT) affects systemic health through its impact on the intestinal microbiota.Hypothesis/Gap Statement. Although the association between oral and gut microbiota has been suggested, there is limited evidence regarding how periodontal therapy may influence intestinal microbial composition. We hypothesized that NSPT in patients with periodontitis would lead to favourable changes in the gut microbiome, which may parallel improvements in clinical periodontal parameters.Aim. This study aimed to investigate the effect of NSPT on both oral and intestinal microbiota and to evaluate whether changes in gut microbial composition correlate with periodontal clinical outcomes.Methodology. Five systemically healthy individuals with grade C periodontitis and five systemically and periodontally healthy individuals were included. Saliva and stool samples were collected at baseline and 1 month after NSPT. DNA extractions were performed and subjected to 16S ribosomal RNA gene sequencing on the Illumina Novaseq at the V3-V4 hypervariable regions.Results. Grade C periodontitis patients displayed distinct oral and gut microbiomes compared to healthy individuals. NSPT resulted in a reduction in the diversity of both saliva and stool samples in healthy individuals (P>0.05). Salivary Fusobacteriota levels (P<0.05) and the gut Firmicutes/Bacteroides ratio decreased after NSPT. Moreover, changes in gut microbiota significantly correlated with improvements in periodontal probing depth and clinical attachment level in periodontitis patients.Conclusion. The improvement in clinical periodontal parameters after NSPT correlates with a positive shift in the gut microbiome towards health. Although the number of participants was limited, these findings support a strong relationship between periodontal and gut status. Further studies with larger cohorts and long-term follow-up are required to confirm these results.},
}

Humans
*Gastrointestinal Microbiome
Male
Female
*Periodontitis/therapy/microbiology
Middle Aged
Adult
Saliva/microbiology
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Bacteria/classification/genetics/isolation & purification
Dysbiosis/microbiology

@article {pmid41066239,
year = {2025},
author = {Cook, RA and Ponsero, AJ and Telatin, A and Yang, Y and Liang, Z and Wang, F and Chen, R and Wang, Z and Adriaenssens, EM and Clokie, MRJ and Millard, AD and Brightling, CE},
title = {Bacteriophage diversity declines with COPD severity in the respiratory microbiome.},
journal = {Cell reports},
volume = {44},
number = {10},
pages = {116413},
doi = {10.1016/j.celrep.2025.116413},
pmid = {41066239},
issn = {2211-1247},
abstract = {Chronic obstructive pulmonary disease (COPD) severity correlates with airway microbial dysbiosis, yet bacteriophage roles remain unexplored. We characterized the lung DNA virome by re-analyzing 135 sputum metagenomes from 99 COPD patients and 36 healthy controls. We identified 1,308 viral operational taxonomic units, revealing progressively lower viral diversity correlating with disease severity. While viral and bacterial diversity typically showed strong positive correlations, patients with frequent exacerbations uniquely exhibited decoupled viral-bacterial relationships, indicating disrupted ecological dynamics. Comparing all COPD patients to controls, phages infecting anaerobic oral bacteria showed disproportionately lower abundance-Porphyromonas phages were 40-fold less abundant, despite only 4-fold lower bacterial abundance-while pathogen-associated phages showed no significant differences. We detected virulence factor-encoding phages, including two neuA-carrying Haemophilus phages in 7.4% of Haemophilus-colonized patients, associated with 82-fold higher bacterial abundance. These findings establish altered bacteriophage ecology as an unrecognized feature of COPD pathobiology, with differential phage-bacteria relationships that reshape lung microbial ecosystems, offering new perspectives for microbiome-targeted interventions.},
}

@article {pmid41066229,
year = {2025},
author = {Lietuvninkas, HB and Chervonsky, A and Golovkina, T},
title = {Cohousing or cross-fostering followed by cohousing does not normalize the microbiomes of genetically distinct adult mice.},
journal = {Cell reports},
volume = {44},
number = {10},
pages = {116402},
doi = {10.1016/j.celrep.2025.116402},
pmid = {41066229},
issn = {2211-1247},
abstract = {It is widely assumed that the horizontal transmission of microorganisms due to coprophagy or colonization of newborns normalizes the microbiomes of genetically distinct mice. Accordingly, cohousing animals of different genetic backgrounds or fostering them as neonates by the same females is commonly used for equilibrating microbial communities in laboratory mice. To assess whether these assumptions hold true under well-controlled experimental conditions, we analyze the composition of the gut commensal bacteria of adult mice from distinct genetic backgrounds either foster nursed by the same dams or cohoused as adults. Despite shared environmental conditions, significant differences in the gut bacterial profiles idiosyncratic to genetic backgrounds persist across all experiments. These findings indicate that host genetics play a crucial role in maintaining specific microbial communities in adult mice that cannot be permanently altered by either foster nursing or cohousing.},
}

@article {pmid41065901,
year = {2025},
author = {ParsaSefat, M and Bahar, A and Khazaei, M and Jahantigh, M and Tahmasebi, H},
title = {How microbiota influence maternal blood disorder in miscarriage.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {1004},
pmid = {41065901},
issn = {1573-4978},
mesh = {Humans ; Female ; Pregnancy ; *Abortion, Spontaneous/microbiology ; *Microbiota/physiology ; Vagina/microbiology ; Gastrointestinal Microbiome/physiology ; *Pregnancy Complications, Hematologic/microbiology ; },
abstract = {The occurrence of miscarriage signifies a significant loss during pregnancy, profoundly affecting many women internationally. The intricate and multifaceted nature of miscarriage causes has led recent investigations to propose that vaginal microbiota may be a contributing factor. A diverse array of microbes constitutes the vaginal microbiome, which plays a vital role in safeguarding vaginal health and reducing the risk of infections. The link between the vaginal microbiome and miscarriage is not yet fully understood. The gut microbiome also serves as a recognized supporting organ, reflecting its many relationships with the overall health of the host individual. Moreover, adverse effects on the microbiomes present in various body systems can significantly compromise overall health. The characterization of microorganisms, known as the microbiota, in relation to human health has involved exploring which organisms exist, how they function in interaction with human cells, and the mechanisms that govern these interactions. The purpose of this review is to investigate how distinct microbiota may influence the risk of miscarriage. Moreover, our research delves into the multiple mechanisms through which maternal blood disorders can impact the likelihood of miscarriage, also looking into the known connections between microbiota and humans, with an emphasis on their impact on blood disorders.},
}

Humans
Female
Pregnancy
*Abortion, Spontaneous/microbiology
*Microbiota/physiology
Vagina/microbiology
Gastrointestinal Microbiome/physiology
*Pregnancy Complications, Hematologic/microbiology

@article {pmid41065880,
year = {2025},
author = {Gates, TJ and Wangmo, D and Bergerud, KMB and Keel, BM and Staley, C and Subramanian, S},
title = {SMAD4 mutation drives gut microbiome shifts toward tumor progression in colorectal cancer.},
journal = {Discover oncology},
volume = {16},
number = {1},
pages = {1841},
pmid = {41065880},
issn = {2730-6011},
abstract = {BACKGROUND: Colorectal cancer (CRC) progression is driven by a series of sequential mutations in key driver genes; however, the factors underlying tumor progression and metastasis remain poorly understood. Mutations in TP53 and SMAD4, in particular, are associated with CRC progression. Although gut microbiome dysbiosis is implicated in CRC initiation and progression, the interactions between the microbiome and specific CRC driver mutations, especially those promoting metastasis, are not well defined.

METHODS: In this study, we utilized triple mutant (Apc, Kras, Tp53; AKP) and quadruple mutant (Apc, Kras, Tp53, Smad4; AKPS) organoid-based orthotopic mouse models of CRC to investigate the impact of the SMAD4 mutation on microbiome composition.

RESULTS: Our results reveal significant differences in metastatic potential and microbial community dynamics between the two tumor models. AKPS tumors exhibited metastasis to the lymph nodes, liver, and lungs, while AKP tumors remained confined to the colon. Longitudinal microbiome analysis showed shifts in microbial composition within each tumor model. Both AKP and AKPS models demonstrated enrichment of Faecalibaculum and a decrease in Dubosiella over time; however, additional shifts were noted with distinct taxa associated with late-stage tumors in each group. Notably, the AKPS model exhibited higher relative abundances of pro-inflammatory taxa, including Turicibacter, Romboutsia, and Akkermansia, suggesting that the SMAD4 mutation promotes a more immunosuppressive and pro-metastatic microbiome profile.

CONCLUSIONS: These findings emphasize  the significance of SMAD4 mutation and microbiome modulation, revealing the interaction between host genetics and gut microbiota in driving colorectal cancer aggressiveness and suggesting potential microbial targets.},
}

@article {pmid41065795,
year = {2025},
author = {Schulz, N and Lange, U and Klemm, P},
title = {[The role of nutrition in osteoprotection].},
journal = {Orthopadie (Heidelberg, Germany)},
volume = {},
number = {},
pages = {},
pmid = {41065795},
issn = {2731-7153},
abstract = {BACKGROUND: Nutrition represents an essential non-pharmacological factor in the prevention of osteoporosis. Evidence-based findings support that adequate intake of protein, calcium, and vitamin D promotes bone health. Vitamin D and calcium, particularly in combination, demonstrate preventive effects. The evidence regarding vitamin K2 supplementation remains inconsistent, and current guidelines do not recommend its use.

FOOD COMPOSITION: Fermented dairy products, calcium-rich mineral waters, and a Mediterranean dietary pattern are associated with higher bone mineral density and a reduced fracture rate. Plant-based diets such as veganism carry an increased fracture risk if macronutrient and micronutrient intake is inadequate. Recent findings also highlight the role of the gut microbiome in osteoprotection. Overall, current data underscore the importance of a balanced, nutrient-rich diet in the prevention of osteoporotic fractures.},
}

@article {pmid41065694,
year = {2025},
author = {Ambar, N and Thurber, MI and Sudakaran, S},
title = {A COMPARATIVE STUDY OF GUT MICROBIOMES IN FOUR SPECIES OF HEALTHY GIBBONS (HYLOBATIDAE) IN A MANAGED SETTING.},
journal = {Journal of zoo and wildlife medicine : official publication of the American Association of Zoo Veterinarians},
volume = {56},
number = {3},
pages = {608-620},
doi = {10.1638/2024-0062},
pmid = {41065694},
issn = {1042-7260},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Hylobates/microbiology ; Feces/microbiology ; *Bacteria/classification/isolation & purification ; Female ; Male ; Species Specificity ; Animals, Zoo ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The microbiome plays a crucial role in human and animal health and welfare; however, no data exists regarding the gibbon microbiome. This study offers the first comprehensive analysis of the gut microbiome of 4 gibbon species in a managed setting, exploring the effects of controlled environmental and dietary conditions on microbial diversity and composition. Three fecal samples were collected from 24 healthy individuals from 4 gibbon species (Hoolock leuconedys, n = 7; Nomascus leucogenys, n = 9; Hylobates pileatus, n = 6; and Hylobates moloch, n = 7) over the course of 1 month. All animals were housed in a single facility with identical environmental conditions and diet. The gut microbiomes were characterized using 16s amplicon sequencing, revealing significant differences in microbial richness across species, with Javan gibbons exhibiting the highest mean diversity (Shannon: 5.347, SD = 0.201) and pileated gibbons the lowest (Shannon: 5.167, SD = 0.241; p < 0.05). Analysis identified 4,070 distinct Amplicon Sequence Variants (ASVs) assigned to 18 phyla, with 70.5% shared across species. Unique microbial genera (ranging from 1%-4.9%) were exclusive to each species, indicating distinct gut microbiome configurations. Additionally, although common microbial genera were found across all species, significant variations in specific bacterial taxa's abundance were observed. This highlights the uniqueness of each species' gut microbiome and challenges the assumption of homogeneity in captive primate microbiomes. Investigations into the enclosure soil microbiomes suggest a minimal impact on the gibbon gut microbial composition. This research emphasizes the complexity of gibbon microbiomes and offers novel insights into their health, management, and conservation.},
}

Animals
*Gastrointestinal Microbiome
*Hylobates/microbiology
Feces/microbiology
*Bacteria/classification/isolation & purification
Female
Male
Species Specificity
Animals, Zoo
RNA, Ribosomal, 16S/genetics

@article {pmid41065403,
year = {2025},
author = {Silva, JVd and Conteville, LC and Bruscadin, JJ and Cardoso, TF and Porto, T and Oliveira, PSNd and Zerlotini, A and Medeiros, SRd and Mourão, GB and Coutinho, LL and Palhares, JCP and Berndt, A and Guan, LL and Andrade, BGN and Regitano, LCdA},
title = {Dietary modulation of the rumen microbiome drives the expression of metabolic and methanogenic pathways in Bos indicus.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0053525},
doi = {10.1128/msphere.00535-25},
pmid = {41065403},
issn = {2379-5042},
abstract = {UNLABELLED: Diet influences ruminal methane emissions by modulating the composition and activity of the rumen microbiome. However, how diet shapes the functional capacity of the rumen microbiome in Nelore cattle (Bos indicus), a key tropical beef breed, remains unclear. This study used metatranscriptomics to investigate how dietary supplementation with agro-industrial by-products affects the active rumen microbiome and its association with residual methane emissions. Rumen samples from 50 Nelore cattle fed either a conventional or by-product-based diet revealed that the active microbiome was dominated by bacteria (88.4% ± 3.16%) and archaea (11.6% ± 3.16%), with no significant taxonomic differences between diets. Despite this, functional profiling identified genes from 193 pathways and 3,512 gene families, with distinct metabolic signatures between diets. Specifically, six pathways and 87 gene families were unique to the conventional diet, while seven pathways and 210 gene families were unique to the by-product diet. The associations between gene families enriched under each diet with residual methane emission revealed that the expression of two gene families exhibited negative correlations, while five were positively correlated with methane emission under conventional diet. In the by-product diet, we identified five gene families positively associated with methane emissions and 14 negatively associated. These results demonstrate that diet alters rumen microbial functions with methane mitigation potential, without affecting taxonomic composition.

IMPORTANCE: Understanding how diet modulates the functional activity of the rumen microbiome is essential for developing strategies to mitigate methane emissions in cattle. This study provides novel insights into how feeding agro-industrial by-products to Nelore cattle (Bos indicus), a key tropical beef breed, reshapes the functional profile of the rumen microbiome. Although no taxonomic shifts were detected, animals fed the by-product diet exhibited a greater number of microbial functions associated with lower methane production potential. These findings suggest that diet-driven modulation of microbial metabolism could contribute to strategies aimed at reducing methane emissions. Moreover, the use of by-products supports circular economy principles, enhancing the sustainability and economic resilience of tropical livestock systems. This work emphasizes the importance of examining the active microbiome through RNA rather than solely profiling taxonomic composition without considering microbial activity. It also contributes to unveiling microbial functions to support future methane mitigation and sustainable feeding strategies.},
}

@article {pmid41065304,
year = {2025},
author = {Ganggang, K and Cheng, G and Gang, L and Wenwu, Z and Di, Z and Yan, L and Baoshu, X and Yiqin, W},
title = {From Molecular Docking to Rat Models: Butyrate From a High-Fiber Diet Inhibits HDAC1 and NLRP3 Inflammasome to Alleviate Oxidative Stress and Inflammation After Spinal Cord Injury.},
journal = {Journal of neurochemistry},
volume = {169},
number = {10},
pages = {e70250},
doi = {10.1111/jnc.70250},
pmid = {41065304},
issn = {1471-4159},
support = {82100124//National Natural Science Foundation of China/ ; 202201011069//Guangzhou Science and Technology Plan Project/ ; },
mesh = {Animals ; *NLR Family, Pyrin Domain-Containing 3 Protein/metabolism/antagonists & inhibitors ; *Spinal Cord Injuries/metabolism/diet therapy ; Rats ; *Oxidative Stress/drug effects/physiology ; *Inflammasomes/metabolism/drug effects/antagonists & inhibitors ; *Butyrates/pharmacology/metabolism/administration & dosage ; *Molecular Docking Simulation/methods ; Rats, Sprague-Dawley ; *Histone Deacetylase 1/metabolism/antagonists & inhibitors ; Male ; Inflammation/metabolism ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Spinal cord injury (SCI) induces complex inflammatory and oxidative stress responses that exacerbate secondary damage and impair functional recovery. This study investigated the role of butyrate-a microbiota-derived short-chain fatty acid (SCFA)-in ameliorating SCI using a combination of in silico, in vitro, and in vivo approaches. We first performed gut microbiota 16S rRNA sequencing and targeted metabolomics to assess microbial dysbiosis and serum SCFA levels in rats post-SCI. A marked reduction in butyrate-producing Firmicutes and serum butyrate concentrations was observed after injury. Molecular docking predicted a direct interaction between butyrate and HDAC1, which was confirmed by a ~40% reduction in HDAC1 expression in spinal cord tissue, as demonstrated by Western blot and immunofluorescence. In microglial cultures, butyrate significantly inhibited LPS + ATP-induced NLRP3 inflammasome activation by approximately 38%. For the in vivo component, a cervical hemi-contusion SCI model at the C5 level was established in rats. To restore butyrate levels, animals were either fed a high-fiber diet (HFD) or received intrathecal butyrate administration. Behavioral assessment revealed a 1.5-fold improvement in Forelimb Locomotor Scale scores at 1 month post-injury, and motor-evoked potential recordings showed nearly a 1.8-fold enhancement, indicating significantly improved locomotor and electrophysiological recovery in HFD-treated rats compared to controls. Furthermore, HFD treatment resulted in reduced oxidative stress (as evidenced by lower MDA and DHE staining), decreased inflammation, while butyrate administration promoted M2-type macrophage/microglia polarization. These findings reveal that butyrate mitigates oxidative stress and inflammation by targeting HDAC1 and the NLRP3 inflammasome. Importantly, HFD-driven restoration of microbial butyrate production represents a promising and translationally relevant non-invasive therapeutic strategy to enhance SCI recovery via the gut-spinal cord axis.},
}

Animals
*NLR Family, Pyrin Domain-Containing 3 Protein/metabolism/antagonists & inhibitors
*Spinal Cord Injuries/metabolism/diet therapy
Rats
*Oxidative Stress/drug effects/physiology
*Inflammasomes/metabolism/drug effects/antagonists & inhibitors
*Butyrates/pharmacology/metabolism/administration & dosage
*Molecular Docking Simulation/methods
Rats, Sprague-Dawley
*Histone Deacetylase 1/metabolism/antagonists & inhibitors
Male
Inflammation/metabolism
Gastrointestinal Microbiome/drug effects

@article {pmid41065279,
year = {2025},
author = {Baima, G and Arce, M and Romandini, M and Van Dyke, T},
title = {Inflammatory and Immunological Basis of Periodontal Diseases.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70040},
pmid = {41065279},
issn = {1600-0765},
abstract = {In its most common form, periodontitis is viewed as a chronic immunoinflammatory disorder of the tooth supporting tissues, shaped by host-microbiome disequilibrium, exaggerated immune activation, and impaired resolution mechanisms. This review explores the periodontal battlefield through its inflammatory and immunological lens, beginning with the transformation of the lesion from silent immune surveillance to sustained inflammation, connective tissue degradation, and alveolar bone loss. The classical Page and Schroeder model is used as a foundation but reinterpreted in light of current evidence derived from advanced molecular techniques. The immunological architecture is subsequently dissected through the involvement of its principal cellular players, acting in a dynamic battleground composed of saliva, crevicular fluid, epithelial barriers, and connective tissues. On the frontlines, neutrophils act as double-edged defenders, capable of both microbial clearance and bystander tissue damage. Like macrophages and dendritic cells, they also serve as strategic sensors and shapers of immunity, bridging innate and adaptive responses. Among these, the T cell arsenal includes inflammatory subsets such as Th1, Th17, and cytotoxic cells, balanced by regulatory T cells. B lymphocytes and plasma cells emerge not only as antibody producers but also as pro-inflammatory effectors, with growing evidence implicating autoreactive subsets in tissue damage, particularly in aggressive forms of the disease. Equally critical are the structural cells: gingival fibroblasts, which transition from matrix architects to immune-active contributors under stress, and osteocytes, recognized as mechanosensitive regulators of bone turnover and immune signaling. Alongside osteoblasts and osteoclasts, these elements form a fragile yet responsive osteoimmune axis that determines the trajectory toward either tissue homeostasis or destruction. The molecular arsenal fueling this conflict-cytokines, chemokines, complement, specialized pro-resolving mediators, neuropeptides, and matrix metalloproteinases-is also examined, highlighting how its dysregulation sustains chronic inflammation and drives structural breakdown. The review also explores how this localized immune conflict echoes systemically, contributing to broader immune activation and comorbidity. By reframing periodontitis as a prototypical immune-mediated disease, this work contributes to a deeper understanding of its pathogenesis and provides a framework for future research aimed at disentangling its immunological complexity and clinical heterogeneity for targeted diagnostic strategies and immune-based therapeutics.},
}

@article {pmid41065113,
year = {2025},
author = {Palacios, N and Gordon, S and Wang, T and Burk, R and Qi, Q and Huttenhower, C and Gonzalez, HM and Knight, R and De Carli, C and Daviglus, M and Lamar, M and Telavera, G and Tarraf, W and Kosciolek, T and Cai, J and Kaplan, RC},
title = {Gut microbiome and cognitive function in the Hispanic Community Health Study/Study of Latinos.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {},
number = {},
pages = {13872877251376911},
doi = {10.1177/13872877251376911},
pmid = {41065113},
issn = {1875-8908},
abstract = {BackgroundThere is limited work on the association between the gut microbiome and Alzheimer's disease and related dementia (AD/ADRD) in Latinos.ObjectiveWe examined, within the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) cohort, the association between gut microbiome and cognitive function.MethodsWe analyzed the fecal metagenomes of 2471 HCHS/SOL participants to identify microbial taxonomic and functional features associated with global cognitive function. Omnibus (PERMANOVA) and feature-wise analyses (MaAsLin2) were conducted to identify microbiome-cognition associations, and specific microbial species and pathways (Kyoto Encyclopedia of Genes and Genomes (KEGG modules) associated with cognition.ResultsEubacterium species (E. siraeum and E. eligens), and C phoceensis, among other species were associated with better cognition. Several KEGG modules, most strongly Ornithine, Serine biosynthesis and Urea Cycle, were associated with worse cognition.ConclusionsIn a large Hispanic/Latino cohort, we identified several microbial taxa and KEGG pathways associated with cognition.},
}

@article {pmid41064842,
year = {2025},
author = {Kuswandi, W and Budiman, C and Khaerunnisa, I and Sumantri, C},
title = {Rearing system and immune status influence the small intestinal microbiota of IPB-D3 chickens: A full-length 16S rRNA metagenomic approach.},
journal = {Veterinary world},
volume = {18},
number = {8},
pages = {2206-2221},
pmid = {41064842},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: The small intestinal microbiota plays a pivotal role in poultry digestion and immune function. Rearing systems can influence their composition, thereby affecting the overall health and performance of the birds. This study aimed to investigate how rearing systems (intensive [IN] vs. free-range [FR]) and immune status, reflected by leukocyte profiles, influence the small intestinal microbiome of IPB-D3 chickens, a genetically improved Indonesian local breed.

MATERIALS AND METHODS: Ninety IPB-D3 chickens were reared for 12 weeks under either IN or FR systems. Hematological profiling was conducted to assess health status, with leukocyte counts used to stratify birds. Microbiota samples from the small intestine were analyzed using full-length 16S ribosomal RNA (V1-V9) sequencing on the Oxford Nanopore platform. Taxonomic identification was performed using the SILVA database. Statistical comparisons were made using t-tests, and microbial diversity was assessed through alpha and beta diversity metrics.

RESULTS: While most hematological parameters did not differ significantly between rearing systems, total leukocyte counts were higher in intensively reared chickens (p = 0.002). FR chickens exhibited significantly greater microbial diversity (p < 0.05) across multiple alpha diversity indices. A total of 1,294 unique species were identified in FR birds versus 720 in the IN group, with 1,761 shared species. Leukocyte level further influenced microbial profiles; chickens with high leukocyte (HL) counts were dominated by Ligilactobacillus aviarius, whereas low-leukocyte chickens had a higher abundance of Bacteroides caecigallinarum. Gallibacterium anatis, a potential pathogen, dominated in IN systems with elevated leukocytes.

CONCLUSION: This study demonstrates that both the rearing environment and immune status substantially influence small intestinal microbial composition in IPB-D3 chickens. FR systems promoted richer, more beneficial microbial communities, while IN systems, especially with HL levels, were associated with opportunistic pathogens. Leukocyte profiling may serve as a non-invasive biomarker for gut health, supporting future development of precision poultry management strategies and immune-responsive probiotics.},
}

@article {pmid41064771,
year = {2025},
author = {Giraldo-Badillo, I and Pineda-Vélez, E and Carbonell-Medina, BA and Ardila, CM},
title = {Microbiological and Pharmacological Aspects Involved in Dentin-Pulp Complex Regeneration: A Scoping Review.},
journal = {Journal of clinical and experimental dentistry},
volume = {17},
number = {9},
pages = {e1149-e1158},
pmid = {41064771},
issn = {1989-5488},
abstract = {BACKGROUND: The regeneration of the dentin-pulp complex represents a pivotal challenge in endodontics, requiring a delicate balance between microbial eradication and tissue repair. This scoping review, conducted in accordance with PRISMA-ScR guidelines, synthesizes current evidence on microbiological and pharmacological factors influencing regenerative outcomes.

MATERIAL AND METHODS: A systematic search of PubMed, Scopus, Web of Science, and Cochrane Library identified 242 studies, with 15 meeting inclusion criteria after screening.

RESULTS: The review highlights the dominance of anaerobic biofilm-forming pathogens (Enterococcus faecalis, Porphyromonas gingivalis) in periapical lesions, their virulence mechanisms (e.g., proteolytic enzymes, immune evasion), and the rising threat of antibiotic resistance driven by β-lactamases and efflux pumps. Pharmacologically, while triple/double antibiotic pastes promote dentin thickening, their cytotoxicity at high concentrations and disruption of commensal microbiota underscore the need for optimized dosing. Emerging alternatives-such as antimicrobial peptides, calcium hypochlorite, and immunomodulatory biomolecules-demonstrate superior biocompatibility and dual action against pathogens while supporting stem cell viability.

CONCLUSIONS: Future directions emphasize microbiome-targeted therapies, advanced biomaterials, and personalized approaches leveraging metagenomics. This review underscores the imperative to integrate selective antimicrobial strategies with regenerative biology to advance endodontic outcomes. Key words:Dentin-pulp regeneration, endodontic infections, biofilm, antimicrobial resistance, regenerative endodontics.},
}

@article {pmid41064643,
year = {2025},
author = {de Oliveira, AM and de Castro, CP},
title = {Perspectives in clinical microbiology for combating multi-drug resistant bacterial infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1695284},
pmid = {41064643},
issn = {2235-2988},
mesh = {Humans ; *Drug Resistance, Multiple, Bacterial ; *Bacterial Infections/diagnosis/microbiology/drug therapy/therapy ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Bacteria/drug effects ; Bacteriophages ; Phage Therapy ; Antimicrobial Peptides/therapeutic use ; },
abstract = {Multidrug-resistant bacterial infections are a major global threat, exacerbated by globalization and poor sanitation. Bacteria develop resistance through mechanisms like enzymatic degradation, efflux pumps, and horizontal gene transfer. Rapid diagnostics and artificial intelligence are crucial for overcoming the limitations of traditional culture methods. Combating this issue requires novel therapeutic strategies, such as bacteriophages, antimicrobial peptides, and microbiome-based therapies. Ultimately, proper antibiotic use, increased research, and global multidisciplinary cooperation are essential to address this complex challenge.},
}

Humans
*Drug Resistance, Multiple, Bacterial
*Bacterial Infections/diagnosis/microbiology/drug therapy/therapy
*Anti-Bacterial Agents/therapeutic use/pharmacology
*Bacteria/drug effects
Bacteriophages
Phage Therapy
Antimicrobial Peptides/therapeutic use

@article {pmid41064399,
year = {2025},
author = {Pławińska-Czarnak, J and Wódz, K and Strzałkowska, ZJ and Kwieciński, P and Żychska, M and Domańska, ED and Kłosińska, D and Orłowska, B and Nowak, T},
title = {Phenotypic and genetic antimicrobial resistance of the intestinal microbiota isolated from two alpacas (Vicugna pacos) post mortem.},
journal = {Journal of veterinary research},
volume = {69},
number = {3},
pages = {345-352},
pmid = {41064399},
issn = {2450-7393},
abstract = {INTRODUCTION: In Poland, alpacas are commonly companion animals and producers of wool. Human-alpaca-environment interactions raise One Health concerns about antimicrobial resistance (AMR). No medications are licensed in Poland for camelids, and so all are prescribed under the cascade; they include β-lactams, cephalosporin, florfenicol, enrofloxacin, marbofloxacin, gentamicin, tetracycline and trimethoprim/sulfamethoxazole. Human and animal bacterial AMR is a matter of global concern. Consequently, the aim of the present study was to determine the prevalence of phenotypic and genotypic AMR among bacteria isolated from alpaca intestines.

MATERIAL AND METHODS: Fifty-four strains were identified using matrix-assisted laser desorption/ionisation-time-of-flight mass spectrometry and biochemical methods. Antibacterial susceptibility was assessed by determining minimum inhibitory concentrations and by the Kirby-Bauer method.

RESULTS: Citrobacter spp., Enterobacter spp. and Serratia spp. exhibited resistance to β-lactams, first-generation cephalosporins and tetracyclines, with Serratia spp. also resistant to colistin, polymyxin B and florfenicol. Enterococcus spp. were resistant to penicillin G, benzylpenicillin and erythromycin, but not to vancomycin, while Staphylococcus spp. showed resistance to amoxicillin and penicillins, but not to methicillin. Bacillus spp. and Corynebacterium spp. were resistant to some penicillins, tetracyclines and trimethoprim-sulfamethoxazole. Enterobacteriaceae isolates carried resistance genes (aadA, dfrA1, tetA, sul1, sul2, strA/strB and floR); therefore, the tested alpacas' microbiomes harboured AMR determinants.

CONCLUSION: Alpacas should be monitored over an extended period to know the risk of transmission of AMR genes from components of their microbiome.},
}

@article {pmid41064256,
year = {2025},
author = {Perumal, R and Somboro, AM and Tulsi, J and Ngcapu, S and Naidoo, K},
title = {The gut and lung microbiome across the TB disease spectrum.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1643900},
pmid = {41064256},
issn = {1664-302X},
abstract = {Tuberculosis (TB) remains a major global health challenge, affecting approximately 10 million people annually. Susceptibility to infection by Mycobacterium tuberculosis, progression to TB, response to antimycobacterial chemotherapy, and the propensity to develop post-infectious sequelae have all been linked to a complex interplay of host and pathogen factors. Studies have revealed that communities of microorganisms colonize the human respiratory and gastrointestinal tracts and regulate regional immunity, with consequent effects on TB acquisition, progression, and resolution. An in-depth understanding of the multifaceted determinants of host susceptibility to TB, including the cross-talk between the host immune system and gut and lung microbiomes, could provide new insights into TB pathogenesis, treatment response, sequelae, and recurrence dynamics. This review explores the role of the gut-lung microbiome axis across the spectrum of TB pathogenesis, including microbial changes during and beyond TB treatment, and assesses their potential effect on treatment outcomes and the risk of TB recurrence.},
}