@article {pmid41395947,
year = {2025},
author = {Bouchali, R and Sentenac, H and Bates, KA and Fisher, MC and Schmeller, DS and Loyau, A},
title = {Unraveling the disease pyramid: the role of environmental micro-eukaryotes in amphibian resistance to the deadly fungal pathogen Batrachochytrium dendrobatidis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0143625},
doi = {10.1128/msystems.01436-25},
pmid = {41395947},
issn = {2379-5077},
abstract = {The disease pyramid conceptualizes the predictors of host infection risk, linking the host, the pathogen, environmental conditions, and both host and environmental microbiomes. However, the importance of the interaction between environmental and host-associated microbiomes in shaping infectious disease dynamics remains poorly understood. While the majority of studies have focused on bacteria, the role of micro-eukaryotes has been seldom investigated. Here, we explore three axes of the disease pyramid using an 18S rRNA gene metabarcoding approach to analyze the micro-eukaryotic assemblages of biofilm, water, and skin samples from three European amphibian species. Skin bacterial communities of the investigated amphibian populations have already been shown to be impacted by the presence of the lethal fungal pathogen Batrachochytrium dendrobatidis (Bd), with a higher abundance of protective bacteria in infected populations and a greater environmental microbial contribution to the skin microbiota in Bd-positive lakes. Here, we explored the relationships between the micro-eukaryotic skin communities of these tadpole populations with their surrounding environment. Tadpoles were sampled at 22 mountain lakes located in the Pyrenees (France), 8 of which harbored amphibian populations infected by Bd. We found that biofilms from Bd-negative lakes had higher environmental micro-eukaryotic diversity and a greater abundance of putative anti-Bd fungi, both in the environment and on the skin microbiota of Bufo spinosus and Rana temporaria, but not of Alytes obstetricans. Bayesian SourceTracker analysis further showed that the environmental contribution from biofilms to amphibian skin micro-eukaryotic assemblages was higher in Bd-positive lakes for B. spinosus and R. temporaria, but not for A. obstetricans.IMPORTANCEResearch on host-associated microbiomes and infectious diseases has mostly focused on bacteria, overlooking the potential contributions of micro-eukaryotes to infection dynamics. Here, we show that environmental and skin-associated micro-eukaryotes-especially putative anti-Batrachochytrium dendrobatidis (Bd) fungi-differ between Bd-positive and Bd-negative amphibian populations in mountain lakes. Our results suggest that micro-eukaryotes influence disease resistance and microbiome assembly, similarly to bacteria. Importantly, environmental reservoirs of micro-eukaryotes appear to contribute differently across infection contexts. These findings demonstrate the importance of adopting a broader microbiome perspective that includes micro-eukaryotes when investigating the ecological mechanisms underlying infectious disease risk.},
}

@article {pmid41395946,
year = {2025},
author = {Jansen, D and Bens, L and Wagemans, J and Green, SI and Hillary, T and Vanhoutvin, T and Van Laethem, A and Vermeire, S and Sabino, J and Lavigne, R and Matthijnssens, J},
title = {Hidradenitis suppurativa patients exhibit a distinctive and highly individualized skin virome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0129025},
doi = {10.1128/msystems.01290-25},
pmid = {41395946},
issn = {2379-5077},
abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory disease characterized by recurring skin lesions. Despite ongoing research, the exact cause underlying initiation and progression of disease remains unknown. While prior research has linked the skin microbiota to HS pathology, the role of viruses has remained unexplored. To investigate the skin virome, metagenomic sequencing of viral particles was performed on 144 skin samples from 57 individuals (39 HS patients and 18 controls). It was found that the virome is not only linked to BMI, but also to the presence and severity of HS, marking a diverging viral profile in the progression of disease. Despite no differences in alpha-diversity, HS patients exhibited a significantly higher beta-diversity compared to healthy controls, indicating a more personalized virome with reduced viral sharing among patients. We identified distinct groups of commonly shared phages, referred to as the core phageome, associated with either healthy controls or patients. Healthy controls displayed a higher abundance of two core Caudoviricetes phages predicted to infect Corynebacterium and Staphylococcus, comprising normal skin commensals. In contrast, HS patients carried previously uncharacterized phages that were more prevalent in advanced stages of the disease, which likely infect Peptoniphilus and Finegoldia, known HS-associated pathogens. Interestingly, genes involved in superinfection exclusion and antibiotic resistance could be found in phage genomes of healthy controls and HS patients, respectively. In conclusion, we report the existence of distinct core phages that may have clinical relevance in HS pathology by influencing skin bacteria through mechanisms such as superinfection exclusion and antibiotic resistance.IMPORTANCEAn increasing body of research showed that the microbiome has an important role in complex human disease. In line with this, here, we analyzed a longitudinal HS cohort and found a relationship between the skin virome and HS pathology. This relationship was defined by distinct groups of phages associated with either healthy controls or HS patients, yet, in both instances, capable of enhancing bacterial fitness. In healthy individuals, these phages were widely shared, fostering symbiosis by ensuring stability of the commensal skin microbiota. Conversely, in HS patients, these phages revealed a more individualistic nature and could contribute to dysbiosis by providing antibiotic resistance genes to bacterial pathogens. Overall, these findings point to a potential clinical significance of the virome in understanding and addressing HS pathology.},
}

@article {pmid41395750,
year = {2025},
author = {Abbas-Egbariya, H and Elwahidi, L and Levy, DJ and Braun, T and Levhar, N and Hadar, R and Efroni, G and Granot, M and Leichtmann-Bardogoo, Y and Maoz, BM and Weiss, B and Gal-Mor, O and Agranovich, B and Abramovich, I and Denson, L and Ben-Horin, S and VanDussen, KL and Amir, A and Haberman, Y},
title = {Supplementation with endogenous healthy gut metabolites reverses the disruptions of in vitro and ex vivo epithelial functions induced by fecal content from IBD patients.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2597568},
doi = {10.1080/19490976.2025.2597568},
pmid = {41395750},
issn = {1949-0984},
mesh = {Humans ; *Feces/microbiology/chemistry ; *Inflammatory Bowel Diseases/microbiology/metabolism ; *Gastrointestinal Microbiome ; Caco-2 Cells ; *Epithelial Cells/metabolism/drug effects ; Female ; Male ; *Intestinal Mucosa/metabolism ; Adult ; Metabolomics ; Middle Aged ; },
abstract = {Despite epithelial involvement in inflammatory bowel disease (IBD) pathogenesis and the gaps in treatment goals with existing immune-directed therapy, epithelial-directed interventions are unavailable. Using patient-based models, we aimed to identify bioactive endogenous metabolites that can improve IBD epithelial dysfunction, are generally regarded as safe, and can enhance epithelial homeostasis. We pooled fecal material from subjects with and without IBD to capture patient heterogeneity and analyzed the fecal contents for microbiome composition and metabolomics. Epithelial cells (Caco-2 cells and patient-derived colonoids) were cultured, and fecal material was applied apically to replicate the gut's physiological orientation. Measurable epithelial outputs included epithelial proinflammatory signals, integrity, and cellular ATP levels. We show that fecal content pools from several independent IBD patients disturb epithelial functions significantly more than does the fecal content from controls. Improved epithelial readouts in the functional patient-based models were linked with several gut metabolite levels, and these findings were further validated in an independent published human biospecimen multi-omics in vivo cohort. This guided the supplementation of five prioritized metabolites (azelate, pyridoxal, fructose-6-phosphate, galactose 1-phosphate, and ribose 5-phosphate) into the IBD fecal content, which reversed the related IBD epithelial dysfunction. We streamline a proof-of-concept pipeline for the prioritization of epithelial-targeted metabolite interventions that can direct safe future novel adjunct interventions.},
}

Humans
*Feces/microbiology/chemistry
*Inflammatory Bowel Diseases/microbiology/metabolism
*Gastrointestinal Microbiome
Caco-2 Cells
*Epithelial Cells/metabolism/drug effects
Female
Male
*Intestinal Mucosa/metabolism
Adult
Metabolomics
Middle Aged

@article {pmid41395693,
year = {2025},
author = {Stone, J and Tripyla, A and Scalise, MC and Balmer, ML and Bally, L and Meinel, DM},
title = {Taxonomic and functional shifts in the microbiome of severely obese, prediabetic patients: Ketogenic diet versus energy-matched standard diet.},
journal = {Diabetes, obesity & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1111/dom.70364},
pmid = {41395693},
issn = {1463-1326},
support = {PCEFP3_194618/1//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; PCEGP3_186978//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; //Stiftung FHNW/ ; //Nestlé Health Science/ ; //Pierre Mercier Foundation/ ; },
abstract = {AIMS: Obesity and type 2 diabetes mellitus (T2DM) are among the leading global health challenges of the 21st century. While caloric restriction remains the cornerstone of weight loss interventions, ketogenic diets (KD), characterised by low carbohydrate and high fat intake, have been shown to improve metabolic health partly by modulating the gut microbiome. This study investigated the effects of a short-term KD on gut microbiome composition and function in severely obese, prediabetic patients, compared to an energy-matched standard diet (SD).

METHODS: In a randomised trial, patients with BMI >35 kg/m[2] and prediabetes underwent either a 2-week KD or isocaloric SD, both inducing a 30% energy deficit. Faecal samples collected before and after the intervention, alongside samples from healthy controls, were analysed by whole-genome metagenomic sequencing.

RESULTS: At baseline, prediabetic patients exhibited greater interindividual variability and lower alpha diversity than healthy controls. KD resulted in a significant reduction of alpha diversity, largely driven by a selective loss of Lachnospiraceae, with a concomitant increase in Bacteroidaceae. Functional profiling revealed that KD, but not SD, altered genes coding for enzymes involved in energy metabolism, amino acid synthesis, nucleic acid activity, RNA modification, and vitamin biosynthesis. Additionally, serum acetate levels increased significantly following KD.

CONCLUSIONS: These findings underscore that KD, independent of caloric intake, acutely remodels the gut microbiome's taxonomic and functional landscape, highlighting the microbiome as a potential mediator of KD's metabolic effects.},
}

@article {pmid41395680,
year = {2025},
author = {Aldewereld, ZT and Megli, CJ and Olson, AC and Morowitz, MJ},
title = {ALARA in Antimicrobial Stewardship: Adapting Radiation Safety Principles to Address Antibiotic Overuse.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciaf688},
pmid = {41395680},
issn = {1537-6591},
abstract = {Despite decades of antimicrobial stewardship programs, antibiotic overuse persists due to imprecise guidelines relying on subjective terms like "optimal" and "appropriate" use. Current stewardship approaches lack a unifying communication framework that effectively bridges technical recommendations with real-world prescribing decisions across medical specialties. We propose adapting ALARA (As Low As Reasonably Achievable) from radiation safety as a transformative framework for antibiotic stewardship. Like radiation, antibiotics provide indisputable benefits while carrying hidden cumulative costs-including microbiome disruption, immune dysfunction, and increased mortality in specific populations. ALARA's three pillars (justification, optimization, dose limitation) map directly to antimicrobial stewardship needs and could standardize prescribing approaches across specialties. This framework addresses the distributed nature of antibiotic prescribing by providing clear principles that transcend subjective judgments. By treating antibiotics as beneficial but inherently risky interventions requiring careful justification, ALARA could reduce unnecessary exposure while maintaining efficacy, ultimately improving both patient outcomes and global antimicrobial resistance patterns.},
}

@article {pmid41395614,
year = {2025},
author = {Zhang, B and Mohd Sahardi, NFN and Chew, KT and Di, W and Shafiee, MN},
title = {Gut microbiome alterations and their clinical and biological implications in ovarian cancer: a systematic review.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1690541},
pmid = {41395614},
issn = {2234-943X},
abstract = {BACKGROUND: Increasing evidence shows the that gut microbiome (GM) plays a crucial role in ovarian cancer (OC) progression, offering potential avenues for microbiome-based intervention strategies. However, research in this area remains limited. This systematic review aimed to synthesize current evidence on microbiome composition and diversity in OC, focusing on its association with disease diagnosis, postoperative changes, and responses to chemotherapy or PARP inhibitor (PARPi) therapy.

METHODS: A literature search was performed in PubMed and Web of Science up to October 2025 using keywords: (gut microb* OR gut bacteri* OR intestinal microb* OR intestinal bacteri*) AND (ovarian cancer OR ovarian carcinoma OR carcinoma of ovary). Only original research articles involving human subjects were included. Data on GM alterations in OC patients, postoperative changes, and responses to chemotherapy or PARP inhibitor (PARPi) therapy were extracted and analysed.

RESULTS: Nine eligible studies, comprising longitudinal and case-control studies were reviewed. At diagnosis, OC patients displayed gut dysbiosis characterised by an increase in Proteobacteria and a decrease in Firmicutes. Genus-level analysis revealed lower levels of Akkermansia and elevated levels of Bacteroides and Prevotella, suggesting disrupted microbial homeostasis. Following surgery, both Firmicutes and Proteobacteria declined, indicating significant microbiome shifts. During chemotherapy, especially neoadjuvant treatment, Firmicutes re-emerged as the dominant phylum. Family-level analyses identified increased Coriobacteriaceae and decreased Ruminococcaceae. Platinum-sensitive patients demonstrated more stable GM profiles than those with platinum resistance Genera such as Angelakisella, Arenimonas, and Roseburia emerged as potential candidates for diagnostic or prognostic markers of chemotherapy resistance. Meanwhile, Phascolarbacterium is identified as a PARPi response in BRCA1/2-negative OC, with higher levels linked to longer progression-free survival.

CONCLUSION: This review highlights a dynamic GM composition in OC across disease stages and treatments, underscoring the need for further research on microbiome-targeted therapeutic strategies.},
}

@article {pmid41395472,
year = {2025},
author = {Son, Y and He, P and Baldwin, M and Li, G and Wang, Z and Gu, AZ and Kao-Kniffin, J},
title = {Geno-pheno characterization of crop rhizospheres: an integrated Raman spectroscopy and microbiome approach in conventional and organic agriculture.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1721013},
pmid = {41395472},
issn = {1664-302X},
abstract = {INTRODUCTION: Agricultural management practices strongly influence soil microbiomes, with broad implications for ecosystem function. Yet, the combined phenotypic and compositional dynamics of rhizosphere microbial communities across conventional and organic farming systems remain poorly characterized, underscoring the need for integrated approaches to understand how management decisions drive microbial assembly and function.

METHODS: We investigated microbial communities associated with conventionally and organically cultivated horticultural crops across multiple farms in New York State. To capture both taxonomic and functional dimensions, community composition was characterized using 16S rRNA gene sequencing, and phenotypic traits were assessed with a newly developed single-cell Raman microspectroscopy (SCRS) approach. This dual strategy allowed us to link microbial identity with metabolic potential and adaptive traits.

RESULTS: Farming practice significantly shaped microbiome clustering, independent of site or plant species. SCRS-based phenotyping revealed distinct biochemical profiles: organic systems favored lipid-accumulating phenotypes linked to energy storage and stress resilience, whereas conventional systems promoted carbon-rich phenotypes associated with rapid assimilation and biomass production. Network analysis identified Pseudomonas and nitrogen-fixing taxa as ecological hubs in conventional systems, while organic soils were enriched in Bacilli class plant growth-promoting rhizobacteria (e.g., Tumebacillus, Bacillus, Paenibacillus, Brevibacillus) and contained microorganisms bearing antibiotic resistance genes.

DISCUSSION: Our findings highlighted that management regimes drive distinct microbial functional traits and community structures. By integrating genotypic and phenotypic analyses, particularly microbial phenotyping via SCRS, we uncovered adaptive traits that differentiate conventional and organic systems, offering new insight into how plant production practices shape microbial assembly and ecological function.},
}

@article {pmid41395471,
year = {2025},
author = {Cheng, YN and Chen, GT and Huang, WC and Chiu, YP and Tang, Y and Fu, PK and Lee, TY},
title = {Lung microbiome signatures and explainable predictive modeling of glucocorticoid response in severe community acquired pneumonia.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1706432},
pmid = {41395471},
issn = {1664-302X},
abstract = {INTRODUCTION: Systemic glucocorticoids (SG) are administered to quell hyper-inflammation in severe community acquired pneumonia (SCAP), yet trials report inconsistent efficacy and no mechanistic explanation.

METHODS: We enrolled 200 ventilated SCAP patients, whom received hydrocortisone within 48 h of ICU admission, and generated longitudinal lower-airway microbiome profiles by 16S rRNA amplicon and metagenomic sequencing on ICU Days 1, 3 and 7. Compositional data were integrated with clinical variables through a fully reproducible bioinformatics analysis workflow.

RESULTS: Baseline community structures did not differ between SG and control cohorts, but by Day 7 survivors exhibited enrichment of Actinobacteria and Gammaproteobacteria whereas non-survivors accumulated Alphaproteobacteria and Campylobacteria. A random-forest model restricted to Bacilli and Alphaproteobacteria achieved AUROC = 0.89 (sensitivity 0.83, specificity 0.81) on a patient-held-out test set, significantly outperforming conventional severity indices like APACHE II, SOFA and mNUTRIC scores.

DISCUSSION: Collectively, our results demonstrate that SG therapy imposes reproducible ecological pressures on the lung microbiome and that a two-feature microbial fingerprint can forecast treatment success with single-sample resolution. These findings show that SG therapy actively reshapes the respiratory ecosystem and that lightweight microbiome-aware machine learning can stratify treatment response, offering a tractable path toward precision corticosteroid stewardship.},
}

@article {pmid41395467,
year = {2025},
author = {Hagarová, L and Kupka, D},
title = {Insights into the microbiome of mine drainage from the Mária mine in Rožňava, Slovakia: a metagenomic approach.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1675058},
pmid = {41395467},
issn = {1664-302X},
abstract = {The Mária mine, particularly the Strieborná vein, in Rožňava, is one of the most important mines in Slovakia, containing Ag-bearing tetrahedrite (40-46 wt% Cu, 26 wt% Sb, ~1 wt% Ag), making it an important source of strategic and critical raw materials. This mine discharges a unique neutral-pH (6.9), metal-rich mine water drainage (402 mg L[-1] SO4 [2-], 4.65 mg L[-1] Fe) that has remained microbiologically uncharacterized. This study presents the first comprehensive shotgun metagenomic survey of this mine effluent, generating ~227 million high-quality reads that assembled into 157,676 contigs and 378,023 non-redundant genes. Taxonomic analysis revealed a community dominated by Betaproteobacteria (> 66%), with abundant lithotrophic genera Sulfuritalea (6.93%), Ferrigenium (5.45%), Gallionella (3.79%), and Sideroxydans (3.65%), alongside the heterotrophic genus Pseudomonas (5.2%). Among the most prevalent neutrophilic iron-oxidizing bacterial strains were Sulfuritalea hydrogenivorans (6.93%), Ferrigenium kumadai (5.45%) and Gallionella capsiferriformas (3.79%). Acidophilic genera (e.g., Thiobacillus sp. at 0.43%, Ferrovum myxofaciens, Acidithiobacillus ferrivorans, Leptospirillum ferrooxidans) collectively accounted for <1% of the community. Functional annotation against KEGG, CAZy, COG, eggNOG, Swiss-Prot, CARD and BacMet databases demonstrated pronounced enrichment of iron cycling (e.g., the iron complex outer-membrane receptor protein TC.FEV.OM), sulfur oxidation (e.g., SoxA, SoxX, SoxB), carbon turnover (glycosyltransferase and glycoside hydrolase families) and nitrogen cycling (e.g., NifH, NifD, NirK, glnA). The antibiotic-resistance profile was dominated (> 95%) by tetracycline and fluoroquinolone determinants, while metal-resistance systems for Ni, Ag, As, Cu and Zn (including CzcD, CzcA, CznA, ArsD and AioX/AoxX) were likewise pervasive. This integrated taxonomic-functional portrait highlights a microbiome finely adapted to this unique geochemistry, combining lithotrophic metabolisms with multi-metal resistance. Our findings establish a critical baseline for long-term monitoring and highlight a high abundance of neutrophilic Fe(II)-oxidizers, suggesting they may represent promising candidates for targeted cultivation and subsequent evaluation in biotechnology applications.},
}

@article {pmid41395466,
year = {2025},
author = {Zou, W and Zheng, R and Lin, S and Lu, C and Xie, B},
title = {Lung and gut microbiota profiling in severe community acquired pneumonia patients: a prospective pilot study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1717822},
pmid = {41395466},
issn = {1664-302X},
abstract = {BACKGROUND: The gut and lung microbiomes play crucial roles in host defense and may serve as predictive markers for severe community-acquired pneumonia (SCAP) patients. However, the simultaneous landscapes of lung and gut microbiomes for SCAP patients remain unclear. The primary objective of this research is to investigate the concomitant landscape of the lung and gut microbiota between the death group and the survival group of SCAP patients and to identify microbial features predictive of clinical parameters.

METHODS: We analyzed 50 respiratory samples and 50 stool samples collected from 50 SCAP patients in this prospective observational study. Patients were categorized into the survival group (n = 41) and the death group (n = 9) according to clinical outcomes. We characterized microbiome compositions, LEfSe analysis, UPGMA analysis and correlation of microbiota features with clinical parameters of respiratory and intestinal flora between two groups using 16S rRNA gene sequencing.

RESULTS: In comparison with the survival group, the death group demonstrated a reduction in alpha diversity, most markedly reflected in the lung microbiota. We found enrichment of specific lung bacterial taxa (Bacteroidales, Streptococcus) in the survival group compared to the death group. Similarly, specific gut bacterial taxa (Anaerotruncus, Peptacetobacter, Rutheniibacterium) were also enriched in the survival group Our study revealed that lung bacteria such as Asteroleplasma, Campylobacter and Acinetobacter and intestinal bacteria such as Bifidobacterium, Ligilactobacillus, Veillonella, and Corynebacterium were positively correlated with inflammatory markers PCT or CRP or neutrophil percentage. Besides, lung bacteria such as Schaalia and intestinal bacteria Alistipes were positively correlated with PaO2/FiO2, while lung bacteria such as Stenotrophomonas was negatively correlated with PaO2/FiO2.

CONCLUSIONS: Our findings reveal distinctive microbial profiles in lung and gut microbiota that correlate with clinical outcomes in SCAP patients. Unraveling these microbial patterns could enable targeted interventions to improve outcomes of SCAP patients.},
}

@article {pmid41395464,
year = {2025},
author = {Gong, J and Lin, M and Chen, L and Xiong, W and Zhang, Y and Liu, C and Chen, S and Lin, W and Zhu, C and Huang, H},
title = {Microbiota-sphingolipid pathway in generalized epilepsy: evidence from Mendelian randomization and clinical metabolomics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1662050},
pmid = {41395464},
issn = {1664-302X},
abstract = {OBJECTIVE: Epilepsy is a complex disorder with growing evidence linking gut microbiota and metabolism, though causal relationships unclear. This study investigated causal effects of gut microbiota on three epilepsy types via metabolic pathways, using Mediation Mendelian randomization (MR), evaluated directional consistency metabolomics of refractory epilepsy (RE) patients before and after medium-chain triglyceride (MCT) diet intervention.

METHODS: Two-step MR was applied to summary statistics for 207 species (Dutch Microbiome Project) and 196 species (MiBioGen consortium), evaluating 871 serum metabolites as mediators of three epilepsy types. For validation, directional consistency in metabolomics was conducted on serum samples from 9 RE patients before and after MCT diet intervention.

RESULTS: Only sphingomyelin (SM; d18:0/20:0, d16:0/22:0) and Glycocholate glucuronide (1) were the metabolites significantly associated with three epilepsy types. Mediation MR analysis revealed Mollicutes RF9 had a unidirectional effect via sphingomyelin (d18:1/22:1, d18:2/22:0, d16:1/24:1) modulation (P = 0.009). In contrast, Gamma-proteobacteria and Oxalobacter demonstrated bidirectional mediation: via glutamine conjugate of C6H10O2(2) and cerotoylcarnitine (C26) (P = 0.026 and P = 0.033, respectively); while these pathways were protective in mediation, higher abundances were associated with increased risk of generalized epilepsy. Notably, no significant mediators were identified for epilepsy or focal epilepsy. Metabolomics further confirmed MCT diet-induced elevations in 7 specific SM species. Among these, SM (d18:1/36:8) remained statistically significant after Benjamini-Hochberg false discovery rate (BH-FDR) correction. Notably, changes in SM (d18:1/36:8) and SM (d18:1/14:3) were positively correlated with seizure control rates.

CONCLUSION: This study identifies both unidirectional and bidirectional microbiota-metabolite pathways modulating generalized epilepsy risk, with converging evidence pointing to sphingomyelin as a potential lipid biomarker and therapeutic target.},
}

@article {pmid41395460,
year = {2025},
author = {Popowski, W and Koseski, D and Domanowska, D and Zalewska, M and Popowska, M},
title = {Bacterial colonization of bone substitute materials used in oral surgery: mechanisms, clinical implications, and preventive strategies-A narrative review.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1715632},
pmid = {41395460},
issn = {1664-302X},
abstract = {The advancement of tissue engineering and the development of novel biomaterials have opened new possibilities for the effective treatment of patients with edentulism and other dental deficiencies, as well as for the prosthetic reconstruction and functional rehabilitation of the stomatognathic system. Bone substitute materials are now widely used in orthopedics, reconstructive surgery, and dentistry to support the regeneration of bone tissue lost due to trauma, inflammation, or tooth extraction. However, surgical procedures within the oral cavity inherently carry a risk of postoperative infection, which can impair healing and compromise treatment outcomes. Unlike natural bone regeneration, bone healing following grafting functions as a repair process that may involve partial resorption of the graft material. Such bone deficiencies can hinder prosthetic reconstruction, making the use of bone substitute materials essential for guided bone regeneration. Bone substitutes can be classified as autogenous, allogenic, xenogenic, or alloplastic, each exhibiting distinct osteoinductive and osteoconductive properties. This review discusses the biological and clinical characteristics of these material groups, with particular attention to their susceptibility to colonization by bacterial strains commonly found in the human oral cavity. It also highlights the risks associated with bacterial biofilm formation and examines its implications for the oral microbiome under dysbiotic conditions.},
}

@article {pmid41395459,
year = {2025},
author = {Li, Q and Liu, Y},
title = {Analyzing the gut liver axis: a dual role of the microbiome in the genesis, progression, and treatment of liver cell carcinoma.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1701101},
pmid = {41395459},
issn = {1664-302X},
abstract = {Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related mortality worldwide, and the poor prognosis highlights the pressing need for innovative therapeutic strategies. The gut-liver axis, a critical bidirectional pathway linking the gut microbiota to the liver, plays a pivotal role in HCC pathogenesis. This review systematically delineates current evidence on how gut dysbiosis, compromised intestinal barrier function, and resultant microbial metabolites (e.g., bacterially metabolized bile acids) drive hepatocarcinogenesis via specific signaling pathways, while also addressing the loss of protective effects due to the depletion of beneficial microbes. Moving beyond descriptive summaries, this article focuses on elucidating the core molecular mechanisms of microbiome-regulated HCC-a key knowledge gap that remains unaddressed-and reconciles conflicting findings into a unified framework. We further explore the translational potential of microbiome signatures as non-invasive biomarkers and evaluate microbiota-targeting interventions (e.g., probiotics, dietary modulation, fecal microbiota transplantation) for enhancing treatment efficacy. Ultimately, this review aims to provide a clear roadmap for developing microbiome-based precision medicine in HCC, with the goal of improving clinical management and patient outcomes.},
}

@article {pmid41395458,
year = {2025},
author = {Sun, N and Wang, Y and Zhang, M and Ma, P and Wang, Z and Zhao, H and Cao, C},
title = {The effect of chili pepper-Chinese chives intercropping on rhizosphere microorganisms and root-stem endophytes.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1716326},
pmid = {41395458},
issn = {1664-302X},
abstract = {INTRODUCTION: This study adopted the intercropping pattern opepper (Capsicum annuum L.) and Chinese chives (Allium tuberosum), combined with high-throughput sequencing and microbial network analysis, to systematically reveal the mechanisms of intercropping on the structural regulation and functional synergy of the crop rhizosphere microbiome and root-stem endophyte communities.

METHODS: Three treatments were set up: blank control, solo cultivation, and intercropping.Combined with high-throughput sequencing and network analysis, the reorganization patterns of rhizosphere and endophyte communities were systematically analyzed.

RESULTS: Intercropping induced differential responses of microbial communities in the two crops: it significantly increased the bacterial α-diversity in Chinese chives leaves, and the Shannon index of pepper roots also showed an upward trend, while the microbial diversity in pepper rhizosphere soil was inhibited. In contrast, among roots, the "pepper intercropped with Chinese chives" group had the highest total number of OTUs and the largest number of unique OTUs. Microbial communities exhibited cross-host transfer characteristics: the migration rate of microbial communities from pepper roots to Chinese chives rhizosphere reached 46.57%, and 69.54% of the microbial communities in Chinese chives roots originated from pepper roots. Specifically, Aureimonas and Sphingomonadaceae were significantly enriched in pepper leaves, the relative abundance of Pantoea in Chinese chives leaves increased by 11.5 times, and the abundance of Flavobacterium in pepper rhizosphere increased by 94%. Microbial co-occurrence network analysis confirmed the optimization of functional synergy: the proportion of positive interactions in pepper leaves increased to 90.45%, and the negative interactions of Bradyrhizobium decreased by 97%, the proportion of positive interactions of functional bacteria in Chinese chives rhizosphere reached 88.96%, and Bacillus enhanced positive connections while maintaining an abundance of 10.23%-20.87%, the number of positive interactions of Streptomyces in pepper rhizosphere doubled. Network stability showed spatial variation: the robustness of stem microbial networks was significantly improved, while the vulnerability of rhizosphere microbial networks increased.

DISCUSSION: This study provides microbial theoretical support for the intercropping system to optimize nitrogen utilization by driving pepper to enrich the growth-promoting bacteria Sphingomonadaceae, and to enhance disease resistance by promoting Chinese chives to recruit the biocontrol bacteria Bacillus, thereby forming a microecological regulation mechanism with functional complementarity.},
}

@article {pmid41395398,
year = {2025},
author = {Chen, X and Mei, XY and Ren, ZM and Chen, SS and Tong, YL and Zhang, CP and Chen, J and Dai, GH},
title = {Corrigendum to "Comprehensive insights into berberine's hypoglycemic mechanisms: A focus on ileocecal microbiome in db/db mice" [Heliyon Volume 10, Issue 13, July 15, 2024, Article e33704].},
journal = {Heliyon},
volume = {11},
number = {16},
pages = {e44124},
doi = {10.1016/j.heliyon.2025.e44124},
pmid = {41395398},
issn = {2405-8440},
abstract = {[This corrects the article DOI: 10.1016/j.heliyon.2024.e33704.].},
}

@article {pmid41395292,
year = {2025},
author = {Ren, H and Wen, J and Liu, J and Wang, L},
title = {Gut microbiota in immunomodulation and infection prevention among multiple myeloma patients after chemotherapy: current evidence and clinical prospects.},
journal = {American journal of cancer research},
volume = {15},
number = {11},
pages = {4621-4638},
pmid = {41395292},
issn = {2156-6976},
abstract = {Multiple Myeloma (MM) is the second most common hematological malignancy, with its pathogenesis involving complex cytogenetic variations, tumor clonal evolution, and dynamic interactions between tumor cells and bone marrow stromal microenvironment. Recent studies highlight the role of the intestinal microbiota, a key component of the tumor-associated microenvironment, in regulates MM occurrence, progression, and treatment response via the "gut-bone marrow axis". Under physiological conditions, it protects the local microenvironment by regulating host metabolism and maintaining immune homeostasis. However, intestinal dysbiosis causes metabolic disorders and immune surveillance defects, promoting tumor growth, drug resistance, and poor prognosis. Though traditional treatments such as chemotherapy and hematopoietic stem cell transplantation have been optimized, chemotherapy disrupts intestinal mucosal integrity and impairs immunity, significantly increasing post-chemotherapy infections. These infections can interrupt treatment, worsen conditions, and reduce quality of life, leaving MM still intractable. Notably, microbiota-targeted interventions (e.g., probiotics, fecal microbiota transplantation [FMT]) have shown potential to reduce infection risk by restoring microbiota balance and repairing intestinal barriers. These interventions may also exert potential anti-tumor effects through immune microenvironment regulation and alleviate chemo/radiotherapy-related adverse reactions (e.g., nausea, diarrhea), offering a new direction for relapsed/refractory MM. This article summarizes the molecular regulatory network of the intestinal microbiota in the pathogenesis of MM and the research progress of microbiota-based interventions, aiming to provide a foundation for developing novel microbiome-oriented precision treatment regimens and improving chemotherapy tolerance and patient prognosis.},
}

@article {pmid41394993,
year = {2025},
author = {Olanrewaju, OS and Glick, BR and Babalola, OO},
title = {Retraction notice to "Beyond correlation: Understanding the causal link between microbiome and plant health" [Heliyon 10 (2024) e40517].},
journal = {Heliyon},
volume = {11},
number = {15},
pages = {e44065},
doi = {10.1016/j.heliyon.2025.e44065},
pmid = {41394993},
issn = {2405-8440},
abstract = {[This retracts the article DOI: 10.1016/j.heliyon.2024.e40517.].},
}

@article {pmid41394959,
year = {2025},
author = {Guo, XY and Song, DY and Wu, MY and Zhang, JQ and Li, JY and Yuan, L},
title = {Parkinson's Disease: The Epidemiology, Risk Factors, Molecular Pathogenesis, Prevention, and Therapy.},
journal = {MedComm},
volume = {6},
number = {12},
pages = {e70540},
pmid = {41394959},
issn = {2688-2663},
abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder with a growing global burden. Current pharmacological therapies remain limited to symptomatic management, owning to an incomplete understanding of the mechanisms driving α‑synuclein aggregation and disease progression. This review provides an integrated overview of PD across epidemiological, etiological, pathophysiological, and clinical dimensions. It emphasizes established and emerging risk factors, including environmental toxins, lifestyle variables, and gut microbiota dysbiosis and delineates how peripheral-central pathways such as the gut-brain, erythrocyte-brain, and kidney-brain axes contribute to PD pathogenesis. At the molecular level, we explore key disruptions including proteostatic failure, aberrant phase separation, oxidative stress, neuroinflammation, synaptic dysfunction, iron dyshomeostasis, and impaired cholesterol metabolism. These encompass microbiome‑targeted interventions and blood-based approaches. We further evaluate a spectrum of management strategies ranging from primary prevention and biomarker‑guided early detection to innovative experimental treatments such as cellular therapies, transfusion‑based modalities, and microbial modulation. By integrating recent advances in systemic pathophysiology with translational perspectives, this review highlights how molecular and cellular dysregulations underlie clinical phenotypes. Finally, we discuss promising biomarkers derived from microbial, inflammatory, and erythrocyte pathways that may facilitate early diagnosis and the development of disease‑modifying therapies.},
}

@article {pmid41394950,
year = {2026},
author = {Krishnan, LRA and Nair, S and Girija, D and Vishnu, BR},
title = {Unravelling the complex bacterial diversity in the rice rhizosphere of Kole lands of Thrissur through the metagenomics approach.},
journal = {3 Biotech},
volume = {16},
number = {1},
pages = {27},
pmid = {41394950},
issn = {2190-572X},
abstract = {UNLABELLED: The Kole wetlands of Kerala are highly productive rice ecosystems that lie below mean sea level and alternate between flooded and dry phases, shaping their ecological structure. This study focused on assessing bacterial diversity in the rice rhizosphere of Thrissur Kole lands. Rhizosphere soil was sampled from three Kole wetland locations, Puzhakkal (Pzk), Mullassery (Mls), and Cherpu (Chr). Bacterial communities were profiled by constructing metagenomic libraries and sequencing the 16S rRNA V3-V4 regions using the Illumina MiSeq platform. The sequences of the samples Pzk, Mls, and Chr were submitted in the SRA portal under the bioaccession numbers SAMN17776076, SAMN17776077, and SAMN17776078, respectively. High-quality, chimera-free sequences were clustered into OTUs using the QIIME pipeline. Taxonomic assignment was performed in MEGAN by matching reads to sequence databases and allocating NCBI-based taxon IDs. Phylum-level bacterial and archaeal diversity was further analyzed using the MG-RAST pipeline. The predominant bacterial phyla identified were Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria, Bacteroidetes, and Nitrospirae, with bacterial relative abundance being highest in the Pzk sample and comparatively lower in the Chr sample. The major archaeal phyla included Euryarchaeota, Crenarchaeota, and Thaumarchaeota. Many members of these bacterial and archaeal groups are known to thrive in waterlogged, oxygen-limited, or anoxic conditions, characteristic of Kole lands. Plant Growth Promoting Rhizobacteria (PGPR) such as Azospirillum, Paenibacillus, and Cellulosimicrobium were detected and could potentially be exploited as acid-tolerant biofertilizers. Biocontrol agents belonging to the genera Bacillus and Pseudomonas were also present. Further investigation is required for the characterization of the 'Unclassified' genera at taxonomic and functional levels to elucidate their ecological functions.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04630-w.},
}

@article {pmid41394893,
year = {2025},
author = {Ramesh, AV and Joseph, SC and Bohm, MS and Grey, EW and Elasy, JH and Hibl, BM and Asunloye, OT and Kim, KS and Doss, TD and Pierre, JF and Cook, KL and Makowski, L and Sipe, LM},
title = {A Standardized Method for Vertical Sleeve Gastrectomy Bariatric Surgery Investigations in Cancer.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {},
pmid = {41394893},
issn = {2813-4338},
abstract = {UNLABELLED: Obesity is a global epidemic that has affected the lives of over 14% of adults worldwide and over a third of Americans. Obesity is associated with the increased risk of thirteen obesity-associated cancers and poor cancer outcomes. Bariatric surgery is the most effective method of sustained weight loss and has been steadily increasing in clinical use over the past 4 decades. Importantly, bariatric surgery is established to decrease cancer risk. Vertical sleeve gastrectomy (VSG) is currently the most common bariatric surgery procedure. To evaluate underlying mechanisms of bariatric associated cancer protection, we developed a robust pre-clinical model of bariatric surgery-induced weight loss in mice. Using multiple strains, we established detailed procedures, defined best practices, and noted specific controls to include to examine mediators critical to cancer onset. This VSG protocol includes stringent pre- and post-operational measures to reduce stress-associated weight loss in obese mice to achieve rigorous and reproducible bariatric surgery-associated weight loss. In addition, we describe collection of fecal and intestinal samples as well as Peyer's patches as important mediators of bariatric surgery's impact on cancer risk. In conclusion, as obesity and weight loss approaches including bariatric surgery are increasingly examined in cancer risk and outcomes including immunotherapy, the establishment of robust pre-clinical interventions will allow the field to address critical underlying mechanisms mediating the benefits of weight loss and cancer.

NEW AND NOTEWORTHY: Obesity increases cancer risk and leads to poor outcomes and survival. Bariatric surgery is an effective method of sustained weight loss. To best model obesity, weight loss, and impacts on cancer risk or outcomes, we developed a robust pre-clinical model of bariatric surgery in mice. Because bariatric surgery leads to sustained impacts on the gut microbiome, which can inform anti-tumor immunity, this protocol provides rigorous methods for the collection of intestinal microbiota and Peyer's patches.},
}

@article {pmid41394880,
year = {2025},
author = {Matera, M and Biagioli, V and Illiceto, MT and Palazzi, CM and Cavecchia, I and Manzi, A and Lugli, S and Pennazzi, L and Meocci, M and Pedaci, FA and Bertuccioli, A},
title = {Pediatric acute-onset neuropsychiatric syndromes and the gut-oral-brain axis: a narrative review of emerging microbiome-immune interactions and therapeutic perspectives.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1726630},
pmid = {41394880},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Autoimmune Diseases/immunology/microbiology/therapy ; Child ; *Streptococcal Infections/immunology/microbiology/therapy ; *Brain/immunology ; *Mouth/microbiology/immunology ; Probiotics/therapeutic use ; Obsessive-Compulsive Disorder ; },
abstract = {BACKGROUND: Pediatric Acute-onset Neuropsychiatric Syndromes (PANS) and Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal infections (PANDAS) are characterized by sudden-onset neuropsychiatric symptoms. Growing evidence indicates that gut and oral microbiota may contribute to disease pathogenesis through immune and inflammatory pathways.

METHODS: This narrative review analyzed approximately 250 studies published between 2000 and 2024, retrieved from PubMed, Scopus, and Google Scholar. The selected works included clinical, immunological, and microbiome-related studies investigating the role of gut-oral-brain interactions in neuroinflammation or in pediatric PANS/PANDAS.

FINDINGS: Alterations in gut and oral microbial communities appear to modulate neuroinflammation through increased intestinal and blood-brain barrier permeability, immune dysregulation, and altered production of neuroactive metabolites. Specific bacterial families, such as Bacteroidaceae, Rikenellaceae, and Odoribacteriaceae, have been associated with pro-inflammatory states, while oral pathogens may exacerbate systemic inflammation via the gut-oral-brain axis.

CONCLUSIONS: The reviewed evidence highlights the potential of microbiome-targeted strategies-including dietary modulation, probiotics, and anti-inflammatory approaches-as promising avenues for future personalized diagnosis and therapy in PANS/PANDAS. However, further controlled studies integrating microbial, immunological, and clinical data are required to confirm causal mechanisms and establish personalized therapeutic protocols.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Autoimmune Diseases/immunology/microbiology/therapy
Child
*Streptococcal Infections/immunology/microbiology/therapy
*Brain/immunology
*Mouth/microbiology/immunology
Probiotics/therapeutic use
Obsessive-Compulsive Disorder

@article {pmid41394872,
year = {2025},
author = {Wang, P and Ge, C and Jing, X and Han, Q and Wang, M and Huang, M and Xiang, Z},
title = {Respiratory microbiome-host interaction on lung carcinogenesis, immunity, and immunotherapy.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1676302},
pmid = {41394872},
issn = {1664-3224},
mesh = {Humans ; *Lung Neoplasms/therapy/immunology/microbiology/pathology/etiology ; *Immunotherapy/methods ; *Microbiota/immunology ; Animals ; Dysbiosis/immunology ; *Carcinogenesis/immunology ; *Host Microbial Interactions/immunology ; Tumor Microenvironment/immunology ; Immune Checkpoint Inhibitors/therapeutic use ; },
abstract = {The respiratory microbiome, as an integral component of the lung cancer microenvironment, exerts pivotal influences on tumorigenesis, immune homeostasis, and therapeutic response through intricate crosstalk with host immunity. Despite advancements, current limitations in lung cancer immunotherapy persist, including heterogeneous therapeutic responses, immune-related adverse events, and the lack of predictive biomarkers. These unmet clinical needs underscore the imperative to delineate the complex immune landscape of respiratory microbiome in lung cancer pathogenesis. This review systematically analyzes the hallmarks of respiratory dysbiosis (reduced α-diversity and enrichment of Streptococcus and Veillonella) and their associations with lung cancer staging, histological subtypes, and prognosis. We further elucidate how these microbial alterations influence tumor progression via metabolic-epigenetic-immune pathways. Additionally, we establish clinical correlations between microbiome signatures and both immune checkpoint inhibitor therapeutic efficacy/toxicity profiles, while examining the paradoxical effects of antibiotic exposure during immunotherapy. Emerging intervention strategies targeting the respiratory microbiome, such as aerosolized probiotics, engineered bacteria (e.g., Escherichia coli), and microbiota-derived nanomaterials, showcase potential in remodeling antitumor immunity and improving therapeutic outcomes. Our findings highlight the double-edged sword effect of the respiratory microbiota as biomarkers and therapeutic targets in lung cancer management, providing critical insights for clinical translation.},
}

Humans
*Lung Neoplasms/therapy/immunology/microbiology/pathology/etiology
*Immunotherapy/methods
*Microbiota/immunology
Animals
Dysbiosis/immunology
*Carcinogenesis/immunology
*Host Microbial Interactions/immunology
Tumor Microenvironment/immunology
Immune Checkpoint Inhibitors/therapeutic use

@article {pmid41394835,
year = {2025},
author = {Mikaelyan, A and Receveur, J and Bernstein, K and Babcock, NJ and Pechal, JL and Welsh, MV and Waters, KA and Yoskowitz, KH and Benbow, ME},
title = {Host-specific microbiomes of blow flies: ecological drivers and implications for pathogen carriage.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1673934},
pmid = {41394835},
issn = {1664-3224},
mesh = {Animals ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Calliphoridae/microbiology ; Male ; Female ; *Diptera/microbiology ; Humans ; },
abstract = {Blow flies (Lucilia sericata and Phormia regina) are necrophagous insects that interact with dense microbial reservoirs and are opportunistic vectors of human and animal pathogens. Despite constant exposure to diverse environmental microbes, it is unclear whether their bacterial communities are primarily acquired stochastically or shaped by host factors that could influence pathogen carriage. We conducted a systematic comparison of wild L. sericata and P. regina collected from seven cities across an urban-rural gradient to determine whether microbiome composition is structured by host species identity or environmental variables. Using 16S rRNA gene sequencing of individual flies, we profiled bacterial communities and applied alpha- and beta-diversity analyses, PERMANOVA, and Random Forest classification to quantify species-level microbiome differentiation. Species identity was the strongest predictor of microbiome composition (PERMANOVA, p = 0.001), while location, land cover type, sampling month, and sex had no significant effects. Random Forest modeling identified multiple bacterial taxa that consistently distinguished the two species, including Ignatzschineria and Dysgonomonas, which were enriched in P. regina, and Vagococcus and Escherichia-Shigella, which were enriched in L. sericata. These taxa are of clinical relevance, with Ignatzschineria in particular increasingly reported from human myiasis and soft-tissue infections, sometimes exhibiting antimicrobial resistance. Our findings demonstrate that wild blow flies maintain species-specific microbiomes despite shared environments, suggesting that host identity strongly filters microbial communities. The presence of opportunistic pathogens within these structured microbiomes underscores the need to understand how blow fly-microbe associations contribute to pathogen persistence and dissemination. By revealing predictable, species-dependent microbiome patterns, this study highlights potential targets for microbiome-based strategies aimed at mitigating blow fly-associated disease risks.},
}

Animals
*Microbiota
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification
*Calliphoridae/microbiology
Male
Female
*Diptera/microbiology
Humans

@article {pmid41394818,
year = {2025},
author = {Lu, Q and Wu, J and Yu, X and Qian, J and Song, Z},
title = {Unveiling the interplay between microbiota and PD1/PD-L1 axis in tumor immunity and immunotherapy.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1690374},
pmid = {41394818},
issn = {1664-3224},
mesh = {Humans ; *B7-H1 Antigen/metabolism/immunology ; *Neoplasms/immunology/therapy/microbiology/metabolism ; *Immunotherapy/methods ; *Programmed Cell Death 1 Receptor/metabolism/immunology ; Tumor Microenvironment/immunology ; Animals ; *Microbiota/immunology ; Immune Checkpoint Inhibitors/therapeutic use ; Signal Transduction ; Gastrointestinal Microbiome ; },
abstract = {Microbial communities across diverse body sites critically shape host immunity and tumor responses. Within this framework, the PD-1/PD-L1 axis emerges as a central pathway governing tumor immune evasion and resistance to therapy. Recent evidence reveals that microbiota-from the gut, lungs, and elsewhere-significantly influence PD-1/PD-L1 signaling, thereby altering immune checkpoint blockade efficacy. This review synthesizes current understanding of the microbiota-PD-1/PD-L1 interplay, examining how microbial composition and metabolites impact immune cell activity, the tumor microenvironment, and immunotherapy outcomes. We detail mechanisms through which microbiota regulate PD-1/PD-L1 expression, fostering immune tolerance and tumor progression while modulating therapeutic responses. The translational potential of microbiota-targeted strategies to enhance PD-1/PD-L1 therapy and overcome resistance is discussed. Integrating microbiota modulation with existing immunotherapies offers promising avenues for precision cancer treatment. Advancing these concepts into clinical practice will require future research to establish microbiome-based interventions as transformative tools in oncology.},
}

Humans
*B7-H1 Antigen/metabolism/immunology
*Neoplasms/immunology/therapy/microbiology/metabolism
*Immunotherapy/methods
*Programmed Cell Death 1 Receptor/metabolism/immunology
Tumor Microenvironment/immunology
Animals
*Microbiota/immunology
Immune Checkpoint Inhibitors/therapeutic use
Signal Transduction
Gastrointestinal Microbiome

@article {pmid41394806,
year = {2025},
author = {Young, MR and Mehta, CC and Staple, T and Herring, GB and Govindaraj, S and Ibegbu, C and Herold, BC and Velu, V and Haddad, LB and Smith, AK},
title = {No change in key HIV target cell markers following initiation of three progestin-based hormonal contraception methods: findings from the CHIME study.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1655678},
pmid = {41394806},
issn = {1664-3224},
mesh = {Humans ; Female ; Adult ; *HIV Infections/immunology ; Young Adult ; Middle Aged ; Adolescent ; Biomarkers ; Medroxyprogesterone Acetate/administration & dosage/adverse effects ; *CD4-Positive T-Lymphocytes/immunology/drug effects ; *Hormonal Contraception/methods/adverse effects ; Receptors, CCR5/metabolism ; Levonorgestrel/administration & dosage ; *Progestins/administration & dosage/adverse effects ; Desogestrel/administration & dosage/adverse effects ; *Contraceptive Agents, Female/administration & dosage ; *Contraceptive Agents, Hormonal/administration & dosage ; },
abstract = {INTRODUCTION: Depot medroxyprogesterone acetate (DMPA) injectable, etonogestrel subdermal implant (ENG-implant), and levonorgestrel intrauterine device (LNG-IUD) are effective, widely used female hormonal contraceptives (HC). Observational studies, but not a randomized trial, suggest increased risk of HIV acquisition with HC use, particularly DMPA. Sexual acquisition of HIV occurs via CD4+ T cells expressing C-C chemokine receptor type 5 (CCR5), though other immunologic cells play a role. This study examined longitudinal changes in CCR5+ T cells and other immunologic cells in the female genital tract following HC initiation.

METHODS: HIV negative participants aged 18-45 years, not using HC, were recruited in Atlanta, Georgia. After two pre-HC visits, participants initiated DMPA, ENG-implant, or LNG-IUD and completed visits every three months for one year. Specimens (peripheral blood, endocervical cells, cervical tissue biopsy, and cervicovaginal lavage [CVL]) were analyzed for immune cellular markers (CD45, CD3, CD4, CCR5, CD69, HLA-DR, CD38, α4β7, CD103, Fox-P3, and Ki-67) using flow cytometry. Effects of CVL on HIV infection of cells in vitro was assessed. Vaginal microbiome was characterized via 16S rRNA gene amplicon sequencing. Multivariable linear mixed effects models estimated association between HC and immune markers (Primary outcome: proportion of CD4+ T cells expressing CCR5; Secondary outcomes: other immune markers, in vitro HIV enhancement). A Bonferroni correction was applied.

RESULTS: Among 118 participants (mean age 25.9; 44.1% self-identified as Black race), 545 visits were completed from 2019-2023. No significant changes were observed in proportion of CCR5+ T cells in any tissue type post-HC. There were statistically significant but moderate absolute decreases in proportion of CD45+ and CD4+ T cells in CVL, and CD4+ T cells in blood, and increased proportion of CD69+ T cells in blood post-HC. Post-HC CVL vs. pre-HC enhanced HIV infection of cells in vitro for all three HC groups (p<0.01) and was modified by the vaginal microbiome. There was also evidence of interaction by time and microbiome parameters for several other immune cells.

DISCUSSION: Our findings suggest that commonly used HC methods do not result in immunologic changes that increase HIV acquisition risk. However, HIV infection enhancement with post-HC CVL in vitro warrants further study.},
}

Humans
Female
Adult
*HIV Infections/immunology
Young Adult
Middle Aged
Adolescent
Biomarkers
Medroxyprogesterone Acetate/administration & dosage/adverse effects
*CD4-Positive T-Lymphocytes/immunology/drug effects
*Hormonal Contraception/methods/adverse effects
Receptors, CCR5/metabolism
Levonorgestrel/administration & dosage
*Progestins/administration & dosage/adverse effects
Desogestrel/administration & dosage/adverse effects
*Contraceptive Agents, Female/administration & dosage
*Contraceptive Agents, Hormonal/administration & dosage

@article {pmid41394752,
year = {2025},
author = {Hillary, LS and Knotts, TA and Adams, SH and Ali, MR and Olm, MR and Emerson, JB},
title = {DNA extraction and virome processing methods strongly influence recovered human gut viral community characteristics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.25.690293},
pmid = {41394752},
issn = {2692-8205},
abstract = {Accurately characterising the human gut virome is critical to understanding virus-microbiome-host interactions. However, widely used methods introduce biases that complicate data interpretation and limit cross-study comparability. For instance, multiple-displacement amplification (MDA) preferentially amplifies single-stranded DNA viruses, while total metagenomes are dominated by non-viral sequences, reducing viral signal. These traditional methods have not been systematically compared to viral size-fraction metagenomes (viromes) prepared without MDA. To address this, we applied four common methods for characterising human gut viral community composition (total metagenomes, viromes with/ without DNase treatment (to remove free DNA), and MDA viromes) to a human stool sample, with technical triplicates for each approach. MDA biased viral community composition to a shocking degree: Microviridae formed ∼90% of MDA viromes compared to just 2% of non-MDA viromes. Removing ssDNA viruses from data analyses substantially reduced, but did not eliminate, MDA bias. Metagenomes were enriched for putative temperate phages and predicted Bacillota-phages , whereas predicted Bacteroidetes -phages dominated all viromes, suggesting that metagenomes and viromes select for different populations within the total viral community. DNase treatment had little-to-no effect on virome richness or community composition. This proof-of-principle experiment demonstrates that preparatory methods for viral community analysis can lead to substantially different conclusions from the same faecal sample, and we provide a comprehensive omic data analysis framework for comparing laboratory methodologies for viral ecology. With sufficient DNA yields now easily achievable from human gut viromes without the use of MDA, our results suggest that this biased amplification method should be avoided in human gut virome studies.},
}

@article {pmid41394746,
year = {2025},
author = {Shoer, S and Godneva, A and Weinberger, A and Pollard, KS and Pilpel, Y and Segal, E},
title = {Bacterial strains in the human gut associate with host physiology.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.30.691432},
pmid = {41394746},
issn = {2692-8205},
abstract = {The human microbiota influences host physiology, yet much of its complexity lies beneath the species level. Here, we analyzed the intra-species genetic diversity of 936 gut bacteria across 24,997 individuals from three countries. Our findings show that highly abundant species exhibit greater strain stability, whereas low-abundance species display increased in-clonal mutations. Clonal strains are often mutually exclusive, while genetically variable strains tend to coexist. Strain turnover is associated with the presence of annotated chemotaxis and sporulation genes in reference genomes, whereas strain coexistence is associated with quorum sensing and secretion systems. Leveraging deep phenotypic data, we constructed an atlas detailing strain-level associations with diverse host physiological domains. For example, Phocaeicola vulgatus sub-types relate to host obesity, Lachnospira eligens to sleep, and Parabacteroides distasonis to iron hemostasis. This resource may guide personalized microbiome-based interventions to improve human health.},
}

@article {pmid41394616,
year = {2025},
author = {Hunt, NK and Liu, C and Liu, J and Tang, Q and Stephen, SJ and Wang, B and Schurman, CA and King, CD and Liu, Q and Vashisth, D and Schilling, B and Hassani, M and Hernandez, CJ},
title = {Modifications to the gut microbiome alter bone matrix proteomics and fracture toughness at the cellular scale.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.21.689836},
pmid = {41394616},
issn = {2692-8205},
abstract = {UNLABELLED: The gut microbiome can regulate the strength of bone matrix but the specific changes in matrix function and composition are not yet understood. Here we introduce micropillar splitting to determine the fracture toughness of matrix at the cellular scale in concert with proteomic analysis of bone matrix when the gut microbiome was altered by oral antibiotics (ampicillin+neomycin). Male mice were divided into four groups (n = 3-4/group): (1) Unaltered (no alteration), (2) Continuous (alteration from 4-24 weeks), (3) Delayed (alteration from 16-24 weeks) and (4) Reconstituted (alteration from 1-16 weeks following by reconstitution). Micropillars (5 µm diameter) were fabricated using focused ion beam milling on femur cross-sections in regions of matrix formed either before or after changes in the microbiome (16 weeks) (n = 4/group). Proteomics was used to identify differences in matrix protein composition. Micropillar fracture toughness differed by group (p < 0.001) and region (p < 0.001). Fracture toughness in the Unaltered group (1.34 ± 0.32 MPa√m, mean ± SD) was substantially greater than the Continuous group (0.95 ± 0.20) and the Delayed group (0.90 ± 0.21) but not different from the Reconstituted group (1.22 ± 0.25). Bone matrix formed from 16-24 weeks of age had lower fracture toughness than matrix formed before 16 weeks of age in all groups. Notably, micropillar splitting was substantially more precise than whole bone testing; whole bone notched 3-point bending tests did not detect differences in fracture toughness. Proteomics identified 46 extracellular matrix proteins that were differentially abundant between groups, including decreased abundance of Periostin (q < 0.001) and Emilin-1 (q < 0.001) in groups with impaired bone matrix. These findings demonstrate that modifications to the gut microbiome lead to changes in bone matrix throughout cortical bone volume and establish micropillar splitting as a high-precision approach for characterizing matrix material properties.

PLAIN LANGUAGE SUMMARY: This study investigated the effect of the gut microbiome on the brittleness of bone as a material. We used a new technique for measuring the brittleness of bone that involves making microscopic pillars on the bone surface and splitting them down the middle to measure a material property called fracture toughness. Mice with altered gut microbiomes had bone with reduced fracture toughness (by 35-40%). Restoration of an altered gut microbiome for two months reversed the effects. The effect of the microbiome on bone occurred throughout the whole bone and was not limited to regions of the bone formed after a change in the gut microbiome.},
}

@article {pmid41394473,
year = {2025},
author = {Chatchatee, P and Breedveld, AC and Eussen, SRBM and Nowak-Wegrzyn, A and Lange, L and Benjaponpitak, S and Chong, KW and Sangsupawanich, P and Wopereis, H and Oude Nijhuis, MM and Langford, JE and Kostadinova, AI and Trendelenburg, V and Pesek, R and Davis, CM and Muraro, A and Erlewyn-Lajeunesse, M and Fox, AT and Michaelis, LJ and Beyer, K},
title = {Effects of a specific synbiotic blend on fecal short-chain fatty acids and gut inflammation in cow's milk-allergic children receiving amino acid-based formula during early life: results of a randomized controlled trial (PRESTO study).},
journal = {Frontiers in allergy},
volume = {6},
number = {},
pages = {1667162},
pmid = {41394473},
issn = {2673-6101},
abstract = {Consumption of an amino acid-based formula (AAF) with added synbiotics [short-chain oligofructose and long-chain inulin (scFOS/lcFOS, 9:1 ratio) and Bifidobacterium breve M-16V] (AAF-S) beneficially impacts the gut microbiome of infants with cow's milk allergy (CMA). We assessed the effect of consuming AAF with or without synbiotics by children with CMA for 12 months on their fecal (branched) short-chain fatty acids (SCFA/BCFA) concentrations, and on gut barrier and inflammation markers (Netherlands Trial Register NTR3725). Feces and saliva were collected from 161 children (≤13 months) with IgE-mediated CMA at baseline, 6 and 12 months after enrollment, and at 24 and 36 months follow-up. Fecal SCFA and BCFA were analyzed by gas chromatography, and gut barrier and inflammation markers were measured in saliva/feces by ELISA or ImmunoCAP. At 6 months, children receiving AAF-S had significantly lower fecal propionate, valerate and BCFA concentrations compared to children consuming AAF. The percentage of propionate from the total 6 SCFA/BCFA (acetate + butyrate + propionate + valerate + isobutyrate + isovalerate) was significantly lower, while the percentage of acetate from the total 6 SCFA/BCFA was significantly higher in the AAF-S group. There were no significant differences between groups in fecal concentrations of butyrate at 6 months, nor in SCFA or BCFA at baseline and after 12, 24 or 36 months. Intestinal inflammation and barrier markers did not differ between groups. Addition of synbiotics to AAF brings concentrations of key fecal microbial metabolites more in line with patterns observed in healthy breastfed infants. The effects on SCFA and BCFA concentrations were transient and only seen at 6 months.},
}

@article {pmid41394296,
year = {2025},
author = {Vasa, SR and Girard, M and Gardiner, GE and Cormican, P and Bee, G and O'Driscoll, K and Lawlor, PG},
title = {Effect of feeding a gestation diet to sows for 5 days post-farrowing and feeding a liquid mixture of milk replacer and starter diet to suckling piglets on growth, selected health parameters and faecal microbiota of suckling pigs on two research farms.},
journal = {Translational animal science},
volume = {9},
number = {},
pages = {txaf138},
pmid = {41394296},
issn = {2573-2102},
abstract = {This study involved 50 sows and was a 2 × 2 factorial arrangement with factors being sow feeding [lactation diet throughout lactation (CON) or gestation diet for the first 5 days of lactation, followed by lactation diet (GEST5)] and creep feeding from day (d) 5 after birth [dry pelleted starter diet (DPS) or liquid mixture of milk replacer and starter diet (LMR+S)]. The study was conducted on two research farms, one in Ireland (IE) and the other in Switzerland (CH). All sows were limit-fed the gestation diet until farrowing. During lactation, both sow treatments followed the same feeding curve with daily digestible energy allocation increasing from 58.1 to 135 MJ between d1 and 28. Sow feed intake, weight and backfat depth and piglet weight and total dry matter disappearance (TDMD) of creep feed during lactation were recorded. On d5 after birth, milk was collected from sows on both farms and sow faeces was collected at CH for short chain fatty acid (SCFA) analysis. Following weaning at d29 ± 0.2 in IE and d25.5 ± 1.3 in CH, pigs were followed until d43 post-weaning (pw) in IE (n = 7 pens/treatment) and d14 pw in CH (n = 11 pens/treatment). In IE, faecal samples were collected from sows before farrowing and on d5, 12 and 26 after birth and from piglets on d2, 5, 12 and 26 after birth and on d7 and d41 pw for microbiota analysis. Feeding GEST5 did not affect overall sow feed intake, backfat depth or weight loss during lactation on both farms (P > 0.05) but reduced the solids, fat and SCFA content of milk and increased faecal SCFA in CH (P < 0.05). In CH, LMR+S-fed pigs had higher TDMD than those fed DPS, while in IE, DPS had higher TDMD than LMR+S (P < 0.05). However, neither GEST5 nor LMR+S influenced pre- or pw pig growth or diarrhoea prevalence on either farm (P > 0.05). In IE, on d5 post-farrowing, GEST5 sows had a higher relative abundance of Prevotella and Succinivibrio in their faeces compared to CON (P < 0.05) and both GEST5 and LMR+S increased bacterial alpha diversity in piglet faeces on d7 pw (P < 0.05). In conclusion, while providing a gestation diet during the first 5 days of lactation increased physical feed intake then, it did not increase overall lactation feed intake in sows. Additionally, creep feeding a liquid mixture of milk replacer and starter diet to suckling piglets did not improve pre- or pw pig growth.},
}

@article {pmid41394287,
year = {2025},
author = {Stögbauer, J and Kämpfer, N and Becker-Dorison, A and Schwiertz, A and Groppa, S and Unger, MM and Fousse, M},
title = {Alterations of fecal short-chain fatty acids solely in the course of multiple sclerosis: rethinking the gut-brain axis in the early stages of MS.},
journal = {Therapeutic advances in neurological disorders},
volume = {18},
number = {},
pages = {17562864251396028},
pmid = {41394287},
issn = {1756-2856},
abstract = {BACKGROUND: The role of gut microbiota in multiple sclerosis (MS) has become increasingly important, intestinal dysbiosis with reduced production of short-chain fatty acids (SCFA) being the prevailing paradigm. However, the direction of causality, that is, whether intestinal changes are cause or consequence of chronic central nervous system inflammation, remains to be elucidated. Previous studies have focused on long-term MS patients. Alteration in fecal SCFA concentrations in early MS, particularly during relapses, remains to be extensively studied.

OBJECTIVES: To compare fecal SCFA concentrations in patients with a first diagnosis of MS with those in patients with long-term MS and in healthy controls (HCs).

DESIGN: Prospective cohort study.

METHODS: The prospective case-control study was conducted on relapsing-remitting MS (RRMS) patients at the time of first, acute relapse without ongoing immunotherapy (Early-RRMS). Clinical and demographic parameters, as well as fecal SCFA concentrations (measured by gas chromatography) were collected. The parameters were compared with those of matched RRMS patients under different, long-term immunotherapy (Late-RRMS) and HCs.

RESULTS: SCFA concentrations of propionate, butyrate, isobutyrate, valerate, and isovalerate were not significantly different between the early-RRMS cohort and HCs, but were lower in the late-RRMS cohort.

CONCLUSION: The findings indicate that reduction in SCFA levels is exclusively observed in patients with RRMS during the further course of the disease and not at the onset. Decrease in SCFA concentration may be rather consequence or related to neurodegeneration than linked to the first demyelinating event. Further investigation related to disease trajectories of immunomodulatory or neuroprotective treatments are required.},
}

@article {pmid41394226,
year = {2025},
author = {Lyu, Z and Zhu, J and Chen, D},
title = {Chronic Periodontitis and Non-Alcoholic Fatty Liver Disease: Recent Advances in Mechanisms of Association.},
journal = {International journal of general medicine},
volume = {18},
number = {},
pages = {7357-7369},
pmid = {41394226},
issn = {1178-7074},
abstract = {BACKGROUND: Chronic periodontitis (CP) and non-alcoholic fatty liver disease (NAFLD) are increasingly prevalent worldwide. Although mechanisms remain incompletely defined, recent studies suggest a close association between these two diseases. This review systematically outlines potential links between periodontitis and NAFLD, emphasizing their pathological mechanisms and interactions within an oral-gut-liver framework.

METHODS: We reviewed observational, interventional, and mechanistic studies evaluating associations between periodontal status/treatment and NAFLD-related outcomes, integrating evidence on dysbiosis, inflammatory mediators, microbial metabolites, oxidative stress, microRNA regulation, and gut barrier function.

RESULTS: Across epidemiological studies, periodontitis is associated with higher risk and greater severity of NAFLD. Mechanistically, oral dysbiosis, especially enrichment of oral pathobionts, is linked to hepatic steatosis and fibrosis. Translocation of microbial products and the resulting cytokine release drive systemic inflammation, impair gut barrier integrity, and induce hepatocellular injury. Microbial metabolites (such as short-chain fatty acids (SCFAs) and trimethylamine N-oxide (TMAO)) and oxidative stress contribute to metabolic dysregulation. Emerging evidence suggests that microRNAs (miRNAs) function as epigenetic regulators linking periodontal inflammation and bone remodeling to immune-metabolic pathways relevant to non-alcoholic fatty liver disease (NAFLD). However, direct evidence on whether treating periodontitis can improve NAFLD outcomes remains limited. Despite heterogeneity in study designs and diagnostic criteria, cumulative evidence supports periodontitis as a modifiable risk factor for the progression of NAFLD.

CONCLUSION: CP and NAFLD appear to be linked through systemic inflammation, dysbiosis, and metabolic disturbances. Future research should prioritize microbiome modulation, advance interdisciplinary care models, and develop personalized prevention and treatment strategies. Integrating oral and liver health within comprehensive management may provide new options for preventing and treating these frequently coexisting diseases.},
}

@article {pmid41394107,
year = {2025},
author = {Yang, Y and Jia, XF and Cui, GH and Huang, QY and Lin, MM and Shi, ZM and Ye, H and Zhang, XZ},
title = {Jinghuaweikang capsule alleviates Helicobacter pylori-infected gastric mucosal inflammation and drug resistance by regulating intestinal microbiota and MAPK pathway.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1628594},
pmid = {41394107},
issn = {2235-2988},
mesh = {Animals ; *Helicobacter Infections/drug therapy/microbiology/pathology ; *Helicobacter pylori/drug effects ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Drugs, Chinese Herbal/administration & dosage/pharmacology ; Disease Models, Animal ; *Gastric Mucosa/pathology/drug effects/microbiology ; *MAP Kinase Signaling System/drug effects ; *Drug Resistance, Bacterial/drug effects ; Anti-Bacterial Agents/pharmacology ; Male ; Inflammation/drug therapy ; *Gastritis/drug therapy/microbiology ; Capsules ; },
abstract = {BACKGROUND: Helicobacter pylori (H. pylori) infection represents a prevalent global health burden. Current eradication strategies are complicated by increasing antibiotic resistance and detrimental alterations to the gut microbiome. Jinghuaweikang capsule (JWC), a traditional Chinese medicine, has demonstrated efficacy against H. pylori, yet its mechanisms involving microbiota-inflammation interactions remain incompletely elucidated.

AIM: This study aimed to investigate the effects of the JWC on gastric mucosal inflammation and the expression of drug-resistance genes in H. pylori-infected mice.

METHODS: Sixty Kunming mice were randomly allocated into six groups, including normal control group (Control), model group (Model), Western medicine triple group (AC), low-dose JWC group (JWCL), medium-dose JWC group (JWCM), and high-dose JWC group (JWCH). A mouse model of H. pylori infection was established by intragastric administration of an H. pylori SS1 solution for two weeks. The efficacy of this model was evaluated using rapid urease test (RUT) and Warthin-Starry (WS) silver stain. Subsequently, the experimental cohort of mice underwent pharmacological intervention. Hematoxylin and eosin (HE) staining, enzyme-linked immunosorbent assay (ELISA), and quantitative real-time polymerase chain reaction (qRT-PCR) were used to assess the impact of JWC on inflammation within the gastric mucosa of mice infected with H. pylori. Metagenomic sequencing technology was used to identify alterations in the intestinal microbiota and antibiotic resistance genes in the murine models. Western blotting was used to assess the expression levels of proteins involved in the mitogen-activated protein kinase (MAPK) signaling pathway.

RESULTS: JWC mitigated gastric mucosal inflammation induced by H. pylori infection and reduced the concentrations of interleukin- (IL-) 6, IL-1β, and tumor necrosis factor-α (TNF-α) while inhibiting gene expression level. Metagenomic sequencing revealed that triple therapy in Western medicine markedly diminished the diversity of the intestinal microbiota while elevating the abundance of antibiotic-resistance genes, including macB, arlR, evgS, tetA(58), and mtrA. The diversity and richness of the intestinal microbiota in the JWC group were comparable to those in the control group, with an increase in the abundance of beneficial bacteria such as Muribaculaceae_bacterium. Furthermore, the expression levels of the antibiotic resistance genes macB, tetA(58), bcrA, oleC, and arlS were downregulated. Moreover, the activation of MAPK signaling pathway components phospho-ERK and phospho-p38 was inhibited.

CONCLUSION: JWC preserves microbial diversity and promotes a beneficial compositional shift, mitigates the risk of antibiotic resistance, modulates the MAPK signaling pathway, and alleviates gastric mucosal inflammation in mice infected with H. pylori.},
}

Animals
*Helicobacter Infections/drug therapy/microbiology/pathology
*Helicobacter pylori/drug effects
*Gastrointestinal Microbiome/drug effects
Mice
*Drugs, Chinese Herbal/administration & dosage/pharmacology
Disease Models, Animal
*Gastric Mucosa/pathology/drug effects/microbiology
*MAP Kinase Signaling System/drug effects
*Drug Resistance, Bacterial/drug effects
Anti-Bacterial Agents/pharmacology
Male
Inflammation/drug therapy
*Gastritis/drug therapy/microbiology
Capsules

@article {pmid41393947,
year = {2025},
author = {Semchyshyn, H},
title = {Balancing the dual nature of glycotoxins: interplay of diet, digestion, and gut microbiome.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1693167},
pmid = {41393947},
issn = {2296-861X},
abstract = {Glycation chemistry, both in vitro and in vivo, is well-studied and known to result in a variety of products-from early glycation products, reactive carbonyl and oxygen species (RCS and ROS, respectively) to advanced glycation end products (AGEs). Exogenous glycation products from the regular diet contribute substantially to the total AGE burden, often exceeding endogenous formation. AGEs and other products of glycation, whether formed endogenously or derived exogenously, may have similar biological effects and are mainly known for their harmful impact, therefore, the term "glycotoxins" is used to emphasize the toxicity of certain of them. Nevertheless, the human body as well as gut microbiome have adapted to the presence of glycation products and can even use them beneficially at low concentrations. Maintaining an appropriate balance of glycotoxins depends largely on digestion in the gastrointestinal tract, mediated by both host and microbiome enzymes. The fate of dietary glycation products in the gut strongly depends on their interaction with the intestinal microbiota. A key open question is how human and microbial enzymes work together to degrade AGEs and maintain their concentrations within a potentially "beneficial" range. This review is focused on the metabolism and digestion of glycation products by both human and microbial enzymes, highlighting their dual nature and overall impact on human health.},
}

@article {pmid41393931,
year = {2025},
author = {Geng, J and Zhang, G and Dong, J and Tian, H and Lou, Z},
title = {Multi-omics techniques revealing the mechanism of Polygonatum sibiricum Huangjiu in alleviating hyperlipidemia in mice.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1705061},
pmid = {41393931},
issn = {2296-861X},
abstract = {INTRODUCTION: Hyperlipidemia poses a serious threat to human health. However, given the significant adverse effect of drug therapy, finding safe and efficient lipid-lowering agents has become a focal point of interest. Polygonatum sibiricum Huangjiu (PSHJ) is hypothesized to exert lipid-lowering effects. This study examined PSHJ's ability to alleviate hyperlipidemia in mice caused by a high-fat diet, and the regulatory mechanism was studied via gut microbiome and fecal lipidomics.

METHODS: A mouse model of hyperlipidemia was established using a high-fat diet. The experimental groups were administered PSHJ, and serum lipid profiles-including triglycerides (TG), total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C)-were measured. Histopathological examinations of the liver, kidney, and small intestine were performed to assess tissue damage. The gut microbiota composition was analyzed to evaluate diversity and the abundance of short-chain fatty acids (SCFAs)-producing bacteria. Fecal lipidomics was employed to investigate alterations in lipid metabolic pathways.

RESULTS: PSHJ treatment significantly increased HDL-C levels while reducing serum TG, TC, and LDL-C levels in hyperlipidemic mice. Histological analysis revealed that PSHJ alleviated damage in the liver, kidney, and small intestine. Furthermore, PSHJ enhanced gut microbial diversity and promoted the proliferation of SCFA-producing bacteria, leading to elevated SCFA levels. Lipidomic analysis indicated that PSHJ modulated metabolic pathways related to glycerophospholipids, glycerolipids, and fatty acids, thereby facilitating the breakdown of TG and diacylglycerol (DG).

DISCUSSION: The findings suggest that polysaccharides in PSHJ function as prebiotics, enriching beneficial gut microbiota and increasing SCFA production. These SCFAs, along with polysaccharides, appear to regulate key lipid metabolic pathways, enhancing the degradation of TG and DG. This study shows that PSHJ has active components that can alleviate hyperlipidemia, thereby laying a theoretical foundation for extracting bioactive substances from Huangjiu for future medical or dietary use.},
}

@article {pmid41393901,
year = {2025},
author = {Wang, JJ and Hu, Y and Jennings, S and Luo, M and Taylor, CM and Nauseef, WM and Wang, G},
title = {Myeloperoxidase gene knockout causes local inflammation and dysbiosis in the murine gut.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {},
pmid = {41393901},
issn = {2993-3935},
abstract = {Myeloperoxidase (MPO), predominantly expressed in neutrophils, catalyzes the production of hypochlorous acid (HOCl) that plays an integral role in the host defense against invading pathogens. However, little is known about its role in maintaining normal gut microbiome and function. Here, we report the comparisons of inflammation and microbiome in the intestines of WT and MPO[-/-] mice. Immune cell profiling demonstrated that the MPO[-/-] mice had significantly more neutrophils and T cells in their intestinal mucosae and significantly more fecal calprotectin as compared to the WT mice. Fluorescent dextran permeability of the bowel showed no difference between the two strains of mice. Carmine Red transit demonstrated that the MPO[-/-] intestines had slower movements than did the WT controls. Sequencing the intestinal 16S rDNA of co-housed MPO[-/-] and WT mice identified 13 bacterial families, 2 of which were unique to MPO[-/-] and 7 to WT mice. Alpha diversity of the microbiome in WT intestines was significantly higher than that of MPO[-/-] ones, and beta diversity of the two microbial communities of the two genotypes also differed significantly. Functional pathway analyses revealed distinct metabolic signatures. Thus, normal MPO function is important to intestinal health and its deficiency leads to gut inflammation and dysbiosis.},
}

@article {pmid41393784,
year = {2025},
author = {Longhi, G and Tarracchini, C and Angelini, L and Anzalone, R and Viappiani, A and Ventura, M and Milani, C and Turroni, F},
title = {Exploring diversity and functional contribution of the microbiome of traditional Italian dry-cured hams.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100516},
pmid = {41393784},
issn = {2666-5174},
abstract = {Traditional dry-cured hams host diverse microbial communities; however, their taxonomic composition, functional capacity, and potential interactions with the human gut remain poorly understood. This study aimed to provide a comprehensive characterization of the microbiota associated with Italian Protected Designation of Origin (PDO) dry-cured hams and to investigate their functional relevance in the food matrix and under simulated intestinal conditions. A total of 96 samples, representing different geographical origins and maturation stages, were analyzed using metagenomics approaches. A conserved microbial core dominated by Staphylococcus equorum (prevalence 80 %) was identified, accompanied by accessory taxa such as Tetragenococcus halophilus (62 %) and Leuconostoc carnosum (10 %). Cluster analyses revealed substantial variability across samples, with community structures influenced more by producer-specific factors than by product type or ripening stage. Functional metagenomics investigation highlighted the presence of metabolic pathways associated with amino acid degradation, carbohydrate metabolism, and lipid transformation, supporting a role for ham-associated microbes in flavor and texture development. Furthermore, cultivation in a simulated gut environment showed a marked reshaping of the microbial community, with low-abundance taxa, including Bacillus spp. and Lactococcus lactis, proliferating under intestinal-like conditions, while the dominance of S. equorum was reduced. Our findings showed that the microbiota of dry-cured ham not only drives key sensory qualities of the product but also comprises a reservoir of live microorganisms capable of tolerating the gut-like conditions. These results highlight the dual role of foodborne microbiota in shaping both food properties and potential interactions with the human host, underscoring the need for further in vivo investigations.},
}

@article {pmid41393412,
year = {2025},
author = {V Manek, P and M, A and Sinha, R and Pradeep, O and Dixit, H and Sharma, D and Tiwari, R},
title = {Daily probiotic supplementation on plaque pH and gingival health in adults: A clinical study.},
journal = {Bioinformation},
volume = {21},
number = {8},
pages = {2365-2368},
pmid = {41393412},
issn = {0973-2063},
abstract = {Oral health is strongly influenced by the balance of the oral microbiome, with plaque pH and gingival status serving as critical indicators of dental and periodontal well-being. A randomized, controlled clinical trial was conducted involving 60 healthy adults aged 20-45 years. The probiotic group exhibited a significant increase in plaque pH (from 5.89 ± 0.12 to 6.52 ± 0.10, p < 0.001) and a marked reduction in gingival index scores (from 1.83 ± 0.18 to 0.97 ± 0.15, p < 0.001). The control group showed no significant changes. Daily probiotic intake effectively enhanced plaque pH and gingival health, supporting its role as a preventive adjunct in routine dental care.},
}

@article {pmid41393294,
year = {2025},
author = {Kellenberger, A and Dewal, RS and de Wouters d'Oplinter, A and Sichert, A and Heine, M and Fuh, MM and Slack, E and Delessa Challa, T and Wolfrum, C},
title = {Antibiotic-induced gut microbiota depletion enhances glucose tolerance linked to GLP-1 signaling.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1684155},
pmid = {41393294},
issn = {1664-2392},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Glucagon-Like Peptide 1/metabolism ; Mice ; *Anti-Bacterial Agents/pharmacology ; Signal Transduction/drug effects ; Mice, Knockout ; Male ; *Glucose Intolerance/metabolism ; Mice, Inbred C57BL ; *Glucose/metabolism ; Glucose Tolerance Test ; Bile Acids and Salts/metabolism ; Glucagon-Like Peptide-1 Receptor/genetics ; Uncoupling Protein 1/metabolism/genetics ; },
abstract = {INTRODUCTION: Depletion of the gut microbiota is known to improve glucose metabolism and modify thermogenic capacity in mice. However, the underlying mechanisms remain unclear. In this study, we aimed to determine whether the browning effect observed after antibiotic treatment contributes to metabolic modifications and to investigate the potential central role of GLP-1 in enhancing glucose metabolism.

METHODS: Using an inducible Ucp1DTR mouse model to transiently ablate UCP1[+] cells, we assessed glucose tolerance, cold sensitivity, and circulating GLP-1 levels following gut microbiota depletion. We additionally examined GLP-1 levels in germ-free mice. Glucose tolerance was compared to GLP1R KO mice following gut microbiota depletion. Bile acid profiling in wild-type mice treated with antibiotics identified regulated bile acids, which were subsequently tested in an in vitro STC-1 cell assay and in vivo in Cyp2c70 mice to identify potential basal GLP-1 secretion inhibitors.

RESULTS: We demonstrate that gut microbiota depletion improved glucose tolerance independent of UCP1[+] cell presence and increased cold sensitivity. Antibiotic treatment increased circulating active GLP-1 levels within one day, and this increase was also observed in germ-free mice, supporting the suggestion that GLP-1 elevation is driven by gut microbiota depletion. The improvement in glucose tolerance was lost in GLP1R KO mice upon oral glucose ingestion. Bile acid profiling and subsequent validation led to the identification of two potential basal GLP-1 secretion inhibitors.

DISCUSSION: Our findings suggest that the metabolic improvements following gut microbiota depletion are primarily driven by GLP-1 signaling, rather than UCP1⁺ cell activation. These results highlight the complex interplay between the gut microbiome and metabolic health, offering insights into potential therapeutic targets for improving glucose metabolism through modulation of basal GLP-1 signaling.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Glucagon-Like Peptide 1/metabolism
Mice
*Anti-Bacterial Agents/pharmacology
Signal Transduction/drug effects
Mice, Knockout
Male
*Glucose Intolerance/metabolism
Mice, Inbred C57BL
*Glucose/metabolism
Glucose Tolerance Test
Bile Acids and Salts/metabolism
Glucagon-Like Peptide-1 Receptor/genetics
Uncoupling Protein 1/metabolism/genetics

@article {pmid41393148,
year = {2025},
author = {Wang, D and Li, J and Wang, L and Tian, H and Zhou, X and Wang, X and Tian, H},
title = {Intestinal dysbiosis in critically ill patients: a case-control study of Enterobacteriaceae enrichment and reduced microbial diversity.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1680262},
pmid = {41393148},
issn = {2296-858X},
abstract = {INTRODUCTION: Critical illness disrupts gut microbiota homeostasis, potentially exacerbating systemic inflammation and adverse outcomes. This study investigates gut dysbiosis patterns in ICU patients, with a focus on Enterobacteriaceae enrichment and microbial diversity loss, to identify biomarkers and therapeutic targets.

METHODS: In this case-control study, 37 ICU patients (sepsis: n = 17; non-sepsis: n = 20) and 20 healthy controls were enrolled. Fecal samples underwent 16S rRNA sequencing (V3-V4 regions). Microbial diversity (Shannon/Simpson indices), beta diversity (Bray-Curtis PCoA), and taxonomic differences (LEfSe, LDA > 2.5) were analyzed using QIIME2 and R.

RESULTS: Critically ill patients showed reduced alpha diversity vs. controls (Shannon p = 0.04; Simpson p = 0.04). Enterobacteriaceae (phylum Proteobacteria) were significantly enriched in ICU patients (LDA = 4.2, p < 0.01), while Ruminococcus dominated controls. Beta diversity differed markedly (PERMANOVA R [2] = 0.199, p = 0.001). No diversity differences were observed between sepsis/non-sepsis subgroups (p > 0.05).

CONCLUSION: ICU patients exhibit gut dysbiosis characterized by Enterobacteriaceae expansion and diversity loss, independent of sepsis status. These findings underscore the gut microbiome's role in critical illness and support exploring microbiota-targeted interventions (e.g., selective probiotics) to improve outcomes.},
}

@article {pmid41393116,
year = {2025},
author = {Ahmed, N and Gaur, V and Kamle, M and Chauhan, A and Chauhan, R and Kumar, P and Singh, NA},
title = {Correction: Microbiome-based therapeutics for metabolic disorders: harnessing microbial intrusions for treatment.},
journal = {Frontiers in medical technology},
volume = {7},
number = {},
pages = {1736962},
doi = {10.3389/fmedt.2025.1736962},
pmid = {41393116},
issn = {2673-3129},
abstract = {[This corrects the article DOI: 10.3389/fmedt.2025.1695329.].},
}

@article {pmid41393108,
year = {2025},
author = {Sun, Y and Yang, H and Zhang, J and Cong, S and Wang, L and Yu, T},
title = {Development and emerging trends in gastrointestinal dysfunction of Parkinson's disease: a decade-long bibliometric analysis.},
journal = {Frontiers in aging neuroscience},
volume = {17},
number = {},
pages = {1712302},
pmid = {41393108},
issn = {1663-4365},
abstract = {Gastrointestinal (GI) dysfunction represents a prevalent non-motor symptom of Parkinson's disease (PD) that not only contributes significantly to disease progression but also substantially compromises patients' quality of life. Over the past decade, research in this domain has expanded considerably. To systematically delineate the knowledge framework and evolving trends, we performed a bibliometric analysis of publications on GI and PD from 2015 to 2025. A total of 924 articles were retrieved from the Web of Science Core Collection (WoSCC). Co-occurrence, clustering, and collaboration network analyses were performed using VOSviewer, CiteSpace, and the R package Bibliometrix. For findings validation, the PubMed database was incorporated as an independent external validation dataset, providing complementary verification of keyword analyses derived from WoSCC. Our analysis revealed a steady annual increase in publication output. China and the United States emerged as the most prolific contributors globally, with the latter attaining the highest total citation count. At the institutional level, Capital Medical University led in publication output, whereas the University of Helsinki ranked highest in both total and average citations. Among journals, Parkinsonism & Related Disorders published the most papers on this topic, while Movement Disorders received the most citations. Keyword cluster analyses identified three primary research frontiers: (1) pathogenesis, focusing on α-synuclein (α-syn), the brain-gut-microbiome axis, and the enteric nervous system; (2) clinical manifestations, especially dysphagia and constipation; and (3) therapeutic interventions, particularly fecal microbiota transplantation and probiotics. By integrating established knowledge and highlighting emerging trends, this review aims to inform and guide future research and clinical practice in the field of gastrointestinal dysfunction in PD.},
}

@article {pmid41392764,
year = {2025},
author = {Wu, Q and Gao, G and Kwok, LY and Qiao, J and Wei, Z and He, Q and Sun, Z},
title = {Bifidobacterium animalis subsp. lactis Bbm-19 ameliorates insomnia by remodeling the gut microbiota and restoring γ-aminobutyric acid and serotonin signaling.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo04374c},
pmid = {41392764},
issn = {2042-650X},
abstract = {Insomnia is associated with dysregulation of the gut-brain axis, yet microbiome-targeted interventions remain underexplored. In this study, we investigated the effects of Bifidobacterium animalis subsp. lactis Bbm-19 (Bbm-19), a strain isolated from human breast milk, in a 4-chloro-DL-phenylalanine-induced mouse model of insomnia. Using integrated behavioral, neurochemical, immunological, and multi-omics approaches, this study demonstrates that insomnia is characterized by shortened sleep duration, prolonged sleep latency, anxiety-like behaviors, and reduced levels of serotonin and gamma-aminobutyric acid in the gut, serum, and brain. Administration of Bbm-19 significantly improved sleep parameters, reduced anxiety-like behaviors, and increased survival. Metagenomic and metabolomic analyses revealed that Bbm-19 restored gut microbiota balance, enriched beneficial taxa, including Muribaculaceae bacterium and Stercoribacter sp., and reprogrammed microbial metabolic modules, particularly those involved in amino acid metabolism (including alanine, aspartate, glutamate, arginine, proline, and tryptophan pathways). Targeted metabolomics confirmed increased levels of gamma-aminobutyric acid and serotonin in fecal and brain tissues, along with normalization of inflammatory cytokine profiles. Spearman correlation analysis linked Bbm-19-enriched taxa to improved neurotransmitter levels and sleep outcomes. Notably, Bbm-19 outperformed lorazepam in modulating gut-specific metabolic functions and synergistically enhanced its effects when co-administered. These findings demonstrate that Bbm-19 ameliorates insomnia through coordinated regulation of the gut microbiota, host metabolism, and neuroimmune signaling, highlighting its potential as a targeted psychobiotic intervention for sleep disorders.},
}

@article {pmid41392395,
year = {2025},
author = {Giangiulio, O and Maccarone, R},
title = {The Blood-Brain Barrier as an Integration Hub in Alzheimer's Disease: How Microbiota Metabolites Modulate Central Signal Processing.},
journal = {CNS neuroscience & therapeutics},
volume = {31},
number = {12},
pages = {e70703},
doi = {10.1002/cns.70703},
pmid = {41392395},
issn = {1755-5949},
mesh = {Humans ; *Alzheimer Disease/metabolism/microbiology/physiopathology ; *Blood-Brain Barrier/metabolism ; *Gastrointestinal Microbiome/physiology ; Animals ; Signal Transduction/physiology ; },
abstract = {BACKGROUND: While both gut-brain axis dysfunction and blood-brain barrier (BBB) breakdown are documented in Alzheimer's disease (AD), current research treats these as separate phenomena. However, emerging evidence suggests that the BBB may function as an active integration interface that processes microbiota-derived metabolites and thereby potentially modulates how peripheral signals influence cognitive health.

OBJECTIVE: This review synthesizes current evidence on microbiota metabolites as modulators of BBB integration capacity, discussing how such mechanisms may contribute to variability in cognitive outcomes despite similar gut microbiome profiles by demonstrating how BBB signal-integration mechanisms determine gut-brain communication effectiveness in AD.

METHODS: We analyzed peer-reviewed literature from 2010 to 2025, focusing on BBB dynamic properties, microbiota metabolite effects on BBB function, and their integration patterns, emphasizing functional evidence supporting the BBB's active signal processing capabilities.

RESULTS: Current evidence suggests that the BBB exhibits integration properties, including dynamic permeability regulation, context-dependent metabolite processing, and coordinated responses to complex signal streams. Short-chain fatty acids enhance integration capacity through HDAC inhibition and coordinated receptor activation, while lipopolysaccharides and trimethylamine N-oxide may overwhelm integration processes through TLR4-mediated disruption. BBB dysfunction precedes classical AD pathology and correlates with altered metabolite processing capacity. Individual variations in BBB integration capacity may help account for why individuals with similar gut microbiome profiles show different cognitive outcomes.

CONCLUSION: Viewing the BBB as an active integration interface offers a useful perspective for organizing current evidence on gut-brain interactions in AD. This conceptual perspective suggests that therapeutic strategies might benefit from supporting BBB integration capacity and optimizing metabolite-processing mechanisms alongside improving gut health.},
}

Humans
*Alzheimer Disease/metabolism/microbiology/physiopathology
*Blood-Brain Barrier/metabolism
*Gastrointestinal Microbiome/physiology
Animals
Signal Transduction/physiology

@article {pmid41392314,
year = {2025},
author = {Abahussin, HM and Alotaibi, MS and Alhazzaa, OA and Alotaibi, AG and Alsaab, SM and Aljawini, NA and Alawad, AO},
title = {Exploring the intricate link between gut microbiota dysbiosis and the aging process: implications for age-related diseases.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-025-00788-z},
pmid = {41392314},
issn = {1757-4749},
abstract = {Aging is a complex process marked by the gradual accumulation of impairments in molecules and tissues, leading to frailty and dysfunction. This decline is a significant risk factor for many debilitating conditions. Recently, gut microbiota dysbiosis has been identified as one of the hallmarks of aging. This review sheds light on the role of gut microbiota dysbiosis in accelerating aging and its relation to age-associated diseases, including neurodegenerative disorders, cardiovascular diseases, cancer and diabetes. Emerging research demonstrates a strong link between the gut microbiome and the aging process, although the underlying mechanisms remain under investigation. Animal studies suggest that targeting the gut microbiome may offer a promising approach to mitigate aging and related diseases. However, further human studies are needed to confirm these findings.},
}

@article {pmid41392229,
year = {2025},
author = {Bernal, SPF and Soares, C and Ottoni, JR and da Costa Silva Gonçalves, C and Lima, N and Passarini, MRZ},
title = {Caracterização taxonômica integrativa de comunidades bacterianas e fúngicas de tripas de cupins e areia de folhas.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {10},
pmid = {41392229},
issn = {1678-4405},
support = {205/2021/PRPPG//Triple Agenda institutional program/ ; },
mesh = {*Isoptera/microbiology ; Animals ; *Fungi/classification/genetics/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; Phylogeny ; Plant Leaves/microbiology ; *Sand/microbiology ; Soil Microbiology ; *Mycobiome ; },
abstract = {The search for microbial cells from different sources is a crucial strategy for discovering new strains with biotechnological potential. Leaf litter fungi, which decompose organic matter, and symbiotic termite bacteria, which digest cellulose, can be harnessed for the development of biotechnologies focused on nutrient recycling, biofuel production, and organic waste treatment. The precise identification of these strains allows the use of their biological capabilities, promoting innovative and sustainable solutions to environmental challenges. In this study, filamentous fungi and bacteria recovered from soil with leaf litter and termite guts were characterized using an integrative taxonomy approach, including classical morphology, ribosomal RNA gene sequencing, MALDI-TOF MS, and FTIR. A total of nine filamentous fungi and nine bacteria were identified. After taxonomic analysis, the bacterial strains were identified as belonging to Rossellomorea marisflavi (n = 2), Bacillus subtilis (n = 2), B. amyloliquefaciens (n = 2), B. cereus (n = 1), Priestia megaterium (n = 1), and Pseudomonas azotoformans (n = 1). The fungal species were identified as Talaromyces mycothecaei (n = 3), Aspergillus fumigatus (n = 1), A. tubingensis (n = 1), A. hiratsukae (n = 1), Trichoderma sp. (n = 1), T. harzianum (n = 1), and Coniochaeta velutina (n = 1). This may be the first report of the isolation of Rossellomorea from the gut microbiome of termites. The results showed that the use of an integrative approach for the taxonomic characterization of microbial strains recovered from environmental samples can improve the accurate identification and understanding of microbial species associated with different environments, such as the termite gut and litter.},
}

*Isoptera/microbiology
Animals
*Fungi/classification/genetics/isolation & purification
*Bacteria/classification/genetics/isolation & purification
Phylogeny
Plant Leaves/microbiology
*Sand/microbiology
Soil Microbiology
*Mycobiome

@article {pmid41392171,
year = {2025},
author = {Chowdhury, J and Milne, N and Wade, M and Sharwood, R and Thuaux, B and Green, P and Last, I and Senior, J and Carnegie, AJ and Anderson, IC and Elms, S and Plett, KL and Plett, JM},
title = {Amino acid biostimulant increases radiata pine photosynthetic efficiency and growth with shifts in mycobiome and nitrogen assimilation.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00835-x},
pmid = {41392171},
issn = {2524-6372},
abstract = {BACKGROUND: Amino-acid biostimulants have emerged as powerful alternatives to conventional inorganic nitrogen fertilisers, yet their potential in forestry species like radiata pine (Pinus radiata) remains largely unexplored. In this study, we reveal physiological mechanisms of enhanced growth of radiata pine seedlings that are achieved by substituting standard inorganic fertigation, either partially or entirely, with amino-acid-based biostimulants.

RESULTS: Amino-acid fertigation notably increased shoot biomass, plant height, and root collar diameter. Critically, this approach reshaped the root fungal community, selectively enriching fungi with diverse ecological roles, including several taxa known for auxin production. These microbial shifts coincided with higher needle auxin, a plausible link that merits testing. Machine learning models further identified key fungal genera that strongly associated with plant biomass, reinforcing microbiome shifts as a contributing mechanism to enhanced growth. Additionally, amino-acid fertigation improved nitrogen assimilation, correlating positively with increased chlorophyll content and photosynthetic efficiency.

CONCLUSIONS: Our findings highlight that the transition from inorganic source to amino-acid biostimulants not only enhances plant growth and nitrogen use but also associated with a shift in the root mycobiome, including taxa often considered beneficial, thereby offering a sustainable pathway to nursery production of radiata pine.},
}

@article {pmid41392089,
year = {2025},
author = {Wilson, BC and Tweedie-Cullen, RY and Albert, BB and Derraik, JGB and Ho, D and Depczynski, M and Creagh, C and Edwards, T and Gali, S and Thabrew, H and Cutfield, WS and O'Sullivan, JM},
title = {Encapsulated faecal microbiota transfer in young women with anorexia nervosa: an open-label feasibility pilot trial.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67267-6},
pmid = {41392089},
issn = {2041-1723},
abstract = {Perturbations of the gut microbiome have been associated with anorexia nervosa (AN) suggesting microbiome-modulation treatments, like faecal microbiota transfer (FMT), may offer therapeutic benefits. This open-label feasibility pilot trial evaluated the tolerability and microbiological impact of encapsulated, multi-donor FMT in 18 young women with AN (Registration: ACTRN12621001504808). Participants completed clinical and microbiome assessments at enrolment (3 weeks pre-treatment), baseline, and 3, 6, and 12 weeks post-treatment. Fifteen participants completed FMT, and 11 completed the final follow-up. The primary outcome was the change in gut microbiome composition from baseline to 3 weeks compared with natural variation between enrolment and baseline. FMT produced a significantly greater shift post-treatment (mean ± SD Bray-Curtis dissimilarity 0.36 ± 0.11; p = 0.0007), with participants gaining 38 ± 16 new species. Donor-derived strains comprised 41 ± 12% of the microbiome at 3 weeks, with engraftment persisting at 6 and 12 weeks. FMT was generally well tolerated; adverse events were mostly mild to moderate and overlapped with typical AN symptomatology. Monitoring of clinical outcomes supported the safety profile and suggested potential improvements in anxiety and metabolic parameters; however, the small sample and absence of a control arm preclude safety and efficacy inference. Overall, these findings warrant further investigation through randomised controlled trials in AN.},
}

@article {pmid41391848,
year = {2025},
author = {Manea, E and Galand, PE and Comeau, S and Ferrier-Pagès, C and Giordano, B and Pezzolesi, L and Raina, JB and Elahee Doomun, SN and Tignat-Perrier, R and Bramanti, L},
title = {Positive Interactions Under Ocean Warming and Acidification: Crustose Coralline Algae Holobionts Enhance Gorgonian Larval Settlement Under Climate Change.},
journal = {Environmental microbiology},
volume = {27},
number = {12},
pages = {e70217},
doi = {10.1111/1462-2920.70217},
pmid = {41391848},
issn = {1462-2920},
support = {101062275//HORIZON European Union programme Marie-Sklodowska Curie Actions/ ; //Prince Albert II of Monaco Foundation/ ; //Scholarship from the University of Cagliari/ ; CA20102//COST Action MAFWORLD/ ; },
mesh = {Animals ; Larva/growth & development/physiology/microbiology ; *Climate Change ; *Anthozoa/microbiology/physiology/growth & development ; Hydrogen-Ion Concentration ; *Rhodophyta/physiology/microbiology ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Seawater/chemistry/microbiology ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; Microbiota ; Global Warming ; Oceans and Seas ; },
abstract = {Crustose coralline algae (CCA) and their bacterial communities can emit chemical cues favoring coral larval settlement. Indeed, larvae of Eunicella singularis (white gorgonian) preferentially settle on CCA. Here, we investigated the effect of two Mediterranean CCA holobionts, Macroblastum dendrospermum and Lithophyllum stictiforme, on E. singularis larvae settlement and their bacterial communities, after warming and acidification treatments. We exposed CCA to temperature and pH expected for 2100 (SSP5-8.5) and to a marine heatwave event. Larval settlement increased 1.8-2.7 times in the presence of CCA exposed to warming and acidification compared to non-exposed CCA. High abundance of bacteria belonging to the Pirellulaceae family was observed in all CCA, while a higher abundance of monosaccharides was found in exudates of exposed CCA. Based on CCA-related 16S rDNA metabarcoding and metabolomics results, we hypothesize that the enhanced larval settlement was driven by the Pirellulaceae breakdown and utilization of CCA polysaccharides, in combination with polysaccharide release through the CCA cell walls likely augmented by decalcification. Furthermore, CCA acted as sources of bacterial taxa that may establish and persist in the adult E. singularis holobiont, independently of climate change effects. We conclude that CCA are key for E. singularis recruitment success, especially under future climate conditions, and contribute to their microbiome development.},
}

Animals
Larva/growth & development/physiology/microbiology
*Climate Change
*Anthozoa/microbiology/physiology/growth & development
Hydrogen-Ion Concentration
*Rhodophyta/physiology/microbiology
Bacteria/classification/genetics/isolation & purification/metabolism
*Seawater/chemistry/microbiology
RNA, Ribosomal, 16S/genetics
Symbiosis
Microbiota
Global Warming
Oceans and Seas

@article {pmid41391818,
year = {2025},
author = {Zhou, H and Gao, and Wu, B and Xu, G and Tian, L and Sun, Y and Yang, F and Ni, K},
title = {Phyllosphere microbiomes in grassland plants harbor a vast reservoir of novel antimicrobial peptides and biosynthetic diversity.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.12.017},
pmid = {41391818},
issn = {2090-1224},
abstract = {INTRODUCTION: The phyllosphere microorganisms colonizing plant surface harbor capacities to synthesize diverse specialized metabolites that mediate communication and interactions with environment and host. However, most known metabolites are derived from a few culturable microorganisms, and the genomic diversity and biosynthetic potential of the vast majority of bacteria associated with plants remain largely unexplored.

OBJECTIVES: Here, we aim to explore the genome architecture, biosynthetic ability, and host specific adaptability of grassland ecosystems, uncovering new perspectives on grassland phyllosphere microbial resources.

METHODS: We employed ultra-deep metagenomic sequencing, functional analysis, host-associated characterization, and bioactivity assays to explore the phyllosphere microbiome across 221 grassland plant samples representing 45 families. This approach revealed host preference in biosynthetic gene clusters (BGCs) and validated the antimicrobial efficacy of phyllosphere-derived antimicrobial peptides (AMPs).

RESULTS: Grassland plant phyllosphere microbiomes encode diverse BGCs. We identified 885,396 potential AMPs from over 68 million non-redundant gene sequences. Then, we reconstructed hundreds of near-complete genomes from phyllosphere metagenomes, and 32.61 % of reconstructed genomes were identified as unclassified genomes, primarily within Pseudomonadota, Actinomycetota, Bacillota and Bacteroidota phyla. Of the near-complete genomes, 91.97 % of the BGCs and 99.76 % of the identified AMPs were previously uncharacterized. Host phylogenetic analysis revealed functional divergence. Poaceae-associated Pseudomonas genomes contain an average of 28 BGCs, significantly higher than those in Asteraceae-associated genomes (mean = 14.76, P = 0.033). Similarly, Poaceae-associated Pantoea genomes carried an average of 9 BGCs, exhibiting significant enrichment compared to genomes from Asteraceae (mean = 7.13, P = 6.1e-05), Lamiaceae (mean = 7, P = 0.015), Ranunculaceae (mean = 8.22, P = 0.0053), and Rosaceae (mean = 7.75, P = 0.00069). ParaFit analyses further confirmed that host phylogeny significantly structures microbial functional repertoires, with intra-family hosts sharing more KEGG pathways than inter-family hosts. These results suggest that host evolutionary relationships are associated with metabolic specialization in phyllosphere microbiomes. All 13 AMPs synthesized via solid-phase peptide synthesis demonstrated antimicrobial activity, inhibiting the growth of at least one tested bacterial strain.

CONCLUSION: This study demonstrates the promise of grassland plant phyllosphere microbiome as a rich source for novel antimicrobial agents.},
}

@article {pmid41391800,
year = {2025},
author = {Li, Y and Li, J and Zhang, F and Liang, Z and Lan, M and Kang, W and Zhang, Y},
title = {The gut-liver axis mediates the protective effect of Cinnamomum chago polysaccharide against acute liver injury: Insights from integrated microbiome and metabolomics analysis.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {149679},
doi = {10.1016/j.ijbiomac.2025.149679},
pmid = {41391800},
issn = {1879-0003},
abstract = {Cinnamomum chago B. S. Sun et H. L. Zhao polysaccharide (CCP) was evaluated for its hepatoprotective effects against carbon tetrachloride (CCl4)-induced acute liver injury (ALI). The results demonstrated that CCP improved liver histopathology in ALI mice, significantly decreased serum biochemical indicators of liver injury, and enhanced hepatic antioxidant capacity. Western blot analysis further revealed that CCP activated the Nrf2/NQO1 signaling pathway, thereby strengthening the antioxidant defense system and alleviating liver damage. Untargeted metabolomics and gut microbiota profiling indicated that CCP increased linoleic acid levels through the biosynthesis of unsaturated fatty acids pathway. The elevated linoleic acid promoted the abundance of Lactobacillus in the gut microbiota, and metabolites produced from their interaction further enhanced systemic antioxidant capacity. Moreover, the CCP-induced increase in linoleic acid activated the hepatic Nrf2 signaling pathway, contributing to the improvement of liver injury. In conclusion, the gut-liver axis plays a crucial protective role in liver health, and the hepatoprotective effects of CCP are mediated by Lactobacillus and linoleic acid through activation of the hepatic Nrf2/NQO1 signaling pathway.},
}

@article {pmid41391761,
year = {2025},
author = {Liu, X and Hu, Y and An, J and Zhang, C and Tan, J and Wei, Y and Zhang, Y},
title = {A pathway for D-cysteinolate degradation in sulfate- and sulfite-reducing bacteria.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {111055},
doi = {10.1016/j.jbc.2025.111055},
pmid = {41391761},
issn = {1083-351X},
abstract = {Sulfonates, characterized by a C-SO3[-] moiety, are widespread in the environment. Sulfate- and sulfite-reducing bacteria (SRB) degrade many naturally occurring sulfonates to produce H2S, playing a vital role in sulfur metabolism in anaerobic environments, including the human gut. One of the most abundant sulfonates in marine environments is D-cysteinolate, which functions as an osmolyte in many marine organisms, though mechanisms for its anaerobic degradation remain unknown. Here, we identify and characterize a gene cluster encoding a D-cysteinolate degradation pathway, found in SRB from both environmental sources and the human gut. In this pathway, D-cysteinolate is first epimerized by a PLP-dependent cysteinolate racemase and oxidized by L-cysteinolate dehydrogenase to produce L-cysteate. Subsequent degradation by the recently characterized PLP-dependent enzymes cysteate racemase and D-cysteate sulfo-lyase yields ammonia, pyruvate, and sulfite, for further reduction to H2S. Given the abundance of cysteinolate in marine-derived foods, our study lays the foundation for further exploring its role in H2S production within the human gut microbiome.},
}

@article {pmid41391742,
year = {2025},
author = {Cui, G and Wu, X and Lei, X and Huang, K and Lü, F and He, P and Xu, Q},
title = {Bioaugmentation influences PBAT biodegradation patterns during composting through associated shifts in plastisphere communities and surface properties.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133792},
doi = {10.1016/j.biortech.2025.133792},
pmid = {41391742},
issn = {1873-2976},
abstract = {The plastisphere microbiome plays a critical yet incompletely resolved role in the biodegradation of bioplastics during aerobic composting. Here, we investigated the degradation of poly(butylene adipate-co-terephthalate) (PBAT) by integrating surface physicochemical characterization with high-throughput microbial profiling under simulated industrial composting conditions. Inoculant amendment significantly enhanced PBAT degradation, yielding a 12.7 % carbon loss compared with 3.2 % in the control. Gel permeation chromatography further confirmed polymer depolymerization, showing pronounced declines in molecular weight (particularly Mz). These structural changes were accompanied by accelerated ester bond hydrolysis, reflected by reduced water contact angle and attenuation of the CO stretching peak. Plastisphere succession revealed that inoculants reshaped surface-associated communities, increasing α-diversity and selectively enriching thermophilic taxa. Temporal community shifts suggested stage-dependent contributions, with hydrolytic genera (Bacillus, Lactobacillus) dominating the thermophilic phase, whereas oxidative taxa (Pseudomonas) became more prominent during maturation. Neutral community model analysis indicated that plastisphere assembly followed a largely deterministic pattern linked to compost stabilization parameters. Although direct functional validation was not performed, the study reveals correlated changes among PBAT depolymerization, surface hydrolysis/oxidation, and plastisphere restructuring. On this basis, we propose a conceptual degradation framework while emphasizing that specific enzymatic pathways and microbial functions require future confirmation. These findings advance understanding of biopolymer-microbe interactions and provide guidance for optimizing inoculant-assisted composting of biodegradable plastics.},
}

@article {pmid41391696,
year = {2025},
author = {Jiang, Q},
title = {The effects of different forms of vitamin E on gut microbiota, mechanisms and implications in disease prevention.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110235},
doi = {10.1016/j.jnutbio.2025.110235},
pmid = {41391696},
issn = {1873-4847},
abstract = {The gut microbiota plays an important role in host health and dysbiosis contributes to disease development. Natural forms of vitamin E consist of eight lipophilic antioxidants, i.e., alpha-, beta-. gamma- and delta-tocopherol (αT, βT, γT and δT) and alpha-, beta-. gamma- and delta-tocotrienol (αTE, βTE, γTE and δTE). Vitamin E forms and their metabolites including 13'-carboxychromanols (13'-COOHs) have been shown to possess anti-inflammatory activities. Interestingly, recent human and animal studies reveal that vitamin E forms and δTE-13'-COOH (metabolite of δTE) can modulate gut microbiota. Specifically, supplementation of αT, γT, tocotrienols or δTE-13'-COOH elevated some beneficial bacteria or attenuated disease-associated decrease of probiotics including butyrate producers. This review focuses on the current knowledge of the effects of different forms of vitamin E and δTE-13'-COOH on gut microbiome. Although the mechanisms underlying modulation of gut microbiota remain to be determined, this author proposes that promotion of beneficial gut microbes by vitamin E forms may in part be rooted in their antioxidant and anti-inflammatory activities as well as protection of intestinal barrier integrity, and that the modulatory effects on gut microbes likely contributes to vitamin E-facilitated disease prevention. Finally, this review discusses knowledge gaps and future research efforts needed to uncover how vitamin E forms interact with gut microbiota and utilize such knowledge for improving human health.},
}

@article {pmid41391685,
year = {2025},
author = {Wang, H and Qiao, Y and Lu, H and Bo, X and Chen, F and Pu, N and Zhou, Y and Cheng, Q},
title = {Central integration mechanisms of neurovascular unit dysfunction and novel synergistic therapeutic strategies.},
journal = {Neurobiology of disease},
volume = {},
number = {},
pages = {107224},
doi = {10.1016/j.nbd.2025.107224},
pmid = {41391685},
issn = {1095-953X},
abstract = {The neurovascular unit (NVU) is a highly integrated multicellular complex composed of neurons, astrocytes, microglia, brain microvascular endothelial cells (BMECs), pericytes, and the extracellular matrix (ECM). It forms the structural and functional basis of the blood-brain barrier (BBB) and is pivotal for maintaining the homeostasis of the brain. Traditional neuroprotective strategies targeting individual cell types have shown limited efficacy in central nervous system (CNS) diseases, mainly due to the neglect of intricate intercellular crosstalk within the NVU. In this review, we first systematically summarize the core mechanisms by which the NVU functional unit causes NVU dysfunction in representative acute CNS injuries (ischemic/hemorrhagic stroke, traumatic brain injury), neurodegenerative diseases (Alzheimer's disease, Parkinson's disease, multiple sclerosis), and systemic diseases (diabetic encephalopathy, depression). Based on this, we innovatively summarize and clarify six major cross-disease pathological mechanisms of NVU dysfunction, including intercellular communication disorders, abnormal epigenetic modifications, microbiome-NVU interaction dysregulation, metabolic reprogramming dysfunction, neuroimmune-vascular coupling imbalance, and mechanical microenvironment imbalance. Additionally, we integrate emerging NVU models (co-culture systems, organoids, microfluidic chips, 3D bioprinting) with multi-omics technologies to establish a cross-scale dynamic research paradigm, and propose multicomponent coordinated regulatory strategies for NVU-targeted therapies. This framework aims to expand the understanding of NVU-centered pathological processes across diverse CNS diseases and provides a novel theoretical basis for precise therapeutic interventions, thereby bridging the gap between basic research and clinical translation.},
}

@article {pmid41391096,
year = {2025},
author = {Ingawale, S},
title = {The Epigenome-Microbiome Axis: Host Regulation of Gut Ecology.},
journal = {The Journal of the Association of Physicians of India},
volume = {73},
number = {12},
pages = {95-96},
doi = {10.59556/japi.73.1257},
pmid = {41391096},
issn = {0004-5772},
}

@article {pmid41391055,
year = {2025},
author = {An, X and Niu, S and Al, MA and Su, E and Chen, L and He, H and Wang, Y and Zhang, S and Yang, Y and Wang, S and Wen, Z and Xu, B and Ming, Y and Zhu, W and Zhao, Z and Wu, K and Yang, Y and Xie, W and He, Z and Yan, Q},
title = {Dietary macroalgae enhances amino acid metabolism via intestinal Shewanella in grass carp (Ctenopharyngodon idella).},
journal = {Advanced biotechnology},
volume = {3},
number = {4},
pages = {36},
pmid = {41391055},
issn = {2948-2801},
support = {2320004002504//Zhuhai Industry-University-Research Cooperation Project/ ; SML2021SP203//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2024SP002//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2024SP022//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; },
abstract = {The gut microbiome plays pivotal roles in the host's metabolic response to dietary interventions. Dietary macroalgae supplementation represents a promising strategy for enhancing animal growth and health via microbiome modulation. However, the underlying mechanism of how macroalgae supplementation regulates microbiome-host interactions in aquatic species remains unclear. This study investigated the effects of three dietary macroalgae-Sargassum hemiphyllum (S), Asparagopsis taxiformis (A), and Gracilaria lemaneiformis (G)-each supplemented at 5% in feed, on the gut microbiome and metabolism of grass carp (Ctenopharyngodon idella), using integrated approaches of 16S rRNA sequencing, metagenomics, and metabolomics. While all three macroalgae influenced host growth, supplementation of S provided the most comprehensive benefits, with significant enhancement of body weight and hepatic superoxide dismutase activity. Integrated multi-omics analysis revealed that dietary macroalgae supplementation increased the relative abundance of the key gut bacterial genus Shewanella, with the most notable effect observed in the supplementation of S. Subsequent analysis of a metagenome-assembled genome (MAG) of Shewanella (MAG C3_bin52) demonstrated its considerable potential for amino acid biosynthesis and metabolism. This genomic potential was further supported by metabolomic profiling, which indicated significant upregulation of amino acid-related metabolites, particularly in the supplementation S. Pathway analysis confirmed enrichment in processes associated with protein digestion and absorption, amino acid biosynthesis, and related metabolic pathways. These findings highlight the modulation of a macroalgae-microbiome-metabolite axis in grass carp, primarily mediated by the enrichment of Shewanella in gut ecosystem for enhancing host amino acid metabolism. This study advances understanding of dietary modulation of the gut microbiome and provides insights for the sustainable development of aquaculture.},
}

@article {pmid41248092,
year = {2025},
author = {Richie, T and Lee, STM},
title = {Decoding the Gut Microbiota: Mechanisms of Host-Microbe Interactions and Inflammatory Pathologies.},
journal = {Digestion},
volume = {},
number = {},
pages = {1-18},
doi = {10.1159/000549457},
pmid = {41248092},
issn = {1421-9867},
abstract = {BACKGROUND: Microbes residing in the gastrointestinal tract are intertwined with the immune development and overall health of the host throughout stages of life. It is well established that these microbes can have both positive and negative impacts on host health. Having foundational knowledge of these interactions with the host is critical in understanding gastrointestinal health.

SUMMARY: This review discusses the importance of high-resolution study of the gut microbiota, which includes potential modern approaches for analyzing the gut microbiota and considers the challenges and aspects necessary for robust investigation of the gut microbiota. Here, we highlight the complex and highly individualized relationship of microbes interacting within the host results in an ever-changing landscape in the gastrointestinal tract, whether due to host conditions or microbial conditions including microbe-microbe and microbe-host interactions. The vastness and complexity of the gut microbiota contribute to the challenge of quantifying not only a community of microbes in the gut environment, but also maintaining resolution to investigate individual microbes, capturing the network of interactions coinciding in the gastrointestinal tract. Furthermore, the review emphasizes the importance of microbial functions and products to host health outcomes in the context of inflammatory diseases.

KEY MESSAGES: Consideration for microbial functions and interactions with the gut immune system is critical for developing effective treatment strategies of inflammatory disorders. Employing high-resolution microbial techniques to investigate microbes with environmental relevance and community functions are a major challenge in the microbiome field. With new techniques and improvements on existing methodologies, investigating microbes at various community levels is feasible and becoming critical in understanding the community interactions with the host influencing the immune status and overall health outcomes.},
}

@article {pmid41390863,
year = {2025},
author = {Tran, L and Deckers, TB and Ho, J and Lansing, L and Cunningham, M and Morfin, N and Pepinelli, M and De la Mora, A and Conflitti, IM and Gregoris, A and Wu, L and Trepanier-Leroux, D and Muntz, L and Newman, T and Vishwakarma, S and Bixby, M and Jabbari, H and Guzman-Novoa, E and Hoover, SE and Currie, RW and Pernal, SF and Giovenazzo, P and Foster, LJ and Zayed, A and Ortega Polo, R and Guarna, MM},
title = {Neonicotinoid-induced signature dysbiosis identified via metagenomic sequencing of the honey bee gut microbiome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30907-4},
pmid = {41390863},
issn = {2045-2322},
support = {Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; },
}

@article {pmid41390845,
year = {2025},
author = {Romero, F and Labouyrie, M and Orgiazzi, A and Ballabio, C and Panagos, P and Jones, A and Tedersoo, L and Bahram, M and Eisenhauer, N and Sünnemann, M and Guerra, CA and Tao, D and Rog, I and Jiao, S and Mocali, S and Rillig, MC and Lehmann, A and Delgado-Baquerizo, M and van der Heijden, MGA},
title = {The soil microbiome as an indicator of ecosystem multifunctionality in European soils.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67353-9},
pmid = {41390845},
issn = {2041-1723},
abstract = {The role of soil microorganisms in supporting multiple ecosystem functions (multifunctionality) remains poorly understood across diverse environmental conditions. Here, we investigate 484 soils from 27 European countries spanning a range of climatic and edaphic contexts. We assess the contribution of climate, soil properties, and soil microbiome traits (i.e., the relative abundance of co-occurring taxa) to explain six key functional proxies related to soil structure, biochemical activity, and productivity. We find the highest multifunctionality values in grasslands, woodlands, loamy and acidic soils, and temperate humid regions, and the lowest in croplands, alkaline soils, and drier regions. Soil properties explain 12-31% of variation in multifunctionality, with microbial biomass and nitrogen content emerging as the strongest predictors. The soil microbiome accounts for 2-14% of unique variance in multifunctionality but explains more than 25% of variation in enzymatic activities and primary productivity in clay-rich soils and soils originating from temperate dry regions. Specific taxa, particularly within Actinobacteria, Acidobacteria, and the fungal genus Mortierella consistently emerge as strong predictors of ecosystem multifunctionality. Our findings highlight that ecosystem multifunctionality is jointly shaped by soil properties and microbial communities. We argue that specific taxa hold potential as context-dependent indicators for multifunctionality monitoring across environmental gradients.},
}

@article {pmid41390780,
year = {2025},
author = {Bommana, S and Olagoke, O and Hu, YJ and Wang, R and Kama, M and Dehdashti, M and Kodimerla, R and Read, TD and Dean, D},
title = {Azithromycin alters the microbiome composition, function and resistome in women with Chlamydia trachomatis infections.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00858-9},
pmid = {41390780},
issn = {2055-5008},
support = {R01 AI151075/AI/NIAID NIH HHS/United States ; R01 AI151075/AI/NIAID NIH HHS/United States ; },
abstract = {Antibiotics disrupt mucosal microbial communities, yet the effects on microbiomes infected with Chlamydia trachomatis (Ct) remain poorly understood. Some data exist on vaginal microbiomes, but none exist for the endocervix or rectum that are primary sites of infection. We applied metagenomic shotgun sequencing to vaginal, endocervical and rectal samples collected longitudinally from women who cleared their infection post-treatment (n = 10), had persistent infection (n = 11), or remained uninfected (n = 18) to evaluate azithromycin-induced changes in microbial composition, function, and the resistome over time. Our results show shifts in composition and function post-treatment that support persistent Ct, nonsynonymous Ct L22 amino acid substitutions that may be linked to azithromycin resistance, and significant endocervical increases in azithromycin resistance genes in Lactobacillus iners and Gardnerella vaginalis strains with moderate/high biofilm formation potential. These findings highlight the unintended ecological consequences of azithromycin treatment, including likely resistance gene propagation, emphasizing the need for novel treatment and microbiome-preserving strategies.},
}

@article {pmid41390744,
year = {2025},
author = {Malik, K and Jousselin, E and Clamens, AL and Sugimoto, S and Wieczorek, K},
title = {Molecular phylogeny of the Acer-feeding aphid subfamily Drepanosiphinae (Insecta: Hemiptera: Aphididae) and the evolution of its endosymbiotic consortia.},
journal = {Zoological letters},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40851-025-00255-2},
pmid = {41390744},
issn = {2056-306X},
}

@article {pmid41390665,
year = {2025},
author = {Cotto, I and Albán, V and Durán-Viseras, A and Jesser, KJ and Zhou, NA and Hemlock, C and Ballard, AM and Fagnant-Sperati, CS and Lee, GO and Hatt, JK and Royer, CJ and Eisenberg, JNS and Trueba, G and Konstantinidis, KT and Levy, K and Fuhrmeister, ER and , },
title = {Environmental exposures associated with the gut microbiome and resistome of pregnant women and children in Northwest Ecuador.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66567-1},
pmid = {41390665},
issn = {2041-1723},
support = {P30 ES007033/ES/NIEHS NIH HHS/United States ; R01AI162867//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 2127509//American Society for Engineering Education (ASEE)/ ; },
abstract = {Inadequate water, sanitation, and hygiene (WASH) infrastructure may increase exposure to antimicrobial resistance (AMR). In addition, close human-animal interactions and unregulated antibiotic use in livestock facilitate the spread of resistant bacteria. We use metagenomic sequence data and multivariate models to assess how animal exposure and WASH conditions affect the gut resistome and microbiome in 53 pregnant women and 84 children in Ecuador. Here we show improving WASH infrastructure and managing animal exposure may be important in reducing AMR but could also reduce taxonomic diversity in the gut. Escherichia coli, Klebsiella pneumoniae, and clinically relevant antimicrobial resistance genes (ARGs) are detected across all age groups, but the highest abundance is found in children compared to mothers. In mothers, higher animal exposure trends towards a higher number of unique ARGs compared to low animal exposure and is significantly associated with greater taxonomic diversity. In addition, mothers with sewer systems or septic tanks and piped drinking water have fewer unique ARGs compared to those without, and mothers with longer duration of drinking water access have lower total ARG abundance. In contrast, few associations are observed in children, likely due to the dynamic nature of the gut microbiome during early childhood.},
}

@article {pmid41390664,
year = {2025},
author = {Cao, Q and Deng, Z and Li, M and Zhu, S and Huo, Y and Dong, H and Aernouts, B and Psifidi, A and Xu, C},
title = {Integrated metagenomic and metabolomic analyses reveal tenacissoside G as a potential non-antimicrobial treatment for bovine endometritis.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02264-x},
pmid = {41390664},
issn = {2049-2618},
support = {No. 2024B02016//the Key Research and Development Program of the Xinjiang Uygur Autonomous Region/ ; 32125038//the National Natural Science Foundation of China/ ; 2023YFD1801100//National Key Research and Development Program of China/ ; CARS-36//China Agriculture Research System/ ; },
abstract = {BACKGROUND: Bovine endometritis is a prevalent uterine disease that directly curtails reproductive performance and indirectly reduces milk production by increasing calving intervals. Postpartum uterine bacterial infection is the primary cause of bovine endometritis, which is typically treated with prostaglandin F2α and antimicrobials. However, abuse of antimicrobials has led to the emergence of multidrug-resistant bacteria, threatening both human and animal health. To explore alternatives to antimicrobial therapy for bovine endometritis, we integrated uterine metagenomic and metabolomic analyses and identified a novel bioactive metabolite with therapeutic potential. The potential antibacterial and anti-inflammatory effects of this metabolite against bovine endometritis were evaluated by assessing its inhibitory effect on the growth of F. necrophorum in vitro, and by quantifying histopathological scores and inflammatory cytokine expression levels in an in vivo mouse model of endometritis, respectively.

RESULTS: A total of 40 Holstein dairy cows at 21 days to 30 days postpartum were assigned into heathy cows (n = 15), subclinical endometritis cows (n = 12) and clinical endometritis cows (n = 13) according to clinical signs and laboratory tests for bovine endometritis. The uterine fluid was collected aseptically for metagenomics and metabolomics sequencing to identify bacterial species associated with bovine endometritis and metabolites that could potentially be used for treatment of bovine endometritis. A total of 17 bacterial species were significantly associated with bovine endometritis, with Fusobacterium necrophorum as the most significantly enriched in cows with clinical endometritis compared to healthy counterparts. In total, 391 metabolites were significantly differentially abundant between healthy and clinical endometritis cows. Among these, a plant-derived compound, tenacissoside G was significantly enriched in healthy cows. Notably, the abundance of F. necrophorum was significantly negatively associated with the concentration of tenacissoside G in clinical endometritis cows. Moreover, tenacissoside G significantly inhibited the growth of F. necrophorum in vitro and ameliorated inflammation in endometritis caused by F. necrophorum in a mice model.

CONCLUSION: This study provides new insights into the relationship between uterine microbiome and metabolites in bovine endometritis, potentially leading to novel strategies for treating bovine endometritis. Furthermore, tenacissoside G exhibits therapeutic effects against endometritis induced by F. necrophorum, and could serve as a potential alternative to antimicrobials for treating endometritis. Video Abstract.},
}

@article {pmid41390654,
year = {2025},
author = {Manzoor, H and Jabeen, I and Saeed, MT and Kayani, MUR and Huang, L},
title = {Metagenomic analyses reveal E. coli-derived siderophores as potential signatures for breast cancer.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-025-07513-z},
pmid = {41390654},
issn = {1479-5876},
}

@article {pmid41390642,
year = {2025},
author = {Vargas Ribera, PR and Parladé, J and Luque, J and Biel, C and Calvet, C and Miarnau, X and Nogales, A},
title = {Rootstock genetic background in almond cultivation influences the composition of root-associated microbial communities and enrichment of taxa associated with plant defense and nutrient availability.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-07895-8},
pmid = {41390642},
issn = {1471-2229},
support = {TED2021-130185B-I00//European Union NextGenerationEU/PRTR/ ; TED2021-130185B-I00//European Union NextGenerationEU/PRTR/ ; TED2021-130185B-I00//European Union NextGenerationEU/PRTR/ ; TED2021-130185B-I00//European Union NextGenerationEU/PRTR/ ; TED2021-130185B-I00//European Union NextGenerationEU/PRTR/ ; TED2021-130185B-I00//European Union NextGenerationEU/PRTR/ ; TED2021-130185B-I00//European Union NextGenerationEU/PRTR/ ; },
abstract = {BACKGROUND: Beneficial root microorganisms play a crucial role in influencing key agronomic traits in rootstocks. However, little is known about the microbial communities naturally associated with almond rootstocks in Spain. To address this gap, we sampled roots of six commercial Prunus rootstocks in a 15-year-old almond orchard representing two different genetic backgrounds: P. cerasifera background (PCB) with Rootpac[®] 20, and Rootpac[®] R; and P. persica background (PPB), with Cadaman, Garnem, GF677, and Rootpac[®] 40. Root-associated bacterial, fungal, and arbuscular mycorrhizal fungi communities were evaluated applying a metabarcoding approach.

RESULTS: Bacterial and fungal communities differed according to the genetic background of the rootstocks. Roots of PCB rootstocks were significantly enriched with amplicon sequence variants (ASVs) identified as Streptomyces, which contain bacterial species known as biocontrol agents. In contrast, PPB rootstocks were significantly enriched with ASVs identified as Hyalorbilia, Rhizoglomus, and Entrophospora, the first one being an ascomycete known for its nematophagous activity, and the two latter for their role as mycorrhizal fungi. Interestingly, taxa including known fungal plant pathogens were significantly enriched in PCB rootstocks, namely ASVs included in Venturiales and Nectriaceae (Hypocreales). Moreover, in PCB rootstocks we identified bacterial and fungal ASVs that were positively correlated with N and P soil concentrations, respectively, thus suggesting their potential role in enhancing nutrient availability for plants. Similarly, a number of bacterial and fungal ASVs were positively and highly correlated with soil Na concentration among PPB rootstocks.

CONCLUSION: These results suggest that the genetic background of the rootstock may influence bacterial and fungal taxa recruitment in field conditions, thus potentially influencing nutrient cycling and plant defense.},
}

@article {pmid41390545,
year = {2025},
author = {Guo, N and Gou, N and Shi, F and Wang, W and Li, S and Bi, S and Jiao, J and Luo, B and Huang, M and Degen, AA and Shang, Z},
title = {Short-chain fatty acids mediate interactions between immune responses and commensal bacteria in high altitude yaks.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-025-09351-7},
pmid = {41390545},
issn = {2399-3642},
support = {U21A20183//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32471581//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {The complex interplay between host and commensal gut microbiota affects the major biological functions such as metabolism and stress adaptation, and displays pronounced seasonality in mammals. However, the seasonal dynamic patterns of immune responses and microbiota, and their interactions remain uncertain in animals inhabiting extreme environments. We analyzed monthly hormones, immunoglobulins and fecal microbiota from yaks grazing on the Tibetan plateau. Clear seasonal patterns were observed: glucocorticoid levels peaked in the cold season, while concentrations of IgA, IgG, IgM, and short-chain fatty acids (SCFAs) increased during the warm season. Yak fecal microbiota also fluctuated seasonally, with lowest diversity in the warm season but accompanied by an enrichment of Firmicutes and Actinobacteria. Taxa such as Alistipes, Bacteroides, Romboutsia and Arthrobacter contributed to seasonal shifts in the levels of SCFAs and immunoglobulins. These results indicate that yaks synchronize peak immune activation and energy production with the nutrient-rich warm season, suggesting a role for microbiome plasticity in driving immune flexibility for high-altitude animals.},
}

@article {pmid41390520,
year = {2025},
author = {Alfaro-Núñez, A and Christensen, S and Ellehauge, J and Eriksen, JO and Andersen, G and Jensen, EA},
title = {Beyond colonoscopy, faecal DNA mutation screening provides a potential and viable path to early colorectal cancer detection.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30802-y},
pmid = {41390520},
issn = {2045-2322},
support = {DNRF148//Danish National Research Foundation/ ; R45-A2128, A1696, and A1009//Research Fund of Naestved, Slagelse and Ringsted Hospitals/ ; R41-A1910 and Kræftplan III//Region Zealand Health Science Research Foundation/ ; },
abstract = {Colorectal cancer (CRC) remains a leading cause of cancer-related morbidity and mortality worldwide, with early detection critical for improving clinical outcomes. In Denmark's CRC screening program, nearly 60% of patients undergoing colonoscopy do not have polyps requiring treatment, highlighting the need for more sensitive and less invasive screening methods to improve early detection and reduce unnecessary procedures. In this study, we assessed the potential of two faecal DNA-based methods for detecting CRC-related mutations. Extracted DNA was analysed using next-generation sequencing (NGS) and digital PCR (dPCR). NGS targeted a gene panel covering the most frequently mutated sites in CRC, while dPCR focused on six specific CRC-associated mutations. A common limitation across both methods was the low abundance of human DNA in faecal samples, which reduced the reliability of variant detection. Nevertheless, both NGS and dPCR showed promise, particularly when DNA input was sufficient. Significant associations were observed between mutation counts and clinical diagnosis, with key CRC mutations reliably detected. The findings suggest that, with further implementation, these methods could serve as a less invasive and more cost-effective alternative to colonoscopy, especially for high-risk individuals. However, the sensitivity of both methods was limited in samples with low DNA yield, likely due to inhibitory effects during sample preservation or extraction. While faecal samples may be better suited for gut microbiome profiling, our findings underscore the potential of human DNA-based faecal screening in CRC and highlight the need for optimized extraction protocols to improve diagnostic accuracy, minimize unnecessary procedures, and provide personalized care for high-risk populations.},
}

@article {pmid41390484,
year = {2025},
author = {Song, D and Feng, G and Ma, Y and Shi, Y and Qian, C and Wang, C and Xu, J and Li, Y and Wang, X and Fan, N and Dong, W and Li, X and Fan, J and Chu, L and Gao, F and He, S and Wang, J and Wang, S and Zhou, H and Gu, Q and Wang, H and Feng, B and Zhang, H and Zhang, X and Li, L and Fan, E and Wang, Y and Wu, M and Zhang, Y and Huang, A and Teng, J and Zhu, Y and Zhai, R and Ding, X and Zhang, C and Peng, Y},
title = {Gut microbiome predicts personalized responses to dietary fiber in prediabetes: a randomized, open-label trial.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66498-x},
pmid = {41390484},
issn = {2041-1723},
abstract = {Gut microbiota contributes to prediabetes progression, however, whether microbiota features can guide targeted prevention and treatment for diabetes requires validation through large-scale clinical trials. Here, in a randomized, open-label trial, we randomly assigned 802 prediabetic subjects to a usual care control group (patient education and dietary recommendations, n = 393) or a dietary fiber intervention group (n = 409) for 6 months. The primary outcome was the percentage change in whole-blood HbA1c, and secondary outcomes were the changes in other glucose, insulin, lipid, liver and kidney function, and anthropometric parameters. There were no statistically significant differences in the primary and secondary outcomes between groups. In post-hoc analysis, we reclassified subjects into four clusters using a multivariate clustering model based on age, BMI, HbA1c, HOMA2-IR and HOMA2-B. These clusters differed in metabolic status, risks of diabetes and its complications, gut microbiome and serum metabolites. Notably, dietary fiber improved glycemic control in Clusters 3 and 4, but not in Clusters 1 and 2, consistent with observed gut microbiota alleviations. By using a LightGBM machine learning model, we calculated a microbiome-based clinical decision score to predict personalized fiber intervention responses and identified individuals who can get glycemic benefits. In conclusion, our study suggests that the gut microbiota response influences the effectiveness of dietary fiber intervention and provides a clinically applicable model to guide microbiome-targeted personalized medicine for prediabetes. Clinical Trial Registry: ChiCTR1900027663.},
}

@article {pmid41390460,
year = {2025},
author = {Sameeha, FNU and Riaz, S and Aslam, MN and Perveen, A},
title = {Association between early-life antibiotic exposure and gut microbiome alterations linked to allergic diseases in children: a systematic review.},
journal = {European journal of medical research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40001-025-03685-y},
pmid = {41390460},
issn = {2047-783X},
abstract = {BACKGROUND: Early-life exposure to antibiotics has been implicated in the disruption of gut microbiota development, potentially contributing to the onset of allergic diseases in childhood. This systematic review aimed to evaluate the association between early antibiotic exposure, gut microbiome alterations, and the risk of developing allergic conditions such as asthma, atopic dermatitis, and allergic rhinitis.

METHODS: This review followed PRISMA 2020 guidelines. A comprehensive search of PubMed, Embase, Web of Science, and the Cochrane Library was conducted up to [insert date]. Eligible studies included observational and interventional designs involving participants from the prenatal stage to 10 years of age. Data were extracted on antibiotic type, exposure timing, microbiome changes, and allergic outcomes. Study quality was assessed using the Newcastle-Ottawa Scale for observational studies and the Cochrane Risk of Bias tool for randomized trials.

RESULTS: Fifteen studies involving over 1.5 million children met the inclusion criteria. The majority reported that antibiotic exposure during the prenatal period or the first two years of life was significantly associated with an increased risk of allergic diseases, particularly asthma and atopic dermatitis. Several studies also documented alterations in gut microbiota composition, including reduced Bifidobacterium and increased Clostridium and Klebsiella spps. Antibiotic type, duration, and timing of exposure were key factors influencing microbiota disruption and allergy development.

CONCLUSION: There is growing evidence that early-life antibiotic exposure may predispose children to allergic diseases through gut microbiota disturbances. These findings support the cautious use of antibiotics during pregnancy and early childhood and underscore the need for further research into microbiota-preserving interventions and long-term outcomes.},
}

@article {pmid41390429,
year = {2025},
author = {Li, G and Jia, L and Li, J and Gao, A and Chen, X and Li, JH and Xia, LJ and Zhou, SY and Lin, YH and Yang, JT and Wan, L and He, YZ and Sun, RY and Ren, H and Lian, XL and Zhao, DH and Liao, XP and Liu, YH and Chen, L and Sun, J},
title = {Carbohydrate competition by Enterobacteriaceae enhances colonization resistance to carbapenem-resistant hypervirulent K. pneumoniae.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02245-0},
pmid = {41390429},
issn = {2049-2618},
support = {32402943//National Natural Science Foundation of China/ ; 32202859//National Natural Science Foundation of China/ ; 2025A1515012412//Guangdong Provincial Natural Science Foundation/ ; 32121004//Foundation for Innovative Research Groups of the National Natural Science Foundation of China/ ; NSF2025CB07//the school level scientific research project of JiangsuAgri-Animal Husbandry Vocational College/ ; 2019BT02N054//Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program/ ; 2020B0301030007//Guangdong Major Project of Basic and Applied Basic Research/ ; D20008//the 111 Center/ ; 2023B10564003//Double First-Class Discipline Promotion Project/ ; },
abstract = {BACKGROUND: Carbapenem-resistant hypervirulent K. pneumoniae (CR-HvKP) is a growing public health threat due to its virulence and limited treatment options. While prevalent in hospitals, its presence in livestock, particularly pigs, is poorly understood. The gut microbiome provides colonization resistance, but how it restricts CR-HvKP remains unclear.

RESULTS: To further elucidate the colonization resistance mechanisms of the gut microbiota against CR-HvKP, we analyzed stool samples from piglets (L), nursery (N), fattening (F), and sows (PS) using microbiome modeling (Micolo) and competition assays. ST290 K. pneumoniae isolated from PS inhibited CR-HvKP via carbohydrate competition, with a pronounced effect observed for sucrose. Niche-specific supplementation with methyl pyruvate was found to partially alleviate this ecological inhibitory effect.

CONCLUSIONS: Carbohydrate-based interventions could be explored as potential therapeutic or prophylactic strategies to combat CR-HvKP colonization, thereby potentially improving animal and public health outcomes. Video Abstract.},
}

@article {pmid41390384,
year = {2025},
author = {Shetty, P and Bhat, R and Padavu, S and Rai, P and B, KK and Shetty, S},
title = {Profiling of microbes associated with chronic irreversible pulpitis using metagenomic next-generation sequencing.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-025-07175-9},
pmid = {41390384},
issn = {1472-6831},
support = {N(DU)/RD/NUFR 1Grant/ABSMIDS/2021-22/01-1//NITTE University/ ; },
abstract = {BACKGROUND: Contemporary molecular analytical methodologies have yielded insufficient characterization of the microbial etiology underlying chronic irreversible pulpitis; a pathological condition characterized by irreversible inflammatory alterations of the dental pulp complex necessitating endodontic intervention. This investigation employed shotgun metagenomic sequencing to comprehensively elucidate the microbiome present in affected pulpal tissues, thereby augmenting our understanding of pulpal pathogenesis.

METHODS: The investigation incorporated six subjects (age range 18-35 years) presenting with clinically diagnosed chronic irreversible pulpitis according to the American Association of Endodontists diagnostic criteria. Pulpal tissue specimens were procured under rubber dam isolation utilizing stringent aseptic protocols following coronal access preparation. Genomic DNA extraction was performed via QIAamp DNA Mini Kit methodology followed by high-throughput sequencing on the Illumina Hiseq platform. Subsequent bioinformatic analysis implemented the WGSA2 pipeline for taxonomic classification, generating approximately 79.906 million paired-end reads per specimen.

RESULTS: Metagenomic analysis of the pulpal microbiome revealed taxonomic predominance of Bacteroidetes (45.095%), Firmicutes (17.424%), Proteobacteria (12.731%), and Actinobacteria (9.071%) at the phylum level. Notably, the investigation identified previously undocumented phyla in pulpal infections, including Euryarchaeota, Thermoproteobacteria, Uroviricota,and Apicomplexa. Propionibacterium acidifaciens emerged as the most consistently detected and ecologically significant species, whereas the conventionally recognized odontopathogen Streptococcus mutans exhibited negligible presence. Shannon diversity indices and taxonomic richness parameters demonstrated substantial inter-subject variability, with species abundance ranging from 574 to 5,468 distinct taxonomic units per pulp sample.

CONCLUSION: This investigation elucidated unprecedented microbial diversity within chronic irreversible pulpitis, fundamentally challenging established understanding of endodontic pathogenesis and clinical therapeutic approaches. The substantial inter-subject taxonomic heterogeneity observed herein suggests that contemporary standardized therapeutic regimens may be insufficiently targeted to address the complex polymicrobial ecosystem characteristic of pulpal pathosis. The identification of archaeal and viral constituents provides mechanistic insight into persistent endodontic infections despite technically adequate treatment modalities. These findings establish a comprehensive basis for evidence-based precision endodontics, facilitating the development of patient-specific antimicrobial strategies and novel therapeutic interventions targeting previously unrecognized microbial components. The comprehensive characterization of pulpal microbiome diversity represents a significant advancement toward molecularly informed clinical decision-making, with profound implications for treatment outcome optimization and the mitigation of therapeutic failures in contemporary endodontic practice.},
}

@article {pmid41390069,
year = {2025},
author = {Wang, Z and Zhang, B and Qi, S and Gao, Q and Zhou, X and Feng, G},
title = {Decade-long Nitrogen Fertilization Differentially Alters Microbiome-mediated Nitrification and Denitrification in Contrasting Soil Types.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123544},
doi = {10.1016/j.envres.2025.123544},
pmid = {41390069},
issn = {1096-0953},
abstract = {The intensive use of nitrogen fertilizers in agriculture, while boosting crop yields, has triggered severe environmental consequences including greenhouse gas emissions and groundwater pollution through disrupted N-cycling. Understanding how fertilizer regimes interact with soil types to govern microbially-driven nitrogen transformations is critical for developing sustainable intensification strategies, yet remains poorly characterized particularly in contrasting soil matrices under identical climatic conditions. This knowledge gap hinders the formulation of soil-specific fertilizer management practices to reconcile agricultural productivity with environmental protection. Through a decade-long field experiment employing split-plot design (soil types: black soil vs. sandy soil; N rates: 0, 168, 312 kg N ha[-1]), we deciphered the microbiome-mediated mechanisms underlying nitrification (NP) and denitrification potentials (DP) using qPCR, high-throughput sequencing, and gas inhibition methods. Nitrogen fertilization significantly altered functional gene abundances (AOA-amoA, AOB-amoA, nirS, nirK, nosZ), reshaped microbial community structure, and induced divergent diversity responses between nitrification and denitrification processes. Structural equation modeling revealed that N addition alters microbial diversity, thereby enhancing NP(4.1 %), whereas stimulated DP(72.6 %) via gene abundance regulation. These soil-dependent microbial adaptation patterns provide mechanistic evidence for optimizing N application strategies: Black soils benefit from moderate N inputs maintaining higher NP, whereas sandy soils require stricter N controls to mitigate denitrification-derived DP. This study provides a theoretical basis for improving nitrogen use efficiency and reducing environmental risks, while offering new insights into the microbial drivers of sustainable agricultural intensification.},
}

@article {pmid41389850,
year = {2025},
author = {Petrov, VA and Schade, S and Laczny, CC and Hallqvist, J and May, P and Jäger, C and Aho, VTE and Hickl, O and Halder, R and Lang, E and Caussin, J and Lebrun, LA and Schulz, J and Unger, MM and Mills, K and Mollenhauer, B and Wilmes, P},
title = {Resistant starch improves Parkinson's disease symptoms through restructuring of the gut microbiome and modulating inflammation.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106217},
doi = {10.1016/j.bbi.2025.106217},
pmid = {41389850},
issn = {1090-2139},
abstract = {Alterations in the gut microbiome and a "leaky" gut are associated with Parkinson's disease (PD), which implies the prospect of rebalancing via dietary intervention. Here, we investigate the impact of a diet rich in resistant starch on the gut microbiome through a multi-omics approach. We conducted a randomized, controlled trial with short-term and long-term phases involving 74 PD patients of three groups: conventional diet, supplementation with resistant starch, and high-fibre diet. Our findings reveal associations between dietary patterns and changes in the gut microbiome's taxonomic composition, functional potential, metabolic activity, and host inflammatory proteome response. Resistant starch supplementation led to an increase in Faecalibacterium species and short-chain fatty acids and a reduction of opportunistic pathogens. Long-term supplementation also increased blood APOA4 and HSPA5 and reduced symptoms of PD. Our study highlights the potential of dietary interventions to modulate the gut microbiome and improve the quality of life for PD patients.},
}

@article {pmid41389504,
year = {2025},
author = {Meenakshi, S and Amrutha, TV and Abubakar, M and Prakash, V and Kumar, N and Murti, K},
title = {Fluoride-induced gut dysbiosis in metabolic disorders: Mechanisms and public health implications.},
journal = {Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS)},
volume = {93},
number = {},
pages = {127806},
doi = {10.1016/j.jtemb.2025.127806},
pmid = {41389504},
issn = {1878-3252},
abstract = {AIM: This review explores the effects of fluoride exposure and metabolic alterations linked to obesity and diabetes, and highlights preventive and therapeutic approaches to mitigate fluoride-driven metabolic risks.

SUMMARY: While fluoride is beneficial to dental health, but excessive exposure disrupts gut microbiota composition, reducing short-chain fatty acids (SCFA) production and impairing intestinal barrier integrity. These disruptions alter the oxidative stress, inflammation and insulin resistance. Evidence from animal and human studies suggest a dose-dependent pattern, with depletion of beneficial bacteria such as Lactobacillus and Faecalibacterium and enrichment of pro-inflammatory microbes. Such microbial imbalances influence bile acid metabolism. lipopolysaccharide (LPS) translocation and glucose regulation. This review discusses potential microbiome modulating strategies include probiotics, prebiotics, synbiotics, fecal microbiota transplantation (FMT) and glucose lowering agents such as metformin and GLP-1 receptor agonists as possible therapeutic interventions to restore microbial balance and improve metabolic outcome However, the long-term and epigenetic effects of fluoride on intestinal and metabolic health remain unclear.

CONCLUSION: Since fluoride contaminates drinking water in areas with an endemic tendency, defluoridation, exposure monitoring, and public awareness are essential preventive strategies. Future mechanistic and clinical studies are necessary to elucidate the pathways linking fluoride metabolic disease progression.},
}

@article {pmid41390064,
year = {2025},
author = {Quan, V and Carey, S},
title = {DIETARY MANAGEMENT OF FUNCTIONAL CONSTIPATION IN DISORDERS OF GUT-BRAIN INTERACTION - A SCOPING REVIEW.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {102849},
doi = {10.1016/j.clnesp.2025.102849},
pmid = {41390064},
issn = {2405-4577},
abstract = {BACKGROUND: Functional constipation is one of the most prevalent disorders of gut-brain interaction, but available dietary interventions haven't been comprehensively collated.

AIMS: The aim of this scoping review was to synthesise the current evidence surrounding dietary-based interventions used to manage functional constipation in adults and to identify any gaps among published dietary management strategies that could warrant further research, namely a systematic review.

METHODS: A comprehensive database search was conducted on MEDLINE, CINAHL and Web of Science capturing the notions of 'dietary management' and 'disorders of gut-brain interaction', from which two rounds of screening were performed.

RESULTS: Forty primary studies and twelve review papers were included in this review. These 52 papers non-exclusively cover a range of dietary domains including fibre supplementation (n=15), microbiome modulation using prebiotics, probiotics or synbiotics (n=26), functional foods (n=10), fluid intake (n=6) and other dietary approaches (n=7). Fiber supplementation with psyllium is the current strongest dietary recommendation, with emerging strong evidence backing functional fruits like kiwifruit and prunes. Meanwhile the efficacy for all other approaches cannot be accurately deduced due to limited well-designed studies or conflicting evidence. However, improvements to constipation severity or symptoms have been observed with probiotics with both Bifidobacterium and Lactobacillus components, galacto-oligosaccharides, partially hydrolysed guar gum and various synbiotic formulations.

CONCLUSIONS: This paper contributes to the growing research around functional constipation where the open-ended approach allowed for identification and synthesis of all nutrition strategies trialed in the literature. We recommend further studies to be conducted on prebiotics, probiotics and synbiotics to determine its potential role in constipation management for this cohort.},
}

@article {pmid41390062,
year = {2025},
author = {Ramuscak, AV and Martincevic, I and Hulst, JM},
title = {A scoping review of the clinical outcomes and use of blenderized tube feeds and commercial food-based formulas in pediatrics.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {102845},
doi = {10.1016/j.clnesp.2025.102845},
pmid = {41390062},
issn = {2405-4577},
abstract = {BACKGROUND & AIMS: Blenderized tube feeding (BTF) is the use of blended whole foods and liquids given into the gastrointestinal (GI) system via an enteral access device, such as a gastrostomy tube. With an increased interest among caregivers as well as clinicians in BTFs, variations have evolved including homemade BTFs (HBTFs), commercially prepared BTFs (CBTFs), and commercial food-based formula (CFBF). Convenient, ready-to-use alternatives to HBTFs, either CBTFs or CFBFs, are considered appealing by tube-fed patients and/or their caregivers, as well as health care providers. While CBTFs or CFBFs may offer similar benefits to HBTFs, research on these products has been sparse. This scoping review aims to map and summarize the currently available literature on CBTFs, CFBFs, or commercially blenderized feeds (CBFs) when undifferentiated in the study, as well as offer recommendations for clinical practice and future research.

METHODS: This scoping review was conducted in accordance with the Preferred Reporting Items for Systematic review and Meta-Analyses Extension for Scoping Reviews (PRISMA-ScR). A comprehensive search strategy was developed and applied across four databases: PubMed, Ovid MEDLINE(R), CINAHL, and Web of Science. Eligible studies were full-text, English language, articles that reported on the use of CBFs among the pediatric population receiving enteral nutrition.

RESULTS: Sixteen studies met the inclusion criteria. Key outcome themes identified included clinical outcomes (GI symptoms, stool patterns, growth and weight, GI microbiome, and emergency department visits and hospitalizations), nutritional adequacy, satisfaction and quality of life, and viscosity and the effects of the administration of CBFs.

CONCLUSIONS: Current evidence suggests that CBFs may improve GI tolerance, support greater gut microdiversity, reduce medical burdens, and enhance quality of life in pediatric patients receiving enteral nutrition. Nevertheless, the limited number and methodological heterogeneity of studies highlight the need for more rigorous research to determine the long-term safety, efficacy, and nutritional adequacy of these formulas.},
}

@article {pmid41390021,
year = {2025},
author = {Bora, S and Priya, B and Pooja, D and Kulhari, H},
title = {Gellan gum-based nanocarriers for the delivery of anticancer agents: A review.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {149660},
doi = {10.1016/j.ijbiomac.2025.149660},
pmid = {41390021},
issn = {1879-0003},
abstract = {Gellan gum (GG) is a naturally occurring anionic polysaccharide that has been used extensively in the delivery of anticancer agents. The application of GG as an effective delivery vehicle is prominently dependent on its adjustable physicochemical characteristics, biocompatibility, and biodegradability. GG has the capability of forming stable hydrogels and diverse nanostructures in physiological conditions. Hence, it is used in the development of multipurpose drug carriers that can effectively carry and deliver a broad spectrum of anticancer drugs at the site of action. Recently, the development of hybrid and composite GG-based systems, where GG is combined with synthetic polymers, nanoparticles, or bioactive peptides, has gained tremendous attention in the scientific community since they provide improved mechanical stability, pharmacokinetic properties, and synergistic biological effects, thereby expanding the therapeutic potential and versatility of GG nanocarriers. However, several obstacles must be addressed before its widespread clinical application can be fathomed. These include ensuring commercial-scale repeatability, long-term stability, precise control of drug release kinetics, and addressing regulatory complications. In addition, further research is required to maximize safety and effectiveness in the interactions of GG nanocarriers with biological settings, such as enzymatic degradation, immunological responses, and microbiome interactions. Interdisciplinary research integrating materials science, pharmacology, and clinical studies will be critical for its further applications. Continued research efforts and collaborative innovation are expected to establish GG-based delivery systems as the core platforms for next-generation anticancer therapies.},
}

@article {pmid41389945,
year = {2025},
author = {Hofmann, C and Geiger, H},
title = {Aging of the Colon - A Mechanistic View.},
journal = {Mechanisms of ageing and development},
volume = {},
number = {},
pages = {112143},
doi = {10.1016/j.mad.2025.112143},
pmid = {41389945},
issn = {1872-6216},
abstract = {The colon is one of the gastrointestinal organs most profoundly affected by aging. Recent advances in our understanding of both colonic physiology and the general mechanisms of aging have significantly expanded our knowledge of the types and underlying processes of colonic aging. In this review, we summarize current insights into the cellular and molecular mechanisms that drive physiological aging of the human colon. We examine the unique structural and functional features of key components of the colon, including the epithelium, local immune system, microbiome, enteric neurons, and smooth muscle cells, and explore how aging affects each of these cell populations, ultimately impacting overall colonic function. In the epithelium, increased mutational burden does not appear to be the primary driver of age-related dysfunction. Instead, dysregulation of signaling pathways such as EGF and Wnt is likely responsible for key phenotypic changes. Aged colonic neurons display protein misfolding and axonal dysfunction reminiscent of aging processes observed in the central nervous system. Similarly, smooth muscle cells exhibit impaired contractility, which is associated with disruptions in calcium homeostasis and deficits in cholinergic signaling. At the same time, age-related activation of the local immune system mirrors broader immunosenescence and may be further influenced by shifts in the gut microbiome, although a consistent aging-associated microbiome signature has yet to be identified. These multifaceted changes, combined with the colon's inherent regional and cellular complexity and the challenges of modeling human colonic aging, continue to fascinate but also pose substantial obstacles for research. Emerging experimental models and clinical strategies offer promising avenues for improving the prevention and treatment of age-associated colonic dysfunction.},
}

@article {pmid41389846,
year = {2025},
author = {Roberts, LA and Gaboriau, DCA and MacIntyre, DA and Marchesi, JR},
title = {Vaginal microbe media (VMM): a novel medium to culture Lactobacillus iners and other fastidious vaginal bacteria.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107358},
doi = {10.1016/j.mimet.2025.107358},
pmid = {41389846},
issn = {1872-8359},
abstract = {A more comprehensive understanding of the bacterial species in the vaginal microbiome and their roles requires their cultivation as pure isolates. However, difficulty in culturing fastidious species, particularly in liquid media, has limited certain types of experimental approaches for studying these organisms. To address this challenge, Vaginal Microbe Medium (VMM) was developed to enable robust growth of Lactobacillus iners within a relatively short period (36 h). A simplified version with fewer components, named VMM2, was subsequently developed. L. iners strains grown in VMM and VMM2 reached higher optical densities in a shorter period compared to NYCIII, supplemented MRS and Columbia broth. Bacterial cells cultured in VMM and VMM2 were significantly longer than those grown in NYCIII. These results indicate that VMM and VMM2 provide superior growth conditions for L. iners as compared to currently available media. Both media also support the growth of a range of other vaginal bacterial species. The development of these media facilitates liquid culture of fastidious bacteria from the vaginal niche, enabling broader experimental capabilities and deeper insights into causal relationships within the microbiome.},
}

@article {pmid41389831,
year = {2026},
author = {McNamara, CG and Cryan, JF},
title = {Unravelling the role of the microbiome in Parkinson's disease.},
journal = {The Lancet. Neurology},
volume = {25},
number = {1},
pages = {7-8},
doi = {10.1016/S1474-4422(25)00452-1},
pmid = {41389831},
issn = {1474-4465},
}

@article {pmid41389810,
year = {2026},
author = {de Castro Fonseca, M and Zanetti, L and Fanourakis, S and Sulzer, DL and Mazmanian, SK},
title = {The gut microbiome, systemic inflammation, and autoimmunity in Parkinson's disease.},
journal = {The Lancet. Neurology},
volume = {25},
number = {1},
pages = {103-114},
doi = {10.1016/S1474-4422(25)00382-5},
pmid = {41389810},
issn = {1474-4465},
mesh = {Humans ; *Parkinson Disease/immunology/microbiology ; *Gastrointestinal Microbiome/immunology/physiology ; *Autoimmunity/immunology/physiology ; *Inflammation/immunology ; Animals ; },
abstract = {Inflammation is a core feature of Parkinson's disease, extending beyond the CNS to include systemic immune activation. The gut microbiome is increasingly recognised as a key regulator of immune function in the gastrointestinal tract, peripheral circulation, and brain. In individuals with Parkinson's disease, gut microbial composition is altered, with reductions in anti-inflammatory taxa and increases in pro-inflammatory bacterial species. Preclinical studies have shown that microbiome alterations can promote α-synuclein aggregation and neuroinflammation, whereas human data suggest early involvement of the gut and immune system. Immune-mediated mechanisms in Parkinson's disease include activation of brain resident microglia and peripheral innate and adaptive immune cells. Emerging evidence suggests the gut microbiome modulates systemic immune activation, through autoreactive T cells that might drive neurodegeneration. An improved understanding of how the microbiome shapes inflammation and autoimmunity in Parkinson's disease could inform the development of therapies that target the immune system or the gut-brain axis.},
}

Humans
*Parkinson Disease/immunology/microbiology
*Gastrointestinal Microbiome/immunology/physiology
*Autoimmunity/immunology/physiology
*Inflammation/immunology
Animals

@article {pmid41389626,
year = {2025},
author = {Kim, Y and Seo, E and Kang, A and Kang, MG and Jang, KB and Oh, S and Kim, Y},
title = {A neuroprotective effect of newly isolated probiotic bacterium Lactobacillus acidophilus SLAM_LAA02 in a rotenone-induced mouse model of Parkinson's disease.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {194},
number = {},
pages = {118896},
doi = {10.1016/j.biopha.2025.118896},
pmid = {41389626},
issn = {1950-6007},
abstract = {The gut microbiota plays a pivotal role in maintaining host health and has increasingly been linked to the pathogenesis of neurodegenerative diseases through the microbiota-gut-brain axis. Parkinson's disease (PD), characterized by dopaminergic dysfunction, neuro inflammation, and pathological alpha-synuclein (α-synuclein) aggregation, is frequently accompanied by gut microbial dysbiosis. Probiotics isolated from human infants could offer distinct neuroprotective and immunomodulatory benefits, yet their effects on integrated gut-brain axis models remain underexplored. In this study, we investigated the therapeutic potential of Lactobacillus acidophilus SLAM_LAA02 (L. acidophilus SLAM_LAA02), a novel infant-derived strain, in modulating PD-related behavioral and neuropathological features via modulation of the gut-brain axis. Following comprehensive safety and functional assessments, we first assessed L. acidophilus SLAM_LAA02 in Caenorhabditis elegans, where supplementation extended lifespan, enhanced antimicrobial defense, improved behavioral responses, and reduced α-synuclein expression in transgenic worms. We then evaluated its effects in a rotenone-induced mouse model that reflects early-stage PD-like features. L. acidophilus SLAM_LAA02 administration ameliorated motor dysfunction, modulated neuroinflammatory signaling, restored gut microbial diversity, and improved intestinal barrier-associated outcomes. These changes were accompanied by a notable reduction in α-synuclein expression and upregulated neuroprotective gene expression, including brain-derived neurotrophic factor (BDNF). Together, these findings suggest that L. acidophilus SLAM_LAA02 exhibits neuroprotective and gut-modulating properties across complementary model systems, supporting its potential as a promising probiotic candidate for alleviating early PD-related dysfunctions through the gut-brain axis.},
}

@article {pmid41389588,
year = {2025},
author = {Oka, S and Yoshida, K and Takefuji, Y},
title = {From bias to reliable insight: Rethinking feature importance in microbiome analytics.},
journal = {Veterinary microbiology},
volume = {312},
number = {},
pages = {110838},
doi = {10.1016/j.vetmic.2025.110838},
pmid = {41389588},
issn = {1873-2542},
}

@article {pmid41389554,
year = {2025},
author = {Yang, T and Zhan, Y and Sha, J and Zhao, J and Wang, C and Peng, T and Zhang, L},
title = {Integrative multi-omics elucidates the impact of microalgae on growth, quality, phytohormones, and rhizosphere microbiome of Angelica sinensis.},
journal = {Microbiological research},
volume = {304},
number = {},
pages = {128418},
doi = {10.1016/j.micres.2025.128418},
pmid = {41389554},
issn = {1618-0623},
abstract = {Microalgae have recently been recognized as sustainable biofertilizers that improve soil fertility while enhancing crop performance. However, their roles in regulating medicinal plant growth and quality, as well as the underlying ecological mechanisms, remain poorly understood. In this study, we systematically assessed the effects of three representative microalgae-Anabaena cylindrica (AC), Phormidium tenue (PT), and Chlorella vulgaris (CV)-on the growth, quality, hormonal regulation, soil nutrient dynamics, and rhizosphere microbiome of Angelica sinensis. Field inoculation trials demonstrated that all three microalgae significantly promoted biomass accumulation and increased antioxidant capacity. AC and CV further enhanced the accumulation of ferulic acid and flavonoids, which are two key quality determinants. Microalgal inoculation significantly altered rhizosphere soil properties by increasing total organic carbon and alkali-hydrolyzable nitrogen, with AC uniquely elevating available phosphorus and iron. Metagenomic analysis revealed that AC and PT stimulated nitrification while suppressing denitrification, thereby reducing nitrogen loss and stabilizing the soil nitrogen pools. Distinct microbial taxa, including Rhodanobacter, Streptomyces, and Pseudomonas, were identified as the major contributors to carbon and nitrogen cycling. Hormone metabolomics showed that microalgal inoculation reprogrammed A. sinensis phytohormone profiles in a species-specific manner. Partial least squares path modeling suggested that AC and CV promote ferulic acid biosynthesis through distinct mechanisms, with AC associated with reduced investment in C-mineralization processes and CV associated with lower salicylic acid levels, whereas PT enhances biomass accumulation mainly by stimulating N-cycle processes. Collectively, this study provides integrated evidence linking microalgae-mediated nutrient cycling, rhizosphere microbiome shifts and hormonal regulation to enhanced quality formation in A. sinensis.},
}

@article {pmid41389450,
year = {2025},
author = {Mittal, A and Sharma, S},
title = {Gut microbiota and nutritional interventions in alcohol-associated liver disease: Mechanisms and therapeutic advances.},
journal = {Nutrition research (New York, N.Y.)},
volume = {145},
number = {},
pages = {8-24},
doi = {10.1016/j.nutres.2025.11.004},
pmid = {41389450},
issn = {1879-0739},
abstract = {Alcohol-associated liver disease (ALD) is a leading cause of liver-related morbidity and mortality worldwide. Despite growing awareness of its burden, treatment options remain limited, with abstinence as the only widely accepted intervention. Recent research underscores the critical role of the gut-liver axis and nutritional status, particularly dietary protein, in modulating ALD pathogenesis and progression. This review aims to integrate current knowledge on the interplay between gut microbiota, dietary protein, and alcohol-induced liver injury, and to evaluate microbiota-targeted therapeutic strategies, including fecal microbiota transplantation (FMT), within this context. We examine how chronic alcohol intake reshapes the gut microbiome, impairs barrier function, and alters microbial metabolism. We discuss how dietary protein, based on source, quantity, and amino acid composition, influences microbial ecology and metabolite profiles, with plant and dairy proteins emerging as beneficial. The review also highlights advances in FMT, which shows promise in improving outcomes in severe alcoholic hepatitis. However, its efficacy is modulated by donor microbial composition and recipient compatibility, both of which may be influenced by diet. Furthermore, we address emerging evidence on the role of fungal and viral communities, which remain understudied contributors to ALD. Despite substantial progress, significant knowledge gaps persist. These include the need for clinical validation of preclinical findings, deeper exploration of nonbacterial microbiota, and a lack of personalized, nutrition-based interventions. Addressing these gaps through integrative, multiomic approaches will be essential to advancing precision therapeutics in ALD.},
}

@article {pmid41389146,
year = {2025},
author = {Vorobeva, M and iAkushev, A and Chen, CC and Orihara, M and Akbar, N and Colley, P and Sehanobish, E and Chung, CHY and Scott, A and O'Brien, E and Chang, CB and Kita, H and Voyich, J and Knoop, K and Jerschow, E},
title = {Impact of Sinus Surgery on Bacteriome Composition in Patients With Chronic Rhinosinusitis With Nasal Polyps.},
journal = {International forum of allergy & rhinology},
volume = {},
number = {},
pages = {},
doi = {10.1002/alr.70082},
pmid = {41389146},
issn = {2042-6984},
support = {R21AI171306 to E.J./TR/NCATS NIH HHS/United States ; CTSA 5KL2TR001071/TR/NCATS NIH HHS/United States ; /NH/NIH HHS/United States ; },
}

@article {pmid41389089,
year = {2025},
author = {Dehghani, S and Khorsandi, H and Hosseinzadegan, R and Rahimi, H and Mottaghi, M and Fallahpour, S and Fazayel, SMA and Bayat, A and Namini, NJ and Karimi, A and Morovatshoar, R and Mobinikhaledi, M and Behfar, Q and Ghasemi, M},
title = {Neuroinflammatory Mechanisms and Therapeutic Targets in Oxaliplatin-Induced Peripheral Neuropathy: a Comprehensive Review.},
journal = {Neurotoxicity research},
volume = {43},
number = {6},
pages = {52},
pmid = {41389089},
issn = {1476-3524},
mesh = {Humans ; *Oxaliplatin/adverse effects/toxicity ; Animals ; *Peripheral Nervous System Diseases/chemically induced/drug therapy/metabolism ; *Neuroinflammatory Diseases/chemically induced/drug therapy/metabolism ; *Antineoplastic Agents/adverse effects/toxicity ; },
abstract = {Oxaliplatin-induced peripheral neuropathy (OIPN) is a severe, dose-limiting complication that significantly reduces quality of life in cancer patients, with no effective preventive or therapeutic options currently available. There is increasing evidence that neuroinflammation plays a central role in OIPN initiation and progression. This review provides a critical and up-to-date analysis of recent studies on the molecular mechanisms of oxaliplatin-induced neuroinflammation, with a particular focus on the integration of mitochondrial dysfunction, immune-mediated inflammation, glial activation, microRNA dysregulation, and gut-nerve axis disruption. Recent findings demonstrate that oxaliplatin disrupts mitochondrial dynamics, increases oxidative stress, and impairs blood-nerve barrier integrity, triggering neuroinflammatory responses. Neuroinflammation in OIPN is mediated through the activation of several key signaling pathways, including MAPK, NF-κB, Wnt/β-catenin, TLR4, and mTOR, which lead to increased production of pro-inflammatory cytokines and activation of glial cells. Furthermore, emerging evidence has identified dysregulation of the gut-nerve axis and alterations in gut microbiota composition as contributing factors that exacerbate oxaliplatin-induced neuroinflammation and neuropathic pain. Various pharmacological and plant-derived compounds, such as naringin, baicalein, and puerarin, as well as selective inhibitors of inflammatory pathways, have shown promising neuroprotective effects in animal models by attenuating inflammatory responses and alleviating neuropathic symptoms. By synthesizing these converging lines of evidence, this review further outlines potential future directions, including the development of combination therapies targeting multiple inflammatory pathways, microbiome-based interventions, and the translation of preclinical findings into well-designed clinical trials.},
}

Humans
*Oxaliplatin/adverse effects/toxicity
Animals
*Peripheral Nervous System Diseases/chemically induced/drug therapy/metabolism
*Neuroinflammatory Diseases/chemically induced/drug therapy/metabolism
*Antineoplastic Agents/adverse effects/toxicity

@article {pmid41389040,
year = {2025},
author = {Ishida, M and Narita, S and Sato, H and Sekine, Y and Kobayashi, M and Kashima, S and Yamamoto, R and Numakura, K and Saito, M and Takahashi, Y and Funahashi, K and Yamauchi, Y and Fukuda, S and Habuchi, T},
title = {Androgen-Deprivation Therapy and Dietary Habits Influence the Gut Microbial Environment in Patients With High-Risk Localized Prostate Cancer.},
journal = {The Prostate},
volume = {},
number = {},
pages = {},
doi = {10.1002/pros.70109},
pmid = {41389040},
issn = {1097-0045},
support = {22K09464//MEXT/JSPS (Kakenhi)/ ; 23K19665//MEXT/JSPS (Kakenhi)/ ; 25K02770//MEXT/JSPS (Kakenhi)/ ; },
abstract = {BACKGROUND: The aim of this study is to investigate the relationship between the gut microbial profiles, occurrence of side effects, total testosterone (TS) levels, and pretreatment dietary habits among patients with high-risk localized prostate cancer who were subjected to androgen-deprivation therapy (ADT).

METHODS: This prospective study included patients diagnosed with high-risk localized prostate cancer who underwent ADT between March 2021 and August 2022. The correlation between the pre- and post (after 3 months)-ADT gut microbial profiles, laboratory tests, body consumption data, and pretreatment dietary habits was analyzed.

RESULTS: No significant differences were observed in the alpha- and beta-diversities of the gut microbiota during pre- and post-ADT. The relative abundance of genus Ruminococcus 2 (p = 0.013) and genus [Eubacterium] ruminantium group (p = 0.043) were significantly higher during post-ADT compared with those during pre-ADT. Twenty percent of the patients with a post-ADT TS level of < 20 ng/dL had a significantly high proportion of genus Ruminococccus 2, whereas no significant proportion was observed in patients with a TS level of ≥ 20 ng/dL. In terms of the impact of the pretreatment dietary habits on the changes of the gut microbiota, genus Romboutsia and genus Fusicatenibacter showed a positive correlation with n-6 polyunsaturated fatty acid intake, whereas the amounts of genus Ruminococcus 2 and genus Veillonella showed a negative correlation with n-3 polyunsaturated fatty acids.

CONCLUSIONS: Short-term ADT was found to increase the proportion of gut genus Ruminococcus 2 in patients with advanced prostate cancer, which was associated with low TS levels and showed a negative correlation with n-3 polyunsaturated fatty acid intake. Further validation is important to identify specific changes in the gut microbiota during ADT in patients with prostate cancer.},
}

@article {pmid41389008,
year = {2025},
author = {Pryor, JC and Hoedt, EC and Soh, WS and Fowler, S and Caban, S and Minahan, K and Sherwin, S and Nieva, C and McCarthy, H and Horvat, J and Hedley, KE and Duncanson, K and Burns, GL and Talley, NJ and Keely, S},
title = {Antibiotics Alter Duodenal Immune Populations Upon Gluten Exposure in Mice: Implications for Non-Coeliac Gluten Sensitivity.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00159.2025},
pmid = {41389008},
issn = {1522-1547},
support = {2004860//DHAC | National Health and Medical Research Council (NHMRC)/ ; 2035319//DHAC | National Health and Medical Research Council (NHMRC)/ ; 1170893//DHAC | National Health and Medical Research Council (NHMRC)/ ; },
abstract = {A growing proportion of the non-celiac population experience adverse symptoms to gluten. The pathogenesis of non-celiac gluten sensitivity (NCGS) is unclear, but elevated duodenal eosinophils and altered mucosa-associated microbiota (MAM) populations have been reported. Given the microbiome's role in gluten digestion and its susceptibility to antibiotics, we hypothesised that altering the microbiome with antibiotics would modify immune responses to gluten in mice. BALB/C mice consuming gluten-free chow received amoxicillin/clavulanate (5mg/kg) or PBS-vehicle daily for 5-days. Mice were then treated with a 3mg wheat-gluten suspension, or vehicle, on days 4 and 5 before sacrifice on day 7. Duodenal immune cells were analysed by histology and flow cytometry, while the duodenal MAM and faecal microbiome were characterised via 16S rRNA and shotgun metagenomic sequencing, respectively. Antibiotic treatment followed by gluten reintroduction significantly reduced Staphylococcus in the duodenal MAM, enriched Bacteroides in faeces, and resulted in altered microbial carbohydrate and lipid metabolism, compared to vehicle controls. Treatment with antibiotics and gluten also increased duodenal eosinophils, which positively correlated with the genus Blautia. Flow cytometry revealed that sequential antibiotic and gluten treatment resulted in a greater proportion of active eosinophils and epithelial γδ T-cells, compared to vehicle control mice. This study demonstrated that modulating the microbiome with antibiotics was sufficient to alter the immune response to gluten in mice, suggesting that the microbiome may determine the capacity for gluten to induce immune responses. These findings contribute valuable insights into possible microbial mechanisms underlying NCGS, such as altered gluten metabolism or production of immunomodulatory metabolites.},
}

@article {pmid41388904,
year = {2025},
author = {Orozco-Mosqueda, MDC and Glick, BR and Santoyo, G},
title = {Cross-talk within plant niches: endophytic and arbuscular mycorrhizal fungi for sustainable crop production.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf063},
pmid = {41388904},
issn = {1574-6976},
abstract = {World agriculture depends in part on the crop-associated microbiome for improved plant growth, health, and productivity. In particular, endophytic fungi (EF) with plant growth-promoting activities fulfill some of these roles and are central as bioinoculant agents. In the case of arbuscular mycorrhizal fungi (AMF), they form a symbiosis with their host plants, enhancing the uptake of water, phosphorus, nitrogen, and other micronutrients, while the plants provide them with photosynthates. This work reviews the differences in the colonization of internal plant niches between these beneficial fungi, as well as other distinctive ecological traits. It also explores mechanisms of seedborne vertical transmission in AMF and their classification. Genomic and transcriptomic advances in fungal endophytes are highlighted, shedding light on genes and expression profiles that define their lifestyle and plant associations. In addition, recent studies on their abilities to promote plant growth are analyzed, especially focusing on Trichoderma spp., Epichloë spp., Serendipita indica (formerly Piriformospora indica), and entomopathogens like Beauveria spp. and Metarhizium spp. Finally, the multiple interactions among EF, AMF, and other members of the plant microbiome-notably plant growth-promoting bacteria (PGPB)-are discussed, emphasizing how these organisms synergistically benefit the host. A deeper understanding of these fungi and their plant-beneficial effects should facilitate commercialization and help farmers achieve sustainable production, especially under challenges posed by global climate change.},
}

@article {pmid41388822,
year = {2025},
author = {Rozenblum, G and Ait-Aissa, K and Zahran, G and Alipour, M and Sahyoun, AM and Munkhsaikhan, U and Kassan, A and Ishrat, T and Wang, Q and Abidi, AH and Kassan, M},
title = {Unraveling the oral microbiome's role in Alzheimer's disease: From pathophysiology to therapeutic potential.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21},
number = {12},
pages = {e71011},
doi = {10.1002/alz.71011},
pmid = {41388822},
issn = {1552-5279},
mesh = {Humans ; *Alzheimer Disease/microbiology/physiopathology ; *Microbiota/physiology ; *Mouth/microbiology ; *Dysbiosis/microbiology/complications ; Fusobacterium nucleatum ; Amyloid beta-Peptides/metabolism ; },
abstract = {Oral dysbiosis contributes to Alzheimer's disease (AD) by promoting neuroinflammation. Pathobionts such as Porphyromonas gingivalis, Treponema denticola, and Fusobacterium nucleatum release virulence factors that induce amyloid beta aggregation and tau hyperphosphorylation, while the loss of commensals like Streptococcus salivarius and Neisseria spp. impairs anti-inflammatory protection, worsening neuronal damage. P. gingivalis is strongly linked to an increased risk of AD, especially in individuals with systemic conditions like diabetes, hypertension, and chronic kidney disease. Its presence in brain tissue correlates with a higher likelihood of AD, while salivary Veillonella and periodontal pathogens in gingival crevicular fluid show potential as non-invasive biomarkers for early AD detection. Therapeutic strategies targeting the oral microbiota, such as gingipain inhibitors, antimicrobials, probiotics, and prebiotics, show promise for mitigating AD risk. However, causal mechanisms and clinical efficacy remain to be fully established. Maintaining microbial balance through preventive and targeted modulation represents an innovative approach to reducing AD susceptibility. HIGHLIGHTS: We identified Porphyromonas gingivalis, Treponema denticola, and Fusobacterium nucleatum as key oral pathogens driving Alzheimer's disease (AD) via gingipain-induced amyloid beta aggregation, systemic inflammation, and blood-brain barrier disruption. Our study revealed diabetes, hypertension, and chronic kidney disease (CKD) amplify AD risk through shared oral dysbiosis, with uremic toxins (CKD) and hyperglycemia (diabetes) exacerbating neuroinflammation. We propose Veillonella in saliva and Porphyromonas gingivalis in gingival crevicular fluid as non-invasive AD biomarkers, correlating with 6 to 10× higher AD risk when detected in brain tissue. Gingipain inhibitors (e.g., COR388), nitrate-reducing probiotics, and integrated dental-neurology care are promising interventions to disrupt the oral-brain axis. We advocate for oral microbiome screening in high-risk populations (apolipoprotein E ε4 carriers, diabetics) and interdisciplinary approaches to AD prevention.},
}

Humans
*Alzheimer Disease/microbiology/physiopathology
*Microbiota/physiology
*Mouth/microbiology
*Dysbiosis/microbiology/complications
Fusobacterium nucleatum
Amyloid beta-Peptides/metabolism

@article {pmid41388767,
year = {2025},
author = {Hou, B and Shao, H and Yuan, D and Tham, EH},
title = {Skin and gut microbiome in atopic dermatitis: Mechanisms and therapeutic opportunities.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {36},
number = {12},
pages = {e70265},
doi = {10.1111/pai.70265},
pmid = {41388767},
issn = {1399-3038},
support = {//National Medical Research Council/ ; },
mesh = {Humans ; *Dermatitis, Atopic/therapy/microbiology/immunology ; *Gastrointestinal Microbiome/immunology ; *Skin/microbiology/immunology ; *Dysbiosis/immunology/therapy ; Probiotics/therapeutic use ; Animals ; Fecal Microbiota Transplantation ; },
abstract = {The pathogenesis of atopic dermatitis (AD) comprises a combination of genetic, immune, and microbial factors. An imbalance in skin and gut microbiota composition, termed dysbiosis, may contribute to AD pathogenesis and severity through overgrowth of pathogenic microbes and suppression of healthy commensal colonization. These, in turn, promote barrier disruption and pro-inflammatory responses. The skin and gut microbiota composition plays crucial roles in AD, namely as early predictive biomarkers of AD onset; indicators of treatment response; and as future novel therapeutics such as probiotics, fecal, and skin microbiota transplantation. Such interventions aim to directly "reset" and restore a healthy microbial equilibrium, thereby fundamentally repairing barrier function, regulating immune homeostasis, and establishing new adjunctive pathways for the long-term management of AD.},
}

Humans
*Dermatitis, Atopic/therapy/microbiology/immunology
*Gastrointestinal Microbiome/immunology
*Skin/microbiology/immunology
*Dysbiosis/immunology/therapy
Probiotics/therapeutic use
Animals
Fecal Microbiota Transplantation

@article {pmid41388723,
year = {2025},
author = {Yang, J and Yao, Y and Zhou, Z},
title = {Osteopontin: a central hub in the pathogenesis and therapeutic intervention of liver disease.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2596538},
doi = {10.1080/07853890.2025.2596538},
pmid = {41388723},
issn = {1365-2060},
mesh = {*Osteopontin/metabolism ; Humans ; *Liver Diseases/metabolism/therapy/pathology ; Liver Neoplasms/metabolism/pathology ; Liver/pathology/metabolism ; Animals ; Biomarkers/metabolism ; Carcinoma, Hepatocellular/metabolism ; Signal Transduction ; Hepatic Stellate Cells/metabolism ; Disease Progression ; },
abstract = {BACKGROUND: Osteopontin (OPN) is a phosphorylated glycoprotein implicated in inflammation and tissue remodeling. Its expression is significantly elevated in various liver diseases, but its precise pathophysiological roles remain complex and context-dependent.

OBJECTIVE: This review systematically examines the mechanisms of OPN in multiple liver diseases, including acute liver injury, alcoholic liver disease, viral hepatitis, metabolic-associated fatty liver disease, and hepatocellular carcinoma. It focuses on its cell-type-specific functions and explores its potential as a diagnostic biomarker and therapeutic target.

RESULTS: OPN exhibits a dual role in liver pathophysiology. It promotes disease progression by activating hepatic stellate cells to drive fibrosis, enhancing collagen deposition, and facilitating HCC invasion and metastasis. Conversely, OPN also demonstrates protective functions. Intestinal OPN preserves gut barrier integrity and microbiome homeostasis, ameliorating alcohol-induced liver injury. Notably, a recent identified mechanism reveals that macrophage-derived OPN activates the OSM-STAT3-ARG2 signaling axis in hepatocytes, enhancing fatty acid oxidation and attenuating hepatic steatosis in MAFLD. Furthermore, OPN shows promise as a clinical biomarker for detecting early-stage HCC and assessing liver fibrosis, potentially outperforming alpha-fetoprotein.

CONCLUSION: Osteopontin serves as a central signaling hub in liver diseases, where it effectively integrates inflammatory, metabolic and fibrogenic networks. Harnessing its therapeutic potential represents the cornerstone for developing future OPN-targeted therapies. This strategic approach will create new avenues for liver disease treatment, enabling precise interventions tailored to specific disease contexts.},
}

*Osteopontin/metabolism
Humans
*Liver Diseases/metabolism/therapy/pathology
Liver Neoplasms/metabolism/pathology
Liver/pathology/metabolism
Animals
Biomarkers/metabolism
Carcinoma, Hepatocellular/metabolism
Signal Transduction
Hepatic Stellate Cells/metabolism
Disease Progression

@article {pmid41388648,
year = {2025},
author = {Peng, Y and Youn, C and Seo, J and Park, EJ and Jang, IC and Kim, CY and Lee, J},
title = {The endophytic Pseudomonas sp. JBR1 alleviates salt stress through integrated host-microbiome mechanisms.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiaf646},
pmid = {41388648},
issn = {1532-2548},
abstract = {Soil salinity is a major abiotic stress that restricts plant growth and agricultural productivity worldwide. Here, we characterized Pseudomonas sp. JBR1, an endophytic bacterium isolated from the halophyte Carex pumila, and evaluated its capacity to enhance salt tolerance in non-halophytic plants. Inoculation with strain JBR1 markedly improved growth of Arabidopsis (Arabidopsis thaliana) and Brassica rapa under saline conditions by reducing reactive oxygen species (ROS) accumulation, enhancing antioxidant enzyme activity, improving Na[+]/K[+] ion homeostasis, and stimulating auxin accumulation in roots. In addition to these direct physiological effects, strain JBR1 markedly altered rhizosphere microbial communities. 16S rRNA amplicon sequencing revealed increased microbial diversity and enrichment of beneficial taxa, particularly Streptomyces and Pseudomonas. Predictive functional profiling indicated upregulation of bacterial motility, chemotaxis, and signal transduction pathways in strain JBR1-treated plants, suggesting enhanced microbial colonization and plant-microbe interactions. These results demonstrate that strain JBR1 confers salt tolerance through a dual mechanism: direct modulation of host physiology and indirect restructuring of the rhizosphere microbiome. The synergistic effects of strain JBR1 highlight its potential as a microbial bioinoculant to improve crop resilience in saline soils and support sustainable agriculture.},
}

@article {pmid41388564,
year = {2025},
author = {Soetaert, C and Itani, M and Triadafilopoulos, G and Spencer, S and Nguyen, L and Neshatian, L},
title = {Evacuation Dysfunction Does Not Impact Breath Test Results.},
journal = {Neurogastroenterology and motility},
volume = {},
number = {},
pages = {e70211},
doi = {10.1111/nmo.70211},
pmid = {41388564},
issn = {1365-2982},
support = {//Belgian American Educational Foundation/ ; },
abstract = {BACKGROUND: Evacuation dysfunction affects gastrointestinal motility, yet its effect on small bowel microbiota is unknown. We aimed to compare the glucose breath test (GBT) and lactulose breath test (LBT) outcomes in patients with or without evacuation dysfunction based on high-resolution anorectal manometry (HR-ARM) and balloon expulsion test (BET).

METHODS: We conducted a retrospective review of patients who received a HR-ARM and either a GBT or LBT from 2018 to 2024.

KEY RESULTS: We studied 344 patients who underwent GBT and 144 who underwent LBT. Clinical characteristics between the two groups were comparable. Abnormal BET was observed in 53% of patients. Rates of abnormal breath tests were comparable among patients with or without abnormal BET. Patients with positive vs. negative breath tests had similar anorectal pressures, rectal sensory function, and BET results. There were significantly more negative breath tests in GBT (64%) versus LBT (35%), with higher rates of small intestinal bacterial overgrowth (SIBO) in LBT versus GBT (SIBO only: 20.1% vs. 7.6%; SIBO+IMO: 21.5% vs. 5.5%; p < 0.001).

CONCLUSIONS AND INFERENCES: The presence of evacuation dysfunction does not impact the results of the breath test. HR-ARM and BET demonstrate a high diagnostic yield in identifying the etiology of abdominal bloating in patients with chronic constipation or IBS without diarrhea, whereas hydrogen breath tests have a low diagnostic yield in this context. The specificity and sensitivity of LBT in this patient population remain less certain.},
}

@article {pmid41388559,
year = {2025},
author = {Uppal, G and Urtecho, G and Richardson, M and Comba, IY and Lee, J and Moody, T and Wang, HH and Gerber, GK},
title = {MCSPACE: inferring microbiome spatiotemporal dynamics from high-throughput co-localization data.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02279-4},
pmid = {41388559},
issn = {2049-2618},
support = {Hanna H. Gray Postdoctoral Fellowship (GT15182)/HHMI/Howard Hughes Medical Institute/United States ; MTM2 2025512//National Science Foundation/ ; R01GM130777//NIH NIGMS/ ; Research Infrastructure Program//Massachusetts Life Sciences Center/ ; President's Scholar Award//Brigham and Women's Hospital/ ; },
abstract = {BACKGROUND: Recent advances in high-throughput approaches for estimating co-localization of microbes, such as SAMPL-seq, allow characterization of the biogeography of the gut microbiome longitudinally and at an unprecedented scale. However, these high-dimensional data are complex and have unique noise properties.

RESULTS: To address these challenges, we developed MCSPACE, a probabilistic AI method that infers, from microbiome co-localization data, spatially coherent assemblages of taxa, their dynamics over time, and their responses to perturbations. To evaluate MCSPACE's capabilities, we generated the largest longitudinal microbiome co-localization dataset to date, profiling spatial relationships of microbes in the guts of mice subjected to serial dietary perturbations over 76 days. Analyses of these data and two existing human longitudinal datasets demonstrated superior benchmarking performance of MCSPACE over existing methods and moreover yielded insights into the spatiotemporal structuring of the gut microbiome, including identifying temporally persistent and dynamic microbial assemblages in the human gut, and shifts in assemblages in the murine gut induced by specific dietary components.

CONCLUSIONS: Our results highlight the utility of MCSPACE, which we make available to the community as an open-source software tool, for elucidating the dynamics of microbiome biogeography and gaining insights into the role of spatial relationships in host-microbial ecosystem function. Video Abstract.},
}

@article {pmid41388485,
year = {2025},
author = {Khan, MAS and Bishir, M and Huang, W and Chidambaram, SB and Chang, SL},
title = {Early upregulation of alpha-7 nicotinic acetylcholine receptor in limbic system correlates with gut dysbiosis in mice exposed to binge ethanol.},
journal = {Alcohol, clinical & experimental research},
volume = {},
number = {},
pages = {},
doi = {10.1111/acer.70210},
pmid = {41388485},
issn = {2993-7175},
support = {AA029925/AA/NIAAA NIH HHS/United States ; },
abstract = {BACKGROUND: Alcohol use disorder (AUD) causes neuroinflammation and disrupts the gut microbiome through bidirectional communication between the brain and gut. However, it remains unclear whether the brain or gut responds first to alcohol exposure. We hypothesized that brain regions respond to alcohol first, preceding changes in the gut microbiome.

METHODS: B6 mice were given ethanol (EtOH; 5 g/kg/day, 42%v/v, i.g.) at various time points. Fecal samples were collected prior to the first EtOH injection (Day 0), at 24 h following the first, second, and third injections (Day 1, Day 2, and Day 3, respectively), and at 96 h after the third injection (Day 6). Brain regions, central amygdala (CeA), hypothalamus (Hyp), and nucleus accumbens (NAc) were isolated at 2 min, 12 h, 24 h, and 192 h following the first and third doses of binge EtOH, respectively. mRNA or protein expression levels of TNF-α, IL-1β, P2Y12, ITGβ2, and α7nAChR were analyzed by qRT-PCR and western blot, respectively. Fecal microbial composition and abundance were assessed using 16S rRNA metagenomic sequencing.

RESULTS: Data revealed increased TNF-α expression in the Amg, Hyp, and NAc and increased IL-1β expression in the Amg and NAc, 12 h after the first EtOH injection. α7nAChR expression in the CeA, Hyp, and NAc was also upregulated at 24 h after the third EtOH dose, compared to the control group. α7nAChR expression in the Hyp was observed at 2 min after the first EtOH dose. CHRNA7 mRNA levels were upregulated 24 h after the third EtOH dose. ITGβ2 showed an increasing trend in the Amg at 12 h after the first dose, followed by a significant reduction at 24 h, and 192 h after the third dose. 16S rRNA sequencing revealed a significant difference in β-diversity on Day 6. The relative abundance of the Prevotellaceae family was higher in EtOH-treated mice compared to controls at Day 3 and Day 6.

CONCLUSION: This study showed that brain inflammation, indicated by α7nAChR upregulation, occurred before EtOH-induced gut dysbiosis, supporting an anterograde sequence of events.},
}

@article {pmid41388434,
year = {2025},
author = {Gustafson, KL and Busi, SB and McAdams, ZL and McCorkle, RE and Khodakivskyi, P and Bivens, NJ and Davis, DJ and Raju, M and Coghill, LM and Goun, EA and Amos-Landgraf, J and Franklin, CL and Wilmes, P and Cortese, R and Ericsson, AC},
title = {Fetal programming by the parental microbiome of offspring behavior, and DNA methylation and gene expression within the hippocampus.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {254},
pmid = {41388434},
issn = {2049-2618},
support = {U42 OD010918/NH/NIH HHS/United States ; R03 OD028259-01/NH/NIH HHS/United States ; },
mesh = {Animals ; Female ; *Hippocampus/metabolism ; *DNA Methylation ; Mice ; *Gastrointestinal Microbiome ; Pregnancy ; *Fetal Development/genetics ; Male ; Behavior, Animal ; Mice, Inbred C57BL ; Anxiety/microbiology ; },
abstract = {BACKGROUND: The microorganisms colonizing the gastrointestinal tract of animals, collectively referred to as the gut microbiome, affect numerous host behaviors dependent on the central nervous system (CNS). Studies comparing germ-free mice to normally colonized mice have demonstrated influences of the microbiome on anxiety-related behaviors, voluntary activity, and gene expression in the CNS. Additionally, there is epidemiologic evidence supporting an intergenerational influence of the maternal microbiome on neurodevelopment of offspring and behavior later in life. There is limited experimental evidence however directly linking the maternal microbiome to long-term neurodevelopmental outcomes, or knowledge regarding mechanisms responsible for such effects.

RESULTS: Here we show that that the maternal microbiome has a dominant influence on several offspring phenotypes including anxiety-related behavior, voluntary activity, and body weight. Adverse outcomes in offspring were associated with features of the maternal microbiome including bile salt hydrolase activity gene expression (bsh), abundance of certain bile acids, and hepatic expression of Slc10a1. In cross-foster experiments, offspring resembled their birth dam phenotypically, despite faithful colonization in the postnatal period with the surrogate dam microbiome. Genome-wide DNA methylation analysis of hippocampal DNA identified microbiome-associated differences in DNA methylation of 196 loci in total, 176 of which show conserved profiles between mother and offspring. Further, single-cell transcriptional analysis revealed accompanying differences in expression of several differentially methylated genes within certain hippocampal cell clusters, and vascular expression of genes associated with bile acid transport. Inferred cell-to-cell communication in the hippocampus based on coordinated ligand-receptor expression revealed differences in expression of neuropeptides associated with satiety.

CONCLUSIONS: Collectively, these data provide proof-of-principle that the maternal gut microbiome has a dominant influence on the neurodevelopment underlying certain offspring behaviors and activities, and selectively affects genome DNA methylation and gene expression in the offspring hippocampus in conjunction with that neurodevelopment. Video Abstract.},
}

Animals
Female
*Hippocampus/metabolism
*DNA Methylation
Mice
*Gastrointestinal Microbiome
Pregnancy
*Fetal Development/genetics
Male
Behavior, Animal
Mice, Inbred C57BL
Anxiety/microbiology

@article {pmid41388368,
year = {2025},
author = {Chen, Y and Nguyen, AD and Lunjani, N and Ndhlovu, G and Kaul, D and De Pessemier, B and Nakatsuji, T and Madzinga, M and Sovershaeva, E and Hlela, C and Levin, M and Mankahla, A and Hightower, G and Callewaert, C and Knight, R and Gallo, RL and Dupont, CL and Dube, F},
title = {Environmental and skin-nasal microbiome variation in South African children with atopic dermatitis.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04589-x},
pmid = {41388368},
issn = {1471-2180},
support = {HREC/REF: 451/2014/GF/NIH HHS/United States ; },
abstract = {BACKGROUND: Atopic dermatitis (AD) in early childhood is associated with microbial dysbiosis. Skin and nasal microbiomes have been linked to AD severity; this relationship has not yet been studied in an African cohort. Here, we aimed to explore how urban and rural stratification, disease severity, and inter-site bacterial overlap shape the skin and nasal microbiomes of South African children with AD.

METHODS: Children were recruited from urban Cape Town (CT) and rural Umtata (UM), South Africa. We profiled the skin and nasal microbiomes of 183 children (84 healthy controls and 99 with AD; ages 9-37 months), totaling 462 samples, including both lesional and non-lesional skin sites in children with AD, in a cross-sectional study design. Using 16S rRNA V4-V5 sequencing for its accessibility, we applied random forest (RF) models to classify AD status based on amplicon sequence variants (ASVs) and analyzed microbiome composition and diversity by region.

RESULTS: We found that RF models could predict AD status using both skin and nasal microbiomes (AUCs: skin = 0.69-0.79; nasal = 0.65), strongly driven by both Streptococcus and Staphylococcus. The correlations between skin and nasal microbiomes were significantly stronger in children with AD compared to controls, with higher correlations observed in rural UM (healthy r = 0.45 to AD r = 0.67) compared to urban CT (healthy r = 0.27 to AD r = 0.65). The skin microbiome diversity was higher in children from rural UM with healthy skin than in those from urban CT (p = 0.004). However, children with AD in both groups showed significant alterations in their microbiome, with those in rural UM exhibiting greater beta diversity changes (p = 0.001-0.002) than their urban CT counterparts (p = 0.002-0.349).

CONCLUSION: In South African children with AD, skin-nasal microbiomes reflect shared reservoirs, and differences in the AD microbiome were observed between environmental regions. These findings highlight the need for geographically diverse studies incorporating skin and mucocutaneous sampling to better understand pediatric AD.},
}