@article {pmid41406967,
year = {2025},
author = {Liu, J and Glukhov, E and De Clerck, O and Gerwick, WH and Donia, MS},
title = {Environmentally controlled production of pagoamide A in marine macroalgae by an intracellular bacterial symbiont.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.11.023},
pmid = {41406967},
issn = {1879-0445},
abstract = {Marine algae are a rich source of diverse molecules, most of which are thought to be produced by the alga itself. We recently reported the discovery of pagoamide A from a cultured marine macroalga collected from American Samoa. Here, we found that the production of pagoamide A is conditional upon environmental temperature. Using comparative metagenomic, metatranscriptomic, and metabolomic analyses of algal cultures, we identified a nonribosomal peptide synthetase biosynthetic gene cluster (NRPS BGC) in the algal microbiome that varies in abundance between producing and non-producing conditions and whose architecture and biosynthetic logic match pagoamide A (named pag). pag belongs to a bacterium that we named "Candidatus Bryopsidiphilus pagoamidifaciens BP1," a new genus in the family Amoebophilaceae and a relative of amoeba, arthropod, and nematode endosymbionts. Ca. B. pagoamidifaciens lives intracellularly in its Bryopsis sp. algal host, harbors a reduced genome (1.7 Mbp), has lost most genes essential for free living, and is enriched in genes containing eukaryotic domains. By quantitatively monitoring longitudinal algal cultures under varying conditions for 9 weeks, we found that the abundance of both Ca. B. pagoamidifaciens and pagoamide A undergoes dramatic fluctuations in response to temperature changes. Finally, we discovered three additional strains of Ca. B. pagoamidifaciens that vary in their NRPS BGCs and eukaryotic domain-containing genes from algal samples of diverse geographical origins. Our findings suggest that symbiont-derived production of algal molecules is more common than previously anticipated and provide a unique case of environmental control of both symbiont and chemical levels in marine algae.},
}

@article {pmid41406907,
year = {2025},
author = {Chen, C and Chen, Q and Zou, H and Zhao, C and Wang, X},
title = {Research Trends in Periodontitis and Alzheimer's Disease: A Bibliometric Analysis Based on Web of Science and Scopus.},
journal = {International dental journal},
volume = {76},
number = {1},
pages = {109327},
doi = {10.1016/j.identj.2025.109327},
pmid = {41406907},
issn = {1875-595X},
abstract = {INTRODUCTION AND AIMS: This study aimed to conduct a comprehensive bibliometric analysis to identify global research trends, key contributors and emerging hot spots in the field investigating the association between periodontitis and Alzheimer's disease (AD).

METHODS: Scientific publications from 2002 to 2025 were retrieved from the Web of Science Core Collection (WoSCC) and Scopus databases. The data were analysed using VOSviewer, CiteSpace and the R package 'bibliometrix' to perform co-authorship, co-occurrence and citation analyses.

RESULTS: A total of 262 articles from WoSCC and 272 from Scopus were included in the analysis. China was the leading contributing country, and Shanghai Jiao Tong University was the most productive institution. The Journal of Alzheimer's Disease was identified as the most influential journal in this domain. Keyword co-occurrence analysis identified central research themes, including 'dementia', 'tooth loss', and 'Porphyromonas gingivalis'. Citation burst analysis indicated that 'oral microbiome' and 'oral health' are currently emerging research frontiers.

CONCLUSION: This is the first bibliometric study to systematically map the intellectual structure and evolution of research linking periodontitis and AD. The findings underscore the strengthening link between oral inflammatory conditions and neurodegeneration.

CLINICAL RELEVANCE: The analysis highlights a shifting focus towards mechanisms such as the oral microbiome and systemic inflammation, pointing to promising directions for future research aimed at novel preventive strategies and therapeutic interventions for AD.},
}

@article {pmid41406905,
year = {2025},
author = {Li, X and Liu, M and Xiang, H and Gui, L and Ma, Y and Dan, X},
title = {Integrated microbiome and metabolome revealing new insight into the combination of lactic acid bacteria in preventing postpartum metritis of dairy cows.},
journal = {Animal reproduction science},
volume = {285},
number = {},
pages = {108078},
doi = {10.1016/j.anireprosci.2025.108078},
pmid = {41406905},
issn = {1873-2232},
abstract = {Probiotics, particularly composite lactic acid bacteria (CLAB), are emerging as a potential alternative to antibiotics for managing bovine metritis. While prior studies have highlighted CLAB's anti-inflammatory effects, limited data exist on its impact on vaginal and uterine microbiomes and systemic metabolism. In this study, Holstein cows received deep vaginal infusions of CLAB (a blend of Lactobacillus rhamnosus, Pediococcus acidilactici and Lactobacillus reuteri; at a standardized 4.5 × 10[10] CFU/dose and a proportion of 25/25/2, respectively) at 20 and 10 days prepartum. We analyzed changes in vaginal and uterine microbiota, plasma metabolomes, and assessed the incidence of metritis, conception rate, and lactation performance postpartum. CLAB administration significantly altered the vaginal microbiota by reducing opportunistic pathogens (Prevotella heparinolytica, Bacteroides and Fusobacteria) and promoting beneficial taxa (Akkermansia and Prevotellaceae). In the uterus, CLAB enriched Rikenellaceae, Christensenellaceae and Lachnospiraceae, while suppressing pathogenic genera such as Cutibacterium and Fournierella. Metabolomic analysis identified pyruvic acid, L-glutamine and L-valine as hub metabolites, with KEGG enrichment revealing involvement in amino acid metabolism and immunomodulatory pathways. Although CLAB infusion did not significantly reduce metritis incidence (5.00 % vs. 5.52 %) or improve conception rate (47.50 % vs. 45.00 %), it showed promising trends without affecting milk production. These findings suggest that prepartum vaginal CLAB infusion modulates reproductive tract microbiota and systemic metabolism, potentially contributing to uterine health maintenance in dairy cows. A key limitation of this study was the absence of significant reductions in metritis incidence and improvements in conception rates, likely attributable to the small sample size and limited study period. Further large-scale studies are warranted to validate its efficacy during high-risk seasons.},
}

@article {pmid41406883,
year = {2025},
author = {Veilleux, C and Erenben, ED and Ismail, N},
title = {Autism and hormones: A perspective from the immune system and the gut microbiome.},
journal = {Hormones and behavior},
volume = {177},
number = {},
pages = {105867},
doi = {10.1016/j.yhbeh.2025.105867},
pmid = {41406883},
issn = {1095-6867},
abstract = {Autism Spectrum Disorder (ASD) affects 2.7 % of individuals worldwide, and it is characterized by abnormal social interactions, communication deficits, restricted interactions, and repetitive behaviors. This disorder appears early in life, and it has been diagnosed more frequently in males than in females. Several factors have been shown to be associated with the onset of ASD. However, the mechanisms underlying the onset of this neurodevelopmental disorder and the higher prevalence in males remain unclear. This review discusses the role of hormonal imbalances, immune system activation during the prenatal (maternal immune activation) and the neonatal periods (neonatal immune activation), immune dysregulation and gut dysbiosis in the development of ASD. It also highlights the many interactions between these systems and demonstrates the true complexity of this disorder.},
}

@article {pmid41406735,
year = {2025},
author = {López-Dávalos, PC and Requena, T and Pozo-Bayón, MÁ and Muñoz-González, C},
title = {In vivo metabolism of fruity carboxylic esters in the human oral cavity is partly driven by microbial enzymes.},
journal = {Food chemistry},
volume = {501},
number = {},
pages = {147554},
doi = {10.1016/j.foodchem.2025.147554},
pmid = {41406735},
issn = {1873-7072},
abstract = {Food flavor perception is shaped by biochemical events during oral processing, with oral metabolism remaining poorly understood. This study investigated the oral fate of fruity carboxylic esters and its relationship with salivary and microbiological parameters. Participants (n = 101) rinsed their mouths with either water (control) or an ester-containing solution for 30 s. Esters and their corresponding acids were analyzed by gas chromatography-mass spectrometry before and after rinsing. Results showed a significant decrease in ester and a marked increase in acid levels, indicating rapid metabolic conversion. Ester recovery was associated with the physicochemical properties of the compounds, participants' body mass index, and salivary esterase activity (SEAC). SEAC also correlated with oral microbiota composition and the abundance of microbial genes encoding carboxylic ester hydrolases, as assessed by shotgun metagenomics. These findings provide the first evidence of rapid ester metabolism in the human mouth and its relationship with the salivary microbiome.},
}

@article {pmid41406635,
year = {2025},
author = {Maeng, LS and Yoon, JH and Chung, BY and Seo, KJ and Lee, HK and Chung, MG and Park, WS and Chae, HS},
title = {Refined photobiomodulation therapy ameliorates inflammatory bowel disease via modulation of immune pathways and gut microbiota.},
journal = {Journal of photochemistry and photobiology. B, Biology},
volume = {274},
number = {},
pages = {113330},
doi = {10.1016/j.jphotobiol.2025.113330},
pmid = {41406635},
issn = {1873-2682},
abstract = {BACKGROUND: Inflammatory bowel diseases (IBD), such as ulcerative colitis and Crohn's disease, are chronic conditions influenced by genetic and environmental factors. Current treatments are costly and not universally effective. This study aimed to evaluate the therapeutic potential of refined photobiomodulation (PBM) therapy by addressing limitations in light delivery and its impact on gut microbiota using a dextran sodium sulfate (DSS)-induced colitis mouse model.

METHODS: PBM therapy was administered using an 830 nm infrared LED with optimized light delivery protocols, including abdominal hair removal and a four-directional irradiation approach. DSS-induced colitis was established in mice, and therapeutic efficacy was assessed through histological analysis, transcriptomic profiling, immune marker expression, and gut microbiota diversity using 16S rRNA sequencing.

RESULTS: PBM therapy significantly ameliorated DSS-induced colitis by reducing inflammatory cell infiltration, crypt damage, and ulceration (p < 0.05). Colon length was restored, and disease activity index scores were reduced (p < 0.001). Transcriptomic profiling revealed modulation of inflammatory pathways, including downregulation of NF-κB signaling and apoptosis-related genes. PBM decreased neutrophil activity (MPO levels) and immune cell marker expression while promoting gut microbiota richness (Chao1 index, p < 0.05). PBM-treated mice exhibited altered microbial composition with increased abundance of protective taxa such as Bacteroides.

CONCLUSIONS: Refined PBM therapy effectively alleviates DSS-induced colitis by modulating immune responses and gut microbiota composition. These findings highlight PBM as a promising non-invasive strategy for IBD management, warranting further translational studies.},
}

@article {pmid41406626,
year = {2025},
author = {Habich, D and Horvath, A and Feldbacher, N and Rebol, L and Nepel, M and Madl, T and Habisch, HJ and Baumann-Durchschein, F and Fürst, S and Plank, J and Rainer, F and Spindelböck, W and Stauber, RE and Tatscher, E and Wagner, M and Zollner, G and Stadlbauer, V},
title = {An observational study on the effect of l-ornithine-l-aspartate (LOLA) on the gut microbiome in liver cirrhosis. A single center phase 4 study.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {56},
number = {},
pages = {106522},
doi = {10.1016/j.clnu.2025.11.007},
pmid = {41406626},
issn = {1532-1983},
abstract = {BACKGROUND & AIMS: Liver cirrhosis is associated with gut microbiome dysbiosis, intestinal inflammation and gut barrier dysfunction, contributing to reduced quality of life and the development of complications. We showed in a retrospective study that l-ornithine-l-aspartate (LOLA) was associated with improvement in taxonomic composition of the microbiome. Here we prospectively studied the influence of LOLA on the gut microbiome, quality of life, sarcopenia and the gut barrier.

METHODS: In this phase 4 study, patients with liver cirrhosis and hepatic encephalopathy grade 0-2 received LOLA 18 g/day orally for 3 months. We studied faecal microbiome composition (primary endpoint abundance of the genus Flavonifractor), microbiome function, quality of life, serum ammonia levels, sarcopenia and frailty, biomarkers of the gut liver axis and the stool, serum and urine metabolome.

RESULTS: We screened 258 patients with liver cirrhosis, included 65, of whom 52 patients (40 % female, age 62 (58; 65)) completed the study. LOLA intake decreased the abundance of the genus Romboutsia, increased the abundance of the genus Enterococcus, but did not alter other microbiome parameters. LOLA improved one out of 8 dimension of quality of life (vitality) and decreased serum ammonia concentrations. The subgroup of patients with improved ammonia concentrations responded with a halt in further muscle mass declined over the study period. Diamine oxidase, a marker of intestinal mucosal condition, decreased and LPS binding protein increased. Metabolomic analysis indicated an increase in alanine concentration.

CONCLUSIONS: LOLA improved one quality of life dimension (vitality) and biomarker of the gut-liver axis, altered innate immune response, faecal microbiome and metabolome. LOLA prevented muscle loss only in patients with elevated ammonia concentrations at baseline. LOLA may therefore be a useful adjunct treatment to improve quality of life in cirrhosis and a promising intervention for muscle loss prevention in hyperammonemic patients.

clinicaltrials.gov NCT05737030.

IMPACT AND IMPLICATION: We conducted a 12-week prospective cohort study to test the effect of the ammonia lowering drug l-ornithine-l-aspartate (LOLA) on the gut microbiome, biomarkers along the gut-liver-axis, muscle health and quality of life in patients with liver cirrhosis and hepatic encephalopathy. Although our primary endpoint was not reached, LOLA slightly altered microbiome composition and function and improved vitality, a clinically relevant patient reported outcome parameter. LOLA also improved biomarkers for the gut-liver-axis, innate immune response and prevented muscle loss in patients with elevated ammonia levels at baseline. LOLA may therefore be a useful adjunct treatment to improve quality of life in cirrhosis and to prevent muscle loss in hyperammonemic patients.},
}

@article {pmid41406001,
year = {2025},
author = {Thornton, CS and Bouzek, DC and Caverly, LJ},
title = {Microbiota, Mucus, and Modulators: CF Infection Pathogenesis in the CFTR Modulator Era.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf626},
pmid = {41406001},
issn = {1537-6613},
abstract = {Cystic fibrosis (CF) lung disease is a result of defective CFTR-mediated ion transport, producing dehydrated mucus, impaired mucociliary clearance and an opportune environment for chronic airway infection. CF airway infections are polymicrobial airway ecosystems often dominated by CF pathogens such as Pseudomonas aeruginosa, Staphylococcus aureus, Burkholderia, Stenotrophomonas, Achromobacter, and nontuberculous mycobacteria that drive cycles of infection, inflammation, and bronchiectasis. Highly effective CFTR modulators, including elexacaftor/tezacaftor/ivacaftor, improve airway hydration and mucociliary clearance and reduce pathogen CF acquisition and density. However, even with CFTR modulator treatment, most individuals with established infection remain chronically infected, and long-term impacts of CFTR modulators on airway infection dynamics and associated clinical outcomes remain unclear. In this review, we address key gaps in understanding chronic infection in the CFTR modulator era, including changes in infection-related lung disease pathogenesis, airway-gut microbiome interactions, approaches to airway infection sampling, and implications for infection management.},
}

@article {pmid41405666,
year = {2025},
author = {Wenbin, T and Feng, D and Jing, L},
title = {The interplay between insect gut microbiota and host immunity in the development and dissemination of antibiotic resistance.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {41405666},
issn = {1874-9356},
support = {25DF0314//China Higher Education Society Higher Education Science Research Planning Project/ ; },
abstract = {The escalating crisis of antibiotic resistance presents a formidable challenge to global public health and food security. Insects are increasingly recognized as significant reservoirs and vectors for antibiotic resistance genes (ARGs) which inhabit diverse ecosystems. This review explores how the insect gut microbiota contributes to the development and spread of antibiotic resistance, focusing on the mediating role of the host immune system. We outline the structural and functional dynamics of the insect gut microbiome and elaborate on direct mechanisms through which microbiota contribute to resistance, including ARG carriage, enzymatic inactivation of antibiotics, and modulation of host detoxification pathways. Special emphasis is placed on the bidirectional crosstalk between gut microbes and the host immune system: we discuss how immune effectors, particularly antimicrobial peptides (AMPs), exert selective pressures that may enrich resistant taxa, and how microbial metabolites reciprocally regulate immune activity. Key immune signaling pathways-Toll, Immune Deficiency(Imd), and Janus kinase-signal transducer and activator of transcription (JAK-STAT)-are explored for their roles in maintaining microbial homeostasis and modulating resistance phenotypes. We also highlight cutting-edge experimental approaches, including gnotobiotic models and multi-omics technologies, that are essential for elucidating causal relationships. We conclude by highlighting outstanding questions and outlining future research priorities that integrate microbiology, immunology, and computational biology. This review aims to establish a holistic framework for understanding the insect gut as a hotspot for antibiotic resistance evolution and to inspire innovative microbiome-based interventions.},
}

@article {pmid41405552,
year = {2025},
author = {Smith, ML and Rillaer, TV and Willmott, T and Lebeer, S and Souza, A and O'Neill, CA and McBain, AJ},
title = {The human skin microbiome remains unchanged after 24 h of sunscreen application.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0147625},
doi = {10.1128/aem.01476-25},
pmid = {41405552},
issn = {1098-5336},
abstract = {UNLABELLED: To ensure safe, long-term use, topical products should be investigated to understand how they interact with the resident skin microbiota to mitigate potential risk. Sunscreens are essential for protecting skin from UV damage, but their effects on skin-resident microbes have not been well characterized. We examined the impact of two sunscreen formulations (containing titanium dioxide or zinc oxide) on both cultured skin bacteria and the skin microbiomes of human volunteers. No loss of viability was observed after a 2 h exposure to either sunscreen in cultures of Staphylococcus epidermidis, Staphylococcus capitis, Staphylococcus hominis, Micrococcus luteus, and Corynebacterium tuberculostearicum. The effects of the sunscreens were then studied across the skin microbiomes of 20 human participants. Skin swabs were collected before application and at 1, 6, and 24 h afterward. DNA was extracted and sequenced at the 16S rRNA V4 region, and sequences were denoised and taxonomically assigned using the nf-core/ampliseq pipeline. Across all time points, alpha diversity (Shannon index, Friedman test) and beta diversity (permutational multivariate analysis of variance) remained stable, with no significant differences in beta dispersion. Differential abundance analysis revealed minor fluctuations in some low-abundance genera, identified as likely transient due to their low prevalence, but overall resident community composition was not significantly altered. These findings suggest that short-term sunscreen application does not disrupt the skin microbiome, supporting their safe use from a microbial standpoint. Outcomes from both in vitro and in vivo experimentation point to the compositional resilience of the skin microbiota to sunscreens.

IMPORTANCE: Understanding how sunscreens affect the skin microbiome is important, given their widespread use and the role of the microbiome in skin health. This study demonstrates that common sunscreens do not significantly alter skin microbiome diversity or viability, including that of the core skin microbiome genera, Staphylococcus, Micrococcus, Kocuria, Cutibacterium, and Corynebacterium. This highlights the resilience of the skin microbiota and supports the microbiome-safe profile of these products.},
}

@article {pmid41405456,
year = {2025},
author = {Pervaiz, K and Tabassum, R and Steidele, C and Brender, N and John, E and Djamei, A},
title = {Transcriptional Response of Magnaporthe oryzae Towards Barley-Microbiome Derived Bacteria.},
journal = {Molecular plant-microbe interactions : MPMI},
volume = {},
number = {},
pages = {},
doi = {10.1094/MPMI-11-25-0158-FI},
pmid = {41405456},
issn = {0894-0282},
abstract = {The composition of the plant microbiome is shaped not only by the host plant and abiotic environmental factors, but also by inter-microbial cooperation and competition. Plant pathogens, therefore must remain competitive within the microbiome in order to establish themselves within their host niche. Magnaporthe oryzae, the blast-disease causing ascomycete fungus, is able to infect economically important hosts including rice, barley and wheat. We sought to identify barley associated bacteria able to antagonize M. oryzae and to characterize the fungal transcriptional responses following confrontation to reveal antimicrobial self-defence mechanisms. From a library of 25 barley-associated bacteria, two strains were identified as moderate and strong antagonists. Through RNA-seq, we demonstrate large-scale transcriptional changes in M. oryzae during their confrontation. Common responses to both strains included an over-representation of genes encoding drug efflux transporters, hydrolases, signalling components, DNA repair and oxidative stress responses. This indicates M. oryzae prioritizes stress adaptation and detoxification. We did not observe a significant increase in secreted proteins of M. oryzae as part of the common response. However, significant strain-specific changes were observed, indicating that independent of host plant, specific microbial antagonists are perceived by M. oryzae leading to altered secretome profiles. Understanding these adaptive strategies provides insight into antimicrobial resistance mechanisms with respective parallels to drug- and fungicide resistance mechanisms in the medical and agricultural context. Additionally, our study provides potential targets on the plant pathogen side to weaken its fitness within the plant microbiome.},
}

@article {pmid41405404,
year = {2025},
author = {Levy, S and McCauley, KE and Strength, R and Robbins, ES and Chen, Q and Namasivyam, S and Maxwell, G and Hourigan, SK},
title = {Colibactin genes are highly prevalent in the developing infant gut microbiome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2604874},
doi = {10.1080/19490976.2025.2604874},
pmid = {41405404},
issn = {1949-0984},
mesh = {Humans ; *Polyketides/metabolism ; *Gastrointestinal Microbiome/genetics ; *Peptides/genetics/metabolism ; Infant ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Infant, Newborn ; Female ; Male ; },
abstract = {Early-life exposure to colibactin-producing pks+ gut bacteria is hypothesized to imprint mutations on the colorectal epithelium, increasing the risk of colorectal cancer later in life. We demonstrate an extremely high prevalence of pks+ bacteria (>50% of infants) during the first 2 y of life, suggesting carriage is likely normal during early-life microbiome development. Further investigation is required to understand the circumstances in which carriage can lead to mutagenesis.},
}

Humans
*Polyketides/metabolism
*Gastrointestinal Microbiome/genetics
*Peptides/genetics/metabolism
Infant
*Bacteria/genetics/classification/isolation & purification/metabolism
Infant, Newborn
Female
Male

@article {pmid41405322,
year = {2025},
author = {Wang, W and Wu, J},
title = {Global clinical landscape of microbiome modulation therapies for non-alcoholic fatty liver disease exploring the role of the gut-liver Axis.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000004431},
pmid = {41405322},
issn = {1743-9159},
}

@article {pmid41405260,
year = {2025},
author = {Liu, H and Song, H and Pu, L and Zhao, J and Yin, X and Liu, B and Zheng, X and Zhu, Y and Yang, J},
title = {Multi-omics analysis reveals microbiome-associated subtypes of esophageal cancer with distinct immune profiles and therapeutic responses.},
journal = {International journal of surgery (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/JS9.0000000000004503},
pmid = {41405260},
issn = {1743-9159},
abstract = {BACKGROUND: Esophageal cancer is an aggressive malignancy with poor prognosis. Comprehensive molecular characterization is crucial for identifying novel therapeutic targets and improving outcomes.

METHODS: We performed an integrative multi-omics analysis of esophageal tumors, profiling the microbiome, transcriptome, epigenome, and clinical data. Unsupervised consensus clustering using ten different algorithms identified robust molecular subtypes, which were further characterized by functional enrichment analyses and experimental validation to uncover subtype-specific features and therapeutic vulnerabilities.

RESULTS: Microbiome profiling revealed distinct taxonomic differences between normal and tumor tissues, with Proteobacteria and Pseudomonas being more abundant in tumors. Two molecular subtypes, C1 (n = 92) and C2 (n = 57), were identified, exhibiting unique clinical, prognostic, and molecular features. Subtype C2 showed higher mutation burden, increased abundance of Pseudomonas species, and an immunologically active microenvironment, with greater infiltration of effector memory CD4 + T cells, regulatory T cells, and M2 macrophages. Subtype C2 also exhibited higher predicted immunotherapy response rates and lower T cell exclusion scores. In contrast, subtype C1 was characterized by elevated expression of specific RNAs and DNA methylation, as well as higher sensitivity to chemotherapy agents and EGFR inhibitors, which was experimentally validated using representative cell lines. Notably, STAT3 inhibitors potentiated the efficacy of PD-L1 blockade in subtype C2 cells by enhancing apoptosis, downregulating PD-L1 expression, suppressing EMT, and attenuating invasion and migration.

CONCLUSION: This multi-omics analysis reveals esophageal cancer's molecular heterogeneity and identifies microbiome and immune signatures associated with prognosis and therapeutic response, providing a framework for developing personalized treatments targeting specific subtypes.},
}

@article {pmid41405224,
year = {2025},
author = {Kok, CR and Morrison, MD and Thissen, JB and Mabery, S and Carson, ML and Kimbrel, JA and Bennett, JW and Tribble, DR and Millar, EV and Mende, K and Be, NA},
title = {Microbiome dynamics in the congregate environment of U.S. Army Infantry training.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0047425},
doi = {10.1128/spectrum.00474-25},
pmid = {41405224},
issn = {2165-0497},
abstract = {Within military training and operational environments, individuals from diverse backgrounds share common spaces, follow structured routines and diets, and engage in physically demanding tasks. While there has been interest in leveraging microbiome features to predict and improve military health and performance, the longitudinal convergence of microbiomes in such constrained environments has not been established. To assess the degree of microbiome convergence, we performed shotgun metagenomic sequencing on swab samples from a military trainee cohort. Samples were taken across four different body sites, three timepoints, and two spatially distinct platoons. We observed evidence of convergence in one platoon, whereby similarity in microbiome composition increased over time, with numerous differentially abundant species. We found no indication of strain transfer between individuals, suggesting that convergence was influenced by external environmental factors, diet, and lifestyle. Microbial shifts observed in the convergence process included a decrease in fungal species, such as Malassezia restricta in nasal cavities, and a decrease in Prevotella species at inguinal regions across time. Shifts in multiple Corynebacterium species were also observed with varying magnitudes depending on the body site. Overall, we provide preliminary evidence of convergence of host microbial communities in military-associated environments that were distinguishable using shotgun metagenomic sequencing approaches. The data presented here on microbiome convergence, dynamics, and stability may inform risk-based mitigation in congregate military settings facilitating development of targeted microbial, dietary, or other interventions to optimize health and performance of military populations.IMPORTANCEMicrobiome convergence in deployed environments could impact the health and readiness of the warfighter, with potential implications for susceptibility to biothreats. This study describes a shotgun metagenomic approach used to study the microbiomes of swab samples collected at different body sites in a military trainee cohort. The results presented here provide a foundation for developing future microbiome-based interventions and protocols to enhance operational readiness.},
}

@article {pmid41405172,
year = {2026},
author = {Molina-Viramontes, JP and Gómez-Acata, ES and Hereira-Pacheco, S and Estrada-Torres, A and Navarro-Noya, YE},
title = {Comparison of Methods to Characterize the Microbiota of Myxomycete Plasmodia.},
journal = {The Journal of eukaryotic microbiology},
volume = {73},
number = {1},
pages = {e70058},
doi = {10.1111/jeu.70058},
pmid = {41405172},
issn = {1550-7408},
support = {CBF2023-2024-1480//Secretaría de Ciencia, Humanidades, Tecnología e Innovación/ ; },
mesh = {*Microbiota ; *Myxomycetes/microbiology/genetics/classification ; *Bacteria/genetics/classification/isolation & purification ; DNA, Bacterial/genetics/isolation & purification ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Myxomycetes are valuable models for studying interactions between single-celled eukaryotes and bacteria; however, little is known about their microbiota or optimal DNA extraction methods. We analyzed the bacterial community of Claustria didermoides plasmodia using commercial and noncommercial DNA extraction methods. A total of 218 amplicon sequence variants (ASVs) were identified, dominated by Pseudomonadota (78%), Bacillota (10%), and Actinomycetota (9%). Achromobacter denitrificans was the most abundant species, with 3-7 codominant ASVs, including opportunistic pathogens. The commercial kit captured higher diversity, while the noncommercial method favored Gram-negatives and preserved DNA integrity longer when phenol was added.},
}

*Microbiota
*Myxomycetes/microbiology/genetics/classification
*Bacteria/genetics/classification/isolation & purification
DNA, Bacterial/genetics/isolation & purification
Phylogeny
Sequence Analysis, DNA

@article {pmid41404904,
year = {2025},
author = {Jensen, EEB and Jespersen, ML and Svendsen, CA and Sonda, T and Otani, S and Aarestrup, FM},
title = {Tanzanian goat gut microbiomes adapt to roadside pollutants and environmental stressors.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0203625},
doi = {10.1128/spectrum.02036-25},
pmid = {41404904},
issn = {2165-0497},
abstract = {The impact of environmental pollution reaching and affecting the gut microbiome is rising. Pollution from vehicle emissions can release compounds harmful to both animal and environmental health, and their effect on the host microbiome is yet to be determined, particularly in understudied locations. Here, we have investigated the potential effect of environmental pollution on the gut microbiome of Tanzanian goats grazing near a heavily trafficked road compared to goats living in a more rural setting. We identified 1,468 metagenome-assembled genomes (MAGs), of which 768 were unidentified species, and created a genomic database to which 52% of the bacterial community could be assigned. We find significant differences in the composition of the bacterial communities and resistomes between rural and road-exposed goats, but not a major difference in antimicrobial resistance (AMR) abundance. Genes involved in pollutant biodegradation were significantly more abundant in the microbiome of goats grazing along the road. This includes genes involved in degradation of naphthalene and toluene (both present in motor vehicle exhaust), as well as the detoxification enzyme, glutathione S-transferase. These findings suggest living near a heavily trafficked road selects for xenobiotic degrading functions within the goat gut microbiome, which might aid the host in detoxification of these compounds.IMPORTANCETo the best of our knowledge, this is the first study on the potential effect of environmental pollution on the gut microbiome of Tanzanian goats. Using shotgun metagenomics, we compare the gut microbiome of goats living near a heavily-trafficked road in Kigoma, Tanzania, with the gut microbiome of goats living in a rural area. We find that genes involved in pollutant biodegradation were significantly more abundant in the gut microbiome of the road-exposed goats, which potentially aids pollutant detoxification in the host. The effect of environmental pollution on the gut microbiome remains poorly understood; however, with this study, we link a potential effect of environmental pollution to changes in the gut microbiome of Tanzanian goats.},
}

@article {pmid41404876,
year = {2025},
author = {Van Beeck, W and Eilers, T and Smets, W and Delanghe, L and Vandenheuvel, D and Tuyaerts, I and Van Malderen, J and Ahannach, S and Michiels, K and Dricot, C and Van de Vliet, N and Huys, AJ and De Boever, P and Lebeer, S},
title = {Sonmat, a citizen-science enabled Kimjang kimchi case study on associations between hand and kimchi microbiota.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0036825},
doi = {10.1128/spectrum.00368-25},
pmid = {41404876},
issn = {2165-0497},
abstract = {UNLABELLED: Kimjang kimchi is traditionally made in Korea in autumn to preserve vegetables during colder winter times after the harvest. Kimjang is an important societal tradition in which families and communities come together to process vegetables, such as cabbage, into kimchi. The origin of the microorganisms that contribute to the flavor and safety during fermentation is still unclear. Although bacteria present on the raw ingredients are considered to be important colonizers of the fermentation, in Korean culture, the term "Sonmat" is often used, which literally translates into "hand flavor," suggesting a role for hand microbiota in the kimchi fermentation. In this citizen-science project, we investigate the impact of the hand microbiome on kimchi fermentation during the Sonmat festival organized in Belgium. The kimchi fermentations contained mainly lactic acid bacteria belonging to the genera Leuconostoc, Weissella, and Latilactobacillus. The hand microbiota was characterized by the presence of Staphylococcus, Corynebacterium, Micrococcus, and Enhydrobacter. Associations were found between the relative abundance of Staphylococcus on the hand and the relative abundance of Latilactobacillus and Leuconostoc found in kimchi, despite limited overlap between the hand and the kimchi microbiome. In addition, different microbiota were found to dominate the kimchi made following the traditional group Kimjang practices compared with individually prepared kimchi. These findings pave the way for future research into how traditional practices and the skin microbiome influence the unique qualities of kimchi, offering exciting possibilities for enhancing fermentation processes and cultural food heritage through citizen science.

IMPORTANCE: Vegetable fermentation has been a staple of human culture for centuries, with deeply rooted traditions behind it. However, the effects of these traditional practices on the microbes in the final fermented product, and their origin, are often not understood. By using participatory citizen-science approaches, it is possible to study these important foods while preserving the authenticity and integrity of the traditional fermentation practices that define them. The results obtained from our citizen-science case study support the importance of exploring traditional fermentation practices and their effect on microbial and sensory properties of fermented foods. Additionally, our case study found associations between microbiota present on the hand and microbiota important in the early successional stage of kimchi fermentation.},
}

@article {pmid41404617,
year = {2025},
author = {Coleman, I and Mametyarova, N and Zaznaev, A and Cai, P and Yu, L and Meydan, Y and Litman, A and Sharma, A and He, L and Simkhovich, A and Seeram, D and Park, H and Nobel, YR and Kav, AB and Pe'er, I and Uhlemann, AC and Korem, T},
title = {Comparative metagenomics using pan-metagenomic graphs.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.24.690211},
pmid = {41404617},
issn = {2692-8205},
abstract = {Identifying microbial genomic factors underlying human phenotypes is a key goal of microbiome research. Sequence graphs are a highly effective tool for genome comparisons because they enable high-resolution de novo analyses that capture and contextualize complex genomic variation. However, applying sequence graphs to complex microbial communities remains challenging due to the scale and complexity of metagenomic data. Existing multi-sample sequence graphs used in these settings are highly complex, computationally expensive, less accurate than single-sample alternatives, and often involve arbitrary coarse-graining. Here, we present copangraph, a multi-sample sequence-graph-based analysis framework for comprehensive comparisons of genomic variation across metagenomes. Copangraph uses a novel homology-based graph, which provides both non-arbitrary, evolutionary-motivated grouping of sequences into the same node as well as flexibility in the scale of variation represented by the graph. Its construction relies on hybrid coassembly, a new coassembly approach in which single-sample graphs are first constructed separately and are then merged to create a multi-sample graph. We also present an algorithm that uses paired-end reads to improve detection of contiguous genomic regions, increasing accuracy. Our results demonstrate that copangraph captures sequence and variant information more accurately than alternative methods, provides graphs that are more suitable for comparative analysis than de Bruijn graphs, and is computationally tractable. We show that copangraph reflects meaningful metagenomic variation across diverse scenarios. Importantly, it enables significantly better performance than other metagenomic representations when predicting the gut colonization trajectories of Vancomycin-resistant Enterococcus. Our results underscore the value of our multi-sample, graph-based framework for comparative metagenomic analyses.},
}

@article {pmid41404442,
year = {2025},
author = {Lee, M and Hwang, SY and Wi, K and Kim, J and Lee, MH and Hwang, IH},
title = {Pharmacological evaluation of 1-acetyl-β-carboline, a naturally occurring compound with anti-skin cancer potential.},
journal = {Molecular therapy. Oncology},
volume = {33},
number = {4},
pages = {201093},
pmid = {41404442},
issn = {2950-3299},
abstract = {The human microbiome comprises microbial communities that reside in the human body and contribute to host health through molecular mediators. Lactobacillus spp. are frequently used as probiotics to restore microbial balance, and L. gasseri has been reported to exert a wide range of beneficial effects. In this study, 1-acetyl-β-carboline (ABC) was identified in L. gasseri cultures and subsequently synthesized via the Pictet-Spengler reaction followed by palladium-catalyzed oxidation. ABC exhibited significant anticancer activity by reducing colony formation and growth of epidermal growth factor-induced JB6 cells and by inhibiting the proliferation of SK-MEL-5 and SK-MEL-28 melanoma cells. Mechanistic studies revealed that ABC induced G2/M phase cell-cycle arrest and promoted apoptosis by regulating related markers, including p27 and caspases-3 and -7. Additionally, ABC significantly inhibited the mitogen-activated protein kinase kinase (MEK)-extracellular signal-regulated kinase (ERK) signaling pathway by reducing phosphorylated MEK and phosphorylated ERK levels. ABC also downregulated cyclooxygenase-2 expression, targeting inflammation-related pathways in melanoma cells. In a mouse model, ABC effectively mitigated 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced epidermal hyperplasia and reduced inflammation. These findings highlight the pharmacological significance of ABC, independent of its origin, and suggest that this naturally occurring compound possesses preventive and therapeutic potential against skin cancer.},
}

@article {pmid41404370,
year = {2025},
author = {Liu, M and Wu, M and Tang, Y and Lin, Z and Ye, C and Huang, X and Zhou, L and Lin, Q and Zheng, D and Lu, Y},
title = {Correlation between oral microbial characteristics and overall bone density of Postmenopausal women based on macrogenomic analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1663645},
pmid = {41404370},
issn = {2235-2988},
mesh = {Humans ; Female ; *Bone Density ; Middle Aged ; Saliva/microbiology ; *Osteoporosis, Postmenopausal/microbiology ; *Postmenopause ; *Microbiota ; Dental Plaque/microbiology ; *Mouth/microbiology ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; Absorptiometry, Photon ; },
abstract = {BACKGROUND: Postmenopausal osteoporosis (PMO), a prevalent bone disease triggered by estrogen deficiency - induced bone mass reduction and deterioration of bone tissue microarchitecture, escalates the risk of fragility fractures. Recent research has highlighted the pivotal role of oral and gut microbiota in PMO development, giving rise to the "oral - gut - bone axis" concept.

METHODS: A total of 21 postmenopausal women, aged 50 - 60, were recruited for the study. Based on bone mineral density (BMD) measurements from dual - energy X - ray absorptiometry (DXA), participants were divided into osteopenia, osteoporosis, and healthy groups. Saliva and dental plaque samples were collected for metagenomic sequencing to analyze microbial diversity and community composition, with differences identified via LEfSe analysis. KEGG pathway analysis was used to reveal variations in microbial functions. Based on these analyses, predictive models for bone density status were constructed using LASSO regression and random forest algorithms.

RESULTS: Significant differences in salivary microbial community structures were found between the osteoporosis and healthy groups (P = 0.041). LEfSe analysis revealed higher abundance of Aggregatibacter, Haemophilus haemolyticus, Haemophilus sputorum, Pasteurellaceae, Neisseria elongata, Aggregatibacter segnis, and Aggregatibacter aphrophilus in the osteopenia group, and higher abundance of Streptococcus pneumoniae and Haemophilus paraphrohaemolyticus in the osteoporosis group compared to the healthy group. The random forest models for osteopenia vs. healthy and osteoporosis vs. healthy yielded AUC values of 0.82 and 0.74, respectively, suggesting potential predictive capability, though further validation in larger cohorts is needed to confirm their generalizability. Functional analysis using LEfSe identified differential KEGG pathways, including glycan biosynthesis and metabolism in cancer, choline metabolism in cancer, and the cGMP-PKG signaling pathway.

CONCLUSION: This exploratory study utilized metagenomic sequencing to analyze the relationship between oral microbiota and PMO while controlling for key confounders. We identified significant compositional and functional alterations in the oral microbiome associated with bone mineral density status, including specific bacterial species showing marked intergroup differences. A model based on differential microbial features exhibited preliminary discriminative capacity, and functional analysis suggested involvement of inflammatory and metabolic pathways. These findings provide initial evidence linking oral microbiota to PMO.},
}

Humans
Female
*Bone Density
Middle Aged
Saliva/microbiology
*Osteoporosis, Postmenopausal/microbiology
*Postmenopause
*Microbiota
Dental Plaque/microbiology
*Mouth/microbiology
Metagenomics
*Bacteria/classification/genetics/isolation & purification
Absorptiometry, Photon

@article {pmid41404120,
year = {2025},
author = {Kim, RY and Kuraji, R and Kapila, YL},
title = {Systemic Health Implications of the Leaky Barriers within the Oral-Gut-Brain Axis and its Pathways of Communication.},
journal = {European Medical Journal (Chelmsford, England)},
volume = {10},
number = {1},
pages = {47-50},
pmid = {41404120},
issn = {2397-6764},
}

@article {pmid41403940,
year = {2025},
author = {Riebelmann, J and Kienzle, N and Sauer, B and Schittek, B},
title = {Commensal Staphylococci attenuate Staphylococcus aureus skin colonization and inflammation via AHR-dependent signaling.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1726557},
pmid = {41403940},
issn = {1664-3224},
mesh = {Humans ; *Receptors, Aryl Hydrocarbon/metabolism/immunology ; Signal Transduction ; *Staphylococcus aureus/immunology ; *Skin/microbiology/immunology/metabolism ; Keratinocytes/immunology/microbiology/metabolism ; Dermatitis, Atopic/immunology/microbiology ; Inflammation/immunology ; *Staphylococcal Skin Infections/immunology/microbiology/metabolism ; Culture Media, Conditioned/pharmacology ; *Staphylococcus/immunology ; Staphylococcus epidermidis ; Microbiota ; *Basic Helix-Loop-Helix Transcription Factors/metabolism ; },
abstract = {INTRODUCTION: Staphylococcus aureus is the leading cause of bacterial skin infections in several inflammatory skin diseases, however, is rarely detected on healthy skin. Skin barrier defects, such as in atopic dermatitis, promote S. aureus colonization by yet unknown mechanism. In our previous work we found that in healthy skin commensal staphylococci including Staphylococcus epidermidis and Staphylococcus lugdunensis (SL) protect against S. aureus skin colonization, however, the microbiome-mediated protection is lost in inflammatory skin. Here, we investigated how microbiome-derived factors contribute to skin defense under homeostatic and inflammatory conditions.

METHODS: We examined how bacterial conditioned media (BCM) from S. epidermidis and S. lugdunensis influence immune responses in primary human keratinocytes, human skin explants, and 3D skin reconstructs. Immune signaling was assessed using LEGENDplex cytokine profiling, RT2 Profiler PCR arrays, and western blotting. To investigate how BCM pretreatment limits S. aureus colonization, we performed inhibitor studies with a focus on aryl hydrocarbon receptor (AHR) signaling. The effects of BCM under inflammatory conditions were analyzed in tape-stripped human skin explants and 3D skin models with an atopic dermatitis-like phenotype.

RESULTS: We show that released factors from SE and SL reduce S. aureus skin colonization by inducing antimicrobial peptides (AMPs) and suppressing inflammatory responses in the skin. Both, factors released by SE and SL, limit S. aureus-induced immune activation in the skin by dampening inflammatory signaling, reducing reactive oxygen species, and suppressing expression of danger-associated molecular patterns (DAMPs). We show that this anti-inflammatory effect is mediated by activation of aryl hydrocarbon receptor (AHR) signaling in keratinocytes. Mechanistically, SE and SL membrane vesicles are involved in activating AHR signaling in keratinocytes via direct vesicle-cell contact as well as by bacterial tryptophan metabolites. This protective effect is lost in inflamed skin, where it instead exacerbated inflammation due to impaired AHR activity in inflamed skin. Interestingly, co-treatment of human AD-like skin equivalents with released SE factors together with an AHR ligand effectively reduces S. aureus colonization pointing out a potential novel AHR- and microbiome-based therapeutic strategy in AD.

DISCUSSION: Together, these findings highlight a context-dependent role of microbiome-derived factors in shaping cutaneous immunity and underscore the therapeutic potential of restoring AHR signaling to enhance the skin's defense against S. aureus, particularly in inflammatory disorders such as AD.},
}

Humans
*Receptors, Aryl Hydrocarbon/metabolism/immunology
Signal Transduction
*Staphylococcus aureus/immunology
*Skin/microbiology/immunology/metabolism
Keratinocytes/immunology/microbiology/metabolism
Dermatitis, Atopic/immunology/microbiology
Inflammation/immunology
*Staphylococcal Skin Infections/immunology/microbiology/metabolism
Culture Media, Conditioned/pharmacology
*Staphylococcus/immunology
Staphylococcus epidermidis
Microbiota
*Basic Helix-Loop-Helix Transcription Factors/metabolism

@article {pmid41403899,
year = {2025},
author = {Shi, W and Wu, L and Qin, Q and Li, Y and Chen, W},
title = {Research progress on the role of microbiome-immune-neurotransmitter network in post-stroke sleep disorders.},
journal = {Frontiers in aging neuroscience},
volume = {17},
number = {},
pages = {1694709},
pmid = {41403899},
issn = {1663-4365},
abstract = {Post-stroke sleep disorders, as a significant complication affecting patient rehabilitation, are closely associated with dysregulation of the microbiome-immune-neurotransmitter network. Following stroke, activation of the hypothalamic-pituitary-adrenal axis and sympathetic nervous system triggers intestinal barrier disruption (reduced tight junction proteins and intestinal permeability) along with microbial imbalance (decreased Bifidobacterium and increased Enterobacteriaceae). Reduced short-chain fatty acids and lipopolysaccharide (LPS) translocation exacerbate systemic inflammatory responses and neurotransmitter imbalances (inhibited serotonin synthesis and excitotoxic glutamate production). These changes further disrupt circadian regulation by the hypothalamic suprachiasmatic nucleus, leading to reduced REM sleep and disrupted slow-wave sleep architecture. Future research should prioritize interventional strategies targeting the gut microbiota, such as probiotics, prebiotics, and fecal microbiota transplantation, integrated with multi-omics technologies and neural circuit modulation approaches, to elucidate the spatiotemporal dynamics of the microbiome-immune-neurotransmitter network and provide a theoretical basis for clinical translation. Restoring brain-gut axis homeostasis is expected to improve post-stroke sleep disorders and neurological functional outcomes in patients.},
}

@article {pmid41403886,
year = {2025},
author = {Tarracchini, C and Bottacini, F and Mancabelli, L and Lugli, GA and Turroni, F and van Sinderen, D and Ventura, M and Milani, C},
title = {Approaches to dissect the vitamin biosynthetic network of the gut microbiota.},
journal = {Microbiome research reports},
volume = {4},
number = {4},
pages = {37},
pmid = {41403886},
issn = {2771-5965},
abstract = {B-group vitamins and vitamin K are essential micronutrients required for numerous cellular processes in both microbial and human physiology. While traditionally considered to originate predominantly from dietary sources, the biosynthetic capacity of the human gut microbiota has recently been recognized as a valuable, though historically underappreciated, endogenous source of these vitamins. In particular, the microbial contribution to the host vitamin pool is increasingly acknowledged as a functionally relevant aspect of vitamin homeostasis, especially in the colon, where microbiota-derived vitamins may be absorbed via specific transport mechanisms. This review provides a comprehensive overview of our current understanding of the biosynthesis of B-group vitamins and vitamin K by human gut-associated bacteria, with particular emphasis on key methodologies employed to assess if, how and to what extent members of the gut microbiota supply their host with such micronutrients. Through an integrated overview of available evidence, we highlight both the progress made and the outstanding challenges in elucidating the microbial contribution to the host vitamin metabolism.},
}

@article {pmid41403881,
year = {2025},
author = {Sun, Y and Huang, Y and Li, R and Zhang, J and Fan, X and Su, X},
title = {Benchmarking and optimizing microbiome-based bioinformatics workflow for non-invasive detection of intestinal tumors.},
journal = {Microbiome research reports},
volume = {4},
number = {4},
pages = {43},
pmid = {41403881},
issn = {2771-5965},
abstract = {Background: The human gut microbiome is closely linked to disease states, offering substantial potential for novel disease detection tools based on machine learning (ML). However, variations in feature types, data preprocessing strategies, feature selection strategies, and classification algorithms can all influence the model's predictive performance and robustness. Methods: To develop an optimized and systematically evaluated workflow, we conducted a comprehensive evaluation of ML methods for classifying colorectal cancer and adenoma using 4,217 fecal samples from diverse global regions. The area under the receiver operating characteristic curve was used to quantify model performance. We benchmarked 6,468 unique analytical pipelines, defined by distinct tools, parameters, and algorithms, utilizing a dual validation strategy that included both cross-validation and leave-one-dataset-out validation. Results: Our findings revealed that shotgun metagenomic (WGS) data generally outperformed 16S ribosomal RNA gene (16S) sequencing data, with features at the species-level genome bin, species, and genus levels demonstrating the greatest discriminatory power. For 16S data, Amplicon Sequence Variant-based features yielded the best disease classification performance. Furthermore, the application of specific feature selection tools, such as the Wilcoxon rank-sum test method, combined with appropriate data normalization, also optimized model performance. Finally, in the algorithm selection phase, we identified ensemble learning models (eXtreme Gradient Boosting and Random Forest) as the best-performing classifiers. Conclusion: Based on the comprehensive evaluation results, we developed an optimized Microbiome-based Detection Framework (MiDx) and validated its robust generalizability on an independent dataset, offering a systematic and practical framework for future 16S and WGS-based intestinal disease detection.},
}

@article {pmid41403880,
year = {2025},
author = {Gargari, G and Meroño, T and Peron, G and Del Bo', C and Marino, M and Cherubini, A and Andres-Lacueva, C and Kroon, PA and Riso, P and Guglielmetti, S},
title = {Effect of a polyphenol-rich dietary pattern on subjects aged ≥ 60 years with higher levels of inflammatory markers: insights into microbiome and metabolome.},
journal = {Microbiome research reports},
volume = {4},
number = {4},
pages = {38},
pmid = {41403880},
issn = {2771-5965},
abstract = {Background: Aging may be associated with low-grade chronic inflammation ("inflammaging") and gut microbiome alterations. Dietary polyphenols have been proposed as modulators of these processes. This study aimed to explore the effects of a polyphenol-rich diet (PR-diet) on inflammatory markers, gut microbiota, and metabolomic profiles in subjects aged ≥ 60 years stratified by baseline inflammation levels. Methods: In this post-hoc analysis of the MaPLE (Microbiome mAnipulation through Polyphenols for managing Leakiness in the Elderly) randomized crossover trial, 50 subjects aged ≥ 60 years were categorized into two subgroups: high inflammation (cH) and low inflammation (cL). Participants received a PR-diet or a control diet for 8 weeks, with a washout period in between. Fecal, blood, and urine samples were analyzed using shallow shotgun metagenomics and untargeted metabolomics. Results: The PR-diet was associated with a significant reduction in key inflammatory markers [e.g., interleukin-6 (IL-6), C-reactive protein] in the cH group. Distinct microbial shifts were observed, including an increase in Blautia and Dorea and a modest improvement in microbial diversity in cH subjects. Metabolomic analysis revealed group-specific changes, notably in polyphenol-derived metabolites. Conclusion: These findings suggest that PR-diets may beneficially modulate inflammation and the gut microbial ecosystem in subjects aged ≥ 60 years with elevated baseline inflammation. Stratification by inflammatory status may improve the targeting and personalization of dietary interventions to support healthy aging.},
}

@article {pmid41403706,
year = {2025},
author = {Ghisleni, G and Armanni, A and Fumagalli, S and Rosatelli, A and Bacchi, YM and Barillari, C and Battista, DA and Benocci, M and Brunelli, A and Cammarano, F and Bovolini, G and Capuano, F and Bulla, N and Colombo, A and Colombo, L and Corneo, L and Evangelista, D and Giorgetti, P and Marin, G and Meziu, A and Riva, M and Rizzo, D and Romano, S and Ronchi, S and Rossi, R and Volpi, R and Zanotti, M and Zenaro, M and Franzetti, A and Casiraghi, M and Bruno, A},
title = {The Bicocca sampling days model: a participatory citizen science approach to environmental microbiome research and education.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf220},
pmid = {41403706},
issn = {2730-6151},
abstract = {Environmental microbiota are essential yet often overlooked, with urbanization driving microbial diversity loss and diseases of civilization. Public misconceptions, exacerbated by COVID-19, have widened the gap between microbiologists and society, highlighting the need for science-society integration. The Bicocca Sampling Days (BSDs) model offers a reproducible "citizen science" framework integrating research, education, and public engagement through large-scale microbiome sampling. Tested while assessing environmental microbiomes in different urbanized outdoors, 76 undergraduates participated in four sampling events, collecting 2429 samples in 8 h of effective sampling, achieving over than 303 samples/hour in 29 288.74 m[2]. Manual metadata curation revealed only 0.58% critical errors and no data loss, emphasizing the effectiveness of structured submission forms in ensuring data quality. Educational outcomes, assessed through a validated survey, significant gains in participants' perceived skills, understanding, and knowledge of microbiome sampling compared to non-participants. The BSDs model, including a step-by-step guide, illustrated protocol, and templates, is freely available for replication. Our findings demonstrate that citizen science can rival or complement traditional microbiome research in efficiency, scale, and data quality while broadening accessibility. BSDs offers a scalable tool to advance educational and societal, empower participation, and support informed decision-making.},
}

@article {pmid41403704,
year = {2025},
author = {Yu, QY and Liu, X and Yao, H and Lü, PP and Yang, GJ and Lü, XT and Han, XG and Guo, LD and Huang, Y},
title = {The adaptability of grassland soil microbiomes to resource and stress shifts is mainly accomplished by niche conservatism under nitrogen deposition.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf215},
pmid = {41403704},
issn = {2730-6151},
abstract = {Atmospheric nitrogen (N) deposition usually alters the ratio of resources to stress in terrestrial ecosystems and has important impacts on soil microbiomes. To elucidate the adaptability of soil microbiomes under N deposition scenarios, we conducted a 6-year N addition experiment in a temperate grassland in Inner Mongolia, applying different levels of ammonium nitrate (AN) and urea (AU) to form different resource-to-stress ratio. Our results reveal that the inborn high yield (Y)-resource acquisition (A)-stress tolerance (S) life history strategies of soil microbiomes collectively drive their adaptability to resources and stress under N deposition. Enriched taxa under AN treatment mainly belonged to Actinomycetota and Chloroflexota with Y and S strategies, while those under AU mainly belonged to Pseudomonadota with A and S strategies. Functional preference analysis indicated that bacterial phyla maintained consistent Y-A-S life history strategies across AN and AU treatments. Moreover, strong purifying selection restricted the pace of adaptive evolution, and horizontal gene transfer expanded the functional repertoire in a complementary rather than essential manner. Thus, the adaptation of microbiomes to shifting resources and stress under N deposition scenarios is mainly accomplished by niche conservatism ("move") rather than niche evolution ("evolve"). Our results support the point that it may be easier for microbial species to move into a befitting niche than to evolve to acclimate a new environment.},
}

@article {pmid41403646,
year = {2025},
author = {Pagano, F and Bemis, DH and Rehman, R and Shapiro, JM and Belenky, P},
title = {Differential impacts of hemin and free iron on amoxicillin susceptibility in ex vivo gut microbial communities.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1629464},
pmid = {41403646},
issn = {1664-302X},
abstract = {INTRODUCTION: The rise of antibiotic-resistant infections worldwide has created a need to enhance the efficacy of existing antibiotics. Modification of metabolism has been shown to potentiate antibiotic lethality. In this study, we employed a novel ex vivo microbiome culture approach to study the effects of different forms of iron on amoxicillin susceptibility.

METHODS: Synthetic and human stool-derived microbiota were cultured and treated with amoxicillin, with growth monitored by optical density. These samples were sequenced using an Oxford nanopore long-read 16S rRNA V4-V9 approach and computationally defined using the Emu algorithm. The validity of this pipeline was confirmed with consortia, murine cecal content, and a human stool sample. The stool-derived community was then cultured for 24 h with ranging concentrations of either hemin, FeSO4, or FeCl3 and concurrent amoxicillin dosage, then profiled to identify the effects of different forms of iron on amoxicillin susceptibility.

RESULTS: Alpha diversity, beta diversity, and normalized relative abundances confirmed the efficacy of the selected ex vivo pipeline, allowing for ~77% species retention over 24 h. Treatment of communities with hemin protected Bacteroides, Escherichia-Shigella, Parabacteroides, and Parasutterella against amoxicillin, while two forms of free iron did not.

DISCUSSION: This ex vivo pipeline enables reproducible assessment of how metabolic modulators like hemin alter amoxicillin susceptibility, highlighting a link between iron-sequestering genera and antibiotic-protection. Future mechanistic insights may support hemin-based strategies to boost antibiotic efficacy.},
}

@article {pmid41403645,
year = {2025},
author = {Lei, H and Li, Z and Deng, J and Lei, H and Li, H and Ding, Z},
title = {Electroacupuncture pretreatment ameliorates anesthesia and surgery-induced cognitive dysfunction in aged rats: insights from gut microbiota modulation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1642337},
pmid = {41403645},
issn = {1664-302X},
abstract = {OBJECTIVE: This study aimed to investigate the effects of electroacupuncture (EA) on postoperative cognitive dysfunction (POCD) and gut microbiota in aged rats anesthetized with propofol.

METHODS: Forty 18-months-old male SD rats were randomly divided into four groups: Sham, Model (MD), Sham Electroacupuncture (JE), and Electroacupuncture (EA), with 10 rats in each group. The Sham group underwent a skin incision without surgery, while the MD, JE, and EA groups received propofol anesthesia followed by right tibial surgery. The EA group received electroacupuncture at Baihui, Shenmen, and bilateral Zusanli points for 5 days prior to surgery, while the JE group received acupuncture without electrical stimulation. Behavioral tests, including the Morris water maze and open field tests, were conducted at 1-, 2-, and 3-weeks post-surgery to assess cognitive function. Gut microbiota composition was analyzed using second-generation sequencing.

RESULTS: At 1-week post-surgery, the MD, JE, and EA groups showed longer latencies and fewer crossings in the behavioral tests. However, at 3- and 4-weeks post-surgery, the EA group exhibited significantly reduced latency and increased crossing times compared to the MD and JE groups. Gut microbiome analysis revealed that the EA group had a higher relative abundance of Bacteroidetes and Proteobacteria, and a reduced relative abundance of Unclassified Lactobacillaceae compared to the MD and JE groups.

CONCLUSION: Electroacupuncture was associated with improved postoperative cognitive function in aged rats after propofol anesthesia and tibial surgery. These effects were accompanied by alterations in gut microbiota composition, suggesting a possible link with the gut-brain axis, although causality remains to be established.},
}

@article {pmid41403643,
year = {2025},
author = {Wang, B and Zhang, Y and Li, J and Wu, M and Shi, Y and Sun, X and Xiao, X and Zhang, P and Shi, Y and Li, Y and Tian, H},
title = {Revealing dietary habits and intestinal microbiome composition of the Beijing swift (Apus apus pekinensis) through regurgitated pellets and fecal samples.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1693396},
pmid = {41403643},
issn = {1664-302X},
abstract = {INTRODUCTION: The Beijing swift, an important insectivorous bird, is a key protected wild animal in Beijing. Current research on this species primarily focuses on distribution surveys and population dynamics, while systematic studies on its diet and intestinal microbiome composition remain lacking, a knowledge gap that constrains in-depth understanding of its ecological adaptability.

METHODS: This study integrated DNA barcoding and high-throughput 16S rRNA gene sequencing to systematically analyze regurgitated pellets and fecal samples from ringed and rescued individuals, revealing the following findings.

RESULTS: The dietary composition primarily encompasses insects from five orders, Diptera, Coleoptera, Hemiptera, Hymenoptera and Lepidoptera, with significant differences observed between adults and nestlings. Dominant intestinal bacterial phyla included Proteobacteria, Firmicutes, Bacteroidota, and Actinobacteriota. Correlation network analysis indicated that Stenotrophomonas, Aminobacter, etc., exhibit extensive mutually promotive interactions with other bacteria, suggesting their potential roles as core functional bacterial communities in the intestine.

DISCUSSION: This research provides the first evidence of dietary differentiation patterns and intestinal microbial composition characteristics of Beijing swifts, providing key foundational data for assessing its survival and adaptation mechanisms. It is highly significant for developing scientific rescue strategies and conservation initiatives.},
}

@article {pmid41403581,
year = {2025},
author = {Alikamali, M and Mohammad-Alizadeh-Charandabi, S and Ahmadi, S and Memar, MY and Shahnazi, M},
title = {The Role of the Vaginal Microbiome in Preterm Premature Rupture of Membranes: A Comprehensive Review of Mechanisms and Clinical Implications.},
journal = {Health science reports},
volume = {8},
number = {12},
pages = {e71484},
pmid = {41403581},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: Preterm premature rupture of membranes (PPROM), a complication in approximately 4.5% of pregnancies, is a leading cause of preterm birth and significant perinatal morbidity. A substantial body of evidence implicates vaginal dysbiosis a departure from a healthy, Lactobacillus-dominant microbiome in the pathogenesis of PPROM. This review synthesizes the current understanding of the mechanistic links between the vaginal microbiome and PPROM and discusses the clinical implications for future therapeutic strategies.

METHODS: A comprehensive literature search was conducted in the PubMed, Scopus, and Google Scholar databases. The selection focused on peer-reviewed articles including systematic reviews, meta-analyses, clinical trials, and influential observational studies (e.g., cohort and case-control), as well as key preclinical studies investigating the vaginal microbiome, PPROM pathogenesis, and relevant therapies.

RESULTS: The synthesized evidence supports a multi-step mechanistic framework wherein ascending pathobionts, characteristic of dysbiosis, trigger a host inflammatory cascade via Toll-like receptors. This inflammatory milieu orchestrates a synergistic attack on fetal membrane integrity through three primary pathways: (1) enzymatic degradation of the extracellular matrix by matrix metalloproteinases (MMPs), (2) programmed cell death (apoptosis) of membrane cells, and (3) damage from oxidative stress. Although conventional therapies such as antibiotics have limitations, emerging strategies, including probiotics, immunomodulators, and antioxidants, are being developed to target these specific mechanistic pathways.

CONCLUSION: This review positions the vaginal microbiome as a central player in the pathophysiology of PPROM, rather than merely a risk factor. This mechanistic understanding shifts the therapeutic focus from broad-spectrum antibiotics toward targeted therapies designed to prevent dysbiosis or neutralize specific downstream inflammatory and degradative pathways. Translating this knowledge into effective clinical practice through rigorous randomized controlled trials remains a critical priority for improving perinatal outcomes.},
}

@article {pmid41403505,
year = {2025},
author = {Sanjrambam, B and Sharma, D and Bakshi, RK and Deka, MB and Agarwala, S and Kalita, A},
title = {Gut microbe's consortium in pregnant women influenced by diet of North-east India: A metagenomic study.},
journal = {Journal of family medicine and primary care},
volume = {14},
number = {11},
pages = {4705-4711},
pmid = {41403505},
issn = {2249-4863},
abstract = {INTRODUCTION: Recent research highlights that the gut microbiota of pregnant women undergoes significant changes throughout pregnancy, influenced by factors such as diet, environment, and sociocultural practices. A diverse gut microbiome during pregnancy is linked to improved metabolic health and the lower risk of complications like gestational diabetes and pre-eclampsia.

OBJECTIVE: This study aimed to investigate the relationship between dietary practices of different communities of Assam and Manipur with the composition of gut microbes during pregnancy.

METHODS: A total of 18 pregnant women completed a survey assessing macronutrient consumption during the first and third trimesters. Dietary data, obtained through questionnaires, were subjected to PCoA (Principal Co-ordinate Analysis) to find similarities and dissimilarities in dietary patterns. Metagenomics analysis of stool samples was done to study the consortium of gut bacteria for the participants.

RESULTS: This study has demonstrated that higher intake of carbohydrates and fats during pregnancy results in a decrease in phylum such as Firmicutes and Actinobacteria. Phylum such as Gemmatimonadetes, Crenarchaeote, Fibrobacteres, and Fusobacteria dominated the gut of most participants.

CONCLUSION: The relationship between gut microbiota composition and dietary habits among pregnant women in Northeast India is essential for designing effective nutritional interventions aimed at improving both maternal and infant health. Future studies should prioritize longitudinal research to better understand these connections and their impact on public health in the region, with a particular focus on identifying the specific foods and dietary patterns responsible for the observed similarities.},
}

@article {pmid41403411,
year = {2025},
author = {García-Ortega, A and Del-Campo-Moreno, R and Sánchez, V and Hervás-Marín, D and Avendaño-Ortiz, J and Rivas-Guerrero, A and Muriel, A and Pedro-Tudela, A and Taberner-Lino, L and De-Juana, C and Barreiro, E and Lobo-Beristain, JL and Jiménez, D and Otero Candelera, R},
title = {Evaluation of microbial-derived metabolites in patients with acute pulmonary embolism: findings from the MICTEP study.},
journal = {ERJ open research},
volume = {11},
number = {6},
pages = {},
pmid = {41403411},
issn = {2312-0541},
abstract = {INTRODUCTION: Functional analysis of microbiome with microbial-derived metabolites (MDMs) has emerged as key for several inflammatory and cardiovascular diseases. However, the data on the relationship of pulmonary embolism (PE) to microbiome are scarce. This study aimed to compare MDM levels between acute PE patients and healthy controls, and to investigate their associations with predisposing factors (i.e. unprovoked, provoked and cancer-associated thrombosis).

METHODS: We collected serum samples from a multicentric cohort, including 96 patients with acute PE at hospital admission and 30 healthy controls. Serum concentrations of MDMs and inflammation/coagulation-related markers were quantified by liquid chromatography-mass spectrometry and flow cytometry, respectively.

RESULTS: Compared with healthy controls, patients with acute PE showed significantly higher serum levels of trimethylamine N-oxide (TMAO) (11.5 μM versus 6.7 μM; p=0.02) and acetate (48.3 μM versus 33.0 μM; p=0.04); and lower levels of propionate (3.8 μM versus 5.3 μM; p=0.007), butyrate (4.03 µM versus 7.68 µM; p=0.009), isobutyrate (5.0 μM versus 7.32 μM; p=0.002) and valerate (0.4 μM versus 0.63 μM; p<0.001). Valerate showed the best discrimination between PE and controls (area under the receiver operating characteristic curve 0.758, 95% CI 0.66-0.86). In the multinomial analysis, higher values of TMAO and acetate were associated with a higher probability of unprovoked PE. MDM levels exhibited different correlation with inflammation-related markers highlighting TGF-β1, CCL2 and CXCL10.

CONCLUSION: These findings reveal imbalances in the serological concentrations of MDMs in patients with acute PE and highlight the potential role of the microbiome and its functional metabolites as novel predisposing risk factors for PE.},
}

@article {pmid41403286,
year = {2025},
author = {Yoshinami, Y and Yamaguchi, S and Shoji, H and Okita, N and Takamaru, H and Hirose, T and Hirano, H and Takashima, A and Imazeki, H and Yamamoto, S and Koyama, S and Ishikawa, D and Terauchi, J and Tanaka, K and Ogawa, K and Watanabe, H and Kato, K},
title = {Feasibility of antibiotic-assisted fecal microbiota transplantation with immunotherapy for esophageal and gastric cancer.},
journal = {Future oncology (London, England)},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/14796694.2025.2599371},
pmid = {41403286},
issn = {1744-8301},
abstract = {AIMS: Immune checkpoint inhibitors (ICIs) have improved outcomes in several malignancies, but survival remains poor for patients with unresectable advanced or recurrent esophageal or gastric cancer. Recent evidence suggests that modulation of the intestinal microbiota may influence the therapeutic response to ICIs. This study aims to evaluate the safety and preliminary efficacy of fecal microbiota transplantation following antibiotic pretreatment (A-FMT) in patients scheduled to receive ICI-containing regimens.

METHODS: This phase I - II, single-institution clinical trial enrolls patients with unresectable advanced or recurrent esophageal or gastric cancer. Participants receive a 1-week course of oral antibiotics (amoxicillin, fosfomycin, and metronidazole) prior to transplantation. A single dose of donor-derived intestinal microbiota solution is administered via colonoscopy, followed by initiation of ICI-based therapy on the next day. The primary endpoint is the incidence of dose-limiting toxicity. Secondary endpoints include response rate, disease control rate, progression-free survival, overall survival, and adverse events. Comprehensive translational research is conducted using stool, blood, and tissue samples to characterize immune responses and identify biomarkers associated with A-FMT and ICI efficacy.Trial registration: jRCTs031240170.The study is ongoing, and patients are currently being enrolled. Enrollment started in June 2024. A total of 7 patients have been enrolled as of August 2025. This protocol is version 3.2.},
}

@article {pmid41403078,
year = {2025},
author = {Moosburner, A and Bilc, M and Anheyer, D and Schleinzer, A and Rahmdel, S and Vitinius, F and Cramer, H},
title = {The effect of MEditerranean DIet and MINdfulness eating on Depression severity in people with major depressive disorder and obesity (MEDIMIND) - a study protocol of a randomized controlled clinical trial with multifactorial design.},
journal = {The British journal of nutrition},
volume = {},
number = {},
pages = {1-25},
doi = {10.1017/S0007114525105849},
pmid = {41403078},
issn = {1475-2662},
abstract = {Obesity and depression are highly prevalent diseases that are strongly correlated. At the same time, there is a growing gap in care, and treatment options should be improved and extended. Positive effects of a mediterranean diet on mental health have already been shown in various studies. Additionally to physiological effects of nutrients, the way how food is eaten, such as mindful eating, seems to play a role. The present study investigates the effect of a mediterranean diet and mindful eating on depression severity in people with clinically diagnosed major depressive disorder and obesity. Participants will be randomized to one of the four intervention groups (mediterranean diet, mindful eating, their combination and a befriending control group). The factorial design allows investigating individual effects as well as potential synergistic effects of the interventions. The study consists of a 12-week intervention period, where five individual appointments will take place, followed by a 12-week follow up. The primary outcome is depression severity. Secondary outcomes are remission of depression, assessor-rated depression severity, quality of life, self-efficacy, BMI, waist-to-hip ratio and body composition, also adherence to mediterranean diet and mindful eating will be assessed. Alongside, mediator and moderator analysis, a microbiome analysis, a qualitative evaluation and an economic analysis will be conducted. The study investigates an important health issue in a vulnerable target group. It allows to draw valuable conclusions regarding effectiveness of different interventions, and therefore contributes to improving available care options for people suffering from depression and obesity.},
}

@article {pmid41402934,
year = {2025},
author = {Liu, B and Li, X and Yang, J and Lu, W and Tang, G and Shi, Y and Li, J and Ding, A and Wang, H and Song, X and Liu, Q and Jiang, X},
title = {Synthetic microbial community in pristine environment promotes the growth of the endangered plant Lilium tsingtauense.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02281-w},
pmid = {41402934},
issn = {2049-2618},
support = {2025CXPT149//Key R&D Program of Shandong Province，China/ ; },
abstract = {BACKGROUND: Habitat fragmentation and degradation have led to the critical endangerment of numerous wild plant species. Although significant achievements in the conservation of endangered wild plants in various regions worldwide, the interaction mechanisms between these plants and their associated rhizosphere microorganisms have yet to be fully elucidated.

RESULTS: Here, we present a communication model between the endangered wild plant Qingdao lily (Lilium tsingtauense) and its associated rhizosphere microorganisms. We isolated a rhizosphere fungus, Trichoderma longibrachiatum QDAU 0920, which effectively colonizes the roots of Qingdao lily and significantly promotes root growth. This growth enhancement is mediated by multiple plant hormones, with auxin playing a particularly prominent role. Further investigation revealed that a non-canonical AUX/IAA protein of the LtIAA16 may augment the transcriptional activation activity of LtARF22 by competitively interacting with LtIAA6, LtIAA17, and LtIAA11, thereby facilitating root growth in Qingdao lily. The growth-promoting effects of this interaction were subsequently validated in several other plant species, including tomato, pepper, corn, pumpkin, and cucumber. Notably, T. longibrachiatum QDAU 0920 forms synthetic microbial consortia (SynComs) in conjunction with other Trichoderma and Penicillium species. These SynComs consistently enhance the growth of Qingdao lily as well as other lily species such as L. lancifolium, Lilium 'Avalon Sunset', and Lilium 'Deliana'.

CONCLUSION: Collectively, these findings underscore the considerable potential of native microorganisms in the development of plant growth-promoting agents and the conservation of endangered plant species. Video Abstract.},
}

@article {pmid41402920,
year = {2025},
author = {Jinato, T and Khamjerm, J and Manprasong, S and Iadsee, N and Tangkijvanich, P and Nookaew, I and Chuaypen, N},
title = {Gut microbiota and host transcriptome interactions reveal diagnostic biomarkers in MASLD-associated hepatocellular carcinoma.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-025-00782-5},
pmid = {41402920},
issn = {1757-4749},
support = {P20GM125503/NH/NIH HHS/United States ; PMU-B-B36G660004//the NSRF via the Program Management Unit for Human Resources & Institutional Development, Research and Innovation/ ; HEAF67300060//Thailand Science research and Innovation Fund Chulalongkorn University/ ; FF67//Fundamental Fund 2024/ ; RA65/039//Ratchadapiseksompotch Fund, Faculty of Medicine Chulalongkorn University/ ; },
abstract = {BACKGROUND: Alterations in the gut microbiome via the gut-liver axis are closely linked to metabolic dysfunction-associated steatotic liver disease (MASLD) and may contribute to hepatocellular carcinoma (HCC) development. However, the interplay between the gut microbiome and host gene expression in MASLD and HCC remains poorly understood.

METHODS: We analyzed the gut microbiome from fecal samples and host transcriptomic profiles from peripheral blood mononuclear cells (PBMCs) in healthy controls and MASLD patients without HCC (mild fibrosis F01 and significant fibrosis F234) and with HCC.

RESULTS: Integrated analysis identified 260 differentially expressed genes (DEGs) and 29 bacterial taxa differentiating MASLD without HCC from MASLD-HCC. Subgroup analysis revealed seven bacterial genera associated with 84 host genes. Notably, Veillonella correlated with regulating synaptic membrane exocytosis 3 (RIMS3), collagen type X alpha 1 (COL10A1), and enabled homolog (ENAH). Real-time PCR validation confirmed COL10A1 as a significant diagnostic biomarker for distinguishing MASLD from MASLD-HCC (AUC = 0.835). Combining COL10A1, and AFP, or Veillonella with AFP, significantly improved differentiation between MASLD and MASLD-HCC, particularly in early-stage fibrosis (F01) (AUC = 0.941 and 0.996, respectively).

CONCLUSIONS: Gut microbiome-host gene interactions appear to play a significant role in MASLD-related HCC progression. Specific bacterial genera and host gene expression profiles may serve as early diagnostic markers for MASLD-HCC.},
}

@article {pmid41402861,
year = {2025},
author = {Chen, Q and Wang, L and Wei, Y and Xu, X and Wei, Z and Peng, Y and Pang, J and Peng, B and Shi, Q and Qudsi, AI and Liang, Q},
title = {Sodium butyrate modulates ocular surface microbiome and attenuates inflammation of meibomian gland dysfunction in ApoE[-/-] mice.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02294-5},
pmid = {41402861},
issn = {2049-2618},
support = {81970765//National Natural Science Foundation of China/ ; 2021YFC2301000//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: The ocular surface microbiome (OSM) in patients with meibomian gland dysfunction (MGD) differs from that of healthy individuals. However, the precise role of OSM in MGD remains unknown. Therefore, we aimed to investigate the mechanism of OSM in the inflammation of MGD and the effects of topical sodium butyrate (SB) treatment in ApoE[-/-] mice.

METHODS: ApoE[-/-] (n = 36) and wild-type C57BL/6J (n = 16) mice served as MGD models and healthy controls, respectively. MGD mice were treated with safety-confirmed concentrations of SB (1, 5, and 10 mM) and PBS for 3 weeks. OSM was analyzed by 16S rRNA gene sequencing (V3-V4). The slit-lamp biomicroscopy, tear cytokines, histopathology (oil red O/PAS/TUNEL staining), and TLR4/MyD88/NF-κB signaling (RT-qPCR, immunohistochemistry, and Western blotting) were evaluated.

RESULTS: Five-month-old ApoE[-/-] mice exhibited typical clinical and histological features of MGD. These mice exhibited elevated tear levels of inflammatory cytokines and activation of the TLR4/NF-κB signaling pathway in the MGs and conjunctivae. Treatment with SB improved the corneal fluorescein staining score of MGD. The ApoE[-/-] mice demonstrated dysbiosis of OSM, characterized by an increase in Proteobacteria and a decrease in Bacteroidota. Additionally, the relative abundance of Muribacter and Muribacter muris increased in ApoE[-/-] mice, while that of Staphylococcus and Staphylococcus lentus decreased, and these alterations were restored by SB treatment. SB also reduced the expression of the TLR4/NF-κB p65 signaling pathway, inflammatory cytokines, and apoptosis in MGs and conjunctival tissues.

CONCLUSION: ApoE[-/-] mice exhibited characteristic features of MGD, accompanied by dysbiosis of OSM. Topical administration of SB modulated the OSM and reduced MGD-associated inflammation. Video Abstract.},
}

@article {pmid41402854,
year = {2025},
author = {Dong, W and Guo, X and Lu, H and Liu, Z and Xie, L and Liu, Y and Wan, Q and Chen, R and Liu, S},
title = {Therapeutic mechanisms of Zi Chong granules against hydroxyurea-induced diminished ovarian reserve based on integrated multi-omics analyses.},
journal = {Journal of ovarian research},
volume = {18},
number = {1},
pages = {295},
pmid = {41402854},
issn = {1757-2215},
support = {2018YFC1704305//Ministry of Science and Technology of the People's Republic of China/ ; },
mesh = {Female ; Animals ; *Hydroxyurea/adverse effects ; *Ovarian Reserve/drug effects ; Mice ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Ovary/drug effects ; Gastrointestinal Microbiome/drug effects ; Metabolomics ; Multiomics ; Animals, Outbred Strains ; },
abstract = {BACKGROUND: Hydroxyurea (HU) is an antitumor drug. However, HU exposure is associated with diminished ovarian reserve (DOR). Zi Chong granules, a Chinese Medicine, can protect against DOR, but little is known regarding its underlying mechanisms of DOR treatment, and thus the target of the present study.

METHODS: Seventy-two female Kunming (KM) mice (4-6 weeks old) were randomly divided into three groups: the control group (Con), the hydroxyurea group (HU), and the Zi Chong group (ZC). The Con group received saline, while the HU and ZC groups were administered hydroxyurea (400 mg/kg/d) by gavage for 21 days to induce diminished ovarian reserve (DOR). Subsequently, the Con and HU groups were given saline, while the ZC group was treated with Zi Chong granules (2.72 g/kg/d) for 15 days. Ovaries and uterus of mice were examined histologically by H&E. The levels of anti-Mullerian hormone (AMH), estradiol (E2), and progesterone (P) were quantified using ELISA kits. The number and quality of oocytes were assessed, and endometrial receptivity was evaluated by immunohistochemistry. 16 S rDNA gene sequencing was used to analyze the composition and abundance of gut microbiome in feces, and non-targeted metabolomics was performed to detect serum metabolite profiles. Correlation analysis was performed to explore the relationships between different gut microbiota and differential metabolites.

RESULTS: ZC granules increased the number of primordial follicles in the ovaries, reduced excessive follicular atresia, restored low AMH, upregulated estrogen and progesterone secretion, and increased the number of mature oocytes after ovulation promotion. It also increased thickness of uterine endometrium and the number of glands, resulting in increased endometrial microvessel density (MVD), enhanced endometrial blood supply, reduced CD138 expression levels and endometrial inflammation. HU decreased the abundance of Lactobacillus spp. in mouse intestines and decreased arachidonic acid metabolism, tryptophan metabolism, spermidine and spermine biosynthesis, steroidogenesis, and nicotinate and nicotinamide metabolism. Correlation analysis revealed that HU exerted its side effects by altering the gut microbiome and bacteria-derived metabolites, while ZC granules could reverse DOR partly depends on regulating gut microbiota and metabolites.

CONCLUSIONS: ZC granules may be a potential therapy for alleviating HU-induced DOR.},
}

Female
Animals
*Hydroxyurea/adverse effects
*Ovarian Reserve/drug effects
Mice
*Drugs, Chinese Herbal/pharmacology/therapeutic use
Ovary/drug effects
Gastrointestinal Microbiome/drug effects
Metabolomics
Multiomics
Animals, Outbred Strains

@article {pmid41402846,
year = {2025},
author = {Huang, YX and Deng, ZC and Cao, KX and Yang, JC and Liu, M and Zhao, L and Zheng, JS and Sun, LH},
title = {Gut microbiome-derived indole-3-carboxaldehyde promotes intestinal development via AHR-NRF2 signaling in the early-life of chicks.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02289-2},
pmid = {41402846},
issn = {2049-2618},
abstract = {BACKGROUND: The development of the small intestine is crucial during early life, with the gut microbiota and microbe-derived metabolites playing key roles in regulating intestinal epithelial barrier function and overall development. However, the underlying mechanism remains unclear. Here, chicks were used to investigate the influences of early-life crosstalk among bacteria, metabolites, and the host on small intestinal development.

RESULTS: We investigated bacterial succession in the small intestine of broiler chicks at four time points during early development. After 3 days post-hatch, Bacillota became the dominant phylum. At the genus level, Lactobacillus and Ligilactobacillus emerged as the two dominant genera, and their abundance was significantly positively correlated with small intestine weight. Metabolome analysis revealed that indole-3-carboxaldehyde (IAld) is derived from both L. gallinarum C2-16-2 (LG) and L. salivarius D7-21 (LS). Moreover, we found that IAld can be converted into bioactive indole-3-carboxylic acid (ICA) in animals, which exhibited greater biological activity than IAld in vitro. Further chick feeding trials revealed that both bacteria (LG and LS) and metabolites (IAld and ICA) promoted epithelial barrier function and enhanced antioxidant capacity during early life in chicks. Moreover, both IAld and ICA promoted tight junction protein expression and enhanced antioxidant capacity by activating AHR-NRF2 signaling.

CONCLUSIONS: These findings suggest that specific bacterial strains (L. gallinarum C2-16-2 and L. salivarius D7-21) and metabolites (IAld and ICA) serve as effective promoters of intestinal epithelial barrier function and antioxidant capacity during early intestinal development in chicks Video Abstract.},
}

@article {pmid41402662,
year = {2025},
author = {Gupta, P and Debnath, B and Ashique, S and Ramzan, M and Yasmin, S and Shorog, E and Mantry, S and Tariq, M and Sridhar, SB and Panigrahy, UP and Sharma, H and Iqbal, A and Prabhakar, PK and Ansari, MY},
title = {The melatonin-microbiome axis: a new frontier in gut health for the immunomodulatory, antioxidant and anti-inflammatory properties.},
journal = {Inflammopharmacology},
volume = {},
number = {},
pages = {},
pmid = {41402662},
issn = {1568-5608},
support = {RGP. 2/8/46//Deanship of Scientific Research, King Khalid University/ ; },
abstract = {Melatonin, primarily produced by the pineal gland, is also synthesized in significant amounts within the gastrointestinal (GI) tract, where its presence surpasses that in the brain. While the pineal gland secretes melatonin to regulate circadian rhythms and promote sleep, gut-derived melatonin plays a crucial role in regulating motility, protecting the mucosa from oxidative stress, and modulating immune function. The interaction between melatonin and gut microbiota is gaining significant attention, as melatonin can influence specific gut microbes and functions, potentially altering the intestinal microbiota, which is essential for maintaining overall health. This review explores the bidirectional relationship between melatonin and gut microbiota, highlighting its influence on microbial composition, intestinal barrier function, microbial metabolism, and immune modulation. Additionally, melatonin indirectly affects the gut microbiota through circadian regulation, further reinforcing its critical role in gut homeostasis. The presence of melatonin receptors in the gut and its interaction with microbial biofilms underline its importance in maintaining a balanced gut environment. Given these multifaceted roles, melatonin emerges as a promising therapeutic candidate for managing gut-related disorders such as irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), and metabolic dysregulation. Despite its promising therapeutic potential, several aspects of melatonin-gut microbiome interactions remain unexplored, necessitating further research into its molecular mechanisms and clinical applications. This review provides an in-depth exploration of melatonin's role in gut microbiome regulation, its therapeutic implications, and future research directions.},
}

@article {pmid41402190,
year = {2025},
author = {Vickers, D and Martynchyk, A and Henden, A and Smibert, OC and Hawkes, EA and Chong, G},
title = {The gut microbiome in B cell lymphoma.},
journal = {Blood reviews},
volume = {},
number = {},
pages = {101357},
doi = {10.1016/j.blre.2025.101357},
pmid = {41402190},
issn = {1532-1681},
abstract = {The gut microbiome (GMB) describes the commensal bacteria which reside in the gastrointestinal tract. Mounting evidence suggests a major role of the GMB in several key aspects of lymphoma development and care. The GMB is implicated in lymphomagenesis, response to therapy and lymphoma-specific outcomes. Moreover, certain gut bacteria can also specifically influence the course of the disease and therapeutic response. In this review we provide an overview of sampling techniques and analytical methodologies for characterising the GMB, a brief outline pertaining to the "healthy" GMB and detailed description of existing literature regarding differences in GMB composition in lymphoma patients, prognostic indicators and the impact of different treatment modalities on the GMB in different lymphoma histologies. Additionally, we describe the relationship of the GMB and treatment of infections in lymphoma patients as well as early-stage research results in GMB manipulation to improve outcomes in patients with B cell lymphomas.},
}

@article {pmid41402129,
year = {2025},
author = {Wang, J and Li, J and Li, Y and Huang, W and Huang, C and Xu, Q and Sun, J and Gong, J and Ma, X and Wang, G and Meng, Y and Li, X},
title = {Angiotensin-(1-7) alleviates intestinal barrier dysfunction and dysbiosis in mice with polymicrobial sepsis.},
journal = {British journal of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bph.70248},
pmid = {41402129},
issn = {1476-5381},
support = {82170641//National Natural Science Foundation of China/ ; 82470663//National Natural Science Foundation of China/ ; 82270089//National Natural Science Foundation of China/ ; 81873583//National Natural Science Foundation of China/ ; 2021A1515012595//Guangdong Provincial Science and Technology Projects under Grant/ ; 2024A1515220136//Guangdong Provincial Science and Technology Projects under Grant/ ; 202312121006//National College Students' Innovation and Entrepreneurship Training Program/ ; S202012121056//Guangdong Provincial Innovation Training Projects under Grant/ ; 2017B020209003//Guangdong Science and Technology Project under Grant/ ; JCYJ20210324112807021//Technical Research and Development Project of Shenzhen/ ; },
abstract = {BACKGROUND AND PURPOSE: The intestine plays a key role in the initiation of sepsis. The gut barrier impedes the translocation of commensal bacteria to the liver in sepsis. Previous studies have reported that angiotensin-(1-7) [Ang-(1-7)] attenuated sepsis-induced organ injury and mortality. However, its role in sepsis-induced intestinal barrier dysfunction remains unclear. Here we have investigated therapeutic effects of Ang-(1-7) on the intestinal barrier dysfunction and dysbiosis in a murine model of sepsis.

EXPERIMENTAL APPROACH: We used a model of sepsis in C57BL/6 mice with caecal ligation and puncture (CLP), to assess mortality and histological and biochemical changes in the gut and liver tissues. Faecal microbiota transplantation (FMT) was used to assess the role of the gut microbiome. 16-s rDNA and metabolomics analyses were performed to characterize differences in the gut microbiome signatures and metabolic profiles.

KEY RESULTS: Plasma Ang-(1-7) was decreased in patients with sepsis. In CLP mice, exogenous Ang-(1-7) attenuated intestinal barrier dysfunction and liver damage. FMT experiments showed that the protective effects of Ang-(1-7) on the gut depended on the gut microbiota. Furthermore, 16-s ribosomal DNA analysis revealed that Ang-(1-7) treatment increased the abundance of Lactobacillus gasseri (L. gasseri) among commensal bacteria. Mechanistically, L. gasseri regulated the production of antimicrobial peptides in intestinal epithelia by activating NLRP6 inflammation.

CONCLUSION AND IMPLICATIONS: Ang-(1-7) protected against sepsis-induced intestine barrier dysfunction and liver injury in mice by modulating gut homeostasis and NLRP6 inflammasome. Ang-(1-7) is a promising candidate drug for protecting intestinal homeostasis in sepsis, offering new insights for clinical treatment.},
}

@article {pmid41401934,
year = {2025},
author = {Chen, W and Peters, DL and Lam, S and Kettal, M},
title = {Bacteriophages as vaccine platforms: Opportunities and challenges in translation.},
journal = {Human vaccines & immunotherapeutics},
volume = {21},
number = {1},
pages = {2599632},
doi = {10.1080/21645515.2025.2599632},
pmid = {41401934},
issn = {2164-554X},
mesh = {Humans ; *Vaccine Development/methods ; *Bacteriophages/immunology/genetics ; Phage Therapy/methods ; Animals ; *Bacterial Vaccines/immunology ; *Viral Vaccines/immunology ; },
abstract = {Bacteriophages (phages) have recently received increased interest as versatile candidates for vaccine development. Their inherent characteristics, such as ease of genetic manipulation, high-density antigen display, intrinsic immunostimulatory properties, demonstrated human safety, and scalability in bacterial hosts, make them attractive as next-generation vaccine platforms. Additionally, their cost-effective production, stability, and existing regulatory approval for food and compassionate phage therapy provide a strong foundation for further development of phage-based vaccines. This commentary summarizes the types of phages, the strategies used, and current advances in phage-based vaccine development for viral and bacterial targets, and discusses the promises and challenges of this platform for novel vaccine development. Phage-based vaccines represent an innovative and promising platform for vaccine development to address significant medical and public health challenges, particularly in antimicrobial resistance, pandemic preparedness, and One Health. Accumulative experimental data have demonstrated that phage-based vaccines induce specific cellular, humoral, and mucosal immune responses at magnitudes comparable to those induced by other vaccine platforms. However, a better understanding of phage biology (interactions with the human immune system and microbiome), more carefully designed preclinical studies, Good Manufacturing Practice production development, the regulatory framework, and ultimately clinical trials are needed before the full potential of this platform is realized.},
}

Humans
*Vaccine Development/methods
*Bacteriophages/immunology/genetics
Phage Therapy/methods
Animals
*Bacterial Vaccines/immunology
*Viral Vaccines/immunology

@article {pmid41401858,
year = {2025},
author = {Memon, FU and Xu, J and Xie, X and Shu, C and Li, Y and Li, K and Xiao, Y and Tian, L},
title = {Strain-specific gut microbiota modulation is linked to resistance to BmNPV infection in silkworms.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108518},
doi = {10.1016/j.jip.2025.108518},
pmid = {41401858},
issn = {1096-0805},
abstract = {Bombyx mori nucleopolyhedrovirus (BmNPV) is a major pathogen threatening sericulture, yet the role of gut microbiota in strain-specific resistance remains poorly understood. This study compared three silkworm strains with high (Xinjiu, XJ), intermediate (AN3, A3), and low (Zhenchixian, ZCX) resistance to BmNPV. Protein assays showed that the resistant XJ strain exhibited the lowest viral EGFP and VP39 expression, minimal weight loss, and highest survival, whereas the susceptible ZCX strain displayed the opposite trend. Shotgun metagenomics revealed strain-specific microbial responses to infection. XJ and A3 maintained significantly higher alpha diversity and more dynamic beta diversity clustering than ZCX, with infection inducing increased microbial gene abundance and emergence of unique taxa in XJ. Taxonomic profiling showed XJ enriched in Firmicutes and beneficial fungal taxa such as Mucoromycota, Ascomycota, Basidiomycota, and Zoopagomycota, alongside reductions in Actinobacteria and Proteobacteria following infection. At finer resolution, resistant strains were enriched in beneficial bacterial classes (Bacilli, Alphaproteobacteria, Opitutae) and fungal classes (Agaricomycetes, Saccharomycetes), with cooperative co-occurrence networks linking these taxa and antagonizing pathogens. In contrast, ZCX was dominated by Gammaproteobacteria, Actinomycetia, and Hydrogenophilalia, consistent with dysbiosis and susceptibility. Functional analysis demonstrated pronounced metabolic reprogramming in resistant strains, especially XJ, with coordinated activation of carbohydrate, amino acid, nucleotide, and lipid metabolism, forming tightly integrated functional networks. Together, these findings reveal that silkworm resistance to BmNPV is associated with microbiome diversity, restructuring toward beneficial taxa, and synergistic metabolic pathways, offering new insights for probiotic-based antiviral strategies.},
}

@article {pmid41401777,
year = {2025},
author = {Bertolini, F and Bovo, S and Bolner, M and Schiavo, G and Ribani, A and Zambonelli, P and Dall'Olio, S and Gallo, M and Fontanesi, L},
title = {Identification of biomarkers for feed efficiency and growth rate by exploring the plasma metabolome of divergent heavy pigs.},
journal = {Animal : an international journal of animal bioscience},
volume = {20},
number = {1},
pages = {101725},
doi = {10.1016/j.animal.2025.101725},
pmid = {41401777},
issn = {1751-732X},
abstract = {Feed represents the largest expense in pig farming and significantly affects the sustainability of the production system. Therefore, enhancing feed efficiency is a key strategy to mitigate these costs and environmental impacts. This is particularly relevant in the context of the heavy pig system in which animals are slaughtered at a heavier live weight than in many other production systems to follow the rules of Protected Designation of Origin (PDO) value chains. Since growth rate is correlated with feed efficiency, and under PDO rules, pigs cannot reach the slaughter weight earlier than a set age limit, the daily gain of the pigs needs to be controlled. In this study, we used untargeted metabolomics to identify plasma metabolites in Italian Large White heavy pigs that may differentiate between animals with divergent feed efficiency and growth rate, and that may constitute biomarkers for one or the other trait. From a starting cohort of 672 performance-tested pigs, two partially overlapping datasets of 200 pigs each, extreme and divergent for feed conversion ratio (FCR) and average daily gain (ADG), were selected. Approximately 700 metabolites were analysed in the plasma of these pigs. Metabolomic data were analysed with the Boruta machine learning algorithm. Discriminant metabolites were further evaluated through univariate and multivariate analyses. Boruta identified 10 and 7 metabolites that differentiate between FCR and ADG extreme pigs, respectively, with an additional metabolite shared by the two datasets. Most metabolites selected in the FCR dataset still show significant abilities to discriminate among high and low ADG pigs, even if they have not been selected in the Boruta analysis, showing medium to high values of Area Under the Curve, and highly significant Mann-Whitney test U P-values, while the opposite was not true. Among the metabolites detected, L-carnitine and O-adipoylcarnitine, both involved in fatty acid metabolism, were significantly higher in pigs with high FCR. Isoleucylhydroxyproline and prolylhydroxyproline, linked to collagen turnover, were higher in low FCR pigs, potentially reflecting more efficient protein metabolism. Other metabolites linked to gut microbiome activity significantly differentiate between high and low FCR and ADG pigs, suggesting a potential role of the microbiota in nutrient utilisation. The identified metabolomic profiles confirm that feed efficiency and growth rate are related yet distinct traits, whose independent consideration will enhance the accuracy of biomarker discovery and genetic selection in Italian heavy pigs.},
}

@article {pmid41401155,
year = {2025},
author = {Supungul, P and Tang, S and Uengwetwanit, T and Uawisetwathana, U and Angthong, P and Arayamethakorn, S and Bunphimpapha, P and Potibut, P and Jangsutthivorawat, W and Visudtiphole, V and Chaiyapechara, S and Rungrassamee, W},
title = {The innate immune IMD pathway is a key regulator of gut microbiome and metabolic homeostasis in the black tiger shrimp (Penaeus monodon).},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0338796},
pmid = {41401155},
issn = {1932-6203},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology/genetics ; *Penaeidae/microbiology/immunology/metabolism/genetics ; *Immunity, Innate/genetics ; *Homeostasis ; Signal Transduction ; Transcriptome ; Myeloid Differentiation Factor 88/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Gene Expression Profiling ; },
abstract = {The gut microbiome plays a fundamental role in host health and homeostasis, yet immune mechanisms regulating this relationship remain poorly understood in commercially important invertebrate such as the black tiger shrimp (Penaeus monodon). We employed a multiomics approach, combining RNA interference (RNAi) with transcriptomic, metabolomic, and 16S rRNA gene profiling, to investigate how the innate immune Toll and IMD pathways regulate gut health. We systematically suppressed key signaling components, MyD88 (Toll) and Relish (IMD), under non-pathogenic conditions. Knockdown of the IMD pathway transcription factor, Relish, triggered a profound and selective response across all measured biological layers. We observed a disproportionately large transcriptomic change, with 1,362 differentially expressed genes (DEGs) in the Relish knockdown group compared to only 333 DEGs in the MyD88 knockdown group. This was accompanied by a targeted alteration in immune effectors, including the upregulation of lysozyme C-like (log2 fold change = 2.44) and a strong suppression of penaeidin 5 (log2 fold change = -3.62). At the microbial level, while overall community structure remained stable, a selective shift was observed, the abundance of specific Gram-negative genera, particularly Photobacterium and Shewanella, was significantly reduced, yet Pseudoalteromonas were enriched in the Relish knockdown group. Metabolomic analysis further revealed that the Relish-suppressed shrimp had a distinct metabolic signature, marked by a decrease in bacterial-associated metabolites like D-alanyl-D-alanine and an increase in pro-inflammatory markers such as succinic acid and 8-HETE. Our findings showed that in P. monodon, the IMD pathway is the primary and central regulator of gut microbiome and metabolic homeostasis. This study provides novel insights into the dynamic interplay between innate immunity and the gut microbiome in a crustacean, identifying the IMD pathway as a promising target for developing strategies to enhance shrimp health and the sustainability of the global aquaculture industry.},
}

Animals
*Gastrointestinal Microbiome/immunology/genetics
*Penaeidae/microbiology/immunology/metabolism/genetics
*Immunity, Innate/genetics
*Homeostasis
Signal Transduction
Transcriptome
Myeloid Differentiation Factor 88/genetics/metabolism
RNA, Ribosomal, 16S/genetics
Gene Expression Profiling

@article {pmid41400850,
year = {2025},
author = {Davoody, S and Vakili, K and Jazi, K and Fathi, M and Heidari-Foroozan, M and Mofidi, SA and Taremi, M and Taherkhani, A and Azadnajafabad, S and Pour, FH and Eslami, S and Zangi, M and Mohamadkhani, A},
title = {Alterations of Gut Microbiota and Microbial Metabolites in Parkinson's Disease: A Systematic Review.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {299},
pmid = {41400850},
issn = {1559-1182},
mesh = {*Gastrointestinal Microbiome/physiology ; *Parkinson Disease/microbiology/metabolism ; Humans ; Fatty Acids, Volatile/metabolism ; },
abstract = {Parkinson's disease (PD) is a significant global health issue, ranking as the second most prevalent neurodegenerative disorder after Alzheimer's disease. Research suggests that changes in the gut microbiota may occur before the onset of the motor symptoms of PD. This study seeks to conduct a systematic review (PROSPERO registration ID: CRD420251118297) to explore the mechanistic exploration and biomarker identification of gut microbiota in PD. The research involved a comprehensive literature search across PubMed, Scopus, and Web of Science databases up to August 2022 using a combination of Medical Subject Heading (MeSH) terms for Parkinson's disease, gut microbiota, and metabolites. Eligible studies included in vivo and in vitro investigations focusing on the metabolite levels produced by the gut microbiota in PD patients. Data extraction was performed by two researchers using Microsoft Excel Software. The Newcastle-Ottawa Scale (NOS) was used to assess the risk of bias. The certainty of the evidence was evaluated using the GRADE framework. The review encompassed 39 selected studies, comprising data from over 3000 participants. Approximately two-thirds of the studies reported a reduction in short-chain fatty acids (SCFAs), notably butyrate and acetate, while almost half reported increased trimethylamine N-oxide (TMAO) levels or altered amino acid and bile acid pathways. Key findings emphasized the comparison of microbiomes in PD patients and healthy controls, highlighting metabolic pathway alterations and their implications for PD development. Studies also delved into the role of inflammation in PD progression, exploring the connection between inflammatory factors and the microbiota. Additionally, the present study examined the influence of PD medications on gut microbiota. This systematic review highlights the potential involvement of gut microbiota in modulating the gut-brain axis in PD. Observed associations suggest links between altered metabolite production, pro-inflammatory states, increased gut permeability, and changes in LPS and α-synuclein dynamics. However, these relationships remain largely correlative, and causal mechanisms are yet to be established. Further longitudinal and mechanistic studies are warranted to confirm these observations and explore their clinical relevance.},
}

*Gastrointestinal Microbiome/physiology
*Parkinson Disease/microbiology/metabolism
Humans
Fatty Acids, Volatile/metabolism

@article {pmid41278729,
year = {2025},
author = {Lu, R and Lee, N and Drake, AK and Fulton, RP and Abutaleb, NS and Seleem, M and Oakland, DN and Garin-Laflam, MP and Pop, M and Luo, XM},
title = {Discovery of Novel Probiotic Species to Improve Infant Health.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41278729},
issn = {2692-8205},
abstract = {UNLABELLED: Selecting an appropriate infant formula can be challenging for parents given the wide range of available options, which may lead to suboptimal choices or frequent switching. Our recent studies in mice demonstrated that the maternal microbiota-particularly Limosilactobacillus reuteri present in breast milk-plays a critical role in shaping neonatal immunity by promoting the production of immunoglobulin A (IgA), a key antibody for defense against enteric pathogens. To extend these findings to humans, we analyzed fecal samples from healthy breastfed infants using shotgun metagenomic sequencing combined with whole-bacterial-cell ELISA to assess associations between specific taxa and pathogen-reactive IgA. We found that members of the Oscillibacter species (including Oscillibacter sp. KLE1728, KLE1745, PC13, PEA192, and O. valericigenes) and Morganella (e.g., M. morganii, Morganella sp. EGD-HP17, and Morganella sp. HMSC11D09) were strongly correlated with IgA responses against Salmonella and Shigella. In contrast, IgA reactive to enterohemorrhagic Escherichia coli (EHEC) was associated with other genera, including Staphylococcus. Notably, Lactobacillus species (L. bombi, L. kefiri, L. equi, and L. rhamnosus) were consistently linked to elevated IgA responses against Salmonella, Shigella, and EHEC. Moreover, levels of anti-Salmonella and anti-Shigella IgA were positively correlated with the use of infant formula containing prebiotic fibers or human milk oligosaccharides (5-HMO). Collectively, these findings highlight novel commensal taxa with potential as probiotic candidates to guide the development of next-generation infant formulas aimed at enhancing mucosal immunity and supporting infant health.

IMPORTANCE: Early-life nutrition shapes immune maturation, yet the microbial factors driving mucosal antibody responses remain poorly defined. Through integrated metagenomic and IgA profiling, this study identifies commensal taxa, particularly Lactobacillus, Oscillibacter, and Morganella, associated with pathogen-specific IgA in infants. These taxa may enhance mucosal defense against enteric pathogens, revealing key microbial contributors to early immune development. The findings provide a foundation for designing next-generation infant formulas that leverage targeted probiotics or prebiotics to promote protective IgA responses and gut health.},
}

@article {pmid41400723,
year = {2025},
author = {Leney, M and Kahale, F and Martin, VM},
title = {Diagnosis and Management of Food Protein-Induced Allergic Proctocolitis.},
journal = {Current gastroenterology reports},
volume = {27},
number = {1},
pages = {76},
pmid = {41400723},
issn = {1534-312X},
mesh = {Humans ; *Proctocolitis/diagnosis/therapy/etiology/immunology ; *Food Hypersensitivity/diagnosis/complications/therapy ; *Dietary Proteins/adverse effects/immunology ; Infant ; Biomarkers/analysis ; Breast Feeding ; },
abstract = {PURPOSE OF REVIEW: Food protein-induced allergic proctocolitis (FPIAP) is a frequent cause of rectal bleeding in otherwise healthy infants. Although benign and self-limited, wide variation in diagnostic and management practices often leads to overdiagnosis, unnecessary dietary restriction, and disruption of breastfeeding. This review summarizes contemporary evidence to guide a pragmatic, challenge-anchored approach to diagnosis and management.

RECENT FINDINGS: Diagnosis of FPIAP remains clinical, based on symptom resolution after elimination and recurrence upon reintroduction of the trigger food; however, confirmatory challenges are seldom performed. Fecal calprotectin and other proposed biomarkers-such as eosinophil-derived neurotoxin, zonulin, and microbiome signatures-show poor reliability in infants and are not ready for clinical use. Management should prioritize the least restrictive diet - maternal dairy elimination for breastfed infants and extensively hydrolyzed formulas for formula-fed infants - only in challenge-proven FPIAP. Growing data support earlier reintroduction once colitis resolves, and early introduction of other allergens may reduce future IgE-mediated allergy risk. A standardized, challenge-confirmed framework minimizes over-restriction and supports continued breastfeeding. Future priorities include validation of non-invasive biomarkers and trials comparing timing and strategies for safe dietary reintroduction in FPIAP.},
}

Humans
*Proctocolitis/diagnosis/therapy/etiology/immunology
*Food Hypersensitivity/diagnosis/complications/therapy
*Dietary Proteins/adverse effects/immunology
Infant
Biomarkers/analysis
Breast Feeding

@article {pmid41400573,
year = {2025},
author = {Wang, L and Chen, Q and Zhang, H and Zhao, X and Dong, J and Wu, D and Lian, Y and Liu, M and Liu, H and Chen, Y and Chen, Q and Lyu, W and Bai, Y},
title = {New Perspectives on Gastric Inflammaging: Integrating Multi-Omics Mechanisms and Gerotherapeutic Strategies in Chronic Gastritis.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2025.1444},
pmid = {41400573},
issn = {2152-5250},
abstract = {Chronic gastritis (CG) is a highly prevalent, age-associated inflammatory disorder of gastric mucosa and a key precursor of gastric cancer in older adults. Beyond Helicobacter pylori infection and environmental insults, accumulating evidence indicates that chronic, low-grade inflammation coupled with aging biology, "gastric inflammaging", plays a central role in driving mucosal degeneration, atrophy, and malignant transformation. Here, we synthesize current mechanistic and multi-omics evidence to conceptualize CG as a tractable model of organ-specific inflammaging. We first summarize how hallmarks of aging-including cellular senescence and the senescence-associated secretory phenotype (SASP), mitochondrial dysfunction, impaired autophagy, immune exhaustion, and microbiome dysbiosis-converge to create a self-perpetuating inflammatory microenvironment in the stomach. We then review emerging single-cell and spatial multi-omics studies that delineate senescence-inflammation niches and reveal how these molecular neighborhoods relate to disease stage and cancer risk. Finally, we discuss therapeutic implications, highlighting geroscience-guided interventions such as senolytics/senomorphics, inflammasome and cGAS-STING pathway modulators, microbiota- and metabolite-targeted strategies, lifestyle interventions, and natural products, and propose a precision framework linking inflammaging biomarkers to patient stratification and clinical endpoints. Reframing CG as a gastric inflammaging model may provide a prototype for organ-specific healthy aging strategies and near-term gerotherapeutic trials aimed at extending healthspan.},
}

@article {pmid41400485,
year = {2025},
author = {Mukherjee, A},
title = {The maternal-infant microbiome axis as an epigenetic and immunometabolic orchestrator: redefining early-life programming and precision interventions for lifelong women's and children's health.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0050225},
doi = {10.1128/iai.00502-25},
pmid = {41400485},
issn = {1098-5522},
abstract = {The maternal-infant microbiome axis represents a dynamic interface that shapes neonatal immune and metabolic development from the earliest stages of life. Microbial communities from the maternal gut, vaginal tract, and breast milk seed the infant microbiome, influencing chromatin remodeling, transcriptional activity, and immunometabolic programming. Rather than functioning solely as a conduit of microbial inheritance, this axis operates as a regulatory network where microbial metabolites such as short-chain fatty acids and indole derivatives modulate histone acetylation, DNA methylation, and noncoding RNA pathways that calibrate immune tolerance and pathogen defense. Perturbations, including cesarean delivery, perinatal antibiotic exposure, or maternal metabolic disorders, disrupt these processes and are associated with altered immune set points, heightened infection susceptibility, and increased risk of inflammatory and metabolic disease. Multi-omics studies now provide mechanistic insights linking microbial signals to epigenetic regulation of neonatal immune responses, while also exposing important controversies, such as the debated presence of a placental microbiome and the variable efficacy of probiotic interventions. Emerging strategies, including maternal dietary modulation of the microbiome, perinatal microbiota restoration, and development of live biotherapeutics, show promise, but their translational potential remains constrained by limited sample sizes, heterogeneous outcomes, and safety concerns. Framing the maternal-infant microbiome axis as an epigenetic and immunometabolic orchestrator highlights both its therapeutic promise and the need for rigorous mechanistic and clinical evaluation to advance preventive strategies for women's and children's health.},
}

@article {pmid41399631,
year = {2025},
author = {Su, J and Hansen, BE and Wang, Z and Sharmenov, A and Xia, X and Broekhuizen, M and Ma, Z and Peppelenbosch, MP},
title = {Yogurt reintroduction and the circulating microbiome in healthy volunteers: protocol for a prospective, longitudinal, species-controlled crossover clinical trial (MAMI).},
journal = {Contemporary clinical trials communications},
volume = {48},
number = {},
pages = {101579},
pmid = {41399631},
issn = {2451-8654},
abstract = {BACKGROUND: Although the gut microbiome plays a crucial role for maintaining overall host homeostasis and metabolism, it is significantly influenced by dietary changes, leading to substantial temporal variations in microbial composition within and between individuals. Despite this, incidental fecal sampling remains the standard method for microbiome assessment. Recently, the blood microbiome, defined by microbial DNA (cmDNA) circulating in the bloodstream, has emerged as a potentially more stable and integrated alternative. Preliminary data suggest that blood microbiome analysis may offer more consistent insights than fecal-based approaches, although the methodological validity of the approach has been questioned.

METHOD/DESIGN: This study aims to establish or rule-out cmDNA as a representative of the gut microbiome. In a prospective, single-arm crossover trial, effects of dairy product withdrawal and reintroduction of a yoghurt with a known consortium of bacteria will be assessed in healthy volunteers aged 18-65. Participants will first abstain from all dairy products, a phase expected to reduce yogurt-associated cmDNA in the bloodstream. Yogurt will then be reintroduced, during which reappearance of cmDNA of specific bacteria (especially LGG, LA-5 and BB-12) is anticipated. Shotgun metagenomic sequencing will be used to track cmDNA dynamics over time. This longitudinal sampling approach will provide experimental evidence supporting the existence and responsiveness of the circulating microbiome, while also revalidating the bioinformatic pipeline used for its analysis.

CONCLUSION: This pilot study will test whether blood-derived microbial DNA can serve as a valid surrogate for gut microbiome composition. If successful, this approach may provide a more stable and integrative alternative to fecal sampling and support future biomarker development and mechanistic research.

CLINICAL TRIAL REGISTRATION: NCT06944002.},
}

@article {pmid41399570,
year = {2025},
author = {Bheemaneni, RS and Sakarkar, P and Nigam, A and Nwachukwu, EC and Sekar Lakshmisai, S and Mohammed, L},
title = {Unraveling the Association Between Fibromyalgia and Irritable Bowel Syndrome: A Systematic Review.},
journal = {Cureus},
volume = {17},
number = {11},
pages = {e96801},
pmid = {41399570},
issn = {2168-8184},
abstract = {Fibromyalgia (FM) and irritable bowel syndrome (IBS) often occur together. Patients with FM and IBS present similar symptoms, such as pain and fatigue; this leads to a delay in diagnosis and management. This systematic review explored the shared pathophysiology of these conditions in adults, focusing on the roles of immune dysfunction, gut dysbiosis, neurotransmitter imbalances, and disturbances in the gut-brain axis. We searched five databases, PubMed, PubMed Central, Google Scholar, Cochrane, and ScienceDirect, for relevant free full-text English articles from 2015 to 2025. Ten studies were selected after screening, identification, and quality assessment, adhering to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines. Our review found that immune system dysregulation involves mast cells and pro-inflammatory cytokines that damage the gut barrier. The gut microbiome and neurotransmitter levels seem to have a reciprocal influence on each other, and their alteration contributes to pathogenesis, with an increase of certain species showing an association with symptom severity. Serotonin and tryptophan metabolism appear to have a crucial role in pain perception, particularly visceral hypersensitivity. Therapeutic strategies targeting the gut microbiome, such as probiotics and fecal microbiota transplantation, have potential but require further research. Overall, this review identified overlapping mechanisms of FM-IBS comorbidity, which can pave the way to effective and combined treatment approaches. Future research should explore gender distinctions in the mechanisms, medications that act on neurotransmitter receptors (especially serotonergic pathways), and the utility of fecal microbiota transplantation and probiotics.},
}

@article {pmid41399387,
year = {2026},
author = {Yu, Y and Zhao, W and Yang, M and Wu, B and Yuan, X},
title = {Tumor-Promoting Gut Microbes in Colorectal Cancer: Mechanisms and Translational Perspectives.},
journal = {International journal of medical sciences},
volume = {23},
number = {1},
pages = {63-75},
pmid = {41399387},
issn = {1449-1907},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/therapy/diagnosis/pathology/immunology ; *Gastrointestinal Microbiome/immunology/physiology ; *Dysbiosis/microbiology/complications/therapy/immunology ; Fecal Microbiota Transplantation/methods ; Probiotics/therapeutic use ; Carcinogenesis/immunology ; Translational Research, Biomedical ; },
abstract = {Colorectal cancer (CRC) represents a predominant global malignancy, characterized by increasing incidence and mortality rates. Recent investigations have underscored the gut microbiota as a pivotal element in the pathogenesis and progression of CRC. This review synthesizes current evidence regarding the association between gut microbial dysbiosis and CRC, with a particular emphasis on pathogenic bacteria such as Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, pks[+] Escherichia coli, and Enterococcus faecalis, among others. The mechanisms through which these microbes contribute to tumorigenesis include the induction of DNA damage, the promotion of chronic inflammation, and the induction of immunosuppression, and the production of oncogenic metabolites. Additionally, the review examines the clinical implications of gut microbiota, highlighting their potential as non-invasive biomarkers for early CRC detection and their impact on the efficacy and toxicity of chemotherapy, radiotherapy, and immunotherapy. Furthermore, emerging microbiota-targeted interventions, such as fecal microbiota transplantation, dietary modification, and probiotics, are evaluated for their therapeutic potential. Despite substantial progress, challenges remain in standardizing microbial markers and optimizing individualized microbiota modulation strategies. Future studies integrating multi-omics and machine learning approaches may pave the way for microbiome-based precision medicine in CRC.},
}

Humans
*Colorectal Neoplasms/microbiology/therapy/diagnosis/pathology/immunology
*Gastrointestinal Microbiome/immunology/physiology
*Dysbiosis/microbiology/complications/therapy/immunology
Fecal Microbiota Transplantation/methods
Probiotics/therapeutic use
Carcinogenesis/immunology
Translational Research, Biomedical

@article {pmid41399344,
year = {2025},
author = {Hillman, EBM and Carson, D and Walters, JRF and Fritzsche, M and Mate, R and Chappell, KE and Chekmeneva, E and Romero, MG and Lewis, SJ and Rijpkema, S and Wellington, EMH and Arasaradnam, R and Amos, GCA},
title = {Ruminococcus gnavus and Biofilm Markers in Feces From Primary Bile Acid Diarrhea Patients Indicate New Disease Mechanisms and Potential for Diagnostic Testing.},
journal = {Gastro hep advances},
volume = {4},
number = {9},
pages = {100712},
pmid = {41399344},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Bile acid diarrhea (BAD) is a common cause of frequent loose stools, urgency, and incontinence, which is under-recognized due to limited diagnostic test availability and unclear pathogenesis. This study aimed to investigate fecal changes in well-defined subjects.

METHODS: Fecal samples were compared in BAD patients (n = 26), diagnosed by SeHCAT testing, and healthy controls (n = 21). Shotgun metagenomic sequencing was used to identify microbiome species and functional genes. An extended set of 38 bile acids was quantified by liquid chromatography mass spectrometry, including various epimers and intermediates, such as iso- (3-beta-OH), oxo (keto), allo (5-alpha), and 3-sulfated forms.

RESULTS: Alpha diversity, reflecting microbial richness, was reduced in BAD patients with severe forms of the disease, while beta diversity demonstrated distinct microbial profiles between groups. Ruminococcus gnavus (R. gnavus) was prevalent in BAD patients but rare in controls (odds ratio = 73), while Firmicutes bacterium CAG110, Eubacterium siraeum and 2 Oscillibacter species were less common in BAD (odds ratios = 25-30). Overall, 99 taxa differed significantly between groups. Bile acidtransforming genes (baiA, baiB, hdhA) were more abundant in BAD samples (P ≤ .0012). Most fecal bile acids, including iso-bile acids and intermediates, were higher in BAD. Elevated ursodeoxycholic acid-3-sulfate and relatively lower lithocholic acid and allo-bile acids, including isoallolithocholic acid, reflect changes in bacterial metabolism. Biofilm-associated genes (bssS, pgaA, pgaB) were markedly elevated in BAD patients (P ≤ .00008). SeHCAT values negatively correlated with R. gnavus (rho -0.53, P = .008) and positively with E ubacterium siraeum (rho 0.41, P = .041).

CONCLUSION: BAD may result from an overgrowth of R. gnavus, associated with intestinal biofilms and an altered bile acid metabolism.},
}

@article {pmid41399266,
year = {2025},
author = {Lee, SG and Lee, JH and Baek, Y and Chu, J and Kim, KH and Ham, S and Shin, CH and Lee, YI},
title = {Efficacy and Safety of Human Skin Microbiome-Derived Strains as Topical Treatment for Acne: An In Vitro and In Vivo Study.},
journal = {Journal of Korean medical science},
volume = {40},
number = {48},
pages = {e327},
doi = {10.3346/jkms.2025.40.e327},
pmid = {41399266},
issn = {1598-6357},
support = {20024192/MOTIE/Ministry of Trade, Industry and Energy/Korea ; },
mesh = {*Acne Vulgaris/microbiology/pathology/therapy/drug therapy ; Humans ; Animals ; *Skin/microbiology ; *Microbiota ; Mice ; Keratinocytes/metabolism/cytology ; Disease Models, Animal ; Staphylococcus epidermidis/isolation & purification ; Propionibacterium acnes ; Cytokines/metabolism ; Male ; Female ; Cyclooxygenase 2/metabolism ; Skin Microbiome ; },
abstract = {BACKGROUND: The skin microbiome plays a crucial role in defending against pathogens and modulating immunity, and its dysregulation is linked to various skin conditions, including acne.

METHODS: In this study, four previously identified strains-Staphylococcus epidermidis B424F-5, S. epidermidis BS47C-1, Dermacoccus profundi BS35F-3, and Streptococcus salivarius BS320F-4- were selected from a skin microbiome database of healthy individuals. The efficacy and safety of these strains against acne-related inflammation were evaluated using in vitro and in vivo animal model experiments.

RESULTS: Cutibacterium acnes exposure increased the expression of acne-associated inflammatory mediators-such as IL-1β, IL-6, IL-8, COX-2, iNOS, and TNF-α-particularly in keratinocytes, without inducing cytotoxicity. Treatment with heat-killed S. epidermidis BS47C-1 (SE2), D. profundi BS35F-3 (DP), and S. salivarius BS320F-4 (SS) significantly reduced these markers in vitro. In vivo, topical application of the strains alleviated inflammation in a C. acnes-induced mouse model, with histological evidence of reduced erythema and immune cell infiltration. Bulk RNA sequencing of keratinocytes showed that SE2 and DP downregulated cytokine and interferon signaling while enhancing skin barrier and antimicrobial gene expression, suggesting a dual anti-inflammatory and barrier-supporting mechanism.

CONCLUSION: These results provide compelling evidence of the efficacy and safety of human skin microbiome-derived strains as potential topical treatments for acne. By targeting both microbial colonization and inflammatory pathways, these strains offer a promising avenue for the development of novel acne therapeutics.},
}

*Acne Vulgaris/microbiology/pathology/therapy/drug therapy
Humans
Animals
*Skin/microbiology
*Microbiota
Mice
Keratinocytes/metabolism/cytology
Disease Models, Animal
Staphylococcus epidermidis/isolation & purification
Propionibacterium acnes
Cytokines/metabolism
Male
Female
Cyclooxygenase 2/metabolism
Skin Microbiome

@article {pmid41399025,
year = {2025},
author = {Zhao, D and Wang, X and Wang, K and Yang, B and Zhu, H and Xu, Y and Ye, C and Li, L and Lv, X and Zhou, S and Ma, C and Chen, X and Yin, F and Zhu, Y and Cao, Z and Li, N and Zuo, T and Qin, H and Chen, Q},
title = {Recipients' native bacteria determine the outcome of FMT treatment in inflammatory bowel disease.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2600055},
doi = {10.1080/19490976.2025.2600055},
pmid = {41399025},
issn = {1949-0984},
mesh = {Humans ; Male ; Female ; Adult ; *Gastrointestinal Microbiome ; *Fecal Microbiota Transplantation/adverse effects ; Middle Aged ; *Bacteria/classification/isolation & purification/genetics ; Treatment Outcome ; Retrospective Studies ; Feces/microbiology ; *Colitis, Ulcerative/therapy/microbiology ; *Inflammatory Bowel Diseases/therapy/microbiology ; *Crohn Disease/therapy/microbiology ; Young Adult ; Prospective Studies ; Aged ; },
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is a promising treatment for inflammatory bowel disease (IBD), achieving clinical response rate of ~50% for ulcerative colitis (UC), and Crohn's disease (CD). While prior research has emphasized donor selection and treatment protocols, the role of the patient's native intestinal microbiota in FMT outcomes remains underexplored.

METHODS: This study analyzed a retrospective cohort of 96 IBD patients (45 CD, 51 UC) undergoing FMT, with 192 paired stool samples collected pre- and post-treatment, alongside 332 healthy donor samples from 18 donors. A prospective cohort of 45 IBD patients provided 45 baseline stool samples, and a validation cohort of 112 non-IBD patients contributed 224 paired samples. Retrospective cohort patients were monitored for 4 weeks to assess FMT responsiveness and 52 weeks for treatment effectiveness. Microbiome analysis identified enterotype-specific bacteria and native bacterial genera influence FMT outcomes. Random forest, permissivity, and mathematical models predicted treatment response, characterized microbiome remodeling, and defined microecological remission thresholds.

RESULTS: The FMT regimen was safe, with no serious adverse events reported. At week 4, the clinical response rates were 58.8% (26/45) for CD patients and 66.7% (34/51) for UC patients; by week 52, the remission rates were 82.4% (37/45) for CD patients and 84.4% (43/51) for UC patients. Microbiome analysis identified 54 bacterial genera linked to enterotype classification, 57 to UC response, and 93 to CD response. Notably, 38 high-frequency retentions of recipient native bacteria after FMT were predictive of FMT responsiveness. The permissivity model revealed a shift toward Bacteroidetes-dominated enterotypes in IBD patients post-FMT, which was validated in 112 non-IBD patients. The abundance ranges of recipients' native bacteria predictive of treatment responsewere determined by mathematical interpretation model.

CONCLUSION: The patient's native microbiota significantly influences FMT efficacy in IBD, influencing microbiome remodeling and clinical outcomes, highlighting the importance of baseline microbial profiles in predicting FMT responsiveness and optimizing therapy.},
}

Humans
Male
Female
Adult
*Gastrointestinal Microbiome
*Fecal Microbiota Transplantation/adverse effects
Middle Aged
*Bacteria/classification/isolation & purification/genetics
Treatment Outcome
Retrospective Studies
Feces/microbiology
*Colitis, Ulcerative/therapy/microbiology
*Inflammatory Bowel Diseases/therapy/microbiology
*Crohn Disease/therapy/microbiology
Young Adult
Prospective Studies
Aged

@article {pmid41399002,
year = {2025},
author = {Ma, C and Ding, W and Li, P and Wang, Q and Li, X and Meng, Z and Ren, H},
title = {ROS-Responsive Hydrogel with M2 Macrophage Nanovesicles for Diabetic Wound Healing: Targeted CO Delivery to Regulate Mitochondrial Metabolism and Reprogram Wound Microbiota.},
journal = {ACS applied materials & interfaces},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsami.5c18140},
pmid = {41399002},
issn = {1944-8252},
abstract = {Macrophage dysregulation and microbial dysbiosis at diabetic chronic wound sites are two of the main drivers that hinder the healing process. To address this, a reactive oxygen species (ROS)-responsive hydrogel wound dressing (NVs@CO-TP) is fabricated through boronic ester bonds between poly(vinyl alcohol) hydroxyl groups and phenylboronic acid moieties, which incorporates M2 macrophage-derived nanovesicles (NVs) loaded with manganese carbonyl (NVs@CO). Upon exposure to a high level of ROS in the wound, the hydrogel responds, scavenges ROS, and subsequently releases NVs@CO, exhibiting the synergistic efficacy of CO gas and NVs. Due to its intrinsic inflammation-tendency ability, NVs@CO specifically targets activated M1 macrophages and releases CO to regulate mitochondrial metabolism, promoting M1 apoptosis and increasing the M2 phenotype. This process decreases the release of inflammatory cytokines and enhances anti-inflammatory processes, promoting chronic diabetic wound healing. More interestingly, the dressing also beneficially modulates the wound microbiota by enhancing the beneficial microbial richness and overall microbiome composition, which further improves the healing microenvironment. Therefore, NVs@CO-TP acts through two primary mechanisms: the targeted delivery of CO to M1 macrophages regulates the mitochondrial metabolism to repolarize macrophages while simultaneously modulating the wound microbiome. This combined anti-inflammatory strategy facilitates chronic wound healing and demonstrates significant potential for clinical translation in treating various difficult-to-heal wounds.},
}

@article {pmid41398941,
year = {2025},
author = {Song, Y and Hou, S and Xiang, Y and Zou, D and Gu, S and Pu, X and Liu, Q and Chu, M},
title = {Dietary energy levels modulate rumen metabolites and function in sheep by regulating the rumen microbiome.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04636-7},
pmid = {41398941},
issn = {1471-2180},
support = {XQSWYZQZ-JBKY-4//Project of State Key Laboratory of Animal Biotech Breeding of China/ ; CAAS-ZDRW202502 and ASTIP-IAS13//Agricultural Science and Technology Innovation Program of China/ ; CARS-38-02//Earmarked Fund for China Agriculture Research System of MOF and MARA/ ; },
abstract = {In intensive ruminant production, high-energy diets are commonly used to enhance animal productivity, as dietary formulation significantly influences rumen fermentation and microbial communities. This study investigated the effects of varying dietary energy levels on the rumen microbial community structure, function, and metabolic profiles in Small-tailed Han (STH) sheep. Thirty 6-month-old sheep were randomly assigned to three groups: high-energy (HE), conventional-energy (CE), and low-energy (LE). All groups were fed iso-nitrogenous diets formulated to provide high-, conventional-, and low-energy levels of 10.8, 9.5, and 8.2 MJ/kg of digestible energy (DE), respectively. Rumen content was collected post-slaughter and analyzed via metagenomic sequencing to assess microbial composition and function, alongside non-targeted metabolomics to characterize the rumen fluid metabolome. Results revealed that Bacteroidota and Bacillota were the dominant phyla. High-energy feeding significantly reduced the relative abundance of Bacteroidota while increasing that of Bacillota, leading to a markedly higher Bacillota-to-Bacteroidota ratio. Functional analysis indicated significant enrichment of carbohydrate metabolism pathways in the HE group, whereas the LE group exhibited enrichment in fundamental cellular processes such as ABC transporters and ribosome, indicating a "survival mode". Metabolomic analysis demonstrated that dietary energy levels substantially reshaped the rumen metabolomic profile. Metabolites in the HE group were enriched in pathways including steroid hormone biosynthesis and the prolactin signaling pathway, while the LE group showed enrichment in histidine metabolism and the TCA cycle. Several aromatic amino acid metabolic pathways were commonly enriched across comparisons. These findings indicate that while the composition of the dominant phyla (Bacteroidota and Bacillota) was conserved across diets with different digestible energy levels, this dietary variation altered community diversity, structure, functional potential, and profoundly reshaped the rumen metabolic environment. This study provides scientific evidence regarding the impact of dietary energy on rumen fermentation and production performance in fattening sheep.},
}

@article {pmid41398793,
year = {2025},
author = {Yang, W},
title = {The causal links between gut microbiota and both acute and chronic renal failure: A two-sample mendelian randomization study.},
journal = {Medicine},
volume = {104},
number = {50},
pages = {e46336},
doi = {10.1097/MD.0000000000046336},
pmid = {41398793},
issn = {1536-5964},
mesh = {Humans ; Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics ; *Acute Kidney Injury/microbiology/genetics ; Genome-Wide Association Study ; *Kidney Failure, Chronic/microbiology/genetics ; Male ; Female ; Middle Aged ; },
abstract = {This study aimed to investigate the potential causal relationships between gut microbiota composition and both acute renal failure (ARF) and chronic renal failure (CRF), using a two-sample Mendelian randomization approach. We characterized the gut microbiota composition at various taxonomic levels (phylum, class, order, family, and genus) and obtained genome-wide association study data for both ARF and CRF from the FinnGen and UK Biobank databases. Subsequently, we employed a two-sample Mendelian randomization approach to explore the causal relationship between the gut microbiota and renal failure. We identified 10 causal relationships between the genetic liability in the gut microbiome and ARF. We found 4 associations between genetic liability in the gut microbiome and CRF. The results indicated that Haemophilus (inverse variance weighted, IVW OR = 0.816, 95% CI = 0.719-0.926, P = .002, q = 0.054) and Ruminococcaceae UCG005 (IVW OR = 0.804, 95% CI = 0.694-0.931, P = .004, q = 0.078) showed negative associations with ARF. Moreover, Ruminococcaceae UCG005 (IVW OR = 1.001, 95% CI = 1.00-1.002, P = .008, q = 0.091) positively correlated with CRF risk. Sensitivity analyses did not provide statistical evidence of bias due to pleiotropy or genetic confounding factors. Our research contributes significantly to the growing body of knowledge linking the gut microbiota to renal health, offering new perspectives for the diagnosis, treatment, and prevention of renal diseases.},
}

Humans
Mendelian Randomization Analysis
*Gastrointestinal Microbiome/genetics
*Acute Kidney Injury/microbiology/genetics
Genome-Wide Association Study
*Kidney Failure, Chronic/microbiology/genetics
Male
Female
Middle Aged

@article {pmid41398791,
year = {2025},
author = {Ye, C and Lian, G and Wang, T and Wang, H and Xie, L},
title = {Causal effects of the gut microbiota, circulating metabolites, and cardiometabolic diseases: A Mendelian randomization study.},
journal = {Medicine},
volume = {104},
number = {50},
pages = {e46523},
doi = {10.1097/MD.0000000000046523},
pmid = {41398791},
issn = {1536-5964},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; Mendelian Randomization Analysis ; Diabetes Mellitus, Type 2/genetics/microbiology ; *Cardiovascular Diseases/microbiology/genetics ; Stroke/genetics/microbiology ; Hypertension/genetics/microbiology ; },
abstract = {The gut microbiota is associated with cardiometabolic disorders (including coronary artery disease, type 2 diabetes, stroke, heart failure, and hypertension) through the gut-heart or gut-brain axis, among which metabolic processes play crucial roles. However, the exact causal mechanisms remain unknown. Our study sought to uncover the causal relationships between the gut microbiota, circulating metabolites and cardiometabolic diseases via Mendelian randomization (MR) analysis. Forward MR was utilized to investigate the causal effects of the gut microbiota and circulating metabolites on the risk of cardiometabolic diseases. Reverse MR was subsequently performed to analyze the significant gut microbiota and circulating metabolites. Two-step MR was employed to examine the impact of circulating metabolites on the relationship between the gut microbiota and cardiometabolic diseases and to determine the mediated fractions. Our results revealed a nominal causal relationship with 23, 23, 22, 20, and 19 gut microbiota constituents for coronary artery disease, type 2 diabetes, stroke, heart failure, and hypertension, respectively. We also identified 2 significant associations and 13 suggestive associations between circulating metabolites and these cardiometabolic diseases. Reverse MR analysis revealed that genetically predicted type 2 diabetes was suggestively associated with 3 circulating metabolites, whereas stroke demonstrated a suggestive association with 3 distinct gut microbiota. Further screening identified 4 circulating metabolites as potential mediators in the pathway from the gut microbiota to cardiometabolic diseases. Our study revealed a causal link between gut microbiome components and cardiometabolic diseases and that circulating metabolites potentially act as intermediaries in this association.},
}

Humans
*Gastrointestinal Microbiome/genetics/physiology
Mendelian Randomization Analysis
Diabetes Mellitus, Type 2/genetics/microbiology
*Cardiovascular Diseases/microbiology/genetics
Stroke/genetics/microbiology
Hypertension/genetics/microbiology

@article {pmid41398743,
year = {2026},
author = {Yang, X and Ji, XH and Li, C and Lai, JL and Luo, XG},
title = {Soil microecosystem collapse and revival: Dual-targeted HMX toxicity versus secretion system-mediated synthetic microbiome restoration.},
journal = {Bioresource technology},
volume = {441},
number = {},
pages = {133557},
doi = {10.1016/j.biortech.2025.133557},
pmid = {41398743},
issn = {1873-2976},
mesh = {*Soil Microbiology ; *Microbiota/drug effects ; Biodegradation, Environmental ; *Soil Pollutants/toxicity/metabolism ; *Soil/chemistry ; Triazines ; },
abstract = {The persistent energetic compound cyclotetramethylene tetranitramine (HMX) poses increasing ecological threats. However, its micro-ecological toxicity mechanisms and effective remediation strategies remain inadequately understood. This study aimed to elucidate HMX's inhibitory mechanisms on soil microecology and develop a synergistic synthetic microbiome for effective remediation. HMX exhibited high persistence (94.4 % residual after 40 days) and acts through a 'dual-target inhibition' mechanism in soil: 1) inhibiting cytochrome c oxidase, disrupting the electron transport chain and reducing ATP synthesis; 2) chelating Zn[2+]/Ni[2+] cofactors, inactivating key enzymes like β-glucosidase (reduced by 63.4 %). These actions culminated in a dual "energy-nutrition" crisis, suppressed functional genes (pccA, nosZ, phoD), and reduced microbial diversity (OTUs decreased by 11.7 %). Metabolomic analysis revealed five HMX transformation pathways in soil. To address this, a synthetic microbiome of six efficient strains (e.g., Bacillus megaterium) was constructed. This consortium achieved HMX degradation via a secretion system-mediated extracellular enzymatic cascade, confirmed by product deposition on cell surfaces (degradation rate: 84.7-96.4 % in 48 h). The ring-opening products were assimilated into the TCA cycle, fueling lipid and nucleotide metabolism. Inoculation with this functional consortium for 40 days successfully restored soil health, achieving 92.4 % HMX removal, a 3.11-fold increase in respiration, and recovered alpha diversity. This study provides a novel "microbiome-enhanced element cycle steady-state" paradigm for remediating military-contaminated sites.},
}

*Soil Microbiology
*Microbiota/drug effects
Biodegradation, Environmental
*Soil Pollutants/toxicity/metabolism
*Soil/chemistry
Triazines

@article {pmid41398701,
year = {2025},
author = {Wang, M and Zhang, C and Zhao, L and Yin, Q and Cui, Z and Chen, X and Ren, J and Wang, Y and Xu, M and Cao, Y and Wu, S and Yao, J},
title = {Unraveling the interaction between the phageome and bacteriome in the rumen and its role in influencing metabolome dynamics in dairy cows at different lactation stages.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02260-1},
pmid = {41398701},
issn = {2049-2618},
support = {2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Although the roles of rumen microbiome in milk yield and milk protein synthesis have been widely recognized, knowledge on how ruminal microbiome dynamic changes affect these two traits during the whole lactation is lacking. Phages have been shown to affect the microbiota, but little is known about the shift patterns of ruminal phages and if they may modulate rumen microbiome during lactation. Herein, a longitudinal study was performed to identify the potential roles of ruminal phageome and bacteriome interactions, and metabolic function shift in affecting milk yield and protein content using metagenomic and metabolomic profiling of rumen microbiome from the peak, early, and later mid-lactation stages.

RESULTS: A total of 780 ruminal bacterial phages were identified, which exhibited two primary shifting patterns: (1) decreasing then increasing; (2) decreasing then stabilizing through the lactation. Bacteriome also showed first increasing then stabilizing or continuously declining besides exhibiting two similar shifting patterns to those of phages. By associating the differentially abundant phages with their host bacteria, we observed that significantly increased Lactococcus phage BM13, Corynebacterium phage P1201, and Campylobacter phage CJIE4-5 in peak lactation, along with Lactobacillus phage Lv-1 in early and later mid-lactation, were positively correlated with the relative abundance of their hosts. However, significantly increased Bacillus phage BCU4 and the Enterococcus phage phiNASRA1 in early mid-lactation were negatively related to their host abundance. In terms of bacteria, Ruminococcus flavefaciens and Faecalibacterium sp. CAG 74 had the highest abundance in peak lactation, whereas most Prevotella species were more abundant in early and later mid-lactation. Notably, ruminal carbohydrate and amino acid metabolism functions were enhanced in early mid-lactation. Further structural equation model and network analysis revealed that abundant Bacillus phage BCU4 and Enterococcus phage phiNASRA1 in early mid-lactation were associated with increased relative abundance of Prevotella species, possibly due to a reduction in Bacillus cereus and Enterococcus faecalis. Additionally, these Prevotella species exhibited positive relationships with rumen metabolites, such as L-phenylalanine, phenylacetylglycine, N-acetyl-D-phenylalanine, and propionate content, which contributed to the improved milk protein yield.

CONCLUSIONS: This study revealed the bacteriome and phageome interactions at different lactation stages, and the key phages and bacteria regulating the rumen function and metabolism thus contributing to the milk traits of cows. The potential regulatory roles of phages in affecting the rumen bacteriome suggest that they can be powerful targets for future interventions to improve rumen functions. Video Abstract.},
}

@article {pmid41398611,
year = {2025},
author = {Chen, X and Zhang, F and Cheng, L and Niu, D and Hu, J and Huang, S and Wang, F and Pang, G and Huang, C and Li, M and Wang, C and Mo, Z},
title = {Dysbiosis of the gut microbiota in calcium oxalate nephrolithiasis is associated with impaired short-chain fatty acid production and systemic metabolomic disruptions.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02224-5},
pmid = {41398611},
issn = {2049-2618},
support = {Guike AB21196022//Guangxi Key Research and Development Project/ ; Guike AA22096032//Guangxi Science and Technology Major Project/ ; AA18118016//Major Project of Guangxi Innovation Driven/ ; 22-35-17//Guangxi key Laboratory for Genomic and Personalized Medicine/ ; 62272065//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The prevalence of calcium oxalate (CaOx) kidney stones is increasing, yet the underlying mechanisms remain incompletely understood. Emerging evidence suggests that gut microbiota-particularly short-chain fatty acid (SCFA)-producing bacteria-may modulate host metabolism and inflammation, thereby influencing stone formation. However, the mechanistic links between gut dysbiosis, metabolic disturbances, and CaOx stone pathophysiology remain to be fully elucidated. This study investigates gut microbiota composition, SCFA levels, and metabolomic alterations in CaOx stone formers (CSF), aiming to uncover potential pathophysiological mechanisms and therapeutic targets.

RESULTS: Among 59 CSF and 60 healthy controls (HC), CSF exhibited significantly reduced microbial richness, with marked depletion of SCFA-producing bacteria such as Faecalibacterium prausnitzii and Eubacterium rectale. This dysbiosis was associated with decreased fecal and plasma SCFA levels, reduced 24-h urinary citrate, and widespread metabolic disturbances, particularly in tryptophan metabolism and the citrate cycle. Plasma SCFA levels were positively correlated with urinary citrate excretion, suggesting a regulatory link within the gut-kidney axis. Mendelian randomization analysis suggested that Bacteroides thetaiotaomicron may be a potential microbial risk factor for stone formation (OR = 1.26, 95% CI: 1.03-1.54, p = 0.028). In a hyperoxaluria rat model, interventions with F. prausnitzii, E. rectale, or sodium butyrate reduced renal CaOx crystal deposition and kidney injury.

CONCLUSIONS: Our findings highlight the central role of SCFA-producing bacteria and their metabolites in maintaining metabolic balance and protecting against CaOx stone formation. Gut dysbiosis and reduced SCFA levels appear to drive metabolic changes that contribute to stone development. B. thetaiotaomicron may increase stone risk, while F. prausnitzii, E. rectale, and sodium butyrate show therapeutic potential. These insights support further exploration of microbiome-based strategies for the prevention and personalized management of kidney stones. Video Abstract.},
}

@article {pmid41398357,
year = {2025},
author = {Yassine, F and Abbas, H and Kurdi, A and Mansour, R and Mourad, FH and Matar, G and Bilen, M},
title = {Gut microbiota profiling in Lebanese ulcerative colitis patients and healthy controls from a pilot study.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-31435-x},
pmid = {41398357},
issn = {2045-2322},
support = {Seed grant//Faculty of Medicine, American University of Beirut/ ; },
abstract = {Ulcerative colitis (UC) is a chronic inflammatory disease of the colon, associated with gut microbiota dysbiosis. While global studies have explored this link, region-specific microbial profiles remain underreported. This pilot study aimed to characterize and compare, for the first time, the gut microbiota of Lebanese UC patients and healthy controls using 16 S rRNA gene sequencing (V3-V4 region). Fecal samples from 11 UC patients and 11 healthy individuals were analyzed. Alpha and beta diversity metrics were computed, and gut microbial composition was assessed across taxonomic levels. Statistical comparisons used Mann-Whitney and Fisher's exact tests. UC patients showed significantly reduced microbial diversity based on Faith's Phylogenetic Diversity and Shannon index (p < 0.05), though evenness was unaffected. Beta diversity also revealed significant group-level dissimilarities (p < 0.05). At the phylum level, Bacteroidota was elevated in UC, while Bacillota and Actinomycetota were reduced. Genera such as Ruminococcus, Bacteroides, and Coprococcus were depleted in UC. Faecalibacterium, commonly reduced in UC, showed no significant difference. This first analysis of gut microbiota in Lebanese UC patients reveals a distinct microbial signature that partially diverges from global trends, supporting the need for region-specific microbiome studies and personalized microbiota-targeted therapies.},
}

@article {pmid41398112,
year = {2025},
author = {Sayin, S and ElGamel, M and Rosener, B and Brehm, M and Mugler, A and Mitchell, A},
title = {Bacterial population dynamics during colonization of solid tumors.},
journal = {Molecular systems biology},
volume = {},
number = {},
pages = {},
pmid = {41398112},
issn = {1744-4292},
support = {R35GM133775//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35GM156451//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; DMS-2245816//National Science Foundation (NSF)/ ; OAC-2117681//National Science Foundation (NSF)/ ; Mellon Fellowship//University of Pittsburgh (Pitt)/ ; },
abstract = {Bacterial colonization of tumors is widespread, yet the dynamics during colonization remain underexplored. Here we discover strong variability in the sizes of intratumor bacterial clones and use this variability to infer the mechanisms of colonization. We monitored bacterial population dynamics in murine tumors after introducing millions of genetically barcoded Escherichia coli cells. Results from intravenous injection revealed that roughly a hundred bacteria seeded a tumor and that colonizers underwent rapid, yet highly nonuniform growth. Within a day, bacteria reached a steady-state and then sustained load and clone diversity. Intratumor injections, circumventing colonization bottlenecks, revealed that the nonuniformity persists and that the sizes of bacterial progenies followed a scale-free distribution. Theory suggested that our observations are compatible with a growth model constrained by a local niche load, global resource competition, and noise. Our work provides the first dynamical model of tumor colonization and may allow distinguishing genuine tumor microbiomes from contamination.},
}

@article {pmid41398090,
year = {2025},
author = {Denisov, N and Springer, F and Brauer-Nikonow, A and Maftei, G and Zeller, G and Selegato, DM and Zimmermann, M},
title = {Development of a GC-MS/MS method to quantify 120 gut microbiota-derived metabolites.},
journal = {Analytical and bioanalytical chemistry},
volume = {},
number = {},
pages = {},
pmid = {41398090},
issn = {1618-2650},
support = {GutTransForm-101078353/ERC_/European Research Council/International ; Mi-EOCRC//Bundesministerium für Bildung und Forschung/ ; 01KD2102E//Bundesministerium für Bildung und Forschung/ ; },
abstract = {The gut microbiota produces metabolites that are important for host physiology and have critical roles in the development of diseases, such as metabolic disorders, cardiovascular diseases, and cancer. Here, we developed a gas chromatography-coupled tandem mass spectrometry (GC-MS/MS) method for the quantification of 120 volatile and semi-volatile compounds produced by gut bacteria, including short-chain fatty acids, indols, nucleotides, organic acids, and amino acid derivatives. The method is based on multiple-reaction-monitoring (MRM) of each analyte and their respective isotopically labeled internal standard, enabling absolute metabolite quantification between 0.45 pmol and 1 nmol. Applying the method to different tissue samples from germfree and conventionally colonized mice, we illustrate the ability to quantify microbiota-produced metabolites in different sample matrices-plasma, liver, feces, and intestinal content-and at different concentrations. Lastly, we demonstrate that this protocol is capable of quantifying microbiota-derived metabolites in stool samples stored in DNA stabilization buffers that are typically used in sequencing-based microbiome studies. Altogether, the developed GC-MS/MS method adds a valuable analytical tool to quantify microbiota-host metabolic interactions.},
}

@article {pmid41397898,
year = {2025},
author = {Gao, B and Luo, J and Nong, X and Yao, Z and Wang, H},
title = {Combined Analysis of Salivary Metabolomics and Microbiota in Type 1 Diabetics With Xerostomia: A Pilot Study.},
journal = {Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jop.70097},
pmid = {41397898},
issn = {1600-0714},
support = {82160187//National Natural Science Foundation of China/ ; 2019GXNSFDA245016//Key Project of Guangxi Natural Science Foundation/ ; 2023JJA141002//General Program of Guangxi Natural Science Foundation/ ; },
abstract = {OBJECTIVE: Given that the oral ecological environment undergoes alterations during the pathological progression of type 1 diabetes mellitus (T1DM) with xerostomia, this study employed microbiomics in conjunction with metabolomics to identify the distinct oral microbiota and salivary metabolites in patients with type 1 diabetic xerostomia and healthy individuals, aiming to elucidate the microorganisms, metabolites, and metabolic pathways potentially implicated in T1DM-associated xerostomia.

METHODS: Saliva samples were obtained from individuals diagnosed with T1DM and xerostomia (patient group, n = 9) as well as from healthy volunteers (control group, n = 9), and were subsequently subjected to microbiota profiling and untargeted metabolomic analysis. Bioinformatics methodologies were applied to assess the microbiota and metabolomics datasets both independently and integratively.

RESULTS: A total of 88 differential metabolites were identified between the patient and control groups. These metabolites were predominantly enriched in the caffeine and Vitamin B6 metabolic pathways. Additionally, an average of 280 operational taxonomic units (OTUs) were detected, with species diversity found to be lower in the patient group compared to the controls. At the genus level, 20 significantly altered microbial taxa were identified. Differential genera, including Leptotrichia and Corynebacterium, exhibited higher abundance in the patient group, whereas genera such as Haemophilus and Streptococcus were predominantly present in the control group. Correlation analysis indicated that the differential microbiota did not exhibit strong associations with the identified differential metabolites. However, certain oral microorganisms were associated with specific metabolites enriched in the caffeine metabolic pathway.

CONCLUSION: In summary, the findings demonstrated notable differences in both oral microbiota composition and salivary metabolite profiles between T1DM patients with xerostomia and healthy individuals. Furthermore, a moderate degree of association between the oral microbiome and metabolome was observed, which may serve as a potential biomarker for T1DM-related xerostomia and contribute to the development of targeted therapeutic strategies.},
}

@article {pmid41397647,
year = {2025},
author = {Guha, R and Lakshmi, S and Krebs, T and Schroers, VJ and Adamek, M and Elumalai, P},
title = {Efficacy of a novel oral bivalent vaccine with fucoidan as adjuvant against Aeromonas hydrophila and Edwardsiella tarda infections in Nile tilapia aquaculture.},
journal = {Fish & shellfish immunology},
volume = {169},
number = {},
pages = {111074},
doi = {10.1016/j.fsi.2025.111074},
pmid = {41397647},
issn = {1095-9947},
abstract = {The emerging diseases caused by Aeromonas hydrophila and Edwardsiella tarda severely impact aquaculture and lead to economic losses. Vaccines, as a safe prophylaxis method, can only protect against specific infections. Therefore, the development of a multivalent vaccine is necessary to enhance protection and cost-effectiveness for sustainable aquaculture. In this study, a bivalent vaccine against A. hydrophila and E. tarda was developed using fucoidan as an adjuvant. The vaccines were administered via the oral route to assess their protective efficacy against challenges. A survival rate of 63 % and 73 % was observed in the orally vaccinated fish where fucoidan was utilized as an adjuvant. Other immunological parameters, such as serum lysozyme, catalase, superoxide dismutase, bactericidal activity, and total IgM production, were measured. TCRβ, IgM, MHCI, MHCII, IFNγ, and IL8 gene expressions were significantly altered in the vaccinated fish. The gut microbiome alterations were noticeable in the vaccinated fish. Although feed-based oral vaccines necessitate antigen stability to withstand degradation in the fish gut, fucoidan used as an adjuvant has enhanced vaccine efficacy in orally vaccinated groups, indicating the potential of fucoidan as a novel immunomodulator and vaccine adjuvant in aquaculture.},
}

@article {pmid41397585,
year = {2025},
author = {Hsu, CY and Polatova, D and Hamad, RH and Patel, PN and Akram, M and Singh, G and Arora, V and Nayak, PP and Kadhem, M and Hamzah, HF},
title = {Phage Therapy in Cancer Treatment: Mechanisms, Emerging Innovations, and Translational Progress.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105085},
doi = {10.1016/j.critrevonc.2025.105085},
pmid = {41397585},
issn = {1879-0461},
abstract = {Bacteriophage therapy has re-emerged as a rapidly advancing field in oncology, bridging antimicrobial precision with tumor-targeted biotherapy. Beyond infection control, phages are now recognized as programmable biological systems capable of eradicating multidrug-resistant (MDR) pathogens, modulating tumor-associated microbiota, activating immune responses, and delivering therapeutic genes or drugs. Preclinical evidence shows that phages can selectively eliminate Fusobacterium nucleatum in oral squamous cell carcinoma, restore microbial balance in colorectal cancer, and enhance immune infiltration via cytokine or antigen display. Engineered constructs including GM-CSF-expressing and MAGE-A1-displaying phages, λ-phage ASPH vaccines, and PEGylated nanocarriers delivering MEG3 or TRAIL have demonstrated strong anti-tumor efficacy across melanoma, hepatocellular, and colorectal cancer models. Additionally, CRISPR-Cas-armed phages precisely remove resistance genes such as bla-CTX-M and mecA, while AI-driven selection pipelines enable data-guided design of personalized phage cocktails. These advances represent a paradigm shift from empirical antibacterial use toward mechanistically engineered, multifunctional phage platforms that integrate microbiome modulation, immune activation, and nanocarrier-mediated gene delivery. Although challenges such as immune clearance, bacterial resistance, and regulatory complexity remain, the convergence of AI, CRISPR, and synthetic biology is accelerating the evolution of phage therapy into a clinically viable precision-oncology strategy. In this context, bacteriophages emerge not merely as antibacterial agents but as intelligent, patient-specific nanomedicines poised to redefine therapeutic boundaries in cancer treatment.},
}

@article {pmid41396813,
year = {2025},
author = {Chirumbolo, S},
title = {Methodological and statistical concerns in MINERVA microbiome-disease knowledge graph.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf673},
pmid = {41396813},
issn = {1477-4054},
}

@article {pmid41396812,
year = {2025},
author = {Langarica, S and Kim, YT and Alkhadrawi, A and Kim, JB and Do, S},
title = {Response to 'Methodological and statistical concerns in MINERVA microbiome-disease knowledge graph' by Salvatore Chirumbolo.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf671},
pmid = {41396812},
issn = {1477-4054},
support = {//HEM Pharma/ ; //AWS Health Equity Initiative/ ; },
}

@article {pmid41396495,
year = {2025},
author = {Sari, DWK and Khamid, NL and Ikhrami, MA and Hardaningsih, I and Satriyo, TB and Suparmin, A},
title = {A Metagenomic Analysis of Gut Microbiome and Growth Performance of Giant Gourami (Osphronemus goramy) Fed with Raw Plant-Based Diet.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {27},
number = {6},
pages = {168},
pmid = {41396495},
issn = {1436-2236},
support = {2938/UN1/PN/PT.01.10/2022//Universitas Gadjah Mada/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Animal Feed/analysis ; Plant Leaves/chemistry ; Aquaculture ; Diet/veterinary ; *Perciformes/growth & development/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Bacteria/classification/genetics ; Diet, Plant-Based ; },
abstract = {The increasing demand for global protein and awareness of environmental issues challenge sustainable aquaculture growth. The freshwater fish giant gourami (Osphronemus goramy) has the potential to be farmed sustainably. The gut microbiome approach is key to sustainable aquaculture by supporting fish health and feed utilization. This study evaluated the effect of taro leaves supplementation on giant gourami growth and gut microbiome composition. Four groups of fish (initial weight 378 ± 26.14 g) were fed commercial feed with 0%, 25%, 50%, and 75% taro leaves substitution for 16 weeks. Growth parameters such as absolute weight gain (AWG), specific growth rate (SGR), protein efficiency ratio (PER), survival rate (SR), and condition factor (CF) were measured, and gut microbiota was analyzed using 16 S rRNA gene sequencing via Oxford Nanopore Technology. The 50% taro leaves group showed significantly higher AWG (78.87 ± 11.96 g, p < 0.05) and PER (1.92 ± 0.37, p < 0.05) compared to the 100% commercial feed (53 ± 5.6 g and 0.54 ± 0.18, respectively). The condition factor of fish in all feeding experiments (1.40-1.55) demonstrated optimal growth conditions. The gut microbiome was dominated by Clostridium, with taro leaves substitution increasing Cellulosilyticum, Fusobacterium, and Ilyobacter, which are linked to cellulose breakdown and SCFA production. These findings suggest that giant gourami do not require solely commercial feed and are promising for sustainable aquaculture practice.},
}

*Gastrointestinal Microbiome/genetics
Animals
*Animal Feed/analysis
Plant Leaves/chemistry
Aquaculture
Diet/veterinary
*Perciformes/growth & development/microbiology
RNA, Ribosomal, 16S/genetics
Metagenomics
Bacteria/classification/genetics
Diet, Plant-Based

@article {pmid41396345,
year = {2025},
author = {Fan, Y and Gu, X and Yang, H and Chen, Y and Fang, C and Deng, H and Dai, L},
title = {Intratumoral microbiome: a crucial regulating factor in development and progression of colorectal cancer.},
journal = {Molecular biomedicine},
volume = {6},
number = {1},
pages = {138},
pmid = {41396345},
issn = {2662-8651},
support = {82372647//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 82203108//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 2024YFFK0381//Program of Sichuan Province, China/ ; 2024YFFK0396//Program of Sichuan Province, China/ ; No. 2025ZNSFSC0549//Natural Science Foundation of Sichuan Province/ ; 2023NSFC1895//Natural Science Foundation of Sichuan Province/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology/therapy/etiology ; Disease Progression ; Tumor Microenvironment ; Animals ; *Gastrointestinal Microbiome ; *Microbiota ; },
abstract = {Colorectal cancer (CRC) is one of the most malignant cancers, and studies have indicated that microbes within tumors play a crucial role in CRC. Advanced methodologies, including single-cell and spatial technologies, high-resolution sequencing, and multi-omic integration, are now unraveling the complex composition and function of the intratumoral microbiome. Mechanistically, these microbial communities contribute to CRC initiation by serving as direct mutagens that induce genomic instability, perpetuating a state of chronic inflammation, and activating specific carcinogenic pathways. Furthermore, they actively promote tumor progression and metastatic dissemination through multiple means, including the modulation of key oncogenic signaling pathways, extensive remodeling of the tumor immune microenvironment, and facilitation of a pro-metastatic niche. Given these profound and multifaceted influences, the intratumoral microbiome shows significant promise as a source of diagnostic and prognostic biomarkers, offering considerable potential for non-invasive monitoring and improved risk stratification in clinical practice. Therapeutically, intervention strategies are rapidly evolving, encompassing approaches such as microbiome modulation to enhance conventional therapies, precise clearance of pathogenic bacteria, utilization of intrinsically antitumor microbes, and the engineering of synthetic bacteria as targeted living therapeutics. This review comprehensively outlines the current research methods, elaborates on the mechanistic insights, and discusses the therapeutic targeting of the intratumoral microbiome, aiming to provide a foundational framework for developing new and effective strategies in CRC precision medicine.},
}

Humans
*Colorectal Neoplasms/microbiology/pathology/therapy/etiology
Disease Progression
Tumor Microenvironment
Animals
*Gastrointestinal Microbiome
*Microbiota

@article {pmid41396065,
year = {2025},
author = {Herrera, G and Zouiouich, S and Diaz-Mayoral, N and Purandare, V and Trabert, B and Wan, Y and Liu, J and Dagnall, CL and Jones, K and Hicks, BD and Hutchinson, A and Li, S and Shi, J and Abnet, CC and Vogtmann, E},
title = {Comparison of oral collection methods for 16S rRNA gene and shotgun metagenomic sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0180625},
doi = {10.1128/spectrum.01806-25},
pmid = {41396065},
issn = {2165-0497},
abstract = {UNLABELLED: To understand how sample collection affects oral microbiome studies, we evaluated the comparability of unpreserved saliva, saliva in glycerol, and mouthwash samples, their room temperature stability, and intraindividual stability over 6 months. Saliva and mouthwash samples were collected from 20 healthy participants 6 months apart. Saliva was divided, with half preserved in glycerol. Some aliquots were frozen immediately, while others were stored at room temperature for a week. DNA was extracted using the PowerSoil Pro and 16S rRNA gene, and shotgun metagenomic sequencing was conducted. Intraclass correlation coefficients (ICCs) from taxonomic and functional tables were compared to assess variability. We estimated sample size requirements based on the intraindividual stability over 6 months. Saliva in glycerol appeared more similar to unpreserved saliva than mouthwash, with higher median ICCs at genus (0.88 vs 0.60), species (0.92 vs 0.64), and gene levels (0.84 vs 0.36; all P < 0.01). Room temperature storage affected saliva in glycerol more than mouthwash (median genus-level ICC = 0.65). No significant differences were observed at the gene level. Intraindividual stability over 6 months was moderate. To detect an odds ratio of 1.5 with one sample per individual, estimated sample sizes ranged from 665 (common species) to 219,547 (rare species). Oral microbiome stability varies by collection method; mouthwash provides greater room temperature stability and may be preferable when immediate freezing is not feasible. For epidemiological studies, consistent use of a single collection method and inclusion of longitudinal sampling can improve reproducibility and power to detect associations with health outcomes.

IMPORTANCE: The oral microbiome plays a key role in health and disease, yet methodological inconsistencies in sample collection and processing can introduce variability and limit comparability across studies. This study investigates the impact of different oral sample collection methods on microbiome profiling and their stability over time. We demonstrate that sample type significantly influences taxonomic and functional microbiome profiles, with mouthwash showing greater stability during delayed processing and saliva in glycerol more closely resembling fresh saliva. Importantly, intraindividual microbial communities were only moderately stable over 6 months, emphasizing the need for consistent sampling protocols and consideration of temporal variation. These findings have direct implications for microbiome study design, highlighting that methodological choices can affect reproducibility, statistical power, and biological interpretation. Our results support the use of mouthwash as a practical alternative when freezing is delayed and underscore the value of longitudinal sampling for detecting biologically meaningful changes.},
}

@article {pmid41395968,
year = {2025},
author = {Almuhaideb, E and Hasan, NA and Grim, C and Rashed, SM and Parveen, S},
title = {Effects of aquaculture practices on Vibrio population dynamics and oyster microbiome.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0198525},
doi = {10.1128/aem.01985-25},
pmid = {41395968},
issn = {1098-5336},
abstract = {Oyster aquaculture is essential for ensuring a sustainable food source. Despite stringent controls, cases of oyster-related illnesses linked to pathogenic Vibrio parahaemolyticus (Vp) and Vibrio vulnificus (Vv) persist. This study investigated the impact of aquaculture practices on the oyster microbiome and pathogen levels, focusing on two common systems: on-bottom and floating cages. From June to November 2019, monthly samples were collected from the Chesapeake Bay, including oysters and water from each aquaculture system. Oyster samples included both fresh and temperature-abused oysters. The study utilized the most probable number and real-time PCR (MPN-qPCR) method to quantify total and pathogenic Vp and Vv in water and oyster samples. DNA was extracted from oyster homogenates and filtered water samples for shotgun metagenomic sequencing. The results revealed significant impacts of aquaculture practices on the diversity of the oyster microbiome, particularly affecting the distribution of phages, antibiotic resistance, and virulence factor genes. Shotgun metagenomic sequencing consistently showed higher genetic representation of Vibrio in floating cages for both fresh and temperature-abused oyster samples. MPN-qPCR results differed between practices, showing higher Vibrio levels in bottom cages for fresh oysters and higher levels in floating cages under temperature abuse. These discrepancies are likely explained by the stable conditions in bottom cages, the effects of temperature abuse, and the growth bias inherent to the MPN method. These results underscore the need for a holistic, time-sensitive approach, taking into account microbial states and the dynamic aspects of the oyster environment to understand the complex relationship between aquaculture practices and the oyster microbiome.IMPORTANCEThis study holds great importance for food safety, antibiotic resistance surveillance, aquaculture management, and environmental health. Unraveling the population dynamics of microbial communities in oysters and their responses to different aquaculture practices enhances our ability to ensure safer seafood, monitor antibiotic resistance, optimize aquaculture methods, and mitigate potential public health challenges. Moreover, it demonstrates the applicability of advanced metagenomic tools for future research. Furthermore, this research addresses critical aspects of food safety, food security, public health, and sustainable aquaculture practices, making it highly relevant in today's context.},
}

@article {pmid41395966,
year = {2025},
author = {Watrous, KM and Larson, MJ and Nelson, AS and Hammer, TJ},
title = {A culture collection of gut bacteria from wild bumble bees (Bombus impatiens).},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0079125},
doi = {10.1128/mra.00791-25},
pmid = {41395966},
issn = {2576-098X},
abstract = {Gut bacteria are important to the ecology and health of social bees. We present a collection of 55 isolates, representing a diverse range of bacterial taxa, from wild- and captive-reared bumble bees (Bombus impatiens). Culture conditions and full-length 16S rRNA gene sequences are provided.},
}

@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.},
}